Adeno-associated virus variants and uses in t cell engineering
Engineered AAV variants with modified capsid polypeptides address inefficiencies in CAR-T cell delivery by targeting human T cells, achieving high transduction efficiency and therapeutic efficacy against malignant B cells.
Patent Information
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- WESTLAKE GENETECH LTD
- Filing Date
- 2025-11-06
- Publication Date
- 2026-05-15
AI Technical Summary
Current CAR-T cell therapies face challenges such as graft-versus-host disease and inefficient delivery of CAR sequences to T cells, particularly in allogenic and in vivo settings, with existing delivery platforms like lipid nanoparticles, lentiviruses, and virus-like particles facing manufacturing hurdles and safety concerns.
Engineered adeno-associated virus (AAV) variants with modified capsid polypeptides are developed to enhance T cell tropism, enabling efficient delivery of CAR sequences to human T cells both ex vivo and in vivo, utilizing engineered AAV9 and AAV6 variants that reduce liver accumulation and target CD62L on T cell surfaces.
The engineered AAV vectors achieve over 95% reduction in liver accumulation and up to 6.4% transduction of human T cells across various organs, effectively inhibiting malignant B cells and controlling their progression, demonstrating a viable platform for in vivo CAR-T cell therapy.
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Abstract
Description
Adeno-associated virus variants and uses in T cell engineeringCROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priorities to International Application No. PCT / CN2024 / 130230, filed on November 6, 2024, and International Application No. PCT / CN2025 / 091712, filed on April 28, 2025, the content of which are incorporated by reference in their entirety. FIELD OF DISCLOSURE
[0002] The present disclosure generally relates to engineered adeno-associated virus and their uses in T cell engineering. Also disclosed are engineered viral capsid polypeptides, vectors, cells, and kits related to the engineered adeno-associated virus, and methods related to the uses thereof. SEQUENCE LISTING
[0003] This application contains a Sequence Listing electronically submitted as an XML file entitled “SEQ. xml” having a size of 10, 436 KB and created on November 5, 2025. The information contained in the Sequence Listing is incorporated by reference herein.BACKGROUND
[0004] Ex vivo CAR-T cell therapy has shown remarkable success in treating both malignant and autoactivated B cells (Baker et al., 2023) . This therapy has led to high rates of long-lasting remission in patients with relapsed or refractory cancers or autoimmune diseases who previously had limited treatment options. Despite its success, challenges remain for the current FDA-approved autologous CAR-T therapy, which is personalized and requires the collection of a patient’s own T cells, genetic modifications to the T cells to express CARs, and lymphodepletion prior to CAR-T cell infusion (Maus, 2022) . Off-the-shelf CAR-T therapy, also called allogenic CAR-T, uses T cells from donors or derived from iPSC, providing immediate availability of the CAR-T cell product (Baker et al., 2023) . However, issues of allogenic CAR-T include life-threatening graft-versus-host diseases (GvHD) and rapid elimination by the host immune system (Depil et al., 2020) .
[0005] In vivo CAR-T cell therapy involves delivering a CAR sequence directly into the patients’ T cells within their body. The CAR sequence is packed by viral or non-viral delivery platforms, which is also “off-the-shelf” while bypassing the GvHD of allogenic CAR-T cell therapy. In this context, in vivo CAR-T is no longer a personalized cell therapy but a ready-to-use gene therapy. Thus, it faces the same challenge as gene therapy: efficiently delivering the CAR sequence to T cells preferentially at a low dose. Several delivery platforms have been used to develop in vivo CAR-T therapy. Lipid nanoparticles (LNP) packing with mRNA-encoding CAR sequence have been conjugated with antibodies, including anti-CD3 antibody, anti-CD8 antibody, and anti-CD5 antibody, to achieve redirection in vivo to T cells rather than the liver (Short et al., 2024; Rurik et al., 2022; Thomsen et al., 2021; Kheirolomoon et al., 2022; Billingsley et al., 2024) . Although the COVID-19 vaccine has proved the safety and scalability of this platform, antibody-conjugated LNPs face significant challenges in manufacturing. Lentivirus (LV) with an engineered envelope with single-chain variable fragments (scFv) anti-CD3, CD4, and CD8 could also be redirected to T cells in vivo (Michels et a., 2021; Pfeiffer et al., 2018; Charitidis et al., 2021; Frank et al., 2020; Huckaby et al., 2021) . LV integrates the CAR sequence into the host cell genome, allowing stable transgene expression through T-cell expansion but also raising safety concerns on sequence integration into the genome of bystander cells and insertional mutagenesis. Virus-like particles (VLPs) resemble viruses but lack viral genetic material, making them non-infectious (Banskota et al., 2022; Hamilton et al., 2021) . VLP allows in vivo delivery of Ribonucleoprotein (RNP) instead of DNA. A recent study engineered VLP by pairing the display of a mutated VSVG with CD3, CD4, and CD28 scFv on Cas9-EDVs (enveloped delivery vehicles) to target T cells in vivo and deliver genome editor and CAR sequences (Hamilton et al., 2024) . Although a proven concept, the less efficient generation of CAR-T cells in vivo and the complicated manufacturing process hurdles its applications in clinics.
[0006] Recombinant AAV vectors (rAAVs) have been widely used in gene therapy due to their safety profile and ability to induce long-term expression of transgenes. Although wild-type rAAVs naturally accumulate in the liver by systematic injection, engineering the variable regions of the capsid protein of rAAV has proved to be effective in redirecting rAAV to non-hepatic organs or tissues (e.g., central nervous systems and muscles) or increasing transduction efficiencies to non-hepatic cells (Li and Samulski, 2020) . For example, Ark313 is a rAAV6 variant targeting murine T cells, which was engineered from three rounds of directed evolution of a capsid library with 7-mer random insertion in the variable region IV (Nyberg et al., 2023) . Infusion of Ark313-generated CAR-T cells demonstrated better efficacy in controlling tumor growth than retrovirus-generated CAR-T cells. However, the question of whether an engineered rAAV variant could enable the targeting of human T cells by systematic delivery has yet to be explored.SUMMARY
[0007] The present disclosure provides engineered viral capsid polypeptide and engineered AAV variants, which have enhanced T cell tropism. The engineered AAV variants could effectively deliver CAR sequences to human T cells ex vivo and in vivo.
[0008] The present disclosure provides examples showing that in a PBMC humanized mouse model, engineered AAV9 and engineered AAV6 variants disclosed herein successfully enabled CAR expression in human T cells by systematic injection, with more than 95%reduction of liver accumulation compared to the wild-type AAV. AAV-CAR injection turned up to 6.4%of human T cells into CAR-T cells across various organs, successfully inhibiting the number of human B cells and controlling the progression of malignant B cells. CRISPR screening identified the CD62L on T cell surfaces as a critical mediator of the enhanced transduction efficiency of the AAV6 variant. These examples showed that AAV-mediated delivery of CAR sequence could enable in vivo generation of functional CAR-T cells, with mechanistic insights from an identified surface receptor expressed in less differentiated T cells. The present disclosure demonstrates that the engineered AAV vector targeting T cells can be a delivery platform for developing in vivo CAR-T therapy. This application of AAV also expands the therapeutic area of the AAV vector to non-inherited diseases.
[0009] In an aspect, the present disclosure provides an engineered viral capsid polypeptide comprising an amino acid sequence, wherein the amino acid sequence is of any one of SEQ ID NOs: 1-2105 and 2149-9287.
[0010] In an aspect, the present disclosure provides an engineered viral capsid polypeptide comprising an amino acid sequence, wherein the amino acid sequence comprises X0X1X2X3X4Y, wherein X0, X1, X2, and X4 are each an amino acid residue, wherein X0 is Aspartate (D) or Glutamate (E) , X3 is an amino acid residue or absent, and Y is Tyrosine. In some embodiments, X3 is absent. In some embodiments, X1 is Lysine (K) . In some embodiments, X4 is Proline (P) , Alanine (A) , Threonine (T) , or Valine (V) . In some embodiments, X4 is Proline (P) . In some embodiments, X4 is Alanine (A) . In some embodiments, X4 is Threonine (T) . In some embodiments, X4 is Valine (V) . In some embodiments, the engineered viral capsid polypeptide comprises any one of SEQ ID NOs: 177, 323, 418, 427, 456, 463, 511, 552, 553, 735, 873, 1142, 1178, 1199, 1303, 1327, 1431, 1439, 1440, 1441, 1443, 1444, 1445, 1449, 1452, 1453, 1473, 1476, 1480, 1486, 1488, 1490, 1491, 1508, 1512, 1513, 1515, 1518, 1522, 1523, 1558, 1679, 1683, 1684, 1685, 1686, 1687, 1688, 1691, 1692, 1693, 1699, 1700, 1705, 1709, 1714, 1715, 1716, 1717, 1723, 1724, 1725, 1726, 1727, 1728, 1779, 1855, 1856, 1861, 1913, 2054, 2141, 2332, 2339, 2366, 2367, 2368, 2375, 2377, 2384, 2386, 2387, 2508, 2509, 2529, 2972, 3051, 3268, 3538, 3888, 4028, 4122, 4252, 4279, 4280, 4720, 4891, 5144, 5148, 5168, 5275, 5343, 5365, 5392, 5528, 5537, 5609, 5670, 5743, 5744, 5745, 5746, 5747, 5873, 6184, 6288, 6309, 6312, 6327, 6328, 6401, 6424, 6511, 6749, 6767, 6769, 6773, 6803, 6816, 6817, 6818, 6905, 6935, 6965, 6972, 6987, 7228, 7269, 7331, 7385, 7416, 7424, 7469, 7470, 7471, 7476, 7481, 7495, 7497, 7508, 7526, 7527, 7539, 7544, 7562, 7623, 7650, 7685, 7770, 7916, 7937, 7938, 7939, 7940, 7941, 7942, 7943, 7944, 7945, 7946, 7947, 7950, 7951, 7952, 7953, 7954, 7955, 7956, 7957, 7958, 7959, 7960, 7961, 7962, 7963, 7964, 7965, 7966, 7967, 7968, 7969, 7970, 7971, 7972, 7973, 7974, 7975, 7976, 7977, 7978, 7979, 7980, 7981, 7982, 7983, 7984, 7985, 7986, 7987, 7988, 7989, 7990, 7991, 7992, 7993, 7994, 7995, 7996, 7997, 7998, 7999, 8000, 8001, 8002, 8003, 8004, 8005, 8006, 8007, 8008, 8009, 8010, 8011, 8012, 8013, 8014, 8015, 8016, 8017, 8018, 8019, 8020, 8021, 8022, 8023, 8024, 8025, 8026, 8027, 8028, 8029, 8030, 8031, 8032, 8033, 8034, 8035, 8036, 8037, 8038, 8039, 8040, 8041, 8042, 8043, 8044, 8045, 8046, 8047, 8048, 8049, 8050, 8052, 8053, 8054, 8055, 8057, 8058, 8059, 8060, 8061, 8062, 8063, 8064, 8065, 8066, 8070, 8071, 8073, 8074, 8075, 8076, 8077, 8078, 8079, 8081, 8082, 8083, 8084, 8085, 8086, 8087, 8088, 8089, 8090, 8091, 8092, 8093, 8094, 8095, 8096, 8097, 8098, 8099, 8100, 8101, 8102, 8103, 8104, 8105, 8106, 8107, 8108, 8109, 8110, 8112, 8113, 8114, 8115, 8116, 8117, 8118, 8119, 8120, 8121, 8122, 8123, 8124, 8315, 8357, 8423, 8445, 8494, 8600, 8697, 8787. In some embodiments, the engineered viral capsid polypeptide comprises any one of SEQ ID NOs: 33, 147, 314, 320, 546, 737, 870, 945, 967, 970, 1037, 1050, 1110, 1142, 1157, 1178, 1199, 1269, 1303, 1327, 1431, 1464, 1476, 1483, 1486, 1490, 1491, 1529, 1549, 1558, 1576, 1625, 1666, 1679, 1714, 1716, 1717, 1734, 1735, 1736, 1752, 1778, 1779, 1855, 1856, 1870, 1913, 2054, 2156, 2331, 2332, 2339, 2366, 2367, 2368, 2375, 2377, 2384, 2386, 2388, 2430, 2504, 2578, 2739, 2740, 2799, 3089, 3090, 3178, 3237, 3252, 3253, 3299, 3404, 3410, 3443, 3467, 3665, 3772, 3876, 3893, 3925, 4028, 4102, 4158, 4276, 4365, 4583, 4589, 4607, 4635, 4658, 4884, 4890, 4990, 5008, 5142, 5148, 5151, 5159, 5305, 5325, 5326, 5365, 5393, 5465, 5479, 5485, 5572, 5670, 5692, 5706, 5770, 5790, 5865, 5928, 5974, 6001, 6005, 6017, 6197, 6236, 6238, 6318, 6319, 6338, 6348, 6349, 6350, 6371, 6452, 6463, 6467, 6610, 6724, 6736, 6748, 6749, 6800, 6804, 6848, 6852, 6920, 6966, 6967, 6975, 7010, 7155, 7197, 7202, 7222, 7243, 7269, 7295, 7424, 7495, 7503, 7504, 7508, 7573, 7603, 7607, 7609, 7610, 7616, 7641, 7650, 7685, 7694, 7695, 7696, 7697, 7702, 7708, 7728, 7729, 7730, 7731, 7733, 7734, 7735, 7746, 7755, 7770, 7791, 7793, 7795, 7815, 7825, 7830, 7834, 7835, 7919, 7920, 7921, 7923, 7924, 7925, 7926, 7927, 7928, 7929, 8125, 8126, 8128, 8129, 8130, 8131, 8138, 8139, 8140, 8141, 8144, 8145, 8146, 8147, 8148, 8149, 8150, 8151, 8152, 8153, 8160, 8161, 8163, 8168, 8170, 8171, 8172, 8174, 8247, 8248, 8249, 8250, 8315, 8331, 8353, 8394, 8423, 8445, 8460, 8462, 8492, 8666, 8734, 8775, 8800, 8813, 8828, 8864, 9189.
[0011] In an aspect, the present disclosure provides an engineered viral capsid polypeptide comprising an amino acid sequence, wherein the amino acid sequence comprises a poly [D|E] motif. In some embodiments, the engineered viral capsid polypeptide comprises any one of SEQ ID NOs: 29, 51, 64, 171, 590, 633, 637, 647, 648, 707, 730, 1025, 1026, 1042, 1045, 1054, 1055, 1061, 1082, 1084, 1100, 1106, 1107, 1108, 1109, 1111, 1124, 1130, 1131, 1141, 1142, 1145, 1148, 1152, 1153, 1154, 1155, 1156, 1161, 1162, 1163, 1178, 1181, 1191, 1192, 1193, 1195, 1196, 1199, 1262, 1268, 1269, 1278, 1279, 1280, 1285, 1293, 1298, 1300, 1303, 1307, 1310, 1321, 1324, 1358, 1366, 1400, 1402, 1415, 1419, 1429, 1430, 1484, 1485, 1493, 1506, 1509, 1534, 1554, 1555, 1556, 1558, 1559, 1563, 1565, 1566, 1568, 1571, 1580, 1581, 1588, 1612, 1616, 1629, 1655, 1657, 1658, 1663, 1680, 1751, 1769, 1779, 1790, 1818, 1823, 1825, 1832, 1833, 1835, 1845, 1846, 1848, 1849, 1850, 1851, 1855, 1856, 1872, 1873, 1874, 1877, 1878, 1880, 1885, 1888, 1889, 1891, 1894, 1895, 1896, 1900, 1902, 1904, 1910, 1911, 1913, 1914, 1942, 1947, 1958, 1959, 1964, 1966, 1975, 1978, 1990, 1991, 2004, 2016, 2017, 2018, 2019, 2020, 2021, 2051, 2053, 2054, 2055, 2059, 2060, 2062, 2065, 2068, 2070, 2071, 2072, 2074, 2075, 2076, 2077, 2078, 2079, 2081, 2082, 2086, 2087, 2089, 2090, 2091, 2100, 2102, 2142, 2157, 2215, 2277, 2279, 2313, 2321, 2331, 2332, 2333, 2335, 2336, 2337, 2338, 2339, 2342, 2343, 2345, 2353, 2357, 2358, 2363, 2367, 2375, 2376, 2377, 2378, 2381, 2385, 2388, 2395, 2396, 2401, 2406, 2407, 2412, 2415, 2416, 2418, 2422, 2428, 2429, 2430, 2431, 2444, 2483, 2484, 2485, 2486, 2487, 2524, 2525, 2530, 2533, 2538, 2539, 2540, 2565, 2576, 2577, 2578, 2634, 2635, 2646, 2692, 2694, 2700, 2709, 2738, 2739, 2740, 2786, 2787, 2788, 2796, 2799, 2801, 2818, 2832, 2838, 2841, 2844, 2849, 2867, 2905, 2915, 2924, 2937, 2994, 2995, 2996, 3001, 3005, 3006, 3007, 3009, 3036, 3049, 3052, 3053, 3064, 3065, 3071, 3075, 3155, 3257, 3276, 3280, 3534, 3566, 3567, 3568, 3569, 3571, 3577, 3578, 3579, 3582, 3590, 3592, 3616, 3617, 3624, 3676, 3704, 3749, 3785, 3793, 3794, 3795, 3796, 3797, 3801, 3802, 3808, 3809, 3832, 3838, 3989, 4006, 4116, 4130, 4181, 4320, 4348, 4349, 4386, 4397, 4500, 4501, 4502, 4503, 4507, 4508, 4509, 4510, 4511, 4512, 4513, 4514, 4515, 4516, 4517, 4518, 4519, 4521, 4522, 4523, 4525, 4526, 4533, 4534, 4535, 4536, 4537, 4538, 4541, 4542, 4562, 4680, 4689, 4690, 4692, 4701, 4702, 4703, 4707, 4726, 4744, 4747, 4758, 4775, 4776, 4778, 4780, 4781, 4793, 4795, 4799, 4819, 4829, 4841, 4842, 4843, 4845, 4878, 4880, 4888, 4968, 5010, 5139, 5152, 5305, 5413, 5609, 5777, 5897, 6007, 6155, 6282, 6290, 6291, 6292, 6306, 6307, 6311, 6312, 6339, 6363, 6365, 6374, 6376, 6390, 6395, 6396, 6408, 6412, 6413, 6423, 6424, 6429, 6431, 6437, 6439, 6460, 6473, 6491, 6502, 6505, 6506, 6507, 6512, 6520, 6521, 6531, 6544, 6554, 6586, 6605, 6606, 6607, 6610, 6617, 6618, 6638, 6665, 6668, 6686, 6707, 6712, 6713, 6716, 6748, 6749, 6750, 6779, 6782, 6783, 6785, 6796, 6803, 6832, 6861, 6862, 6863, 6866, 6867, 6868, 6869, 6870, 6871, 6892, 6895, 6896, 6915, 6920, 6923, 6924, 6933, 6947, 6953, 6955, 6958, 6965, 6967, 6970, 6973, 6975, 6976, 6977, 6985, 7004, 7005, 7007, 7010, 7016, 7020, 7030, 7045, 7046, 7052, 7056, 7057, 7058, 7059, 7063, 7074, 7075, 7076, 7173, 7179, 7181, 7182, 7184, 7185, 7187, 7194, 7196, 7197, 7198, 7203, 7218, 7223, 7224, 7225, 7226, 7227, 7228, 7235, 7254, 7257, 7271, 7275, 7280, 7283, 7285, 7290, 7292, 7298, 7302, 7314, 7322, 7326, 7331, 7339, 7372, 7378, 7398, 7399, 7404, 7405, 7408, 7421, 7422, 7423, 7424, 7426, 7427, 7435, 7446, 7449, 7460, 7462, 7477, 7483, 7484, 7486, 7490, 7491, 7495, 7496, 7502, 7509, 7514, 7516, 7545, 7549, 7582, 7589, 7592, 7597, 7601, 7623, 7632, 7633, 7647, 7650, 7651, 7652, 7653, 7654, 7655, 7664, 7670, 7685, 7706, 7708, 7710, 7711, 7712, 7713, 7714, 7724, 7725, 7726, 7727, 7741, 7742, 7745, 7748, 7749, 7750, 7751, 7752, 7753, 7754, 7759, 7768, 7770, 7771, 7777, 7778, 7782, 7785, 7788, 7789, 7792, 7798, 7799, 7802, 7806, 7807, 7819, 7824, 7827, 7839, 7843, 7845, 7848, 7856, 7857, 7860, 7863, 7867, 7877, 7886, 7891, 7896, 7897, 7898, 7914, 8068, 8156, 8164, 8188, 8191, 8201, 8204, 8222, 8232, 8278, 8279, 8285, 8292, 8298, 8309, 8313, 8318, 8320, 8334, 8335, 8353, 8359, 8360, 8362, 8363, 8364, 8365, 8366, 8368, 8377, 8378, 8393, 8394, 8397, 8410, 8411, 8412, 8413, 8415, 8417, 8423, 8424, 8425, 8426, 8428, 8445, 8453, 8454, 8458, 8460, 8461, 8468, 8470, 8471, 8472, 8477, 8484, 8488, 8491, 8493, 8494, 8497, 8498, 8499, 8506, 8507, 8508, 8510, 8537, 8543, 8591, 8603, 8604, 8608, 8609, 8612, 8618, 8622, 8625, 8627, 8630, 8639, 8644, 8654, 8660, 8662, 8669, 8670, 8674, 8681, 8688, 8690, 8712, 8720, 8742, 8759, 8760, 8767, 8780, 8787, 8789, 8819, 8820, 8829, 8838, 8850, 8860, 8861, 8870, 8883, 8885, 8886, 8898, 8900, 8905, 8917, 8919, 8920, 8950, 8952, 8953, 8965, 8973, 8977, 8982, 8985, 8986, 8997, 9011, 9012, 9014, 9048, 9057, 9059, 9100, 9105, 9106, 9114, 9118, 9123, 9124, 9126, 9127, 9140, 9169, 9172, 9174, 9175, 9187, 9188, 9189, 9207, 9212, 9213, 9227, 9228, 9234, 9236, 9237, 9247, 9265, 9267.
[0012] In an aspect, the present disclosure provides an engineered viral capsid polypeptide comprising an amino acid sequence, wherein the amino acid sequence comprises poly [A|G|S] motif. In some embodiments, the engineered viral capsid polypeptide comprises any one of SEQ ID NOs: 3, 4, 6, 7, 8, 9, 14, 15, 16, 17, 19, 20, 30, 31, 32, 34, 35, 36, 37, 38, 40, 43, 45, 46, 54, 61, 67, 76, 93, 102, 110, 112, 113, 114, 115, 116, 117, 118, 119, 120, 122, 123, 124, 127, 128, 132, 135, 141, 142, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 159, 160, 162, 176, 178, 179, 180, 181, 182, 184, 186, 187, 188, 191, 197, 198, 199, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 247, 248, 255, 269, 274, 282, 283, 284, 291, 293, 294, 296, 300, 302, 303, 305, 310, 314, 315, 318, 326, 330, 338, 340, 341, 342, 346, 353, 360, 363, 368, 387, 395, 403, 416, 427, 429, 430, 432, 439, 444, 445, 446, 447, 450, 451, 452, 460, 467, 475, 476, 485, 486, 488, 489, 496, 502, 504, 506, 507, 508, 513, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 529, 532, 540, 544, 545, 549, 554, 566, 568, 569, 578, 588, 589, 592, 593, 594, 595, 596, 597, 598, 600, 601, 602, 603, 604, 605, 616, 622, 624, 629, 642, 649, 650, 655, 656, 659, 663, 665, 669, 672, 684, 720, 732, 778, 779, 780, 793, 795, 813, 849, 851, 852, 853, 854, 855, 856, 857, 858, 862, 863, 864, 865, 867, 876, 877, 878, 882, 883, 884, 889, 890, 891, 893, 900, 901, 902, 904, 905, 906, 907, 908, 909, 910, 911, 912, 913, 914, 917, 922, 923, 924, 925, 926, 927, 928, 929, 930, 931, 933, 937, 938, 939, 942, 943, 944, 947, 952, 953, 954, 955, 956, 960, 961, 965, 966, 967, 971, 973, 974, 979, 980, 981, 984, 985, 986, 987, 988, 989, 992, 996, 997, 998, 999, 1000, 1002, 1008, 1009, 1010, 1011, 1013, 1015, 1099, 1017, 1020, 1021, 1022, 1023, 1024, 1028, 1039, 1041, 1042, 1044, 1047, 1048, 1077, 1078, 1082, 1086, 1087, 1088, 1089, 1090, 1091, 1092, 1093, 1094, 1096, 1097, 1113, 1115, 1116, 1121, 1126, 1134, 1135, 1143, 1157, 1158, 1174, 1175, 1179, 1182, 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7602, 7611, 7620, 7621, 7622, 7624, 7625, 7626, 7628, 7629, 7630, 7634, 7635, 7636, 7637, 7638, 7639, 7643, 7644, 7655, 7658, 7660, 7661, 7662, 7664, 7665, 7666, 7668, 7669, 7676, 7677, 7705, 7715, 7737, 7760, 7761, 7765, 7766, 7767, 7773, 7774, 7776, 7781, 7783, 7786, 7803, 7808, 7809, 7811, 7813, 7816, 7818, 7820, 7833, 7838, 7840, 7841, 7851, 7853, 7857, 7859, 7868, 7871, 7874, 7875, 7878, 7883, 7884, 7895, 7904, 7910, 7912, 7914, 7917, 7918, 7933, 7936, 7937, 8047, 8056, 8070, 8072, 8128, 8135, 8156, 8157, 8159, 8162, 8166, 8167, 8176, 8177, 8181, 8185, 8188, 8192, 8193, 8194, 8195, 8196, 8197, 8198, 8199, 8200, 8201, 8202, 8203, 8204, 8205, 8206, 8207, 8208, 8209, 8210, 8211, 8212, 8213, 8214, 8215, 8216, 8217, 8218, 8219, 8220, 8222, 8223, 8224, 8225, 8226, 8227, 8228, 8229, 8230, 8231, 8232, 8233, 8234, 8235, 8236, 8237, 8238, 8239, 8240, 8241, 8242, 8243, 8244, 8245, 8246, 8254, 8256, 8257, 8259, 8260, 8261, 8262, 8263, 8264, 8265, 8266, 8267, 8268, 8269, 8270, 8271, 8272, 8273, 8280, 8281, 8289, 8290, 8291, 8295, 8296, 8297, 8298, 8299, 8300, 8301, 8302, 8303, 8304, 8305, 8307, 8308, 8313, 8319, 8324, 8325, 8337, 8338, 8339, 8340, 8341, 8342, 8343, 8344, 8345, 8346, 8347, 8348, 8349, 8350, 8351, 8352, 8354, 8355, 8356, 8357, 8361, 8363, 8364, 8365, 8366, 8367, 8368, 8369, 8372, 8373, 8379, 8380, 8382, 8383, 8384, 8385, 8391, 8392, 8395, 8398, 8400, 8401, 8402, 8403, 8404, 8405, 8406, 8407, 8408, 8409, 8410, 8412, 8414, 8418, 8420, 8421, 8422, 8427, 8431, 8433, 8434, 8435, 8436, 8437, 8438, 8439, 8440, 8441, 8442, 8443, 8444, 8445, 8446, 8447, 8448, 8449, 8450, 8451, 8452, 8455, 8456, 8457, 8458, 8459, 8461, 8474, 8478, 8481, 8483, 8486, 8495, 8513, 8516, 8517, 8518, 8523, 8524, 8525, 8526, 8530, 8531, 8532, 8538, 8540, 8542, 8546, 8547, 8548, 8563, 8568, 8571, 8573, 8574, 8577, 8578, 8579, 8580, 8582, 8584, 8585, 8587, 8588, 8589, 8590, 8592, 8593, 8594, 8598, 8602, 8605, 8606, 8610, 8611, 8614, 8615, 8616, 8617, 8618, 8619, 8620, 8621, 8622, 8623, 8624, 8636, 8646, 8648, 8649, 8651, 8652, 8653, 8657, 8659, 8680, 8688, 8690, 8695, 8702, 8703, 8706, 8707, 8708, 8709, 8710, 8711, 8715, 8716, 8721, 8722, 8728, 8731, 8742, 8758, 8759, 8767, 8768, 8774, 8785, 8793, 8794, 8795, 8796, 8798, 8804, 8805, 8807, 8811, 8825, 8826, 8827, 8829, 8834, 8835, 8837, 8844, 8865, 8874, 8875, 8876, 8887, 8890, 8891, 8905, 8921, 8933, 8934, 8939, 8940, 8944, 8945, 8946, 8947, 8955, 8957, 8960, 8961, 8962, 8963, 8964, 8996, 8999, 9000, 9004, 9005, 9006, 9007, 9015, 9038, 9045, 9049, 9052, 9056, 9059, 9060, 9061, 9062, 9063, 9065, 9066, 9067, 9068, 9069, 9070, 9071, 9072, 9073, 9074, 9075, 9076, 9077, 9079, 9080, 9081, 9082, 9083, 9084, 9086, 9087, 9088, 9091, 9092, 9093, 9095, 9096, 9097, 9098, 9099, 9101, 9102, 9103, 9104, 9108, 9109, 9110, 9111, 9112, 9113, 9130, 9131, 9132, 9135, 9136, 9138, 9139, 9141, 9142, 9143, 9144, 9145, 9147, 9148, 9149, 9150, 9151, 9152, 9153, 9154, 9155, 9156, 9157, 9158, 9159, 9161, 9164, 9165, 9166, 9167, 9169, 9170, 9171, 9178, 9179, 9180, 9181, 9182, 9185, 9186, 9187, 9192, 9193, 9194, 9195, 9196, 9197, 9198, 9199, 9200, 9201, 9202, 9203, 9204, 9205, 9206, 9208, 9209, 9210, 9216, 9217, 9218, 9219, 9220, 9221, 9222, 9223, 9224, 9225, 9226, 9227, 9228, 9229, 9230, 9231, 9232, 9233, 9236, 9238, 9239, 9248, 9250, 9251, 9252, 9253, 9254, 9255, 9256, 9257, 9258, 9259, 9261, 9262, 9263, 9264, 9269, 9270, 9271, 9274, 9276, 9277, 9278, 9279, 9280, 9282, 9283, 9284, 9285.
