Abstract: Method for determining tissue positions using an array, which comprise location sequences, the location sequences bind to the tissue samples via ligands. The tissue section which allows localisation tags to be assigned to areas of the tissue comprising a single or plurality of cells or organelles, e.g. about two to ten cells. By triangulation of the localisation tags it is possible to assign a unique relative position in the tissue per cell or organelle.

Abstract: Disclosed are methods and systems for diagnosing, staging, stratifying, prognosing, and/or treating bladder cancer. In particular, the invention relates to methods and systems for classifying Stage T1 bladder cancer. The disclosed methods may include generating an mRNA expression profile for a sample of Stage T1 bladder cancer and classifying the sample based on the expression profile.

Abstract: The present invention relates to methods for predicting the survival time of patients suffering from a micro satellite unstable cancer. In particular, the present invention relates to a method for predicting the survival time of a patient suffering from a micro satellite unstable cancer comprising i) determining the expression level of at least one gene encoding for an immune checkpoint protein in a tumor tissue sample obtained from the patient, ii) comparing the expression level determined at step i) with a predetermined reference value and iii) concluding that the patient will have a long survival time when the level determined at step i) is lower than the predetermined reference value or concluding that the patient will have a short survival time when the level determined at step i) is higher than the predetermined reference value.

Abstract: The invention relates to method for treating cancer. Through whole exome sequencing, the inventors analyzed 47 MSI CRC and results were confirmed in a series of 53 MSI CRC. Negatively selected coding alterations in MSI CRC were further investigated for their functional role in CRC cell lines and survival impact in a cohort of 164 MSI CRC patients. Five coding negatively selected, MSI-related mutational events were demonstrated to have deleterious effects on tumor expansion, while they were associated with worse prognosis inpatients. The inventors investigated the functional consequences of the silencing of WNK1, HMGXB4, GART, and/or PRRC2C using siRNA and/or shRNA in CRC cell lines in vitro and in vivo using xenograft models. Their inactivation in CRC cells led to deleterious effects on apoptosis, proliferation and/or cell migration. The deleterious effects were greatly enhanced when several of the targets were concomitantly silenced.

Abstract: A method for predicting the risk of prostate cancer recurrence in a subject affected with prostate cancer, including: (a) providing a sample from the subject, (b) determining the TMPRSS/ERG fusion status of the sample, (c) if the sample is positive for TMPRSS/ERG fusion (Fus+), determining a molecular signature of the sample by measuring the expression level of at least 6 prostate cancer markers selected from the ANPEP, AZGP1, CHRNA2, COMP, KHDRBS3 and SFRP4, (d) comparing the molecular signature to a reference signature, and (e) assigning the subject to a risk group based on the correlation of the molecular signature with the reference signature, thereby predicting the risk of cancer recurrence in the subject.

Abstract: The present invention relates to methods for predicting the survival time of patients suffering from a micro satellite unstable cancer. In particular, the present invention relates to a method for predicting the survival time of a patient suffering from a micro satellite unstable cancer comprising i) determining the expression level of at least one gene encoding for an immune checkpoint protein in a tumor tissue sample obtained from the patient, ii) comparing the expression level determined at step i) with a predetermined reference value and iii) concluding that the patient will have a long survival time when the level determined at step i) is lower than the predetermined reference value or concluding that the patient will have a short survival time when the level determined at step i) is higher than the predetermined reference value.

Abstract: The present invention concerns a method to determine the gene expression profile on a sample previously obtained from a patient diagnosed for a liver tumor, comprising assaying the expression of a set of genes in this sample and determining the gene expression profile (signature). In a particular embodiment, said method enables to determine the grade of the liver tumor, such as hepatoblastoma (HB) or a hepatocellular carcinoma (HCC). The invention is also directed to kits comprising a plurality of pairs of primers or a plurality of probes specific for a set of genes, as well as to solid support or composition comprising a set of probes specific for a set of genes. These methods are useful to determine the grade of a liver tumor in a sample obtained from a patient, to determine the risk of developing metastasis and/or to define the therapeutic regimen to apply to a patient.

Abstract: The present invention relates to the technical field of liver diseases, their classification and diagnosis. It provides a new method for classifying a liver sample between non-hepatocellular sample; hepatocellular carcinoma (HCC) sample with further classification into one of subgroups G1 to G6; focal nodule dysplasia (FNH) sample; hepatocellular adenoma (HCA) sample with further classification into HNF1A mutated HCA, inflammatory HCA, ? catenin mutated HCA or other HCA sample; and other benign liver sample, based on determination in vitro of genes expression profiles and analysis of the expression profile using algorithms calibrated with reference samples. The invention also provides kits for the classification of liver samples, and methods of treatment of liver disease in a subject based on a preliminary classification of a liver sample of said subject.

