WO2018078142A1 - Moyens et procédés de détermination de l'efficacité du fluorouracile (5-fu) dans une thérapie du cancer colorectal (crc) - Google Patents

Moyens et procédés de détermination de l'efficacité du fluorouracile (5-fu) dans une thérapie du cancer colorectal (crc) Download PDF

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WO2018078142A1
WO2018078142A1 PCT/EP2017/077693 EP2017077693W WO2018078142A1 WO 2018078142 A1 WO2018078142 A1 WO 2018078142A1 EP 2017077693 W EP2017077693 W EP 2017077693W WO 2018078142 A1 WO2018078142 A1 WO 2018078142A1
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transcript variant
gene
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Marie-Laure Yaspo
Thomas Risch
Christine JANDRASITS
Hans Lehrach
Bodo Lange
Moritz SCHÜTTE
Jens Hoffmann
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MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V.
Alacris Theranostics Gmbh
Experimentelle Pharmakologie Und Onkologie (Epo) Berlin-Buch Gmbh
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Publication of WO2018078142A1 publication Critical patent/WO2018078142A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • the present invention relates to a method for determining the susceptibility/responsiveness of (a) cancer cell(s), preferably (a) colorectal cancer cell(s), to the treatment with fluorouracil (5- FU). Further, the present invention relates to a method of selecting (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) of colorectal cancer (CRC) with susceptibility to fluorouracil (5-FU).
  • an in vitro method for the identification of a responder for or a subject, preferably a human patient, suffering from colorectal cancer (CRC) to fluorouracil (5-FU) is disclosed.
  • the present invention also relates to a method of monitoring the efficacy of a treatment of the colorectal cancer (CRC) with fluorouracil (5-FU).
  • Colorectal cancer represents the third most frequent cancer worldwide. The five-year survival rate of patients diagnosed with metastasis is below 10%. CRC is refractory to most chemotherapeutic agents. Only fluorouracil (5-FU), irinotecan and oxaliplatin have documented responses in metastatic diseases such as colorectal cancer (CRC). Antibodies targeting the epidermal growth factor receptor (EGFR), such as cetuximab offer therapeutic options for a fraction of metastatic colorectal cancers (CRCs) but have failed in the adjuvant setting (Nelson V.M. et al. Gastrointest Oncol. 4(3) (2013), 245-252).
  • EGFR epidermal growth factor receptor
  • Regorafenib monotherapy a multi tyrosine kinase inhibitor
  • CRC metastatic colorectal cancer
  • Colorectal cancers are heterogeneous tumors which can be classified within characteristic molecular groups, however the clinical utility of this classification has not been demonstrated so far (De Sousa E.M.F. et al. Nat Med 19 (2013), 614-618; Guinney J. et al, Nat Med 21 (2015), 1350-1356; Marisa L. et al, PLoS Med 10 (2013), el 001453; Sadanandam A.
  • WO-A2 2008/115419 discloses marker gene(s) and methods for prediction of patient response to fluorouracil (5-FU); see also WO-A1 2007/147877; WO-A2 2006/015742; WO-A1 2009/114836; WO-A1 2014/197543; Ju et al, Journal of Cellular Biochemistry 116(2) (2015), 277-286.
  • fluorouracil 5-FU
  • the technical problem underlying the present invention is the provision of means and methods for the evaluation of (a) cell(s), in particular (a) cancer cell(s), (a) cancer tissue or tumor sample(s) obtained from a subject suffering from cancer, for their susceptibility or responsiveness to the treatment with an anti-cancer treatment.
  • the present invention relates to a method for determining the susceptibility or responsiveness of (a) cancer cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject/patient suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU), comprising (a) obtaining (a) cancer cell(s), cancer tissue(s) or tumor sample(s) from a subject/patient suffering from colorectal cancer (CRC); and (b) determining the expression level of one or more gene(s) as shown in Table 1 ( Figure 1), more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3) in said cancer cell(s), cancer tissue(s) or tumor sample(s), wherein said expression level is indicative of whether said subject/patient is responsive or susceptible to the treatment with fluorouracil (5-FU).
  • the present invention is based on the unexpected finding that by determining the expression of one or more gene(s) shown in Table 1 ( Figure 1), more preferably by determining the expression of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3) it is possible to predict in a reliable manner whether or not a subject suffering from colorectal cancer (CRC) is susceptible or responsive to a treatment with fluorouracil (5-FU).
  • the methods of the present invention allow the prediction or determination of the responsiveness or susceptibility to a treatment with fluorouracil (5-FU) in a subject suffering from colorectal cancer (CRC).
  • the present invention generally relates to a method of selecting (a) subject(s) suffering from colorectal cancer (CRC) with susceptibility or responsiveness to fluorouracil (5-FU), comprising the steps of: (a) determining the expression level of one or more gene(s) shown in Table 1 ( Figure 1), more preferably determining the expression level of (at least) 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 ( Figure 3) in (a) cancer cell(s), (a) cancer tissue(s) or tumor sample(s) of said subject; and (b) selecting (a) subject(s)/patient(s) suffering from colorectal cancer (CRC) characterized by a differential expression level of one or more gene(s) as shown in Table 1 ( Figure 1), more preferably characterized by a differential expression level of (at least) 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 ( Figure 3).
  • the method may additionally comprise (i) contacting (a) cancer cell(s), (a) cancer tissue(s) or tumor sample(s) with fluorouracil (5-FU) and (ii) evaluating susceptibility or responsiveness of said cancer cell(s), cancer tissue(s) or tumor sample(s) contacted with fluorouracil (5-FU). It is of note that steps (i) and (ii) may be performed prior to step (a) but also after step (a) or, optionally, after step (b). Said steps (i) and (ii) may in particular serve as further experimental proof that the selected subject(s) is responsive or susceptible in its viability to fluorouracil (5-FU).
  • cancer cell(s), cancer tissue(s) or tumor sample(s) is not only limited to (an) isolated cell(s), (a) tissue(s), (a) tumor sample(s) and cell culture(s) from a carcinogenic tissue, preferably from colorectal cancer (CRC), but also comprises the use of (a) sample(s), i.e. (a) biological, medical or pathological sample(s) that consist of fluids such as blood, ascites, tear fluid, pleura effusion, liquor, lymph, urine, cerebral fluid, faeces or hair roots and comprise such (a) carcinogenic cell(s) or parts, fragments of carcinogenic cell(s).
  • sample(s) i.e.
  • biological, medical or pathological sample(s) that consist of fluids such as blood, ascites, tear fluid, pleura effusion, liquor, lymph, urine, cerebral fluid, faeces or hair roots and comprise such (a) carcinogenic cell(s) or parts, fragments of carcinogenic cell(s).
  • the gist of the present invention lies in the fact that a method is provided that allows the determination of the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) for the anti-cancer or anti-proliferative treatment with fluorouracil (5-FU).
  • CRC colorectal cancer
  • 5-FU fluorouracil
  • the present invention provides a method for selecting (a) cell(s), (a) cancer tissue(s) or (a) tumor sample(s) which are susceptible or responsive to fluorouracil (5-FU), but also for an in vitro method for assessing a subject suffering from colorectal cancer (CRC), i.e.
  • the present invention provides not only the possibility to select (a) cell(s), (a) cancer tissue(s), (a) tumor sample(s) that are susceptible or responsive to the treatment with fluorouracil (5-FU) but also for a method to evaluate whether a given subject, preferably a subject suffering from colorectal cancer (CRC), is a responder or non-responder for a fluorouracil (5-FU) treatment.
  • a given subject preferably a subject suffering from colorectal cancer (CRC)
  • CRC colorectal cancer
  • the present invention relates to a method for determining the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU) which comprises the step of: (a) determining the expression level of one or more gene(s) as shown in Table 1 ( Figure 1), more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3).
  • the expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 is determined. Accordingly, in the herein described method for determining the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU) the activity or expression of one or more gene(s), preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes selected from the group consisting of DDX43 (NCBI accession no.: NM_018665; version no.: NM 018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.
  • DDX43 NCBI accession no.:
  • DDX43 NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:2223521478
  • FTL NCBI accession no.: NMJ300146; version no.: NM 000146.3; GL56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI:150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM_024501 ; version no.: NM_024501 ; version no.: NM_024501 ; version no.: NM_02450
  • the selection method of an fluorouracil (5-FU) responding cell or a responding subject, preferably a human patient comprises the steps of (a) obtaining (a) cell(s), (a) cancer tissue(s) or (a) tumor sample(s) from a subject/patient suffering from colorectal cancer (CRC); and (b) determining the expression level of one or more gene(s) as shown in Table 1 ( Figure 1), more preferably determining the expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3).
  • the method for the identification of a responder to fluorouracil (5-FU) or a subject sensitive to fluorouracil (5-FU) comprises the step of obtaining (a) cell(s), (a) cancer tissue(s) or (a) tumor sample(s) from a subject suffering from CRC with (a) differential gene expression of 1 , 2, 3,
  • the present invention relates in particular to a method for determining the responsiveness or susceptibility of colorectal tumor cell(s), colorectal cancer cell(s) or colorectal cancer tissue(s) obtained from a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU), said method comprises determining the gene expression level of one or more gene(s) shown in Table 1 ( Figure 1), preferably of 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 of the gene(s) as shown in Table 3 ( Figure 3), more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3) in said colorectal tumor cell(s), colorectal cancer cell(s) or colorectal cancer tissue(s), wherein said gene expression level is indicative of whether the cell is likely to respond or is responsive to the fluorouracil (5-FU) treatment.
  • Table 1 Figure 1
  • Figure 3 preferably of 1 , 2, 3, 4, 5, 6,
  • Such a determination may take place on (an) individual, isolated tumor cell(s). Such an evaluation may also be carried out on biological/medical/pathological sample(s), like body fluids, isolated body tissue samples and the like, wherein said sample(s) preferably comprise cells or cell debris to be analyzed.
  • Subject of the present invention is a method for diagnosing a subject/patient suffering from colorectal cancer (CRC) who is to be subjected to or is being subjected to an anti-cancer treatment or an anti-proliferative treatment to assess the responsiveness or susceptibility to fluorouracil (5-FU) prior, during and/or after fluorouracil (5-FU) treatment which comprises the steps of (a) detection of the gene expression level of one or more gene(s) as shown in Table 1 ( Figure 1), preferably of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 gene(s) as shown in Table 3 ( Figure 3), more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3) in (a) biological/medical/pathological sample(s) wherein the differential gene expression level of at least one of said gene(s) is (are) indicative for the responsiveness or susceptibility to fluorouracil (5-FU), treatment prior, during and/or after treatment with flu
  • the invention provides for the first time markers in (a) subject(s) suffering from colorectal cancer (CRC) which can predict the outcome of an anti-cancer/anti-proliferative treatment with fluorouracil (5-FU) prior to the treatment with fluorouracil (5-FU).
  • CRC colorectal cancer
  • the presence of (a) differential expression level of one or more gene(s) as shown in Table 1 ( Figure 1 ), Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes shown in Table 3 ( Figure 3) was identified as a marker/predictor for responsiveness or susceptibility to the treatment of a subject suffering from colorectal cancer (CRC) with 5 -fluorouracil (5-FU).
  • fluorouracil is to be administered to a subject/patient after determination of the expression level of one or more gene(s) as shown in Table 1 ( Figure 1 ), Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably after the determination of the expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes shown in Table 3 ( Figure 3) in a cancer cell(s), cancer tissue(s) or tumor sample(s) obtained from said patient/subject.
  • the present invention solves the above identified technical problem since, as documented herein below and in the appended Examples, it was surprisingly found that the presence of (a) differential gene expression of one or more gene(s) as shown in Table 1 ( Figure 1), Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes shown in Table 3 ( Figure 3) in (a) cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a patient suffering from colorectal cancer (CRC) is predictive for susceptibility of said cell(s), tissue(s) or tumor sample(s) to fluorouracil (5-FU).
