WO2016134416A1 - Méthode d'évaluation du pronostic d'un lymphome - Google Patents

Méthode d'évaluation du pronostic d'un lymphome Download PDF

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WO2016134416A1
WO2016134416A1 PCT/AU2016/050118 AU2016050118W WO2016134416A1 WO 2016134416 A1 WO2016134416 A1 WO 2016134416A1 AU 2016050118 W AU2016050118 W AU 2016050118W WO 2016134416 A1 WO2016134416 A1 WO 2016134416A1
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subject
score
immune
survival
ratio
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PCT/AU2016/050118
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Maher GANDHI
Colm Gerard KEANE
Kim-Anh LE CAO
Francesco VARI
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The University Of Queensland
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Publication of WO2016134416A1 publication Critical patent/WO2016134416A1/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
    • 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
    • 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
    • C12Q2600/118—Prognosis of disease development
    • 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 invention relates to methods, devices and kits for providing prognosis of subjects having lymphoma.
  • the methods relate to determining likelihood of survival, recurrence or treatment outcome in B-cell lymphoma patients.
  • Lymphomatous B-cells develop within a complex tumour microenvironment
  • TME T-cell-effector
  • DLBCL Diffuse large B-cell lymphoma
  • DLBCL Diffuse large B-cell lymphoma
  • tumour biopsies display 'adaptive resistance' in which checkpoints are triggered in response to immune-effectors. Whether a similar relationship between immune-effectors and checkpoints is present in DLBCL remains to be determined.
  • Diffuse large B-cell lymphoma is an aggressive B-cell lymphoma.
  • DLBCL Diffuse large B-cell lymphoma
  • R-CHOP Refractory B. J Clin Oncol 2005; 23(26): 6387-93.
  • New therapeutic strategies are in development, but their application requires accurate identification of patients likely to fail induction.
  • pre-treatment prognosticators such as the cell-of-origin (COO) and international prognostic index (IPI) and/or revised-international prognostic index (R-IPI), (Alizadeh AA, et al.
  • the present invention provides a method for providing a prognosis of a subject having diffuse large B-cell lymphoma (DLBCL) responding to a treatment regime including an anthracycline and a B-cell depleting antibody, the method comprising: determining an immune score for the subject based upon the ratio of a level of any one or more of CD137, CD4, CD8, CD56, TNFa (alpha) and LM02 in the subject to a level of any one or more of PD-1 , PD-L1 , CD163, CD68, PD-L2, LAG 3, TIM3 and SCYA3(CCL3) in the subject, comparing the immune score to a reference score; wherein the immune score in comparison with the reference score is indicative of the subject's prognosis of responding to a treatment regime including an anthracycline and a B-cell depleting antibody.
  • the B-cell depleting antibody is an anti- CD20 antibody.
  • the present invention also provides a method for providing a prognosis of a subject having diffuse large B-cell lymphoma responding to a treatment regime including an anthracycline and a B-cell depleting antibody, the method comprising determining an immune score for the subject based upon the ratio of a level of any one or more of CD137, CD4, CD8, CD56, TNFa (alpha) and LM02 in the subject to a level of any one or more of PD-1 , PD-L1 , CD163, CD68, PD-L2, LAG3, TIM3 and SCYA3(CCL3) in the subject, comparing the immune score to a reference score; wherein the reference score is a score above which correlates with an increased probability of recurrence free survival or overall survival of the subject at a later time, and below which correlates with a decreased probability of recurrence free survival or overall survival of the subject at the later time, thereby providing a prognosis of the subject for responding to a treatment regime including
  • the present invention also provides a method for predicting the likelihood of overall survival of a subject having diffuse large B-cell lymphoma if treated with a regime including an anthracycline and a B-cell depleting antibody, the method comprising: determining an immune score for the subject based upon the ratio of a level of any one or more of CD137, CD4, CD8, CD56, TNFa (alpha) and LM02 in the subject to a level of any one or more of PD-1 , PD-L1 , CD163, CD68, PD-L2, LAG3, TIM3 and SCYA3(CCL3) in the subject, comparing the immune score to a reference score; wherein the reference score is a score above which correlates with an increased probability of recurrence free survival or overall survival of the subject at a later time, and below which correlates with a decreased probability of recurrence free survival or overall survival of the subject, thereby providing a prognosis of the subject for responding to a treatment regime including an an
  • determining an immune score for the subject may be based upon the ratio of a level of any one or more of CD137, CD4, CD8 and CD56 in the subject to a level of any one or more of PD-1 , PD-L1 , CD 163 and CD68 in the subject.
