Marker, molecular typing model and application thereof
Through the application of targeted sequencing and molecular typing models, the markers of CD30 were screened and molecular typing models were constructed, which solved the problem of difficult understanding of CD30 regulation mechanism in PTCL in the prior art, and achieved the genetic mutation background of PTCL patients. Understand and target the targeted treatment.
Patent Information
- Application Number
- CN202411600438.3
- Authority / Receiving Office
- CN · China
- Patent Type
- Applications(China)
- Current Assignee / Owner
- Filing Date
- 2024-11-11
- Publication Date
- 2025-02-07
AI Technical Summary
It is difficult for the prior art to effectively explore and understand the CD30 regulatory mechanism in peripheral T-cell lymphoma (PTCL), especially its prognostic significance and targeted therapeutic value in different pathological subtypes.
Through targeted sequencing, the gene mutations in PTCL tumor tissue were detected, and CD30 markers were screened, such as SETD2, STAT3 and PTPRS were screened to construct molecular typing models, and typed according to the patient's gene mutation characteristics and immune microenvironment characteristics, and target different subsubs Targeted therapy.
It has achieved an understanding of the genetic mutation background of PTCL patients, predicted the prognosis of patients through molecular typing, and carried out targeted treatments for different subtypes, which has improved the targetedness and effectiveness of the treatment.
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Abstract
Description
Technical Field
[0001] The present invention relates to the field of biological detection, and in particular to markers, molecular typing models and applications thereof. Background Art
[0002] In recent years, the incidence of malignant lymphoma has been increasing year by year, posing a serious threat to human health. Peripheral T-cell lymphoma (PTCL) is a type of malignant lymphoproliferative disease originating from postthymic mature T cells or NK / T cells. In recent years, the incidence of PTCL has increased year by year, and the incidence in Asia is higher than in Europe and the United States. PTCL is highly heterogeneous and invasive. According to a report released by the World Health Organization in 2022, PTCL has more than 30 different pathological subtypes with different clinical manifestations and pathogenesis; except for anaplastic lymphoma kinase (ALK)-positive anaplastic large cell tumor (ALCL), the first-line anthracycline-based CHOP (cyclophosphamide, doxorubicin, vincristine, prednisone) regimen has a complete remission rate of less than 40%, and the total remission rate of patients entering second-line salvage treatment is only 20%~42%. Nucleolar phosphoprotein 1 (NPM1)-ALK is the most common translocation in the ALK+ALCL subtype, present in 75%~80% of patients, promoting the activation of downstream signaling pathways and the proliferation of tumor cells. However, the pathogenesis of other subtypes of PTCL is still unclear and needs further exploration. In recent years, with the development of DNA sequencing, whole-cell RNA and single-cell RNA sequencing technologies, it has become possible to explore the molecular mechanisms related to PTCL tumor evolution, the state of the immune microenvironment and predict patient survival outcomes.
[0003] According to the 2022 WHO classification, PTCL has more than 30 different pathological subtypes, among which the most common primary nodal PTCLs include nodal follicular helper T-cell lymphoma (nTFHL) derived from follicular helper T cells (TFH), peripheral T-cell neoplasm not otherwise specified (PTCL-NOS), ALK+ALCL and ALK-negative anaplastic large cell tumor (ALK-ALCL), with different clinical manifestations and pathogenesis. With the development of sequencing technology, multi-omics studies have focused on tumor origin (TFH, PTCL-TBX21 and PTCL-GATA3), genomic characteristics (TET2, RHOA mutations, CDKN2A / B copy number variations, TP63, DUSP22 gene rearrangements), surface antigens (CD30), transcription factors (JUN, FOS, BATF3), viral regulation (Epstein-Barr virus), etc., which have promoted the progress of the regulatory mechanism of peripheral T-cell lymphoma.