  • 5-FU fluorouracil
  • marker for responsiveness to the treatment with fluorouracil (5-FU) and “predictor for responsiveness to the treatment with fluorouracil (5-FU)” can be used interchangeably and refer to (a) gene amplification(s) of said gene(s), whereby the amplification status is indicative for susceptibility or responsiveness to fluorouracil (5-FU).
  • the expression level(s) of the gene(s) as shown in Table 1 ( Figure 1), Table 2 ( Figure 2) , Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes shown in Table 3 ( Figure 3) are indicative for the susceptibility or responsiveness of (a) cell(s), (a) cancer tissue(s), or (a) tumor sample(s) to the treatment with fluorouracil (5- FU).
  • a differential gene expression level is defined herein as an expression level of the gene above or below a corresponding reference expression level.
  • the differential gene expression level is defined as the up- or down-regulation of the gene(s) as determined in (a sample from) a subject/patient (responder) compared to the gene expression level determined in (a sample from) a reference subject/patient (non- responder), wherein the extent of the difference between the gene expression determined in (a sample from) a subject/patient (responder) and said reference gene expression is indicative of whether said subject/patient is responsive or susceptible to the treatment with fluorouracil (5- FU).
  • the term "responder” refers in this context to a subject/patient which responds/is responsive/is susceptible to the treatment with fluorouracil (5-FU).
  • non-responder refers in this context to a subject/patient which does not respond/is not responsive/is not susceptible to the treatment with fluorouracil (5-FU). Whether a subject/patient is classified as a "responder” or “non-responder” with respect to the gene expression analysis can be evaluated by the skilled person on the basis of the read per kilo-base per million (RPKM) value/cut off value.
  • RPKM read per kilo-base per million
  • a “responder” may be, for example, a subject/patient characterized by (i) a down regulated expression level of the genes DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), GATAD1 (NCBI accession no.: NM_021167; version no.: NM_021167.4; GL392307002), MYRIP (NCBI accession no.: NM_015460; version no.: NM 015460.3; GI:548923902), PACS2 (NCBI accession no.: NMJH5197; version no.: NM_015197.3; GI:341604746
  • a patient i.e. responder
  • a "non-responder” may be a subject/patient characterized by (i) an up regulated expression level of the genes DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GL56682960), SUPT7L (NCBI accession no.: NM 014860; version no.: NM_014860.2; GL544186059), GATADl (NCBI accession no.: NM_021167; version no.: NM 021167.4; GI:392307002), MYRIP (NCBI accession no.: NM 015460; version no.: NM_015460.3; GI:548923902), PACS2 (NCBI accession no.: NM_015197; version no.: NM_015197.3; GI:3416047
  • the expression level(s) of the corresponding gene(s) is (are) disclosed in Table 1 , Table 2 and/or Table 3. Whether (a) gene(s) is (are) differentially expressed may be also determined by using bioinformatic approaches. A gene was considered differentially expressed if the False Discovery Rate (FDR) was equal or less than 1 % (0.01). Further, in the context of the present invention, different bioinformatic setups were used in order to identify differentially expressed genes. For setups a, b, c (as indicated in Table 1 ( Figure 1), Table 2 ( Figure 2) and/or Table 3 ( Figure 3)) the differential gene expression was determined by
  • the differential gene expression was determined by FDR ⁇ 0.01 and a dispersion of ⁇ 4.
  • a machine learning technique can be used in order to identify whether a patient is responsive or susceptible to the treatment with fluorouracil (5- FU).
  • a machine learning technique can be used in order to classify (a) sample(s) from a subject/patient into (a) patient(s)/subject(s) which is (are) responsive or susceptible to the treatment with fluorouracil (5-FU) (responder) or into (a) patient(s)/subject(s) which is (are) not responsive or susceptible to the treatment with fluorouracil (5-FU) (non-responder).
  • Machine learning techniques which can be used in the context of the present invention are known to the skilled person (see e.g., Larranaga, et al., Bioinform.
  • Machine learning involves training a machine learning algorithm to perform some task, rather than directly programming the system to perform the task.
  • the system observes some data, i.e. the expression level of one or more gen(s) as shown in Table 1 ( Figure 1), more preferably the expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes shown in Table 3 ( Figure 3) in (a) cancer cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject/patient suffering from CRC, and automatically determines some structure of the data for the classification whether or not said patient(s) is (are) responsive or susceptible to the treatment with fluorouracil (5-FU).
  • 5-FU fluorouracil
  • SVM support vector machine
  • Bennet et al SIGKDD Explorations 2, (2000); Cortes et al., Machine Learning 20 (1995), 273-297). Additional details related to SVM-based prediction are provided below in the appended Examples. Briefly, the data set was randomly split into two respective training and independent test cohorts. Then differentially expressed genes were identified using an appropriate statistical test and a learning model was trained on the identified genes. Using this approach, the algorithm would learn to discriminate between the respective subtypes based on gene expression data in the given patient cohort.
  • the present invention relates to a method for predicting the susceptibility or responsiveness of a patient/subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU) comprising the step of: a) determining the expression profile of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,
  • the present invention relates to a method for predicting the susceptibility or responsiveness of a patient/subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU) comprising the step of: a) determining the expression profile of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90,
  • three normalization procedures can be applied: 1 ) After the determination of the expression profile, a single sample is positioned against the cohort that was used to train the classifier. The training cohort is used to calculate the mean and standard deviation of expression for each gene in the expression profile. The gene expression values of the single sample are normalized by calculating a z-score per gene, which is based on the mean and standard deviation values that are derived from the training cohort. If the established expression values do not follow a normal distribution, the expression values of the training cohort and the single sample need to be log-transformed before the normalization by taking the logarithm (e.g. base two). 2) The expression values are normalized against one or more reference genes that are established with the expression profile.
  • the training of the SVM comprises the steps: a) establishing the gene expression profile comprising 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, 99, 100, 101 , 102, 103, 104
  • susceptibility to fluorouracil (5-FU) or responsiveness to the treatment with fluorouracil (5-FU) are well known in the art.
  • susceptibility to fluorouracil (5-FU)/responsiveness to fluorouracil (5-FU) may be determined by contacting (a) cell(s), (a) cancer tissue(s), or (a) tumor sample(s) which are obtained from a subject, preferably a human patient, suffering from colorectal cancer (CRC) with fluorouracil (5-FU) and determining the viability of said cell(s), cancer tissue(s), or tumor sample(s) after contacting.
  • CRC colorectal cancer
  • determining the susceptibility to fluorouracil (5-FU)/responsiveness to treatment with fluorouracil (5-FU) may, for example, comprise an evaluation/determination step, which may, for example, include determining the viability of the cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject, preferably a human patient, suffering from colorectal cancer (CRC) contacted with/exposed to fluorouracil (5- FU), or (a) colorectal cancer cell(s), colorectal cancer tissue(s) or colorectal tumor sample(s) treated with fluorouracil (5-FU).
  • an evaluation/determination step may, for example, include determining the viability of the cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject, preferably a human patient, suffering from colorectal cancer (CRC) contacted with/exposed to fluorouracil (5- FU), or (a) colorectal cancer cell(s), colorectal cancer tissue(
  • cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a subject suffering from colorectal cancer (CRC) described herein above may show decreased viability upon contacting/exposing/treating with fluorouracil (5- FU).
  • the cell(s), cancer tissue(s) or tumor sample(s) obtained from a subject suffering from colorectal cancer (CRC) may show an at least 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 % and, most preferably, 90 % reduction in viability compared to reference/control cell(s), cancer tissue(s) or tumor sample(s) obtained from a patient suffering from CRC not contacted/exposed/treated with fluorouracil (5-FU).
  • CRC colorectal cancer
  • the referece/control cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a subject suffering from colorectal cancer (CRC) will be identical to the cell(s), (a) cancer tissue(s) or tumor sample (s) to be tested as described herein with the only exception that the reference(s)/control(s) refer to (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) that are obtained from a subject not suffering from CRC or to (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) that are obtained from the subject suffering from CRC before treatment with fluorouracil (5-FU) has been started.
  • CRC colorectal cancer
  • cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a subject suffering from colorectal cancer (CRC) contacted/exposed/treated with fluorouracil (5-FU), and showing, for example, a decreased viability as described herein above, can be considered as being susceptible or responsible to fluorouracil (5-FU).
  • cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) as obtained from a subject suffering from CRC treated with fluorouracil (5-FU) showing such a decreased viability can be considered as responsive to treatment with fluorouracil (5-FU).
  • a reduction in viability may, for example, be reflected in a decreased proliferation, such as 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 % and, most preferably, 90 % reduction in proliferation compared to reference/control cancer cell(s), cancer tissue(s) or tumor sample(s) not contact ed/exposed/treated with fluorouracil (5-FU).
  • the decreased proliferation may be quantified, for example, by measuring the total cell volume, tissue volume or tumor sample volume using standard techniques.
  • the difference in proliferation between contacted/exposed/treated cancer cell(s), cancer tissue(s) or tumor sample(s) as obtained from a subject and corresponding references/controls as defined herein may, for example, be evaluated/determined by measuring the volume of the cancer cell(s), tissue(s) or cell culture(s) taking advantage of standard techniques.
  • Said evaluation/determination may be performed in various points in time, for example, 15 minutes, 30 minutes, 60 minutes, 2 hours, 5 hours, 18 hours, 24 hours, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 4 weeks and/or more than 4 weeks after contacting/treating said cell(s), tissue(s) or tumor sample(s) with fluorouracil (5-FU), or exposing said cell(s), tissue(s) or tumor sample(s) to fluorouracil (5-FU). It is envisaged herein that said evaluation/determination may be performed repeatedly, for example, at 15 minutes, 30 minutes and 60 minutes after said contacting/exposing/treating.
  • said cell(s), tissue(s) or tumor sample(s) may be contacted/treated not only once with fluorouracil (5-FU) or exposed to fluorouracil (5-FU) but several times (e.g. 2 times, 3 times, 5 times, 10 times or 20 times) under various conditions (e.g. same concentration of inhibitor, different concentration of inhibitor, inhibitor comprised in a composition with different stabilizers, diluents, and/or carriers and the like). Accordingly, said optionally repeated evaluation/determination may be performed after the final contacting/treating with or exposing to fluorouracil (5-FU) or in between said above-mentioned various contacting/exposing/treating steps.
  • a Patient Derived Xenograft from (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a patient suffering from said cancer, like in the present application CRC, are known to the skilled person (Fichtner et al., Eur J Cancer 40, 298-307 (2004)).
  • the Patient Derived Xenograft (PDX) models are known to be closely reflective of tumors or infections in patients for both their histopathological and genetic profiles.
  • PDX model(s) was (were) generated from tumor tissue of individuals of a population of 106 patients suffering from colorectal cancer, comprising 89 primary tumors (stages I to IV), and 27 metastases.
  • parameters of the subject may be considered as well for the prediction of the response, etc.
  • Such parameters in a multivariate model may include gender, age, histological evaluation, and other markers.
  • a Cox- Proportional-Hazard regression predicts the dependent variable based on one or more independent variables. These predictors can either be measured (as e.g. level of a biomarker) or categorical data.
  • diagnostic/predictive markers only give a certain degree of sensitivity and specificity, as also outlined herein.
  • different further parameters might be considered in order to increase both, like previous response of the patient to the drug.
  • the present invention provides (a) new and superior marker(s) for predicting the response as defined herein.
  • the presence of one or more further diagnostic/predictive markers for the response is detected in the sample.