[0013] In some embodiments of the engineered viral capsid polypeptide, the amino acid sequence is located within a variable region in the viral capsid polypeptide.
[0014]
[0015] In some embodiments of the engineered viral capsid polypeptide, the engineered viral capsid polypeptide has tropism to T cells. In some embodiments, the T cells are primary T cells. In some embodiments, the T cells are human T cells.
[0016] In some embodiments of the engineered viral capsid polypeptide, the viral capsid polypeptide is a viral capsid polypeptide of an adeno associated virus (AAV) .
[0017] In some embodiments of the engineered viral capsid polypeptide, the engineered viral capsid polypeptide is a viral capsid polypeptide of an engineered adeno associated virus derived from a parental virus selected from AAV1, AAV2, AAV3, AAV3B, AAV4, AAV5, AAV6, AAV6.2, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, AAV13, AAVrh74, AAVrh10, AAVDJ, AAVDJ / 8, AAV-PHP. eB, AAV-PHP. S, AAV2-retro, AAV2-QuadYF, AAV2.7m8, and Avian AAV.
[0018] In some embodiments, the engineered viral capsid polypeptide is a viral capsid polypeptide of an engineered AAV9, and the amino acid sequence is any one of SEQ ID NOs: 1-1007, 2149-2261, and 2945-6269. In some embodiments, the amino acid sequence is inserted into a location analogous to a location between A581 and T593 of SEQ ID NO: 2107. In some embodiments, the engineered viral capsid polypeptide is capable of binding to SLC35C2. In some embodiments, the engineered viral capsid polypeptide comprises SEQ ID NO: 109 and is capable of binding to SLC35C2.
[0019] In some embodiments, the engineered viral capsid polypeptide is a viral capsid polypeptide of an engineered AAV6, and the amino acid sequence is any one of SEQ ID NOs: 1008-2105, 2262-2944, and 6270-9287. In some embodiments, the amino acid sequence is inserted into a location analogous to a location between A581 and T593 of SEQ ID NO: 2106. In some embodiments, the engineered viral capsid polypeptide is capable of binding to CD62L. In some embodiments, the engineered viral capsid polypeptide comprises SEQ ID NO: 1660 and is capable of binding to CD62L.
[0020] In another aspect, the present disclosure provides a polynucleotide encoding the engineered viral capsid polypeptide disclosed herein.
[0021] In another aspect, the present disclosure provides a vector comprising the engineered viral capsid polypeptide disclosed herein, or the polynucleotide disclosed herein.
[0022] In some embodiments, the vector is a plasmid, a viral vector, a lipid nanoparticle (LNP) vector, or a non-viral vector.
[0023] In another aspect, the present disclosure provides a cell comprising the engineered viral capsid polypeptide disclosed herein, the polynucleotide disclosed herein, or the vector disclosed herein.
[0024] In another aspect, the present disclosure provides an engineered adeno-associated virus (AAV) comprising the engineered viral capsid polypeptide disclosed herein.
[0025] In some embodiments, the engineered adeno-associated virus (AAV) further comprises an expression cassette which comprises a single-strand DNA encoding a chimeric antigen receptor (CAR) . In some embodiments, the chimeric antigen receptor (CAR) is selected from CD19-CAR, BCMA-CAR, CD22-CAR, CD30-CAR, CD7-CAR, CD38-CAR, CD20-CAR, GD2-CAR, HER2-CAR, IL13Ra2-CAR, EGFR-CAR, Mesothelin-CAR, Claudin-18.2-CAR, PSMA-CAR, and GPC3-CAR.
[0026] In some embodiments of the engineered adeno-associated virus (AAV) disclosed herein, the expression cassette further comprises a promoter selected from CMV, EF-1α, SV40, PGK1, CAG, ubc, human beta actin, TRE, UA5, Ac5, Polyhedrin, CaMKIIa, GAL1, GAL10, TEF1, GDS, ADH1, CaMV355, Ubi, and SFFV. In some embodiments, the promoter is EF-1α.
[0027] In some embodiments, the expression cassette further comprises a 5’ ITR, a 3’ ITR, a Flag, a poly (A) , a WPRE, or a miRNA target.
[0028] In some embodiments, the engineered adeno-associated virus has tropism to T cells. In some embodiments, the T cells are primary T cells. In some embodiments, the T cells are human T cells.
[0029] In some embodiments, the engineered adeno associated virus derived from a parental virus selected from AAV1, AAV2, AAV3, AAV3B, AAV4, AAV5, AAV6, AAV6.2, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, AAV13, AAVrh74, AAVrh10, AAVDJ, AAVDJ / 8, AAV-PHP. eB, AAV-PHP. S, AAV2-retro, AAV2-QuadYF, AAV2.7m8, and Avian AAV.
[0030] In some embodiments, the engineered adeno-associated virus is an engineered AAV9, and the engineered viral capsid polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 1-1007, 2149-2261, and 2945-6269. In some embodiments, the amino acid sequence replaces a sequence in the viral capsid polypeptide analogous to a sequence from T582 to Q592 of SEQ ID NO: 2107. In some embodiments, the engineered adeno-associated virus (AAV) is capable of binding to SLC35C2. In some embodiments, the engineered adeno-associated virus (AAV) comprises SEQ ID NO: 109 and is capable of binding to SLC35C2.
[0031] In some embodiments, the engineered adeno-associated virus is an engineered AAV6, and the engineered viral capsid polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 1008-2105, 2262-2944, and 6270-9287. In some embodiments, the amino acid sequence replaces a sequence in the viral capsid polypeptide analogous to a sequence from V582 to A592 of SEQ ID NO: 2106. In some embodiments, the engineered adeno-associated virus (AAV) is capable of binding to CD62L. In some embodiments, the engineered adeno-associated virus (AAV) comprises SEQ ID NO: 1660 and is capable of binding to CD62L.
[0032] In another aspect, the present disclosure provides a kit comprising the engineered adeno-associated virus (AAV) disclosed herein, and a gene editing system. In some embodiments, the gene editing system comprises a Cas9 protein and a guide RNA, or one or more polynucleotide encoding thereof. In some embodiments, the gene editing system comprises a Cas9 / gRNA ribonucleoprotein (RNP) .
[0033] In another aspect, the present disclosure provides an engineered T cell which is transduced by the engineered AAV disclosed herein.
[0034] In some embodiments, the engineered T cell further comprises at least one chimeric antigen receptor (CAR) . In some embodiments, the chimeric antigen receptor (CAR) is selected from CD19-CAR, BCMA-CAR, CD22-CAR, CD30-CAR, CD7-CAR, CD38-CAR, CD20-CAR, GD2-CAR, HER2-CAR, IL13Ra2-CAR, EGFR-CAR, Mesothelin-CAR, Claudin-18.2-CAR, PSMA-CAR, and GPC3-CAR.
[0035] In some embodiments, the T cell is a primary T cell. In some embodiments, the T cell is a human T cell.
[0036] In another aspect, the present disclosure provides a method of delivering a payload polynucleotide into a cell, comprising contacting the cell with the engineered adeno-associated virus (AAV) disclosed herein, wherein the engineered adeno-associated virus (AAV) comprises the payload polynucleotide.
[0037] In some embodiments, the method is carried out in vivo.
[0038] In some embodiments, the method further comprises administering a gene editing system into the cell. In some embodiments, the cell is a T cell. In some embodiments, the cell is a primary T cell. In some embodiments, the cell is a human T cell.
[0039] In some embodiments, the payload polynucleotide encodes a chimeric antigen receptor (CAR) . In some embodiments, the chimeric antigen receptor (CAR) is selected from CD19-CAR, BCMA-CAR, CD22-CAR, CD30-CAR, CD7-CAR, CD38-CAR, CD20-CAR, GD2-CAR, HER2-CAR, IL13Ra2-CAR, EGFR-CAR, Mesothelin-CAR, Claudin-18.2-CAR, PSMA-CAR, and GPC3-CAR.
[0040] In another aspect, the present disclosure provides a method of engineering a T cell, comprising contacting the T cell with the engineered adeno-associated virus (AAV) disclosed herein, wherein the engineered AAV comprises an expression cassette which comprises a single-strand DNA encoding a chimeric antigen receptor (CAR) .
[0041] In some embodiments, the method is carried out in vivo.
[0042] In some embodiments, the method further comprises administering a gene editing system into the T cell. In some embodiments, the T cell is electroporated with a Cas9 / gRNA ribonucleoprotein (RNP) .
[0043] In another aspect, the present disclosure provides a method of engineering a T cell in a subject, comprising administering into the subject an effective amount of engineered adeno-associated virus (AAV) disclosed herein. In some embodiments, the engineered AAV comprises an expression cassette which comprises a single-strand DNA encoding a chimeric antigen receptor (CAR) . In some embodiments, the engineered adeno-associated virus (AAV) is systematically administered to the subject. In some embodiments, the engineered adeno-associated virus (AAV) is an engineered AAV, and the engineered viral capsid polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 1-2105 and 2149-9287, and the effective amount of engineered adeno-associated virus (AAV) is more than 1× 1011 vg / kg, 1× 1012 vg / kg, or 1× 1013 vg / kg, e.g., less than 1× 1015 vg / kg. In some embodiments, the engineered adeno-associated virus (AAV) is an engineered AAV, and the engineered viral capsid polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 1-2105 and 2149-9287, and the effective amount is a low dose. In some embodiments, the effective amount of engineered adeno-associated virus (AAV) is from about 1× 1011 vg / kg to about 1× 1013 vg / kg. In some embodiments, the effective amount of engineered adeno-associated virus (AAV) is no more than 1× 1013 vg / kg. In some embodiments, the effective amount of engineered adeno-associated virus (AAV) is no more than 1× 1011 vg / kg, 1× 1012 vg / kg, or 1× 1013 vg / kg. In some embodiments, the engineered adeno-associated virus (AAV) is an engineered AAV6, and the engineered viral capsid polypeptide comprising an amino acid sequence of any one of SEQ ID NOs: 1008-2105, 2262-2944, and 6270-9287, and the effective amount is no more than 1× 1012 vg / kg. In some embodiments, the engineered adeno-associated virus (AAV) is an engineered AAV9, and the engineered viral capsid polypeptide comprising an amino acid sequence of any one of SEQ ID NOs: 1-1007, 2149-2261, and 2945-6269, and the effective amount is no more than 1× 1013 vg / kg.
[0044] In another aspect, the present disclosure provides a method of reducing the amount of B cell is a subject, comprising administering a therapeutically effective amount of engineered adeno-associated virus (AAV) disclosed herein which comprises a single-strand DNA encoding a chimeric antigen receptor (CAR) . In some embodiments, the engineered adeno-associated virus (AAV) is systematically administered to the subject. In some embodiments, the engineered adeno-associated virus comprises an expression cassette which comprises a single-strand DNA encoding a CD19-CAR. In some embodiments, the B cell is a malignant B cell. In some embodiments, the B cell is a CD19+ B cell. In some embodiments, the engineered adeno-associated virus (AAV) is systematically administered to the subject. In some embodiments, the engineered adeno-associated virus (AAV) is an engineered AAV6, and the engineered viral capsid polypeptide comprising an amino acid sequence of any one of SEQ ID NOs: 1008-2105, 2262-2944, and 6270-9287, and the therapeutically effective amount is no more than 1× 1012 vg / kg. In some embodiments, the present disclosure provides a method for treating B-cell malignancy by reducing the amount of B cell with the method disclosed herein. In some embodiments, B-cell malignancy includes, but not limited to B-cell lymphoma, chronic lymphocytic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma.
[0045] In an aspect, the present disclosure provides a targeting moiety comprising one or more polypeptides selected from SEQ ID NOs: 1-2105 and 2149-9287, and optionally a polynucleotide, a lipid, a polymer, a sugar, or any combination thereof.
[0046] In some embodiments, the present disclosure provides a composition comprising the targeting moiety disclosed herein and a payload. BRIEF DESCRIPTION OF THE FIGURES
[0047] Figure 1 shows that AAV9-M1 shows superior transduction efficiencies in human primary T cells.
[0048] Fig. 1A is a schematic view of quantifying the transduction efficiencies of AAV9-EGFP in human primary T cells.
[0049] Fig. 1B are representative multi-histogram plots showing EGFP expression levels in human primary T cells following AAV9-WT-EGFP or AAV9-M-EGFP transduction at four different MOIs. The cells were collected three days post-transduction.
[0050] Fig. 1C shows the percentage of EGFP+ cells in human primary T cells following AAV9-WT-EGFP and AAV9-M-EGFP variants transduction (n=2 in each group) .
[0051] Fig. 1D shows the MFI of EGFP in human primary T cells following AAV9-WT-EGFP and AAV9-M-EGFP variants transduction (n=2 in each group) .
[0052] Data were presented as mean ±SEM. P values were calculated by Two-way ANOVA analysis. *P≤0.05; **P≤0.01; ***P≤0.001, ****P≤0.0001.
[0053] Figure 2. Illustrates how AAV9-M1 delivered CAR sequence to human T cells in vitro.
[0054] Fig. 2A is a schematic view of delivering AAV-CAR into human T cells to generate CAR-T cells with transient CAR expression.
[0055] Fig. 2B is a representative FCM plot of CAR expression in CAR-T cells.
[0056] Fig. 2C shows the percentage of CAR-T cells in all human T cells at different time points post AAV transduction (n=3 in each group) .
[0057] Fig. 2D shows the cytotoxicity of CAR-T cells at different time points post-AAV transduction (n=3 in each group) .
[0058] Fig. 2E is a schematic view of integrating CAR sequences into the PDCD1 loci in human T cells. The CAR-tagBFP template was delivered by AAV. The Cas9 / gRNA RNP was delivered by electroporation. The gRNA targets the first exon of PDCD1.
[0059] Fig. 2F is a representative FCM plot of CAR expression in CAR-T cells with stable CAR expression.
[0060] Fig. 2G shows the percentage of CAR-T cells in all human T cells at different time points after Cas9 / RNP electroporation and AAV9-M1-CAR or AAV9-WT-CAR transduction (n=4 in each group) .
[0061] Fig. 2H shows the cytotoxicity of the stable CAR-T cells at different time points after AAV9-M1-CAR transduction. Each point represents data collected from one donor (n=4 in each group) .
[0062] Data were presented as mean±SEM. P values were calculated by Two-way ANOVA analysis. *P≤0.05; **P≤0.01; ***P≤0.001, ****P≤0.0001.
[0063] Figure 3 illustrates how AAV9-M1 delivers CAR sequences in vivo to generate functional CAR-T cells in a humanized mouse model.
[0064] Fig. 3A is a schematic view of the PBMC humanized mouse model. The corresponding dates of conducting operations are indicated below. AAV9-M1-CAR was dosed at 2 × 1011 vg / mouse, which is about 1 × 1013 vg / kg. (at day 14: n=6 in PBS group, n=8 in AAV9-M1-CAR group; at day 28: n=5 in PBS group, n=6 in AAV9-M1-CAR group. PBMC were from 3~4 donors) .
[0065] Fig. 3B shows the percentage of CAR-T cells in human T cells in multiple organs at day 14 after AAV9-M1-CAR delivery.
[0066] Fig. 3C shows the percentage of human B cells in all alive cells in multiple organs at day 14 after AAV9-M1-CAR delivery.
[0067] Fig. 3D shows the percentage of CAR-T cells in human T cells in multiple organs at day 28 after AAV9-M1-CAR delivery.
[0068] Fig. 3E shows the percentage of human B cells in all alive cells in multiple organs at day 28 after AAV9-M1-CAR delivery.
[0069] Fig. 3F is a schematic view of the PBMC+CDX humanized mouse model. The corresponding dates of conducting operations are indicated below. (at day 14: n=4 in PBS group, n=6 in AAV9-M1-CAR group; at day 28: n=8 in PBS group, n=9 in AAV9-M1-CAR group. PBMC were from 3~4 donors) .
[0070] Fig. 3G shows the percentage of CAR-T cells in human T cells in multiple organs at day 14 after AAV9-M1-CAR delivery.
[0071] Fig. 3H shows the percentage of human B cells in all alive cells in multiple organs at day 14 after AAV9-M1-CAR delivery.
[0072] Fig. 3I shows the percentage of NALM6 cells in all alive cells in multiple organs at day 14 after AAV9-M1-CAR delivery.
[0073] Fig. 3J shows the percentage of NALM6 cells in all alive cells in multiple organs at day 28 after AAV9-M1-CAR delivery.
[0074] Fig. 3K is an in vivo imaging of NLAM6 signal in humanized mice at day 0 and day 28 after AAV9-M1-CAR delivery.
[0075] Data were presented as mean±SEM; P values were calculated by unpaired T-test analysis in Fig. 3C, Fig. 3E, Fig. 3H, Fig. 3I, and Fig. 3J. *P≤0.05; **P≤0.01; ***P≤0.001, ****P≤0.0001.
[0076] Figure 4. AAV6-M2 generates functional CAR-T cells in a humanized mouse model.
[0077] Fig. 4A is a representative multi-histogram showing EGFP expression levels in human primary T cells following AAV6-WT-EGFP or AAV6-M-EGFP transduction at four different MOIs. The cells were collected three days post-transduction.
[0078] Fig. 4B is a schematic view of the PBMC humanized mouse model. The corresponding dates of conducting operations are indicated below. AAV6-M2-CAR was dosed at 2 × 1010 vg / mouse (~1 × 1012 vg / kg) or 2 × 109 vg / mouse (~1 × 1011 vg / kg) .
[0079] Fig. 4C shows the percentage of CAR-T cells in human T cells in multiple organs at day 14 after AAV delivery.
[0080] Fig. 4D shows the percentage of human B cells in all alive cells in multiple organs at day 14 after AAV delivery.
[0081] Fig. 4E shows the quantitative PCR quantified the accumulation of viral copies in the liver of the humanized mouse 14 days post AAV transduction.
[0082] Fig. 4F shows the percentage of CAR-T cells in human T cells in multiple organs at d28 after AAV delivery.
[0083] Fig. 4G shows the percentage of human B cells in all alive cells in multiple organs at d28 after AAV delivery.
[0084] Fig. 4H shows the quantitative PCR quantified the accumulation of viral copies in the liver of the humanized mouse 28 days post AAV transduction.
[0085] Data were presented as mean ± SEM. P values were calculated for Fig. 4D and Fig. 6G by unpaired T-test and Fig. 4E, Fig. 4F, and Fig. 4H by Two-way ANOVA analysis. *P≤0.05; **P≤0.01; ***P≤0.001, ****P≤0.0001.
[0086] Figure 5.
[0087] Fig. 5A is a schematic view of the genome-wide CRISPR knockout screening.
[0088] Fig. 5B is a volcano plot depicting genes ranked by MAGeCK LFC (log fold changes) and MAGeCK score in AAV6-M2 transduction screening. The top 10 genes enriched in the bottom 20%over the top 20%cells were shown in rectangles.
[0089] Fig. 5C is a volcano plot depicting genes ranked by MAGeCK LFC (log fold changes) and MAGeCK score in AAV6-WT transduction screening. The top 10 genes enriched in the bottom 20%over the top 20%cells were shown in rectangles.
[0090] Fig. 5D shows the percentage of EGFP+ Jurkat-Cas9 cells with indicated gene knocked out following AAV6-M2 transduction. Signals were collected on day 3 post AAV transduction. Each point represents data collected from a Jurkat-Cas9 clone.
[0091] Fig. 5E shows the percentage of EGFP+ Jurkat-Cas9 cells with indicated gene knocked out following AAV6-WT transduction. Signals were collected on day 3 post AAV transduction. Each point represents data collected from a Jurkat-Cas9 clone.
[0092] Data were presented as mean ± SEM. P values were calculated for Fig. 5D and Fig. 5E by One-way ANOVA analysis. *P≤0.05; **P≤0.01; ***P≤0.001, ****P≤0.0001.
[0093] Figure 6.
[0094] Fig. 6A shows the percentage of EGFP+ human primary T cells transduced with AAV9-WT-EGFP and AAV9-M-EGFP at MOI=104 at multiple time points.
[0095] Fig. 6B shows the packing efficiencies of AAV9-WT-EGFP and AAV9-M1-EGFP.
[0096] Fig. 6C shows the cell proliferation of human primary T cells transduced with AAV9-WT-EGFP and AAV9-M-EGFP at MOI=104 at multiple time points.
[0097] Fig. 6D shows the cell proliferation of human primary T cells transduced with AAV9-WT-EGFP and AAV9-M-EGFP at various MOI.
[0098] Data were presented as mean ± SEM. P values were calculated for Fig. 6A, Fig. 6C, and Fig. 6D by Two-way ANOVA analysis and Fig. 6B by Unpaired T-test. *P≤0.05; **P≤0.01; ***P≤0.001, ****P≤0.0001.
[0099] Figure 7.
[0100] Fig. 7A shows the cell number of human primary T cells transduced with AAV9-WT-CAR and AAV9-M1-CAR. Measurements were done at different time points post-transduction.
[0101] Fig. 7B shows the cell viability of human primary T cells transduced with AAV9-WT-CAR and AAV9-M1-CAR. Measurements were done at different time points post-transduction.
[0102] Fig. 7C is a representative gel image showing the PCR amplification products of junction sequences of the template insertion loci. M: marker; Left: 5’ junction; Right: 3’ junction.
[0103] Fig. 7D shows the cell number of human primary T cells electroporated with Cas9 / gRNA RNP and transduced with AAV9-WT-CAR and AAV9-M1-CAR. Measurements were done at different time points post-transduction.
[0104] Fig. 7E shows the cell viability of human primary T cells electroporated with Cas9 / gRNA RNP and transduced with AAV9-WT-CAR and AAV9-M1-CAR. Measurements were done at different time points post-transduction.
[0105] Data were presented as mean ± SEM. P values were calculated for Fig. 7A, Fig. 7B, Fig. 7D, and Fig. 7E by Two-way ANOVA analysis. *P≤0.05; **P≤0.01; ***P≤0.001, ****P≤0.0001.
[0106] Figure 8.
[0107] Fig. 8A shows the percentage of human T cells in all alive cells in multiple organs at d14 after AAV9-M1-CAR transduction into a PMBC humanized mouse model. n=6 in PBS group, n=8 in AAV9-M1-CAR group.
[0108] Fig. 8B shows the percentage of human T cells in all alive cells in multiple organs at d28 after AAV9-M1-CAR delivery. n=5 in PBS group, n=6 in AAV9-M1-CAR group.
[0109] Fig. 8C shows weight loss of mice at multiple time points after AAV9-M1-CAR transduction. n=5 inPBS group, n=6 in AAV9-M1-CAR group.
[0110] Data were presented as mean ± SEM. P values were calculated by unpaired T test analysis for Fig. 8A and Fig. 8B and by Two-way ANOVA analysis for Fig. 8C. *P≤0.05; **P≤0.01; ***P≤0.001, ****P≤0.0001.
[0111] Figure 9.
[0112] Fig. 9A shows the percentage of human T cells in all alive cells in multiple organs at d14 after AAV9-M1-CAR injection into a PMBC humanized mouse model with NALM6 transplanted. n=4 in PBS group, n=6 in AAV9-M1-CAR group.
[0113] Fig. 9B shows the percentage of human T cells in all alive cells in multiple organs at d28 after AAV9-M1-CAR injection. n=8 in PBS group, n=9 in AAV9-M1-CAR group.
[0114] Fig. 9C shows the weight loss of mice at multiple time points after AAV9-M1-CAR delivery. n=8 in PBS group, n=9 in AAV9-M1-CAR group.
[0115] Fig. 9D shows the percentage of CAR+ cells in human T cells in multiple organs at d28 after AAV9-M1-CAR injection. n=8 in PBS group, n=9 in AAV9-M1-CAR group.
[0116] Fig. 9E shows the percentage of human B cells in all alive cells in multiple organs at d28 after AAV9-M1-CAR injection. n=8 in the PBS group, n=9 in the AAV9-M1-CAR group.
[0117] Data were presented as mean ± SEM. P values were calculated for Fig. 9C by Two-way ANOVA analysis and Fig. 9A, Fig. 9B, and Fig. 9E by unpaired T-test. *P≤0.05; **P≤0.01; ***P≤0.001, ****P≤0.0001.
[0118] Figure 10.
[0119] Fig. 10A shows the percentage of EGFP+ cells in human primary T cells following AAV6-WT-EGFP, AAV6-M1-EGFP, and AAV6-M2-EGFP transduction at various MOI. Measurements were done three days post-transduction. n=3 in each group.
[0120] Fig. 10B shows the EGFP MFI in human primary T cells after AAV6-WT-EGFP, AAV6-M1-EGFP, and AAV6-M2-EGFP transduction at various MOI. Measurements were done three days post-transduction. n=2 in each group.
[0121] Fig. 10C shows the packing efficiencies of AAV6-WT-CAR, AAV6-M1-CAR, and AAV6-M2-CAR.
[0122] Fig. 10D shows the weight loss of mice at multiple time points after AAV6-M2-CAR injection.
[0123] Fig. 10E shows the percentage of human T cells in all alive cells in multiple organs at d14 after AAV6-M2-CAR injection.
[0124] Fig. 10F shows the percentage of human T cells in all alive cells in multiple organs at d28 after AAV6-M2-CAR injection.
[0125] Fig. 10G shows the quantification of AAV9-WT-CAR or AAV9-M1-CAR in the liver of humanized mouse at d14 post AAV injection. n=7 in AAV9-WT-CAR group, n=8 in AAV9-M1-CAR group.
[0126] Fig. 10H shows the quantification of AAV9-WT-CAR or AAV9-M1-CAR in the liver of humanized mouse at d28 post AAV injection. n=6 in AAV9-WT-CAR group, n=6 in AAV9-M1-CAR group.
[0127] Data were presented as mean ± SEM. P values were calculated for Fig. 10A, Fig. 10B, Fig. 10D by Two-way ANOVA analysis, Fig. 10C by One-way ANOVA analysis, and Fig. 10E and Fig. 10F by unpaired T-test. *P≤0.05; **P≤0.01; ***P≤0.001, ****P≤0.0001.
[0128] Figure 11.
[0129] Fig. 11A shows a predicted interaction interface between the engineered loop region of AAV6-M2 and CD62L. Top: Sticks indicate the interacting amino acids of the U-shaped loop of AAV6-M2 and in the binding pocket of CD62L, with one-letter amino acids labels on the side; predicted interactions were shown in dashed lines; Bottom: surface view of the binding pocket of CD62L and stick view of the U-shaped loop of AAV6-M2.
[0130] Fig. 11B is a volcano plot depicting genes ranked by MAGeCK LFC (log fold changes) and MAGeCK score in AAV9-M1 transduction screening. The top 10 genes enriched in the bottom 20%over the top 20%cells were shown in rectangles. KIAA0319L (AAVR) and TM9SF2 were in red. SLC35C2 was in green.
[0131] Fig. 11C shows the percentage of EGFP+ cells in Jurkat-Cas9 with indicated gene knockout following AAV9-M1 transduction at d3 post-transduction in multiple cell clones.
[0132] Fig. 11D is a volcano plot depicting genes ranked by MAGeCK LFC (log fold changes) and MAGeCK score in AAV9-WT transduction screening. The top 10 genes enriched in the bottom 20%over the top 20%cells were shown in rectangles. KIAA0319L (AAVR) and TM9SF2 were in red. SLC35C2 was in green.
[0133] Fig. 11E shows the percentage of EGFP+ cells in Jurkat-Cas9 with indicated gene knockout following AAV9-WT transduction at d3 post-transduction in multiple cell clones.
[0134] Figure 12.
[0135] Figs. 12A, 12B, 12C, and 12D show Seq-logo plots illustrating motifs with blood cell tropism.DETAILED DESCRIPTIONDefinitions
[0136] All publications, patents, and patent applications referred to herein are incorporated by reference in their entirety to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference in its entirety.
[0137] In the present disclosure, unless otherwise specified, the scientific and technical terms used herein have meanings generally understood by a person skilled in the art. Although any methods and materials similar or equivalent to those described herein find use in the practice of the present disclosure, the preferred methods and materials are described herein. Accordingly, the terms defined herein are more fully described by reference to the Specification as a whole.
[0138] As used herein, the singular terms “a, ” “an, ” and “the” include the plural reference unless the context clearly indicates otherwise.
[0139] As used herein, “and / or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative ( “or” ) . Moreover, the present invention also contemplates that in some embodiments of the invention, any feature or combination of features set forth herein can be excluded or omitted.
[0140] Unless the context requires otherwise, the terms “comprise, ” “comprises, ” and “comprising, ” or similar terms are intended to mean a non-exclusive inclusion, such that a recited list of elements or features does not include those stated or listed elements solely, but may include other elements or features that are not listed or stated.
