Colorectal cancer subtype identifier

Abstract

This invention relates to an identifier for colorectal cancer subtypes based on percent splice-in (PSI) values ​​from alternative splicing events. Furthermore, this invention relates to a method for predicting outcomes in colorectal cancer patients using PSI values. Furthermore, this invention relates to a kit for predicting outcomes in colorectal cancer patients using PSI values. Furthermore, this invention relates to the use of PSI values ​​as an outcome marker in colorectal cancer patients. Furthermore, this invention relates to a method for treating colorectal cancer patients using PSI values ​​to obtain CMS likelihood for disease outcomes.

Description

Technical Field

[0001] The present invention relates to identifiers for colorectal cancer subtypes based on percent splice-in (PSI) values from alternative splicing events. Further, the present invention relates to methods for predicting the outcome of colorectal cancer patients using PSI values. Further, the present invention relates to kits for predicting the outcome of colorectal cancer patients using PSI values. Further, the present invention relates to the use of PSI values as outcome markers for colorectal cancer patients. Further, the present invention relates to a method of treating colorectal cancer patients using PSI values to obtain a CMS likelihood related to disease outcome. Background of the Invention

[0002] Colorectal cancer (CRC) (also called colon cancer or bowel cancer) is the third most common cancer in the world. In 2020, more than 1.9 million new CRC cases were identified, and more than 500,000 patients die annually from this disease ultimately ("Colorectal Cancer Facts and Figures 2020 - 2022", American Cancer Society, Atlanta, Georgia). Patients in the early stages usually undergo colectomy, followed by radiotherapy or systemic chemotherapy based on the macroscopic features of the tumor and the stage of the tumor. In some patients who receive chemotherapy after colectomy, the 5-year recurrence-free survival rate improves, but in other patients, this statistic is not improved.

[0003] Clinical experience and colorectal cancer research have led to the understanding that colorectal cancer is not a single disease but arises as multiple distinct subtypes. These subtypes are distinguished by characteristic gene expression patterns that influence or determine the biological characteristics of the tumor. Numerous papers have been published on methods for classifying colon tumors into molecularly distinguishable subtypes. For example, see M. Pratap Singh et al., Genes & Diseases, 2021, 8, 133-145; G. Valenzuela et al., World J. Clin. Oncol., 2021, 12(11), 1000-1008; DG Menter et al., Curr. Gastroenterol. Rep., 2019, 21(5), 1-12; G. Martini et al., Ther. Adv. Med. Oncol., 2020, 12(1), 1-18; and E. Fontana et al., Annals of oncology, 2019, 30, 520-527. Recognizing the similarities among many of these subtype classification systems, an expert consortium was formed to derive a single subtype classification system that inherits the best features of each system.

[0004] The Consensus Molecular Subtype (CMS) classification system classifies colorectal cancer into four distinct groups called subtypes. Each subtype, namely CMS1, CMS2, CMS3, and CMS4, has different biological and molecular characteristics. These subgroups were established using tumor gene expression profiles. CMS1 (MSI immunotype) tumors exhibit microsatellite instability and high immune cell infiltration. CMS2 (standard type) is an epithelial subtype with marked upregulation of WNT and MYC downstream targets, and chromosomal instability (CIN) is a prominent feature of this subtype. CMS3 (metabolic type) has epithelial characteristics similar to CMS2, but with lower CIN. Furthermore, CMS3 subtypes are rich in KRAS mutations and exhibit abnormal expression of metabolic genes. CMS4 (mesenchymal type) is a mesenchymal subtype with activation of pathways that regulate epithelial-mesenchymal transition (EMT) and stem cell characteristics. The CMS subtype classification system has a very high potential to play a crucial role in treatment selection for colorectal cancer.

[0005] Identifying molecular subtypes of colorectal cancer (CRC) has potential value in predicting patient prognosis and diagnosis, but a reliable subtype classification has yet to be established. The current consensus molecular subtype (CMS) classification in colorectal cancer is based on complex RNA expression patterns quantified at the gene level.

[0006] The following references provide the technical background for this invention: WO2021 / 101452, Jianyi et al., Molecular Carcinogenesis, 60 (4), 2021, p. 279-293, Haifeng et al., BCM Gastroenterology, 20 (1), 2020, and Guinney et al., Nature Medicine, 21 (11), 2015, p. 1350-1356.

[0007] Zhiyuan et al., Genomic Academic Press, 2020, 112 (6), pp. 4032-4040, presents a study on alternative splicing (AS) in the recurrence of colorectal cancer (CRC). Furthermore, a prognostic signature predicting recurrence in stage I-III CRS has been constructed based on alternative splicing. It should be noted that stages I-III of colorectal cancer (CRC) do not correspond to subtypes CM1-CM4 of colorectal cancer.

[0008] Haitao et al., BMC Cancer, 20 (1), 2020, is a study on the identification and validation of alternative splicing signatures based on alternative splicing events associated with survival.

[0009] Yongfu et al., Ebiomedicine, 36, 2018, pp. 183-195, describes a study that profiles genome-wide alternative splicing in a CRC cohort to identify CRC-related alternative splicing events and analyze their association with clinical outcomes. Four clusters, C1, C2, C3, and C4, were identified (these do not correspond to CMS1-CMS4). Furthermore, it is stated that the distribution among clusters of different CMS, TNM stages, KRASm, and survival status in the CRS sample was not random overall.

[0010] Eilertsen et al., Int. J. of Cancer, 144 (4), 2018, 841-847, is a study on the impact of mutation-related KRAS alternative splicing on prognosis.

[0011] Tong et al., Department of Pathology, Erasmus University Medical Cancer, 11 (7), 2022, study alternative splicing that causes phenotypic plasticity in epithelial malignancies in colorectal cancer. This study focuses on alternative splicing of the CD44 and NUMB genes.

[0012] WO2019173647 discloses a kit and method for predicting or determining the consensus molecular subtype (CMS) of colorectal cancer in human patients. The kit includes multiple oligonucleotide primers configured to bind complementarily to a portion of the cDNA of at least 12 RNA transcripts derived from a colorectal cancer tissue sample and to prime the polymerase chain reaction of the cDNA, wherein these at least 12 RNA transcripts comprise at least three RNA transcripts from each of four genetic element groups, each of which defines a CMS gene expression profile specific to one of four different CMS1, CMS2, CMS3, and CMS4.

[0013] WO2020206136 relates to a method for classifying the cancer status of colorectal cancer patients. (a) Take a tumor sample from the subject; (b) Measure the expression levels of multiple genes in the tumor sample; (c) Generate an expression profile based on a comparison of the expression levels of several genes in a sample derived from a subject with the corresponding expression levels obtained from a reference sample from another subject with a known cancer status; and (d) Classify the cancer status of the subjects based on their expression profiles.

[0014] WO2021061990 discloses a method for determining whether a subject has a Cl subtype of colorectal cancer (CRC), which involves measuring the expression level of at least one Cl subtype-related gene in the test sample.

[0015] To date, the characteristics of CMS and current CMS classification methods rely on the expression patterns of hundreds of genes. Barriers to the clinical application of these technologies include the uncertainty in patient-to-patient sample evaluation commonly encountered in clinical settings, susceptibility to batch effects in gene-level expression quantification, and the high costs associated with evaluating the gene expression levels of hundreds of genes.

[0016] Therefore, conventional consensus molecular subtype (CMS) determination of colorectal cancer tumors has several shortcomings that need to be addressed. As a result, there is an urgent need for time- and cost-effective clinical trials to determine consensus molecular subtypes of colorectal tumors and their associated prognoses.

[0017] Therefore, an object of the present invention is to provide a method for classifying molecular subtypes (CMS) of colorectal cancer patients. Furthermore, an object of the present invention is to provide a method for predicting outcomes of colorectal cancer patients.

[0018] Surprisingly, it was found that consensus molecular subtypes (CMS) could be classified using colorectal cancer subtype identifiers based on percentage splice-in rates (PSI) obtained from alternative splicing events. [Overview of the Initiative]

[0019] The present invention relates to a colorectal cancer subtype identifier that classifies tumors by PSI values ​​based on the occurrence of at least one alternative splicing event.

[0020] The present invention further relates to a method for predicting the outcome of a subject with colorectal cancer using a PSI value based on the occurrence of at least one alternative splicing event, and includes the following steps: a) The process of taking a sample from a tumor of a subject who has cancer; b) The process of determining PSI values, specifically at least three, and in particular at least five PSI values; c) A process of converting PSI values ​​to determine disease outcome indicators.

[0021] The present invention further relates to a kit for predicting outcomes in subjects with colorectal cancer using PSI values, specifically at least three, and more particularly at least five, PSI values, based on the occurrence of at least one alternative splicing event.

[0022] The present invention further relates to using PSI values, particularly at least three, and especially at least five, PSI values ​​based on the occurrence of alternative splicing, as outcome markers for subjects with colorectal cancer.

[0023] The present invention further relates to a method for treating a subject with colorectal cancer using PSI values ​​based on the occurrence of alternative splicing, and includes the following steps: d) The process of taking a sample from a tumor of a subject who has cancer; e) The process of determining PSI values, specifically at least three, and in particular at least five PSI values; f) A step of converting PSI values ​​to determine disease outcome indicators. Description of the Invention

[0024] The colorectal cancer subtype identifier and method according to the present invention have the following advantages. - To classify patients into subtypes CMS1, CMS2, CMS3, and CMS4, and to help determine additional treatment and / or observation as an alternative to no intervention. - Consensus molecular subtypes of colorectal cancer can be identified by converting PSI values ​​from a small number of alternative splicing events per CMS, which can be measured using RT-PCR, multiplex assay, or targeted sequencing. - PSI values ​​provide the proportion of a particular splice variant. The built-in normalization process for calculating PSI values ​​enhances the method's resistance to batch effects that could negatively impact the quantification of gene-level expression. Enabling the evaluation of a single sample by providing four probability values each representing the likelihood that the sample belongs to a specific subtype. Showing performance superior to that of a classifier based on gene expression.

[0025] CMS1 (MSI immune type) tumors have microsatellite instability (MSI) and significant infiltration of immune cells. The pathway leading to carcinogenesis has the following characteristics: 1) occurrence in the proximal colon, 2) high BRAFV600E mutation rate, 3) loss of tumor suppressor function due to hypermethylation of CpG islands (CpG island methylation phenotype [CIMP]), 4) association with defects in the DNA mismatch repair (MMR) system, and 5) infiltration of immunogenic lymphocytes into the tumor microenvironment. Patients with CMS1 tumors have a better prognosis compared to patients with CMS2, CMS3, or CMS4 tumors.

[0026] CMS2 (standard type) is an epithelial subtype with activated WNT-β-catenin and MYC signaling pathways, and chromosomal instability (CIN) is characteristic of this subtype. Tumors classified as CMS2 arise from the progression of standard adenomas to cancer. CMS2 tumors are usually treated with standard adjuvant chemotherapy. The 5-year overall survival rate at all stages of CMS2 is higher than that of any other subtype.

[0027] CMS3 (metabolic type) has characteristics of epithelial cells but low CIN. Furthermore, the CMS3 subtype is rich in KRAS mutations and shows abnormal expression of metabolism-related genes. Also, CMS3 has more MSI than CMS2 and 4. CMS3 is considered to be most similar to normal colon tissue at the gene expression level. As a result of pathway analysis, CMS3 mRNA was abundantly observed in 9 pathways including glutamine, fatty acid, and lysophospholipid metabolism among the 10 metabolic pathways investigated.

[0028] CMS4 (mesenchymal type) is a mesenchymal subtype in which pathways controlling epithelial-mesenchymal transition (EMT) and stem symmetry are activated. CMS4 tumors exhibit extremely low levels of high-frequency mutations. CMS4 CRCs exhibit a mesenchymal phenotype with a genetic signature consistent with activated stroma, namely angiogenesis, integrin binding to matrix proteins, TGFβ signaling characteristic of cancer-associated fibroblasts (CAFs), and an inflammatory microenvironment with prominent innate immune cells. In contrast to the antitumor immune environment of CMS1 cancer, the CMS4 tumor microenvironment is pro-inflammatory and contains Treg cells, T helper 17 cells, myeloid suppressor cells, and pro-tumor macrophages. CMS4 cancer is often diagnosed at an advanced stage, has a poor prognosis, and has the lowest 5-year overall survival rate.

[0029] In this invention, the term "subject" refers to any human or animal. (Non-human) animals include all vertebrates, such as mammals and non-mammals (cattle, sheep, pigs, goats, horses, poultry, dogs, cats, non-human primates, rodents, etc.). In one embodiment, the subject is a human.

[0030] As used herein, the term "marker" refers to the PSI value used to determine the CMS1, CMS2, CMS3, and / or CMS4 groups.

[0031] In this invention, the term "outcome" refers to the result of treatment or a series of treatments for a specific disease.

[0032] Outcomes are determined at a point in time during or after treatment, based on one or more criteria. Considering outcomes helps to assess the effectiveness and appropriateness of medical interventions and evaluate them in relation to alternatives, particularly no intervention.

[0033] Disease outcomes can be defined in various ways, including by using different endpoints. One way to determine an outcome is "long-term" survival, which refers to survival for a specific period after diagnosis and / or initial treatment, for example, at least three years. Another method is "recurrence-free survival" (RFS), which refers to survival (usually in years) from diagnosis and / or initial treatment to cancer recurrence or death due to cancer recurrence. Yet another method is "overall survival" (OS), which refers to survival (usually in years) from diagnosis and / or initial treatment to death from any cause. Yet yet another method is "disease-free survival" (DFS), which refers to survival (usually in years) from diagnosis and / or initial treatment to the first cancer recurrence or death from any cause.

[0034] Outcome analysis often focuses on changes in quality of life, and therefore allows for the evaluation of each preventive or therapeutic measure in a more meaningful way for future subjects than using so-called surrogate markers, parameters, or endpoints (measurable variables not directly relevant to the subject, such as measured values ​​and clinical laboratory values, tumor size, etc.).

[0035] The overall situation should be defined as precisely as possible, rather than relying on surrogate parameters or intuitive descriptions of the case (such as "cured" or "uncured").

[0036] In a first embodiment, the present invention relates to a colorectal cancer subtype identifier that classifies tumors based on PSI values ​​associated with at least one alternative splicing event.

[0037] The reference genome is named GRCh38, and the annotation is Gencode v28 (primary assembly).

