(19) *EP003677693A1* (11) EP 3 677 693 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 08.07.2020 Bulletin 2020/28 C12Q 1/6886 (2018.01) (21) Application number: 19150151.9 (22) Date of filing: 03.01.2019 (84) Designated Contracting States: (72) Inventors: AL AT BE BG CH CY CZ DE DK EE ES FI FR GB • TRONO, Didier GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO 1134 Vufflens-Chateau (CH) PL PT RO RS SE SI SK SM TR • SIMO RIUDALBAS, Laia Designated Extension States: 1004 Lausanne (CH) BA ME • PLANET LETSCHERT, Evarist Designated Validation States: 1113 ST-Saphorin-sur-Morges (CH) KH MA MD TN • DUC, Julien 1004 Lausanne (CH) (71) Applicants: • Ecole Polytechnique Federale De Lausanne (74) Representative: KATZAROV S.A. (EPFL) EPFL-TTO European Patent Attorneys 1015 Lausanne (CH) 12, Avenue des Morgines • Aarhus University 1213 Petit-Lancy (CH) 8000 Aarhus C (DK) (54) TRANSPOCHIMERIC GENE TRANCRIPTS (TCGTS) AS CANCER BIOMARKERS (57) The invention relates to methods for detecting or predicting the likelihood of a cancer in a subject as well as to compositions, pharmaceutical compositions and methods of treatment of cancer. EP 3 677 693 A1 Printed by Jouve, 75001 PARIS (FR) EP 3 677 693 A1 Description FIELD OF THE INVENTION 5 [0001] The invention relates to methods for detecting or predicting the likelihood of a cancer in a subject as well as to compositions, pharmaceutical compositions and methods of treatment of cancer. BACKGROUND OF THE INVENTION 10 [0002] Overall, current cancer drugs are inefficient in close to 75% of patients, and it is increasingly recognized that the future of cancer management lies in personalized approaches, whereby therapies are selected not just based on a tumor’s organ of origin but rather on a precise characterization of its molecular make-up and of the patient’s genetic background. New methods are needed to discover novel therapeutic targets as well as biomarkers for staging tumors, predicting their sensitivity to particular treatments, monitoring therapeutic responses and detecting relapses as early as 15 possible. [0003] A newly available signature for an in-depth characterization of healthy and tumoral human cells is the expression pattern of transposable elements (TEs). TEs, some 4.5 millions of which can be readily identified in the human genome, may account for up to 80% of our DNA, hence are the repository of a major part of our genetic heritage. TEs have been linked to cancer through different mechanisms, such as insertional activation of oncogenes and disruption of tumor 20 suppressor genes, chromosomal rearrangements, or TE-gene chimeric transcripts that activate oncogenes. Particular TEs have been found overexpressed in cancer but, due to a lack of proper technologies, a comprehensive characterization of their global expression patterns in human cancer is far from complete. The use of improved DNA and RNA sequencing (RNA-seq) methodology combined with in-house optimized bioinformatics pipelines has allowed us to define and start deciphering the TE-derived transcriptome in healthy and cancerous human tissues. 25 Colorectal cancer (CRC) has been the focus of our studies because its treatment is an unmet clinical need and its step- wise development has been extremely well documented. Furthermore, samples of tumor and healthy tissues are systematically obtained during surgery. CRC is the third most common cancer in men, the second in women and it represents almost a 10% of the annual global cancer incidence. 90% of new cases occur in people above 50 years and the risk of developing colon cancer is 3 times greater in cases 30 with a family history. The preventable risk factors of CRC include consumption of processed meat, consumption of alcoholic beverages, tobacco smoking, and excess of body fat, whereas consumption of dietary fiber and diary products and increased levels of physical activity decrease the risk. CRC screening can prevent the disease through the detection and removal of precancerous lesions and detect cancer at an early stage, when treatment is usually more successful. Current CRC therapy is based on surgery often accompanied by radio- and chemotherapy. Although advances in therapy 35 over the last 20 years have led to improvements in survival, 50% of all CRC patients die from metastatic disease. In this application, we aimed to fill this uncovered clinical need by exploiting the information yielded by the TEs in our genomes. SUMMARY OF THE INVENTION 40 [0004] This object has been achieved by providing a method for detecting and/or predicting the likelihood of a cancer in a subject, the method comprising detecting, directly or indirectly, in a biological sample of said subject, the presence or absence of at least one nucleic acid sequence comprising i) at least one transposable element (TE) a fragment or variant thereof, and 45 ii) a gene sequence, a fragment