  • the present invention also provides a method for predicting the likelihood of overall survival of a subject having diffuse large B-cell lymphoma if treated with a regime including an anthracycline and a B-cell depleting antibody, the method comprising: analysing levels of at least one of CD137, CD4, CD8, CD56, TNFa (alpha) and
  • LM02 and at least one of PD-1 , PD-L1 , CD163, CD68, PD-L2, LAG 3, TIM3 and SCYA3(CCL3) in a biological sample obtained from the subject determining an immune score for the subject based upon the ratio of a level of any one or more of CD137, CD4, CD8, CD56, TNFa (alpha) and LM02 in the subject to a level of any one or more of PD-1 , PD-L1 , CD163, CD68, PD-L2, LAG3, TIM3 and SCYA3(CCL3), comparing the immune score to a reference score, wherein the reference score has been derived from a patient cohort of known survival outcome treated with a regime including an anthracycline and a B-cell depleting antibody, and assigning the subject to a risk group based on whether the immune score is higher or lower than the reference score, wherein an immune score higher than the reference score indicates a high likelihood of overall survival and an immune score lower than the reference
  • the B- cell depleting antibody is an anti-CD20 antibody.
  • the method of the invention includes the following steps: analysing levels of at least one of CD137, CD4, CD8 and CD56, and at least one of PD-1 , PD-L1 , CD163 and CD68 in a biological sample obtained from the subject determining an immune score for the subject based upon the ratio of a level of any one or more of CD137, CD4, CD8 and CD56 in the subject to a level of any one or more of PD-1 , PD-L1 , CD163 and CD68.
  • the immune score for the subject may be based upon the ratio of a level of each of CD137, CD4, CD8, CD56, TNFa (alpha) and LM02 in the subject to a level of each of PD-1 , PD-L1 , CD163, CD68, PD-L2, LAG 3, TIM3 and SCYA3(CCL3) in the subject.
  • the immune score for the subject may be based upon the ratio of a level of each of CD137, CD4, CD8 and CD56 in the subject to a level of PD-1 , PD-L1 , CD163 and CD68 in the subject.
  • the present invention provides a method for providing a prognosis of a subject having diffuse large B-cell lymphoma responding to a treatment regime including an anthracycline and anti-CD20 antibody, the method comprising: determining an immune score for the subject based upon the ratio of the product of levels of each of CD4, CD8, CD137(TNFR9), TNFa (alpha) and LM02 in the subject to the product of levels of PD-L1 , PD-1 , CD163, CD68 and SCYA3(CCL3) in the subject, wherein the ratio is defined by
  • the present invention provides a method for providing a prognosis of a subject having diffuse large B-cell lymphoma responding to a treatment regime including an anthracycline and anti-CD20 antibody, the method comprising: determining an immune score for the subject based upon the ratio of the product of levels of each of CD4 and CD8 in the subject to the product of levels of PD-L1 , CD163 and CD68 in the subject, wherein the ratio is defined by CD4xCD8.div.M2xPD- L1 , wherein M2 is (CD163.div.CD68), comparing the immune score to a reference score; wherein the immune score in comparison with the reference score is indicative of the subject's prognosis of responding to a treatment regime including an anthracycline and anti-CD20 antibody.
  • the level of more than one of CD137, CD4, CD8, CD56, TNFa (alpha) and LM02 is used in the ratio
  • the mathematical product of their values is used.
  • the level of CD163 and CD68 can be present in the ratio as a ratio of CD163.div.CD68 (i.e. CD163:CD68, or ' ⁇ 2').