[0038] The term "PSI" is an abbreviation for "percent spliced ​​in" and refers to exon inclusion. It is a known statistic used to measure alternative splicing events. Alternative splicing is the process by which a gene is transcribed into multiple isoforms (or mRNA transcripts). PSI is defined as the ratio obtained by dividing the relative abundance of all isoforms containing a given exon by the relative abundance of all isoforms of the gene containing that exon. In other words, the PSI value defines how frequently an exon appears in all isoforms of the gene containing that exon. The PSI value of an alternative splicing event reflects the intensity / frequency of such an event and has been widely used to detect exons that have undergone different splicing.

[0039] Alternative splicing (AS) events contribute to the complexity of gene expression patterns and can be classified into five distinct types: (1) exon skipping (ES), (2) intron retention (IR), (3) alternative 5' splicing (A5SS), (4) alternative 3' splicing (A3SS), and (5) mutually exclusive exon use (MXE) events. These events are regulated in a tissue and cell type-specific manner, resulting in qualitative changes to the existing RNA pool and adding a new layer of biological information.

[0040] Preferably, the PSI value is based on at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, or 141 alternative splicing events, or a combination thereof.

[0041] The alternative splicing event is preferably at least one exon skipping event.

[0042] An advantage is that colorectal cancer subtype identifiers classify tumors as CMS1, CMS2, CMS3, or CMS4.

[0043] There are two types of alternative splicing patterns that can be used to identify subtypes of colorectal cancer. The first type is subtype-specific alternative splicing events.

[0044] Preferably, for the identification of CMS1, there are at least one, preferably at least five, more preferably at least ten, and especially at least 20, and especially at least 25, exon skipping events, which are selected from the following: ITGAE (ENSG00000083457.11) in the exon at genomic coordinates chr17:3723287-3723383, CCNDBP1 (ENSG00000166946.13) in the exon at genomic coordinates chr15:43194080-43194137, CPT1B (ENSG00000205560.12) in the exon at genomic coordinates chr22:50573807-50573921, and CDC16 in the exon at genomic coordinates chr13:114236644-114236699. (ENSG00000130177.14), PTPN6 in the exon at genomic coordinates chr12:6951458-6951520 (ENSG00000111679.16), PTPN6 in the exon at genomic coordinates chr12:6951463-6951520 (ENSG00000111679.16), ACCS in the exon at genomic coordinates chr11:44073446-44073517 (ENSG00000110455.13), EXOSC9 in the exon at genomic coordinates chr4:121816143-121816194 EXOSC9 in the exon at genomic coordinates chr4:121816368-121816447 (ENSG00000123737.12), ZNF611 in the exon at genomic coordinates chr19:52707468-52707542 (ENSG00000213020.9), MRRF in the exon at genomic coordinates chr9:122285779-122285946 (ENSG00000148187.17), NUP153 in the exon at genomic coordinates chr6:17668974-17669028 (ENSG00000124789.11), WARS in exon chr14:100375282-100375350 (ENSG00000140105.17) WARS (ENSG00000140105.17) in the exon at genomic coordinates chr14:100375282-100375403, WARS (ENSG00000140105.17) in the exon at genomic coordinates chr14:100375282-100375406, D2HGDH (ENSG00000180902.17) in the exon at genomic coordinates chr2:241748864-241749929, LUC7L (ENSG00000007392.16) in the exon at genomic coordinates chr16:228332-228402, EPB41 in the exon at genomic coordinates chr1:29058588-29058645 (ENSG00000159023.20), DGUOK in the exon at genomic coordinates chr2:73938909-73939022 (ENSG00000114956.19), MDM4 in the exon at genomic coordinates chr1:204537429-204537497 (ENSG00000198625.12), MDM4 in the exon at genomic coordinates chr1:204537458-204537497 (ENSG00000198625.12), PTP4A2 in the exon at genomic coordinates chr1:31915894-31915987 (ENSG00000184007.19), MKNK2 in exon at genomic coordinates chr19:2039630-2039856 (ENSG00000099875.14), CCDC112 in exon at genomic coordinates chr5:115269702-115269798 (ENSG00000164221.12), FRYL in exon at genomic coordinates chr4:48593929-48594016 (ENSG00000075539.14), CEP78 in exon at genomic coordinates chr9:78265858-78265906 (ENSG00000148019.13), FNBP1 in the exon at genome coordinates chr9:129923843-129923996 (ENSG00000187239.16), FNBP1 in the exon at genome coordinates chr9:129923843-129924026 (ENSG00000187239.16) ECT2 in the exon at genomic coordinates chr3:172752149-172752472 (ENSG00000114346.13), ECT2 in the exon at genomic coordinates chr3:172755482-172755575 (ENSG00000114346.13), ANKRD26 in the exon at genomic coordinates chr10:27044156-27044190 (ENSG00000107890.16), ZMIZ2 in the exon at genomic coordinates chr7:44760150-44760228 (ENSG00000122515.14), C6orf48 in the exon at genomic coordinates chr6:31836423-31836517 (ENSG00000204387.12), and USPL1 in the exon at genomic coordinates chr13:30621072-30621239 (ENSG00000132952.11).

[0045] In particular, for the identification of CMS1, there are 1, 2, 3, 4, 5, 6, 7, 8, and 9 exon skipping events, which are selected from the following: ITGAE in the exon at genomic coordinates chr17:3723287-3723383 (ENSG00000083457.11), MRRF in the exon at genomic coordinates chr9:122285779-122285946 (ENSG00000148187.17), LUC7L in the exon at genomic coordinates chr16:228332-228402 (ENSG00000007392.16), and MDM4 in the exon at genomic coordinates chr1:204537458-204537497 (ENSG00000198625.12). CCDC112 (ENSG00000164221.12) in exon chr5:115269702-115269798, FRYL (ENSG00000075539.14) in exon chr4:48593929-48594016, CEP78 (ENSG00000148019.13) in exon chr9:78265858-78265906, FNBP1 (ENSG00000187239.16) in exon chr9:129923843-129923996, ANKRD26 in exon chr10:27044156-27044190 (ENSG00000107890.16).

[0046] Preferably, for the identification of CMS2, there are at least one, preferably at least five, more preferably at least ten, and especially at least fifteen exon skipping events, which are selected from the following: ZMIZ2 (ENSG00000122515.14) in the exon at genomic coordinates chr7:44760150-44760228, C6orf48 (ENSG00000) in the exon at genomic coordinates chr6:31836423-31836517 USPL1 (ENSG00000132952.11) in the exon at genomic coordinates chr13:30621072-30621239, RBM39 (ENSG00000131051.22) in the exon at genomic coordinates chr20:35740524-35740597, MIS12 (ENSG00000167842.15) in the exon at genomic coordinates chr17:5488195-5488589, and genomic coordinate chr17:782046 AFMID (ENSG00000183077.15) in exon 55-78204741, MACROD1 (ENSG00000133315.10) in exon genomic coordinates chr11:63998837-63998872, FN1 (ENSG00000115414.18) in exon genomic coordinates chr2:215380810-215381080, WBP1 (E NSG00000239779.6), XPO1 in the exon at genomic coordinates chr2:61525269-61525333 (ENSG00000082898.16), PTPN18 in the exon at genomic coordinates chr2:130359232-130359309 (ENSG00000072135.12), ARHGAP27 in the exon at genomic coordinates chr17:45404268-45404334 (ENSG00000159314.11), genomic coordinates C16orf13 (ENSG00000130731.15) in the exon chr16:635280-635340, and C16orf13 (ENSG00000130731.) in the exon chr16:635517-635774.15) C16orf13 (ENSG00000130731.15) in the exon at genome coordinates chr16:635611-635774.

[0047] In particular, for the identification of CMS2, there are 1, 2, 3, 4, or 5 exon skipping events, which are selected from the following: USPL1 in the exon at genomic coordinates chr13:30621072-30621239 (ENSG00000132952.11), MACROD1 in the exon at genomic coordinates chr11:63998837-63998872 (ENSG00000133315.10), ENAH in the exon at genomic coordinates chr1:225504990-225505053 (ENSG00000154380.17), and FNIP1 in the exon at genomic coordinates chr5:131710577-131710661 (ENSG00000217128.11), and SORBS1 in exon genomic coordinates chr10:95414493-95414862 (ENSG00000095637.21).

[0048] Preferably, for the identification of CMS3, there are at least 1, preferably at least 5, more preferably at least 15, especially at least 30, and especially at least 41 exon skipping events, which are selected from the following: C16orf13 (ENSG00000130731.15) in the exon at genomic coordinates chr16:635280-635340, C16orf13 (ENSG00000130731.15) in the exon at genomic coordinates chr16:635517-635774, C16orf13 (ENSG00000130731.15) in the exon at genomic coordinates chr16:635611-635774, and AURKA in the exon at genomic coordinates chr20:56388686-56388784 (ENSG00000087586.17), EPB41L3 in the exon at genomic coordinates chr18:5394676-5394793 (ENSG00000082397.17), KALRN in the exon at genomic coordinates chr3:124637207-124637303 (ENSG00000160145.15), ADAM15 in the exon at genomic coordinates chr1:155061903-155061975 (ENSG00000143537.13), KRAS in the exon at genomic coordinates chr12:25215436-25215560 (ENSG00000133703.11), SLC39A14 in the exon at genomic coordinates chr8:22412036-22412206 (ENSG00000104635.13), MYO9A in the exon at genomic coordinates chr15:71951776-71951896 (ENSG00000066933.15), TPM1 in the exon at genomic coordinates chr15:63044026-63044152 (ENSG00000140416.20), TPM1 in the exon at genomic coordinates chr15:63061197-63061273 (ENSG00000140416.20), TPM1 in the exon at genomic coordinates chr15:63061712-63061788 (ENSG00000140416.20), MYO6 in the exon at genomic coordinates hr6:75894813-75894840 (ENSG00000196586.13) MYO6 (ENSG00000196586.13) in the exon at genomic coordinates chr6:75898372-75898411, KIAA1217 (ENSG00000120549.17) in the exon at genomic coordinates chr10:24494499-24494604, KIAA1217 (ENSG00000120549.17) in the exon at genomic coordinates chr10:24542692-24542770, KIAA1217 (ENSG00000120549.17) in the exon at genomic coordinates chr10:24542882-24544481, GIT2 in the exon at genomic coordinates chr12:109945259-109945349 (ENSG00000139436.20), MYL6 in the exon at genomic coordinates chr12:56160625-56160670 (ENSG00000092841.18), CTNND1 in the exon at genomic coordinates chr11:57789036-57789155 (ENSG00000198561.13), CTNND1 in the exon at genomic coordinates chr11:57791384-57791673 (ENSG00000198561.13), CTNND1 in the exon at genomic coordinates chr11:57791491-57791673 (ENSG00000198561.13), CD44 in the exon at genomic coordinates chr11:35208104-35208206 (ENSG00000026508.18), CD44 in the exon at genomic coordinates chr11:35211245-35211449 (ENSG00000026508.18), APBB2 in the exon at genomic coordinates chr4:40935076-40935139 (ENSG00000163697.16), SEC31A in the exon at genomic coordinates chr4:82830936-82830975 (ENSG00000138674.16), SEC31A in the exon at genomic coordinates chr4:82830936-82830975 (ENSG00000138674.16), SEC31A in the exon at genomic coordinates chr4:82842139-82842481 (ENSG00000138674.16) SEC31A in the exon at genomic coordinates chr4:82842184-82842481 (ENSG00000138674.16), SYTL2 in the exon at genomic coordinates chr11:85717482-85717530 (ENSG00000137501.17), MYOF in the exon at genomic coordinates chr10:93392916-93392955 (ENSG00000138119.16), NAV2 in the exon at genomic coordinates chr11:20051288-20051333 (ENSG00000166833.19), GAB1 in the exon at genomic coordinates chr4:143434087-143434168 (ENSG00000109458.8), PLEKHM2 in the exon at genomic coordinates chr1:15721328-15721388 (ENSG00000116786.12), CLSTN1 in the exon at genomic coordinates chr1:9737497-9737554 (ENSG00000171603.16), CLSTN1 in the exon at genomic coordinates chr1:9756480-9756510 (ENSG00000171603.16), GOLGA4 in the exon at genomic coordinates chr3:37361242-37361305 (ENSG00000144674.16), PBX1 in the exon at genomic coordinates chr1:164820071-164820184 (ENSG00000185630.18), FKBP14 in the exon at genomic coordinates chr7:30020212-30020304 (ENSG00000106080.10), and XPO1 in the exon at genomic coordinates chr2:61525269-61525333 (ENSG00000082898.16).

[0049] In particular, for the identification of CMS3, there are 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, and 11 exon skipping events, which are selected from the following: XPO1 in the exon at genomic coordinates chr2:61525269-61525333 (ENSG00000082898.16), C16orf13 in the exon at genomic coordinates chr16:635517-635774 (ENSG00000130731.15), PXN in the exon at genomic coordinates chr12:120224642-120224727 (ENSG00000089159.16), and ENAH in the exon at genomic coordinates chr1:225504990-225505053 (ENSG00000154380.17), AURKA in the exon at genomic coordinates chr20:56388686-56388784 (ENSG00000087586.17), EPB41L3 in the exon at genomic coordinates chr18:5394676-5394793 (ENSG00000082397.17), KALRN in the exon at genomic coordinates chr3:124637207-124637303 (ENSG00000160145.15), TPM1 in the exon at genomic coordinates chr15:63061197-63061273 (ENSG00000140416.20), KIAA1217 in the exon at genomic coordinates chr10:24542692-24542770 (ENSG00000120549.17), MYOF in the exon at genomic coordinates chr10:93392916-93392955 (ENSG00000138119.16), and PBX1 in the exon at genomic coordinates chr1:164820071-164820184 (ENSG00000185630.18).