[0141] Unless otherwise indicated, nucleic acids are written left to right in the 5' to 3' orientation, and amino acid sequences are written left to right in amino to carboxy orientation, respectively. A number “n” , when used in the context of an amino acid sequence, refers to the nth amino acid in the amino acid sequence counting from the amino end. For example, “amino acid 15” refers to the 15th amino acid in a certain amino acid sequence. As used herein, in some embodiments, amino acid is written as a combination of letter and number, such as “A581” and “T593” . The letter before the number represents the original amino acid at a certain position in a particular sequence. The number represents the position of the amino acid in the particular sequence, counting from N terminus. For example, “A581” refers to the 581st amino acid, which is an alanine (A) , in a certain amino acid sequence. “T593” refers to the 593rd amino acid, which is a threonine (T) , in a certain amino acid sequence.
[0142] It is to be understood that this disclosure is not limited to the particular methodology, protocols, and reagents described, as these may vary, depending upon the context in which they are used by those skilled in the art.
[0143] As used herein, the term “about” will be understood by persons of ordinary skill in the art and will vary to some extent depending on the context in which it is used. In some embodiments, the term “about” when referring to a value is meant to encompass art-accepted variations. In some embodiments, the term “about” when referring to such values, is meant to encompass variations of ±20%or ±10%, more preferably ±5%, even more preferably ±1%, and still more preferably ±0.1%from the specified value, as such variations are appropriate in the context in which the term “about” is used.
[0144] As used herein, the terms “percent identity” and “%identity, ” as applied to nucleic acid or polynucleotide sequences, refer to the percentage of residue matches between at least two nucleic acid or polynucleotide sequences aligned using a standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize alignment between two sequences, and therefore achieve a more meaningful comparison of the two sequences.
[0145] Percent identity between nucleic acid or polynucleotide sequences may be determined using a suite of commonly used and freely available sequence comparison algorithms provided by the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) (Altschul, S. F. et al. J. Mol. Biol. 215: 403-410, (1990) ) , which is available from several sources, including the NCBI, Bethesda, Md., and on the Internet at http: / / www. ncbi. nlm. nih. gov / BLAST / .
[0146] Nucleic acid or polynucleotide sequences that do not show a high degree of identity may nevertheless encode similar amino acid sequences due to the degeneracy of the genetic code. It is understood that changes in a nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid sequences that all encode substantially the same protein. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and / or deoxyinosine residues (Batzer et al. (1991) Nucleic Acid Res 19: 5081; Ohtsuka et al. (1985) J Biol Chem 260: 2605-2608; Cassol et al. (1992) ; Rossolini et al. (1994) Mol Cell Probes 8: 91-98) . The term “nucleic acid” refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single-or double-stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogues of natural nucleotides which have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. The term nucleic acid is used interchangeably with polynucleotide, and (in appropriate contexts) gene, cDNA, and mRNA encoded by a gene. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) , alleles, orthologs, SNPs, and complementary sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and / or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19: 5081 (1991) ; Ohtsuka et al., J. Biol. Chem. 260: 2605-2608 (1985) ; and Rossolini et al., Mol. Cell. Probes 8: 91-98 (1994) ) .
[0147] As used herein, “percent (%) amino acid sequence identity” with respect to a peptide, polypeptide or protein sequence is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in another peptide or polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Percent amino acid sequence identity in the current disclosure is measured using BLAST software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
[0148] An amino acid substitution refers to the replacement of one amino acid in a polypeptide with another amino acid. Amino acid substitutions can be conservative or non-conservative substitutions. Amino acid substitutions may be introduced into a protein of interest and the products screened for a desired activity, for example, retained / improved biological activity.
[0149] Amino acids may be grouped according to common side-chain properties:
[0150] (1) hydrophobic: Norleucine, Met, Ala, Val, Leu, Ile;
[0151] (2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gln;
[0152] (3) acidic: Asp, Glu;
[0153] (4) basic: His, Lys, Arg;
[0154] (5) residues that influence chain orientation: Gly, Pro;
[0155] (6) aromatic: Trp, Tyr, Phe.
[0156] The term “polypeptide” is intended to encompass a singular “polypeptide” as well as plural “polypeptides, ” and refers to a molecule composed of monomers (amino acids) linearly linked by amide bonds (also known as peptide bonds) . The term “polypeptide” refers to any chain or chains of two or more amino acids, and does not refer to a specific length of the product. Thus, “peptides, ” “protein” , or any other term used to refer to a chain or chains of two or more amino acids, are included within the definition of “polypeptide, ” and the term “polypeptide” may be used instead of, or interchangeably with any of these terms. The term “polypeptide” is also intended to refer to the products of post-expression modifications of the polypeptide, including without limitation glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting / blocking groups, proteolytic cleavage, or modification by non-naturally occurring amino acids. A polypeptide may be derived from a natural biological source or produced by recombinant technology, but is not necessarily translated from a designated nucleic acid sequence. It may be generated in any manner, including by chemical synthesis.
[0157] As used herein, the term “encode” or “encoding” as it is applied to polynucleotides refers to a polynucleotide which is said to “encode” a polypeptide if, in its native state or when manipulated by methods well known to those skilled in the art, it can be transcribed and / or translated to produce the mRNA for the polypeptide and / or a fragment thereof. The antisense strand is the complement of such a nucleic acid, and the encoding sequence can be deduced therefrom.
[0158] The term “genetic modification” and its grammatical equivalents, as used herein can refer to one or more alterations of a nucleic acid, e.g., the nucleic acid within an organism’s genome. For example, genetic modification can refer to alterations, additions, and / or deletion of genes or portions of genes or other nucleic acid sequences. A genetically modified cell can also refer to a cell with an added, deleted, and / or altered gene or portion of a gene. A genetically modified cell can also refer to a cell with an added nucleic acid sequence that is not a gene or gene portion. Genetic modifications include, for example, both transient knock-in or knock-down mechanisms, and mechanisms that result in permanent knock-in, knock-down, or knock-out of target genes or portions of genes or nucleic acid sequences. Genetic modifications include, for example, both transient knock-in and mechanisms that result in permanent knock-in of nucleic acids sequences. Genetic modifications also include, for example, reduced or increased transcription, reduced or increased mRNA stability, reduced or increased translation, and reduced or increased protein stability.
[0159] Unless otherwise specified, a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. The phrase nucleotide sequence that encodes a protein or an RNA may also include introns to the extent that the nucleotide sequence encoding the protein may in some version contain an intron (s) .
[0160] The term “expression” refers to the transcription and / or translation of a particular nucleotide sequence driven by its promoter.
[0161] The term “effective amount” or “therapeutically effective amount” is used interchangeably herein, and refer to an amount of a compound, formulation, material, or composition, as described herein effective to achieve a particular biological result. The term “endogenous” refers to any material from or produced inside an organism, cell, tissue or system.
[0162] As used herein, a composition refers to any mixture of two or more products, substances, or compounds, including cells.
[0163] The term “transfer vector” or “vector” refers to a composition of matter which comprises an isolated nucleic acid and which can be used to deliver the isolated nucleic acid to the interior of a cell. Numerous vectors are known in the art including, but not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses. The term “transfer vector” includes an autonomously replicating plasmid or a virus. The term should also be construed to further include non-plasmid and non-viral compounds which facilitate transfer of nucleic acid into cells, such as, for example, a polylysine compound, liposome, and the like. Examples of viral transfer vectors include, but are not limited to, adenoviral vectors, adeno-associated virus vectors, retroviral vectors, lentiviral vectors, and the like.
[0164] As used herein, “subject” refers to any animals, such as human.
[0165] As used herein, recombinant AAV (rAAV) refers to an AAV with rearranged DNA. In some embodiments, an rAAV is produced by removing the viral DNA from an AAV and replacing it with the transgene of interest. In some embodiments, the replication (rep) and capsid protein (cap) genes in an AAV is replaced by a transgene to obtain a rAAV.
[0166] As used herein, an amino acid sequence in a polypeptide which is analogous to a reference sequence in a reference polypeptide refers to an amino acid sequence that is similar or identical to the reference sequence, wherein the two amino acid sequences are in a conserved region shared by both polypeptides. In some embodiments, the “analogous” sequence is identified by (1) aligning the polypeptides’s equences, (2) identify the conserved region shared by the two polypeptides, (3) aligning the conserved region of the two polypeptides and the sequence that aligned with the reference sequence is the “analogous sequence. ” In some embodiments, the analogous sequence has at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%sequence identity to the reference sequence. A conserved region shared by two polypeptides refers to the similar or identical regions in the two polypeptides, which may be responsible for a specific structural characteristic of the polypeptides. In some embodiments, the conserved regions of the two polypeptides have at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%sequence identity. Engineered Viral Capsid Polypeptides
[0167] The present disclosure provides engineered viral capsid polypeptide and engineered AAV variants with enhanced T cell tropism. In some embodiments, the engineered viral capsid polypeptide is obtained by genetically modification in the variable region (VR) .
[0168] A capsid is the protein shell of a virus, enclosing its genetic material. There are multiple types of capsids, including spiral-shaped capsid, icosahedral-shaped capsid, and sphere capsid. The wild-type adeno-associated virus (AAV) capsid is made up of three different capsid protein isoforms (VP1, VP2, and VP3) . The entire sequence of VP3 is contained within VP2, and all VP2 is contained within VP1, which has a unique N-terminal (VP1u) domain. Only the common VP3 region is observed in all of the capsid structures of AAV serotypes determined to date. Comparisons of the AAV structures show that the core of each VP contains an eight-stranded β-barrel motif (βB to βI) and an α-helix (αA) that are also conserved in autonomous parvovirus capsids. Structurally variable regions (VRs) occur in the surface loops that connect the β-strands, which cluster to produce local variations in the capsid surface. Differences in the conformations of the VRs are predicted to dictate the variability of cellular tropism (both in vitro and in vivo) , tissue transduction efficiency, and antigenic reactivity that is observed among the serotypes. AAVs have 12 variable regions (also referred to as hypervariable regions) (see e.g., Weitzman and Linden. 2011. “Adeno-Associated Virus Biology. ” In Snyder, R. O., Moullier, P. (eds. ) Totowa, N. J. : Humana Press) .
[0169] In an aspect, the present disclosure provides an engineered viral capsid polypeptide, comprising an amino acid sequence of any one of SEQ ID NOs: 1-2105 and 2149-9287. In some embodiments of the engineered viral capsid polypeptide, the amino acid sequence is located within a variable region in the viral capsid polypeptide.
[0170] In some embodiments of the engineered viral capsid polypeptide, the engineered viral capsid polypeptide has tropism to T cells. In some embodiments, the T cells are primary T cells. In some embodiments, the T cells are human T cells. In some embodiments, the T cell is a CD4+ T cell. In some embodiments, the T cell is a CD8+ T cell. Table 1A presents the fold changes in the tropism to T cells of each of the engineered viral capsid polypeptide disclosed herein, compared to the parental or wild-type capsid polypeptide. The fold change was calculated by dividing the mean value of the viral copies transduced into human primary T cells by an AAV variant by the mean value of the viral copies transduced into human primary T cells by a parental or wild-type AAV, wherein the AAV variant is an AAV that uses a different capsid protein compared to its parental or wild-type AAV. A higher fold change indicates that the engineered viral capsid polypeptide has stronger tropism to T cells and / or higher transduction efficiencies. In some embodiments, the fold changes range from about 1 to about 20 folds, such as, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 folds. In some embodiments, the fold changes range from about 1 to about 2 folds. In some embodiments, the fold changes range from about 2 to about 8 folds. In some embodiments, the fold changes range from about 8 to about 10 folds. In some embodiments, the fold changes range from about 8 to about 15 folds. In some embodiments, the fold change is more than 8 folds. As used in Table 1A, “n+ fold” refers to a fold change larger than n. for example, “8+ fold” means that the fold change is larger than 8.
[0171] As used herein, “tropism” or “tropic” refers to increased target cell specificity and / or reduced non-target cell specificity, e.g., as compared to a parental or wildtype capsid polypeptide or as compared to a parental or wildtype AAV. The target cell can be any cells of a subject, such as a neuronal cell, a neural stem cell, an astrocyte, an oligodendrocyte, a microglia cell, a retinal cell, a tumor cell, a hematopoietic stem cell, an insulin producing beta cell, a lung epithelium cell, an endothelial cell, a liver cell, a skeletal muscle cell, a muscle stem cell, a muscle satellite cell, or a cardiac muscle cell.
[0172] For example, an engineered viral capsid polypeptide having tropism to a cell, a tissue, an organ, or a species means that a viral particle containing the viral capsid polypeptide has an increased uptake, delivery rate, transduction rate, efficiency, amount, or a combination thereof in a target cell, a target tissue, a target organ, or a target species as compared to a viral particle comprising a parental or wild-type viral capsid polypeptide. As another example, an engineered virus having increased tropism to a cell, a tissue, an organ, or a species means that the virus has an increased uptake, delivery rate, transduction rate, efficiency, amount, or a combination thereof in a target cell, a target tissue, a target organ, or a target species as compared to a parental or wild-type virus.
[0173] In some embodiments of the engineered viral capsid polypeptide, the viral capsid polypeptide is a viral capsid polypeptide of an adeno-associated virus (AAV) .
[0174] Engineered viral capsids can be variants of a parental viral capsid such as a wild-type viral capsid. For example, in some embodiments, the engineered AAV capsids can be variants of wild-type AAV capsids. In some embodiments, the serotype of the reference (also called “parental” herein) wild-type AAV capsid can be AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV8, AAV9, etc., or any combination thereof. In some embodiments, the serotype of the wild-type AAV capsid is AAV9 or AAV6. The engineered AAV capsids can have a different tropism than that of the reference wild-type AAV capsid.
[0175] As used herein, the term "serotype" is a distinction used to refer to an AAV having a capsid that is serologically distinct from other AAV serotypes. Serologic distinctiveness is determined on the basis of the lack of cross-reactivity between antibodies to one AAV as compared to another AAV. Such cross-reactivity differences are usually due to differences in capsid protein sequences / antigenic determinants (e.g., due to VP1, VP2, and / or VP3 sequence differences of AAV serotypes) .
[0176] In some embodiments of the engineered viral capsid polypeptide, the engineered viral capsid polypeptide is a viral capsid polypeptide of an engineered adeno associated virus derived from a parental virus selected from AAV1, AAV2, AAV3, AAV3B, AAV4, AAV5, AAV6, AAV6.2, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, AAV13, AAVrh74, AAVrh10, AAVDJ, AAVDJ / 8, AAV-PHP. eB, AAV-PHP. S, AAV2-retro, AAV2-QuadYF, AAV2.7m8, and Avian AAV.
[0177] In some embodiments, the engineered viral capsid polypeptide is a viral capsid polypeptide of an engineered AAV9, and the amino acid sequence is any one of SEQ ID NOs: 1-1007, 2149-2261, and 2945-6269. In some embodiments, the amino acid sequence replaces a sequence in the viral capsid polypeptide analogous to a sequence from T582 to Q592 of SEQ ID NO: 2107. In some embodiments, the engineered viral capsid polypeptide is capable of binding to SLC35C2. In some embodiments, the engineered viral capsid polypeptide comprises SEQ ID NO: 109 and is capable of binding to SLC35C2. Solute carrier family 35 member C2 (SLC35C2) is a protein that in human is encoded by the SLC35C2 gene (Ensembl: ENSG00000080189) . SLC35C2 is related to endosomal / Golgi trafficking, which plays a role in AAV transduction (Meyer and Chapman, 2021) .
[0178] MAADGYLPDWLEDNLSEGIREWWALKPGAPQPKANQQHQDNARGLVLPGY KYLGPGNGLDKGEPVNAADAAALEHDKAYDQQLKAGDNPYLKYNHADAEFQERLKE DTSFGGNLGRAVFQAKKRLLEPLGLVEEAAKTAPGKKRPVEQSPQEPDSSAGIGKSGAQ PAKKRLNFGQTGDTESVPDPQPIGEPPAAPSGVGSLTMASGGGAPVADNNEGADGVGSS SGNWHCDSQWLGDRVITTSTRTWALPTYNNHLYKQISNSTSGGSSNDNAYFGYSTPWG YFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTDNNGVKTIANNLTST VQVFTDSDYQLPYVLGSAHEGCLPPFPADVFMIPQYGYLTLNDGSQAVGRSSFYCLEYF PSQMLRTGNNFQFSYEFENVPFHSSYAHSQSLDRLMNPLIDQYLYYLSKTINGSGQNQQ TLKFSVAGPSNMAVQGRNYIPGPSYRQQRVSTTVTQNNNSEFAWPGASSWALNGRNSL MNPGPAMASHKEGEDRFFPLSGSLIFGKQGTGRDNVDADKVMITNEEEIKTTNPVATES YGQVATNHQSAQAQAQTGWVQNQGILPGMVWQDRDVYLQGPIWAKIPHTDGNFHPS PLMGGFGMKHPPPQILIKNTPVPADPPTAFNKDKLNSFITQYSTGQVSVEIEWELQKENS KRWNPEIQYTSNYYKSNNVEFAVNTEGVYSEPRPIGTRYLTRNL (SEQ ID NO: 2107) is a reference AAV9 capsid sequence where exemplary insertion site are highlighted (bolded and underlined) . In some embodiments, the engineered polypeptide sequences can be inserted between any two contiguous amino acids within the insertion site. In some embodiments, other genetic modifications are introduced into the insertion site, including amino acid insertion, deletion, and substitution. In some embodiments, the 11 underlined amino acids in the insertion site as shown in SEQ ID NO: 2107 are replaced by any of SEQ ID NOs: 1-1007, 2149-2261, and 2945-6269. A person skilled in the art would be able to identify an analogous sequence in other analogous AAV viral capsid polypeptides by aligning the analogous AAV viral capsid polypeptide sequence with SEQ ID NO: 2107. Sequence alignment tools, such as the Basic Local Alignment Search Tool (BLAST) , are readily available. In some embodiments, the insertion site is located within the variable region VIII (VR-VIII) of the AAV9 capsid protein.
[0179] In some embodiments, the engineered viral capsid polypeptide is a viral capsid polypeptide of an engineered AAV6, and the amino acid sequence is any one of SEQ ID NOs: 1008-2105, 2262-2944, and 6270-9287. In some embodiments, the amino acid sequence replaces a sequence in the viral capsid polypeptide analogous to a sequence from V582 to A592 of SEQ ID NO: 2106. In some embodiments, the engineered viral capsid polypeptide is capable of binding to CD62L. In some embodiments, the engineered viral capsid polypeptide comprises SEQ ID NO: 1660 and is capable of binding to CD62L. CD62L, also known as L-selectin, is a cell adhesion molecule found on the surface of leukocytes and the blastocyst. CD62L is encoded by the SELL gene (Ensembl: ENSG00000188404) .
[0180] MAADGYLPDWLEDNLSEGIREWWDLKPGAPKPKANQQKQDDGRGLVLPGY KYLGPFNGLDKGEPVNAADAAALEHDKAYDQQLKAGDNPYLRYNHADAEFQERLQED TSFGGNLGRAVFQAKKRVLEPFGLVEEGAKTAPGKKRPVEQSPQEPDSSSGIGKTGQQP AKKRLNFGQTGDSESVPDPQPLGEPPATPAAVGPTTMASGGGAPMADNNEGADGVGN ASGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWG YFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANNLTST VQVFSDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYF PSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLNRTQNQSGSAQN KDLLFSRGSPAGMSVQPKNWLPGPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRE SIINPGTAMASHKDDKDKFFPMSGVMIFGKESAGASNTALDNVMITDEEEIKATNPVAT ERFGTVAVNLQSSSTDPATGDVHVMGALPGMVWQDRDVYLQGPIWAKIPHTDGHFHP SPLMGGFGLKHPPPQILIKNTPVPANPPAEFSATKFASFITQYSTGQVSVEIEWELQKENS KRWNPEVQYTSNYAKSANVDFTVDNNGLYTEPRPIGTRYLTRPL (SEQ ID NO: 2106) is a reference AAV6 capsid sequence where exemplary insertion site are highlighted (bolded and underlined) . In some embodiments, the engineered polypeptide sequences can be inserted between any two contiguous amino acids within the insertion site. In some embodiments, other genetic modifications are introduced into the insertion site, including amino acid insertion, deletion, and substitution. In some embodiments, the 11 underlined amino acids in the insertion site as shown in SEQ ID NO: 2106 are replaced by any of SEQ ID NOs: 1008-2105, 2262-2944, and 6270-9287. A person skilled in the art would be able to identify an analogous sequence in other analogous AAV viral capsid polypeptides by aligning the analogous AAV viral capsid polypeptide sequence with SEQ ID NO: 2106. Sequence alignment tools, such as the Basic Local Alignment Search Tool (BLAST) , are readily available. In some embodiments, the insertion site is located within the variable region VIII (VR-VIII) of the AAV9 capsid protein.
[0181] In some embodiments, the engineered viral capsid polypeptide comprises an amino acid sequence, wherein the amino acid sequence comprises a motif with a string of amino acid residues having a particular pattern. In some embodiments, the motif comprises a string of five to eight six amino acid residues having a particular pattern.
[0182] In some embodiments, the engineered viral capsid polypeptide comprises an amino acid sequence, wherein the amino acid sequence comprises a motif represented as X0X1X2X3X4Y, wherein X0, X1, X2, and X4 are each an amino acid residue, wherein X0 is Aspartate (D) or Glutamate (E) , X3 is an amino acid residue or absent, and Y is Tyrosine. For example, this motif can be denoted as [D|E] X1X2X3X4Y. In some embodiments, X3 is absent such that the motif can be represented as [D|E] X1X2X4Y. In some embodiments, X1 is Lysine (K) . In some embodiments, X4 is Proline (P) , Alanine (A) , Threonine (T) , or Valine (V) . In some embodiments, X4 is Proline (P) . In some embodiments, X4 is Alanine (A) . In some embodiments, X4 is Threonine (T) . In some embodiments, X4 is Valine (V) . In some embodiments, X4 is preferably Proline (P) or Alanine (A) . In some embodiments, the engineered viral capsid polypeptide comprises any one of SEQ ID NOs: 177, 323, 418, 427, 456, 463, 511, 552, 553, 735, 873, 1142, 1178, 1199, 1303, 1327, 1431, 1439, 1440, 1441, 1443, 1444, 1445, 1449, 1452, 1453, 1473, 1476, 1480, 1486, 1488, 1490, 1491, 1508, 1512, 1513, 1515, 1518, 1522, 1523, 1558, 1679, 1683, 1684, 1685, 1686, 1687, 1688, 1691, 1692, 1693, 1699, 1700, 1705, 1709, 1714, 1715, 1716, 1717, 1723, 1724, 1725, 1726, 1727, 1728, 1779, 1855, 1856, 1861, 1913, 2054, 2141, 2332, 2339, 2366, 2367, 2368, 2375, 2377, 2384, 2386, 2387, 2508, 2509, 2529, 2972, 3051, 3268, 3538, 3888, 4028, 4122, 4252, 4279, 4280, 4720, 4891, 5144, 5148, 5168, 5275, 5343, 5365, 5392, 5528, 5537, 5609, 5670, 5743, 5744, 5745, 5746, 5747, 5873, 6184, 6288, 6309, 6312, 6327, 6328, 6401, 6424, 6511, 6749, 6767, 6769, 6773, 6803, 6816, 6817, 6818, 6905, 6935, 6965, 6972, 6987, 7228, 7269, 7331, 7385, 7416, 7424, 7469, 7470, 7471, 7476, 7481, 7495, 7497, 7508, 7526, 7527, 7539, 7544, 7562, 7623, 7650, 7685, 7770, 7916, 7937, 7938, 7939, 7940, 7941, 7942, 7943, 7944, 7945, 7946, 7947, 7950, 7951, 7952, 7953, 7954, 7955, 7956, 7957, 7958, 7959, 7960, 7961, 7962, 7963, 7964, 7965, 7966, 7967, 7968, 7969, 7970, 7971, 7972, 7973, 7974, 7975, 7976, 7977, 7978, 7979, 7980, 7981, 7982, 7983, 7984, 7985, 7986, 7987, 7988, 7989, 7990, 7991, 7992, 7993, 7994, 7995, 7996, 7997, 7998, 7999, 8000, 8001, 8002, 8003, 8004, 8005, 8006, 8007, 8008, 8009, 8010, 8011, 8012, 8013, 8014, 8015, 8016, 8017, 8018, 8019, 8020, 8021, 8022, 8023, 8024, 8025, 8026, 8027, 8028, 8029, 8030, 8031, 8032, 8033, 8034, 8035, 8036, 8037, 8038, 8039, 8040, 8041, 8042, 8043, 8044, 8045, 8046, 8047, 8048, 8049, 8050, 8052, 8053, 8054, 8055, 8057, 8058, 8059, 8060, 8061, 8062, 8063, 8064, 8065, 8066, 8070, 8071, 8073, 8074, 8075, 8076, 8077, 8078, 8079, 8081, 8082, 8083, 8084, 8085, 8086, 8087, 8088, 8089, 8090, 8091, 8092, 8093, 8094, 8095, 8096, 8097, 8098, 8099, 8100, 8101, 8102, 8103, 8104, 8105, 8106, 8107, 8108, 8109, 8110, 8112, 8113, 8114, 8115, 8116, 8117, 8118, 8119, 8120, 8121, 8122, 8123, 8124, 8315, 8357, 8423, 8445, 8494, 8600, 8697, 8787. In some embodiments, the engineered viral capsid polypeptide comprises any one of SEQ ID NOs: 33, 147, 314, 320, 546, 737, 870, 945, 967, 970, 1037, 1050, 1110, 1142, 1157, 1178, 1199, 1269, 1303, 1327, 1431, 1464, 1476, 1483, 1486, 1490, 1491, 1529, 1549, 1558, 1576, 1625, 1666, 1679, 1714, 1716, 1717, 1734, 1735, 1736, 1752, 1778, 1779, 1855, 1856, 1870, 1913, 2054, 2156, 2331, 2332, 2339, 2366, 2367, 2368, 2375, 2377, 2384, 2386, 2388, 2430, 2504, 2578, 2739, 2740, 2799, 3089, 3090, 3178, 3237, 3252, 3253, 3299, 3404, 3410, 3443, 3467, 3665, 3772, 3876, 3893, 3925, 4028, 4102, 4158, 4276, 4365, 4583, 4589, 4607, 4635, 4658, 4884, 4890, 4990, 5008, 5142, 5148, 5151, 5159, 5305, 5325, 5326, 5365, 5393, 5465, 5479, 5485, 5572, 5670, 5692, 5706, 5770, 5790, 5865, 5928, 5974, 6001, 6005, 6017, 6197, 6236, 6238, 6318, 6319, 6338, 6348, 6349, 6350, 6371, 6452, 6463, 6467, 6610, 6724, 6736, 6748, 6749, 6800, 6804, 6848, 6852, 6920, 6966, 6967, 6975, 7010, 7155, 7197, 7202, 7222, 7243, 7269, 7295, 7424, 7495, 7503, 7504, 7508, 7573, 7603, 7607, 7609, 7610, 7616, 7641, 7650, 7685, 7694, 7695, 7696, 7697, 7702, 7708, 7728, 7729, 7730, 7731, 7733, 7734, 7735, 7746, 7755, 7770, 7791, 7793, 7795, 7815, 7825, 7830, 7834, 7835, 7919, 7920, 7921, 7923, 7924, 7925, 7926, 7927, 7928, 7929, 8125, 8126, 8128, 8129, 8130, 8131, 8138, 8139, 8140, 8141, 8144, 8145, 8146, 8147, 8148, 8149, 8150, 8151, 8152, 8153, 8160, 8161, 8163, 8168, 8170, 8171, 8172, 8174, 8247, 8248, 8249, 8250, 8315, 8331, 8353, 8394, 8423, 8445, 8460, 8462, 8492, 8666, 8734, 8775, 8800, 8813, 8828, 8864, 9189.