[0004] CD30 is encoded by the TNFRSF8 gene and is a 120 kd type I transmembrane glycoprotein of the tumor necrosis factor receptor (TNFR) superfamily. It is widely expressed in PTCL and has important diagnostic, prognostic and targeted therapeutic significance. CD30 is specifically and highly expressed in Hodgkin's lymphoma, anaplastic large cell lymphoma and cutaneous CD30-positive lymphoproliferative diseases such as cutaneous anaplastic T-cell lymphoma (CTCL) and lymphomatoid papulosis (LyP), while other pathological subtypes such as PTCL-NOS, AITL, mycosis fungoides (MF) and diffuse large B-cell lymphoma (DLBCL) have also been found to be expressed to varying degrees. CD30 exerts its physiological effects through a series of different signaling pathways. After receiving stimulation, tumor necrosis factor receptor-associated protein (TRAF) trimerizes and further activates downstream signaling pathways such as nuclear factor-κB (NFκB) and mitogen-activated protein kinase (MAPK), promoting cell proliferation.
[0005] In PTCL, previous studies have mainly explored the progression and evolution mechanisms of ALCL subtypes. Activation of the JAK-STAT3 signaling pathway that depends on NPM1-ALK is mainly seen in ALK+ALCL. Alternative mechanisms of JAK-STAT3 activation that are independent of NPM1-ALK include mutations in JAK1 and / or STAT3 and fusions involving ROS1 and TYK2. Further exploration is needed to understand the regulatory mechanism of CD30 in more pathological subtypes of PTCL; however, no studies have conducted subgroup analysis on CD30+PTCL to explore the prognostic significance and targeted therapeutic value of CD30 in different subtypes of PTCL. Summary of the invention
[0006] In view of this, the present invention provides markers, molecular typing models and their applications. The present invention detects gene mutations in peripheral T-cell lymphoma tumor tissues through targeted sequencing, understands the genetic background of peripheral T-cell lymphoma patients, and divides patients into three groups with different gene mutation characteristics, transcriptome characteristics and immune microenvironment characteristics through correlation analysis of the mutated genes of patients. Molecular typing can predict the prognosis of patients and perform targeted treatment based on the molecular biological characteristics of patients.
[0007] In order to achieve the above-mentioned object of the invention, the present invention provides the following technical solutions:
[0008] The present invention provides a method for screening markers, comprising the following steps:
[0009] S1: Obtain the protein expression of CD30 in samples of patients with peripheral T-cell lymphoma;
[0010] S2: dividing the peripheral T-cell lymphoma patient samples into a peripheral T-cell lymphoma CD30 positive group and a peripheral T-cell lymphoma CD30 negative group according to the protein expression level;
[0011] S3: Statistical analysis is performed on the frequencies of differentially expressed genes between the positive group and the negative group, and genes with statistical differences are the markers.
[0012] In some embodiments of the present invention, when the protein expression level in the above screening method S2 is greater than 10%, it is the positive group of the peripheral T cell lymphoma CD30;
[0013] When the protein expression level is less than 10%, it is the negative group of the peripheral T cell lymphoma CD30.
[0014] The present invention also provides markers, including one or more of SETD2, STAT3 and PTPRS.
[0015] The present invention also provides the use of the above marker in preparing a product for down-regulating the protein expression of CD30 in peripheral T-cell lymphoma.
[0016] In some embodiments of the present invention, in the above application, when the SETD2 is activated, the STAT3 is inactivated or the PTPRS is activated, the protein expression level of the CD30 is downregulated.
[0017] The present invention also provides the use of the above markers in constructing a molecular typing model for peripheral T cell lymphoma.
[0018] The present invention also provides a method for constructing a peripheral T-cell lymphoma molecular typing model, comprising the following steps:
[0019] S1: Group the above markers;
[0020] S2: Analyze the groups obtained in S1 according to the database to obtain the relevant genes of the groups;
[0021] S3: Typing the sample to be tested according to the marker or the related gene.
[0022] In some embodiments of the present invention, in the above construction method, the grouping includes: ,Group and Group ;
[0023] The group The marker is SETD2;
[0024] The group The marker is STAT3;
[0025] The group The marker is PTPRS.