[0050] Preferably, for the identification of CMS4, there are at least 1, preferably 5, more preferably 15, and especially at least 30, and especially at least 55 exon skip events, which are selected from the following: Myo9a (endg00000066933.15) in the exon at genomic coordinates CHR15:7195176-71951896, TPM1 (ENSG00000140416.20) in the exon at genomic coordinates chr15:63044026-63044152, TPM1 (ENSG00000140416.20) in the exon at genomic coordinates chr15:63061197-63061273, and TPM1 in the exon at genomic coordinates chr15:63061712-63061788. (ENSG00000140416.20), MYO6 in the exon at genomic coordinates chr6:75894813-75894840 (ENSG00000196586.13), MYO6 in the exon at genomic coordinates chr6:75898372-75898411 (ENSG00000196586.13), KIAA1217 in the exon at genomic coordinates chr10:24494499-24494604 (ENSG00000120549.17), KIAA1217 in the exon at genomic coordinates chr10:24542692-24542770 (ENSG00000120549.17), KIAA1217 in the exon at genomic coordinates chr10:24542882-24544481 (ENSG00000120549.17), GIT2 in the exon at genomic coordinates chr12:109945259-109945349 (ENSG00000139436.20), MYL6 in the exon at genomic coordinates chr12:56160625-56160670 (ENSG00000092841.18), BPTF in the exon at genomic coordinates chr17:67875555-67875744 (ENSG00000171634.17), MYH11 in the exon at genomic coordinates chr16:15708802-15708841 (ENSG00000133392.17), NUMB in the exon at genomic coordinates chr14:73279280-73279424 (ENSG00000133961.20) TEAD1 in the exon at genomic coordinates chr11:12878888-12878900 (ENSG00000187079.16), SPAG9 in the exon at genomic coordinates chr17:50975862-50975901 (ENSG00000008294.20), FAT1 in the exon at genomic coordinates chr4:186590367-186590403 (ENSG00000083857.13), TNS1 in the exon at genomic coordinates chr2:217830366-217830390 (ENSG00000079308.17), ESYT2 in the exon at genomic coordinates chr7:158752780-158752843 (ENSG00000117868.15), SLMAP in the exon at genomic coordinates chr3:57925844-57925934 (ENSG00000163681.14), AKAP9 in the exon at genomic coordinates chr7:91992157-91992211 (ENSG00000127914.16), RUBCN in the exon at genomic coordinates chr3:197691073-197691148 (ENSG00000145016.15), ATP2B4 in the exon at genomic coordinates chr1:203733222-203733400 (ENSG00000058668.14), LRRFIP2 in the exon at genomic coordinates chr3:37091466-37091538 (ENSG00000093167.17), TBC1D23 in the exon at genomic coordinates chr3:100311832-100311877 (ENSG00000036054.12), EHBP1 in the exon at genomic coordinates chr2:62987930-62988038 (ENSG00000115504.14), SLK in the exon at genomic coordinates chr10:104010815-104010908 (ENSG00000065613.13), WDFY3 in the exon at genomic coordinates chr4:84726860-84726911 (ENSG00000163625.15), SMARCC2 in the exon at genomic coordinates chr12:56164302-56164368 (ENSG00000139613.11) KIF13A in exon chr6:17771113-17771218 (ENSG00000137177.19), MPRIP in exon chr17:17180606-17180669 (ENSG00000133030.20), LRRFIP1 in exon chr2:237769625-237769818 (ENSG00000124831.18), NIN in exon chr14:50756491-50758630 (ENSG00000100503.23), RPS24 in exon chr10:78040203-78040225 (ENSG00000138326.19), ACTN1 in the exon at genomic coordinates chr14:68878988-68879069 (ENSG00000072110.13), CTNND1 in the exon at genomic coordinates chr11:57789036-57789155 (ENSG00000198561.13), CTNND1 in the exon at genomic coordinates chr11:57791384-57791673 (ENSG00000198561.13), CTNND1 in the exon at genomic coordinates chr11:57791491-57791673 (ENSG00000198561.13), CD44 in the exon at genomic coordinates chr11:35208104-35208206 (ENSG00000026508.18), CD44 in the exon at genomic coordinates chr11:35211245-35211449 (ENSG00000026508.18), APBB2 in the exon at genomic coordinates chr4:40935076-40935139 (ENSG00000163697.16), SEC31A in the exon at genomic coordinates chr4:82830936-82830975 (ENSG00000138674.16), SEC31A in the exon at genomic coordinates chr4:82830936-82830975 (ENSG00000138674.16), SEC31A in the exon at genomic coordinates chr4:82842139-82842481 (ENSG00000138674.16) SEC31A in the exon at genomic coordinates chr4:82842184-82842481 (ENSG00000138674.16), SYTL2 in the exon at genomic coordinates chr11:85717482-85717530 (ENSG00000137501.17), MYOF in the exon at genomic coordinates chr10:93392916-93392955 (ENSG00000138119.16), NAV2 in the exon at genomic coordinates chr11:20051288-20051333 (ENSG00000166833.19), GAB1 in the exon at genomic coordinates chr4:143434087-143434168 (ENSG00000109458.8), PLEKHM2 in the exon at genomic coordinates chr1:15721328-15721388 (ENSG00000116786.12), CLSTN1 in the exon at genomic coordinates chr1:9737497-9737554 (ENSG00000171603.16), CLSTN1 in the exon at genomic coordinates chr1:9756480-9756510 (ENSG00000171603.16), GOLGA4 in the exon at genomic coordinates chr3:37361242-37361305 (ENSG00000144674.16), PBX1 in the exon at genomic coordinates chr1:164820071-164820184 (ENSG00000185630.18), and FKBP14 in the exon at genomic coordinates chr7:30020212-30020304 (ENSG00000106080.10).

[0051] In particular, for the identification of CMS4, there are 1, 2, 3, 4, 5, 6, 7, and 8 exon skipping events, which are selected from the following: ENAH in the exon at genomic coordinates chr1:225504990-225505053 (ENSG00000154380.17), TPM1 in the exon at genomic coordinates chr15:63061197-63061273 (ENSG00000140416.20), MYO6 in the exon at genomic coordinates chr6:75898372-75898411 (ENSG00000196586.13), and SLMAP in the exon at genomic coordinates chr3:57925844-57925934. (ENSG00000163681.14), KIF13A in the exon at genomic coordinates chr6:17771113-17771218 (ENSG00000137177.19), MPRIP in the exon at genomic coordinates chr17:17180606-17180669 (ENSG00000133030.20), SEC31A in the exon at genomic coordinates chr4:82842184-82842481 (ENSG00000138674.16), and MYOF in the exon at genomic coordinates chr10:93392916-93392955 (ENSG00000138119.16).

[0052] The second type of exon skipping event exhibits a complex PSI pattern that distinguishes multiple classes simultaneously.

[0053] Preferably, in order to distinguish CMS2 and CMS3 from CMS1 and CMS4, there must be at least one, preferably at least five, more preferably at least ten, and especially at least 20, and especially at least 23, exon skipping events, which are selected from the following: FCGRT (ENSG00000104870.12) in the exon at genomic coordinates chr19:49521694-49521813, DOCK6 (ENSG00000130158.13) in the exon at genomic coordinates chr19:11229297-11229390, EXOC7 (ENSG00000182473.21) in the exon at genomic coordinates chr17:76090328-76090397, and BPTF in the exon at genomic coordinates chr17:67875555-67875744. (ENSG00000171634.17), PXN in the exon at genomic coordinates chr12:120224642-120224727 (ENSG00000089159.16), EXOC1 in the exon at genomic coordinates chr4:55888887-55888932 (ENSG00000090989.17), PLOD2 in the exon at genomic coordinates chr3:146077861-146077924 (ENSG00000152952.11), CD47 in the exon at genomic coordinates chr3:108049618-108049651 CD47 in the exon at genomic coordinates chr3:108050577-108050602 (ENSG00000196776.15), ARHGEF11 in the exon at genomic coordinates chr1:156938417-156938513 (ENSG00000132694.18), PBRM1 in the exon at genomic coordinates chr3:52558248-52558413 (ENSG00000163939.18), MAGI1 in the exon at genomic coordinates chr3:65448021-65448057 (ENSG00000151276.23), MBNL1 in the exon at genome coordinates chr3:152446703-152446757 (ENSG00000152601.17) TNC in the exon at genomic coordinates chr9:115064646-115064919 (ENSG00000041982.15), ENAH in the exon at genomic coordinates chr1:225504990-225505053 (ENSG00000154380.17), BAZ2B in the exon at genomic coordinates chr2:159397073-159397100 (ENSG00000123636.17), RAI14 in the exon at genomic coordinates chr5:34813573-34813660 (ENSG00000039560.13), FNIP1 in the exon at genomic coordinates chr5:131710577-131710661 (ENSG00000217128.11), MAP3K7 in the exon at genomic coordinates chr6:90544551-90544632 (ENSG00000135341.17), ERBIN in the exon at genomic coordinates chr5:66068876-66069020 (ENSG00000112851.14), SULF2 in the exon at genomic coordinates chr20:47659398-47659452 (ENSG00000196562.14), SORBS1 in the exon at genomic coordinates chr10:95414493-95414655 (ENSG00000095637.21), and SORBS1 (ENSG00000095637.21) in the exon at genomic coordinates chr10:95414493-95414862.

[0054] Preferably, in order to distinguish CMS2 and CMS4 from CMS1 and CMS3, there must be at least one, preferably at least five, more preferably at least eight, and especially at least eleven, exon skipping events, which are selected from the following: SRSF6 (ENSG00000124193.14) in the exon at genomic coordinates chr20:43459152-43459420, WASH3P (ENSG00000185596.16) in the exon at genomic coordinates chr15:101972595-101972694, OPA1 (ENSG00000198836.9) in the exon at genomic coordinates chr3:193626091-193626202, and GOLGB1 in the exon at genomic coordinates chr3:121719645-121719753. (ENSG00000173230.15), GOLGB1 in the exon at genomic coordinates chr3:121719645-121719768 (ENSG00000173230.15), APLP2 in the exon at genomic coordinates chr11:130137255-130137291 (ENSG00000084234.16), CPNE1 in the exon at genomic coordinates chr20:35658929-35659014 (ENSG00000214078.12), WIPF1 in the exon at genomic coordinates chr2:174597600-174597858 (ENSG00000115935.17), ATG9A in exon genomic coordinates chr2:219228433-219228482 (ENSG00000198925.11), NUBP2 in exon genomic coordinates chr16:1786737-1786955 (ENSG00000095906.16), and ANO1 in exon genomic coordinates chr11:70111125-70111191 (ENSG00000131620.17).

[0055] A preferred embodiment is a colorectal cancer subtype identifier, where alternative splicing is based on at least one exon skipping event in at least one, particularly at least 50, particularly at least 116 genes selected from the following: ITGAE (ENSG00000083457.11), CCNDBP1 (ENSG00000166946.13), CPT1B (ENSG00000205560.12), CDC16 (ENSG00000130177.14), PTPN6 (ENSG00000111679.16), ACCS (ENSG00000110455.13), EXOSC9 (ENSG00000123737.12), ZNF611 (ENSG00000213020.9), MRRF (ENSG00000148187.17), NUP153 (ENSG00000124789.11), WARS (ENSG00000140105.17), D2HGDH (ENSG00000180902.17), LUC7L (ENSG00000007392.16), EPB41 (ENSG00000159023.20), DGUOK (ENSG00000114956.19), MDM4 (ENSG00000198625.12), PTP4A2 (ENSG00000184007.19), MKNK2 (ENSG00000099875.14), CCDC112 (ENSG00000164221.12), FRYL (ENSG00000075539.14), CEP78 (ENSG00000148019.13), FNBP1 (ENSG00000187239.16), ECT2 (ENSG00000114346.13), ANKRD26 (ENSG00000107890.16), ZMIZ2 (ENSG00000122515.14), C6orf48 (ENSG00000204387.12), USPL1 (ENSG00000132952.11), RBM39 (ENSG00000131051.22), MIS12 (ENSG00000167842.15), AFMID (ENSG00000183077.15), MACROD1 (ENSG00000133315.10), FN1 (ENSG00000115414.18)、WBP1 (ENSG00000239779.6)、XPO1 (ENSG00000082898.16)、PTPN18 (ENSG00000072135.12)、ARHGAP27 (ENSG00000159314.11)、C16orf13 (ENSG00000130731.15)、FCGRT (ENSG00000104870.12)、DOCK6 (ENSG00000130158.13)、EXOC7 (ENSG00000182473.21)、BPTF (ENSG00000171634.17)、PXN (ENSG00000089159.16)、EXOC1 (ENSG00000090989.17)、PLOD2 (ENSG00000152952.11)、CD47 (ENSG00000196776.15)、ARHGEF11 (ENSG00000132694.18)、PBRM1 (ENSG00000163939.18)、MAGI1 (ENSG00000151276.23)、MBNL1 (ENSG00000152601.17)、TNC (ENSG00000041982.15)、ENAH (ENSG00000154380.17)、BAZ2B (ENSG00000123636.17)、RAI14 (ENSG00000039560.13)、FNIP1 (ENSG00000217128.11)、MAP3K7 (ENSG00000135341.17)、ERBIN (ENSG00000112851.14)、SULF2 (ENSG00000196562.14)、SORBS1 (ENSG00000095637.21)、SRSF6 (ENSG00000124193.14)、WASH3P (ENSG00000185596.16)、OPA1 (ENSG00000198836.9)、GOLGB1 (ENSG00000173230.15)、APLP2 (ENSG00000084234.16)、CPNE1 (ENSG00000214078.12)、WIPF1 (ENSG00000115935.17)、ATG9A (ENSG00000198925.11)、NUBP2 (ENSG00000095906.16)、ANO1 (ENSG00000131620.17)、AURKA (ENSG00000087586.17)、EPB41L3 (ENSG00000082397.17)、KALRN (ENSG00000160145.15)、ADAM15 (ENSG00000143537.13)、KRAS (ENSG00000133703.11)、SLC39A14 (ENSG00000104635.13)、MYO9A (ENSG00000066933.15)、TPM1 (ENSG00000140416.20)、MYO6 (ENSG00000196586.13)、KIAA1217 (ENSG00000120549.17)、GIT2 (ENSG00000139436.20)、MYL6 (ENSG00000092841.18)、MYH11 (ENSG00000133392.17)、NUMB (ENSG00000133961.20)、TEAD1 (ENSG00000187079.16)、SPAG9 (ENSG00000008294.20)、FAT1 (ENSG00000083857.13)、TNS1 (ENSG00000079308.17)、ESYT2 (ENSG00000117868.15)、SLMAP (ENSG00000163681.14)、AKAP9 (ENSG00000127914.16)、RUBCN (ENSG00000145016.15)、ATP2B4 (ENSG00000058668.14)、LRRFIP2 (ENSG00000093167.17)、TBC1D23 (ENSG00000036054.12)、EHBP1 (ENSG00000115504.14)、SLK (ENSG00000065613.13)、WDFY3 (ENSG00000163625.15)、SMARCC2 (ENSG00000139613.11)、KIF13A (ENSG00000137177.19)、MPRIP (ENSG00000133030.20)、LRRFIP1 (ENSG00000124831.18)、NIN (ENSG00000100503.23)、RPS24 (ENSG00000138326.19)、ACTN1 (ENSG00000072110.13)、CTNND1 (ENSG00000198561.13)、CD44 (ENSG00000026508.18), APBB2 (ENSG00000163697.16), SEC31A (ENSG00000138674.16), SYTL2 (ENSG00000137501.17), MYOF (ENSG00000138119.16), NAV2 (ENSG00000166833.19), GAB1 (ENSG00000109458.8), PLEKHM2 (ENSG00000116786.12), CLSTN1 (ENSG00000171603.16), GOLGA4 (ENSG00000144674.16), PBX1 (ENSG00000185630.18), and FKBP14 (ENSG00000106080.10).