[0183] In some embodiments, the engineered viral capsid polypeptide comprises an amino acid sequence, wherein the amino acid sequence comprises a poly [D|E] motif. A “poly [D|E] motif” as used herein means that within a string of five or six amino acid residues in an engineered viral capsid polypeptide, the string includes no less than three D, or no less than three E, or no less than a three-letter (three amino acid residues) combination of D and E. In some embodiments, the amino acid residues D and / or E are consecutively connected. In some embodiments, the engineered viral capsid polypeptide comprises any one of SEQ ID NOs: 29, 51, 64, 171, 590, 633, 637, 647, 648, 707, 730, 1025, 1026, 1042, 1045, 1054, 1055, 1061, 1082, 1084, 1100, 1106, 1107, 1108, 1109, 1111, 1124, 1130, 1131, 1141, 1142, 1145, 1148, 1152, 1153, 1154, 1155, 1156, 1161, 1162, 1163, 1178, 1181, 1191, 1192, 1193, 1195, 1196, 1199, 1262, 1268, 1269, 1278, 1279, 1280, 1285, 1293, 1298, 1300, 1303, 1307, 1310, 1321, 1324, 1358, 1366, 1400, 1402, 1415, 1419, 1429, 1430, 1484, 1485, 1493, 1506, 1509, 1534, 1554, 1555, 1556, 1558, 1559, 1563, 1565, 1566, 1568, 1571, 1580, 1581, 1588, 1612, 1616, 1629, 1655, 1657, 1658, 1663, 1680, 1751, 1769, 1779, 1790, 1818, 1823, 1825, 1832, 1833, 1835, 1845, 1846, 1848, 1849, 1850, 1851, 1855, 1856, 1872, 1873, 1874, 1877, 1878, 1880, 1885, 1888, 1889, 1891, 1894, 1895, 1896, 1900, 1902, 1904, 1910, 1911, 1913, 1914, 1942, 1947, 1958, 1959, 1964, 1966, 1975, 1978, 1990, 1991, 2004, 2016, 2017, 2018, 2019, 2020, 2021, 2051, 2053, 2054, 2055, 2059, 2060, 2062, 2065, 2068, 2070, 2071, 2072, 2074, 2075, 2076, 2077, 2078, 2079, 2081, 2082, 2086, 2087, 2089, 2090, 2091, 2100, 2102, 2142, 2157, 2215, 2277, 2279, 2313, 2321, 2331, 2332, 2333, 2335, 2336, 2337, 2338, 2339, 2342, 2343, 2345, 2353, 2357, 2358, 2363, 2367, 2375, 2376, 2377, 2378, 2381, 2385, 2388, 2395, 2396, 2401, 2406, 2407, 2412, 2415, 2416, 2418, 2422, 2428, 2429, 2430, 2431, 2444, 2483, 2484, 2485, 2486, 2487, 2524, 2525, 2530, 2533, 2538, 2539, 2540, 2565, 2576, 2577, 2578, 2634, 2635, 2646, 2692, 2694, 2700, 2709, 2738, 2739, 2740, 2786, 2787, 2788, 2796, 2799, 2801, 2818, 2832, 2838, 2841, 2844, 2849, 2867, 2905, 2915, 2924, 2937, 2994, 2995, 2996, 3001, 3005, 3006, 3007, 3009, 3036, 3049, 3052, 3053, 3064, 3065, 3071, 3075, 3155, 3257, 3276, 3280, 3534, 3566, 3567, 3568, 3569, 3571, 3577, 3578, 3579, 3582, 3590, 3592, 3616, 3617, 3624, 3676, 3704, 3749, 3785, 3793, 3794, 3795, 3796, 3797, 3801, 3802, 3808, 3809, 3832, 3838, 3989, 4006, 4116, 4130, 4181, 4320, 4348, 4349, 4386, 4397, 4500, 4501, 4502, 4503, 4507, 4508, 4509, 4510, 4511, 4512, 4513, 4514, 4515, 4516, 4517, 4518, 4519, 4521, 4522, 4523, 4525, 4526, 4533, 4534, 4535, 4536, 4537, 4538, 4541, 4542, 4562, 4680, 4689, 4690, 4692, 4701, 4702, 4703, 4707, 4726, 4744, 4747, 4758, 4775, 4776, 4778, 4780, 4781, 4793, 4795, 4799, 4819, 4829, 4841, 4842, 4843, 4845, 4878, 4880, 4888, 4968, 5010, 5139, 5152, 5305, 5413, 5609, 5777, 5897, 6007, 6155, 6282, 6290, 6291, 6292, 6306, 6307, 6311, 6312, 6339, 6363, 6365, 6374, 6376, 6390, 6395, 6396, 6408, 6412, 6413, 6423, 6424, 6429, 6431, 6437, 6439, 6460, 6473, 6491, 6502, 6505, 6506, 6507, 6512, 6520, 6521, 6531, 6544, 6554, 6586, 6605, 6606, 6607, 6610, 6617, 6618, 6638, 6665, 6668, 6686, 6707, 6712, 6713, 6716, 6748, 6749, 6750, 6779, 6782, 6783, 6785, 6796, 6803, 6832, 6861, 6862, 6863, 6866, 6867, 6868, 6869, 6870, 6871, 6892, 6895, 6896, 6915, 6920, 6923, 6924, 6933, 6947, 6953, 6955, 6958, 6965, 6967, 6970, 6973, 6975, 6976, 6977, 6985, 7004, 7005, 7007, 7010, 7016, 7020, 7030, 7045, 7046, 7052, 7056, 7057, 7058, 7059, 7063, 7074, 7075, 7076, 7173, 7179, 7181, 7182, 7184, 7185, 7187, 7194, 7196, 7197, 7198, 7203, 7218, 7223, 7224, 7225, 7226, 7227, 7228, 7235, 7254, 7257, 7271, 7275, 7280, 7283, 7285, 7290, 7292, 7298, 7302, 7314, 7322, 7326, 7331, 7339, 7372, 7378, 7398, 7399, 7404, 7405, 7408, 7421, 7422, 7423, 7424, 7426, 7427, 7435, 7446, 7449, 7460, 7462, 7477, 7483, 7484, 7486, 7490, 7491, 7495, 7496, 7502, 7509, 7514, 7516, 7545, 7549, 7582, 7589, 7592, 7597, 7601, 7623, 7632, 7633, 7647, 7650, 7651, 7652, 7653, 7654, 7655, 7664, 7670, 7685, 7706, 7708, 7710, 7711, 7712, 7713, 7714, 7724, 7725, 7726, 7727, 7741, 7742, 7745, 7748, 7749, 7750, 7751, 7752, 7753, 7754, 7759, 7768, 7770, 7771, 7777, 7778, 7782, 7785, 7788, 7789, 7792, 7798, 7799, 7802, 7806, 7807, 7819, 7824, 7827, 7839, 7843, 7845, 7848, 7856, 7857, 7860, 7863, 7867, 7877, 7886, 7891, 7896, 7897, 7898, 7914, 8068, 8156, 8164, 8188, 8191, 8201, 8204, 8222, 8232, 8278, 8279, 8285, 8292, 8298, 8309, 8313, 8318, 8320, 8334, 8335, 8353, 8359, 8360, 8362, 8363, 8364, 8365, 8366, 8368, 8377, 8378, 8393, 8394, 8397, 8410, 8411, 8412, 8413, 8415, 8417, 8423, 8424, 8425, 8426, 8428, 8445, 8453, 8454, 8458, 8460, 8461, 8468, 8470, 8471, 8472, 8477, 8484, 8488, 8491, 8493, 8494, 8497, 8498, 8499, 8506, 8507, 8508, 8510, 8537, 8543, 8591, 8603, 8604, 8608, 8609, 8612, 8618, 8622, 8625, 8627, 8630, 8639, 8644, 8654, 8660, 8662, 8669, 8670, 8674, 8681, 8688, 8690, 8712, 8720, 8742, 8759, 8760, 8767, 8780, 8787, 8789, 8819, 8820, 8829, 8838, 8850, 8860, 8861, 8870, 8883, 8885, 8886, 8898, 8900, 8905, 8917, 8919, 8920, 8950, 8952, 8953, 8965, 8973, 8977, 8982, 8985, 8986, 8997, 9011, 9012, 9014, 9048, 9057, 9059, 9100, 9105, 9106, 9114, 9118, 9123, 9124, 9126, 9127, 9140, 9169, 9172, 9174, 9175, 9187, 9188, 9189, 9207, 9212, 9213, 9227, 9228, 9234, 9236, 9237, 9247, 9265, 9267.
[0184] In some embodiments, the engineered viral capsid polypeptide comprises an amino acid sequence, wherein the amino acid sequence comprises a poly [A|G|S] motif. A “poly [A|G|S] motif” as used herein means that within a string of five amino acid residues, the string includes no less than four amino acid residues selected from A, G, and S. In some embodiments, the engineered viral capsid polypeptide comprises any one of SEQ ID NOs: 3, 4, 6, 7, 8, 9, 14, 15, 16, 17, 19, 20, 30, 31, 32, 34, 35, 36, 37, 38, 40, 43, 45, 46, 54, 61, 67, 76, 93, 102, 110, 112, 113, 114, 115, 116, 117, 118, 119, 120, 122, 123, 124, 127, 128, 132, 135, 141, 142, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 159, 160, 162, 176, 178, 179, 180, 181, 182, 184, 186, 187, 188, 191, 197, 198, 199, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 247, 248, 255, 269, 274, 282, 283, 284, 291, 293, 294, 296, 300, 302, 303, 305, 310, 314, 315, 318, 326, 330, 338, 340, 341, 342, 346, 353, 360, 363, 368, 387, 395, 403, 416, 427, 429, 430, 432, 439, 444, 445, 446, 447, 450, 451, 452, 460, 467, 475, 476, 485, 486, 488, 489, 496, 502, 504, 506, 507, 508, 513, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 529, 532, 540, 544, 545, 549, 554, 566, 568, 569, 578, 588, 589, 592, 593, 594, 595, 596, 597, 598, 600, 601, 602, 603, 604, 605, 616, 622, 624, 629, 642, 649, 650, 655, 656, 659, 663, 665, 669, 672, 684, 720, 732, 778, 779, 780, 793, 795, 813, 849, 851, 852, 853, 854, 855, 856, 857, 858, 862, 863, 864, 865, 867, 876, 877, 878, 882, 883, 884, 889, 890, 891, 893, 900, 901, 902, 904, 905, 906, 907, 908, 909, 910, 911, 912, 913, 914, 917, 922, 923, 924, 925, 926, 927, 928, 929, 930, 931, 933, 937, 938, 939, 942, 943, 944, 947, 952, 953, 954, 955, 956, 960, 961, 965, 966, 967, 971, 973, 974, 979, 980, 981, 984, 985, 986, 987, 988, 989, 992, 996, 997, 998, 999, 1000, 1002, 1008, 1009, 1010, 1011, 1013, 1015, 1099, 1017, 1020, 1021, 1022, 1023, 1024, 1028, 1039, 1041, 1042, 1044, 1047, 1048, 1077, 1078, 1082, 1086, 1087, 1088, 1089, 1090, 1091, 1092, 1093, 1094, 1096, 1097, 1113, 1115, 1116, 1121, 1126, 1134, 1135, 1143, 1157, 1158, 1174, 1175, 1179, 1182, 1203, 1204, 1205, 1207, 1209, 1210, 1211, 1212, 1213, 1214, 1215, 1216, 1217, 1218, 1219, 1220, 1221, 1222, 1223, 1224, 1225, 1226, 1227, 1228, 1229, 1230, 1231, 1232, 1233, 1234, 1235, 1236, 1237, 1238, 1239, 1240, 1241, 1242, 1243, 1244, 1245, 1246, 1247, 1248, 1249, 1250, 1251, 1252, 1253, 1254, 1255, 1256, 1257, 1258, 1259, 1260, 1261, 1263, 1264, 1265, 1266, 1274, 1276, 1277, 1281, 1283, 1287, 1290, 1296, 1302, 1305, 1311, 1312, 1314, 1316, 1321, 1323, 1328, 1331, 1333, 1334, 1335, 1337, 1339, 1340, 1345, 1351, 1353, 1354, 1355, 1356, 1359, 1363, 1365, 1368, 1370, 1371, 1372, 1373, 1375, 1376, 1377, 1381, 1383, 1384, 1385, 1386, 1387, 1388, 1391, 1393, 1394, 1396, 1401, 1403, 1408, 1411, 1416, 1417, 1418, 1420, 1421, 1425, 1434, 1438, 1439, 1440, 1441, 1452, 1475, 1487, 1501, 1507, 1521, 1522, 1527, 1529, 1531, 1532, 1535, 1536, 1537, 1539, 1540, 1541, 1542, 1545, 1547, 1560, 1570, 1620, 1622, 1623, 1626, 1627, 1633, 1634, 1635, 1636, 1637, 1638, 1664, 1665, 1667, 1683, 1684, 1686, 1692, 1719, 1722, 1729, 1734, 1740, 1741, 1742, 1743, 1744, 1748, 1750, 1764, 1772, 1782, 1783, 1784, 1786, 1797, 1798, 1800, 1801, 1802, 1803, 1804, 1805, 1806, 1808, 1809, 1810, 1812, 1815, 1818, 1822, 1823, 1824, 1825, 1827, 1828, 1829, 1830, 1831, 1841, 1844, 1853, 1859, 1860, 1862, 1864, 1866, 1868, 1869, 1870, 1879, 1888, 1890, 1901, 1902, 1905, 1906, 1909, 1911, 1916, 1919, 1934, 1941, 1948, 1949, 1954, 1957, 1965, 1967, 1968, 1969, 1970, 1973, 1974, 1975, 1976, 1977, 1978, 1979, 1980, 1981, 1982, 1983, 1984, 1985, 1986, 1987, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2001, 2003, 2005, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024, 2025, 2026, 2027, 2028, 2029, 2030, 2031, 2032, 2033, 2034, 2035, 2036, 2037, 2038, 2039, 2041, 2044, 2045, 2046, 2047, 2050, 2056, 2063, 2072, 2073, 2075, 2077, 2080, 2083, 2092, 2093, 2097, 2104, 2113, 2114, 2115, 2116, 2117, 2118, 2119, 2120, 2121, 2122, 2123, 2124, 2125, 2126, 2127, 2128, 2129, 2130, 2132, 2133, 2134, 2135, 2136, 2137, 2139, 2144, 2145, 2146, 2147, 2148, 2149, 2150, 2152, 2154, 2156, 2158, 2160, 2171, 2179, 2188, 2191, 2203, 2204, 2217, 2232, 2238, 2241, 2250, 2251, 2258, 2260, 2261, 2262, 2263, 2264, 2265, 2266, 2267, 2268, 2269, 2270, 2271, 2272, 2273, 2274, 2276, 2278, 2281, 2282, 2288, 2289, 2290, 2291, 2292, 2297, 2300, 2301, 2305, 2306, 2317, 2321, 2324, 2325, 2326, 2327, 2328, 2329, 2337, 2340, 2352, 2356, 2360, 2368, 2380, 2381, 2382, 2388, 2390, 2391, 2392, 2394, 2400, 2402, 2404, 2410, 2413, 2414, 2417, 2421, 2422, 2426, 2427, 2433, 2434, 2436, 2437, 2443, 2447, 2452, 2454, 2455, 2473, 2475, 2476, 2477, 2489, 2494, 2498, 2499, 2501, 2523, 2534, 2535, 2547, 2550, 2556, 2561, 2570, 2571, 2583, 2585, 2588, 2590, 2593, 2600, 2601, 2605, 2610, 2615, 2616, 2617, 2621, 2625, 2668, 2670, 2679, 2681, 2737, 2743, 2746, 2762, 2763, 2764, 2766, 2773, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2820, 2826, 2827, 2828, 2829, 2830, 2833, 2834, 2835, 2836, 2837, 2839, 2840, 2848, 2851, 2852, 2853, 2854, 2856, 2860, 2869, 2870, 2875, 2882, 2883, 2884, 2885, 2886, 2887, 2889, 2892, 2903, 2918, 2921, 2922, 2925, 2927, 2940, 2941, 2947, 2956, 2960, 2961, 2967, 2974, 2986, 2987, 2988, 2989, 2990, 2991, 2992, 2993, 2995, 2997, 3000, 3003, 3004, 3018, 3020, 3021, 3022, 3023, 3037, 3051, 3059, 3060, 3064, 3076, 3077, 3078, 3079, 3080, 3081, 3082, 3083, 3085, 3086, 3087, 3095, 3096, 3097, 3100, 3101, 3105, 3106, 3107, 3108, 3109, 3110, 3111, 3112, 3113, 3114, 3115, 3116, 3117, 3118, 3119, 3120, 3121, 3122, 3123, 3124, 3125, 3126, 3127, 3128, 3129, 3130, 3131, 3137, 3138, 3139, 3143, 3147, 3151, 3157, 3158, 3164, 3165, 3168, 3169, 3170, 3171, 3172, 3173, 3174, 3175, 3176, 3177, 3178, 3179, 3180, 3181, 3183, 3184, 3185, 3189, 3190, 3191, 3192, 3193, 3194, 3195, 3196, 3197, 3198, 3199, 3200, 3201, 3202, 3203, 3204, 3205, 3206, 3207, 3208, 3209, 3210, 3211, 3212, 3213, 3214, 3215, 3216, 3217, 3218, 3219, 3220, 3221, 3222, 3223, 3224, 3225, 3226, 3227, 3228, 3229, 3230, 3231, 3232, 3233, 3234, 3235, 3236, 3241, 3244, 3249, 3251, 3252, 3255, 3256, 3258, 3262, 3264, 3265, 3267, 3270, 3271, 3272, 3273, 3279, 3283, 3284, 3285, 3286, 3287, 3288, 3293, 3308, 3317, 3321, 3322, 3324, 3325, 3326, 3328, 3331, 3333, 3335, 3339, 3345, 3350, 3353, 3378, 3383, 3387, 3391, 3392, 3396, 3397, 3399, 3406, 3408, 3411, 3413, 3431, 3435, 3437, 3438, 3439, 3440, 3441, 3442, 3444, 3445, 3446, 3449, 3451, 3452, 3453, 3454, 3455, 3456, 3457, 3458, 3460, 3461, 3462, 3463, 3471, 3473, 3475, 3478, 3479, 3483, 3494, 3496, 3499, 3536, 3537, 3540, 3541, 3542, 3543, 3544, 3546, 3547, 3558, 3559, 3597, 3598, 3599, 3600, 3601, 3602, 3603, 3606, 3607, 3608, 3609, 3618, 3635, 3636, 3653, 3665, 3685, 3688, 3692, 3739, 3744, 3750, 3757, 3758, 3759, 3762, 3763, 3768, 3770, 3780, 3789, 3791, 3792, 3794, 3799, 3810, 3812, 3815, 3816, 3817, 3818, 3819, 3823, 3828, 3830, 3831, 3839, 3840, 3852, 3853, 3855, 3856, 3857, 3858, 3859, 3861, 3862, 3863, 3864, 3865, 3866, 3867, 3868, 3869, 3870, 3871, 3875, 3877, 3881, 3882, 3883, 3889, 3890, 3891, 3892, 3893, 3894, 3895, 3896, 3897, 3900, 3901, 3902, 3903, 3904, 3905, 3907, 3914, 3915, 3916, 3924, 3937, 3938, 3942, 3946, 3947, 3948, 3954, 3955, 3957, 3958, 3959, 3963, 3970, 3971, 3972, 3973, 3974, 3975, 3979, 3980, 3981, 3982, 3988, 3990, 3992, 3994, 3997, 3998, 4000, 4003, 4010, 4017, 4025, 4030, 4040, 4047, 4053, 4055, 4063, 4064, 4069, 4071, 4078, 4079, 4085, 4086, 4096, 4103, 4104, 4105, 4109, 4110, 4119, 4124, 4125, 4126, 4127, 4128, 4132, 4133, 4134, 4135, 4136, 4144, 4151, 4167, 4168, 4169, 4170, 4172, 4177, 4179, 4183, 4184, 4187, 4191, 4192, 4194, 4196, 4204, 4205, 4206, 4207, 4208, 4209, 4210, 4214, 4215, 4216, 4217, 4218, 4223, 4224, 4225, 4226, 4227, 4228, 4229, 4232, 4236, 4251, 4255, 4257, 4262, 4269, 4270, 4272, 4273, 4274, 4281, 4282, 4286, 4287, 4288, 4290, 4293, 4307, 4308, 4309, 4310, 4311, 4313, 4317, 4322, 4331, 4335, 4337, 4339, 4355, 4356, 4357, 4360, 4361, 4363, 4364, 4366, 4368, 4370, 4372, 4394, 4428, 4435, 4441, 4442, 4443, 4444, 4447, 4448, 4452, 4453, 4455, 4456, 4461, 4473, 4489, 4496, 4506, 4507, 4524, 4531, 4543, 4547, 4548, 4549, 4550, 4551, 4552, 4553, 4563, 4568, 4569, 4570, 4571, 4572, 4573, 4574, 4575, 4576, 4577, 4578, 4579, 4580, 4581, 4582, 4583, 4584, 4585, 4586, 4587, 4588, 4589, 4606, 4610, 4613, 4616, 4625, 4631, 4635, 4636, 4640, 4641, 4655, 4657, 4658, 4659, 4661, 4662, 4663, 4664, 4665, 4669, 4686, 4706, 4708, 4712, 4713, 4715, 4725, 4726, 4730, 4737, 4745, 4748, 4751, 4787, 4788, 4789, 4790, 4825, 4848, 4849, 4855, 4856, 4858, 4860, 4861, 4862, 4863, 4864, 4865, 4866, 4867, 4868, 4869, 4870, 4871, 4872, 4873, 4890, 4899, 4900, 4903, 4904, 4906, 4907, 4908, 4909, 4911, 4912, 4913, 4914, 4915, 4916, 4917, 4918, 4919, 4920, 4921, 4926, 4931, 4937, 4940, 4954, 4955, 4956, 4957, 4968, 4973, 4974, 4976, 4983, 4987, 4988, 4989, 4990, 4991, 4992, 4993, 4994, 4995, 4996, 4997, 4998, 4999, 5000, 5001, 5002, 5003, 5004, 5005, 5006, 5007, 5008, 5015, 5016, 5022, 5023, 5024, 5025, 5026, 5027, 5028, 5029, 5030, 5031, 5032, 5033, 5036, 5037, 5039, 5048, 5049, 5054, 5055, 5056, 5057, 5058, 5069, 5073, 5074, 5076, 5077, 5078, 5079, 5080, 5081, 5082, 5083, 5084, 5085, 5086, 5087, 5088, 5089, 5090, 5091, 5092, 5093, 5094, 5095, 5096, 5097, 5098, 5099, 5101, 5102, 5103, 5104, 5105, 5106, 5107, 5108, 5113, 5116, 5117, 5121, 5122, 5123, 5124, 5129, 5132, 5137, 5145, 5149, 5150, 5158, 5162, 5167, 5175, 5177, 5181, 5182, 5185, 5186, 5188, 5189, 5192, 5193, 5195, 5196, 5197, 5198, 5199, 5200, 5201, 5202, 5203, 5205, 5208, 5209, 5210, 5211, 5212, 5213, 5214, 5215, 5216, 5217, 5219, 5226, 5229, 5230, 5231, 5232, 5234, 5235, 5236, 5237, 5238, 5239, 5240, 5241, 5242, 5244, 5246, 5247, 5248, 5249, 5250, 5251, 5252, 5253, 5254, 5255, 5256, 5257, 5260, 5263, 5264, 5267, 5270, 5272, 5273, 5277, 5279, 5282, 5285, 5287, 5288, 5290, 5294, 5295, 5296, 5297, 5302, 5304, 5305, 5308, 5310, 5321, 5323, 5325, 5330, 5337, 5338, 5344, 5346, 5348, 5354, 5356, 5359, 5360, 5364, 5370, 5372, 5373, 5374, 5376, 5382, 5387, 5393, 5404, 5406, 5414, 5416, 5417, 5425, 5428, 5430, 5432, 5433, 5434, 5435, 5436, 5440, 5446, 5447, 5448, 5452, 5454, 5463, 5467, 5469, 5472, 5474, 5475, 5477, 5478, 5480, 5481, 5483, 5484, 5487, 5488, 5489, 5490, 5491, 5492, 5497, 5499, 5500, 5504, 5506, 5507, 5508, 5511, 5528, 5534, 5547, 5551, 5564, 5566, 5567, 5577, 5580, 5585, 5586, 5587, 5593, 5594, 5595, 5596, 5597, 5598, 5603, 5604, 5605, 5606, 5607, 5608, 5610, 5613, 5622, 5623, 5627, 5628, 5629, 5630, 5631, 5634, 5636, 5637, 5638, 5639, 5640, 5643, 5644, 5645, 5646, 5647, 5648, 5649, 5650, 5651, 5654, 5655, 5660, 5662, 5663, 5664, 5665, 5673, 5674, 5680, 5689, 5690, 5691, 5694, 5695, 5696, 5704, 5705, 5711, 5723, 5724, 5725, 5726, 5729, 5730, 5731, 5732, 5733, 5740, 5741, 5744, 5746, 5759, 5764, 5768, 5775, 5779, 5793, 5794, 5795, 5796, 5797, 5798, 5799, 5802, 5804, 5805, 5806, 5807, 5808, 5809, 5810, 5820, 5829, 5831, 5832, 5835, 5836, 5844, 5849, 5853, 5864, 5867, 5874, 5875, 5876, 5877, 5887, 5892, 5895, 5915, 5916, 5921, 5922, 5923, 5924, 5925, 5926, 5927, 5934, 5935, 5936, 5937, 5938, 5939, 5940, 5941, 5942, 5944, 5945, 5947, 5949, 5951, 5952, 5958, 5959, 5960, 5963, 5964, 5965, 5966, 5975, 5976, 5988, 5999, 6002, 6006, 6010, 6020, 6023, 6026, 6030, 6032, 6033, 6037, 6038, 6040, 6041, 6042, 6047, 6048, 6055, 6058, 6059, 6072, 6074, 6075, 6080, 6090, 6099, 6109, 6111, 6112, 6116, 6127, 6129, 6136, 6137, 6138, 6142, 6147, 6149, 6151, 6152, 6160, 6161, 6162, 6163, 6165, 6166, 6167, 6168, 6169, 6171, 6172, 6173, 6174, 6175, 6177, 6180, 6181, 6183, 6184, 6186, 6194, 6198, 6200, 6201, 6202, 6203, 6207, 6209, 6211, 6212, 6214, 6215, 6216, 6217, 6218, 6219, 6220, 6224, 6233, 6234, 6249, 6251, 6256, 6258, 6263, 6267, 6275, 6277, 6278, 6279, 6280, 6281, 6282, 6283, 6284, 6287, 6289, 6290, 6291, 6292, 6293, 6294, 6295, 6296, 6297, 6298, 6299, 6300, 6301, 6302, 6303, 6304, 6305, 6308, 6313, 6320, 6333, 6334, 6335, 6336, 6340, 6341, 6342, 6343, 6344, 6346, 6352, 6357, 6366, 6367, 6368, 6369, 6380, 6381, 6382, 6383, 6384, 6385, 6386, 6387, 6388, 6389, 6391, 6392, 6393, 6394, 6395, 6396, 6397, 6398, 6399, 6404, 6420, 6422, 6427, 6432, 6433, 6435, 6467, 6472, 6479, 6480, 6481, 6482, 6483, 6484, 6485, 6486, 6487, 6488, 6489, 6490, 6491, 6492, 6493, 6494, 6495, 6496, 6497, 6498, 6499, 6500, 6501, 6502, 6503, 6504, 6511, 6517, 6518, 6519, 6520, 6521, 6522, 6523, 6527, 6529, 6531, 6533, 6537, 6545, 6546, 6547, 6548, 6549, 6551, 6559, 6562, 6566, 6567, 6568, 6569, 6570, 6571, 6572, 6573, 6574, 6575, 6576, 6577, 6578, 6579, 6580, 6581, 6582, 6583, 6584, 6585, 6586, 6587, 6588, 6589, 6590, 6591, 6592, 6593, 6594, 6595, 6596, 6597, 6598, 6599, 6600, 6601, 6602, 6603, 6604, 6605, 6606, 6607, 6608, 6609, 6610, 6611, 6612, 6613, 6614, 6615, 6616, 6617, 6618, 6619, 6620, 6621, 6622, 6623, 6624, 6625, 6626, 6627, 6628, 6629, 6630, 6631, 6632, 6633, 6634, 6635, 6636, 6637, 6638, 6639, 6640, 6641, 6642, 6643, 6644, 6645, 6646, 6647, 6648, 6649, 6650, 6651, 6652, 6653, 6654, 6655, 6656, 6657, 6658, 6659, 6660, 6661, 6662, 6663, 6664, 6665, 6666, 6667, 6668, 6669, 6670, 6671, 6672, 6673, 6674, 6675, 6676, 6677, 6678, 6679, 6680, 6681, 6682, 6683, 6684, 6685, 6686, 6687, 6688, 6689, 6690, 6691, 6692, 6693, 6694, 6695, 6696, 6697, 6698, 6699, 6700, 6701, 6702, 6703, 6704, 6705, 6706, 6707, 6708, 6709, 6710, 6714, 6715, 6716, 6717, 6718, 6719, 6720, 6721, 6722, 6723, 6725, 6727, 6735, 6737, 6738, 6739, 6742, 6743, 6751, 6762, 6767, 6769, 6770, 6772, 6774, 6775, 6776, 6777, 6781, 6782, 6786, 6787, 6788, 6790, 6792, 6793, 6794, 6796, 6797, 6798, 6810, 6812, 6814, 6816, 6817, 6822, 6823, 6825, 6830, 6834, 6835, 6836, 6837, 6839, 6840, 6841, 6842, 6843, 6844, 6851, 6852, 6853, 6854, 6855, 6856, 6857, 6858, 6859, 6860, 6864, 6872, 6874, 6875, 6876, 6877, 6878, 6879, 6880, 6881, 6882, 6883, 6885, 6886, 6887, 6888, 6889, 6893, 6897, 6898, 6899, 6900, 6901, 6902, 6903, 6904, 6905, 6906, 6907, 6908, 6909, 6910, 6911, 6912, 6913, 6914, 6915, 6916, 6917, 6918, 6919, 6920, 6921, 6924, 6925, 6926, 6927, 6929, 6931, 6934, 6935, 6939, 6940, 6941, 6942, 6945, 6949, 6951, 6979, 6980, 6981, 6986, 6988, 6995, 6997, 6998, 7014, 7028, 7031, 7033, 7034, 7035, 7036, 7039, 7040, 7044, 7047, 7048, 7049, 7061, 7066, 7070, 7077, 7085, 7102, 7105, 7115, 7116, 7127, 7129, 7132, 7133, 7145, 7154, 7155, 7158, 7176, 7186, 7190, 7191, 7192, 7193, 7195, 7199, 7201, 7202, 7204, 7209, 7210, 7211, 7212, 7213, 7214, 7216, 7217, 7230, 7237, 7241, 7246, 7247, 7251, 7256, 7258, 7262, 7263, 7267, 7268, 7272, 7286, 7294, 7295, 7296, 7299, 7300, 7301, 7302, 7303, 7304, 7305, 7306, 7307, 7308, 7309, 7310, 7311, 7312, 7313, 7314, 7315, 7316, 7319, 7320, 7322, 7342, 7349, 7354, 7355, 7360, 7362, 7365, 7367, 7377, 7379, 7389, 7393, 7394, 7413, 7418, 7430, 7441, 7442, 7464, 7475, 7521, 7531, 7537, 7538, 7551, 7560, 7563, 7566, 7577, 7584, 7585, 7586, 7587, 7588, 7590, 7591, 7592, 7602, 7611, 7620, 7621, 7622, 7624, 7625, 7626, 7628, 7629, 7630, 7634, 7635, 7636, 7637, 7638, 7639, 7643, 7644, 7655, 7658, 7660, 7661, 7662, 7664, 7665, 7666, 7668, 7669, 7676, 7677, 7705, 7715, 7737, 7760, 7761, 7765, 7766, 7767, 7773, 7774, 7776, 7781, 7783, 7786, 7803, 7808, 7809, 7811, 7813, 7816, 7818, 7820, 7833, 7838, 7840, 7841, 7851, 7853, 7857, 7859, 7868, 7871, 7874, 7875, 7878, 7883, 7884, 7895, 7904, 7910, 7912, 7914, 7917, 7918, 7933, 7936, 7937, 8047, 8056, 8070, 8072, 8128, 8135, 8156, 8157, 8159, 8162, 8166, 8167, 8176, 8177, 8181, 8185, 8188, 8192, 8193, 8194, 8195, 8196, 8197, 8198, 8199, 8200, 8201, 8202, 8203, 8204, 8205, 8206, 8207, 8208, 8209, 8210, 8211, 8212, 8213, 8214, 8215, 8216, 8217, 8218, 8219, 8220, 8222, 8223, 8224, 8225, 8226, 8227, 8228, 8229, 8230, 8231, 8232, 8233, 8234, 8235, 8236, 8237, 8238, 8239, 8240, 8241, 8242, 8243, 8244, 8245, 8246, 8254, 8256, 8257, 8259, 8260, 8261, 8262, 8263, 8264, 8265, 8266, 8267, 8268, 8269, 8270, 8271, 8272, 8273, 8280, 8281, 8289, 8290, 8291, 8295, 8296, 8297, 8298, 8299, 8300, 8301, 8302, 8303, 8304, 8305, 8307, 8308, 8313, 8319, 8324, 8325, 8337, 8338, 8339, 8340, 8341, 8342, 8343, 8344, 8345, 8346, 8347, 8348, 8349, 8350, 8351, 8352, 8354, 8355, 8356, 8357, 8361, 8363, 8364, 8365, 8366, 8367, 8368, 8369, 8372, 8373, 8379, 8380, 8382, 8383, 8384, 8385, 8391, 8392, 8395, 8398, 8400, 8401, 8402, 8403, 8404, 8405, 8406, 8407, 8408, 8409, 8410, 8412, 8414, 8418, 8420, 8421, 8422, 8427, 8431, 8433, 8434, 8435, 8436, 8437, 8438, 8439, 8440, 8441, 8442, 8443, 8444, 8445, 8446, 8447, 8448, 8449, 8450, 8451, 8452, 8455, 8456, 8457, 8458, 8459, 8461, 8474, 8478, 8481, 8483, 8486, 8495, 8513, 8516, 8517, 8518, 8523, 8524, 8525, 8526, 8530, 8531, 8532, 8538, 8540, 8542, 8546, 8547, 8548, 8563, 8568, 8571, 8573, 8574, 8577, 8578, 8579, 8580, 8582, 8584, 8585, 8587, 8588, 8589, 8590, 8592, 8593, 8594, 8598, 8602, 8605, 8606, 8610, 8611, 8614, 8615, 8616, 8617, 8618, 8619, 8620, 8621, 8622, 8623, 8624, 8636, 8646, 8648, 8649, 8651, 8652, 8653, 8657, 8659, 8680, 8688, 8690, 8695, 8702, 8703, 8706, 8707, 8708, 8709, 8710, 8711, 8715, 8716, 8721, 8722, 8728, 8731, 8742, 8758, 8759, 8767, 8768, 8774, 8785, 8793, 8794, 8795, 8796, 8798, 8804, 8805, 8807, 8811, 8825, 8826, 8827, 8829, 8834, 8835, 8837, 8844, 8865, 8874, 8875, 8876, 8887, 8890, 8891, 8905, 8921, 8933, 8934, 8939, 8940, 8944, 8945, 8946, 8947, 8955, 8957, 8960, 8961, 8962, 8963, 8964, 8996, 8999, 9000, 9004, 9005, 9006, 9007, 9015, 9038, 9045, 9049, 9052, 9056, 9059, 9060, 9061, 9062, 9063, 9065, 9066, 9067, 9068, 9069, 9070, 9071, 9072, 9073, 9074, 9075, 9076, 9077, 9079, 9080, 9081, 9082, 9083, 9084, 9086, 9087, 9088, 9091, 9092, 9093, 9095, 9096, 9097, 9098, 9099, 9101, 9102, 9103, 9104, 9108, 9109, 9110, 9111, 9112, 9113, 9130, 9131, 9132, 9135, 9136, 9138, 9139, 9141, 9142, 9143, 9144, 9145, 9147, 9148, 9149, 9150, 9151, 9152, 9153, 9154, 9155, 9156, 9157, 9158, 9159, 9161, 9164, 9165, 9166, 9167, 9169, 9170, 9171, 9178, 9179, 9180, 9181, 9182, 9185, 9186, 9187, 9192, 9193, 9194, 9195, 9196, 9197, 9198, 9199, 9200, 9201, 9202, 9203, 9204, 9205, 9206, 9208, 9209, 9210, 9216, 9217, 9218, 9219, 9220, 9221, 9222, 9223, 9224, 9225, 9226, 9227, 9228, 9229, 9230, 9231, 9232, 9233, 9236, 9238, 9239, 9248, 9250, 9251, 9252, 9253, 9254, 9255, 9256, 9257, 9258, 9259, 9261, 9262, 9263, 9264, 9269, 9270, 9271, 9274, 9276, 9277, 9278, 9279, 9280, 9282, 9283, 9284, 9285.