  • the ratio is not the level of CD4 to PD-1 , CD56 to PD-1 or CD56 to PDL-1 (shown in Table 3 as the last 3 rows as CD4.div.PD-1 , CD56.div.PD-1 and CD56.div.PD-L1 ).
  • a method may be used for providing a prognosis for recurrence free survival, overall survival, four year survival or other clinically or biochemically detectable response to a treatment regime.
  • the treatment regime is a chemo-immunotherapy treatment including, or consisting of, an anthracycline and a B-cell depleting antibody.
  • the B-cell depleting antibody is an anti-CD20 antibody.
  • the anthracycline may be doxorubicin, daunorubicin, idarubicin or epirubicin
  • the B-cell depleting antibody may be inotuzumab or an anti-CD20 antibody such as rituximab, obinutuzumab or ofatumumab.
  • the chemotherapy including an anthracycline and anti-CD20 antibody is R-CHOP (Rituximab, Cyclophosphamide, Hydroxydaunorubicin, Oncovin (vincristine), and Prednisone or Prednisolone), R-CHOP-14, R-CHOP-21 , DA-EPOCH- R (dose-adjusted etoposide, doxorubicin, and cyclophosphamide with vincristine, prednisone, and rituximab) or R-ACVBP (rituximab, doxorubicin, cyclophosphamide, vindesine, bleomycin, and prednisone). More preferably, the chemotherapy is R-CHOP.
  • a high likelihood of overall survival is at least 95%, 94%, 93%, 92%, 91 %, 90%, 85%, 80%, 75% or 70%.
  • a low likelihood of overall survival is less than 60%, 55%, 54%, 53%, 52%, 51 %, 50%, 49%, 48%, 47%, 46%, 45% or 44%.
  • Determining the immune score for a subject may be by any one of the ratios listed in Table 3 or Table 5.
  • the ratio is one that has a p-value difference between survival curves as shown in Table 3 or 5 of less than 1 E-1 1 (i.e. 1 x 10-1 1 ), 1 E-10, 1 E-09, 1 E-08, 1 E-07, 1 E-06, 1 E-05, 1 E-04, 1 E-03, 1 E-02 or 0.05.
  • the immune score for a subject is determined using any one of the following ratios: 2,
  • the immune score for a subject is determined using the ratio CD4xCD8.div.M2xPD-L1 , or CD4xCD8xCD137.TNFR9xTNF.AIphaxLM02.div.M2xSCYA3.CCL3xPD.1xPD.L1.
  • SCYA3 and CCL3 refer to the same single marker, both terms have been used as that marker may be referred to by a skilled person as either SCYA3 or CCL3 (i.e. SCYA3.CCL3 or SCYA3(CCL3) refer only to a single marker).
  • CD137.TNFR9 refers to the same single marker that may be referred to by the skilled person as either CD137 or TNFR9.
  • the reference score and immune score are determined using the same biomarkers in the same ratios.
  • the immune score and reference score are determined using the same statistical method or the same ratio described herein.
  • the immune score and reference score may be determined using the same ratio being any of those described in Table 3 or 5, preferably CD4xCD8.div.M2xPD-L1 or CD4xCD8xCD137.TNFR9xTNF.AIphaxLM02.div.M2xSCYA3.CCL3xPD.1xPD.L1 .
  • the prognosis requires that a reference score has previously been determined for those specific biomarker ratios, which can be done by the methods described in this specification.
  • PD-L1 , CD163, CD68, PD-L2, LAG3, TIM3 and SCYA3(CCL3) may be determined from a biological sample derived from the subject or may be determined from information obtained from a previously analyzed biological sample.
  • determining the level of any one of the biomarkers described herein in the subject may be by determining the level in a biological sample obtained from the subject or from expression information previously obtained from a biological sample.
  • the level of a biomarker is determined by the amount or relative amount of a nucleic acid encoding, or complementary to a nucleic acid encoding, a biomarker as described herein in a biological sample.
  • the nucleic acid is RNA, more preferably mRNA.
  • the method further comprises a step of obtaining a biological sample from the subject.