  • fluorouracil (5-FU) and like expressions encompass within their meaning response to treatment comprising fluorouracil (5-FU) as monotherapy, or in combination with other agents, or as prodrugs, or together with local therapies such as surgery and radiation, or as adjuvant or neoadjuvant chemotherapy, or as part of a multimodal approach to the treatment of neoplastic disease.
  • the general mechanism of action of fluorouracil (5-FU) is its activity as a pyrimidine antimetabolite. In fluorouracil (5-FU), the smaller fluorine at position 5 allows the molecule to mimic uracil biochemically.
  • the fluorine-carbon bond is much tighter than that of C-H and prevents methylation of the 5 position of fluorouracil (5- FU) by thymidylate synthase.
  • the fluoropyrimidine locks the enzyme in an inhibited state and prevents the synthesis of thymidylate, a required DNA precursor.
  • a fluorouracil (5-FU) combination refers to a combination of fluorouracil (5-FU) and another agent.
  • a number of agents have been combined with fluorouracil (5-FU) to enhance the cytotoxic activity through biochemical modulation.
  • Addition of exogenous folate in the form of 5-formyl-tetrahydrofolate (leucovorin) sustains inhibition of thymidylate synthase.
  • Methotrexate by inhibiting purine synthesis and increasing cellular pools of certain substrates for reactivity with 5-FU, enhances the activation of fluorouracil (5-FU).
  • the combination of cisplatin and 5-FU increases the antitumor activity of fluorouracil (5-FU).
  • Oxaliplatin is commonly used with 5-FU and leucovorin for treating colorectal cancer, and it may inhibit catabolism of 5-FU, perhaps by inhibiting dihydropyrimidine dehydrogenase (the enzyme that is responsible for the catabolism of fluorouracil (5-FU)), and may also inhibit expression of thymidylate synthase.
  • the combination of fluorouracil (5-FU) and irinotecan, a topoisomerase-1 inhibitor is a treatment that combines fluorouracil (5-FU) with an agent that has a different mechanism of action.
  • Eniluracil which is an inactivator of dihydropyrimidine dehydrogenase, leads to another strategy for improving the efficacy of fluorouracil (5-FU).
  • fluorouracil (5-FU) prodrugs have been developed.
  • One is capecitabine (N4- pentoxycarbonyl-5'-deoxy-5-fluorcytidine). This orally administered agent is converted to 5'- deoxy-5-fluorcytidine by the ubiquitous enzyme cytidine deaminase.
  • the final step in its activation occurs when thymidine phosphorylase cleaves off the 5'-deoxy sugar, leaving intracellular fluorouracil (5-FU).
  • Capecitabine Xeloda(R)
  • Another fluoropyrimidine that acts as a prodrug for fluorouracil (5-FU) is ftorafur.
  • fluorouracil (5-FU) is applied intravenously.
  • fluorouracil (5-FU) and 5 -fluorouracil (5- FU) are used interchangeably.
  • HTS high throughput screening
  • cancer cell(s), cancer tissue(s) and/or tumor sample(s) obtained from a subject, preferably a patient, suffering from colorectal cancer (CRC) for responsiveness/sensitivity to fluorouracil (5-FU), preferably cetuximab.
  • CRC colorectal cancer
  • Suitable (HTS) approaches are known in the art. Screening-assays are usually performed in liquid phase, wherein for each cell/tissue/cell culture to be tested at least one reaction batch is made. Typical containers to be used are micro titer plates having, for example, 384, 1536, or 3456 wells (i.e. multiples of the "original" 96 reaction vessels).
  • Robotics, data processing and control software and sensitive detectors are further commonly used components of a HTS device.
  • robot system which transport micro titer plates from station to station for addition and mixing of sample(s) and reagent(s), incubating the reagents, and final readout (detection).
  • HTS can be used in the simultaneous preparation, incubation, and analysis of many plates.
  • the assay can be performed in a single reaction (which is usually preferred), may, however, also comprise washing and/or transfer steps. Detection can be performed taking advantage of radioactivity, luminescence or fluorescence, like fluorescence- resonance-energytransfer (FRET), fluorescence polarisation (FP) and the like.
  • FRET fluorescence- resonance-energytransfer
  • FP fluorescence polarisation
  • cellular assays and in vivo assays can be employed in HTS.
  • Cellular assays may also comprise cellular extracts, i.e. extracts from cells, tissues and the like.
  • preferred herein is the use of cancer cell(s), cancer tissue(s) or tumor sample(s) as biological sample (in particular a sample obtained from a patient/subject suffering or being prone to suffer from colorectal cancer (CRC)), whereas in vivo assays (wherein suitable animal models are employed, e.g. the herein described mouse models) are particularly useful in the validation/monitoring of the treatment with fluorouracil (5-FU).
  • follow up assays can be performed by re-running the experiment to collect further data on a narrowed set (e.g. samples found "positive" in the first assay), confirming and refining observations.
  • a suitable readout in animal (in vivo) models is tumor growth (or respectively the complete or partial inhibition of tumor growth and/or its remission).
  • the herein described HTS methods for the detection of copy number changes include but are not limited to sequencing technologies such as whole genome sequencing and exome sequencing.
  • the exome sequencing is a techniques for sequencing all the differentially expressed genes in a genome (known as the exome) of, e.g., extracts from cells, tissues or tumor samples obtained from a patient (responder and/or non- responder).
  • the meaning of the terms "cell(s)", “tissue(s)” and “sample(s)” is well known in the art and may, for example, be deduced from “The Cell” (Garland Publishing, Inc.).
  • the term “cell(s)” used herein refers to a single cell or a plurality of cells.
  • pluripotent cells means in the context of the present invention a group of cells comprising more than a single cell. Thereby, the cells out of said group of cells may have a similar function. Said cells may be connected cells and/or separate cells.
  • tissue in the context of the present invention particularly means a group of cells that perform a similar function.
  • sample refers in context of the present invention to all biological tissues, all fluids such as blood, ascites, sputum, broncho-alveolar lavage, tear fluid, pleura effusion, liquor, lymph, urine, cerebral fluid, faeces or hair roots. Tissues may be, e.g.
  • sample is collected from the patient or subjected to the method or treatment according to the invention.
  • a “tumor sample” is a sample of the tumor to be treated. Such sample may be for example taken from an excised tumor, for example, tumor tissue retrieved by surgery.
  • the cell(s), tissue(s) or tumor sample(s) to be selected comprise/are derived from or are (a) tumor cell(s), preferably (a) colorectal cancer cell(s).
  • the tumor cell(s) may, for example, be obtained from a biopsy, in particular a biopsy/biopsies from a patient/subject suffering from or being prone to suffering from colorectal cancer (CRC). It is preferred herein that said subject is a human.
  • the cancer cell(s) may be obtained from a biopsy, in particular a biopsy/biopsies from a patient/subject suffering from colorectal cancer (CRC)".
  • said tumor sample(s) or cancer cell(s) may be obtained from any biological source/organism, particularly any biological source/organism, suffering from or being prone to suffer from colorectal cancer (CRC).
  • the (tumor) cell(s) or (cancer) cell to be contacted is (are) obtained/derived from a subject, preferably a patient, suffering from colorectal cancer (CRC).
  • said tumor/cancer cell(s) may be (are) derived from an animal or mammal.
  • the meaning of the terms "animal” or “mammal” is well known in the art and can, for example, be deduced from Wehner und Gehring (1995; Thieme Verlag).
  • Non-limiting examples for mammals are even-toed ungulates such as sheep, cattle and pig, odd-toed angulates such as horses as well as carnivores such as cats and dogs.
  • DNA samples are derived from organisms that are economically, agronomically or scientifically important.
  • Scientifically or experimentally important organisms include, but are not limited to, mice, rats, rabbits, guinea pigs and pigs.
  • the tumor cell(s) may also be obtained carnivores such as cats or dogs or, for example, from primates which comprise dogs, cates, lemurs, monkeys and apes.
  • the meaning of the terms "dogs”, “cats”, “primate”, “lemur”, “monkey” and “ape” is known and may, for example, be deduced by an artisan from Wehner und Gehring (1995, Thieme Verlag).
  • the tumor or cancer cell(s) is (are) most preferably derived from a human being suffering from the above-mentioned colorectal cancer.
  • particular useful cells in particular tumor or cancer cells, are, accordingly, human cells. These cells can be obtained from e.g. biopsies or from biological samples but the term "cell” also relates to in vitro cultured cells.
  • the present invention relates to an in vitro method for the identification of a responder to fluorouracil (5-FU) or a subject sensitive to fluorouracil (5-FU), said method comprising the following steps:
  • an expression of at least one of said genes is indicative for a responding subject or is indicative for a sensitivity of said patient to fluorouracil (5-FU).
  • the present invention relates to a method for the identification of a responder to fluorouracil (5-FU) or a subject sensitive to fluorouracil (5-FU), said method comprising determining the gene expression of one or more gene(s) as shown in Table 1 ( Figure 1), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2), whereby an expression of at least one of said genes is indicative for a responding subject or is indicative for a sensitivity of said patient to fluorouracil (5-FU).
  • the present invention also relates to a method of monitoring the efficacy of a fluorouracil (5- FU) treatment of colorectal cancer (CRC) in a subject suffering from said disease comprising the steps of:
  • sample(s) may, for example, be obtained by (a) biopsy (biopsies).
  • said sample is obtained from a subject/patient suffering from colorectal cancer (CRC).
  • said sample is obtained from (a) tumor(s) and, accordingly, is (a) tumor cell(s) or (a) tumor tissue(s).
  • tumor sample(s) may be obtained from subjects/patients suffering from colorectal cancer (CRC).
  • Particularly preferred is the use of one or more gene(s) as shown in Table 1 ( Figure 1), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13 or 14 genes shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2) as marker gene(s).
  • the gene expression/amplification status of at least one additional gene selected from the group of FOS (NCBI accession no.: NM 005252; version no.: NM_005252.3; GL254750707) and S100A2 (NCBI accession no.: NM_005978; version no.: NM_005978.3; GI:45269153) (as shown in Table 2 ( Figure 2)) is assessed or determined.
  • Exemplarily combination which may be determined in this context are FOS (NCBI accession no.: NM_005252; version no.: NM_005252.3; GI:254750707) and one, or more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as selected from the group consisiting iDDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NMJ314860; version no
  • NCBI accession no.: NM_005978; version no.: NM_005978.3; GL45269153 (as shown in Table 2) and one, or more preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as selected from the group consisiting of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM _004367.5; GI: 150417991 (transcript variant 1 ); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: DDX43 (NCBI accession no.:
  • FOS NCBI accession no.: NM_005252; version no.: NM 005252.3; GL254750707) and S100A2 (NCBI accession no.: NM_005978; version no.: NM_005978.3; GL45269153) and one, or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as selected from the group consisiting of DDX43 (NCBI accession no.: NM 018665; version no.: NM 018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NMJD04367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos
  • “Expression” refers to transcription and translation occurring within a host cell.
  • the level of expression of a DNA molecule in a host cell may be determined on the basis of either the amount of corresponding mRNA that is present within the cell or the amount of the protein encoded by the respective gene produced by the host cells. Further detail for the term “ • expression” within the context of the present invention can be obtained via a review of Sambrook et al. (2012), A Laboratory Manual, Fourth Edition, ISBN 978-1 -9361 13-41-5.
  • the expression of said gene(s) is determined by determining RNA levels of the respective gene(s) or protein level(s) encoded by the respective gene(s).
  • the present invention has been exemplified by using the expression determination through determination of mRNA levels using RNA sequencing techniques. The skilled person will however acknowledge that the method may likewise be performed using different techniques and detection methods suited for determining the expression level of genes.
  • Methods for determining the expression level of a gene on the nucleic acid level, i.e. on RNA levels are known by those skilled in the art and include hybridization-based, PCR-based and sequencing-based methods, including next generation sequencing (NGS). Such methods are generally known by those skilled in the art.