[0185] In some embodiments, the engineered viral capsid polypeptide comprises one or more (e.g., 2, 3, or 4) motifs. In some embodiments, the engineered viral capsid polypeptide may comprise a string of amino acid residues that can be characterized under more than one motif. For example, a string of amino acid residues can fall within the category of a [D|E] X1X2X3X4Y motif and the category of a poly [D|E] motif.
[0186] Exemplary sequences that correspond to the [D|E] X1X2X3X4Y motif, [D|E] X1X2X4Y motif, poly [D|E] motif, and / or the poly [A|G|S] motif are shown in lower case letters (amino acid residues) in Table 1A.
[0187] As used herein, the engineered viral capsid polypeptide sequences can be encoded by engineered polynucleotides which can be included in a polynucleotide that is configured to be a viral genome donor in a viral vector system that can be used to generate engineered viral particles described elsewhere herein.
[0188] In another aspect, the present disclosure provides a polynucleotide encoding the engineered viral capsid polypeptide disclosed herein.
[0189] In some embodiments, the polynucleotide encoding the engineered AAV capsid polypeptide is included in a polynucleotide that is configured to be an AAV genome donor in an AAV vector system that can be used to generate engineered AAV particles described herein. In some embodiments, the polynucleotide encoding the engineered AAV capsid polypeptide is operably linked to a poly adenylation tail, a 5’ -ITR, and / or 3’ -ITR. In some embodiments, the poly adenylation tail can be an SV40 poly adenylation tail. In some embodiments, the polynucleotide encoding the engineered AAV capsid polypeptide is operably coupled to a promoter. In some embodiments, the promoter can be a constitutive promoter. Suitable tissue specific promoters and constitutive promoters are discussed elsewhere herein and are generally known in the art and can be commercially available. Suitable constitutive promoters include, but are not limited to CMV, RSV, SV40, EF1alpha, CAG, and beta-actin. In some embodiments, the promoter is selected from CMV, EF-1α, SV40, PGK1, CAG, ubc, human beta actin, TRE, UA5, Ac5, Polyhedrin, CaMKIIa, GAL1, GAL10, TEF1, GDS, ADH1, CaMV355, Ubi, and SFFV.
[0190] The polynucleotides disclosed herein can be obtained by methods known in the art. For example, the polynucleotide can be obtained from cloned DNA (e.g., from a DNA library) , by chemical synthesis, by cDNA cloning, or by the cloning of genomic DNA or fragments thereof, purified from the desired cell. When the polynucleotides are produced by recombinant means, any method known to those skilled in the art for identification of nucleic acids that encode desired genes can be used. Any method available in the art can be used to obtain a full length (i.e., encompassing the entire coding region) cDNA or genomic DNA encoding a desired protein, such as from a cell or tissue source. Modified or variant polynucleotides can be engineered from a wildtype polynucleotide using standard recombinant DNA methods. Polynucleotides can be cloned or isolated using any available methods known in the art for cloning and isolating nucleic acid molecules. Such methods include PCR amplification of nucleic acids and screening of libraries, including nucleic acid hybridization screening, antibody-based screening, and activity-based screening.
[0191] In another aspect, the present disclosure provides a vector comprising the engineered viral capsid polypeptide disclosed herein, or the polynucleotide disclosed herein.
[0192] In some embodiments, the vector is a plasmid, a viral vector, a lipid nanoparticle (LNP) vector, or a non-viral vector.
[0193] Any methods known in the art for the insertion of DNA fragments into a vector can be used to construct expression vectors comprising a polynucleotide disclosed herein. These methods can include in vitro recombinant DNA and synthetic techniques and in vivo (genetic) recombination. The polynucleotide disclosed herein can be operably linked to control sequences in the expression vector (s) to ensure protein expression. Such control sequences may include, but are not limited to, leader or signal sequences, promoters (e.g., naturally associated or heterologous promoters) , ribosomal binding sites, enhancer or activator elements, translational start and termination sequences, and transcription start and termination sequences, and are chosen to be compatible with the host cell chosen to express the proteins. Constitutive or inducible promoters as known in the art are also contemplated. The promoters may be either naturally occurring promoters, hybrid promoters that combine elements of more than one promoter, or synthetic promoters. An expression construct may be present in a cell on an episome, such as a plasmid, or the expression construct may be inserted in a chromosome such as in a gene locus. In some embodiment, the expression vector includes a selectable marker gene to allow the selection of transformed host cells. In some embodiments, the vector is an expression vector comprising a nucleotide sequence encoding a variant polypeptide operably linked to at least one regulatory control sequence. Regulatory control sequences for use herein include promoters, enhancers, and other expression control elements. In some embodiments, the expression vector is designed for the choice of the host cell to be transformed, the particular variant polypeptide desired to be expressed, the vector's copy number, the ability to control that copy number, and / or the expression of any other protein encoded by the vector, such as antibiotic markers.
[0194] In another aspect, the present disclosure provides a cell comprising the engineered viral capsid polypeptide disclosed herein, the polynucleotide disclosed herein, or the vector disclosed herein.
[0195] In another aspect, the viral capsid polypeptide described herein can also be implemented in other delivery systems to deliver a payload to T cells. In some embodiments, a polypeptide of SEQ ID NOs: 1-2105 and 2149-9287 are isolated polypeptides which function as targeting moieties for T cells. For example, one or more of polypeptides of SEQ ID NOs: 1-2105 and 2149-9287 can be introduced into any feasible delivery systems and serve as a targeting moiety or part thereof. In some embodiments, polypeptides of SEQ ID NOs: 1-2105 and 2149-9287 are targeting moieties or part thereof for a nanobody. In some embodiments, polypeptides of SEQ ID NOs: 1-2105 and 2149-9287 are targeting moieties or part thereof for peptide nucleic acids. In some embodiments, a targeting moiety comprises one of more (e.g., 2, 3, or 4, etc. ) of the sequences from SEQ ID NOs: 1-2105 and 2149-9287. In some embodiments, a targeting moiety comprises one or more (e.g., 2, 3, or 4, etc. ) motifs selected from polypeptides of SEQ ID NOs: 1-2105 and 2149-9287 and any combinations thereof. In some embodiments, the targeting moiety disclosed herein further comprises a polypeptide, a polynucleotide, a peptide nucleic acid, a lipid, a polymer, a sugar, or any combination thereof. In some embodiments, a composition comprises a targeting moiety disclosed herein and a payload. In some embodiments, the payload can be any known therapy that is effective for treating T cell-related disease, such as autoimmune diseases, immunodeficiency disorders, neoplasms, and T-cell lymphoma. The payload may be a small molecule drug, a therapeutic peptide, a therapeutic transgene, an antisense oligonucleotide, an antibody, or a polynucleotide that encodes a therapy. The payload may be attached to the targeting moiety by covalent linkage or is associated with the targeting moiety non-covalently.
[0196] In an aspect, the present disclosure provides a targeting moiety comprising one or more polypeptides selected from SEQ ID NOs: 1-2105 and 2149-9287, and optionally a polynucleotide, a lipid, a polymer, a sugar, or any combination thereof.
[0197] In some embodiments, the composition comprises the targeting moiety disclosed herein and a payload. Engineered AAV Variants and Uses thereof
[0198] In another aspect, the present disclosure provides an engineered adeno-associated virus (AAV) comprising the engineered viral capsid polypeptide disclosed herein.
[0199] In some embodiments, the engineered adeno-associated virus (AAV) further comprises an expression cassette which comprises a single-strand DNA encoding a protein of interest.
[0200] In some embodiments, the engineered adeno-associated virus (AAV) further comprises an expression cassette which comprises a single-strand DNA encoding a chimeric antigen receptor (CAR) . In some embodiments, the chimeric antigen receptor (CAR) is selected from CD19-CAR, BCMA-CAR, CD22-CAR, CD30-CAR, CD7-CAR, CD38-CAR, CD20-CAR, GD2-CAR, HER2-CAR, IL13Ra2-CAR, EGFR-CAR, Mesothelin-CAR, Claudin-18.2-CAR, PSMA-CAR, and GPC3-CAR.
[0201] Chimeric antigen receptors (CARs) are receptor proteins that are designed to bind to specific proteins on cancer cells and help T cells find and destroy them. CARs are also known as chimeric immunoreceptors, chimeric T cell receptors, or artificial T cell receptors. In some embodiments, the CAR comprises an antigen binding domain, a hinge region, a transmembrane domain, and an intracellular signaling domain. (Sterner, 2021) .
[0202] The antigen binding domain is the portion of the CAR that confers target antigen specificity. In some embodiments, the antigen binding domain is an antibody or a fragment thereof. In some embodiments, the antigen-binding domain is a single-chain variable fragment (scFv) derived from the variable heavy (VH) and light (VL) chains of monoclonal antibodies. In some embodiments, the antigen binding domain targets extracellular surface cancer antigens resulting in major histocompatibility complex (MHC) -independent T cell activation. In some embodiments, the antigen binding domain of an MHC-dependent, T cell receptor (TCR) -mimic CAR recognizes intracellular tumor-associated antigens. In some embodiments, in order to recognize antigens on tumor cells, induce CAR signaling, and activate T cells, the CARs antigen binding affinity are designed to be sufficiently high but not high enough to result in activation induced death of the CAR expressing T cell and trigger toxicities.
[0203] The hinge or spacer region is defined as the extracellular structural region that extends the binding units from the transmembrane domain. The hinge functions to provide flexibility to overcome steric hindrance and contributes to the length in order to allow the antigen-binding domain to access the targeted epitope.
[0204] The transmembrane domain anchors the CAR to the cell membrane. It is reported that the transmembrane domains also influence CAR expression level, stability, and can be active in signaling or synapse formation, and dimerize with endogenous signaling molecules. In some embodiments, the transmembrane domain is derived from natural proteins such as CD3ζ, CD4, CD8α, or CD28. In some embodiments, the transmembrane domain is derived from CD3ζ, which can mediate CAR dimerization and incorporation into endogenous TCRs, and thus facilitate CAR-mediated T cell activation.
[0205] Intracellular signaling domain is important in CAR co-stimulation. In some embodiments, the CAR activates the CAR-expressing cells (such as CAR-T cells) through CD3ζ derived immunoreceptor tyrosine-based activation motifs. In some embodiments, the intracellular signaling domain is derived from a costimulatory molecule, such as CD28 or CD137 (4-1BB) . In some embodiments, the costimulatory molecule is inducible T cell co-stimulator (ICOS) , CD27, MYD88, CD40, and OX40 (CD134) .
[0206] In some embodiments of the engineered adeno-associated virus (AAV) disclosed herein, the expression cassette further comprises a promoter selected from CMV, EF-1α, SV40, PGK1, CAG, ubc, human beta actin, TRE, UA5, Ac5, Polyhedrin, CaMKIIa, GAL1, GAL10, TEF1, GDS, ADH1, CaMV355, Ubi, and SFFV. In some embodiments, the promoter is EF-1α.
[0207] In some embodiments, the expression cassette further comprises a 5’ ITR, a 3’ ITR, a Flag, a poly (A) , a WPRE, or a miRNA target.
[0208] Inverted terminal repeat (ITR) serves as the origin of replication and are required for replication, packaging, and vector persistence. They work in conjunction with the viral rep (replication) and cap (capsid) proteins, which bind to the ITRs and initiate replication. ITRs are cis-acting elements. In some embodiments, the ITR consists of palindromic arms (A-A’, B-B’, and C-C’) that give the feature its characteristic T-shape. The arrangement of the B-B’ and C-C’ palindromic sequences determines the orientation of the ITR, which can either be “flip” or “flop” . In some embodiments, the ITR contains a 4-nucleotide Rep binding element (RBE) that serves as a binding site for Rep78 and Rep68 to initiate replication and a terminal resolution site that serves as the target site for Rep proteins. In some embodiments, a transgene in a recombinant AAV is flanked by two ITRs (5’ -ITR and 3’ -ITR) .
[0209] A flag, or flag tag, refers to an epitope protein with DYKDDDDK sequence, or the polynucleotide encoding the protein.
[0210] Poly (A) , or polyadenylation, refers to a long chain of adenine nucleotides. In some embodiments, the poly (A) is located at the end of the AAV genome, upstream of the final ITR and downstream of the WPRE.
[0211] The Woodchuck Hepatitis Virus (WHP) Posttranscriptional Regulatory Element (WPRE) forms a tertiary structure when transcribed, which aids in nuclear export of mRNA and helps increase the expression of your transgene. In some embodiments, the WPRE is located at the end of the AAV genome, just upstream of the final ITR.
[0212] MicroRNA (miRNA) target refers to the miRNA binding site. In some embodiments, inclusion of miRNA binding site in the expression cassette enables endogenous miRNA-mediated regulation. miRNA is a type of non-coding RNA (ncRNA) that regulates gene expression and is found in plants, animals, and some viruses. miRNAs are small, single-stranded molecules that contain 21–24 nucleotides. They are involved in RNA silencing and post-transcriptional regulation of gene expression.
[0213] In some embodiments, the engineered adeno-associated virus has tropism to T cells. In some embodiments, the T cells are primary T cells. In some embodiments, the T cells are human T cells. In some embodiments, the T cell is a CD4+ T cell. In some embodiments, the T cell is a CD8+ T cell. Table 1A presents the fold changes in the tropism of exemplary engineered viral capsid polypeptide to T cells, compared to the parental or wild-type capsid polypeptide. In some embodiments, an AAV comprising an engineered viral capsid polypeptide which has higher fold change exhibits stronger tropism to T cells. In some embodiments, an AAV comprising an engineered viral capsid polypeptide which has higher fold change exhibits increased transduction efficiencies to T cells.
[0214] In some embodiments, the engineered adeno associated virus derived from a parental virus selected from AAV1, AAV2, AAV3, AAV3B, AAV4, AAV5, AAV6, AAV6.2, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, AAV13, AAVrh74, AAVrh10, AAVDJ, AAVDJ / 8, AAV-PHP. eB, AAV-PHP. S, AAV2-retro, AAV2-QuadYF, AAV2.7m8, and Avian AAV.
[0215] In some embodiments, the engineered adeno-associated virus is an engineered AAV9, and the engineered viral capsid polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 1-1007, 2149-2261, and 2945-6269. In some embodiments, the amino acid sequence replaces a sequence in the viral capsid polypeptide analogous to a sequence from T582 to Q592 of SEQ ID NO: 2107. In some embodiments, the engineered adeno-associated virus (AAV) is capable of binding to SLC35C2. In some embodiments, the engineered adeno-associated virus (AAV) comprises SEQ ID NO: 109 and is capable of binding to SLC35C2. In some embodiments, the engineered adeno-associated virus (AAV) comprising an engineered capsid polypeptide of SEQ ID NO: 2110 is capable of binding to SLC35C2.
[0216] In some embodiments, the engineered polypeptide sequences can be inserted between any two contiguous amino acids within the insertion site. A person skilled in the art would be able to identify an analogous position of insertion site in other analogous AAV viral capsid polypeptides by aligning the analogous AAV viral capsid polypeptide sequence with SEQ ID NO: 2107. Sequence alignment tools, such as the Basic Local Alignment Search Tool (BLAST) , are readily available. In some embodiments, the insertion site is located within the variable region VIII (VR-VIII) of the AAV9 capsid protein.
[0217] In some embodiments, the engineered adeno-associated virus is an engineered AAV6, and the engineered viral capsid polypeptide comprising an amino acid sequence of any one of SEQ ID NOs: 1008-2105, 2262-2944, and 6270-9287. In some embodiments, the amino acid replaces a sequence in the viral capsid polypeptide analogous to a sequence from V582 to A592 of SEQ ID NO: 2106. In some embodiments, the engineered adeno-associated virus (AAV) is capable of binding to CD62L. In some embodiments, the engineered adeno-associated virus (AAV) comprises SEQ ID NO: 1660 and is capable of binding to CD62L.
[0218] In some embodiments, the engineered polypeptide sequences can be inserted between any two contiguous amino acids within the insertion site. A person skilled in the art would be able to identify an analogous position of insertion site in other analogous AAV viral capsid polypeptides by aligning the analogous AAV viral capsid polypeptide sequence with SEQ ID NO: 2106. Sequence alignment tools, such as the Basic Local Alignment Search Tool (BLAST) , are readily available. In some embodiments, the insertion site is located within the variable region VIII (VR-VIII) of the AAV6 capsid protein.
[0219] In another aspect, the present disclosure provides a kit comprising the engineered adeno-associated virus (AAV) disclosed herein, and a gene editing system. In some embodiments, the gene editing system is a CRISPR-Cas based system, such as a CRISPR-Cas9 system. In some embodiments, the gene editing system comprises a TALE nuclease, or zinc-finger nuclease.
[0220] In some embodiments, the gene editing system comprises a Cas9 protein and a guide RNA, or one or more polynucleotide encoding thereof. In some embodiments, the gene editing system comprises a Cas9 / gRNA ribonucleoprotein (RNP) .
[0221] In another aspect, the present disclosure provides an engineered T cell which is transduced by the engineered AAV disclosed herein. In some embodiments, the T cell is engineered by transduction of an AAV comprising the engineered viral capsid polypeptide disclosed herein.
[0222] In some embodiments, the engineered T cell further comprises at least one chimeric antigen receptor (CAR) . In some embodiments, the chimeric antigen receptor (CAR) is selected from CD19-CAR, BCMA-CAR, CD22-CAR, CD30-CAR, CD7-CAR, CD38-CAR, CD20-CAR, GD2-CAR, HER2-CAR, IL13Ra2-CAR, EGFR-CAR, Mesothelin-CAR, Claudin-18.2-CAR, PSMA-CAR, and GPC3-CAR.
[0223] In some embodiments, the T cell is a primary T cell. In some embodiments, the T cell is a human T cell. In some embodiments, the T cell is a CD4+ T cell. In some embodiments, the T cell is a CD8+ T cell.
[0224] In another aspect, the present disclosure provides a method of delivering a payload polynucleotide into a cell, comprising contacting the cell with the engineered adeno-associated virus (AAV) disclosed herein, wherein the engineered adeno-associated virus (AAV) comprises the payload polynucleotide. In some embodiments, the method is carried out in vivo. Methods and protocols for AAV transduction are well known in the art and are further disclosed in the Examples of this disclosure.
[0225] In some embodiments, the method further comprises administering a gene editing system into the cell. In some embodiments, the cell is a T cell. In some embodiments, the cell is a primary T cell. In some embodiments, the cell is a human T cell. In some embodiments, the components of the gene editing system are transduced into the cell by electroporation. In some embodiments, when both the engineered AAV disclosed herein and the gene editing system are introduced into the cell, the payload polynucleotide carried by the engineered AAV is integrated into the genome of the cell.
[0226] In some embodiments, the payload polynucleotide encodes a chimeric antigen receptor (CAR) . In some embodiments, the chimeric antigen receptor (CAR) is selected from CD19-CAR, BCMA-CAR, CD22-CAR, CD30-CAR, CD7-CAR, CD38-CAR, CD20-CAR, GD2-CAR, HER2-CAR, IL13Ra2-CAR, EGFR-CAR, Mesothelin-CAR, Claudin-18.2-CAR, PSMA-CAR, and GPC3-CAR.
[0227] In another aspect, the present disclosure provides a method of engineering a T cell, comprising contacting the T cell with the engineered adeno-associated virus (AAV) disclosed herein, wherein the engineered AAV comprises an expression cassette which comprises a single-strand DNA encoding a chimeric antigen receptor (CAR) . In some embodiments, the method is carried out in vivo.
[0228] In some embodiments, the method further comprises administering a gene editing system into the T cell. In some embodiments, the T cell is electroporated with a Cas9 / gRNA ribonucleoprotein (RNP) .
[0229] In another aspect, the present disclosure provides a method of engineering a T cell in a subject, comprising administering into the subject an effective amount of engineered adeno-associated virus (AAV) disclosed herein. In some embodiments, the engineered AAV comprises an expression cassette which comprises a single-strand DNA encoding a chimeric antigen receptor (CAR) . In some embodiments, the engineered adeno-associated virus (AAV) is an engineered AAV, and the engineered viral capsid polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 1-2105 and 2149-9287, and the effective amount of engineered adeno-associated virus (AAV) is more than 1× 1011 vg / kg, 1× 1012 vg / kg, or 1× 1013 vg / kg. In some embodiments, the engineered adeno-associated virus (AAV) is an engineered AAV, and the engineered viral capsid polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 1-2105 and 2149-9287, and the effective amount of engineered adeno-associated virus (AAV) is no more than 1× 1014 vg / kg, or 1× 1015 vg / kg. In some embodiments, the engineered adeno-associated virus (AAV) is systematically administered to the subject. In some embodiments, the engineered adeno-associated virus (AAV) is an engineered AAV, and the engineered viral capsid polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 1-2105 and 2149-9287, and the effective amount is a low dose. In some embodiments, the effective amount of engineered adeno-associated virus (AAV) is from about 1× 1011 vg / kg to about 1× 1013 vg / kg. In some embodiments, the effective amount of engineered adeno-associated virus (AAV) is no more than 1× 1013 vg / kg. In some embodiments, the effective amount of engineered adeno-associated virus (AAV) is no more than 1× 1011 vg / kg, 1× 1012 vg / kg, or 1× 1013 vg / kg. In some embodiments, the engineered adeno-associated virus (AAV) is an engineered AAV6, and the engineered viral capsid polypeptide comprising an amino acid sequence of any one of SEQ ID NOs: 1008-2105, 2262-2944, and 6270-9287, and the effective amount is no more than 1× 1012 vg / kg. In some embodiments, the engineered adeno-associated virus (AAV) is an engineered AAV9, and the engineered viral capsid polypeptide comprising an amino acid sequence of any one of SEQ ID NOs: 1-1007, 2149-2261, and 2945-6269, and the effective amount is no more than 1× 1013 vg / kg.
[0230] In another aspect, the present disclosure provides a method of reducing the amount of B cell is a subject, comprising administering a therapeutically effective amount of engineered adeno-associated virus (AAV) disclosed herein which comprises a single-strand DNA encoding a chimeric antigen receptor (CAR) . In some embodiments, the engineered adeno-associated virus (AAV) is systematically administered to the subject. In some embodiments, the engineered adeno-associated virus comprises an expression cassette which comprises a single-strand DNA encoding a CD19-CAR. In some embodiments, the B cell is a malignant B cell. In some embodiments, the B cell is a CD19+ B cell. In some embodiments, the engineered adeno-associated virus (AAV) is systematically administered to the subject. In some embodiments, the engineered adeno-associated virus (AAV) is an engineered AAV6, and the engineered viral capsid polypeptide comprising an amino acid sequence of any one of SEQ ID NOs: 1008-2105, 2262-2944, and 6270-9287, and the therapeutically effective amount is no more than 1× 1012 vg / kg.
[0231] In some embodiments, the present disclosure provides a method for treating B-cell malignancy by reducing the amount of B cell with the method disclosed herein. In some embodiments, B-cell malignancy includes, but is not limited to, B-cell lymphoma, chronic lymphocytic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma.
