Exosome isolation method

Abstract

The present invention relates to methods for isolating exosomes. Specifically, the methods include providing a sample containing exosomes; identifying cell surface polypeptides on the exosomes; and isolating exosomes using the cell surface polypeptides on the exosomes. Exosomes isolated by the methods of the present invention can be tested to identify biomarkers, understand biological function and disease, and explore ways to target them with therapeutic agents.

Description

[Background technology]

[0001] Exosomes are a type of cell-derived small extracellular membrane vesicles (50–100 nm in diameter) actively secreted by numerous healthy and pathological cell types. Exosomes can mediate microcommunications at the cell, tissue, and organ levels by shuttle proteins, mRNAs, and microRNAs under normal and pathological conditions.

[0002] Exosomes are now believed to mediate intercellular communication between different cell types in the body, thereby influencing normal and pathological conditions. Multiple biological entities within exosomes (e.g., proteins, mRNAs, and microRNAs) are closely related to the pathogenesis of most human malignancies, and they can be used as highly valuable biomarkers for disease diagnosis, prognosis, and treatment. Many different cell types and tissues secrete exosomes, and the content and properties of exosomes vary depending on the cell type or tissue of origin. Therefore, the function of exosomes and their relevance to specific pathologies may also vary depending on the tissue of origin. For these reasons, it is becoming increasingly important to isolate tissue-specific subtypes of exosomes.

[0003] Therefore, exosome purification and analysis is a rapidly growing field of research, but despite several advances in exosome purification and analysis methods, research still faces several challenges.

[0004] Studying exosomes to identify biomarkers, understand biological function and disease, and explore ways to target them with therapeutic agents first requires isolating these microscopic structures from the plethora of other molecules and structures present in blood and other biological fluids.

[0005] Therefore, there is a need to provide methods for isolating exosomes. Summary of the Invention

[0006] In a first aspect of the present invention, there is provided a method for isolating exosomes, the method comprising: (a) providing a sample containing exosomes; (b) identifying cell surface polypeptides on exosomes; and (c) isolating exosomes using the cell surface polypeptides on exosomes; Including, wherein said cell surface polypeptide is dystroglycan (DAG).

[0007] Optionally, the method includes: (a) providing a sample containing exosomes; (b) identifying cell surface polypeptides on exosomes; (c) providing a binding partner for said cell surface polypeptide; (d) contacting the binding partner with the sample; (e) isolating the binding partner; and (f) isolating exosomes; Including, wherein said cell surface polypeptide is dystroglycan (DAG).

[0008] Optionally, the sample is a biological sample. Still optionally, the sample is a human biological sample.

[0009] Optionally, the sample is a biological fluid sample. Still optionally, the sample is a human biological fluid sample.

[0010] Optionally, the biological fluid sample is selected from cerebrospinal fluid (CSF), peritoneal fluid, pleural fluid, amniotic fluid, interstitial fluid, intravascular fluid, intercellular fluid, and intracellular fluid. Optionally, the human biological fluid sample is selected from cerebrospinal fluid (CSF), peritoneal fluid, pleural fluid, amniotic fluid, interstitial fluid, intravascular fluid, intercellular fluid, and intracellular fluid.

[0011] Optionally, the sample is a blood sample. Still optionally, the sample is a human blood sample. Optionally, the sample is a whole blood sample. Still optionally, the sample is a human whole blood sample. Optionally, the sample is a serum sample. Still optionally, the sample is a human serum sample. Preferably, the sample is a human serum sample.

[0012] Optionally, the sample is a biological tissue sample. Still optionally, the sample is a human biological tissue sample. Optionally, the sample comprises biological tissue. Still optionally, the sample comprises human biological tissue.

[0013] Optionally, the sample is a soft biological tissue sample. Further optionally, the sample is a soft biological tissue sample from a human. Optionally, the sample comprises soft biological tissue. Further optionally, the sample comprises soft biological tissue from a human.