or variant thereof, wherein the at least one additional nucleic acid is selected from the group listed in Table 1 and/or Table 2, or a variant or fragment thereof. [0005] A further object of the present invention is to provide a method for classifying a cancer subject, the method 50 comprising i) detecting, directly or indirectly, in a biological sample of said subject, the presence or absence of at least one nucleic acid sequence comprising at least one transposable element (TE) or a fragment thereof, and a gene se- quence, a fragment or variant thereof, wherein the at least one additional nucleic acid is selected from the group 55 listed in Table 1 and/or Table 2 or a variant or fragment thereof and ii) classifying the cancer subject - as having a favourable prognosis based on the absence of the at least one nucleic acid sequence in the biological 2 EP 3 677 693 A1 sample or - as having a poor prognosis based on the presence of the at least one nucleic acid sequence in the biological. [0006] A further object of the present invention is to provide a method for classifying a cancer subject, the method 5 comprising 1) detecting, directly or indirectly, in a biological sample of said subject, the presence or absence of - at least one nucleic acid sequence correlating with an increase of survival (POSITIVE PROGNOSIS), said 10 nucleic acid sequence comprising at least one transposable element (TE) a fragment or variant thereof, and a gene sequence selected from the group comprising CSNK1G2, LPIN1 and YIPF4, a fragment or variant thereof, and - at least one nucleic acid sequence correlating with a decrease of survival (NEGATIVE PROGNOSIS), said nucleic acid sequence comprising at least one transposable element (TE) a fragment or variant thereof, and a 15 gene sequence selected from the group comprising POU5F1B, AHRR, AKAP7, MCUR1, PPP1R16A, SEC24B, SNED1 and ZNF558, a fragment or variant thereof, 2) scoring the number of nucleic acid sequences correlating with an increase of survival (POSITIVE PROGNOSIS) and the number of nucleic acid sequences correlating with a decrease of survival (NEGATIVE PROGNOSIS ), 20 wherein the - number of protective events > number of harmful events is indicative of increase in survival (POSITIVE PROG- NOSIS). - number of harmful events > number of protective events is indicative of decrease in survival (NEGATIVE PROG- 25 NOSIS). [0007] A further object of the present invention is to provide a method for classifying a cancer subject, the method comprising 30 1) detecting, directly or indirectly, in a biological sample of said subject, the presence or absence of - at least one nucleic acid sequence correlating with an increase of survival (POSITIVE PROGNOSIS), said nucleic acid sequence comprising at least one transposable element (TE) a fragment or variant thereof, and a gene sequence selected from the group comprising CAPN1, IGJ and TMEM131, a fragment or variant thereof, 35 and - at least one nucleic acid sequence correlating with a decrease of survival (NEGATIVE PROGNOSIS), said nucleic acid sequence comprising at least one transposable element (TE) a fragment or variant thereof, and a gene sequence selected from the group comprising ADTRP, CAST, CNOT1, DZIP1, PEX13 and TMEM248, a fragment or variant thereof, 40 2) scoring the number of nucleic acid sequences correlating with an increase of survival (POSITIVE PROGNOSIS) and the number of nucleic acid sequences correlating with a decrease of survival (NEGATIVE PROGNOSIS), wherein the 45 - number of protective events > number of harmful events is indicative of increase in survival (POSITIVE PROG- NOSIS), and - number of harmful events > number of protective events is indicative of decrease in survival (NEGATIVE PROG- NOSIS). 50 [0008] A further object of the present invention is to provide a method for staging a cancer in a subject, the method comprising measuring, directly or indirectly, in a biological sample of said subject, the level of expression or activity of at least one nucleic acid sequence and comparing said level of expression or activity to a control value or range, wherein said at least one nucleic acid sequence comprises 55 i) at least one transposable element (TE) a fragment or variant thereof, and ii) a gene sequence, a fragment or variant thereof, wherein the at least one additional nucleic acid is selected from the group listed in Table 1 and/or Table 2, or a variant 3 EP 3 677 693 A1 or fragment thereof.. FIGURES 5 [0009] Figure 1. (a) Representation of patients (rows) expressing TcGTs (columns) in the primary tumor (n=11 genes), which are either directly correlated with a decrease or an increase in survival. For every patient, the number of TcGTs correlating with an increase (protective) of survival minus the ones correlated with a decrease (harmful) of 10 survival is computed. This is shown in the bar at the left of the plot.