  • the methods may be applied to detect the expression of one or more certain genes.
  • hybridization probes and/or primers are used to detect and/or amplify a certain nucleic acid sequence. It will be understood by the skilled person that it may be desirable to reverse transcribe the mRNA prior to detection. Reverse transcription using Reverse-Transcriptase is also commonly known (see inter alia Sambrook et al. (2012), A Laboratory Manual, Fourth Edition, ISBN 978-1-936113-41 -5). Likewise there are kits and assays available allowing sequencing the entire genome or transcriptome. It may hence be preferred to sequence the entire transcriptome of a sample in order to gain information about the entire transcription levels. The assessment of certain expression levels, e.g.
  • RNAseq libraries may be prepared to include modifications preserving strand-specific information (Parkhomchuk D, et al., Nucleic Acids Res. 37(18) (2009), el23). Sequencing of the so generated libraries may be performed by common methods.
  • RNAseq libraries either prepared using TruSeq RNA Sample Prep Kit v2 (Illumina, set A: RS-122-2001 ; set B: RS-122-2002) with modifications preserving strand- specific information or using TruSeq Stranded mRNA Sample Prep Kit (Illumina, set A: RS- 122-2101 ; set B: RS- 122-2102).
  • TruSeq Stranded mRNA Sample Prep Kit Illumina, set A: RS- 122-2101 ; set B: RS- 122-2102.
  • Ribo-ZeroTM Magnetic Gold Kit Epicentre, MRZG 12324
  • Sequencing (2 51 bp) was performed on HiSeq 2000/2500 instruments with v3 chemistry. In the context of the present invention the use of those kits and assays is preferred.
  • Oligonucleotide primers and probes having the desired sequence may be prepared using any suitable method, such as, for example, the phosphotriester and phosphodiester methods or automated embodiments thereof.
  • diethylophosphoramidites are used as starting materials and may be synthesized (see Beaucage et al, Tetrahedron Letters, 22 (1981), 1859-1862).
  • One method for synthesizing oligonucleotides on a modified solid support is described in US Bl 4,458,006. It is also possible to use a primer which has been isolated from a biological source (such as a restriction endonuclease digestion).
  • Preferred primers or hybridization probes have a length of from about 15-100, more preferably about 20-50, most preferably about 20-40 bases.
  • RNA reads may be first aligned to the sequences of a database to identify the gene(s). Such alignment may be for example performed against hgl9 (Kent et al, Genome Res. 12(6) (2002), 996-1006; Kent et al, Nature. 409(6822) (2001), 860-921 ) using BWA (Li et al, Bioinformatics 25 (2009), 1754-1760) and SAMtools (Li et al, Bioinformatics 25 (2009), 2078-2079). Mapped reads may be annotated, e.g. using Ensembl v70.
  • Gene expression levels may then be quantified by detecting the relative amount of an RNA of a certain gene, e.g. using reads per kilobase of exon model per million mapped reads (RPKM) as a measure (see Mortazavi A. et al, Nat Methods.5(7) (2008), 621-628).
  • RPKM per million mapped reads
  • RNA levels for example mRNA levels
  • the expression level of said gene(s) is determined by determining RNA levels by a method selected from the group consisting of hybridization based methods, PCR based methods, real-time-PCR, microarray methods, and RNA sequencing (RNAseq).
  • the expression level may, for example, be detected, assessed or evaluated by an in situ hybridization method, an in situ sequencing method, comparative genomic hybridisation and single-nucleotide polymorphism arrays.
  • exemplary in situ hybridisations are, inter alia, fluorescent in situ hybridisation (FISH), chromogenic in situ hybridisation (CISH) and silver in situ hybridisation (SISH).
  • FISH fluorescent in situ hybridisation
  • CISH chromogenic in situ hybridisation
  • SISH silver in situ hybridisation
  • the expression level of said gene(s) can be determined by the assessment, determination, detection or evaluation of the RNA levels by a method selected from the group consisting of hybridization based methods, PCR based methods, real-time-PCR, microarray methods and RNA sequencing.
  • the expression level may be determined by determining in the sample the amount of protein encoded by the gene. This may be performed using common techniques known by those skilled in the art. These techniques include immunoassays. Suitable immunoassays may be selected from the group of immunoprecipitation, enzyme immunoassay (EIA), enzyme-linked immunosorbent assays (ELISA), radioimmunoassay (RIA), fluorescent immunoassay, a cytometric bead array (CBA), a chemiluminescent assay, an agglutination assay, nephelometric assay, turbidimetric assay, a Western Blot, a competitive immunoassay, a non-competitive immunoassay, a homogeneous immunoassay a heterogeneous immunoassay, a bioassay and a reporter assay such as a luciferase assay.
  • the immunoassay is an enzyme linked immunosorbent assay (ELISA)
  • the present invention also relates to a method of diagnosing (colorectal cancer (CRC)) in a subject/patient suspected of suffering from colorectal cancer or suspected of being prone to suffering from colorectal cancer (CRC) comprising the steps of a) determining in a cell or tumor sample obtained from said subject/patient the gene expression or protein level of one or more gene(s) as shown in Table 1 ( Figure 1), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2); and b) comparing the expression or activity of said at least one marker gene determined in a) with a reference gene expression level of said one or more gene(s) determined in (a sample from) a reference/control subject/patient (healthy subject), wherein said colorectal cancer (CRC
  • the present invention also relates to a method of monitoring the efficacy of a treatment of a colorectal cancer (CRC) in a subject/patient suffering from said cancer or being prone to suffer from said cancer comprising the steps of a) determining in (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from said subject/patient the gene expression or protein level of one or more gene(s) as shown in Table 1 ( Figure 1), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2), and/or preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2); and b) comparing the gene expression or protein level of said one or more marker gene(s) determined in a) with a reference gene expression or protein level of said one or more marker gene(s), optionally determined in (a sample from)
  • the term "gene expression level" as used herein refers to the gene expression status as described elsewhere herein.
  • the method of monitoring the efficacy of a treatment of a cancer may comprise a step of determining in a cell or tissue sample obtained from a subject/patient suffering from colorectal cancer (CRC) (e.g. a biopsy) the gene expression status of one or more gene(s) as shown in Table 1 ( Figure 1), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2).
  • CRC colorectal cancer
  • the present invention also relates to a method of predicting the efficacy of a treatment of a colorectal cancer (CRC) for a subject/patient suffering from said disease comprising the steps of a) determining in (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from said subject/patient the expression of one or more gene(s) as shown in Table 1 ( Figure 1), optionally in combination the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2); and b) comparing the expression of said one or more gene(s) determined in (a sample from) a reference/control subject/patient (responder and/or non-responder) in a) and said reference expression is indicative for the predicted efficacy of a treatment of a colore
  • the treatment of colorectal cancer may comprise the administration of fluorouracil (5- FU) as described herein.
  • the colorectal cancer (CRC) is a malignant tumor that arises from cells of the colon or the rectum.
  • CRC is classified into hypermutated or non-hypermutated, chromosomal instable tumors. Hypermutated case show either microsatellite instability (MSI) caused by defects in the mismatch repair mechanism or mutations in POLE or POLDl .
  • MSI microsatellite instability
  • Chromosomal instable CRC is characterized by extensive chromosomal rearrangements.
  • a recent attempt to define four consensus molecular subtypes in CRC was published by Guinney et al.
  • the patient/subject suffering from colorectal cancer may be a subject/patient characterized by having a colorectal cancer (CRC) which can be classified into hypermutated, non-hypermutated, and/or chromosomal instable tumors.
  • the subject/patient suffering from colorectal cancer may be a subject/patient characterized by having a colorectal cancer (CRC) which does not have (a) KRAS, BRAS and/or NRAS mutation(s) (see Gong J. et al.,. J. Gastrointest. Oncol. 7 (2016), 687-704).
  • the cell(s), tissue(s) or sample(s) obtained from the patient/subject suffering from CRC is (are) characterized by not having (a) KRAS, BRAS and/or NRAS mutation(s).
  • the cell(s), tissue(s) or sample(s) obtained from the patient/subject suffering from CRC is (are) characterized by having (a) KRAS, BRAS and/or NRAS mutation(s).
  • cell(s), tissue(s) or tumor sample(s) obtained from the patient/subject suffering from CRC which is (are) characterized by not having (a) KRAS, BRAS and/or NRAS mutation(s).
  • the differential expression of one or more gene(s) as shown in Table 1 ( Figure 1 ), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2) as disclosed herein act as markers/predictors for susceptibility to fluorouracil (5-FU).
  • a responder to fluorouracil (5-FU) or a subject/patient sensitive to fluorouracil (5-FU) may be identified in accordance with the present method.
  • the present invention provides the possibility to recognize changes of any one of the genes shown in Table 1 ( Figure 1), Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2) immediately once they occur, for example, by determining the gene expression level of said marker gene(s).
  • the assessment/evaluation/detection of the expression status of any of the above marker genes is sufficient for determining whether a subject/patient is likely to respond to or is sensitive to fluorouracil (5- FU), whether a (tumor) cell of a colorectal cancer is likely to respond or is responsive to treatment with fluorouracil (5-FU).
  • the assessment/evaluation/detection of the expression status of any of the above marker genes (and their combinations) is also sufficient for diagnosing sensitivity to fluorouracil (5-FU).
  • the expression status alone of any of the above marker genes is indicative for a sensitivity/responsiveness to fluorouracil (5-FU) and the expression level/activity of the gene products of the above marker genes need not be determined in addition to the gene expression status.
  • the present invention relates to means, methods and uses which are based on the early recognition of (an) expression change(s) of one or more gene(s) as shown in Table 1 ( Figure 1), Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3) and/or the protein level of the respective gene(s).
  • "early” particularly means prior to (the onset of) a (complete or partial) cytogenetic or hematological response or a response measured by any imaging technique and/or to the outbreak of colorectal cancer (CRC).
  • "early" monitoring the efficacy of a therapy/treatment of said colorectal cancer may be at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 10, or at least 14 days prior to (the onset of) a (complete) cytogenetic or hematological response or a response measured by any type of imaging technique to said therapy/treatment and/or at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 10, at least 12, at least 15, or at least 18 month prior a complete cytogenetic or hematological response or a response measured by any type of imaging technique to said therapy/treatment (of the patient or control patient (responder)), wherein the longer periods are preferred.
  • "early” monitoring the efficacy of a therapy/treatment of said cancer may also be at most 1, at most 2, at most 3, at most 4, at most 5, at most 6, at most 7, at most 10, or at most 14 days after (onset of) the therapy/treatment of said cancer, wherein the shorter periods are preferred. Most preferably, it is envisaged to already monitor the efficacy of a therapy/treatment of said cancer at the day the therapy/treatment was initiated, i.e.
  • expression of one or more gene(s) as shown in Table 1 may be determined daily during the first week after initiation of the therapy/treatment, weekly during the first month of the therapy/treatment and, afterwards, monthly.
  • the reference activity/expression level may be taken at the day the therapy/treatment is initiated, from the subject/patient to be treated and/or from a corresponding reference/control subject/patient (responder/non-responder); see below.
  • "early" predicting the efficacy of a therapy/treatment of the cancer defined herein may be at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 10, or at least 14 days prior to (the onset of) a (complete) cytogenetic or hematological response to said therapy/treatment and/or at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 10, at least 12, at least 15, or at least 18 month prior a complete cytogenetic or hematological response or a response measured by any type of imaging technique to said therapy/treatment, wherein the longer periods are preferred.
  • "early" predicting the efficacy of a therapy/treatment of the cancer defined herein may also be at most 1 , at most 2, at most 3, at most 4, at most 5, at most 6, at most 7, at most 10, or at most 14 days after (onset of) the therapy/treatment of the cancer defined herein, wherein the shorter periods are preferred. Most preferably, it is envisaged to already monitor the efficacy of a therapy/treatment of said colorectal cancer (CRC) at the day the therapy/treatment was initiated, i.e.