[0014] Optionally, the biological tissue is selected from endodermal tissue, mesodermal tissue, and ectodermal tissue. Optionally, the sample comprises biological tissue selected from endodermal tissue, mesodermal tissue, and ectodermal tissue. Further optionally, the sample comprises human biological tissue selected from endodermal tissue, mesodermal tissue, and ectodermal tissue.

[0015] Optionally, said mesodermal tissue is paraxial mesodermal tissue.

[0016] Optionally, said mesodermal tissue is muscle tissue.

[0017] Optionally, the muscle tissue is selected from skeletal (striated) muscle tissue; smooth (non-striated) muscle tissue; and cardiac (semi-striated) muscle tissue.

[0018] Optionally, the muscle tissue comprises cells selected from skeletal (striated) muscle cells; smooth (non-striated) muscle cells; and cardiac (semi-striated) muscle cells.

[0019] Optionally, the muscle tissue comprises cells selected from skeletal (striated) myoblasts; smooth (non-striated) myoblasts; and cardiac (semi-striated) myoblasts.

[0020] Optionally, the muscle tissue comprises cells selected from skeletal (striated) myotubes; smooth (non-striated) myotubes; and cardiac (semi-striated) myotubes. Preferably, the muscle tissue comprises smooth (non-striated) myotubes.

[0021] Optionally, the cell surface polypeptide is human dystroglycan (DAG).

[0022] Optionally, the cell surface polypeptide is human dystroglycan (DAG), as defined by UniProtKB accession number Q14118.

[0023] Optionally, the cell surface polypeptide is selected from alpha-dystroglycan and beta-dystroglycan.

[0024] Optionally, the cell surface polypeptide is selected from human alpha-dystroglycan and human beta-dystroglycan. Preferably, the cell surface polypeptide is human alpha-dystroglycan.

[0025] Optionally, a binding partner of the cell surface polypeptide is capable of binding to the cell surface polypeptide.

[0026] Optionally, the binding partner of the cell surface polypeptide is an antibody capable of binding to the cell surface polypeptide.

[0027] Optionally, the antibody is selected from a monoclonal antibody capable of binding to the cell surface polypeptide and a polyclonal antibody capable of binding to the cell surface polypeptide. Preferably, the antibody is a monoclonal antibody capable of binding to the cell surface polypeptide.

[0028] Optionally, the antibody is of the IgG isotype. Further optionally, the antibody is of the IgG2 isotype. Even more optionally, the antibody is of the IgG2a isotype. Even more optionally, the antibody is of the MIgG2a isotype. Preferably, the antibody is of the MIgG2a isotype.

[0029] Optionally, the binding partner of the cell surface polypeptide comprises an antibody capable of binding to the cell surface polypeptide and a solid support.

[0030] Optionally, the solid support is a bead.

[0031] Optionally, the solid support is a hydrophilic bead.

[0032] Optionally, or in addition, the solid support is a pH-neutral bead.

[0033] Optionally, the solid support is an epoxy bead. Still more optionally, the solid support is an epoxy-coated bead. Still more optionally, the solid support is an epoxy-group bearing bead.

[0034] Optionally, the solid support is a magnetic bead. Still more optionally, the solid support is a paramagnetic bead. Still more optionally, the solid support is a superparamagnetic bead. Preferably, the solid support is a superparamagnetic bead.

[0035] Optionally, the beads have a diameter of 1.0 to 4.5 μm. Preferably, the beads have a diameter of 2.8 μm. Hereinafter, embodiments of the present invention will be described with reference to the accompanying drawings. [Brief explanation of the drawings]

[0036] [Figure 1] Western blot analysis of culture media of myoblasts from healthy human subjects, differentiated into myotubes in culture. [Figure 2] Western blot analysis of cell culture exosomes immunocaptured from serum. [Figure 3A] FIG. 1 is a schematic diagram of muscle exosome isolation. [Figure 3B] Western blot analysis of circulating vesicles pulled down (precipitated) with an antibody capable of binding to a cell surface polypeptide (muscle membrane protein). [Figure 4] Western blot analysis of immunocaptured circulating muscle exosomes from a healthy subject (H).