  • the biological sample may be selected from the group consisting of formalin fixed embedded tissue or cells, processed tissue, frozen tissue, and a biopsy.
  • more than one immune score is determined using ratios of different biomarkers (such as those in Table 3 or 5), and compared to the corresponding reference score, to improve prognosis accuracy for a subject.
  • the method further comprises a step of conducting a COO, R-IPI and/or IPI analysis to further stratify the subject into a group based on likelihood of overall survival, recurrence free survival or response to therapy.
  • the subject may be stratified into one of the following groups R-IPI - 'very good/good' (VG/G) equivalent to IPI 0-2, 'Poor' equivalent to IPI:3-5, COO - germinal centre B-cell (GCB) and non-GCB (activated B-cell and unclassified combined), each group may then have a subgroup based on an immune score that is above the reference score (a high immune score) or an immune score below the reference score (a low immune score).
  • kits or article of manufacture for providing a prognosis of a subject having diffuse large B-cell lymphoma responding to a treatment regime including an anthracycline and anti-CD20 antibody including one or more nucleic acid primers or probes for determining the level of any of the biomarkers for determining an immune score as described here using any one or more of the ratios in Table 3 or 5.
  • kits comprising one or more nucleic acid primers or probes for determining the level of any of the biomarkers for determining an immune score as described here using any one or more of the ratios in Table 3 or 5.
  • the kit or article of manufacture includes written instructions for implementing an above described method.
  • the kit comprises reagents for quantitative amplification of nucleic acid, preferably RNA, of a biomarker that can be used to determine an immune score as described herein.
  • the kit may comprise a microarray.
  • the kits may contain 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 18, 20, 25, 30, 40, 50, 75, 100, 200, 500 or more probes or primers.
  • the primer or probe is a nucleic acid having a sequence sharing at least 70% nucleotide sequence identity, preferably 75% identity, preferably 80% identity, preferably 85% identity, preferably 90% identity, preferably 95% identity, preferably 98 or 99 % identity with the sequence of the relevant nucleic acid encoding, or complementary to a nucleic acid encoding, a biomarker as described herein.
  • the invention also includes a device for determining levels of any one or more of the biomarkers described herein and visual means for reporting (a) an immune score as described herein, and / or (ii) a difference from a reference score.
  • kit, device or article of manufacture of the invention further include instructions for practicing the methods of the invention.
  • the current invention provides the clinician or physician caring for a subject with DLBCL information about the likelihood of response to treatment and overall survival.
  • the clinician or physician can (i) avoid treating a subject with a treatment regime that the subject is unlikely to respond to, (ii) avoid treating a subject with a treatment regime that will provide side effects and unlikely to provide any benefit in treating the disease, (iii) enroll the patient in clinical trials for new therapies for DLBCL, (iv) treat the subject with alternative therapies, such as those which target the immune biomarkers, (v) discuss the likely treatment and outcome scenarios with the subject, (vi) provide more regular or extensive post- treatment surveillance for a subject identified as having a low response or survival rate, and / or (vi) proceed to treat a subject identified as likely to response with added confidence the treatment is likely to provide benefit to the subject.
  • Figure 1 Kaplan-Meier estimates of survival of the Australian-tissue cohort of DLBCL patients treated with R-CHOP for high and low immune-ratio CD4*CD8:M2*PD- L1 .
  • Figure 3 Kaplan-Meier estimate of survival of the validation cohort of 233 DLBCL patients treated with R-CHOP-like therapy. Patients stratified by the high and low immune-ratio CD4 * CD8:M2 * PD-L1 quantified using the Affymetrix platform on frozen tissue.
  • the instant invention overcomes several major problems with current cancer prognosis in providing methods, devices, kits and compositions using novel combinations of biomarkers identified by expression profiling and survival analysis of diffuse large B-cell lymphoma (DLBCL) patients.
  • particular biomarkers have been identified that may be used to predict response to chemotherapy and clinical outcome, e.g., overall survival or disease-free survival, in DLBCL patients.