  • CRC colorectal cancer
  • "early" predicting the efficacy of a therapy/treatment of the cancer defined herein may also be at most 1 , at most 2, at most 3, at most 4, at most 5, at most 6, at most 7, at most 10, or at most 14 days after diagnosis of the cancer, wherein the shorter periods are preferred. Most preferably, it is envisaged to already predict the efficacy of fluorouracil (5- FU) therapy/treatment of said colorectal cancer (CRC) at the day of diagnosis. As mentioned, the present invention is particularly useful for monitoring the efficacy of a fluorouracil (5-FU) therapy/treatment of the colorectal cancer (CRC) as defined herein. Corresponding means, uses and methods are provided herein.
  • monitoring the efficacy of a certain kind of a fluorouracil (5-FU) therapy/treatment is regularly applied in clinical routine.
  • the skilled person is aware of the meaning of monitoring the efficacy of a certain kind of fluorouracil (5-FU) therapy/treatment.
  • the meaning of the term “monitoring” encompasses the meaning of terms like “tracking”, “discovering” etc.
  • the term "monitoring the efficacy of a fluorouracil (5-FU) therapy/treatment of colorectal cancer (CRC) as used herein refers to monitoring whether a subject/patient suffering from said disease (or being prone to suffering from said cancer) responds at all to a fluorouracil (5-FU) therapy/treatment of said disease and/or how the course of said respond is (e.g. how fast/slow the respond is and/or to what extent the respond is).
  • the present invention is further useful for predicting the efficacy of a therapy/treatment of the colorectal cancer (CRC) as defined herein.
  • CRC colorectal cancer
  • predicting the efficacy of a fluorouracil (5-FU) therapy/treatment is highly desired in clinical routine, since it allows for preventing the disease (colorectal cancer (CRC)) and/or increasing the efficiency of a fluorouracil (5-FU) therapy/treatment and hence, leads to savings in cost and time and to a higher lifespan/likelihood of survival or of 'Genesung' of the affected patient.
  • the term "predicting the efficacy of a therapy/treatment of colorectal cancer (CRC) for a subject/patient” is used in basically the same sense like determining whether, and/or to what extent, a subject/patient exhibits susceptibility to such a fluorouracil (5-FU) therapy/treatment, i.e. whether said subject/patient will or would respond at all to a fluorouracil (5-FU) therapy/treatment of said disease and/or how the course of said respond will or would be (e.g.
  • a subject/patient exhibits susceptibility to said colorectal cancer (CRC) in accordance with this invention, when its (amplified) activity/expression level of one or more gene(s) as shown in Table 1 ( Figure 1 ) (and/or any other gene(s) as shown in Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2)) is differential.
  • said expression level is differential as defined herein.
  • the "predicting the efficacy of a therapy/treatment of the colorectal cancer (CRC)" in accordance with this invention may be performed after initiation of the fluorouracil (5-FU) therapy/treatment, i.e. during the already ongoing fluorouracil (5-FU) therapy/treatment.
  • said "predicting” may be performed during the herein described monitoring the efficacy of a fluorouracil (5-FU) therapy/treatment of said colorectal cancer, preferably early after the beginning of said monitoring.
  • the predicting may be based on results from said monitoring obtained at a certain point in time of the ongoing fluorouracil (5-FU) therapy/treatment.
  • said point in time is an early point in time, like, for example that point in time, when a first result from said monitoring has been obtained.
  • predicting the efficacy of a fluorouracil (5-FU) therapy/treatment of the colorectal cancer (CRC) as defined herein is performed during an already ongoing fluorouracil (5-FU) therapy/treatment, it refers to the following/subsequent efficacy of said fluorouracil (5-FU) therapy/treatment.
  • the "predicting the efficacy of a fluorouracil (5-FU) therapy/treatment of the colorectal cancer (CRC)” may be performed (immediately) after diagnosis but, however, prior to initiation of the fluorouracil (5-FU) therapy/treatment.
  • "predicting the efficacy of a fluorouracil (5-FU) therapy/treatment of said colorectal cancer (CRC)” refers to the efficacy of a fluorouracil (5-FU) therapy/treatment which has not yet been initiated (or has been initiated substantially at the same point in time when the "predicting" was performed).
  • one non-limiting example of a healthy reference/control subject/patient is one having, e.g. (a) non-amplified gene(s) as shown in Table 1 ( Figure 1) (and/or any other gene(s) shown in Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of the expression of 1 or 2 gene(s) as shown in Table 2 ( Figure 2)).
  • a non-amplified gene(s) as shown in Table 1 ( Figure 1) (and/or any other gene(s) shown in Table 2 ( Figure 2), Table 3 ( Figure 3), and/or more preferably of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of the expression of 1 or 2 gene(s) as shown in Table 2 ( Figure 2)).
  • DDX43 NCBI accession no.: NM_018665; version no.: NMJD18665.2; GL2223521478
  • FTL NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5; GL 150417991 (transcript variant 1); NCBI accession no.: NM_ 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NMJH4860; version no.: NM_014860.2; GI:544186059
  • HOXD1 NCBI accession no.: N _024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_00
  • the reference/control subject/patient is, in one embodiment, envisaged to be a subject/patient suffering from said cancer, i.e.
  • a subject/patient having, for example, an differential activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; Gl:399154168; (NCBI accession no.:
  • DDX43 NCBI accession no.: NM_018665; version no.: NM_018665.2; GL2223521478
  • FTL NCBI accession no.: NM 000146; version no.: NM_000146.3; Gl:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1 ); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GL150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM 024501
  • DDX43 NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:2223521478
  • FTL NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM 004367; version no.: NM 004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NMJB 1409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NMJH4860; version no.: NM_014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM_2450
  • DDX43 NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:2223521478
  • FTL NCBI accession no.: NM_000146; version no.: NM 000146.3; GL56682960
  • CCR6 NCBI accession no.: NM 004367; version no.: NM_ 004367.5; GI: 150417991 (transcript variant 1 ); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM 014860; version no.: NM 014860.2; GL544186059
  • HOXD1 NCBI accession no.: NM_
  • different, higher or lower means at least 1.0 fold, at least 1.5 fold, at least 2 fold, at least 2.5 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 7 fold, at least 10 fold, at least 15 fold, at least 25 fold, at least 50 fold, at least 100 fold, at least 200 fold different, higher or lower, wherein the higher values are preferred. Whether, in which direction (i.e., in which direction (i.e., in which direction (i.e.
  • the reference/control subject/patient is subjected to the same fluorouracil (5-FU) treatment of the colorectal cancer (CRC) as the subject/patient suffering from colorectal cancer (CRC) described and defined herein.
  • Said reference/control subject/patient may be a responder (positive reference/control) or non- responder (negative reference/control) to this treatment.
  • a subject/patient is a "responder” or “non-responder” with respect to a colorectal cancer (CRC) fluorouracil (5-FU) treatment/therapy can be evaluated by the skilled person on the basis of his common general knowledge and/or the teaching provided herein, hi particular, a "responder” may be a subject/patient whose cytological/hematological parameters and/or (aberrant) DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_ 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript
  • a “responder” may be a subject/patient not suffering from one of the herein defined resistances.
  • a “non-responder” may be a subject/patient whose cytological/hematological parameters and/or (aberrant) activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.
  • CRC fluorouracil (5-FU) fluorouracil (5-FU) treatment/therapy if the activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GL 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GF.544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM 2450), HOXD1
  • DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148)
  • FTL NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM 004367; version no.: NM_004367.5; GL 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_00524
  • a reduction in expression/ activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM 018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154
  • CRC colorectal cancer fluorouracil
  • DDX43 NCBI accession no.: NM 018665; version no.: NM 018665.2; GI:2223521478
  • FTL NCBI accession no.: NM _000146; version no.: NM_000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GL150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059
  • HOXD1 NCBI accession no.: NM 024501
  • a person skilled in the art may also determine cytological/hematological parameters characteristic for a specific colorectal cancer (CRC) in order to assess whether a patient responds to a fluorouracil (5-FU) treatment/therapy.
  • CRC colorectal cancer
  • a patient who does not respond to a fluorouracil (5-FU) treatment/therapy does not show a reduced expression level/activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM _004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.:
  • one non-limiting example of a diseased reference/control subject/patient (responder and/or non-responder) suffering from a colorectal cancer (CRC) defined herein (or being prone to suffering from a susceptibility thereto) is one having an amplified DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GF.222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NMJ)04367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2;
  • the subject/patient is a "responder”. If the response of a subject/patient is as fast (or even faster) than the "typical/desired response", the subject/patient is a "responder". If the response of a subject/patient is slower than the "typical/desired response", the subject/patient is a "non-responder" (when no substantial response can be seen) or "weak-responder".
  • the efficacy of a cancer treatment/therapy can be determined taking account of the change in the activity/expression level of DDX43 (NCBI accession no.: NMJ) 18665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM _031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NMJH4860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2;
  • a skilled person is able to assess the efficacy of a treatment by evaluating the activity/expression level of the above marker gene(s) at various points in time during the treatment (e.g. prior to the treatment, after start of the treatment, and subseqently in intervals during the treatment).
  • a (desired) efficacy of a treatment of a cancer described herein or susceptibility thereto is indicated/predicted, when the aberrant (i.e. enhanced or decreased) activity or expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 ( Figure 3) is shifted back towards the "normal level" of a (healthy) reference/control subject/patient or to "normal level” of a defined responder ("positive control") due to/in consequence of said treatment of the cancer or susceptibility thereto.
  • a (desired) efficacy of a treatment of a cancer described herein or susceptibility thereto is indicated/predicted, when the aberrant (i.e.
  • the efficacy of a treatment of the cancer defined herein is high, when the subject/patient (to be) treated responds as fast (or even faster) and as complete as a "responder”, i.e. exhibits a "typical/desired response".
  • the efficacy of a fluorouracil (5-FU) treatment of the colorectal cancer (CRC) is high, if the patient treated shows a "typical/desired response".
  • the efficacy is high, when the activity/expression level of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 ( Figure 3) in said patient reach a "normal” activity/level as rapidly as in a "typical/desired response".
  • the efficacy of a fluorouracil (5-FU) treatment of the colorectal cancer (CRC) is high, if the patient treated shows a "typical/desired response".
  • the efficacy is high, when the activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NMJ300146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NMJH4860.2; GL544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.
  • the efficacy of a fluorouracil (5-FU) treatment of the cancer defined herein is moderate/low, when the subject/patient (to be) treated responds not as fast and/or not as complete as a "responder”, i.e. does not exhibit a "typical/desired response".
  • the efficacy is low, when the activity/expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NMJM4860.2; GI:544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM _24501.2; GI:399154168; (NCBI accession
  • DDX43 NCBI accession no.: NM_018665; version no.: NM 018665.2; GI:2223521478
  • FTL NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5
  • GI: 150417991 transcription variant 1
  • NCBI accession no.: NM_031409 version nos.: NM_031409.3
  • GI: 150417990 transcription variant 2
  • SUPT7L NCBI accession no.: NM_014860; version no.: NM 014860.2; GL544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168;
  • Such an "own" reference sample may be obtained prior to (or at the beginning of) the treatment/therapy.
  • the "reference/control subject/patient” would be the subject/patient to be treated itself.
  • the efficacy of the fluorouracil (5-FU) treatment would then be assessed on the basis of how the activity or expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GF222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GL56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.:
  • a fluorouracil (5-FU) treatment of the colorectal cancer is assessed in accordance with specific embodiments of this invention, on the basis that the activity/expression level of DDX43 (NCBI accession no.: NM 018665; version no.: NM 018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_ 031409; version nos.