[0026] In some embodiments of the present invention, in the above construction method, the group The related genes include: one or more of KMT2A, KMT2C, KMT2D, SETD2, SETD1B, BCOR, CREBBP and NCOR2;
[0027] The group The related genes include: one or more of JAK1, JAK3, SOCS1, STAT3, STAT5B, NOTCH1, NOTCH2 and EBER;
[0028] The group The related genes include one or more of FYN, PTPN13, PTPRC, PTPRS, ARID1A, ARID1B, ARID2, ASLX3, CHDB, SMARCA2, HLA-A, HLA-B and TAL1.
[0029] In some embodiments of the present invention, in the above construction method, the typing judgment criteria are:
[0030] If the sample to be tested contains any one of the markers, it corresponds to the group , the group or the group ;or
[0031] If the sample to be tested contains any two or three of the markers, it corresponds to the group , the group and / or the group Then clustering is performed according to the frequency of the related genes, and the genes with high frequency are the corresponding genes in the group , the group or the group ;or
[0032] If the sample to be tested does not contain the marker, clustering is performed according to the frequency of the related genes, and the gene with the highest frequency corresponds to the group. , the group or the group .
[0033] The present invention also provides a molecular typing model obtained by the above construction method.
[0034] The present invention also provides the use of the above markers and / or the above molecular typing model in any of the following items:
[0035] (I) preparing a product for predicting peripheral T-cell lymphoma; and / or
[0036] ( ), preparing products for predicting the prognosis of peripheral T-cell lymphoma; and / or
[0037] ( ), prognosis prediction for patients with peripheral T-cell lymphoma; and / or
[0038] ( ), screening targeted drugs for the treatment of peripheral T-cell lymphoma.
[0039] The present invention also provides a method for constructing a prognostic model for predicting peripheral T-cell lymphoma. The prognostic model for peripheral T-cell lymphoma is obtained according to the typing results of the above molecular typing model.
[0040] In some embodiments of the present invention, in the above construction method, when the group , the prognosis is poor.
[0041] This study detected gene mutations in peripheral T-cell lymphoma tumor tissues through targeted sequencing to understand the genetic background of peripheral T-cell lymphoma patients. By performing correlation analysis on the mutated genes of the patients, the patients were divided into three groups with different gene mutation characteristics, transcriptome characteristics, and immune microenvironment characteristics. Molecular typing can predict the prognosis of patients and provide targeted treatment based on the molecular biological characteristics of the patients. BRIEF DESCRIPTION OF THE DRAWINGS
[0042] In order to more clearly illustrate the embodiments of the present invention or the technical solutions in the prior art, the drawings required for use in the embodiments or the description of the prior art are briefly introduced below.
[0043] Figure 1 Flow chart showing the analysis of PTCL patients
[0044] Figure 2 Showing the gene mutation characteristics of CD30+PTCL patients
[0045] Figure 3 Shows the regulatory effect of seed genes on CD30; from left to right: SETD2, STAT3, PTPRS;
[0046] Figure 4 It shows the construction of molecular classification of CD30+PTCL;
[0047] Figure 5The prognostic prediction of the constructed CD30+PTCL molecular classification is shown; wherein: A shows the effect of CD30+PTCL molecular classification on progression-free survival; B shows the effect of CD30+PTCL molecular classification on overall survival; C shows the multivariate analysis of progression-free survival of CD30+PTCL; D shows the multivariate analysis of overall survival of CD30+PTCL. DETAILED DESCRIPTION
[0048] The invention discloses a marker, a molecular typing model and applications thereof.
[0049] It should be understood that the expression "one or more of..." includes each of the items recited after the expression individually and in various different combinations of two or more of the recited items, unless otherwise understood from the context and usage. The expression "and / or" in combination with three or more recited items should be understood to have the same meaning, unless otherwise understood from the context.
[0050] The use of the terms "comprising", "having" or "containing", including their grammatical synonyms, should generally be understood as open and non-restrictive, for example not excluding other unrecited elements or steps, unless otherwise specifically stated or otherwise understood from the context.