[0037] Materials and Methods Participants and ethical review approval Deltoid muscle biopsies from healthy subjects were obtained from the BTR (Bank of Tissues for Research, partner of the EU network EuroBioBank) according to European recommendations and French legislation.

[0038] Serum samples were obtained from patients with Parkinson's disease and age- and sex-matched healthy subjects. This protocol (NCT02305147) was approved by the local ethics committee and all subjects signed informed consent in accordance with institutional guidelines.

[0039] Muscle stem cell extraction and culture Briefly, muscle biopsies were mechanically dissociated and plated in growth medium (1 volume M199, 4 volumes Dulbecco's modified Eagle's medium (DMEM), 20% fetal bovine serum (v:v), 25 μg / ml fetuin, 0.5 ng / ml bFGF, 5 ng / ml EGF, and 5 μg / ml insulin) as previously described (Bigot et al., 2015). Myogenic cell populations were enriched using CD56 magnetic beads, and their myogenicity was confirmed by enrichment using an anti-desmin antibody, as previously described (Bigot et al., 2015). A minimum of 80% of the cell population was positive for desmin. Myoblasts were then immortalized as previously described (Thorley et al., 2016). The immortalized myoblasts were then differentiated into myotubes by rinsing them three times with DMEM, removing all residual FBS, and culturing them in DMEM for 3 days.

[0040] Serum samples Briefly, blood samples were collected by venipuncture using red-top blood collection tubes and allowed to clot for 30 min at room temperature. After centrifugation at 4,000 g for 10 min at 4°C, serum was snap-frozen on dry ice and stored at -80°C until processing.

[0041] Example Embodiments of the present invention will now be described with reference to the following non-limiting examples.

[0042] Example 1 Muscle exosome isolation To determine whether the polypeptide dystroglycan (DAG) is present inside muscle exosomes or on their surface (embedded in the membrane and therefore accessible to antibodies), we investigated whether commercially available anti-DAG antibodies (anti-DAG antibodies targeting different forms of the polypeptide) could bind to muscle exosomes extracted from cell culture medium.

[0043] To do this, two types of tests were used that are inversely related: (1) Are exosomes pulled down (precipitated) with a commercially available anti-DAG antibody positive for exosome markers? and (2) Are exosomes pulled down (precipitated) with exosome markers positive for the polypeptide dystroglycan (DAG)? In this way, positive results in both tests should be obtained only if the form of the polypeptide dystroglycan (DAG) targeted by the commercially available anti-DAG antibody is present on the exosome surface. Using this approach, we have shown that we can determine whether α-dystroglycan (encoded by the DAG1 gene) is accessible to antibodies and therefore suitable for immunoaffinity pull-down (see Figure 1).

[0044] Briefly, myoblasts were isolated from muscle biopsies of healthy human subjects and cultured to differentiate into myotubes as described above. After 3 days of culture, exosomes were isolated from the culture medium of 800,000 muscle cells using a total exosome isolation reagent according to the manufacturer's instructions.

[0045] To isolate exosomes from cell culture medium, Total Exosome Isolation Reagent (for isolation from cell culture medium; Life Technologies™) was added to the cell culture medium at a volume ratio of 1:2 and incubated overnight at 4°C. Exosomes were then pelleted by centrifugation at 10,000 x g for 60 minutes, and the exosome-free medium was discarded. The exosome pellet was resuspended in 200 μl of PBS and stored at -80°C until needed.

[0046] Exosomes isolated from the culture medium were then purified by immunoaffinity using either anti-CD63 antibody, anti-DAG antibody VIA41, or anti-DAG antibody DAG-6F4. For co-immunoprecipitation (Co-IP) of muscle exosomes isolated from cell culture medium, α-DAG antibody (DAG-6F4; DSHB) was coupled to Dynabeads™ M-270 epoxy beads (Life Technologies™) using a Dynabeads™ antibody coupling kit (Life Technologies™) according to the manufacturer's instructions.