  • a fluorouracil (5-FU) treatment of the colorectal cancer is assessed based on the comparison of the activity/ expression level of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM _014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 02
  • DDX43 NCBI accession no.: NM O 18665; version no.: NM_018665.2; GI:2223521478
  • FTL NCBI accession no.: NM_000146; version no.: NM _000146.3; GI:56682960
  • CCR6 NCBI accession no.: NMJ304367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM_24501.2
  • different, higher or lower means at least 1.5 fold, at least 2 fold, at least 2,5 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 7 fold, at least 10 fold, at least 15 fold, at least 25 fold, at least 50 fold, at least 100 fold or at least 200 fold different, higher or lower, wherein the higher values are preferred.
  • a certain type of colorectal cancer can be associated with increased activity/expression level of any one of the above marker gene(s) or with a decreased increased activity/expression level of any one of the above marker gene(s). Since a skilled person will be aware of reference activity/expression levels of the marker gene(s) (e.g. in a healthy person), he will be readily in the position to determine whether the activity/expression level of any one of the above marker genes is increased or decreased when compared to the reference activity/expression level.
  • a responder shows expression/ activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM
  • a responder may show reduced or increased expression level/activity of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1 ); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXDl (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.:
  • CRC colorectal cancer
  • DDX43 NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:2223521478
  • FTL NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GL 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM_02450
  • the cancer is characterised by a low expression level/activity of at least one of the marker gene(s) and if expression/ activity of DDX43 (NCBI accession no.: NMJM 8665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GL56682960), CCR6 (NCBI accession no.: NM _004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NMJ
  • DDX43 NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:2223521478
  • FTL NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM 004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1 ); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM_24501 .2; GI
  • a reference/control sample can be obtained from a non-responder or can be obtained prior to/at the beginning of a therapy/treatment of a cancer. Accordingly, if the difference between the expression level/activity of DDX43 (NCBI accession no.: NM_ 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM _031409; version nos.: NM 031409.3; GL 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.
  • a responder shows a reduced expression level/activity of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM 024501 ; version no.:
  • the reference activity/reference expression level of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM 24501.2; GI:399154168; (NCBI accession no.: X
  • CCR6 NCBI accession no.: NM 004367; version no.: NM_004367.5;
  • GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.:
  • NM 014860 version no.: NM_014860.2; GL544186059
  • HOXD1 NCBI accession no.:
  • NM_024501 version no.: NM 24501.2; GI:399154168; (NCBI accession no.:
  • XM 005246507 version nos.: XM_005246507.3; GL1034613502 (predicted transcript variant XI)
  • MRAP2 NCBI accession no.: NMJ38409; version no.: NM 138409.2; Gil 56523250
  • GATAD1 NCBI accession no.: NM 021167; version no.: NM_021167.4;
  • TNFSF13 NCBI accession no.: NM_003808; version no.: NM_003808.3;
  • SLC9A8 (NCBI accession no.: NM 015266; version no.: NM 015266.2; GI:386781491) and/or LI CAM (NCBI accession no.: NM _024003; version no.: NM_024003.3;
  • CCR6 NCBI accession no.: NM_004367; version no.: NM 004367.5;
  • GL150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.:
  • NM_024501 version no.: NM_24501.2; GL399154168; (NCBI accession no.:
  • XM_005246507 version nos.: XM_005246507.3; GL 1034613502 (predicted transcript variant XI )), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ38409.2;
  • GATAD1 NCBI accession no.: NM_021167; version no.: NM 021167.4; GI:392307002
  • RHBDL2 NCBI accession no.: NMJH7821 ; version no.: NM_017821.4;
  • TNFSF13 NCBI accession no.: NM_003808; version no.: NM_003808.3;
  • GI:341604746 MAGEA11 (NCBI accession no.: NM_ 005366; version no.: NM_005366.4), SLC9A8 (NCB1 accession no.: NM_015266; version no.: NM_015266.2; GI:386781491 ) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_024003.3; GI:497239882) (and/or any other gene(s) shown in Table 1 ( Figure 1), Table 2 ( Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2)), for example with respect to the course of the therapy/treatment.
  • MAGEA11 NCBI accession no.: NM_ 005366; version no.: NM_005366.4
  • DDX43 NCBI accession no.: NM_018665; version no.: NM 018665.2; GL2223521478
  • FTL NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NMJ304367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI:150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM 014860; version no.: NM_014860.2; GL544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM_005246507; version
  • activity/expression level of DDX43 (NCBI accession no.: NM 018665; version no.: NMJH 8665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_ 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NMJD24501 ; version no.: NM_24501.2; GL399154168; (NCBI accession no.: XM 005246507;
  • DDX43 activities/expression levels of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM _000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM
  • Non-limiting examples of schemes of determining activities/expression levels of DDX43 (NCBI accession no.: NM 018665; version no.: NM 018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 014860; version no.: NM 014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI:399154168; (NCBI accession no.: XM 005
  • the present invention also relates to the use of a (transgenic) cell or a (transgenic) non-human animal having at least one gene marker/predictor as defined herein for screening and/or validation of a fluorouracil (5-FU) medicament for the treatment of colorectal cancer (CRC).
  • the term "cell" as used in this context may also comprise a plurality of cells as well as cells comprised in a tissue.
  • a cell to be used may, for example, be a primary tumor cell.
  • the tumor cell or cell to be used in the screening or validation method may be obtained from samples from a (transgenic) non-human animal suffering from colorectal cancer (CRC).
  • the tumor cell or cell may also be obtained from patient samples (e.g.
  • the tumor cell or cell may be a human tumor cell.
  • such a cell to be used in the present screening or validation methods may be comprised in a tissue or tissue sample, like in a sample biopsy.
  • the used non-human animal or cell may be transgenic or non transgenic.
  • Transgenic in this context particularly means that at least one of the marker gene(s) as described or defined herein is over- or under- expressed or has a higher or lower activity.
  • DDX43 NCBI accession no.: NM_018665; version no.: NM_018665.2; GL2223521478
  • FTL NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)
  • DDX43 NCBI accession no.: NM 018665; version no.: NM_018665.2; GL2223521478
  • FTL NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5
  • GI: 150417991 transcription variant 1
  • NCBI accession no.: NM_031409 version nos.: NM_031409.3
  • GI: 150417990 transcription variant 2
  • SUPT7L NCBI accession no.: NM_ 014860; version no.: NM _014860.2; GL544186059
  • HOXD1 NCBI accession no.: NM_024501 ; version no.: NM J24501.2; GI:399154168; (NCBI accession no.: X
  • Transgenic in this context may also mean that DDX43 (NCBI accession no.: NM_ 018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.:
  • XM_005246507 version nos.: XM_005246507.3; GI: 1034613502 (predicted transcript variant XI)), MRAP2 (NCBI accession no.: NM 138409; version no.: NMJ38409.2;
  • GATAD1 NCBI accession no.: NM 021167; version no.: NM _021167.4;
  • GI:392307002 NCBI accession no.: NM 017821 ; version no.: NM 017821.4; GI:754171734), TNFSF13 (NCBI accession no.: NM_003808; version no.: NM_003808.3;
  • SLC9A8 (NCBI accession no.: NM_015266; version no.: NM_015266.2; GI:386781491) and/or L1CAM (NCBI accession no.: NM_024003; version no.: NM_ 024003.3; GL497239882) (and/or any other gene(s) shown in Table 1 ( Figure 1), Table 2 ( Figure 2), and/or of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 genes as shown in Table 3 ( Figure 3), optionally in combination with the additional determination of 1 or 2 gene(s) as shown in Table 2 ( Figure 2)) is over- or under-expressed, and/or that the DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.
  • DDX43 NCBI accession no.: NM_018665; version no.: NM_018665.2; GL2223521478
  • FTL NCBI accession no.: NM 000146; version no.: NM_000146.3; GI:56682960
  • CCR6 NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)
  • SUPT7L NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059
  • HOXD1 NCBI accession no.: NM 024501 ; version no.: M_24501.2; GI:399154168; (NCBI accession no.: XM_005246507
  • a preferred (transgenic) non-human animal or (transgenic) cell in context of the invention suffers from colorectal cancer (CRC) for the treatment of which the medicament is to be screened and/or validated.
  • CRC colorectal cancer
  • the (transgenic) non-human animal or (transgenic) cell is particularly intended to suffer from DDX4S (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GL150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM 031409;
  • transgenic non-human animal or “transgenic cell” as used herein refers to a non- human animal or cell, not being a human that comprises genetic material different from the genetic material of a corresponding wild-type animal/cell.
  • Genetic material in this context may be any kind of a nucleic acid molecule, or analogues thereof, for example a nucleic acid molecule, or analogues thereof as defined herein.
  • “Different” in this context means additional or fewer genetic material with respect to the genome of the wild-type animal/cell and/or rearranged genetic material, i.e. genetic material present at a different locus of the genome with respect to the genome of the wild-type animal/cell.
  • the (transgenic) non-human animal or (transgenic) cell is or is derived from a mammal.
  • Non-limiting examples of the (transgenic) non-human animal or derived (transgenic) cell are selected from the group consisting of a mouse, a rat, a rabbit, a guinea pig and a Drosophila.
  • the (transgenic) cell in accordance with this invention may be an animal cell, for example, a non-human animal cell.
  • human cells are envisaged to be employed as cells in context of the present invention.
  • such cell may be an embryonic stem cell (ES cell), particularly a non- human animal ES, like, for example, a mouse or rat ES cell.
  • the (transgenic) cell as described herein, particularly the ES cell, may also be used for generating the (transgenic) non-human animal as described herein.
  • the ES cell technology for generating transgenic animals is well known in the art and for example is described in Pirity et.al. (Methods Cell Biol, 1998, 57:279).
  • the (transgenic) cell may be a prokaryotic or eukaryotic cell.
  • the (transgenic) cell may be a bacterial, yeast, fungus, plant or animal cell.
  • the transformation or genetically engineering of a cell with a nucleic acid construct or vector can be carried out by standard methods, as for instance described in Sambrook and Russell (2001), Molecular Cloning: A Laboratory Manual, CSH Press, Cold Spring Harbor, NY, USA; Methods in Yeast Genetics, A Laboratory Course Manual, Cold Spring Harbor Laboratory Press, 1990.
  • the (transgenic) non-human animal or (transgenic) cell as described or defined in context of this invention is particularly useful in methods for screening and/or validation of a medicament for the treatment of cancers as defined and described herein.
  • These screening methods may, in particular, performed in vivo using, for example, (transgenic) animals as described herein (e.g. rats, mice and the like) and/or animals comprising (a) colorectal cancer (CRC) cell(s), (a) tissue(s) or (a) cell culture(s).
  • Said (a) cell(s), (a) tissue(s) or (a) cell culture(s) may, for example, be obtained/derived from (a) colorectal cancer (CRC) tumor cell(s)/tumor(s).
  • said (a) cell(s), (a) tissue(s) or (a) cell culture(s) may be obtained from a subject/patient suffering from a CRC.
  • These in vivo screening methods may in particular comprise measuring and determining differences in tumor volume, for example, in the (transgenic) animals described herein above.
  • the present invention also relates to a method for screening and/or validation of a fluorouracil (5-FU) for the treatment of a colorectal cancer (CRC).
  • Said method may comprise the steps of
  • screening and/or validation of medicaments means, on the one hand, whether a given set of compounds comprises one or more compound(s) that can function as (a) medicament(s), and/or, on the other hand, whether (a) given compound(s) can function as (a) medicament(s). It is particularly intended that the medicaments to be screened and/or validated in context of this invention are medicaments for the treatment, prevention and/or amelioration of a cancer as defined herein.
  • the compound(s)/medicament(s) to be screened and/or validated may be administered to the non-human (transgenic) animal or cell described herein, and, afterwards (for example after a certain period of time sufficient to allow a compound to effect on a cancer as described herein), it is analyzed whether the cancer, or a symptom thereof, of said animal/cell is ameliorated.