Abstract: The present invention relates to the technical field of hepatocellular carcinoma (HCC) management, and more precisely to the prognosis of HCC aggressiveness and associated therapeutic decisions. The invention provides a new prognosis method of HCC aggressiveness, based on determination in vitro and analysis of an expression profile comprising genes TAF9, RAMP3, HN1, KRT19, and RAN. The invention also provides kits for the prognosis of HCC aggressiveness, and methods of treatment of HCC in a subject based on a preliminary prognosis of said subject HCC aggressiveness.

Abstract: Methodology for the in vitro classification and/or prognosis of hepatocellular carcinoma (HCC) from a HCC sample is based on the determination of the expression profile of particular gene combinations. For example, in one embodiment, a method comprises measuring the expression level in an HCC sample of at least 8 genes selected from the group consisting of: RAB1A, REG3A, NRAS, RAMP3, MERTK, PIR, EPHA1, LAMA3, G0S2, HN1, PAK2, AFP, CYP2C9, CDH2, HAMP, SAE1, ADH6, DCN, FLJ10159, ALDH1L1, IGF1, LECT2, SLC38A1, SPARCL1, CTNNA2, GLUL, LEF1, MATN2, MME, PFN2, SPINT2, TBX3, and FGFR2; b) calculating 6 subgroup distances from the expression profile; and c) classifying the HCC tumor in the subgroup for which the subgroup distance is the lowest, wherein the 6 subgroups G1, G2, G3, G4, G5, and G6 are defined by the presence (+) or absence (?) of their clinical and genetic features.

Abstract: Methodology for the in vitro classification and/or prognosis of hepatocellular carcinoma (HCC) from a HCC sample is based on the determination of the expression profile of particular gene combinations. For example, in one embodiment, a method comprises measuring the expression level in an HCC sample of at least 8 genes selected from the group consisting of: RAB1A, REG3A, NRAS, RAMP3, MERTK, PIR, EPHA1, LAMA3, G0S2, HN1, PAK2, AFP, CYP2C9, CDH2, HAMP, SAE1, ADH6, DCN, FLJ10159, ALDH1L1, IGF1, LECT2, SLC38A1, SPARCL1, CTNNA2, GLUL, LEF1, MATN2, MME, PFN2, SPINT2, TBX3, and FGFR2; b) calculating 6 subgroup distances from the expression profile; and c) classifying the HCC tumor in the subgroup for which the subgroup distance is the lowest, wherein the 6 subgroups G1, G2, G3, G4, G5, and G6 are defined by the presence (+) or absence (?) of their clinical and genetic features.

Abstract: The present invention concerns a method to determine the gene expression profile on a sample previously obtained from a patient diagnosed for a liver tumor, comprising assaying the expression of a set of genes in this sample and determining the gene expression profile (signature). In a particular embodiment, said method enables to determine the grade of liver tumor, such as hepatoblastoma (HB) or a hepatocellular carcinoma (HCC). The invention is also directed to kits comprising a plurality of pairs of primers or a plurality of probes specific for a set of genes, as well as to solid support or composition comprising a set of probes specific for a set of genes. These methods are useful to determine the grade of a liver tumor in sample obtained from a patient, to determine the risk of developing metastasis and/or to define the therapeutic regimen to apply to a patient.

Abstract: The present invention concerns a method to determine the gene expression profile on a sample previously obtained from a patient diagnosed for a liver tumor, comprising assaying the expression of a set of genes in this sample and determining the gene expression profile (signature). In a particular embodiment, said method enables to determine the grade of the liver tumor, such as hepatoblastoma (HB) or a hepatocellular carcinoma (HCC). The invention is also directed to kits comprising a plurality of pairs of primers or a plurality of probes specific for a set of genes, as well as to solid support or composition comprising a set of probes specific for a set of genes. These methods are useful to determine the grade of a liver tumor in a sample obtained from a patient, to determine the risk of developing metastasis and/or to define the therapeutic regimen to apply to a patient.

Abstract: Methodology for the in vitro classification and/or prognosis of hepatocellular carcinoma (HCC) from a HCC sample is based on the determination of the expression profile of particular gene combinations.