[0056] Another embodiment of the present invention relates to a method for predicting the outcome of a subject with colorectal cancer using a PSI value based on the occurrence of at least one alternative splicing event, preferably at least one exon skipping event, and includes the following steps: a) Preferably a step of taking a sample from a tumor of a subject having cancer of epithelial cell origin; b) The process of determining the PSI value; c) A process of converting PSI values ​​to determine disease outcome indicators.

[0057] In step a), a sample is taken from the tumor of a subject who has cancer.

[0058] Suitable samples include tumor-derived tissue or cells from a subject with epithelial cell-derived cancer. Samples preferably include biopsy samples such as tumor biopsies, primary tissues, and metastatic tissues. In particular, specimens can be collected by needle biopsy, image-guided biopsy, surgical (excisional) biopsy, shear / punch biopsy, endoscopic biopsy, laparoscopic biopsy, and combinations thereof.

[0059] In step b) of the method of the present invention, the PSI value is determined.

[0060] The PSI value represents the exon inclusion rate and is calculated / determined by dividing the number of reads from the upstream and downstream splice junctions of the selective exon and / or the selective exon itself (called inclusion reads) by the total number of reads from all splice junctions in the splice region. This total includes reads from the splice junction connecting the upstream exon to the downstream exon (called skipping reads) and inclusion reads. The effective length of the isoform is used to normalize the inclusion and skipping reads, which is a mathematical conversion between sequencing read length and exon length.

[0061] For example, PSI values ​​can be estimated from RNA-Seq data using computational tools such as rMATS-turbo (https: / / github.com / Xinglab / rmats-turbo) or MISO (https: / / miso.readthedocs.io / en / fastmiso / ).

[0062] There are several methods for converting PSI values ​​to determine disease outcomes.

[0063] One option is to convert the calculated PSI values ​​into CMS probabilities through mathematical transformation. Preferably, the calculated PSI values ​​are converted into CMS probability estimates by mathematically transforming the dot product of the PSI values ​​and the respective weights obtained from the reference dataset. The transformation method is as follows: PSI and θ represent the vector representation of the PSI values ​​for the new sample and the weights associated with the consensus molecule subtype estimated from a penaltyed polynomial logistic regression model on the reference dataset, respectively.

number

number

number

[0064] Another possible method for converting PSI values ​​to CMS classifications is to measure the distance between the sample's PSI value and the median PSI for each CMS in the reference dataset. By ranking these distances, the CMS with the smallest distance can be assigned to the sample. If there are n PSI values, the CMSs are assigned as follows:

number

[0065] In step c) of the method of the present invention, the tumor is classified as CMS1, CMS2, CMS3, or CMS4 by converting the PSI value to determine the disease outcome index. Preferably, the conversion of the PSI value to determine the disease outcome index is used to determine whether the subject will receive treatment with antitumor therapy and / or follow-up of disease progression.

[0066] The identification of CMS1 is defined above.

[0067] The identification of CMS2 is defined above.

[0068] The identification of CMS3 is defined above.

[0069] The identification of CMS4 is defined above.

[0070] Preferably, alternative splicing is based on at least one exon skipping event in at least one, particularly at least 50, particularly at least 116, genes selected from the following: ITGAE (ENSG00000083457.11), CCNDBP1 (ENSG00000166946.13), CPT1B (ENSG00000205560.12), CDC16 (ENSG00000130177.14), PTPN6 (ENSG00000111679.16), ACCS (ENSG00000110455.13), EXOSC9 (ENSG00000123737.12), ZNF611 (ENSG00000213020.9), MRRF (ENSG00000148187.17), NUP153 (ENSG00000124789.11), WARS (ENSG00000140105.17), D2HGDH (ENSG00000180902.17), LUC7L (ENSG00000007392.16), EPB41 (ENSG00000159023.20), DGUOK (ENSG00000114956.19), MDM4 (ENSG00000198625.12), PTP4A2 (ENSG00000184007.19), MKNK2 (ENSG00000099875.14), CCDC112 (ENSG00000164221.12), FRYL (ENSG00000075539.14), CEP78 (ENSG00000148019.13), FNBP1 (ENSG00000187239.16), ECT2 (ENSG00000114346.13), ANKRD26 (ENSG00000107890.16), ZMIZ2 (ENSG00000122515.14), C6orf48 (ENSG00000204387.12), USPL1 (ENSG00000132952.11), RBM39 (ENSG00000131051.22), MIS12 (ENSG00000167842.15), AFMID (ENSG00000183077.15), MACROD1 (ENSG00000133315.10), FN1 (ENSG00000115414.18), WBP1 (ENSG00000239779.6)、XPO1 (ENSG00000082898.16)、PTPN18 (ENSG00000072135.12)、ARHGAP27 (ENSG00000159314.11)、C16orf13 (ENSG00000130731.15)、FCGRT (ENSG00000104870.12)、DOCK6 (ENSG00000130158.13)、EXOC7 (ENSG00000182473.21)、BPTF (ENSG00000171634.17)、PXN (ENSG00000089159.16)、EXOC1 (ENSG00000090989.17)、PLOD2 (ENSG00000152952.11)、CD47 (ENSG00000196776.15)、ARHGEF11 (ENSG00000132694.18)、PBRM1 (ENSG00000163939.18)、MAGI1 (ENSG00000151276.23)、MBNL1 (ENSG00000152601.17)、TNC (ENSG00000041982.15)、ENAH (ENSG00000154380.17)、BAZ2B (ENSG00000123636.17)、RAI14 (ENSG00000039560.13)、FNIP1 (ENSG00000217128.11)、MAP3K7 (ENSG00000135341.17)、ERBIN (ENSG00000112851.14)、SULF2 (ENSG00000196562.14)、SORBS1 (ENSG00000095637.21)、SRSF6 (ENSG00000124193.14)、WASH3P (ENSG00000185596.16)、OPA1 (ENSG00000198836.9)、GOLGB1 (ENSG00000173230.15)、APLP2 (ENSG00000084234.16)、CPNE1 (ENSG00000214078.12)、WIPF1 (ENSG00000115935.17)、ATG9A (ENSG00000198925.11)、NUBP2 (ENSG00000095906.16)、ANO1 (ENSG00000131620.17)、AURKA (ENSG00000087586.17)、EPB41L3 (ENSG00000082397.17)、 KALRN (ENSG00000160145.15)、ADAM15 (ENSG00000143537.13)、KRAS (ENSG00000133703.11)、SLC39A14 (ENSG00000104635.13)、MYO9A (ENSG00000066933.15)、 TPM1 (ENSG00000140416.20)、 MYO6 (ENSG00000196586.13)、KIAA1217 (ENSG00000120549.17)、GIT2 (ENSG00000139436.20)、MYL6 (ENSG00000092841.18)、MYH11 (ENSG00000133392.17)、NUMB (ENSG00000133961.20)、TEAD1 (ENSG00000187079.16)、SPAG9 (ENSG00000008294.20)、FAT1 (ENSG00000083857.13)、TNS1 (ENSG00000079308.17)、ESYT2 (ENSG00000117868.15)、SLMAP (ENSG00000163681.14)、AKAP9 (ENSG00000127914.16)、RUBCN (ENSG00000145016.15)、ATP2B4 (ENSG00000058668.14)、LRRFIP2 (ENSG00000093167.17)、TBC1D23 (ENSG00000036054.12)、EHBP1 (ENSG00000115504.14)、SLK (ENSG00000065613.13)、WDFY3 (ENSG00000163625.15)、SMARCC2 (ENSG00000139613.11)、KIF13A (ENSG00000137177.19)、MPRIP (ENSG00000133030.20)、LRRFIP1 (ENSG00000124831.18)、NIN (ENSG00000100503.23)、RPS24 (ENSG00000138326.19)、ACTN1 (ENSG00000072110.13)、CTNND1 (ENSG00000198561.13)、CD44 (ENSG00000026508.18), APBB2 (ENSG00000163697.16), SEC31A (ENSG00000138674.16), SYTL2 (ENSG00000137501.17), MYOF (ENSG00000138119.16), NAV2 (ENSG00000166833.19), GAB1 (ENSG00000109458.8), PLEKHM2 (ENSG00000116786.12), CLSTN1 (ENSG00000171603.16), GOLGA4 (ENSG00000144674.16), PBX1 (ENSG00000185630.18), and FKBP14 (ENSG00000106080.10).

[0071] The method of the present invention has the advantage that an evaluation scale can be established using a PSI value based on the occurrence of at least one alternative splicing event. This evaluation scale has the advantage that it can be used to determine whether a subject is likely to experience a poor outcome. In particular, the PSI value can be used to classify tumors as CMS1, CMS2, CMS3, or CMS4. Furthermore, it can be used to determine whether a subject should be treated with antitumor therapy and / or monitored for disease progression. This method allows for a very early stage of the disease. At this stage, markers used in state-of-the-art procedures (e.g., other tumor markers or the occurrence of metastasis) are usually not yet detectable.

[0072] A further embodiment of the present invention relates to a kit for predicting outcomes in colorectal cancer patients based on PSI values ​​derived from the occurrence of at least one alternative splicing event. The kit comprises means for determining the PSI value.

[0073] Preferably, alternative splicing is based on at least one exon skipping event, in particular at least one exon skipping event in at least one, in particular at least 50, in particular at least 116 genes selected from the following: ITGAE (ENSG00000083457.11), CCNDBP1 (ENSG00000166946.13), CPT1B (ENSG00000205560.12), CDC16 (ENSG00000130177.14), PTPN6 (ENSG00000111679.16), ACCS (ENSG00000110455.13), EXOSC9 (ENSG00000123737.12), ZNF611 (ENSG00000213020.9), MRRF (ENSG00000148187.17), NUP153 (ENSG00000124789.11), WARS (ENSG00000140105.17), D2HGDH (ENSG00000180902.17), LUC7L (ENSG00000007392.16), EPB41 (ENSG00000159023.20), DGUOK (ENSG00000114956.19), MDM4 (ENSG00000198625.12), PTP4A2 (ENSG00000184007.19), MKNK2 (ENSG00000099875.14), CCDC112 (ENSG00000164221.12), FRYL (ENSG00000075539.14), CEP78 (ENSG00000148019.13), FNBP1 (ENSG00000187239.16), ECT2 (ENSG00000114346.13), ANKRD26 (ENSG00000107890.16), ZMIZ2 (ENSG00000122515.14), C6orf48 (ENSG00000204387.12), USPL1 (ENSG00000132952.11), RBM39 (ENSG00000131051.22), MIS12 (ENSG00000167842.15), AFMID (ENSG00000183077.15), MACROD1 (ENSG00000133315.10), FN1 (ENSG00000115414.18)、WBP1 (ENSG00000239779.6)、XPO1 (ENSG00000082898.16)、PTPN18 (ENSG00000072135.12)、ARHGAP27 (ENSG00000159314.11)、 C16orf13 (ENSG00000130731.15)、FCGRT (ENSG00000104870.12)、DOCK6 (ENSG00000130158.13)、EXOC7 (ENSG00000182473.21)、BPTF (ENSG00000171634.17)、PXN (ENSG00000089159.16)、EXOC1 (ENSG00000090989.17)、PLOD2 (ENSG00000152952.11)、CD47 (ENSG00000196776.15)、ARHGEF11 (ENSG00000132694.18)、PBRM1 (ENSG00000163939.18)、MAGI1 (ENSG00000151276.23)、MBNL1 (ENSG00000152601.17)、TNC (ENSG00000041982.15)、ENAH (ENSG00000154380.17)、BAZ2B (ENSG00000123636.17)、RAI14 (ENSG00000039560.13)、FNIP1 (ENSG00000217128.11)、MAP3K7 (ENSG00000135341.17)、ERBIN(ENSG00000112851.14)、SULF2(ENSG00000196562.14)、SORBS1(ENSG00000095637.21)、SRSF6(ENSG00000124193.14)、WASH3P(ENSG00000185596.16)、OPA1(ENSG00000198836.9)、GOLGB1(ENSG00000173230.15)、APLP2(ENSG00000084234.16)、CPNE1(ENSG00000214078.12)、WIPF1(ENSG00000115935.17)、ATG9A(ENSG00000198925.11)、NUBP2 (ENSG00000095906.16)、ANO1 (ENSG00000131620.17)、AURKA (ENSG00000087586.17), EPB41L3 (ENSG00000082397.17), KALRN (ENSG00000160145.15), ADAM15 (ENSG00000143537.13), KRAS (ENSG00000133703.11), SLC39A14 (ENSG00000104635.13), MYO9A (ENSG00000066933.15), TPM1 (ENSG00000140416.20), MYO6 (ENSG00000196586.13), KIAA1217 (ENSG00000120549.17), GIT2 (ENSG00000139436.20), MYL6 (ENSG00000092841.18), MYH11 (ENSG00000133392.17), NUMB (ENSG00000133961.20), TEAD1 (ENSG00000187079.16), SPAG9 (ENSG00000008294.20), FAT1 (ENSG00000083857.13), TNS1 (ENSG00000079308.17), ESYT2 (ENSG00000117868.15), SLMAP (ENSG00000163681.14), AKAP9(ENSG00000127914.16), RUBCN(ENSG00000145016.15), ATP2B4(ENSG00000058668.14), LRR FIP2 (ENSG00000093167.17), TBC1D23 (ENSG00000036054.12), EHBP1 (ENSG00000115504.14), SLK. .

[0074] The identification of CMS1 is defined above.

[0075] The identification of CMS2 is defined above.

[0076] The identification of CMS3 is defined above.

[0077] The identification of CMS4 is defined above.