  • the present invention also relates to a fluorouracil (5-FU) for use in the treatment of colorectal cancer (CRC) if (a) cancer cell(s), (a) cancer tissue(s) or (a) tumor sample(s) obtained from a subject to be treated exhibits expression of at least one or more gene(s) as shown in Table 1.
  • the present invention relates to fluorouracil (5-FU) for use in the treatment of colorectal cancer (CRC), wherein said fluorouracil (5-FU) is administered to the subject to be treated if (a) cancer cell(s), (a) cancer tissue(s) or tumor sample(s) obtained from the subject to be treated exhibits expression of at least one or more gene(s) as shown in Table 1.
  • the subject to be treated has been predicted to be responsive or susceptible to the treatment with a fluorouracil (5-FU) in a method of the present invention.
  • the present invention also relates to a kit useful for carrying out the method or used of this invention.
  • said kit comprises oligonucleotides or polynucleotides capable of detecting the amplification status of at least one gene selected from the group of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GF56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GL150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM _014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version
  • said kit may comprise (a) compound(s) required for specifically determining the amplification status of at least one gene of DDX4S (NCBI accession no.: NM 018665; version no.: NM_018665.2; GL222352148), FTL (NCBI accession no.: NM_000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM 004367; version no.: NM_004367.5; GI:150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GI:544186059), HOXD1 (NCBI accession no.: NM_024501 ; version no.: NM_24501.2; GI
  • the kit (to be prepared in context) of this invention is a diagnostic kit.
  • the kit (to be prepared in context) of this invention or the methods and uses of the invention may further comprise or be provided with (an) instruction manual(s).
  • said instruction manual(s) may guide the skilled person (how) to determine amplification status of at least one gene of DDX43 (NCBI accession no.: NM 018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM 000146; version no.: NM 000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM_004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM 031409; version nos.: NM 031409.3; GI: 150417990 (transcript variant 2)), SUPT7L (NCBI accession no.: NM_014860; version no.: NM_014860.2; GL544186059), HOXD1 (NCBI accession no.: NM 024501 ; version no.: NM_24501.2; GL399154168;
  • the kit (to be prepared in context) of this invention may further comprise substances/chemicals and/or equipment suitable/required for carrying out the methods and uses of this invention.
  • substances/chemicals and/or equipment are solvents, diluents and/or buffers for stabilizing and/or storing (a) compound(s) required for specifically determining the amplification status of at least one gene of DDX43 (NCBI accession no.: NM_018665; version no.: NM_018665.2; GI:222352148), FTL (NCBI accession no.: NM_000146; version no.: NM_000146.3; GI:56682960), CCR6 (NCBI accession no.: NM_004367; version no.: NM 004367.5; GI: 150417991 (transcript variant 1); NCBI accession no.: NM_031409; version nos.: NM_031409.3; GI: 150417990 (transcript variant 2)), SUPT7
  • the present invention also relates to the use of an oligo- or polynucleotide capable of detecting the expression level(s) of one or more of the gene(s) of Table 1 ( Figure 1) for predicting the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU).
  • Figure 1 an oligo- or polynucleotide capable of detecting the expression level(s) of one or more of the gene(s) of Table 1 ( Figure 1) for predicting the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU).
  • oligonucleotide(s) is (are) about 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15 to 100 nucleotides in length.
  • the expression of at least 1 additional gene selected from the group consisting of FOS (NCBI accession no.: NM 005252; version no.: NM_005252.3; GL254750707), and S100A2 (NCBI accession no.: NM_005978; version no.: NM_005978.3; GI:45269153) is (are) detected for predicting the susceptibility or responsiveness of a subject suffering from colorectal cancer (CRC) to the treatment with fluorouracil (5-FU).
  • CRC colorectal cancer
  • Figure 1 Novel fluorouracil (5-FU) sensitivity related genes (see Table 1).
  • EIR expression in responders
  • a RPKM expression level
  • Down regulated genes indicate likelihood for response to cetuximab below the cutoff.
  • Up regulated genes indicate likelihood for response to cetuximab above the cutoff.
  • logFC log 2 normalized fold change.
  • FDR false discovery rate (Benjamini- Hochberg procedure). Please see the methods for further details on setups a-d.
  • EER expression in responders indicates if a certain gene is up or down regulated in responding PDX models compared to non-responding PDX models.
  • a RPKM (expression level) cutoff that indicates likelihood for response to cetuximab is listed in column "RPKM cutoff”.
  • Down regulated genes indicate likelihood for response to cetuximab below the cutoff.
  • Up regulated genes indicate likelihood for response to cetuximab above the cutoff.
  • logFC - log2 normalized fold change.
  • FDR false discovery rate (Benjamini- Hochberg procedure). Please see the methods for further details on setups a-d.
  • Figure 3 14-gene mini-classifier (see Table 3). Selection of fluorouracil (5-FU) sensitivity related genes.
  • EIR expression in responders indicates if a certain gene is up or down regulated in responding PDX models compared to non-responding PDX models.
  • a RPKM (expression level) cutoff that indicates likelihood for response to cetuximab is listed in column "RPKM cutoff'.
  • Down regulated genes indicate likelihood for response to cetuximab below the cutoff.
  • Up regulated genes indicate likelihood for response to cetuximab above the cutoff.
  • FDR false discovery rate (Benjamini-Hochberg procedure). Please see the methods for further details on setups a-d and the selection of the genes using SVM.
  • FIG. 4 Response to fluorouracil (5-FU) in xenografts (PDXs): Heatmap of genes that correlate in their expression to fluorouracil (5-FU) sensitivity.
  • PDX samples and genes are clustered using hierarchical clustering. The drug sensitivity is determined by a treatment in comparison to control (T/C) (as illustrated in a continuous grey scale color code) in PDX: black - strongly responding models, grey - resistant models
  • T/C control
  • Heatmap includes genes that are not reported to be associated with fluorouracil (5-FU) sensitivity (236 genes)
  • Heatmap includes genes known to be associated with fluorouracil (5-FU) sensitivity.
  • FIG. 5 Performance range of the downsized sub-signatures of the 14-gene mini- classifier.
  • the plot shows the upper range of the balanced accuracy for sub- signatures with a signature size of two up to 13 genes. Sub-signatures were randomly generated out of the 14-gene mini-classifier. For each signature size 120 unique sub-signatures were generated. Hyperparameter fitting and and SVM training was performed on the OncoTrack PDX cohort as described. The upper bound shows the maximum of balanced accuracy. The lower bound shows the median of balanced accuracy. The small vertical line marks the 75% quartile of balanced accuracy. The balanced accuracy of the downsized sub- signatures was evaluated on the OncoTrack PDX cohort and plotted over the signature size. The mini-gene classifier accuracy is stable or stays in an acceptable range, i.e. the performance of the 14-gene mini-classifier is more or less independent of the number of applied genes.
  • tissue samples were used to generate a collection of pre-clinical patient-derived experimental models.
  • the genomes, exomes and transcriptomes of the donor cohort as well as of the matched untreated PDX models were sequenced.
  • RNA reads were aligned to hgl 9 (GCA_000001405.1) using BWA and SAMtools. Mapped reads were annotated using Ensembl v70. Gene expression levels were quantified in reads per kilobase of exon per million mapped reads (RPKM) (Mortazavi A. et al, Nat Methods. 5(7) (2008), 621 -8).
  • DNA reads were aligned to the human reference genome hgl 9 using BWA (Li H. et al, Bioinformatics 25 (2009), 1754-1760) (bwa0.7.7-r441-mem for 75/101bp, bwa0.5.9-rl6-aln for 51bp reads).
  • BWA Li H. et al, Bioinformatics 25 (2009), 1754-1760
  • PDX xenograft
  • Somatic SNVs were detected using established pipelines based on VarScan2 (Koboldt D.C. et al, Genome Res 22 (2012), 568-576) combined with RNAseq data and functional annotation of the variants based on Ensembl v.70. Somatic indels were detected using SAMtools and Dindel (Albers C.A. et al, Genome Res 21 (2011), 961- 973). Development and characterization of patient derived xenografts (PDX)
  • Resected tumor tissues were transplanted to immunodeficient mice (NMRI nude or NOG, Taconic, Bomholdtgard, DK- Tac:NMRI-Foxnlnu, females, 6-8 weeks at start of transplantation) using previously described methods by Fichtner et al. (Fichtner I. et ah, Eur J Cancer 40 (2004), 298-307). Animal experiments were carried out in accordance with the United Kingdom Coordinating Committee on Cancer Research regulations for the Welfare of Animals and of the German Animal Protection Law and approved by the local responsible authorities. Experimental Pharmacology and Oncology Berlin-Buch GmbH (EPO) strictly follows the EU guideline European convention for the protection of vertebrate animals used for experimental and other scientific purposes.
  • mice were monitored 3 times weekly for tumor engraftment for up to 3 month. Engrafted tumors at a size of about 1cm 3 were surgically excised and smaller fragments re-transplanted to naive NMRI nu/nu mice for further passage. Within passage 1 to 3 numerous samples were cryo-conserved (DMSO-medium) for further experiments. Tumors were passaged not more than 6 times. For confirmation of tumor histology, tumor tissue was formalin fixed and paraffin embedded (FFPE) and 5 ⁇ sections were prepared. Samples were stained according to a standard protocol for hematoxilin, eosin and Ki67 to ensure xenograft comparability to the original specimen. Cases with changed histological pattern were sent for pathological review and outgrowth of lymphoproliferative diseases was excluded. In this study, no blinding was done.
  • FFPE paraffin embedded
  • mice were randomized to treatment or control groups consisting of 5-6 animals each. Doses and schedules were chosen according to previous experience in animal experiments and represent maximum tolerated or efficient doses.
  • the applied schedule for 5-FU was as follows: Application route: i.p. (intraperitoneal injection); Schedule: Once per week; Day: Monday; number of cycles: 4; Dose: 100 mg/kg. The injection volume was 0.1-0.2 ml/20 g body weight.
  • Treatment was continued over a period of four weeks (4 cycles) or till tumor size exceeded 1 cm 3 or animals showed loss of >15% body weight. From the first treatment day onwards the tumor volumes and body weights were recorded twice weekly. At the end of the treatment period animals were sacrificed, blood and tumor samples collected, and stored in liquid nitrogen immediately.
  • RTV relative tumor volume
  • xenograft samples of the 52 xenografts (PDX) that derived from one colorectal carcinoma (CRC) (150 MET1) shared highly similar global expression profiles. They were merged into one artificial single sample to avoid analysis bias by taking an average of the reads per kilobase of exon per million mapped (RPKM) (Mortazavi A, et al, Nat Methods 5 (2008), 621 -628)-values and of the T/C -values per gene or drug, i.e. 5-FU. Taking the artificial sample for 150JVIET1 into account 48 PDX were included into the drug response analysis. Drug response related gene signatures in xenografts (PDX)
  • DGE analysis using the R package edgeR (Robinson MD et al., Bioinformatics 26 (2010), 139-140) to identify signatures associated with drug, i.e. 5-FU, response results in form of T/C values for PDX: strong, moderate, minor, resistant (see the above section 6).
  • DGE analysis was applied in different setups as follows: a) combined strong+moderate vs combined minor+resistant, b) combined strong+moderate+minor vs. resistant, and c): 20 most sensitive vs. 20 least sensitive PDX. Genes were filtered by a false discovery rate (FDR) ⁇ 0.01,
  • FDR false discovery rate
  • the IC 50 or T/C values as phenotype vector in a general linear model (GLM) provided by the edgeR package was used.
  • Genes were filtered by FDR ⁇ 0.01 and dispersion ⁇ 4.