[0232] Table 1A
[0233] Table 1B References
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[0265] 32 Sterner, R. C., Sterner, R. M. CAR-T cell therapy: current limitations and potential strategies. Blood Cancer J. 11, 69 (2021) . https: / / doi. org / 10.1038 / s41408-021-00459-7 EXAMPLESExample 1 Design engineered capsid for AAV9 variants
[0266] To design a capsid library with a better chance of identifying variants with specific tropism, functional peptides reported from various databases and literature are collected and analyzed. Fragments with 6-12 amino acids from the collected sequences were randomly chosen and inserted between A581 and T593 of the AAV9 capsid protein (SEQ ID NO: 2017) , resulting in a library with 480,000 AAV9 variants. Based on a AAV9 variant screening in human primary T cells, candidates that showed increased transduction efficiencies compared to the wild-type AAV9 (AAV9-WT) were identified. Three leading candidates, AAV9-M1 (SEQ ID NO: 2110) , M2 (SEQ ID NO: 2111) , and M3 (SEQ ID NO: 2112) , were identified from the capsid screening. These AAV9 variants were assembled by engineered capsid proteins with mutations between A581 and T593. The mutated peptides between A581 and T593 locate in the protrusion of AAV particles and interact directly with host cells.
[0267] To validate the transduction efficiencies of the leading candidates in human primary T cells, self-complementary AAVs were packed with constructs encoding EGFP using the three AAV9-M variants and compared to AAV9-WT (Figure 1A) . The percentage of fluorescent T cells was used to represent the transduction efficiencies of AAV at days 3, 7, and 14 post AAV transduction. Across various MOI (1 × 102, 1 × 103, 1 × 104, and 1 × 105) and different examining time points, AAV9-M1 consistently showed the highest transduction efficiencies among the variants, and all the AAV9-M variants showed higher transduction efficiencies than AAV9-WT (Figure 1B-C, Figure 6A) . The mean fluorescent intensity (MFI) showed the same trend (Figure 1D) . Remarkably, at the lowest MOI we tested (1 × 102) , AAV9-M1 successfully transduced ~23%of T cells, which is beyond the ~16%EGFP-positive T cells transduced with AAV9-WT at MOI of 1×105. These data demonstrated that the AAV9-M variants exhibited superior transduction efficiencies to human primary T cells than AAV9-WT. Moreover, we examined the packing efficiencies of AAV9-M1, the most efficient variant, and found it’s comparable to the AAV9-WT (Figure 6B) . And the transduction of AAV9-M1-EGFP does not negatively impact T-cell proliferation (Figure 6C-D) . These features collectively indicate that AAV9-M1 can be a delivery vector to human primary T cells.Example 2 Deliver CAR sequence to human T cells in vitro using AAV9-M1
[0268] The capability of AAV9-M1 to deliver anti-CD19 CAR sequences into human T cells was tested. The transient CAR-expressing T cells (transient CAR-T cells) was generated by delivering the CAR sequence as a transgene. The stable CAR-expressing T cells (stable CAR-T cells) was generated following Cas9 / gRNA ribonucleoprotein (RNP) electroporation.
[0269] To generate the transient CAR-T cells by AAV9-M1, a construct encoding CAR sequence followed by the EGFP gene, driven by an EF1α promoter (AAV9-M1-CAR) was designed (Figure 2A) . Active human primary T cells were transduced by AAV9-M1-CAR or AAV9-WT-CAR, and the percentages of CAR-positive T cells were measured (Figure 2B) . Notably, at MOI= 5 × 104, AAV9-M1-CAR produced 32.0%CAR-positive T cells, compared to less than 1%CAR-T cells produced by AAV9-WT-CAR. The percentage of CAR-T cells was monitored every three days till day 12 post-transduction. Around 27%of T cells were CAR positive at day three post-transduction, then dropped to about 1%after six days, as active T cells proliferated rapidly (Figure 2C) . In independent replicates, the cytotoxicity of AAV-transduced T cells was examined by co-culturing CAR-T cells with NALM6 cells. NALM6 cytotoxicity was detected from day 1 to day 6 after co-culture (Figure 2D) , which was longer than the duration that CAR-T cells could be detected. Moreover, the proliferation and viability of AAV-transduced T cells were comparable to the non-transduction control (Figures 7A and 7B) , indicating that AAV transduction did not impact T cell proliferation. Together, AAV9-M1 effectively delivers CAR sequence into human primary T cells in vitro, resulting in functional CAR-T cells with demonstrated NALM6 cytotoxicity and normal self-proliferation and viability.
[0270] Stable CAR T cells was generated by integrating the CAR sequence into the T cell genome via homology-directed repair (HDR) (Figure 2E) . The first exon of the PDCD1 gene was chosen to accommodate the CAR sequence, by which the cytotoxicity of CAR-T cells would presumably be further enhanced by knocking out the immune checkpoint gene. Cas9 / gRNA RNP was electroporated into T cells before AAV transduction to enable genome editing, and the CAR sequence integration was confirmed by PCR (Figure 7C) . Three days post AAV transduction, 51.6%of T cells from the AAV9-M1-CAR group turned to CAR-T cells, compared to 16.8%CAR-T cells in the AAV9-WT-CAR group (Figure 2F) . In independent replicates, the percentage of CAR-positive T cells remained stable from day 3 to day 9, then slightly increased at day 12 post AAV transduction (Figure 2G) . By engineering T cells from four different donors, we confirmed that AAV9-M1-CAR-transduced T cells almost wholly eliminated NALM6 cells, and the cytotoxicity was retained at least nine days after co-culture (Figure 2H) . RNP electroporation appears to have impacted T cell proliferation (Figure 7D) , while the cell viability remained unchanged (Figure 7E) . Collectively, we demonstrated that electroporating Cas9 / gRNA RNP followed by delivering CAR sequence as HDR template via AAV9-M1 could enable stable CAR expression and cytotoxicity to NALM6 cells in human T cells in vitro.Example 3 Deliver CAR sequence to human T cells in vivo using AAV9-M1
[0271] Based on the successful AAV-mediated CAR-T cell generation in Example 2, further exploration of the in vivo application of AAV9-M1 was conducted. This example aims to test whether the superior transduction efficiency of AAV9-M1 to human T cells could enable the generation of CAR-T cells in vivo through systematic injection to bypass the complex manufacturing of ex vivo CAR-T cell therapy. A humanized mouse model was generated by injecting human peripheral blood mononuclear cells (PBMCs) into immunodeficient mice (Figure 3A) . Animals with comparable levels of engrafted human T-cell were injected with AAV9-M1-CAR at 1×1013 vg / kg or PBS through the tail vein and sacrificed after 14 or 28 days. The CAR-EGFP construct used in the in vitro assay was packed by AAV9-M1 (Figure 2A) . The percentages of T-cell engraftment were examined to confirm the successful construction of the PMBC humanized mouse model, and there were no differences in animal weight between the mice injected with AAV or PBS (Figure 8) .
[0272] Fourteen days after the AAV injection, the percentage of CAR-T cells was quantified in the peripheral blood (PB) , bone marrow (BM) , spleen, lung, and liver. It was observed that around 5%of human T cells were turned into CAR-T cells in these organs (Figure 3B) . Interestingly, these anti-CD19 CAR-T cells appeared functional to inhibit the engrafted human B cells in mice, as the percentages of B cells in the mice injected with AAV9-M1-CAR were significantly lower than the baseline levels in the mice injected PBS, especially in bone marrow and spleen (Figure 3C) . Twenty-eight days post AAV injection, although CAR-T cells remained present in multiple organs and peripheral blood, the percentages dropped (Figure 3D, Figure 8B) . Meanwhile, the percentages of human B cells were still at low levels (Figure 3E) . Collectively, these data demonstrated that systematic injection of AAV9-M1-CAR could generate CAR-T cells in vivo, which appeared to inhibit the number of CD19+ human B cells in mice.
[0273] To investigate whether the growth of malignant CD19+ B cells could also be controlled by the in vivo generated CAR-T cells, luciferase-expressing NALM6 lymphoma cells were transplanted into the humanized mice (Figure 3F, Figure 9A-C) . Fourteen days post AAV injection, with the presence of ~5%CAR-T cells, the percentage of normal human B cells decreased as previously observed, but there was no significant difference in NALM6 cells at this time point between the PBS and AAV-M1-CAR groups (Figure 3G-I) . Interestingly, after two more weeks, although the percentage of CAR-T cells dropped to ~1% (Figure 9D) , the percentage of both NALM6 cells decreased compared to the control, especially in bone marrow (Figure 3J and Figure 9E) . The luciferase-expressing NALM6 also allowed tumor growth to be monitored in live animals (Figure 3K) . Tumor signals was found presented in 7 out of eight mice (87.5%) in the PBS group. Tumor signals in the thighs appeared the strongest compared to the other parts of the mouse body, implying tumors expanded rapidly in bone marrow, consistent with the highest percentage of NALM6 cells (Figure 3J) . In contrast, tumor signals presented in 4 out of nine mice (44.9%) injected with AAV9-M1-CAR to a much lesser extent and restricted areas compared to the control group, indicating the injection of AAV9-M1-CAR inhibited the growth of NALM6, presumably through the in vivo generated CAR-T cells. Investigations on the NALM6-transplanted humanized mouse model further demonstrated that the AAV9-M1-mediated in vivo CAR-T cells could control the progression of CD19+ malignant B cells.Example 4 Design engineered capsid for AAV6 variants
[0274] To further reduce the AAV-CAR dose for in vivo CAR-T cell generation, the same capsid engineering was conducted as in Example 1 for variants derived from AAV6, which possesses congenital tropism in human primary T cells compared to the other AAV serotypes. Two capsids, AAV6-M1 (SEQ ID NO: 2108) and AAV6-M2 (SEQ ID NO: 2109) , were chosen as leading candidates and used to deliver the transgene sequence into human T cells. An in vitro pilot study verified that both AAV6-M1-EGFP and AAV6-M2-EGFP transduced human T cells more efficiently than AAV6-WT-EGFP across various MOI (Figure 4A) , as quantified by the percentage of EGFP-positive T cells and the MFI of the transduced T cells (Figure 10A-B) . After examining the packing efficiencies of the two AAV6 variants, AAV6-M2 was chosen to deliver the CAR sequence in vivo (Figure 10C) .Example 5 Deliver CAR sequence to human T cells in vivo using AAV6-M2 at low dose
[0275] To assess the dose range of AAV6-M2 to generate CAR-T cells in vivo, AAV6-M2-CAR was systematically injected into PBMC humanized mice at two different doses (Figure 4B) . The injection did not change animal weights (Figure 10D) . When 1×1012 vg / kg of AAV6-M2-CAR was administrated, which is 10%of the dose used by AAV9-M1-CAR, flow cytometry identified 2.6-2.9%CAR-T cells in the peripheral blood and multiple organs at 14 days post-AAV injection (Figure 4C, Figure 10E) . Twenty-eight days post-injection, there were still ~0.5%CAR-T cells in the BM, PB, and spleen and ~1%in the liver and lung (Figure 4F, Figure 10F) . In the presence of CAR-T cells, the percentage of human B cells decreased in the peripheral blood and other organs compared to the control group, and the decrease in the BM, spleen, and liver is statistically significant (Figure 4D &4G) .
[0276] When further decreasing the dose of AAV6-M2-CAR to 1 × 1011 vg / kg, which is 1%of AAV9-M1-CAR, it was still able to identify 0.6-1.3%CAR-T cells in peripheral blood and organs at day 14 (Figure 4C) and 0.5-1.1%CAR-T cells at day 28 (Figure 4F) . Notably, although the percentages of CAR-T cells decreased than that of administrating 1 × 1012 vg / kg AAV, they did not proportionally decrease as the dose of AAV. Significantly, this amount of CAR-T cells still successfully inhibited the number of human B cells. For example, 0.10%of B cells remained in the spleen with the presence of CAR-T cells at day 28, compared to the 1.10%in the control group (Figure 4G) . In vivo data indicated that AAV6-M2 could deliver CAR sequences to T cells through 1 × 1011 -1012 vg / kg systematic administration, implying its translational potential for in vivo CAR-T therapies at low doses.
[0277] To assess the hepatoxicity of systematically administrating AAV6-M2, the AAV6-M2 viral copies in the liver were estimated. Fourteen days post intravenous injection of AAV6 at 1 ×1012 vg / kg, the viral copy identified in the liver of the mice injected with AAV6-M2-CAR was 0.7%of the amount determined in the liver of the mice injected with AAV6-WT-CAR (Figure 4E) . This percentage was 0.8%at day 28 post-injection (Figure 4H) . When administrating a further reduced dose of 1 × 1011 vg / kg, the mouse liver accumulated 2.8%viral copies of that injected with AAV6-WT-CAR. A sharp reduction of viral accumulation was observed in the liver of mice injected with AAV9-M1-CAR at 1 × 1013 vg / kg compared to AAV9-WT-CAR (Figure 10G-H) . The reduced liver accumulation suggested that the engineered AAV6-M2, as well as AAV9-M1, de-targeted from the mouse liver on top of their in vivo tropism to human T cells, which could potentially translate to a low-dose and effective in vivo CAR-T therapy via systematic administration of AAV-CAR.Example 6 Explore the superiority of AAV6-M2 in T-cell transduction
[0278] To understand the superiority of AAV6-M2 in T-cell transduction over the AAV6-WT, whole genome CRISPR knockout screening was performed in Jurkat cells and identified genes that significantly impacted AAV6-M2 and AAV6-WT transduction (Figure 5A) . The CRISPR screening was conducted in Jurkat cells with stable Cas9 expression (Jurkat-Cas9) so that the editing outcome of each cell was given the same Cas9 expression level. In brief, Jurkat-Cas9 cells were transduced by the lentiviral Brunello CRISPR library, and the successfully transduced cells were further transduced by either AAV6-WT-EGFP or AAV6-M2-EGFP. Both the top 20%and the bottom 20%fluorescent cells were collected. It was reasoned that sgRNAs enriched in the bottom 20%of cells compared to the top 20%represented genes disrupting the AAV attachment, internalization, or trafficking to host cells. This workflow was used to identify potential cell surface receptors or co-receptors that might be hijacked by the engineered capsids to enter host cells.
[0279] The top 10 genes enriched in each screening were analyzed (Figure 5B-C) . Both screenings identified genes that are known to be essential to AAV transduction and trafficking, including KIAA0319L and TM9SF2, demonstrating that the screenings are effective. Among genes only identified in the AAV6-M2 screening, SELL is the only protein that shows cell surface localization, potentially mediating the attachment or entry of AAV6-M2. Also known as CD62L or L-selectin, SELL is essential for the binding and subsequent rolling of lymphocytes on endothelial cells, facilitating their migration into secondary lymphoid organs. In a recent study, researchers modified lentivirus envelopes with CD62L-specific scFv for efficient CAR sequence delivery into less differentiated human T cells (Kapitza et al., 2023) . Indeed, knocking out CD62L (SELL) from Jurkat-Cas9 cells decreased the AAV6-M2 transduction efficiencies (Figure 5D) . The reduction of transduction efficiencies was at a similar level when AAVR was knocked out, suggesting the critical role of CD62L in mediating AAV6-M2 entry to T cells. Interestingly, CD62L-KO (SELL-KO) did not impact the AAV6-WT transduction, indicating CD62L-mediated AAV entry is unique to AAV6-M2 and potentially contributes to AAV6-M2’s tropism to T cells (Figure 5E) . Maestro was used to predict the binding between CD26L and AAV6-M2 (Sastry et al., 2013) . The predicted interaction interface indicated that the engineered variable region of AAV6-M2 forms a U-shaped loop and fits well in a well-characterized CD26L binding pocket. The negatively charged loop sequences and the positively charged amino acids at the surface of the binding pocket may contribute to their high affinity (Figure 11A) . Example 7 Plot sequence logos
[0280] To investigate the sequence patterns in the AAV capsid protein and identify critical amino acid at specific positions, sequence logo plots were generated based on the sequences disclosed in Table 1A. We used the Meme software and regular expressions to extract motifs from enriched sequence patterns. The process of determining the enriched sequence patterns involved manual curations.
[0281] Figs. 12A and 12B illustrate two similar sequence motifs. The motif in Fig. 12A can be denoted as [D|E] X1X2X3X4Y, and the motif in Fig. 12B can be denoted as [D|E] X1X2X4Y. These two motifs contain a string of five or six amino acid residues, starting with D or E and ending with Y. The amino acid residues at the first position and the ending position of these motifs are critical. The amino acid residues in between also show patterns. For example, the amino acid residue X1 in [D|E] X1X2X4Y and the amino acid residue X1 in [D|E] X1X2X3X4Y prefer K. For another example, the amino acid residue X4 in [D|E] X1X2X4Y and the amino acid residue X4 in [D|E] X1X2X3X4Y prefer P and A.
[0282] The motif in Fig. 12C represents a poly [D|E] pattern. Within a string of five or six letters, this motif includes no less than three D, or no less than three E, or no less than a three-letter combination of D and E. The letters D and / or E are preferentially, but not required, consecutive.
[0283] The motif in Fig. 12D represents a poly [A|G|S] pattern. Within a string of five letters, this motif includes no less than four letters from a selection of A, G, and S. For visualization purposes, amino acid residues with small frequencies are not shown or not clearly visible in the sequence logo plots in Fig. 12A, 12B, 12C, and 12D.
[0284] The sequence patterns in Figs. 12A, 12B, 12C, and 12D are exemplified in Tables 7A, 7B, 7C, and 7D, where the rows (A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y) denote the 20 amino acid residues and the columns denote the positions in the motifs. The numbers in Tables 7A to 7D represent estimated frequency levels of a particular amino acid residue in a given position in the motifs. The frequency level 0, 1, 2, 3, or 4 represents an estimated likelihood of an amino acid residue that may occur at a given position, where the larger the number, the higher the likelihood. Table 7A Table 7B Table 7C Table 7D
[0285] Tables 7A-7D are exemplary position matrix tables illustrating estimated frequency level of a particular amino acid at a given position in a motif. While the specific frequency of an amino acid residue at a particular position may change if a given different set of input sequences is given, the frequency levels in Tables 7A-7D were helpful in determining the importance of an amino acid at a specific position. For example, as shown in Table 7A, amino acid residues P and A at position X4 have a higher level of frequency than other amino acid residues.Discussion
[0286] The examples disclosed herein showcased that a clinically demonstrated delivery platform, the recombinant AAV vector, could deliver transgenes into human T cells in high-efficiency ex vivo and in vivo. They showed that AAV9-M1, a leading AAV9 variant, successfully generated T cells with stable CAR expression by integrating CAR sequence into the PDCD1 loci in the genome of human T cells, following electroporation of Cas9 / gRNA RNP. In addition, AAV9-M1 and AAV6-M2 generated functional CAR-T cells in vivo by systematically administrating AAV-CAR at different doses. Inhibition on the number of human B cells was observed 28 days after AAV6-M2-CAR injection at 1 × 1011 vg / kg, and viral copies accumulated in the liver of a humanized mouse model was 4%of the mouse injected with AAV6-WT-CAR. Moreover, mechanistic insights were provided by CRISPR screening, which identified CD62L as a key mediator of enhanced AAV6-M2 transduction efficiency in human T cells.
[0287] Among the various drug delivery platforms, lentivirus, LNP, and VLP have already been used to engineer human T cells in vivo. However, no study has shown that systematic injection of AAV could enable the generation of functional human CAR-T cells in vivo, although AAV vector has already been used in eight gene therapies approved by the FDA. As natural AAV significantly accumulates in the liver by systematic administration, engineering AAV vectors to non-hepatic organs and cells is critical to bringing AAV into the regime of in vivo CAR-T therapy. This study showcased that capsid engineering could enhance the transduction efficiencies of AAV vectors to T cells as the other therapeutically relevant organs (e.g., CNS and muscles) . Through capsid engineering and screening in human T cells, the present disclosure successfully identified AAV9-M1 and AAV6-M2 as leading candidates. They could effectively deliver CAR sequences into human T cells both ex vivo and in vivo. Indeed, in a PBMC humanized mouse model, the in vivo-generated CAR-T cells led to a significant reduction in the number of engrafted human B cells and controlled the progression of transplanted malignant B cells, which proved the concept of AAV-mediated in vivo CAR-T therapy for autoimmune disease and hematological malignancies.
[0288] Identifying CD62L in mediating AAV6-M2 transduction to human T cells provides structural interpretation of the successful generation of CAR-T cells in vivo. The CD62L surface marker decorated and early-memory T cells with higher plasticity and greater ability to proliferate, which are favored by CAR-T cell therapy. In the present disclosure, the engineered AAV6-M2 appears to hijack the CD62L to enter T cells. The engineered peptide sequence could potentially be incorporated with other therapeutic modalities as a targeting moiety for CD62L+ T cells. Also, the homing of CD62L+ T cells could redirect AAV6-M2 to secondary lymphoid organs, where T cells are abundant. Collectively, this targeted delivery increases the likelihood of AAV6-M2 encountering and transducing T cells.
[0289] Among the eight FDA-approved AAV gene therapies, Zolgensma and Elevidys are the only two to target non-hepatic organs by systematic injection; both are prescribed > 1 × 1014 vg / kg to patients (Wang et al., 2024) . In this study, functional CAR-T cells were generated by administrating AAVs at three doses, from 1 × 1013 vg / kg of AAV9-M1 to 1 × 1012 or 1 × 1011 vg / kg of AAV6-M2, which are around 2 × 109 -2 × 1011 vg / animal. The one to three orders of magnitude lower doses provide a low-dose gene therapy. Additionally, across all doses and different AAV variants, the viral copies accumulation in the liver showed a sharp reduction (>95%) compared to the wild-type AAV vectors. These profiles indicated a low dose and low hepatoxicity in vivo CAR-T gene therapy.
[0290] It was noticed that AAV9-M1 might use different receptors / co-receptors than AAV6-M2 (Figure 11B-E) , suggesting distinct cellular factors could be utilized by different AAV variants for cell entry. AAV variants using other receptors / co-receptors to mediate stronger T cell tropism may also be possible. Meanwhile, the identified receptors can also be used to guide the design of the capsid protein.
[0291] We demonstrate that engineered AAVs such as AAV9 and AAV6 variants with enhanced transduction efficiencies in human T cells can deliver CAR sequences via systematic administration and generate functional CAR-T cells in vivo. This study provides a novel in vivo CAR-T platform with a well-studied and clinic-approved delivery vector. It also expands the scope of AAV-mediated gene therapy to non-inherited diseases.MethodsAAV production and titration
[0292] ITR-containing cargo plasmid was utilized for packaging with different AAV capsid plasmid and adenovirus helper plasmids using polyethyleneimine (24765-1, Polysciences) . 293T cells were purchased from ATCC. To pack AAV, 293T cells were seeded in 150 mm plates; The cargo plasmid, capsid plasmid, and helper plasmid were added at a ratio = 1: 1: 1 (Table 2) . After 72 hours, the transfected 293T cells were collected in SAN digestion buffer and lysed by three rounds of rapid freeze / thawing, followed by a 1 h incubation at 37℃ with 100 units / ml Benzonase (20156ES60, Yeasen) . AAV was further purified following cell harvest and PEG precipitation using iodixanol (OptiPrep, #07820, StemCell Technologies) gradient ultracentrifugation. The purified AAV was treated with DNaseI (AM2238, Invitrogen) and Proteinase K (W0013, Qiagen) . The titer of AAV was determined by qPCR with ChamQ Universal SYBR qPCR Master Mix (Q711, Vazyme) via 96 (Roche) . Relative quantity was estimated compared to a serial dilution of a plasmid standard of known concentration. Primers for AAV titration were listed in Table 3. The engineered capsids were listed in Table 4. Cell culture and AAV transduction
[0293] Human primary cells
[0294] Human periphery blood from healthy donors was obtained with ethical approval at Liquan Hospital, Shanghai, Boren Hospital, Beijing, and The Affiliated People’s Hospital of Ningbo University, Ningbo. Human primary T cells were isolated from PBMC using the Pan T Cell Isolation Kit (Miltenyi Biotec, 130-096-535) and stored in liquid nitrogen until used.
[0295] To transduce human T cells with AAV, T cells were activated by EnceedTM T cell Activation reagent (L00899, Genescript) for 48 h in RPMI 1640 (Sigma) supplemented with 10%FBS and IL-2 at 100U / mL (Jiangsu Kingsley Pharmaceutical Co., Ltd. ) . Then, AAV was added to the cell culture at certain MOIs. After incubation overnight, the AAV-containing medium was exchanged for fresh medium with IL-2 (100 U / ml) for further cell culture. The cell number and viability were monitored, and the culture medium was half-changed every three days. In AAV-EGFP transduction, the EGFP expression in cells was detected by flow cytometry at indicated time points. In AAV-CAR transduction, anti-human Fab was added in cells to detect CAR expression via flow cytometry at indicated time points.
[0296] NALM6 cells
[0297] NALM6 cells were transduced by lentivirus containing luciferase sequence with hygromycin resistance. Then, the NALM6 cells with stable luciferase expression were selected and expanded in 50ug / ml hygromycin.
[0298] Jurkat cells
[0299] Jurkat cells were used in CRISPR screening and candidate gene validation. Jurkat cells were purchased from ATCC and cultured in RPMI 1640 supplemented with 10%FBS. To generate Jurkat-Cas9 cells, Jurkat cells were transduced by LentiCas9-Blast (Addgene, 52962) . After blasticidin selection, monoclones of Jurkat-Cas9 cells were established via limited dilution. Then, monoclones were expanded in the presence of blasticidin.In vitro experiment
[0300] Electroporation
[0301] To generate stable CAR-T cells in vitro, T cells were first electroporated in P3 buffer (Lonza #V4XP-3032) with Cas9 / gRNA RNP using a 4D-Nucleofector X unit (Lonza #AAF-1003X) . RNP was freshly prepared. For each reaction, 30 pmol Cas9 protein (Takara #632641) and 75 pmol sgRNA (GenScript) were incubated at 25 ℃. A total of 1 × 106 human T cells were electroporated with RNP per well under the Lonza EO-115 program. After nucleofection, cells were resuspended in a fresh culture medium. Afterward, AAV-CAR was added to the cell culture within 15 min after electroporation at an MOI of 5×104. The cell culture was incubated at 37℃ overnight. The medium was exchanged the next day, and the cells were maintained at a density of approximately 1×106 cells per ml for expansion.
[0302] PCR amplification of joining sequences flanking the HDR insertion
[0303] At d3 post electroporation and AAV addition, the genomic DNA of cells was extracted by TIANamp Genomic DNA Kit (TIANGEN, DP304-03) . Then, joining sequences flanking the HDR insertion were amplified using Q5 master mix (2×) (NEB #M0544S) . Primers used in PCR amplification of 5’ and 3’ joining sequences flanking the HDR insertion were listed in Table 3.
[0304] Cytotoxicity assays
[0305] To evaluate the cytotoxicity of CAR-T cells, 3 × 105 NALM6 cells and 3 × 105 effector CAR-T cells were co-cultured in the medium at a final concentration of 1×106 cells / mL in a 12-well plate. Twenty-four hours later, the co-cultured cells were collected for flow cytometry tests. Anti-human CD45 and anti-human CD19 were added into cell suspension to identify NALM6 cells and human T cells. The cytotoxicity for each sample was determined by the formula: 100%× (CD19+%in blank -CD19+%in AAV9-M1) / CD19+%in blank.
[0306] Flow cytometry data collection and analysis
[0307] Backman CytoFLEX was used for EGFP expression assay, CAR expression assay, and cytotoxicity assay. Flow cytometry data were analyzed via FlowJo.
[0308] Humanized mouse model
[0309] NOD-PrkdcscidIl2rgnull / Shjh (NPSG) mice were purchased from Shanghai Jihui Laboratory Animal Care Co., Ltd. And housed in standard individually ventilated and pathogen-free conditions in the laboratory animal resource center of Westlake University. All mice were used following Institutional Animal Care and Use Committee (IACUC) guidelines at Westlake University. 24h before human PBMC injection, 4-6 weeks-old mice were radiated by X-ray at 1Gy. Then, 5 × 106 PBMC was adoptively transferred into each mouse recipient via intravenous (i.v. ) injection. At 10~11 days after human PBMC injection, AAV-WT-CAR or AAV-M-CAR were given to each mouse at indicated doses via i.v. injection. One day before human PBMC injection, human CD45+ cell engraftment in the periphery blood of each mouse was tested by flow cytometry. Mice with human CD45+ cell engraftment >50%or <3%were excluded. In the humanized model with tumor transplantation, 2 × 106 NALM6 cells were transplanted into each humanized mouse via i.v. Injection at d5 after human PBMC injection. In the following month, after the AAV injection, the weight loss of mice was monitored every week.In vivo imaging
[0310] At days 0 and 28 after AAV injection, the NALM6 signals in mice were detected by in vivo imaging via PHOTON IMAGERTM OPTIMA, in which luciferin (D-Luciferin potassium salt, Beyotime) was administered intraperitoneally 5 minutes before signal collection.
[0311] Detection of human T cell, human B cell, and NLAM6 cell in humanized mice
[0312] At d14 or d28 post AAV injection, mice were sacrificed for periphery blood, spleen, liver, lung, and bone marrow (from femur) collection. The erythrocytes were lysed in 1X BD Pharm lyse solution (BD Bioscience) before antibody staining for periphery blood processing. For other organs, tissues were cut into small pieces and passed through 100um cell mesh. Then, the passed cells were resuspended into 1X BD Pharm lyse solution to deplete erythrocytes. Finally, partial cell suspension was taken for antibody staining. In antibody staining, anti-human CD45, anti-human CD19, and anti-human CD3, were added to each sample and kept on ice for 30mins. Then, all cell suspensions were washed with PBS before the flow cytometry test. All flow cytometry data were analyzed using FlowJo version 10. Antibodies were listed in Table 5.
[0313] AAV accumulation test in the liver of humanized mice
[0314] A 50-80mg minced mouse liver was taken for homogenization and further genomic DNA extraction by TIANamp Genomic DNA Kit (TIANGEN, DP304-03) . Then, a QPCR assay of AAV-CAR was performed.