[0051] It should be understood that the order of steps or the order in which certain actions are performed is not important as long as the present invention remains operable. In addition, two or more steps or actions may be performed simultaneously.
[0052] The use of any and all examples or exemplary language, such as "for example" or "including", herein is intended only to better illustrate the invention and does not limit the scope of the invention unless otherwise claimed. No language in this specification should be construed as indicating that any non-claimed element is essential to the practice of the invention.
[0053] In addition, the numerical ranges and parameters used to define the present invention are approximate values, and the relevant values in the specific embodiments have been presented as accurately as possible. However, any numerical value inherently inevitably contains standard deviations due to individual test methods. Therefore, unless otherwise expressly stated, it should be understood that all ranges, quantities, values and percentages used in this disclosure are modified by "about". Here, "about" generally means that the actual value is within plus or minus 10%, 5%, 1% or 0.5% of a specific value or range.
[0054] In Examples 1 to 5 of the present invention, all the raw materials and reagents used can be purchased from the market.
[0055] The present invention will be further described below in conjunction with embodiments:
[0056] Example 1 Pathological subtypes included, sequencing content and grouping method
[0057] like Figure 1 As shown, 317 PTCL patients with CD30 immunohistochemistry results, including ALK+ALCL, ALK-ALCL, nTFHL and PTCL-NOS, were selected. With 10% (CD30 protein expression) as the CD30 cutoff value, a total of 119 patients were defined as CD30+PTCL and had DNA sequencing data (for subsequent grouping), and 105 patients were defined as CD30-PTCL.
[0058] Example 2 Mutation characteristics of CD30+PTCL
[0059] The mutation data of CD30+PTCL and CD30-PTCL patients grouped in Example 1 were analyzed by chi-square test (P<0.050 for genes with significant differences), as shown in Figure 2 As shown, CD30+PTCL patients have more SETD2, STAT3, and PTPRS mutations.
[0060] Example 3 Gene regulation on CD30
[0061] The cell lines with knockdown and overexpression of SETD2, STAT3, and PTPRS in two T lymphoma cell lines H9 and JURKAT were constructed, and the expression of CD30 was detected by WB. Figure 3 As shown, inactivation of SETD2 ( Figure 3 Left), STAT3 activation ( Figure 3 middle) and inactivation of PTPRS ( Figure 3 Right) can upregulate the expression of CD30.
[0062] Example 4 Construction of molecular typing of CD30+PTCL
[0063] like Figure 4As shown, based on the above results, SETD2, STAT3, and PTPRS were defined as the seed genes of three CD30+PTCL subtypes, namely HMA, JNE, and PCT subgroups, and according to the pathways and literature annotated in the GO and KEGG databases, KMT2A, KMT2C, KMT2D, SETD2, SETD1B, BCOR, CREBBP, and NCOR2 were defined as the integral items of HMA, JAK1, JAK3, SOCS1, STAT3, STAT5B, NOTCH1, NOTCH2 genes and EBER expression were defined as the integral items of JNE, and FYN, PTPN13, PTPRC, PTPRS, ARID1A, ARID1B, ARID2, ASLX3, CHDB, SMARCA2, HLA-A, HLA-B, and TAL1 were defined as the integral items of PCT. The process of grouping patients is as follows: if the patient has any seed gene, he will be divided into the corresponding subgroup. If the patient does not have the seed gene, the integral items of the three groups will be integrated, with each item accumulating 1 point. Finally, the patient will be assigned to the subgroup with the highest score.
[0064] Example 5 Prognostic prediction of the constructed CD30+PTCL molecular classification
[0065] There were significant differences in PFS and OS among the three molecular subtypes of CD30+ PTCL patients, and the JNE subtype had a worse prognosis than the HMA subtype (PFS p=0.025, OS p=0.003) and PCT subtype (PFS p=0.039, OS p=0.030). Univariate and multivariate models between clinical parameters and molecular subtypes of CD30+ PTCL were established. JNE was strongly associated with lower PFS (p=0.012) and OS (p=0.002) and was considered an independent adverse prognostic factor for PFS (hazard ratio [HR]=1.709, 95%CI 1.025-2.849, p=0.040) and OS (HR=2.803, 95%CI 1.320-5.953, p=0.007).