[0078] Another embodiment of the present invention involves using PSI values ​​based on the occurrence of alternative splicing events as an outcome marker for subjects with colorectal cancer. Preferably, the alternative splicing event is at least one exon skipping event.

[0079] The identification of CMS1 is defined above.

[0080] The identification of CMS2 is defined above.

[0081] The identification of CMS3 is defined above.

[0082] The identification of CMS4 is defined above.

[0083] Preferably, alternative splicing is based on at least one exon skipping event in at least one, particularly at least 50, particularly at least 116, genes selected from the following: ITGAE (ENSG00000083457.11), CCNDBP1 (ENSG00000166946.13), CPT1B (ENSG00000205560.12), CDC16 (ENSG00000130177.14), PTPN6 (ENSG00000111679.16), ACCS (ENSG00000110455.13), EXOSC9 (ENSG00000123737.12), ZNF611 (ENSG00000213020.9), MRRF (ENSG00000148187.17), NUP153 (ENSG00000124789.11), WARS (ENSG00000140105.17), D2HGDH (ENSG00000180902.17), LUC7L (ENSG00000007392.16), EPB41 (ENSG00000159023.20), DGUOK (ENSG00000114956.19), MDM4 (ENSG00000198625.12), PTP4A2 (ENSG00000184007.19), MKNK2 (ENSG00000099875.14), CCDC112 (ENSG00000164221.12), FRYL (ENSG00000075539.14), CEP78 (ENSG00000148019.13), FNBP1 (ENSG00000187239.16), ECT2 (ENSG00000114346.13), ANKRD26 (ENSG00000107890.16), ZMIZ2 (ENSG00000122515.14), C6orf48 (ENSG00000204387.12), USPL1 (ENSG00000132952.11), RBM39 (ENSG00000131051.22), MIS12 (ENSG00000167842.15), AFMID (ENSG00000183077.15), MACROD1 (ENSG00000133315.10), FN1 (ENSG00000115414.18), WBP1 (ENSG00000239779.6)、XPO1 (ENSG00000082898.16)、PTPN18 (ENSG00000072135.12)、ARHGAP27 (ENSG00000159314.11)、C16orf13 (ENSG00000130731.15)、FCGRT (ENSG00000104870.12)、DOCK6 (ENSG00000130158.13)、EXOC7 (ENSG00000182473.21)、BPTF (ENSG00000171634.17)、PXN (ENSG00000089159.16)、EXOC1 (ENSG00000090989.17)、PLOD2 (ENSG00000152952.11)、CD47 (ENSG00000196776.15)、ARHGEF11 (ENSG00000132694.18)、PBRM1 (ENSG00000163939.18)、MAGI1 (ENSG00000151276.23)、MBNL1 (ENSG00000152601.17)、TNC (ENSG00000041982.15)、ENAH (ENSG00000154380.17)、BAZ2B (ENSG00000123636.17)、RAI14 (ENSG00000039560.13)、FNIP1 (ENSG00000217128.11)、MAP3K7 (ENSG00000135341.17)、ERBIN (ENSG00000112851.14)、SULF2 (ENSG00000196562.14)、SORBS1 (ENSG00000095637.21)、SRSF6 (ENSG00000124193.14)、WASH3P (ENSG00000185596.16)、OPA1 (ENSG00000198836.9)、GOLGB1 (ENSG00000173230.15)、APLP2 (ENSG00000084234.16)、CPNE1 (ENSG00000214078.12)、WIPF1 (ENSG00000115935.17)、ATG9A (ENSG00000198925.11)、NUBP2 (ENSG00000095906.16)、ANO1 (ENSG00000131620.17)、AURKA (ENSG00000087586.17)、EPB41L3 (ENSG00000082397.17)、KALRN (ENSG00000160145.15)、ADAM15 (ENSG00000143537.13)、KRAS (ENSG00000133703.11)、SLC39A14 (ENSG00000104635.13)、MYO9A (ENSG00000066933.15)、TPM1 (ENSG00000140416.20)、MYO6 (ENSG00000196586.13)、KIAA1217 (ENSG00000120549.17)、GIT2 (ENSG00000139436.20)、MYL6 (ENSG00000092841.18)、MYH11 (ENSG00000133392.17)、NUMB (ENSG00000133961.20)、TEAD1 (ENSG00000187079.16)、SPAG9 (ENSG00000008294.20)、FAT1 (ENSG00000083857.13)、TNS1 (ENSG00000079308.17)、ESYT2 (ENSG00000117868.15)、SLMAP (ENSG00000163681.14)、 AKAP9 (ENSG00000127914.16)、RUBCN (ENSG00000145016.15)、ATP2B4 (ENSG00000058668.14)、LRRFIP2 (ENSG00000093167.17)、TBC1D23 (ENSG00000036054.12)、EHBP1 (ENSG00000115504.14)、SLK(ENSG00000065613.13)、WDFY3(ENSG00000163625.15)、SMARCC2(ENSG00000139613.11)、KIF13A(ENSG00000137177.19)、MPRIP(ENSG00000133030.20)、LRRFIP1(ENSG00000124831.18)、NIN(ENSG00000100503.23)、RPS24(ENSG00000138326.19)、ACTN1(ENSG00000072110.13)、CTNND1(ENSG00000198561.13)、CD44(ENSG00000026508.18)、APBB2 (ENSG00000163697.16) SEC31A (ENSG00000138674.16), SYTL2 (ENSG00000137501.17), MYOF (ENSG00000138119.16), NAV2 (ENSG00000166833.19), GAB1 (ENSG00000109458.8), PLEKHM2 (ENSG00000116786.12), CLSTN1 (ENSG00000171603.16), GOLGA4 (ENSG00000144674.16), PBX1 (ENSG00000185630.18), and FKBP14 (ENSG00000106080.10).

[0084] Another embodiment of the present invention is a method for treating a subject with colorectal cancer using PSI values ​​based on the occurrence of alternative splicing, and includes the following steps: d) Preferably a step of taking a sample from a tumor of a subject having cancer of epithelial cell origin; e) The process of determining the PSI value; f) A process of converting PSI values ​​to determine disease outcome indicators.

[0085] Preferably, the alternative splicing event is at least one exon skipping event.

[0086] The identification of CMS1 is defined above.

[0087] The identification of CMS2 is defined above.

[0088] The identification of CMS3 is defined above.

[0089] The identification of CMS4 is defined above.

[0090] Preferably, alternative splicing is based on at least one exon skipping event in at least one, particularly at least 50, particularly at least 116, genes selected from the following: ITGAE (ENSG00000083457.11), CCNDBP1 (ENSG00000166946.13), CPT1B (ENSG00000205560.12), CDC16 (ENSG00000130177.14), PTPN6 (ENSG00000111679.16), ACCS (ENSG00000110455.13), EXOSC9 (ENSG00000123737.12), ZNF611 (ENSG00000213020.9), MRRF (ENSG00000148187.17), NUP153 (ENSG00000124789.11), WARS (ENSG00000140105.17), D2HGDH (ENSG00000180902.17), LUC7L (ENSG00000007392.16), EPB41 (ENSG00000159023.20), DGUOK (ENSG00000114956.19), MDM4 (ENSG00000198625.12), PTP4A2 (ENSG00000184007.19), MKNK2 (ENSG00000099875.14), CCDC112 (ENSG00000164221.12), FRYL (ENSG00000075539.14), CEP78 (ENSG00000148019.13), FNBP1 (ENSG00000187239.16), ECT2 (ENSG00000114346.13), ANKRD26 (ENSG00000107890.16), ZMIZ2 (ENSG00000122515.14), C6orf48 (ENSG00000204387.12), USPL1 (ENSG00000132952.11), RBM39 (ENSG00000131051.22), MIS12 (ENSG00000167842.15), AFMID (ENSG00000183077.15), MACROD1 (ENSG00000133315.10), FN1 (ENSG00000115414.18), WBP1 (ENSG00000239779.6)、XPO1 (ENSG00000082898.16)、PTPN18 (ENSG00000072135.12)、 ARHGAP27 (ENSG00000159314.11)、C16orf13 (ENSG00000130731.15)、FCGRT (ENSG00000104870.12)、DOCK6 (ENSG00000130158.13)、EXOC7 (ENSG00000182473.21)、 BPTF (ENSG00000171634.17)、PXN (ENSG00000089159.16)、EXOC1 (ENSG00000090989.17)、PLOD2 (ENSG00000152952.11)、CD47 (ENSG00000196776.15)、ARHGEF11 (ENSG00000132694.18)、PBRM1 (ENSG00000163939.18)、MAGI1 (ENSG00000151276.23)、MBNL1 (ENSG00000152601.17)、TNC (ENSG00000041982.15)、ENAH (ENSG00000154380.17)、BAZ2B (ENSG00000123636.17)、RAI14 (ENSG00000039560.13)、FNIP1(ENSG00000217128.11)、MAP3K7(ENSG00000135341.17)、ERBIN(ENSG00000112851.14)、SULF2(ENSG00000196562.14)、SORBS1(ENSG00000095637.21)、SRSF6(ENSG00000124193.14)、WASH3P(ENSG00000185596.16)、OPA1(ENSG00000198836.9)、GOLGB1(ENSG00000173230.15)、APLP2(ENSG00000084234.16)、CPNE1(ENSG00000214078.12)、WIPF1 (ENSG00000115935.17)、ATG9A (ENSG00000198925.11)、NUBP2 (ENSG00000095906.16)、ANO1 (ENSG00000131620.17)、AURKA (ENSG00000087586.17)、EPB41L3 (ENSG00000082397.17)、KALRN (ENSG00000160145.15)、ADAM15 (ENSG00000143537.13)、KRAS (ENSG00000133703.11)、SLC39A14 (ENSG00000104635.13)、MYO9A (ENSG00000066933.15)、TPM1 (ENSG00000140416.20)、MYO6 (ENSG00000196586.13)、KIAA1217 (ENSG00000120549.17)、GIT2 (ENSG00000139436.20)、MYL6 (ENSG00000092841.18)、MYH11 (ENSG00000133392.17)、NUMB (ENSG00000133961.20)、TEAD1 (ENSG00000187079.16)、SPAG9 (ENSG00000008294.20)、FAT1 (ENSG00000083857.13)、TNS1 (ENSG00000079308.17)、ESYT2 (ENSG00000117868.15)、SLMAP (ENSG00000163681.14)、 AKAP9 (ENSG00000127914.16)、RUBCN (ENSG00000145016.15)、ATP2B4 (ENSG00000058668.14)、LRRFIP2 (ENSG00000093167.17)、TBC1D23 (ENSG00000036054.12)、EHBP1 (ENSG00000115504.14)、SLK (ENSG00000065613.13)、WDFY3 (ENSG00000163625.15)、SMARCC2 (ENSG00000139613.11)、KIF13A (ENSG00000137177.19)、MPRIP (ENSG00000133030.20)、LRRFIP1 (ENSG00000124831.18)、NIN (ENSG00000100503.23)、 RPS24 (ENSG00000138326.19)、ACTN1 (ENSG00000072110.13)、CTNND1 (ENSG00000198561.13)、CD44 (ENSG00000026508.18)、APBB2 (ENSG00000163697.16) SEC31A (ENSG00000138674.16), SYTL2 (ENSG00000137501.17), MYOF (ENSG00000138119.16), NAV2 (ENSG00000166833.19), GAB1 (ENSG00000109458.8), PLEKHM2 (ENSG00000116786.12), CLSTN1 (ENSG00000171603.16), GOLGA4 (ENSG00000144674.16), PBX1 (ENSG00000185630.18), and FKBP14 (ENSG00000106080.10).

[0091] The method of the present invention has the advantage that an evaluation scale can be established using a PSI value based on the occurrence of at least one alternative splicing event. This evaluation scale has the advantage that it can be used to determine whether a subject is likely to experience a poor outcome. In particular, the PSI value can be used to classify tumors as CMS1, CMS2, CMS3, or CMS4. Furthermore, it can be used to determine whether a subject should be treated with antitumor therapy and / or monitored for disease progression. This method enables a decision at a very early stage of the disease. At this stage, markers used in state-of-the-art procedures (e.g., other tumor markers or the occurrence of metastasis) are usually not yet detectable. Exemplary Embodiments