[0047] Briefly, 5 μg of antibody was conjugated to 1 mg of beads and incubated for 16–24 hours at room temperature (RT) with gentle shaking. The beads were then washed with the provided wash buffer and stored as directed until needed.

[0048] α-DAG-coated beads were then dispensed at 1 mg into each immunoprecipitation condition and washed with 900 μl of 1x IP buffer (Life Technologies™) containing 100 mM NaCl. The beads were then captured using a PureProteome™ magnetic stand, and 400 μl of the exosome suspension prepared as described above was added to the α-DAG-bound beads and incubated for 3 hours at room temperature with end-over-end rotation.

[0049] The beads were then magnetically captured, and the supernatant was saved for exosome depletion analysis. The beads were then washed twice with 1 ml of PBS-BSA (0.1%), and the exosomes were either directly lysed or eluted from the beads, depending on their subsequent use.

[0050] For Western blotting and detection of CD63 and CD81 tetraspanin proteins, exosomes were lysed under non-reducing conditions by adding 15 μl of 4x NuPAGE™ LDS buffer to the beads and incubating on ice for 30 minutes. The beads were then magnetically captured, and the protein was transferred to a new tube and heated at 70°C for 10 minutes. Next, 45 μl of protein was loaded onto a NuPAGE™ 4-12% Bis-tris Midi gel (Life Technologies™) and run at 200V for 50 minutes in 1x NuPAGE™ MOPS SDS running buffer (Life Technologies™) before being transferred to a polyvinylidene fluoride (PVDF) membrane using the iBlot™ Dry Blotting System (Life Technologies™).

[0051] Immunoblotting was performed using the ibind™ Flex Western System and primary antibodies (CD81, clone M38 & CD63, clone Ts63; 1:1,000 dilution; Life Technologies™) with appropriate secondary antibodies (goat anti-mouse HRP, 1:4,000 dilution). Chemiluminescent signals were detected using Pierce™ ECL Western blotting substrate and a UVP ChemiDoc-It2 imager.

[0052] In both cases, the precipitates were positive for the CD63 exosome marker, indicating that anti-DAG can precipitate muscle exosomes.

[0053] Example 2 Immunocapture of cell culture exosomes in serum To test whether immunocapture of muscle exosomes from complex starting materials such as serum is hindered by competition from endogenous serum IgG, muscle exosomes from cell culture media were injected into human serum samples obtained from Parkinson's disease patients and age- and sex-matched healthy subjects (protocol NCT02305147, as described above), and co-immunoprecipitation (Co-IP) was performed as described above.

[0054] Briefly, muscle exosomes secreted into the medium by 800,000 myoblasts differentiated into myotubes during 3 days of culture were injected into 200 μl of serum from a healthy subject (H). Approximately 6.7 × 10 cells coated with anti-DAG1 antibody (DAG-6F4, deposited with the Developmental Studies Hybridoma Bank (DSHB) by Morris, GE as DSHB Hybridoma Product DAG-6F4) were then injected into the medium. 7Exosome-injected serum was incubated with magnetic beads for 3 hours. A magnetic stand was used to capture and wash the beads as described above. The captured muscle exosomes were then dissolved in NuPAGE buffer, loaded onto gels as described above, and subjected to Western blot analysis using antibodies specific for the exosome markers CD63 and CD81.

[0055] Exosomes from cell culture media were successfully isolated from human serum samples, confirming that anti-DAG1 beads can capture exosomes from biological fluids without significant interference from endogenous antigens (see Figure 2).

[0056] Example 3 Extraction of circulating muscle exosomes Serum from human subjects was used to investigate whether circulating muscle exosomes could be isolated from serum using an anti-DAG1 immunoaffinity approach.