  • Gene signatures associated with a given drug response were generated by combining results from setups a-d.
  • Low expressed genes were filtered by an expression > 1 RPKM in minimum five PDX and by a mean expression > 0.8 RPKM. In total 253 genes correlate in their expression with the response to 5-FU. Building drug response classifiers for 5-FU
  • SVM linear support vector machine
  • samples can be classified into groups (Bennet K.P. et al., SIGBCDD Explorations 2 (2000); Cortes et al, Machine Learning 20 (1995), 273-297).
  • An important factor for a proper classification is the selection of features (genes) that define the data space and the SVM learns from. From the preselected genes that are associated to drug response, the SVM itself was used to rank features and the probably most important one were selected. The application of the SVM is described in further details below.
  • a class weighted SVM was used and the hyperparameter C was tuned for each of classes resistance and response ⁇ C res i S , C resp ).
  • the feature (gene) selection included feature ranking and feature size selection.
  • SVM- RFE SVM recursive feature elimination
  • a SVM-RFE includes following steps: 1) hyperparameter tuning, 2) train multiple SVMs on subsamples of the original training set, 3) calculate a ranking score per feature based on the trained SVMs, 4) note the relative position in the final ranking vector of m features with the lowest ranking score, 5) eliminate m features with the lowest ranking score from the feature space, 6) repeat step 1 -5 until all features are ranked in the final ranking vector.
  • the bootstrap was separately applied on the responder and resistance set with a sample size of 13 and 31 , respectively.
  • the performance of a hyperparameter set was evaluated using the Fi- score.
  • For the leave-n-out resampling two and five samples of the responder and resistance set were left out from the training set, respectively.
  • the calculation of the ranking score was based on the weight vector w of a linear SVM and not w 2 as described from Duan et al.
  • the 5-FU mini classifier (14 genes) was cross-validated on the OT PDX cohort via a 100 times repeated 10-fold cross-validation. Performance values were averaged over the repeats. The performance of the classifier was estimated from the number of true positive (TP), false positive (FP), true negative (TN) and false negative (FN) predictions as well as the sensitivity, specificity and balanced accuracy. Additional information

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Abstract

La présente invention concerne un procédé de détermination de la sensibilité/réactivité de (a) cellule(s) cancéreuse(s), de préférence (a) de cellule(s) cancéreuse(s) colorectale(s), au traitement avec le fluorouracile (5-FU). De plus, la présente invention concerne un procédé de sélection (a) d'une (de) cellule(s) cancéreuse(s), (a) d'un (de) tissu(s) cancéreux ou (a) d'un (d') échantillon(s) tumoral (tumoraux) du cancer colorectal (CRC) présentant une sensibilité au fluorouracile (5-FU). En outre, l'invention concerne un procédé in vitro d'identification d'un répondeur au fluorouracile (5-FU) ou d'un sujet sensible au fluorouracile (5-FU), de préférence un patient humain, souffrant d'un cancer colorectal (CRC). La présente invention concerne également un procédé de surveillance de l'efficacité d'un traitement du cancer colorectal (CRC) avec du fluorouracile (5-FU).
PCT/EP2017/077693 2016-10-28 2017-10-27 Moyens et procédés de détermination de l'efficacité du fluorouracile (5-fu) dans une thérapie du cancer colorectal (crc) WO2018078142A1 (fr)

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Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20220262494A1 (en) * 2018-11-30 2022-08-18 Caris Mpi, Inc. Next-generation molecular profiling

Citations (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4458006A (en) 1982-06-21 1984-07-03 Hoechst Aktiengesellschaft Photopolymerizable mixture and photopolymerizable copying material prepared therewith
WO2006015742A2 (fr) 2004-08-04 2006-02-16 Friedrich-Alexander- Universität Erlangen- Nürnberg Marqueur tumoral destine au diagnostic de carcinomes et/ou des metastases issues de ces carcinomes
WO2007147877A1 (fr) 2006-06-22 2007-12-27 Oryzon Genomics, S.A. Procédé de pronostic dans le cancer colorectal
WO2008115419A2 (fr) 2007-03-15 2008-09-25 Genomic Health, Inc. Marqueurs d'expression de gène pour la prévision de la réponse d'un patient à une chimiothérapie
WO2009114836A1 (fr) 2008-03-14 2009-09-17 Genomic Health, Inc. Marqueurs d’expression génique pour la prédiction de la réponse d’un patient à une chimiothérapie
US20120136583A1 (en) * 2009-07-08 2012-05-31 Worldwide Innovative Network Method for predicting efficacy of drugs in a patient
WO2014197543A1 (fr) 2013-06-04 2014-12-11 University Of Miami Dosages, procédés et kits d'analyse de la sensibilité et de la résistance à des médicaments anticancéreux, donnant un pronostic de patient cancéreux, et stratégies thérapeutiques personnalisées

Patent Citations (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4458006A (en) 1982-06-21 1984-07-03 Hoechst Aktiengesellschaft Photopolymerizable mixture and photopolymerizable copying material prepared therewith
WO2006015742A2 (fr) 2004-08-04 2006-02-16 Friedrich-Alexander- Universität Erlangen- Nürnberg Marqueur tumoral destine au diagnostic de carcinomes et/ou des metastases issues de ces carcinomes
WO2007147877A1 (fr) 2006-06-22 2007-12-27 Oryzon Genomics, S.A. Procédé de pronostic dans le cancer colorectal
WO2008115419A2 (fr) 2007-03-15 2008-09-25 Genomic Health, Inc. Marqueurs d'expression de gène pour la prévision de la réponse d'un patient à une chimiothérapie
WO2009114836A1 (fr) 2008-03-14 2009-09-17 Genomic Health, Inc. Marqueurs d’expression génique pour la prédiction de la réponse d’un patient à une chimiothérapie
US20120136583A1 (en) * 2009-07-08 2012-05-31 Worldwide Innovative Network Method for predicting efficacy of drugs in a patient
WO2014197543A1 (fr) 2013-06-04 2014-12-11 University Of Miami Dosages, procédés et kits d'analyse de la sensibilité et de la résistance à des médicaments anticancéreux, donnant un pronostic de patient cancéreux, et stratégies thérapeutiques personnalisées

Non-Patent Citations (74)

* Cited by examiner, † Cited by third party
Title
"Affymetrix GeneChip Human Genome U133 Array Set HG-U133A", GEO,, 11 March 2002 (2002-03-11), XP002355386 *
"Methods in Yeast Genetics, A Laboratory Course Manual", 1990, COLD SPRING HARBOR LABORATORY PRESS
"NCBI", Database accession no. NM 000146
"NCBI", Database accession no. NM 005252
"NCBI", Database accession no. NM 005366
"NCBI", Database accession no. NM 017821
"NCBI", Database accession no. NM 031409
"NCBI", Database accession no. NM_005252
"NCBI", Database accession no. NM_005978
"NCBI", Database accession no. NM-004367
ALBERS C.A. ET AL., GENOME RES, vol. 21, 2011, pages 961 - 973
BEAUCAGE ET AL., TETRAHEDRON LETTERS, vol. 22, 1981, pages 1859 - 1862
BENNET ET AL., SIGKDD EXPLORATIONS, vol. 2, 2000
BENNET K.P. ET AL., SIGKDD EXPLORATIONS, vol. 2, 2000
BILLMAN-JACOBE, CURRENT OPINION IN BIOTECHNOLOGY, vol. 7, 1996, pages 500 - 504
BITTER ET AL., METHODS IN ENZYMOLOGY, vol. 153, 1987, pages 516 - 544
CORTES ET AL., MACHINE LEARNING, vol. 20, 1995, pages 273 - 297
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM _018665
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM 015197
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM 015460
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM 024501
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_000146
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_003808
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_003808.3
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_004367
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_005366
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_014860
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_015197
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_015266
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_015460
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_017821
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_018665
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_021167
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_024003
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_024501
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_031409
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_138409
DATABASE Genbank [O] retrieved from NCBI Database accession no. NM_138409.2
DATABASE Genbank [O] retrieved from ncbi Database accession no. XM_005246507
DATABASE Genbank [O] retrieved from v Database accession no. XM_005246507
DE SOUSA E.M.F. ET AL., NAT MED, vol. 19, 2013, pages 614 - 618
DIMITRIADOU E. ET AL., THE LANCET E1071 PACKAGE, 2005
DUAN K.B. ET AL., IEEE TRANSACTIONS ON NANOBIOSCIENCE, vol. 4, 2005, pages 228 - 234
EISENHAUER E.A. ET AL., EUR J CANCER, vol. 45, 2009, pages 228 - 247
FICHTNER ET AL., EUR J CANCER, vol. 40, 2004, pages 298 - 307
FICHTNER I. ET AL., EUR J CANCER, vol. 40, 2004, pages 298 - 307
GONG J. ET AL., J. GASTROINTEST. ONCOL., vol. 7, 2016, pages 687 - 704
GRIFFITHS ET AL., METHODS IN MOLECULAR BIOLOGY, vol. 75, 1997, pages 427 - 440
GROTHEY ET AL., LANCET, vol. 381, no. 9863, 2013, pages 303 - 312
GUINNEY J. ET AL., NAT MED, vol. 21, 2015, pages 1350 - 1356
HOCKNEY, TRENDS IN BIOTECHNOLOGY, vol. 12, 1994, pages 456 - 463
JU ET AL., JOURNAL OF CELLULAR BIOCHEMISTRY, vol. 116, no. 2, 2015, pages 277 - 286
KENT ET AL., GENOME RES., vol. 12, no. 6, 2002, pages 996 - 1006
KENT ET AL., NATURE, vol. 409, no. 6822, 2001, pages 860 - 921
KOBOLDT D.C. ET AL., GENOME RES, vol. 22, 2012, pages 568 - 576
LARRANAGA ET AL., BIOINFORM., vol. 7, 2006, pages 86 - 112
LI ET AL., BIOINFORMATICS, vol. 25, 2009, pages 1754 - 1760
LI ET AL., BIOINFORMATICS, vol. 25, 2009, pages 2078 - 2079
LI H. ET AL., BIOINFORMATICS, vol. 25, 2009, pages 1754 - 1760
LIBBRECHT; NOBLE, NAT REV GENET, vol. 16, 2015, pages 321 - 332
MARISA L. ET AL., PLOS MED, vol. 10, 2013, pages e1001453
METHODS IN ENZYMOLOGY, vol. 153, 1987, pages 385 - 516
MORTAZAVI A ET AL., NAT METHODS, vol. 5, 2008, pages 621 - 628
MORTAZAVI A. ET AL., NAT METHODS, vol. 5, no. 7, 2008, pages 621 - 628
MORTAZAVI A. ET AL., NAT METHODS, vol. 5, no. 7, 2008, pages 621 - 8
NELSON V.M. ET AL., GASTROINTEST ONCOL., vol. 4, no. 3, 2013, pages 245 - 252
PARKHOMCHUK D ET AL., NUCLEIC ACIDS RES., vol. 37, no. 18, 2009, pages e123
PIRITY, METHODS CELL BIOL, vol. 57, 1998, pages 279
ROBINSON MD ET AL., BIOINFORMATICS, vol. 26, 2010, pages 139 - 140
SADANANDAM A. ET AL., NAT MED, vol. 19, 2013, pages 619 - 625
SAMBROOK ET AL.: "A Laboratory Manual. 4th ed.", 2012
SAMBROOK; RUSSELL: "Molecular Cloning: A Laboratory Manual", 2001, CSH PRESS
SAWERS ET AL., APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, vol. 46, 1996, pages 1 - 9
SCHLICKER A. ET AL., BMC MED GENOMICS, vol. 5, 2012, pages 66

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20220262494A1 (en) * 2018-11-30 2022-08-18 Caris Mpi, Inc. Next-generation molecular profiling

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