[0092] 1. A colorectal cancer subtype identifier that classifies tumors by PSI values ​​based on the occurrence of at least one alternative splicing event. 2. A colorectal cancer subtype identifier according to Embodiment 1, wherein the alternative splicing event is at least one exon skipping event. 3. A colorectal cancer subtype identifier according to any one of the embodiments described above, for classifying tumors as CMS1, CMS2, CMS3, or CMS4. 4. A colorectal cancer subtype identifier according to any one of Embodiments 1 to 3, wherein at least one exon skipping event selected from the following exists for the identification of CMS1: ITGAE in the exon at genomic coordinates chr17:3723287-3723383, CCNDBP1 in the exon at genomic coordinates chr15:43194080-43194137, CPT1B in the exon at genomic coordinates chr22:50573807-50573921, CDC16 in the exon at genomic coordinates chr13:114236644-114236699, PTPN6 in the exon at genomic coordinates chr12:6951458-6951520, and in the exon at genomic coordinates chr12:6951463-6951520 PTPN6, ACCS in the exon at genomic coordinates chr11:44073446-44073517, EXOSC9 in the exon at genomic coordinates chr4:121816143-121816194, EXOSC9 in the exon at genomic coordinates chr4:121816368-121816447, ZNF611 in the exon at genomic coordinates chr19:52707468-52707542, MRRF in the exon at genomic coordinates chr9:122285779-122285946, genomic coordinates chr6:17668974- NUP153 in exon 17669028, WARS in exon at genomic coordinates chr14:100375282-100375350, WARS in exon at genomic coordinates chr14:100375282-100375403, WARS in exon at genomic coordinates chr14:100375282-100375406, D2HGDH in exon at genomic coordinates chr2:241748864-241749929, LUC7L in exon at genomic coordinates chr16:228332-228402, genomic coordinates ch EPB41 in exons r1:29058588-29058645, DGUOK in exons chr2:73938909-73939022, MDM4 in exons chr1:204537429-204537497, MDM4 in exons chr1:204537458-204537497, PTP4A2 in exons chr1:31915894-31915987, MKNK2 in exons chr19:2039630-2039856,CCDC112 in exon chr5:115269702-115269798, FRYL in exon chr4:48593929-48594016, CEP78 in exon chr9:78265858-78265906, FNBP1 in exon chr9:129923843-129923996, FNBP1 in exon chr9:129923843-129924026, chr3:172752149- ECT2 in exon 172752472, ECT2 in exon genomic coordinates chr3:172755482-172755575, ANKRD26 in exon genomic coordinates chr10:27044156-27044190, ZMIZ2 in exon genomic coordinates chr7:44760150-44760228, C6orf48 in exon genomic coordinates chr6:31836423-31836517, and USPL1 in exon genomic coordinates chr13:30621072-30621239. 5. A colorectal cancer subtype identifier according to any one of Embodiments 1 to 3, wherein at least one exon skipping event selected from the following exists for the identification of CMS2: ZMIZ2 in exon chr7:44760150-44760228, C6orf48 in exon chr6:31836423-31836517, USPL1 in exon chr13:30621072-30621239, RBM39 in exon chr20:35740524-35740597, MIS12 in exon chr17:5488195-5488589, AFMID in exon chr17:78204655-78204741, MACROD1 in exon chr11:63998837-63998872, chr2:215380810-2 FN1 in exon 15381080, WBP1 in exon at genomic coordinates chr2:74459477-74459562, XPO1 in exon at genomic coordinates chr2:61525269-61525333, PTPN18 in exon at genomic coordinates chr2:130359232-130359309, ARHGAP27 in exon at genomic coordinates chr17:45404268-45404334, C16orf13 in exon at genomic coordinates chr16:635280-635340, C16orf13 in exon at genomic coordinates chr16:635517-635774, and C16orf13 in exon at genomic coordinates chr16:635611-635774. 6. A colorectal cancer subtype identifier according to any one of Embodiments 1 to 3, wherein at least one exon skipping event selected from the following exists for the identification of CMS3: C16orf13 in the exon at genomic coordinates chr16:635280-635340, C16orf13 in the exon at genomic coordinates chr16:635517-635774, C16orf13 in the exon at genomic coordinates chr16:635611-635774, AURKA in the exon at genomic coordinates chr20:56388686-56388784, EPB41L3 in the exon at genomic coordinates chr18:5394676-5394793, and in the exon at genomic coordinates chr3:124637207-124637303 KALRN, ADAM15 in the exon at genomic coordinates chr1:155061903-155061975, KRAS in the exon at genomic coordinates chr12:25215436-25215560, SLC39A14 in the exon at genomic coordinates chr8:22412036-22412206, MYO9A in the exon at genomic coordinates chr15:71951776-71951896, TPM1 in the exon at genomic coordinates chr15:63044026-63044152, genomic coordinates chr15:63061197-630 TPM1 in exon 61273, TPM1 in exon genomic coordinates chr15:63061712-63061788, MYO6 in exon genomic coordinates chr6:75894813-75894840, MYO6 in exon hr6:75898372-75898411, KIAA1217 in exon genomic coordinates chr10:24494499-24494604, KIAA1217 in exon genomic coordinates chr10:24542692-24542770, genomic coordinate chr10:2454 KIAA1217 in exon 2882-24544481, GIT2 in exon genomic coordinates chr12:109945259-109945349, MYL6 in exon genomic coordinates chr12:56160625-56160670, CTNND1 in exon genomic coordinates chr11:57789036-57789155, CTNND1 in exon genomic coordinates chr11:57791384-57791673, CTNND1 in exon genomic coordinates chr11:57791491-57791673,CD44 in the exon at genomic coordinates chr11:35211245-35211449, APBB2 in the exon at genomic coordinates chr4:40935076-40935139, SEC31A in the exon at genomic coordinates chr4:82830936-82830975, SEC31A in the exon at genomic coordinates chr4:82842139-82842481, SEC31A in the exon at genomic coordinates chr4:82842184-82842481, genomic coordinates chr11:8 SYTL2 in exons 5717482-85717530, MYOF in exons at genomic coordinates chr10:93392916-93392955, NAV2 in exons at genomic coordinates chr11:20051288-20051333, GAB1 in exons at genomic coordinates chr4:143434087-143434168, PLEKHM2 in exons at genomic coordinates chr1:15721328-15721388, CLSTN1 in exons at genomic coordinates chr1:9737497-9737554, and genomic coordinates chr1:9756480-9756510 CLSTN1 in the exon, GOLGA4 in the exon at genomic coordinates chr3:37361242-37361305, PBX1 in the exon at genomic coordinates chr1:164820071-164820184, FKBP14 in the exon at genomic coordinates chr7:30020212-30020304, and XPO1 in the exon at genomic coordinates chr2:61525269-61525333. 7. A colorectal cancer subtype identifier according to any one of Embodiments 1 to 3, wherein at least one exon skipping event selected from the following exists for the identification of CMS4: MYO9A in the exon at genomic coordinates chr15:71951776-71951896, TPM1 in the exon at genomic coordinates chr15:63044026-63044152, TPM1 in the exon at genomic coordinates chr15:63061197-63061273, TPM1 in the exon at genomic coordinates chr15:63061712-63061788, MYO6 in the exon at genomic coordinates chr6:75894813-75894840, and M in the exon at genomic coordinates chr6:75898372-75898411. YO6, KIAA1217 in the exon at genomic coordinates chr10:24494499-24494604, KIAA1217 in the exon at genomic coordinates chr10:24542692-24542770, KIAA1217 in the exon at genomic coordinates chr10:24542882-24544481, GIT2 in the exon at genomic coordinates chr12:109945259-109945349, MYL6 in the exon at genomic coordinates chr12:56160625-56160670, genomic coordinates chr17:67875555- BPTF in exon 67875744, MYH11 in exon at genomic coordinates chr16:15708802-15708841, NUMB in exon at genomic coordinates chr14:73279280-73279424, TEAD1 in exon at genomic coordinates chr11:12878888-12878900, SPAG9 in exon at genomic coordinates chr17:50975862-50975901, FAT1 in exon at genomic coordinates chr4:186590367-186590403, genomic coordinate chr2:21 TNS1 in exon 7830366-217830390, ESYT2 in exon genomic coordinates chr7:158752780-158752843, SLMAP in exon genomic coordinates chr3:57925844-57925934, AKAP9 in exon genomic coordinates chr7:91992157-91992211, RUBCN in exon genomic coordinates chr3:197691073-197691148, ATP2B4 in exon genomic coordinates chr1:203733222-203733400,LRRFIP2 in the exon at genomic coordinates chr3:37091466-37091538, TBC1D23 in the exon at genomic coordinates chr3:100311832-100311877, EHBP1 in the exon at genomic coordinates chr2:62987930-62988038, SLK in the exon at genomic coordinates chr10:104010815-104010908, WDFY3 in the exon at genomic coordinates chr4:84726860-84726911, and exon at genomic coordinates chr12:56164302-56164368 SMARCC2 in Son, KIF13A in exon at genomic coordinates chr6:17771113-17771218, MPRIP in exon at genomic coordinates chr17:17180606-17180669, LRRFIP1 in exon at genomic coordinates chr2:237769625-237769818, NIN in exon at genomic coordinates chr14:50756491-50758630, RPS24 in exon at genomic coordinates chr10:78040203-78040225, genomic coordinate chr14:68878988 ACTN1 in exon -68879069, CTNND1 in exon at genomic coordinates chr11:57789036-57789155, CTNND1 in exon at genomic coordinates chr11:57791384-57791673, CTNND1 in exon at genomic coordinates chr11:57791491-57791673, CD44 in exon at genomic coordinates chr11:35208104-35208206, CD44 in exon at genomic coordinates chr11:35211245-35211449, genomic coordinates chr APBB2 in exon 4:40935076-40935139, SEC31A in exon chr4:82830936-82830975, SEC31A in exon chr4:82830936-82830975, SEC31A in exon chr4:82842139-82842481, SEC31A in exon chr4:82842184-82842481, SYTL2 in exon chr11:85717482-85717530,MYOF in the exon at genomic coordinates chr10:93392916-93392955, NAV2 in the exon at genomic coordinates chr11:20051288-20051333, GAB1 in the exon at genomic coordinates chr4:143434087-143434168, PLEKHM2 in the exon at genomic coordinates chr1:15721328-15721388, and genomic coordinate chr1:973749 CLSTN1 in exon 7-9737554, CLSTN1 in exon genomic coordinates chr1:9756480-9756510, GOLGA4 in exon genomic coordinates chr3:37361242-37361305, PBX1 in exon genomic coordinates chr1:164820071-164820184, and FKBP14 in exon genomic coordinates chr7:30020212-30020304. 8. A colorectal cancer subtype identifier according to any one of the embodiments described above, wherein at least one exon skipping event selected from the following exists to distinguish CMS2 and CMS3 from CMS1 and CMS4: FCGRT in the exon at genomic coordinates chr19:49521694-49521813, DOCK6 in the exon at genomic coordinates chr19:11229297-11229390, EXOC7 in the exon at genomic coordinates chr17:76090328-76090397, BPTF in the exon at genomic coordinates chr17:67875555-67875744, PXN in the exon at genomic coordinates chr12:120224642-120224727, and in the exon at genomic coordinates chr4:55888887-55888932 EXOC1, PLOD2 in the exon at genomic coordinates chr3:146077861-146077924, CD47 in the exon at genomic coordinates chr3:108049618-108049651, CD47 in the exon at genomic coordinates chr3:108050577-108050602, ARHGEF11 in the exon at genomic coordinates chr1:156938417-156938513, PBRM1 in the exon at genomic coordinates chr3:52558248-52558413, genomic coordinates chr3:65448021-65 MAGI1 in exon 448057, MBNL1 in exon at genomic coordinates chr3:152446703-152446757, TNC in exon at genomic coordinates chr9:115064646-115064919, NAH in exon at genomic coordinates chr1:225504990-225505053, BAZ2B in exon at genomic coordinates chr2:159397073-159397100, RAI14 in exon at genomic coordinates chr5:34813573-34813660, genomic coordinate chr5:131 FNIP1 in exon 710577-131710661, MAP3K7 in exon genomic coordinates chr6:90544551-90544632, ERBIN in exon genomic coordinates chr5:66068876-66069020, SULF2 in exon genomic coordinates chr20:47659398-47659452, SORBS1 in exon genomic coordinates chr10:95414493-95414655, and ORBS1 in exon genomic coordinates chr10:95414493-95414862. 9. A colorectal cancer subtype identifier according to any one of the embodiments described above, wherein at least one exon skipping event selected from the following exists to distinguish CMS2 and CMS4 from CMS1 and CMS3: SRSF6 in the exon at genomic coordinates chr20:43459152-43459420, WASH3P in the exon at genomic coordinates chr15:101972595-101972694, OPA1 in the exon at genomic coordinates chr3:193626091-193626202, GOLGB1 in the exon at genomic coordinates chr3:121719645-121719753, GOLGB1 in the exon at genomic coordinates chr3:121719645-121719768, and genomic coordinate chr11:1301372 APLP2 in exon 55-130137291, CPNE1 in exon genomic coordinates chr20:35658929-35659014, WIPF1 in exon genomic coordinates chr2:174597600-174597858, ATG9A in exon genomic coordinates chr2:219228433-219228482, NUBP2 in exon genomic coordinates chr16:1786737-1786955, and ANO1 in exon genomic coordinates chr11:70111125-70111191. 10. A colorectal cancer subtype identifier according to any one of the embodiments described above, wherein the alternative splicing event is based on at least one exon skipping event in at least one gene selected from the following: ITGAE, CCNDBP1, CPT1B, CDC16, PTPN6, ACCS, EXOSC9, ZNF611, MRRF, NUP153, WARS, D2HGDH, LUC7L, EPB41, D GUOK, MDM4, PTP4A2, MKNK2, CCDC112, FRYL, CEP78, FNBP1, ECT2, ANKRD26, ZMIZ2, C6orf48, USPL1, RBM39, MI S12, AFMID, MACROD1, FN1, WBP1, XPO1, PTPN18, ARHGAP27, C16orf13, FCGRT, DOCK6, EXOC7, BPTF, PXN, EXOC1 , PLOD2, CD47, ARHGEF11, PBRM1, MAGI1, MBNL1, TNC, ENAH, BAZ2B, RAI14, FNIP1, MAP3K7, ERBIN, SULF2, SORB S1, SRSF6, WASH3P, OPA1, GOLGB1, APLP2, CPNE1, WIPF1, ATG9A, NUBP2, ANO1, AURKA, EPB41L3, KALRN, ADAM15 , KRAS, SLC39A14, MYO9A, TPM1, MYO6, KIAA1217, GIT2, MYL6, MYH11, NUMB, TEAD1, SPAG9, FAT1, TNS1, ESYT2, SLMAP, AKAP9, RUBCN, ATP2B4, LRRFIP2, TBC1D23, EHBP1, SLK, WDFY3, SMARCC2, KIF13A, MPRIP, LRRFIP1, NIN, RPS24, ACTN1, CTNND1, CD44, APBB2, SEC31A, SYTL2, MYOF, NAV2, GAB1, PLEKHM2, CLSTN1, GOLGA4, PBX1, and FKBP14. 11. A method for predicting the outcome of a subject with colorectal cancer using a PSI value based on the occurrence of at least one alternative splicing event, comprising the following steps: a) The process of taking a sample from a tumor of a subject who has cancer; b) The process of determining the PSI value; c) A process of converting PSI values ​​to determine disease outcome indicators. 12. A method according to Embodiment 11, wherein the alternative splicing event is at least one exon skipping event. 13. A method according to Embodiment 12, wherein at least one exon skipping event is at least one exon skipping event in at least one gene selected from the following: ITGAE, CCNDBP1, CPT1B, CDC16, PTPN6, ACCS, EXOSC9, ZNF611, MRRF, NUP153, WARS, D2HGDH, LUC7L, EPB41, D GUOK, MDM4, PTP4A2, MKNK2, CCDC112, FRYL, CEP78, FNBP1, ECT2, ANKRD26, ZMIZ2, C6orf48, USPL1, RBM39, M IS12, AFMID, MACROD1, FN1, WBP1, XPO1, PTPN18, ARHGAP27, C16orf13, FCGRT, DOCK6, EXOC7, BPTF, PXN, EX OC1, PLOD2, CD47, ARHGEF11, PBRM1, MAGI1, MBNL1, TNC, ENAH, BAZ2B, RAI14, FNIP1, MAP3K7, ERBIN, SULF2, SORBS1, SRSF6, WASH3P, OPA1, GOLGB1, APLP2, CPNE1, WIPF1, ATG9A, NUBP2, ANO1, AURKA, EPB41L3, KALRN, ADAM15, KRAS, SLC39A14, MYO9A, TPM1, MYO6, KIAA1217, GIT2, MYL6, MYH11, NUMB, TEAD1, SPAG9, FAT1, TNS1, ESYT2, SLMAP, AKAP9, RUBCN, ATP2B4, LRRFIP2, TBC1D23, EHBP1, SLK, WDFY3, SMARCC2, KIF13A, MPRIP, LRRFIP1, NIN, RPS24, ACTN1, CTNND1, CD44, APBB2, SEC31A, SYTL2, MYOF, NAV2, GAB1, PLEKHM2, CLSTN1, GOLGA4, PBX1, and FKBP14. 14. A method according to Embodiment 11, wherein the conversion of PSI values ​​for determining disease outcome indicators classifies tumors as CMS1, CMS2, CMS3, or CMS4. 15. A method according to Embodiment 11, wherein the conversion of PSI values ​​for determining a disease outcome index is used to determine whether a subject receives treatment with antitumor therapy and / or follow-up of disease progression. 16. A kit for predicting the outcome of a subject with colorectal cancer, comprising means for determining a PSI value, using a PSI value based on the occurrence of at least one alternative splicing event, preferably at least one exon skipping event, in at least one gene selected from the following genes: ITGAE, CCNDBP1, CPT1B, CDC16, PTPN6, ACCS, EXOSC9, ZNF611, MRRF, NUP153, WARS, D2HGDH, LUC7L, EP B41, DGUOK, MDM4, PTP4A2, MKNK2, CCDC112, FRYL, CEP78, FNBP1, ECT2, ANKRD26, ZMIZ2, C6orf48, USP L1, RBM39, MIS12, AFMID, MACROD1, FN1, WBP1, XPO1, PTPN18, ARHGAP27, C16orf13, FCGRT, DOCK6, EXO C7, BPTF, PXN, EXOC1, PLOD2, CD47, ARHGEF11, PBRM1, MAGI1, MBNL1, TNC, ENAH, BAZ2B, RAI14, FNIP1, MAP3K7, ERBIN, SULF2, SORBS1, SRSF6, WASH3P, OPA1, GOLGB1, APLP2, CPNE1, WIPF1, ATG9A, NUBP2, ANO1, AURKA, EPB41L3, KALRN, ADAM15, KRAS, SLC39A14, MYO9A, TPM1, MYO6, KIAA1217, GIT2, MYL6, MYH11, NUMB, TEAD1, SPAG9, FAT1, TNS1, ESYT2, SLMAP, AKAP9, RUBCN, ATP2B4, LRRFIP2, TBC1D23, EHBP1, SLK, WDFY3, SMARCC2, KIF13A, MPRIP, LRRFIP1, NIN, RPS24, ACTN1, CTNND1, CD44, APBB2, SEC31A, SYTL2, MYOF, NAV2, GAB1, PLEKHM2, CLSTN1, GOLGA4, PBX1, and FKBP14. 17. Use of at least one PSI value based on the occurrence of alternative splicing as an outcome marker in subjects with colorectal cancer. 18. A method for treating a subject with colorectal cancer using PSI values ​​based on the occurrence of alternative splicing, comprising the following steps: d) The process of taking a sample from a tumor of a subject who has cancer; e) A step of determining at least one PSI value; f) A process of converting PSI values ​​to determine disease outcome indicators. 19. A method according to Embodiment 18, wherein a tumor is classified as CMS1, CMS2, CMS3, or CMS4 by converting PSI values ​​for determining disease outcome indicators. 20. A method relating to Embodiment 11 or 18, wherein the subject is a human.