[0315] Absolute quantification of AAV-CAR via QPCR was based on 100ng gDNA per sample. In the QPCR assay, primers (QCAR-F, QCAR-R) and probes (QCAR-Probe) targeting the CAR sequence were designed as listed in Table 3. The PCR amplification was performed using Hot Start Taq 2× Master Mix (NEB#M0496S) as 95 ℃ for the 30s, followed by 40 cycles of 95 ℃ for 15s, 52 ℃ for 30s, and 68 ℃ for 20s. Finally, the Ct values were transformed into the AAV vector genome (Vg) according to the standard curve.Genome-wide CRISPR / Cas9 screening
[0316] Prepare lentivirus Brunello library
[0317] The transfer plasmid (LentiGuide-Puro) , the pMD2. G (Addgene, 12259) envelope plasmid, and the psPAX2 (Addgene, 12260) packaging plasmid were mixed at the mass ratio 5: 2: 3 and incubated for 15 mins at room temperature. The mixture was dropped to HEK293T cells at 80%confluency. Lentiviral supernatant was collected at 48 and 72 h post-transfection, filtered through a 0.45 μm filter (Millipore, SLHV033RB) , and then concentrated by ultracentrifuging at 70 000g at 4℃ for 2 h. Finally, the concentrated lentivirus was aliquoted and stored at -80℃.
[0318] CRISPR / Cas9 screening in Jurkat-Cas9 cells
[0319] Human CRISPR Brunello lentiviral pooled library targeting 19, 114 genes (76, 441 sgRNAs) was packaged and transduced in Jurkat with stable Cas9 expression (Jurkat-Cas9) . The screening was performed in two Jurkat-Cas9 mono clones. For each replicate, 7 × 107 Cas9-expressing Jurkat cells (~300X coverage) were transduced with the lentiviral library at MOI ≤ 0.3 by infection and incubated overnight. Flow cytometry confirmed transduction efficiencies at around 30%in each replicate for mKate2+%expression at 72h after lentivirus transduction. Cas9-expressing Jurkat cells (Jurkat-Cas9) were selected and expanded in a culture medium with puromycin. When mKate2+%achieved above 95%, 2.3 × 107 cells per replicate were transduced with scrAAV-WT-EGFP or scrAAV-M-EGFP at the indicated MOI to allow the percentage of EGFP+ cells reached ≥ 80%. At 72 h after AAV transduction, cells collected for the top 20%and bottom 20%were sorted via Flow Cytometer. BD FACSAriaTM Fusion and SONY MA900 were used for cell sorting. Flow cytometry data were analyzed via FlowJo.
[0320] After sorting, genomic DNA was extracted by TIANamp Genomic DNA Kit (TIANGEN, DP304-03) . Then, sgRNA sequences were amplified using Q5 master mix (2×) (NEB #M0544S) and purified using SPRI beads (Beckman #A63882) for NGS. PCR primers with P5 and P7 adapters (NGS-Lib-KO-F and NGS-Lib-KO-R) were listed in Table 3. sgRNA sequences used in validation were listed in Table 6.
[0321] Screening data analysis
[0322] The CRISPR screening was analyzed using MAGeCK (Li et al., 2014) . The difference in genes between the bottom 20%of cells and the top 20%of cells was evaluated by the reads count of corresponding gRNAs. In addition, the negative gRNAs were input as background with parameter (--control-sgrna) . The MAGeCK score and log2 fold change were used to rank genes from the CRISPR screening. The log2 fold change was calculated as the log2 transformed ratio between the normalized read counts in the bottom 20%sample and the top 20%sample. Normalization was based on the sequencing depth of each sample.
[0323] Candidate gene knockout cell line generation
[0324] Stable candidate knockout cell lines were generated using Jurkat-Cas9 cells transduced with lentivirus encoding indicated sgRNA under the U6 promoter. From day 2 after lentivirus transduction, Jurkat cells were selected with puromycin (2 μg / mL) for 7-10 days. Then, the genomic DNA of the Jurkat cells was extracted for PCR amplification of the target gene sequence. The indel%of the target gene was assessed via SYNTEGO analysis based on Sanger sequencing of PCR products. Primers used in sanger sequencing for KO validation were listed in Table 3.
[0325] Validation of candidate gene via AAV-EGFP transduction
[0326] For each validation candidate, as well as the positive control and negative control, a total of 1 × 105 cells were transduced with self-complementary AAV-WT-EGFP or AAV-M-EGFP. Seventy-two hours after AAV transduction, cells were collected and tested for EGFP expression via flow cytometry.Statistical analysis
[0327] Statistical analysis was performed using GraphPad Prism v8, and the specific tests were indicated in the brief descriptions of the figures.
Claims
1.An engineered viral capsid polypeptide, comprising an amino acid sequence, wherein the amino acid sequence is of any one of SEQ ID NOs: 1-2105 and 2149-9287.2.An engineered viral capsid polypeptide, comprising an amino acid sequence, wherein the amino acid sequence comprises X0X1X2X3X4Y,wherein X0, X1, X2, and X4 are each an amino acid residue, wherein X0 is Aspartate (D) or Glutamate (E) ,X3 is an amino acid residue or absent, andY is Tyrosine.3.The engineered viral capsid polypeptide of claim 2, wherein X3 is absent.4.The engineered viral capsid polypeptide of claim 2 or 3, wherein X1 is Lysine (K) .5.The engineered viral capsid polypeptide of claim 2 or 3, wherein X4 is Proline (P) or Alanine (A) .6.The engineered viral capsid polypeptide of claim 2, wherein the amino acid sequence comprises any one of SEQ ID NOs: 177, 323, 418, 427, 456, 463, 511, 552, 553, 735, 873, 1142, 1178, 1199, 1303, 1327, 1431, 1439, 1440, 1441, 1443, 1444, 1445, 1449, 1452, 1453, 1473, 1476, 1480, 1486, 1488, 1490, 1491, 1508, 1512, 1513, 1515, 1518, 1522, 1523, 1558, 1679, 1683, 1684, 1685, 1686, 1687, 1688, 1691, 1692, 1693, 1699, 1700, 1705, 1709, 1714, 1715, 1716, 1717, 1723, 1724, 1725, 1726, 1727, 1728, 1779, 1855, 1856, 1861, 1913, 2054, 2141, 2332, 2339, 2366, 2367, 2368, 2375, 2377, 2384, 2386, 2387, 2508, 2509, 2529, 2972, 3051, 3268, 3538, 3888, 4028, 4122, 4252, 4279, 4280, 4720, 4891, 5144, 5148, 5168, 5275, 5343, 5365, 5392, 5528, 5537, 5609, 5670, 5743, 5744, 5745, 5746, 5747, 5873, 6184, 6288, 6309, 6312, 6327, 6328, 6401, 6424, 6511, 6749, 6767, 6769, 6773, 6803, 6816, 6817, 6818, 6905, 6935, 6965, 6972, 6987, 7228, 7269, 7331, 7385, 7416, 7424, 7469, 7470, 7471, 7476, 7481, 7495, 7497, 7508, 7526, 7527, 7539, 7544, 7562, 7623, 7650, 7685, 7770, 7916, 7937, 7938, 7939, 7940, 7941, 7942, 7943, 7944, 7945, 7946, 7947, 7950, 7951, 7952, 7953, 7954, 7955, 7956, 7957, 7958, 7959, 7960, 7961, 7962, 7963, 7964, 7965, 7966, 7967, 7968, 7969, 7970, 7971, 7972, 7973, 7974, 7975, 7976, 7977, 7978, 7979, 7980, 7981, 7982, 7983, 7984, 7985, 7986, 7987, 7988, 7989, 7990, 7991, 7992, 7993, 7994, 7995, 7996, 7997, 7998, 7999, 8000, 8001, 8002, 8003, 8004, 8005, 8006, 8007, 8008, 8009, 8010, 8011, 8012, 8013, 8014, 8015, 8016, 8017, 8018, 8019, 8020, 8021, 8022, 8023, 8024, 8025, 8026, 8027, 8028, 8029, 8030, 8031, 8032, 8033, 8034, 8035, 8036, 8037, 8038, 8039, 8040, 8041, 8042, 8043, 8044, 8045, 8046, 8047, 8048, 8049, 8050, 8052, 8053, 8054, 8055, 8057, 8058, 8059, 8060, 8061, 8062, 8063, 8064, 8065, 8066, 8070, 8071, 8073, 8074, 8075, 8076, 8077, 8078, 8079, 8081, 8082, 8083, 8084, 8085, 8086, 8087, 8088, 8089, 8090, 8091, 8092, 8093, 8094, 8095, 8096, 8097, 8098, 8099, 8100, 8101, 8102, 8103, 8104, 8105, 8106, 8107, 8108, 8109, 8110, 8112, 8113, 8114, 8115, 8116, 8117, 8118, 8119, 8120, 8121, 8122, 8123, 8124, 8315, 8357, 8423, 8445, 8494, 8600, 8697, and 8787.7.The engineered viral capsid polypeptide of claim 3, wherein the amino acid sequence comprises any one of SEQ ID NOs: 33, 147, 314, 320, 546, 737, 870, 945, 967, 970, 1037, 1050, 1110, 1142, 1157, 1178, 1199, 1269, 1303, 1327, 1431, 1464, 1476, 1483, 1486, 1490, 1491, 1529, 1549, 1558, 1576, 1625, 1666, 1679, 1714, 1716, 1717, 1734, 1735, 1736, 1752, 1778, 1779, 1855, 1856, 1870, 1913, 2054, 2156, 2331, 2332, 2339, 2366, 2367, 2368, 2375, 2377, 2384, 2386, 2388, 2430, 2504, 2578, 2739, 2740, 2799, 3089, 3090, 3178, 3237, 3252, 3253, 3299, 3404, 3410, 3443, 3467, 3665, 3772, 3876, 3893, 3925, 4028, 4102, 4158, 4276, 4365, 4583, 4589, 4607, 4635, 4658, 4884, 4890, 4990, 5008, 5142, 5148, 5151, 5159, 5305, 5325, 5326, 5365, 5393, 5465, 5479, 5485, 5572, 5670, 5692, 5706, 5770, 5790, 5865, 5928, 5974, 6001, 6005, 6017, 6197, 6236, 6238, 6318, 6319, 6338, 6348, 6349, 6350, 6371, 6452, 6463, 6467, 6610, 6724, 6736, 6748, 6749, 6800, 6804, 6848, 6852, 6920, 6966, 6967, 6975, 7010, 7155, 7197, 7202, 7222, 7243, 7269, 7295, 7424, 7495, 7503, 7504, 7508, 7573, 7603, 7607, 7609, 7610, 7616, 7641, 7650, 7685, 7694, 7695, 7696, 7697, 7702, 7708, 7728, 7729, 7730, 7731, 7733, 7734, 7735, 7746, 7755, 7770, 7791, 7793, 7795, 7815, 7825, 7830, 7834, 7835, 7919, 7920, 7921, 7923, 7924, 7925, 7926, 7927, 7928, 7929, 8125, 8126, 8128, 8129, 8130, 8131, 8138, 8139, 8140, 8141, 8144, 8145, 8146, 8147, 8148, 8149, 8150, 8151, 8152, 8153, 8160, 8161, 8163, 8168, 8170, 8171, 8172, 8174, 8247, 8248, 8249, 8250, 8315, 8331, 8353, 8394, 8423, 8445, 8460, 8462, 8492, 8666, 8734, 8775, 8800, 8813, 8828, 8864, and 9189.8.An engineered viral capsid polypeptide, comprising an amino acid sequence, wherein the amino acid sequence comprises a poly [D|E] motif.9.The engineered viral capsid polypeptide of claim 8, wherein the amino acid sequence comprises any one of SEQ ID NOs: 29, 51, 64, 171, 590, 633, 637, 647, 648, 707, 730, 1025, 1026, 1042, 1045, 1054, 1055, 1061, 1082, 1084, 1100, 1106, 1107, 1108, 1109, 1111, 1124, 1130, 1131, 1141, 1142, 1145, 1148, 1152, 1153, 1154, 1155, 1156, 1161, 1162, 1163, 1178, 1181, 1191, 1192, 1193, 1195, 1196, 1199, 1262, 1268, 1269, 1278, 1279, 1280, 1285, 1293, 1298, 1300, 1303, 1307, 1310, 1321, 1324, 1358, 1366, 1400, 1402, 1415, 1419, 1429, 1430, 1484, 1485, 1493, 1506, 1509, 1534, 1554, 1555, 1556, 1558, 1559, 1563, 1565, 1566, 1568, 1571, 1580, 1581, 1588, 1612, 1616, 1629, 1655, 1657, 1658, 1663, 1680, 1751, 1769, 1779, 1790, 1818, 1823, 1825, 1832, 1833, 1835, 1845, 1846, 1848, 1849, 1850, 1851, 1855, 1856, 1872, 1873, 1874, 1877, 1878, 1880, 1885, 1888, 1889, 1891, 1894, 1895, 1896, 1900, 1902, 1904, 1910, 1911, 1913, 1914, 1942, 1947, 1958, 1959, 1964, 1966, 1975, 1978, 1990, 1991, 2004, 2016, 2017, 2018, 2019, 2020, 2021, 2051, 2053, 2054, 2055, 2059, 2060, 2062, 2065, 2068, 2070, 2071, 2072, 2074, 2075, 2076, 2077, 2078, 2079, 2081, 2082, 2086, 2087, 2089, 2090, 2091, 2100, 2102, 2142, 2157, 2215, 2277, 2279, 2313, 2321, 2331, 2332, 2333, 2335, 2336, 2337, 2338, 2339, 2342, 2343, 2345, 2353, 2357, 2358, 2363, 2367, 2375, 2376, 2377, 2378, 2381, 2385, 2388, 2395, 2396, 2401, 2406, 2407, 2412, 2415, 2416, 2418, 2422, 2428, 2429, 2430, 2431, 2444, 2483, 2484, 2485, 2486, 2487, 2524, 2525, 2530, 2533, 2538, 2539, 2540, 2565, 2576, 2577, 2578, 2634, 2635, 2646, 2692, 2694, 2700, 2709, 2738, 2739, 2740, 2786, 2787, 2788, 2796, 2799, 2801, 2818, 2832, 2838, 2841, 2844, 2849, 2867, 2905, 2915, 2924, 2937, 2994, 2995, 2996, 3001, 3005, 3006, 3007, 3009, 3036, 3049, 3052, 3053, 3064, 3065, 3071, 3075, 3155, 3257, 3276, 3280, 3534, 3566, 3567, 3568, 3569, 3571, 3577, 3578, 3579, 3582, 3590, 3592, 3616, 3617, 3624, 3676, 3704, 3749, 3785, 3793, 3794, 3795, 3796, 3797, 3801, 3802, 3808, 3809, 3832, 3838, 3989, 4006, 4116, 4130, 4181, 4320, 4348, 4349, 4386, 4397, 4500, 4501, 4502, 4503, 4507, 4508, 4509, 4510, 4511, 4512, 4513, 4514, 4515, 4516, 4517, 4518, 4519, 4521, 4522, 4523, 4525, 4526, 4533, 4534, 4535, 4536, 4537, 4538, 4541, 4542, 4562, 4680, 4689, 4690, 4692, 4701, 4702, 4703, 4707, 4726, 4744, 4747, 4758, 4775, 4776, 4778, 4780, 4781, 4793, 4795, 4799, 4819, 4829, 4841, 4842, 4843, 4845, 4878, 4880, 4888, 4968, 5010, 5139, 5152, 5305, 5413, 5609, 5777, 5897, 6007, 6155, 6282, 6290, 6291, 6292, 6306, 6307, 6311, 6312, 6339, 6363, 6365, 6374, 6376, 6390, 6395, 6396, 6408, 6412, 6413, 6423, 6424, 6429, 6431, 6437, 6439, 6460, 6473, 6491, 6502, 6505, 6506, 6507, 6512, 6520, 6521, 6531, 6544, 6554, 6586, 6605, 6606, 6607, 6610, 6617, 6618, 6638, 6665, 6668, 6686, 6707, 6712, 6713, 6716, 6748, 6749, 6750, 6779, 6782, 6783, 6785, 6796, 6803, 6832, 6861, 6862, 6863, 6866, 6867, 6868, 6869, 6870, 6871, 6892, 6895, 6896, 6915, 6920, 6923, 6924, 6933, 6947, 6953, 6955, 6958, 6965, 6967, 6970, 6973, 6975, 6976, 6977, 6985, 7004, 7005, 7007, 7010, 7016, 7020, 7030, 7045, 7046, 7052, 7056, 7057, 7058, 7059, 7063, 7074, 7075, 7076, 7173, 7179, 7181, 7182, 7184, 7185, 7187, 7194, 7196, 7197, 7198, 7203, 7218, 7223, 7224, 7225, 7226, 7227, 7228, 7235, 7254, 7257, 7271, 7275, 7280, 7283, 7285, 7290, 7292, 7298, 7302, 7314, 7322, 7326, 7331, 7339, 7372, 7378, 7398, 7399, 7404, 7405, 7408, 7421, 7422, 7423, 7424, 7426, 7427, 7435, 7446, 7449, 7460, 7462, 7477, 7483, 7484, 7486, 7490, 7491, 7495, 7496, 7502, 7509, 7514, 7516, 7545, 7549, 7582, 7589, 7592, 7597, 7601, 7623, 7632, 7633, 7647, 7650, 7651, 7652, 7653, 7654, 7655, 7664, 7670, 7685, 7706, 7708, 7710, 7711, 7712, 7713, 7714, 7724, 7725, 7726, 7727, 7741, 7742, 7745, 7748, 7749, 7750, 7751, 7752, 7753, 7754, 7759, 7768, 7770, 7771, 7777, 7778, 7782, 7785, 7788, 7789, 7792, 7798, 7799, 7802, 7806, 7807, 7819, 7824, 7827, 7839, 7843, 7845, 7848, 7856, 7857, 7860, 7863, 7867, 7877, 7886, 7891, 7896, 7897, 7898, 7914, 8068, 8156, 8164, 8188, 8191, 8201, 8204, 8222, 8232, 8278, 8279, 8285, 8292, 8298, 8309, 8313, 8318, 8320, 8334, 8335, 8353, 8359, 8360, 8362, 8363, 8364, 8365, 8366, 8368, 8377, 8378, 8393, 8394, 8397, 8410, 8411, 8412, 8413, 8415, 8417, 8423, 8424, 8425, 8426, 8428, 8445, 8453, 8454, 8458, 8460, 8461, 8468, 8470, 8471, 8472, 8477, 8484, 8488, 8491, 8493, 8494, 8497, 8498, 8499, 8506, 8507, 8508, 8510, 8537, 8543, 8591, 8603, 8604, 8608, 8609, 8612, 8618, 8622, 8625, 8627, 8630, 8639, 8644, 8654, 8660, 8662, 8669, 8670, 8674, 8681, 8688, 8690, 8712, 8720, 8742, 8759, 8760, 8767, 8780, 8787, 8789, 8819, 8820, 8829, 8838, 8850, 8860, 8861, 8870, 8883, 8885, 8886, 8898, 8900, 8905, 8917, 8919, 8920, 8950, 8952, 8953, 8965, 8973, 8977, 8982, 8985, 8986, 8997, 9011, 9012, 9014, 9048, 9057, 9059, 9100, 9105, 9106, 9114, 9118, 9123, 9124, 9126, 9127, 9140, 9169, 9172, 9174, 9175, 9187, 9188, 9189, 9207, 9212, 9213, 9227, 9228, 9234, 9236, 9237, 9247, 9265, and 9267.10.An engineered viral capsid polypeptide, comprising an amino acid sequence, wherein the amino acid sequence comprises a poly [A|G|S] motif.11.The engineered viral capsid polypeptide of claim 10, wherein the amino acid sequence comprises any one of SEQ ID NOs: 3, 4, 6, 7, 8, 9, 14, 15, 16, 17, 19, 20, 30, 31, 32, 34, 35, 36, 37, 38, 40, 43, 45, 46, 54, 61, 67, 76, 93, 102, 110, 112, 113, 114, 115, 116, 117, 118, 119, 120, 122, 123, 124, 127, 128, 132, 135, 141, 142, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 159, 160, 162, 176, 178, 179, 180, 181, 182, 184, 186, 187, 188, 191, 197, 198, 199, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 247, 248, 255, 269, 274, 282, 283, 284, 291, 293, 294, 296, 300, 302, 303, 305, 310, 314, 315, 318, 326, 330, 338, 340, 341, 342, 346, 353, 360, 363, 368, 387, 395, 403, 416, 427, 429, 430, 432, 439, 444, 445, 446, 447, 450, 451, 452, 460, 467, 475, 476, 485, 486, 488, 489, 496, 502, 504, 506, 507, 508, 513, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 529, 532, 540, 544, 545, 549, 554, 566, 568, 569, 578, 588, 589, 592, 593, 594, 595, 596, 597, 598, 600, 601, 602, 603, 604, 605, 616, 622, 624, 629, 642, 649, 650, 655, 656, 659, 663, 665, 669, 672, 684, 720, 732, 778, 779, 780, 793, 795, 813, 849, 851, 852, 853, 854, 855, 856, 857, 858, 862, 863, 864, 865, 867, 876, 877, 878, 882, 883, 884, 889, 890, 891, 893, 900, 901, 902, 904, 905, 906, 907, 908, 909, 910, 911, 912, 913, 914, 917, 922, 923, 924, 925, 926, 927, 928, 929, 930, 931, 933, 937, 938, 939, 942, 943, 944, 947, 952, 953, 954, 955, 956, 960, 961, 965, 966, 967, 971, 973, 974, 979, 980, 981, 984, 985, 986, 987, 988, 989, 992, 996, 997, 998, 999, 1000, 1002, 1008, 1009, 1010, 1011, 1013, 1015, 1099, 1017, 1020, 1021, 1022, 1023, 1024, 1028, 1039, 1041, 1042, 1044, 1047, 1048, 1077, 1078, 1082, 1086, 1087, 1088, 1089, 1090, 1091, 1092, 1093, 1094, 1096, 1097, 1113, 1115, 1116, 1121, 1126, 1134, 1135, 1143, 1157, 1158, 1174, 1175, 1179, 1182, 1203, 1204, 1205, 1207, 1209, 1210, 1211, 1212, 1213, 1214, 1215, 1216, 1217, 1218, 1219, 1220, 1221, 1222, 1223, 1224, 1225, 1226, 1227, 1228, 1229, 1230, 1231, 1232, 1233, 1234, 1235, 1236, 1237, 1238, 1239, 1240, 1241, 1242, 1243, 1244, 1245, 1246, 1247, 1248, 1249, 1250, 1251, 1252, 1253, 1254, 1255, 1256, 1257, 1258, 1259, 1260, 1261, 1263, 1264, 1265, 1266, 1274, 1276, 1277, 1281, 1283, 1287, 1290, 1296, 1302, 1305, 1311, 1312, 1314, 1316, 1321, 1323, 1328, 1331, 1333, 1334, 1335, 1337, 1339, 1340, 1345, 1351, 1353, 1354, 1355, 1356, 1359, 1363, 1365, 1368, 1370, 1371, 1372, 1373, 1375, 1376, 1377, 1381, 1383, 1384, 1385, 1386, 1387, 1388, 1391, 1393, 1394, 1396, 1401, 1403, 1408, 1411, 1416, 1417, 1418, 1420, 1421, 1425, 1434, 1438, 1439, 1440, 1441, 1452, 1475, 1487, 1501, 1507, 1521, 1522, 1527, 1529, 1531, 1532, 1535, 1536, 1537, 1539, 1540, 1541, 1542, 1545, 1547, 1560, 1570, 1620, 1622, 1623, 1626, 1627, 1633, 1634, 1635, 1636, 1637, 1638, 1664, 1665, 1667, 1683, 1684, 1686, 1692, 1719, 1722, 1729, 1734, 1740, 1741, 1742, 1743, 1744, 1748, 1750, 1764, 1772, 1782, 1783, 1784, 1786, 1797, 1798, 1800, 1801, 1802, 1803, 1804, 1805, 1806, 1808, 1809, 1810, 1812, 1815, 1818, 1822, 1823, 1824, 1825, 1827, 1828, 1829, 1830, 1831, 1841, 1844, 1853, 1859, 1860, 1862, 1864, 1866, 1868, 1869, 1870, 1879, 1888, 1890, 1901, 1902, 1905, 1906, 1909, 1911, 1916, 1919, 1934, 1941, 1948, 1949, 1954, 1957, 1965, 1967, 1968, 1969, 1970, 1973, 1974, 1975, 1976, 1977, 1978, 1979, 1980, 1981, 1982, 1983, 1984, 1985, 1986, 1987, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2001, 2003, 2005, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024, 2025, 2026, 2027, 2028, 2029, 2030, 2031, 2032, 2033, 2034, 2035, 2036, 2037, 2038, 2039, 2041, 2044, 2045, 2046, 2047, 2050, 2056, 2063, 2072, 2073, 2075, 2077, 2080, 2083, 2092, 2093, 2097, 2104, 2113, 2114, 2115, 2116, 2117, 2118, 2119, 2120, 2121, 2122, 2123, 2124, 2125, 2126, 2127, 2128, 2129, 2130, 2132, 2133, 2134, 2135, 2136, 2137, 2139, 2144, 2145, 2146, 2147, 2148, 2149, 2150, 2152, 2154, 2156, 2158, 2160, 2171, 2179, 2188, 2191, 2203, 2204, 2217, 2232, 2238, 2241, 2250, 2251, 2258, 2260, 2261, 2262, 2263, 2264, 2265, 2266, 2267, 2268, 2269, 2270, 2271, 2272, 2273, 2274, 2276, 2278, 2281, 2282, 2288, 2289, 2290, 2291, 2292, 2297, 2300, 2301, 2305, 2306, 2317, 2321, 2324, 2325, 2326, 2327, 2328, 2329, 2337, 2340, 2352, 2356, 2360, 2368, 2380, 2381, 2382, 2388, 2390, 2391, 2392, 2394, 2400, 2402, 2404, 2410, 2413, 2414, 2417, 2421, 2422, 2426, 2427, 2433, 2434, 2436, 2437, 2443, 2447, 2452, 2454, 2455, 2473, 2475, 2476, 2477, 2489, 2494, 2498, 2499, 2501, 2523, 2534, 2535, 2547, 2550, 2556, 2561, 2570, 2571, 2583, 2585, 2588, 2590, 2593, 2600, 2601, 2605, 2610, 2615, 2616, 2617, 2621, 2625, 2668, 2670, 2679, 2681, 2737, 2743, 2746, 2762, 2763, 2764, 2766, 2773, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2820, 2826, 2827, 2828, 2829, 2830, 2833, 2834, 2835, 2836, 2837, 2839, 2840, 2848, 2851, 2852, 2853, 2854, 2856, 2860, 2869, 2870, 2875, 2882, 2883, 2884, 2885, 2886, 2887, 2889, 2892, 2903, 2918, 2921, 2922, 2925, 2927, 2940, 2941, 2947, 2956, 2960, 2961, 2967, 2974, 2986, 2987, 2988, 2989, 2990, 2991, 2992, 2993, 2995, 2997, 3000, 3003, 3004, 3018, 3020, 3021, 3022, 3023, 3037, 3051, 3059, 3060, 3064, 3076, 3077, 3078, 3079, 3080, 3081, 3082, 3083, 3085, 3086, 3087, 3095, 3096, 3097, 3100, 3101, 3105, 3106, 3107, 3108, 3109, 3110, 3111, 3112, 3113, 3114, 3115, 3116, 3117, 3118, 3119, 3120, 3121, 3122, 3123, 3124, 3125, 3126, 3127, 3128, 3129, 3130, 3131, 3137, 3138, 3139, 3143, 3147, 3151, 3157, 3158, 3164, 3165, 3168, 3169, 3170, 3171, 3172, 3173, 3174, 3175, 3176, 3177, 3178, 3179, 3180, 3181, 3183, 3184, 3185, 3189, 3190, 3191, 3192, 3193, 3194, 3195, 3196, 3197, 3198, 3199, 3200, 3201, 3202, 3203, 3204, 3205, 3206, 3207, 3208, 3209, 3210, 3211, 3212, 3213, 3214, 3215, 3216, 3217, 3218, 3219, 3220, 3221, 3222, 3223, 3224, 3225, 3226, 3227, 3228, 3229, 3230, 3231, 3232, 3233, 3234, 3235, 3236, 3241, 3244, 3249, 3251, 3252, 3255, 3256, 3258, 3262, 3264, 3265, 3267, 3270, 3271, 3272, 3273, 3279, 3283, 3284, 3285, 3286, 3287, 3288, 3293, 3308, 3317, 3321, 3322, 3324, 3325, 3326, 3328, 3331, 3333, 3335, 3339, 3345, 3350, 3353, 3378, 3383, 3387, 3391, 3392, 3396, 3397, 3399, 3406, 3408, 3411, 3413, 3431, 3435, 3437, 3438, 3439, 3440, 3441, 3442, 3444, 3445, 3446, 3449, 3451, 3452, 3453, 3454, 3455, 3456, 3457, 3458, 3460, 3461, 3462, 3463, 3471, 3473, 3475, 3478, 3479, 3483, 3494, 3496, 3499, 3536, 3537, 3540, 3541, 3542, 3543, 3544, 3546, 3547, 3558, 3559, 3597, 3598, 3599, 3600, 3601, 3602, 3603, 3606, 3607, 3608, 3609, 3618, 3635, 3636, 3653, 3665, 3685, 3688, 3692, 3739, 3744, 3750, 3757, 3758, 3759, 3762, 3763, 3768, 3770, 3780, 3789, 3791, 3792, 3794, 3799, 3810, 3812, 3815, 3816, 3817, 3818, 3819, 3823, 3828, 3830, 3831, 3839, 3840, 3852, 3853, 3855, 3856, 3857, 3858, 3859, 3861, 3862, 3863, 3864, 3865, 3866, 3867, 3868, 3869, 3870, 3871, 3875, 3877, 3881, 3882, 3883, 3889, 3890, 3891, 3892, 3893, 3894, 3895, 3896, 3897, 3900, 3901, 3902, 3903, 3904, 3905, 3907, 3914, 3915, 3916, 3924, 3937, 3938, 3942, 3946, 3947, 3948, 3954, 3955, 3957, 3958, 3959, 3963, 3970, 3971, 3972, 3973, 3974, 3975, 3979, 3980, 3981, 3982, 3988, 3990, 3992, 3994, 3997, 3998, 4000, 4003, 4010, 4017, 4025, 4030, 4040, 4047, 4053, 4055, 4063, 4064, 4069, 4071, 4078, 4079, 4085, 4086, 4096, 4103, 