[0057] Briefly, to isolate exosomes from human serum samples, 200 μl of serum was first cleared of cellular debris by centrifugation at 2000 × g for 30 minutes. Exosomes were then isolated using Whole Exosome Isolation Reagent (for isolation from serum; Life Technologies™) according to the manufacturer's instructions, but with modified volumes. Specifically, 20 μl of isolation reagent was added to the serum sample instead of the recommended 40 μl. The sample was vortexed and incubated on ice for 30 minutes, followed by centrifugation at 10,000 × g for 10 minutes. The supernatant was then separated and saved for subsequent exosome depletion analysis. The pellet was resuspended in 200 μl of PBS and stored at -80°C until needed.

[0058] Exosomes were precipitated from 200 μl of serum as described above. Total circulating exosomes were then incubated with anti-DAG1 antibody-coated magnetic beads for 3 hours. The beads were then isolated and washed using a magnet as described above. Proteins were then extracted from muscle exosomes using NuPAGE buffer and loaded onto a gel for Western blot analysis (see Figure 3A). Western blot analysis showed that vesicles pulled down by antibodies targeting muscle membrane proteins were positive for the exosome markers CD63 and CD81, demonstrating the feasibility of using an immunoaffinity approach using anti-DAG1 to isolate muscle exosomes from serum (see Figure 3B).

[0059] Example 4 Immunocapture of circulating muscle exosomes from healthy subjects To determine whether circulating muscle exosomes could be isolated from serum of healthy controls using anti-DAG1 beads, immunoprecipitation was performed as described above, but the sample volume was increased to 500 μl. The ability of different elution buffers to elute captured exosomes from the anti-DAG1 isolation beads was also tested.

[0060] Briefly, exosomes were precipitated from 500 μl of serum. Total circulating exosomes were then incubated with anti-DAG1 antibody-coated magnetic beads for 3 hours, as described above. A magnetic stand was used to capture and wash the beads, as described above. Captured muscle exosomes were then eluted with either NuPAGE buffer (NP), 8 M urea buffer, or commercial elution buffer (EB), loaded onto gels as described above, and subjected to Western blot analysis using antibodies specific for the exosome markers CD63 and CD81.

[0061] After increasing the sample volume, muscle exosomes positive for CD63 and CD81 were successfully captured from the serum of healthy controls (see Figure 4). Furthermore, testing of different elution buffers showed that NuPAGE buffer and 8M urea buffer were most effective in eluting the captured exosomes compared to low pH elution buffers.

Claims

1. 1. A method for isolating exosomes, said method comprising: (a) providing a binding partner for a cell surface polypeptide, wherein said cell surface polypeptide is dystroglycan (DAG); (b) contacting the binding partner with a sample containing exosomes; (c) isolating the binding partner; and (d) isolating the exosomes; A method comprising:

2. 10. The method of claim 1, wherein the sample is a biological fluid sample.

3. 3. The method of claim 1 or 2, wherein the sample is a serum sample.

4. The method of any one of claims 1 to 3, wherein the sample comprises a biological tissue.

5. The method according to any one of claims 1 to 4, wherein the sample comprises a biological tissue selected from endodermal tissue, mesodermal tissue, and ectodermal tissue.

6. 6. The method of claim 5, wherein said mesodermal tissue is muscle tissue.

7. 7. The method of claim 6, wherein the muscle tissue comprises cells selected from skeletal muscle cells; smooth muscle cells; and cardiac muscle cells.

8. The method of any one of claims 1 to 7, wherein the cell surface polypeptide is alpha-dystroglycan.

9. The method of any one of claims 1 to 8, wherein the binding partner of the cell surface polypeptide is an antibody capable of binding to the cell surface polypeptide.

10. The method of any one of claims 1 to 9, wherein the binding partner of the cell surface polypeptide comprises an antibody capable of binding to the cell surface polypeptide and a solid support.

11. 11. The method of claim 10, wherein the solid support is a magnetic bead.

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