[0093] The present invention will be further described with reference to the following embodiments, but its scope will not be limited to the specific embodiments described. The present invention includes any non-exclusive combination of the described features, and particularly preferred features. Detailed Description of the Invention

[0094] CMS identifiers were constructed and validated using data from colorectal cancer patients, particularly with detectable alternative splicing events (AS) present in 675 human colorectal cancers (data obtained from Indivumed Inc / G GmbH, Indivumed cohort). CMS labels were generated for the entire cohort using two different expression-based classification indices: CMS Caller (Eide et al., Sci Rep. 2017;7(1):16618) and CMS Classifier (Guinney et al., Nat Med. 2015;21(11):1350-6). Unsupervised clustering was used to measure the strength of association between different categories of AS and CMS. Ground truth for CMS labels was obtained from gene-level quantified expression data to construct the classification indices. Feature selection was performed using bootstrap and L1-penalized estimation. Using the obtained feature space, a multiple logistic regression model was trained with CRCs from 300 patients in the Indivumed cohort. The model's performance was evaluated using undetected CRCs obtained from two independent sources. A colorectal cancer subtype identifier (CRCi) was developed based on 29 exon skipping events, accurately classifying undetected tumors (Indivumed AUC = 0.95, TCGA AUC = 0.93), and outperforming the expression-based CMS classification index. [Brief explanation of the drawing]

[0095] Figure 1: This figure shows exon skipping events that are strongly associated with the consensus molecular subtype (CMS) of colorectal cancer. (A) This figure shows the distribution of CMS labels identified by two independent expression-based methods in the Indivumed colorectal cancer cohort (n=429). (B) This figure shows the strength of association between clusters and CMSs that emerged from NMF-based consensus clustering of percent splice-in (PSI) values ​​from alternative splicing events. The strength of association is determined by Cramer's V (an index of effect size in the chi-squared independence test). (C) This figure shows the distribution of samples in NMF-based clusters ordered in relation to CMS (n=429).

[0096] Figure 2: This figure shows the performance of the colorectal cancer subtype identifier (CRCi), with the receiver operating curves showing the performance of CRCi in (A) a randomly selected trial cohort (Indivumed, n = 129) and (B) a validation cohort (TCGA, n = 99).

[0097] Figure 3: This figure shows that CRCi better reflects known molecular signals than expression-based methods in subtype classification of mismatched samples. (A) This shows the results of calling mismatched tumor samples by the expression-based closest CMS using two expression-based classification indices. (B) The heatmap of CMS-related molecular signals shows the -log10 transformed p-values ​​of competitive gene set tests in the consensus cohort. Black indicates downregulation, and white indicates upregulation. (C) The heatmap of CMS-related molecular signals shows the -log10 transformed p-values ​​of competitive gene set tests comparing a consensus subtype or a subtype of a disagreement cohort to all other consensus subtypes. (D) Cosine similarity is shown, calculated based on the converted p-values ​​of competitive gene set tests comparing specific subtypes of the consensus cohort and the discrepancy cohort with all other subtypes of the consensus cohort.

[0098] Figure 4: This figure shows the results of RT-PCR verification of the major exon skipping events underlying CRCi. The scatter plot shows the correlation strength of PSI values ​​estimated from RT-PCR (reverse transcription polymerase chain reaction) and RNA-Seq in tumor samples (n=16) from colorectal cancer patients, measured using the Pearson correlation coefficient.

[0099] Figure 5: (A) This figure shows the results of detecting major exon skipping events underlying CRCi by RT-PCR. Six major exon skipping events were detected using RNA samples extracted from 16 colorectal cancer specimens. Specimens 1-4, 5-8, 9-12, and 13-16 are classified as CMS1, CMS2, CMS3, and CMS4, respectively. The boxes indicate the number of exons contained in the amplicon, with skipped exons shown in white boxes and constitutive exons in black boxes. Two different primer sets were designed to evaluate the expression of these variants in order to detect TPM1 alternative splicing, which is characterized by mutually exclusive exon inclusion containing two isomorphic exons. OAT mRNA expression was used as a criterion for normalization between independent PCR reactions (OAT amplicons are shown as dotted boxes). (B) OAT mRNA expression was used as a normalization criterion between independent PCR reactions in TPM1 variant detection. The box plot shows OAT expression in tumors classified by CMS (n=429).

[0100] Figure 6: This figure shows that the PSI values ​​underlying CRCi correlate between human colorectal cancer samples and human colorectal cancer cell lines. (A) The scatter plot shows the correlation between the median PSI values ​​of 29 exon skipping events estimated by the CRCi model in colorectal tumors (n=429) and colorectal cancer cell lines (n=46). The strength of the correlation is measured by the Pearson correlation coefficient. (B) RT-PCR was performed on six major exon skipping events using RNA extracted from colorectal cancer cell lines. The Lovo cell line was classified as CMS1, the NCIH-508 cell line as CMS2, the HT-29 cell line as CMS3, and the NCIH-747 and HCT116 cell lines as CMS4.

Claims

1. A colorectal cancer subtype identifier that classifies tumors by PSI values ​​based on the occurrence of at least one alternative splicing event.

2. The colorectal cancer subtype identifier according to claim 1, wherein the alternative splicing event is at least one exon skipping event.

3. A colorectal cancer subtype identifier according to claim 1 or 2 for classifying tumors as CMS1, CMS2, CMS3, or CMS4.

4. A colorectal cancer subtype identifier according to any one of claims 1 to 3, wherein at least one exon skipping event selected from the following exists for the identification of CMS1: ITGAE in the exon at genomic coordinates chr17:3723287-3723383, CCNDBP1 in the exon at genomic coordinates chr15:43194080-43194137, CPT1B in the exon at genomic coordinates chr22:50573807-50573921, CDC16 in the exon at genomic coordinates chr13:114236644-114236699, PTPN6 in the exon at genomic coordinates hr12:6951458-6951520, and in the exon at genomic coordinates chr12:6951463-6951520 PTPN6, ACCS in the exon at genomic coordinates chr11:44073446-44073517, EXOSC9 in the exon at genomic coordinates chr4:121816143-121816194, EXOSC9 in the exon at genomic coordinates chr4:121816368-121816447, ZNF611 in the exon at genomic coordinates chr19:52707468-52707542, MRRF in the exon at genomic coordinates chr9:122285779-122285946, genomic coordinates chr6:17668974- NUP153 in exon 17669028, WARS in exon at genomic coordinates chr14:100375282-100375350, WARS in exon at genomic coordinates chr14:100375282-100375403, WARS in exon at genomic coordinates chr14:100375282-100375406, D2HGDH in exon at genomic coordinates chr2:241748864-241749929, LUC7L in exon at genomic coordinates chr16:228332-228402, genomic coordinates ch EPB41 in exons r1:29058588-29058645, DGUOK in exons chr2:73938909-73939022, MDM4 in exons chr1:204537429-204537497, MDM4 in exons chr1:204537458-204537497, PTP4A2 in exons chr1:31915894-31915987, MKNK2 in exons chr19:2039630-2039856,CCDC112 in exon chr5:115269702-115269798, FRYL in exon chr4:48593929-48594016, CEP78 in exon chr9:78265858-78265906, FNBP1 in exon chr9:129923843-129923996, FNBP1 in exon chr9:129923843-129924026, and chr3:172752149-1 ECT2 in exon 72752472, ECT2 in exon genomic coordinates chr3:172755482-172755575, ANKRD26 in exon genomic coordinates chr10:27044156-27044190, ZMIZ2 in exon genomic coordinates chr7:44760150-44760228, C6orf48 in exon genomic coordinates chr6:31836423-31836517, and USPL1 in exon genomic coordinates chr13:30621072-30621239.

5. A colorectal cancer subtype identifier according to any one of claims 1 to 3, wherein at least one exon skipping event selected from the following exists for the identification of CMS2: ZMIZ2 in the exon at genomic coordinates chr7:44760150-44760228, C6orf48 in the exon at genomic coordinates chr6:31836423-31836517, USPL1 in the exon at genomic coordinates chr13:30621072-30621239, RBM39 in the exon at genomic coordinates chr20:35740524-35740597, MIS12 in the exon at genomic coordinates chr17:5488195-5488589, AFMID in the exon at genomic coordinates chr17:78204655-78204741, MACROD1 in the exon at genomic coordinates chr11:63998837-63998872, Geno FN1 in the exon at genomic coordinates chr2:215380810-215381080, WBP1 in the exon at genomic coordinates chr2:74459477-74459562, XPO1 in the exon at genomic coordinates chr2:61525269-61525333, PTPN18 in the exon at genomic coordinates chr2:130359232-130359309, ARHGAP27 in the exon at genomic coordinates hr17:45404268-45404334, C16orf13 in the exon at genomic coordinates chr16:635280-635340, C16orf13 in the exon at genomic coordinates chr16:635517-635774, and genomic coordinates C16orf13 in exons of chr16:635611-635774.

6. A colorectal cancer subtype identifier according to any one of claims 1 to 3, wherein at least one exon skipping event selected from the following exists for the identification of CMS3: C16orf13 in the exon at genomic coordinates chr16:635280-635340, C16orf13 in the exon at genomic coordinates chr16:635517-635774, C16orf13 in the exon at genomic coordinates chr16:635611-635774, AURKA in the exon at genomic coordinates chr20:56388686-56388784, EPB41L3 in the exon at genomic coordinates chr18:5394676-5394793, and genomic coordinates chr3:124637207-1246373 KALRN in exon 03, ADAM15 in exon at genomic coordinates chr1:155061903-155061975, KRAS in exon at genomic coordinates chr12:25215436-25215560, SLC39A14 in exon at genomic coordinates chr8:22412036-22412206, MYO9A in exon at genomic coordinates chr15:71951776-71951896, TPM1 in exon at genomic coordinates chr15:63044026-63044152, genomic coordinates TPM1 in the exon chr15:63061197-63061273, TPM1 in the exon chr15:63061712-63061788, MYO6 in the exon chr6:75894813-75894840, MYO6 in the exon chr6:75898372-75898411, KIAA1217 in the exon chr10:24494499-24494604, KIAA1217 in the exon chr10:24542692-24542770, genome coordinates KIAA1217 in the exon chr10:24542882-24544481, GIT2 in the exon chr12:109945259-109945349, MYL6 in the exon chr12:56160625-56160670, CTNND1 in the exon chr11:57789036-57789155, CTNND1 in the exon chr11:57791384-57791673, CTNND1 in the exon chr11:57791491-57791673,CD44 in the exon at genomic coordinates chr11:35208104-35208206, CD44 in the exon at genomic coordinates chr11:35211245-35211449, APBB2 in the exon at genomic coordinates chr4:40935076-40935139, SEC31A in the exon at genomic coordinates chr4:82830936-82830975, genomic coordinates chr4:82830936-828 SEC31A in exon 30975, SEC31A in exon at genomic coordinates chr4:82842139-82842481, SEC31A in exon at genomic coordinates chr4:82842184-82842481, SYTL2 in exon at genomic coordinates chr11:85717482-85717530, MYOF in exon at genomic coordinates chr10:93392916-93392955, NAV2 in the exon at genomic coordinates chr11:20051288-20051333, GAB1 in the exon at genomic coordinates chr4:143434087-143434168, PLEKHM2 in the exon at genomic coordinates chr1:15721328-15721388, CLSTN1 in the exon at genomic coordinates chr1:9737497-9737554, and genomic coordinates chr1:9756480-9756 CLSTN1 in exon 510, GOLGA4 in exon genomic coordinates chr3:37361242-37361305, PBX1 in exon genomic coordinates chr1:164820071-164820184, FKBP14 in exon genomic coordinates chr7:30020212-30020304, and XPO1 in exon genomic coordinates chr2:61525269-61525333.