[0066] The above is only a preferred embodiment of the present invention. It should be pointed out that for ordinary technicians in this technical field, several improvements and modifications can be made without departing from the principle of the present invention. These improvements and modifications should also be regarded as the scope of protection of the present invention.
Claims
1. A method for screening a marker, characterized in that: The steps include: S1: Obtain the protein expression of CD30 in samples of patients with peripheral T-cell lymphoma; S2: dividing the peripheral T-cell lymphoma patient samples into a peripheral T-cell lymphoma CD30 positive group and a peripheral T-cell lymphoma CD30 negative group according to the protein expression level; S3: Statistical analysis is performed on the frequencies of differentially expressed genes between the positive group and the negative group, and genes with statistical differences are the markers.
2. The screening method according to claim 1 or 2, characterized in that In S2, when the protein expression level is greater than 10%, it is the positive group of the peripheral T cell lymphoma CD30; When the protein expression level is less than 10%, it is the negative group of the peripheral T cell lymphoma CD30.
3. A marker, characterized in that include: One or more of SETD2, STAT3 and PTPRS.
4. Use of the marker according to claim 3 in preparing a product for downregulating the protein expression of CD30 in peripheral T-cell lymphoma.
5. The use according to claim 4, characterized in that When the SETD2 is activated, the STAT3 is inactivated or the PTPRS is activated, the protein expression level of the CD30 is downregulated.
6. Use of the marker as claimed in claim 3 in constructing a molecular typing model for peripheral T-cell lymphoma.
7. A method for constructing a molecular typing model for peripheral T-cell lymphoma, characterized in that: The steps include: S1: grouping the markers as claimed in claim 3; S2: Analyze the groups obtained in S1 according to the database to obtain the relevant genes of the groups; S3: Typing the sample to be tested according to the marker or the related gene.
8. The construction method according to claim 7, characterized in that: The groups include: Group I, Group II and Group III; The marker of group I is SETD2; The marker of Group II is STAT3; The marker of Group III is PTPRS.
9. The construction method according to claim 7 or 8, characterized in that: The related genes of group I include: one or more of KMT2A, KMT2C, KMT2D, SETD2, SETD1B, BCOR, CREBBP and NCOR2; The related genes of group II include: one or more of JAK1, JAK3, SOCS1, STAT3, STAT5B, NOTCH1, NOTCH2 and EBER; The related genes of group III include: one or more of FYN, PTPN13, PTPRC, PTPRS, ARID1A, ARID1B, ARID2, ASLX3, CHDB, SMARCA2, HLA-A, HLA-B and TAL1.
10. The construction method according to claim 9, characterized in that: The classification criteria are: If the sample to be tested contains any one of the markers, it corresponds to Group I, Group II or Group III; or If the sample to be tested contains any two or three of the markers, it corresponds to group I, group II and / or group III, and then clustering is performed according to the frequency of the related genes, and the genes with higher frequencies correspond to group I, group II or group III; or If the sample to be tested does not contain the marker, clustering is performed according to the frequency of the related genes, and the genes with higher frequencies correspond to group I, group II or group III.
11. The molecular typing model obtained by the construction method according to any one of claims 7 to 10.
12. Use of the marker according to claim 3 and / or the molecular typing model according to claim 11 in any of the following items; (I) preparing a product for predicting peripheral T-cell lymphoma; and / or (II) preparing a product for predicting the prognosis of peripheral T-cell lymphoma; and / or (III) Prediction of prognosis of patients with peripheral T-cell lymphoma; and / or (IV) Screening targeted drugs for the treatment of peripheral T-cell lymphoma.
13. A method for constructing a prognostic model for predicting peripheral T-cell lymphoma, characterized in that: According to the typing results of the molecular typing model as claimed in claim 11, the peripheral T-cell lymphoma prognosis model is obtained.
14. The construction method according to claim 13, characterized in that: When it is the Group II, the prognosis is poor.