4104, 4105, 4109, 4110, 4119, 4124, 4125, 4126, 4127, 4128, 4132, 4133, 4134, 4135, 4136, 4144, 4151, 4167, 4168, 4169, 4170, 4172, 4177, 4179, 4183, 4184, 4187, 4191, 4192, 4194, 4196, 4204, 4205, 4206, 4207, 4208, 4209, 4210, 4214, 4215, 4216, 4217, 4218, 4223, 4224, 4225, 4226, 4227, 4228, 4229, 4232, 4236, 4251, 4255, 4257, 4262, 4269, 4270, 4272, 4273, 4274, 4281, 4282, 4286, 4287, 4288, 4290, 4293, 4307, 4308, 4309, 4310, 4311, 4313, 4317, 4322, 4331, 4335, 4337, 4339, 4355, 4356, 4357, 4360, 4361, 4363, 4364, 4366, 4368, 4370, 4372, 4394, 4428, 4435, 4441, 4442, 4443, 4444, 4447, 4448, 4452, 4453, 4455, 4456, 4461, 4473, 4489, 4496, 4506, 4507, 4524, 4531, 4543, 4547, 4548, 4549, 4550, 4551, 4552, 4553, 4563, 4568, 4569, 4570, 4571, 4572, 4573, 4574, 4575, 4576, 4577, 4578, 4579, 4580, 4581, 4582, 4583, 4584, 4585, 4586, 4587, 4588, 4589, 4606, 4610, 4613, 4616, 4625, 4631, 4635, 4636, 4640, 4641, 4655, 4657, 4658, 4659, 4661, 4662, 4663, 4664, 4665, 4669, 4686, 4706, 4708, 4712, 4713, 4715, 4725, 4726, 4730, 4737, 4745, 4748, 4751, 4787, 4788, 4789, 4790, 4825, 4848, 4849, 4855, 4856, 4858, 4860, 4861, 4862, 4863, 4864, 4865, 4866, 4867, 4868, 4869, 4870, 4871, 4872, 4873, 4890, 4899, 4900, 4903, 4904, 4906, 4907, 4908, 4909, 4911, 4912, 4913, 4914, 4915, 4916, 4917, 4918, 4919, 4920, 4921, 4926, 4931, 4937, 4940, 4954, 4955, 4956, 4957, 4968, 4973, 4974, 4976, 4983, 4987, 4988, 4989, 4990, 4991, 4992, 4993, 4994, 4995, 4996, 4997, 4998, 4999, 5000, 5001, 5002, 5003, 5004, 5005, 5006, 5007, 5008, 5015, 5016, 5022, 5023, 5024, 5025, 5026, 5027, 5028, 5029, 5030, 5031, 5032, 5033, 5036, 5037, 5039, 5048, 5049, 5054, 5055, 5056, 5057, 5058, 5069, 5073, 5074, 5076, 5077, 5078, 5079, 5080, 5081, 5082, 5083, 5084, 5085, 5086, 5087, 5088, 5089, 5090, 5091, 5092, 5093, 5094, 5095, 5096, 5097, 5098, 5099, 5101, 5102, 5103, 5104, 5105, 5106, 5107, 5108, 5113, 5116, 5117, 5121, 5122, 5123, 5124, 5129, 5132, 5137, 5145, 5149, 5150, 5158, 5162, 5167, 5175, 5177, 5181, 5182, 5185, 5186, 5188, 5189, 5192, 5193, 5195, 5196, 5197, 5198, 5199, 5200, 5201, 5202, 5203, 5205, 5208, 5209, 5210, 5211, 5212, 5213, 5214, 5215, 5216, 5217, 5219, 5226, 5229, 5230, 5231, 5232, 5234, 5235, 5236, 5237, 5238, 5239, 5240, 5241, 5242, 5244, 5246, 5247, 5248, 5249, 5250, 5251, 5252, 5253, 5254, 5255, 5256, 5257, 5260, 5263, 5264, 5267, 5270, 5272, 5273, 5277, 5279, 5282, 5285, 5287, 5288, 5290, 5294, 5295, 5296, 5297, 5302, 5304, 5305, 5308, 5310, 5321, 5323, 5325, 5330, 5337, 5338, 5344, 5346, 5348, 5354, 5356, 5359, 5360, 5364, 5370, 5372, 5373, 5374, 5376, 5382, 5387, 5393, 5404, 5406, 5414, 5416, 5417, 5425, 5428, 5430, 5432, 5433, 5434, 5435, 5436, 5440, 5446, 5447, 5448, 5452, 5454, 5463, 5467, 5469, 5472, 5474, 5475, 5477, 5478, 5480, 5481, 5483, 5484, 5487, 5488, 5489, 5490, 5491, 5492, 5497, 5499, 5500, 5504, 5506, 5507, 5508, 5511, 5528, 5534, 5547, 5551, 5564, 5566, 5567, 5577, 5580, 5585, 5586, 5587, 5593, 5594, 5595, 5596, 5597, 5598, 5603, 5604, 5605, 5606, 5607, 5608, 5610, 5613, 5622, 5623, 5627, 5628, 5629, 5630, 5631, 5634, 5636, 5637, 5638, 5639, 5640, 5643, 5644, 5645, 5646, 5647, 5648, 5649, 5650, 5651, 5654, 5655, 5660, 5662, 5663, 5664, 5665, 5673, 5674, 5680, 5689, 5690, 5691, 5694, 5695, 5696, 5704, 5705, 5711, 5723, 5724, 5725, 5726, 5729, 5730, 5731, 5732, 5733, 5740, 5741, 5744, 5746, 5759, 5764, 5768, 5775, 5779, 5793, 5794, 5795, 5796, 5797, 5798, 5799, 5802, 5804, 5805, 5806, 5807, 5808, 5809, 5810, 5820, 5829, 5831, 5832, 5835, 5836, 5844, 5849, 5853, 5864, 5867, 5874, 5875, 5876, 5877, 5887, 5892, 5895, 5915, 5916, 5921, 5922, 5923, 5924, 5925, 5926, 5927, 5934, 5935, 5936, 5937, 5938, 5939, 5940, 5941, 5942, 5944, 5945, 5947, 5949, 5951, 5952, 5958, 5959, 5960, 5963, 5964, 5965, 5966, 5975, 5976, 5988, 5999, 6002, 6006, 6010, 6020, 6023, 6026, 6030, 6032, 6033, 6037, 6038, 6040, 6041, 6042, 6047, 6048, 6055, 6058, 6059, 6072, 6074, 6075, 6080, 6090, 6099, 6109, 6111, 6112, 6116, 6127, 6129, 6136, 6137, 6138, 6142, 6147, 6149, 6151, 6152, 6160, 6161, 6162, 6163, 6165, 6166, 6167, 6168, 6169, 6171, 6172, 6173, 6174, 6175, 6177, 6180, 6181, 6183, 6184, 6186, 6194, 6198, 6200, 6201, 6202, 6203, 6207, 6209, 6211, 6212, 6214, 6215, 6216, 6217, 6218, 6219, 6220, 6224, 6233, 6234, 6249, 6251, 6256, 6258, 6263, 6267, 6275, 6277, 6278, 6279, 6280, 6281, 6282, 6283, 6284, 6287, 6289, 6290, 6291, 6292, 6293, 6294, 6295, 6296, 6297, 6298, 6299, 6300, 6301, 6302, 6303, 6304, 6305, 6308, 6313, 6320, 6333, 6334, 6335, 6336, 6340, 6341, 6342, 6343, 6344, 6346, 6352, 6357, 6366, 6367, 6368, 6369, 6380, 6381, 6382, 6383, 6384, 6385, 6386, 6387, 6388, 6389, 6391, 6392, 6393, 6394, 6395, 6396, 6397, 6398, 6399, 6404, 6420, 6422, 6427, 6432, 6433, 6435, 6467, 6472, 6479, 6480, 6481, 6482, 6483, 6484, 6485, 6486, 6487, 6488, 6489, 6490, 6491, 6492, 6493, 6494, 6495, 6496, 6497, 6498, 6499, 6500, 6501, 6502, 6503, 6504, 6511, 6517, 6518, 6519, 6520, 6521, 6522, 6523, 6527, 6529, 6531, 6533, 6537, 6545, 6546, 6547, 6548, 6549, 6551, 6559, 6562, 6566, 6567, 6568, 6569, 6570, 6571, 6572, 6573, 6574, 6575, 6576, 6577, 6578, 6579, 6580, 6581, 6582, 6583, 6584, 6585, 6586, 6587, 6588, 6589, 6590, 6591, 6592, 6593, 6594, 6595, 6596, 6597, 6598, 6599, 6600, 6601, 6602, 6603, 6604, 6605, 6606, 6607, 6608, 6609, 6610, 6611, 6612, 6613, 6614, 6615, 6616, 6617, 6618, 6619, 6620, 6621, 6622, 6623, 6624, 6625, 6626, 6627, 6628, 6629, 6630, 6631, 6632, 6633, 6634, 6635, 6636, 6637, 6638, 6639, 6640, 6641, 6642, 6643, 6644, 6645, 6646, 6647, 6648, 6649, 6650, 6651, 6652, 6653, 6654, 6655, 6656, 6657, 6658, 6659, 6660, 6661, 6662, 6663, 6664, 6665, 6666, 6667, 6668, 6669, 6670, 6671, 6672, 6673, 6674, 6675, 6676, 6677, 6678, 6679, 6680, 6681, 6682, 6683, 6684, 6685, 6686, 6687, 6688, 6689, 6690, 6691, 6692, 6693, 6694, 6695, 6696, 6697, 6698, 6699, 6700, 6701, 6702, 6703, 6704, 6705, 6706, 6707, 6708, 6709, 6710, 6714, 6715, 6716, 6717, 6718, 6719, 6720, 6721, 6722, 6723, 6725, 6727, 6735, 6737, 6738, 6739, 6742, 6743, 6751, 6762, 6767, 6769, 6770, 6772, 6774, 6775, 6776, 6777, 6781, 6782, 6786, 6787, 6788, 6790, 6792, 6793, 6794, 6796, 6797, 6798, 6810, 6812, 6814, 6816, 6817, 6822, 6823, 6825, 6830, 6834, 6835, 6836, 6837, 6839, 6840, 6841, 6842, 6843, 6844, 6851, 6852, 6853, 6854, 6855, 6856, 6857, 6858, 6859, 6860, 6864, 6872, 6874, 6875, 6876, 6877, 6878, 6879, 6880, 6881, 6882, 6883, 6885, 6886, 6887, 6888, 6889, 6893, 6897, 6898, 6899, 6900, 6901, 6902, 6903, 6904, 6905, 6906, 6907, 6908, 6909, 6910, 6911, 6912, 6913, 6914, 6915, 6916, 6917, 6918, 6919, 6920, 6921, 6924, 6925, 6926, 6927, 6929, 6931, 6934, 6935, 6939, 6940, 6941, 6942, 6945, 6949, 6951, 6979, 6980, 6981, 6986, 6988, 6995, 6997, 6998, 7014, 7028, 7031, 7033, 7034, 7035, 7036, 7039, 7040, 7044, 7047, 7048, 7049, 7061, 7066, 7070, 7077, 7085, 7102, 7105, 7115, 7116, 7127, 7129, 7132, 7133, 7145, 7154, 7155, 7158, 7176, 7186, 7190, 7191, 7192, 7193, 7195, 7199, 7201, 7202, 7204, 7209, 7210, 7211, 7212, 7213, 7214, 7216, 7217, 7230, 7237, 7241, 7246, 7247, 7251, 7256, 7258, 7262, 7263, 7267, 7268, 7272, 7286, 7294, 7295, 7296, 7299, 7300, 7301, 7302, 7303, 7304, 7305, 7306, 7307, 7308, 7309, 7310, 7311, 7312, 7313, 7314, 7315, 7316, 7319, 7320, 7322, 7342, 7349, 7354, 7355, 7360, 7362, 7365, 7367, 7377, 7379, 7389, 7393, 7394, 7413, 7418, 7430, 7441, 7442, 7464, 7475, 7521, 7531, 7537, 7538, 7551, 7560, 7563, 7566, 7577, 7584, 7585, 7586, 7587, 7588, 7590, 7591, 7592, 7602, 7611, 7620, 7621, 7622, 7624, 7625, 7626, 7628, 7629, 7630, 7634, 7635, 7636, 7637, 7638, 7639, 7643, 7644, 7655, 7658, 7660, 7661, 7662, 7664, 7665, 7666, 7668, 7669, 7676, 7677, 7705, 7715, 7737, 7760, 7761, 7765, 7766, 7767, 7773, 7774, 7776, 7781, 7783, 7786, 7803, 7808, 7809, 7811, 7813, 7816, 7818, 7820, 7833, 7838, 7840, 7841, 7851, 7853, 7857, 7859, 7868, 7871, 7874, 7875, 7878, 7883, 7884, 7895, 7904, 7910, 7912, 7914, 7917, 7918, 7933, 7936, 7937, 8047, 8056, 8070, 8072, 8128, 8135, 8156, 8157, 8159, 8162, 8166, 8167, 8176, 8177, 8181, 8185, 8188, 8192, 8193, 8194, 8195, 8196, 8197, 8198, 8199, 8200, 8201, 8202, 8203, 8204, 8205, 8206, 8207, 8208, 8209, 8210, 8211, 8212, 8213, 8214, 8215, 8216, 8217, 8218, 8219, 8220, 8222, 8223, 8224, 8225, 8226, 8227, 8228, 8229, 8230, 8231, 8232, 8233, 8234, 8235, 8236, 8237, 8238, 8239, 8240, 8241, 8242, 8243, 8244, 8245, 8246, 8254, 8256, 8257, 8259, 8260, 8261, 8262, 8263, 8264, 8265, 8266, 8267, 8268, 8269, 8270, 8271, 8272, 8273, 8280, 8281, 8289, 8290, 8291, 8295, 8296, 8297, 8298, 8299, 8300, 8301, 8302, 8303, 8304, 8305, 8307, 8308, 8313, 8319, 8324, 8325, 8337, 8338, 8339, 8340, 8341, 8342, 8343, 8344, 8345, 8346, 8347, 8348, 8349, 8350, 8351, 8352, 8354, 8355, 8356, 8357, 8361, 8363, 8364, 8365, 8366, 8367, 8368, 8369, 8372, 8373, 8379, 8380, 8382, 8383, 8384, 8385, 8391, 8392, 8395, 8398, 8400, 8401, 8402, 8403, 8404, 8405, 8406, 8407, 8408, 8409, 8410, 8412, 8414, 8418, 8420, 8421, 8422, 8427, 8431, 8433, 8434, 8435, 8436, 8437, 8438, 8439, 8440, 8441, 8442, 8443, 8444, 8445, 8446, 8447, 8448, 8449, 8450, 8451, 8452, 8455, 8456, 8457, 8458, 8459, 8461, 8474, 8478, 8481, 8483, 8486, 8495, 8513, 8516, 8517, 8518, 8523, 8524, 8525, 8526, 8530, 8531, 8532, 8538, 8540, 8542, 8546, 8547, 8548, 8563, 8568, 8571, 8573, 8574, 8577, 8578, 8579, 8580, 8582, 8584, 8585, 8587, 8588, 8589, 8590, 8592, 8593, 8594, 8598, 8602, 8605, 8606, 8610, 8611, 8614, 8615, 8616, 8617, 8618, 8619, 8620, 8621, 8622, 8623, 8624, 8636, 8646, 8648, 8649, 8651, 8652, 8653, 8657, 8659, 8680, 8688, 8690, 8695, 8702, 8703, 8706, 8707, 8708, 8709, 8710, 8711, 8715, 8716, 8721, 8722, 8728, 8731, 8742, 8758, 8759, 8767, 8768, 8774, 8785, 8793, 8794, 8795, 8796, 8798, 8804, 8805, 8807, 8811, 8825, 8826, 8827, 8829, 8834, 8835, 8837, 8844, 8865, 8874, 8875, 8876, 8887, 8890, 8891, 8905, 8921, 8933, 8934, 8939, 8940, 8944, 8945, 8946, 8947, 8955, 8957, 8960, 8961, 8962, 8963, 8964, 8996, 8999, 9000, 9004, 9005, 9006, 9007, 9015, 9038, 9045, 9049, 9052, 9056, 9059, 9060, 9061, 9062, 9063, 9065, 9066, 9067, 9068, 9069, 9070, 9071, 9072, 9073, 9074, 9075, 9076, 9077, 9079, 9080, 9081, 9082, 9083, 9084, 9086, 9087, 9088, 9091, 9092, 9093, 9095, 9096, 9097, 9098, 9099, 9101, 9102, 9103, 9104, 9108, 9109, 9110, 9111, 9112, 9113, 9130, 9131, 9132, 9135, 9136, 9138, 9139, 9141, 9142, 9143, 9144, 9145, 9147, 9148, 9149, 9150, 9151, 9152, 9153, 9154, 9155, 9156, 9157, 9158, 9159, 9161, 9164, 9165, 9166, 9167, 9169, 9170, 9171, 9178, 9179, 9180, 9181, 9182, 9185, 9186, 9187, 9192, 9193, 9194, 9195, 9196, 9197, 9198, 9199, 9200, 9201, 9202, 9203, 9204, 9205, 9206, 9208, 9209, 9210, 9216, 9217, 9218, 9219, 9220, 9221, 9222, 9223, 9224, 9225, 9226, 9227, 9228, 9229, 9230, 9231, 9232, 9233, 9236, 9238, 9239, 9248, 9250, 9251, 9252, 9253, 9254, 9255, 9256, 9257, 9258, 9259, 9261, 9262, 9263, 9264, 9269, 9270, 9271, 9274, 9276, 9277, 9278, 9279, 9280, 9282, 9283, 9284, and 9285.12.The engineered viral capsid polypeptide of any one of claims 1-11, wherein the amino acid sequence is located within a variable region in the viral capsid polypeptide.13.The engineered viral capsid polypeptide of any one of claims 1-12, wherein the engineered viral capsid polypeptide has tropism to T cells.14.The engineered viral capsid polypeptide of claim 13, wherein the T cells are primary T cells.15.The engineered viral capsid polypeptide of any one of claims 13-14, wherein the T cells are human T cells.16.The engineered viral capsid polypeptide of any one of claims 1-15, wherein the viral capsid polypeptide is a viral capsid polypeptide of an adeno associated virus (AAV) .17.The engineered viral capsid polypeptide of claim 16, wherein the engineered viral capsid polypeptide is a viral capsid polypeptide of an engineered adeno associated virus derived from a parental virus selected from AAV1, AAV2, AAV3, AAV3B, AAV4, AAV5, AAV6, AAV6.2, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, AAV13, AAVrh74, AAVrh10, AAVDJ, AAVDJ / 8, AAV-PHP. eB, AAV-PHP. S, AAV2-retro, AAV2-QuadYF, AAV2.7m8, and Avian AAV.18.The engineered viral capsid polypeptide of any one of claims 1 and 12-17, wherein the engineered viral capsid polypeptide is a viral capsid polypeptide of an engineered AAV9, and the amino acid sequence is any one of SEQ ID NOs: 1-1007, 2149-2261, and 2945-6269.19.The engineered viral capsid polypeptide of claim 18, wherein the amino acid sequence replaces a sequence in the viral capsid polypeptide analogous to a sequence from T582 to Q592 of SEQ ID NO: 2107.20.The engineered viral capsid polypeptide of any one of claims 18-19, wherein the engineered viral capsid polypeptide comprises SEQ ID NO: 109 and is capable of binding to SLC35C2.21.The engineered viral capsid polypeptide of any one of claims 1 and 12-17, wherein the engineered viral capsid polypeptide is a viral capsid polypeptide of an engineered AAV6, and the amino acid sequence is any one of SEQ ID NOs: 1008-2105, 2262-2944, and 6270-9287.22.The engineered viral capsid polypeptide of claim 21, wherein the amino acid sequence replaces a sequence in the viral capsid polypeptide analogous to a sequence from V582 to A592 of SEQ ID NO: 2106.23.The engineered viral capsid polypeptide of any one of claims 21-22, wherein the engineered viral capsid polypeptide comprises SEQ ID NO: 1660 and is capable of binding to CD62L.24.A polynucleotide encoding the engineered viral capsid polypeptide of any one of claims 1-23.25.A vector comprising the engineered viral capsid polypeptide of any one of claims 1-13 or the polynucleotide of claim 24.26.The vector of claim 25, wherein the vector is a plasmid, a viral vector, a lipid nanoparticle (LNP) vector, or a non-viral vector.27.A cell comprising the engineered viral capsid polypeptide of any one of claims 1-23, the polynucleotide of claim 24, or the vector of claim 25.28.An engineered adeno-associated virus (AAV) comprising the engineered viral capsid polypeptide of any one of claims 1-23.29.The engineered adeno-associated virus (AAV) of claim 28, further comprising an expression cassette which comprises a single-strand DNA encoding a chimeric antigen receptor (CAR) .30.The engineered adeno-associated virus (AAV) of claim 29, wherein the chimeric antigen receptor (CAR) is selected from CD19-CAR, BCMA-CAR, CD22-CAR, CD30-CAR, CD7-CAR, CD38-CAR, CD20-CAR, GD2-CAR, HER2-CAR, IL13Ra2-CAR, EGFR-CAR, Mesothelin-CAR, Claudin-18.2-CAR, PSMA-CAR, and GPC3-CAR.31.The engineered adeno-associated virus (AAV) of any one of claims 29-30, wherein the expression cassette further comprises a promoter selected from CMV, EF-1α, SV40, PGK1, CAG, ubc, human beta actin, TRE, UA5, Ac5, Polyhedrin, CaMKIIa, GAL1, GAL10, TEF1, GDS, ADH1, CaMV355, Ubi, and SFFV.32.The engineered adeno-associated virus (AAV) of claim 31, wherein the promoter is EF-1α.33.The engineered adeno-associated virus (AAV) of any one of claims 29-32, wherein the expression cassette further comprises a 5’ ITR, a 3’ ITR, a Flag, a poly (A) , a WPRE, or a miRNA target.34.The engineered adeno-associated virus (AAV) of any one of claims 28-33, wherein the engineered adeno-associated virus has tropism to T cells.35.The engineered adeno-associated virus (AAV) of claim 34, wherein the T cells are primary T cells.36.The engineered adeno-associated virus (AAV) of any one of claims 34-35, wherein the T cells are human T cells.37.The engineered adeno-associated virus (AAV) of any one of claims 28-36, wherein the engineered adeno associated virus is derived from a parental virus selected from AAV1, AAV2, AAV3, AAV3B, AAV4, AAV5, AAV6, AAV6.2, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, AAV13, AAVrh74, AAVrh10, AAVDJ, AAVDJ / 8, AAV-PHP. eB, AAV-PHP. S, AAV2-retro, AAV2-QuadYF, AAV2.7m8, and Avian AAV.38.The engineered adeno-associated virus (AAV) of any one of claims 28-37, wherein the engineered adeno-associated virus is an engineered AAV9, and the engineered viral capsid polypeptide comprising an amino acid sequence of any one of SEQ ID NOs: 1-1007, 2149-2261, and 2945-6269.39.The engineered adeno-associated virus (AAV) of claim 38, wherein the amino acid sequence replaces a sequence in the viral capsid polypeptide analogous to a sequence from T582 to Q592 of SEQ ID NO: 2107.40.The engineered adeno-associated virus (AAV) of any one of claims 38-39, wherein the engineered adeno-associated virus (AAV) comprises SEQ ID NO: 109 and is capable of binding to SLC35C2.41.The engineered adeno-associated virus (AAV) of any one of claims 28-37, wherein the engineered adeno-associated virus is an engineered AAV6, and the engineered viral capsid polypeptide comprising an amino acid sequence of any one of SEQ ID NOs: 1008-2105, 2262-2944, and 6270-9287.42.The engineered adeno-associated virus (AAV) of claim 41, wherein the amino acid sequence replaces a sequence in the viral capsid polypeptide analogous to a sequence from V582 to A592 of SEQ ID NO: 2106.43.The engineered adeno-associated virus (AAV) of any one of claims 41-42, wherein the engineered adeno-associated virus (AAV) comprises SEQ ID NO: 1660 and is capable of binding to CD62L.44.A kit comprising the engineered adeno-associated virus (AAV) of any one of claims 28-43, and a gene editing system.45.The kit of claim 44, wherein the gene editing system comprises a Cas9 protein and a guide RNA, or one or more polynucleotide encoding thereof.46.The kit of claim 45, wherein the gene editing system comprises a Cas9 / gRNA ribonucleoprotein (RNP) .47.An engineered T cell which is transduced by the engineered AAV of any one of claims 28-43.48.The engineered T cell of claim 47, further comprising at least one chimeric antigen receptor (CAR) .49.The engineered T cell of claim 47, wherein the chimeric antigen receptor (CAR) is selected from CD19-CAR, BCMA-CAR, CD22-CAR, CD30-CAR, CD7-CAR, CD38-CAR, CD20-CAR, GD2-CAR, HER2-CAR, IL13Ra2-CAR, EGFR-CAR, Mesothelin-CAR, Claudin-18.2-CAR, PSMA-CAR, and GPC3-CAR.50.The engineered T cell of any one of claims 47-49, wherein the T cell is a primary T cell.51.The engineered T cell of any one of claims 47-50, wherein the T cell is a human T cell.52.A method of delivering a payload polynucleotide into a cell, comprising contacting the cell with the engineered adeno-associated virus (AAV) of any one of claims 28-43, wherein the engineered adeno-associated virus (AAV) comprises the payload polynucleotide.53.The method of claim 52, wherein the method is carried out in vivo.54.The method of claim 52, further comprising administering a gene editing system into the cell.55.The method of any one of claims 52-54, wherein the cell is a T cell.56.The method of claim 55, wherein the cell is a primary T cell.57.The method of any one of claims 55-56, wherein the cell is a human T cell.58.The method of any one of claims 52-57, wherein the payload polynucleotide encodes a chimeric antigen receptor (CAR) .59.The method of claim 58, wherein the chimeric antigen receptor (CAR) is selected from CD19-CAR, BCMA-CAR, CD22-CAR, CD30-CAR, CD7-CAR, CD38-CAR, CD20-CAR, GD2-CAR, HER2-CAR, IL13Ra2-CAR, EGFR-CAR, Mesothelin-CAR, Claudin-18.2-CAR, PSMA-CAR, and GPC3-CAR.60.A method of engineering a T cell, comprising contacting the T cell with the engineered adeno-associated virus (AAV) of any one of claims 28-43.61.The method of claim 60, wherein the method is carried out in vivo.62.The method of claim 60, further comprising administering a gene editing system into the T cell.63.The method of claim 62, wherein the T cell is electroporated with a Cas9 / gRNA ribonucleoprotein (RNP) .64.A method of engineering a T cell in a subject, comprising administering into the subject an effective amount of engineered adeno-associated virus (AAV) of any one of claims 28-43.65.The method of claim 64, wherein the engineered adeno-associated virus (AAV) is systematically administered to the subject.66.The method of any one of claims 64-65, wherein the engineered adeno-associated virus (AAV) is any one of claims 41-43, and the effective amount is no more than 1× 1012 vg / kg.67.A method of reducing the amount of B cell in a subject, comprising administering into the subject a therapeutically effective amount of engineered adeno-associated virus (AAV) of any one of claims 28-43.68.The method of claim 67, wherein the engineered adeno-associated virus (AAV) is systematically administered to the subject.69.The method of any one of claims 67-68, wherein the engineered adeno-associated virus comprises an expression cassette which comprises a single-strand DNA encoding a CD19-CAR.70.The method of any one of claims 67-69, wherein the B cell is a malignant B cell.71.The method of any one of claims 67-70, wherein the B cell is a CD19+ B cell.72.The method of any one of claims 67-71, wherein the engineered adeno-associated virus (AAV) is any one of claims 41-43, and the therapeutically effective amount is no more than 1× 1013 vg / kg.73.A method for treating B-cell malignancy in a subject comprising reducing the amount of B-cell in the subject according to a method of any one of claims 67-72.74.The method of claim 73, wherein the B-cell malignancy is selected from B-cell lymphoma, chronic lymphocytic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma.75.A targeting moiety comprising one or more polypeptides selected from SEQ ID NOs: 1-2105 and 2149-9287, and optionally a polynucleotide, a lipid, a polymer, a sugar, or any combination thereof.76.A composition comprising the targeting moiety of claim 75 and a payload.