7. A colorectal cancer subtype identifier according to any one of claims 1 to 3, wherein at least one exon skipping event selected from the following exists for the identification of CMS4: MYO9A in the exon at genomic coordinates chr15:71951776-71951896, TPM1 in the exon at genomic coordinates chr15:63044026-63044152, TPM1 in the exon at genomic coordinates chr15:63061197-63061273, TPM1 in the exon at genomic coordinates chr15:63061712-63061788, MYO6 in the exon at genomic coordinates chr6:75894813-75894840, MYO6 in the exon at genomic coordinates chr6:75898372-75898411, and in the exon at genomic coordinates chr10:24494499-24494604 KIAA1217 in the exon at genomic coordinates chr10:24542692-24542770, KIAA1217 in the exon at genomic coordinates chr10:24542882-24544481, GIT2 in the exon at genomic coordinates chr12:109945259-109945349, MYL6 in the exon at genomic coordinates chr12:56160625-56160670, BPTF in the exon at genomic coordinates chr17:67875555-67875744, genomic coordinates ch MYH11 in exon r16:15708802-15708841, NUMB in exon chr14:73279280-73279424, TEAD1 in exon chr11:12878888-12878900, SPAG9 in exon chr17:50975862-50975901, chr4:186590367-186590403 FAT1 in the exon, TNS1 in the exon at genomic coordinates chr2:217830366-217830390, ESYT2 in the exon at genomic coordinates chr7:158752780-158752843, SLMAP in the exon at genomic coordinates chr3:57925844-57925934, AKAP9 in the exon at genomic coordinates chr7:91992157-91992211, RUBCN in the exon at genomic coordinates chr3:197691073-197691148, ATP2B4 in the exon at genomic coordinates chr1:203733222-203733400,LRRFIP2 in the exon at genomic coordinates chr3:37091466-37091538, TBC1D23 in the exon at genomic coordinates chr3:100311832-100311877, EHBP1 in the exon at genomic coordinates chr2:62987930-62988038, SLK in the exon at genomic coordinates chr10:104010815-104010908, WDFY3 in the exon at genomic coordinates chr4:84726860-84726911, and exon at genomic coordinates chr12:56164302-56164368 SMARCC2 in Son, KIF13A in exon at genomic coordinates chr6:17771113-17771218, MPRIP in exon at genomic coordinates chr17:17180606-17180669, LRRFIP1 in exon at genomic coordinates chr2:237769625-237769818, NIN in exon at genomic coordinates chr14:50756491-50758630, RPS24 in exon at genomic coordinates chr10:78040203-78040225, genomic coordinate chr14:68878988 ACTN1 in exon -68879069, CTNND1 in exon at genomic coordinates chr11:57789036-57789155, CTNND1 in exon at genomic coordinates chr11:57791384-57791673, CTNND1 in exon at genomic coordinates chr11:57791491-57791673, CD44 in exon at genomic coordinates chr11:35208104-35208206, CD44 in exon at genomic coordinates chr11:35211245-35211449, genomic coordinates chr APBB2 in exon 4:40935076-40935139, SEC31A in exon chr4:82830936-82830975, SEC31A in exon chr4:82830936-82830975, SEC31A in exon chr4:82842139-82842481, SEC31A in exon chr4:82842184-82842481, SYTL2 in exon chr11:85717482-85717530,MYOF in the exon at genomic coordinates chr10:93392916-93392955, NAV2 in the exon at genomic coordinates chr11:20051288-20051333, GAB1 in the exon at genomic coordinates chr4:143434087-143434168, PLEKHM2 in the exon at genomic coordinates chr1:15721328-15721388, and genomic coordinates chr1:9737497-973 CLSTN1 in exon 7554, CLSTN1 in exon genomic coordinates chr1:9756480-9756510, GOLGA4 in exon genomic coordinates chr3:37361242-37361305, PBX1 in exon genomic coordinates chr1:164820071-164820184, and FKBP14 in exon genomic coordinates chr7:30020212-30020304.

8. A colorectal cancer subtype identifier according to any one of claims 1 to 7, wherein at least one exon skipping event selected from the following exists to distinguish CMS2 and CMS3 from CMS1 and CMS4: FCGRT in the exon at genomic coordinates chr19:49521694-49521813, DOCK6 in the exon at genomic coordinates chr19:11229297-11229390, EXOC7 in the exon at genomic coordinates chr17:76090328-76090397, BPTF in the exon at genomic coordinates chr17:67875555-67875744, PXN in the exon at genomic coordinates chr12:120224642-120224727, and genomic coordinates chr4:55888887-558889 EXOC1 in 32 exons, PLOD2 in exon at genomic coordinates chr3:146077861-146077924, CD47 in exon at genomic coordinates chr3:108049618-108049651, CD47 in exon at genomic coordinates chr3:108050577-108050602, ARHGEF11 in exon at genomic coordinates chr1:156938417-156938513, PBRM1 in exon at genomic coordinates chr3:52558248-52558413, genome MAGI1 in the exon at coordinates chr3:65448021-65448057, MBNL1 in the exon at genomic coordinates chr3:152446703-152446757, TNC in the exon at genomic coordinates chr9:115064646-115064919, ENAH in the exon at genomic coordinates chr1:225504990-225505053, BAZ2B in the exon at genomic coordinates chr2:159397073-159397100, and genomic coordinates chr5:34813573-34813660 RAI14 in the exon, FNIP1 in the exon at genomic coordinates chr5:131710577-131710661, MAP3K7 in the exon at genomic coordinates chr6:90544551-90544632, ERBIN in the exon at genomic coordinates chr5:66068876-66069020, SULF2 in the exon at genomic coordinates chr20:47659398-47659452, SORBS1 in the exon at genomic coordinates chr10:95414493-95414655, and SORBS1 in the exon at genomic coordinates chr10:95414493-95414862.

9. A colorectal cancer subtype identifier according to any one of claims 1 to 8, wherein at least one exon skipping event selected from the following exists to distinguish CMS2 and CMS4 from CMS1 and CMS3: SRSF6 in the exon at genome coordinates chr20:43459152-43459420, WASH3P in the exon at genome coordinates chr15:101972595-101972694, OPA1 in the exon at genome coordinates chr3:193626091-193626202, GOLGB1 in the exon at genome coordinates chr3:121719645-121719753, GOLGB1 in the exon at genome coordinates chr3:121719645-121719768, APLP2 in the exon at genomic coordinates chr11:130137255-130137291, CPNE1 in the exon at genomic coordinates chr20:35658929-35659014, WIPF1 in the exon at genomic coordinates chr2:174597600-174597858, ATG9A in the exon at genomic coordinates chr2:219228433-219228482, NUBP2 in the exon at genomic coordinates chr16:1786737-1786955, and ANO1 in the exon at genomic coordinates chr11:70111125-70111191.

10. A colorectal cancer subtype identifier according to any one of claims 1 to 9, wherein the alternative splicing event is based on at least one exon skipping event in at least one gene selected from the following: ITGAE, CCNDBP1, CPT1B, CDC16, PTPN6, ACCS, EXOSC9, ZNF611, MRRF, NUP153, WARS, D2HGDH, LUC7L, EPB41, D GUOK, MDM4, PTP4A2, MKNK2, CCDC112, FRYL, CEP78, FNBP1, ECT2, ANKRD26, ZMIZ2, C6orf48, USPL1, RBM39, MI S12, AFMID, MACROD1, FN1, WBP1, XPO1, PTPN18, ARHGAP27, C16orf13, FCGRT, DOCK6, EXOC7, BPTF, PXN, EXOC1 , PLOD2, CD47, ARHGEF11, PBRM1, MAGI1, MBNL1, TNC, ENAH, BAZ2B, RAI14, FNIP1, MAP3K7, ERBIN, SULF2, SORB S1, SRSF6, WASH3P, OPA1, GOLGB1, APLP2, CPNE1, WIPF1, ATG9A, NUBP2, ANO1, AURKA, EPB41L3, KALRN, ADAM15 , KRAS, SLC39A14, MYO9A, TPM1, MYO6, KIAA1217, GIT2, MYL6, MYH11, NUMB, TEAD1, SPAG9, FAT1, TNS1, ESYT2, SLMAP, AKAP9, RUBCN, ATP2B4, LRRFIP2, TBC1D23, EHBP1, SLK, WDFY3, SMARCC2, KIF13A, MPRIP, LRRFIP1, NIN, RPS24, ACTN1, CTNND1, CD44, APBB2, SEC31A, SYTL2, MYOF, NAV2, GAB1, PLEKHM2, CLSTN1, GOLGA4, PBX1, and FKBP14.

11. A method for predicting the outcome of a subject with colorectal cancer using a PSI value based on the occurrence of at least one alternative splicing event, comprising the following steps: a) The process of taking a sample from a tumor of a subject who has cancer; b) The process of determining the PSI value; c) A process of converting PSI values ​​to determine disease outcome indicators.

12. A method according to claim 11, wherein the alternative splicing event is at least one exon skipping event, and in particular, the at least one exon skipping event is at least one exon skipping event in at least one gene selected from the following: ITGAE, CCNDBP1, CPT1B, CDC16, PTPN6, ACCS, EXOSC9, ZNF611, MRRF, NUP153, WARS, D2HGDH, LUC7L, EPB41, D GUOK, MDM4, PTP4A2, MKNK2, CCDC112, FRYL, CEP78, FNBP1, ECT2, ANKRD26, ZMIZ2, C6orf48, USPL1, RBM39, MI S12, AFMID, MACROD1, FN1, WBP1, XPO1, PTPN18, ARHGAP27, C16orf13, FCGRT, DOCK6, EXOC7, BPTF, PXN, EXOC1 , PLOD2, CD47, ARHGEF11, PBRM1, MAGI1, MBNL1, TNC, ENAH, BAZ2B, RAI14, FNIP1, MAP3K7, ERBIN, SULF2, SORB S1, SRSF6, WASH3P, OPA1, GOLGB1, APLP2, CPNE1, WIPF1, ATG9A, NUBP2, ANO1, AURKA, EPB41L3, KALRN, ADAM1 5, KRAS, SLC39A14, MYO9A, TPM1, MYO6, KIAA1217, GIT2, MYL6, MYH11, NUMB, TEAD1, SPAG9, FAT1, TNS1, ESYT2 SLMAP, AKAP9, RUBCN, ATP2B4, LRRFIP2, TBC1D23, EHBP1, SLK, WDFY3, SMARCC2, KIF13A, MPRIP, LRRFIP1, NIN, RPS24, ACTN1, CTNND1, CD44, APBB2, SEC31A, SYTL2, MYOF, NAV2, GAB1, PLEKHM2, CLSTN1, GOLGA4, PBX1, and FKBP14.

13. A method according to claim 11, wherein the conversion of PSI values ​​for determining disease outcome indicators classifies tumors as CMS1, CMS2, CMS3, or CMS4.

14. A method according to claim 11, wherein the conversion of PSI values ​​for determining a disease outcome index is used to determine whether a subject receives treatment with antitumor therapy and / or follow-up of disease progression.

15. A kit for predicting the outcome of a subject with colorectal cancer, comprising means for determining a PSI value, using a PSI value based on the occurrence of at least one alternative splicing event, preferably at least one exon skipping event, in at least one gene selected from the following genes: ITGAE, CCNDBP1, CPT1B, CDC16, PTPN6, ACCS, EXOSC9, ZNF611, MRRF, NUP153, WARS, D2HGDH, LUC7L, EPB41, DG UOK, MDM4, PTP4A2, MKNK2, CCDC112, FRYL, CEP78, FNBP1, ECT2, ANKRD26, ZMIZ2, C6orf48, USPL1, RBM39, MIS1 2, AFMID, MACROD1, FN1, WBP1, XPO1, PTPN18, ARHGAP27, C16orf13, FCGRT, DOCK6, EXOC7, BPTF, PXN, EXOC1, PL OD2, CD47, ARHGEF11, PBRM1, MAGI1, MBNL1, TNC, ENAH, BAZ2B, RAI14, FNIP1, MAP3K7, ERBIN, SULF2, SORBS1, S RSF6, WASH3P, OPA1, GOLGB1, APLP2, CPNE1, WIPF1, ATG9A, NUBP2, ANO1, AURKA, EPB41L3, KALRN, ADAM15, KRA S, SLC39A14, MYO9A, TPM1, MYO6, KIAA1217, GIT2, MYL6, MYH11, NUMB, TEAD1, SPAG9, FAT1, TNS1, ESYT2, SLMAP AKAP9, RUBCN, ATP2B4, LRRFIP2, TBC1D23, EHBP1, SLK, WDFY3, SMARCC2, KIF13A, MPRIP, LRRFIP1, NIN, RPS24, ACTN1, CTNND1, CD44, APBB2, SEC31A, SYTL2, MYOF, NAV2, GAB1, PLEKHM2, CLSTN1, GOLGA4, PBX1, and FKBP14.

16. Use of at least one PSI value based on the occurrence of alternative splicing as an outcome marker in subjects with colorectal cancer.

17. A method for treating a subject with colorectal cancer using PSI values ​​based on the occurrence of alternative splicing, comprising the following steps: d) The process of taking a sample from a tumor of a subject who has cancer; e) A step of determining at least one PSI value; f) A step of converting PSI values ​​to determine disease outcome indicators, wherein the conversion of PSI values ​​for determining disease outcome indicators is a step of classifying tumors as CMS1, CMS2, CMS3, or CMS4.

18. A method according to claim 11 or 17, wherein the subject is a human.

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