  • the present invention is based on the relationship between immune effectors (beneficial host response to tumour) and inhibitory host-checkpoint response (negative host and/or tumour response to adapt to and evade immune surveillance).
  • the inventors for the first time determine that the net-tumoural immunity, being the relationship of the antagonistic forces of immune effectors and inhibitory checkpoint response, have significant prognostic value.
  • the net-tumoural immunity as determined by an immune-ratio of immune effectors to inhibitory check-point response can predict a subjects response to a therapy treatment including an anthracycline and a B-cell depleting antibody (e.g. any anti-CD20 antibody), for example R-CHOP treatment.
  • An advantage of the present invention is that the prognostic value is independent of existing pre-treatment prognosticators such as cell-of-origin (COO), international prognostic index (IPI) and/or the revised-international prognostic index (R-IPI).
  • COO cell-of-origin
  • IPI international prognostic index
  • R-IPI revised-international prognostic index
  • the present invention can be used in conjunction with COO, IPI or R-IPI to better predict overall survival and response to initial therapy.
  • the present invention is a valuable prognosticator as it segregates patients into distinct categories, those categories containing a high proportion of patients and can be used independently of, or in conjunction with to enhance, the discriminatory ability of COO, R-IPI and IPI.
  • Those subjects identified as having a low likelihood to respond to treatment or a low likelihood of survival can then be treated using regimes other than anthracycline and anti-CD20 monoclonal antibody based chemo-immunotherapy (e.g. R-CHOP), such as those which block the PD-1/PD-L1 axis.
  • subjects identified as having a low likelihood to respond to treatment or a low likelihood of survival may still be treated with anthracycline and anti-CD20 monoclonal antibody based chemo- immunotherapy (e.g. R-CHOP) but are instead subject to an increased level of post- therapy surveillance.
  • anthracycline and anti-CD20 monoclonal antibody based chemo-immunotherapy e.g. R-CHOP
  • the methods described herein can be used to determine the likelihood of recurrence-free survival or overall survival if the chemo-immunotherapy was applied.
  • those patients determined to have a low likelihood of recurrence-free survival or overall survival in other words stratified by their immune score into a group having a low probability of recurrence-free survival or overall survival, they can be treated by more aggressive or alternative treatments, for example checkpoint-blockage treatments.
  • prognosis' generally refers to a forecast or prediction of the probable course or outcome of the cancer.
  • prognosis includes the forecast or prediction of any one or more of the following: duration of survival of a patient susceptible to or diagnosed with diffuse large B-cell lymphoma, duration of recurrence-free survival, duration of progression free survival of a patient susceptible to or diagnosed with diffuse large B-cell lymphoma, response rate in a group of patients susceptible to or diagnosed with diffuse large B-cell lymphoma, and/or duration of response in a patient or a group of patients susceptible to or diagnosed with a diffuse large B-cell lymphoma.
  • Prognosis also includes prediction of favorable responses to cancer treatments, such as a conventional cancer therapy, for example a treatment regime including an anthracycline and anti-CD20 antibody'.
  • a treatment regime including an anthracycline and anti-CD20 antibody'.
  • the prediction may need not be correct for 100% of the subjects evaluated. The term, however, requires that a statistically significant portion of subjects can be identified as having an increased probability of having a given outcome.
  • 'Responding to a treatment regime' refers to a clinically or biochemically favorable detectable response to a treatment, such as a conventional cancer therapy.
  • a favorable response is survival measured at a later time point after treatment, for example, 1 , 2, 3, or 4 years post treatment.
  • OS' is well known to one of skill in the art and refers to the fate of the patient after an event, preferably after the start or end of a treatment regime, despite the possibility that the cause of death in a patient is not directly due to the effects of the disease (cancer). In other words, it refers to the prognosis that the patient will not die because of DLBCL, preferably within at least 1 year, at least 2 years, at least 3 years, at least 4 years, at least 5 years, at least 10 years or at least 15 years.
  • a 'treatment regime including an anthracycline and anti-CD20 antibody' refers to any treatment administrable to a subject for cancer therapy that includes an anthracycline and anti-CD20 antibody.
  • Exemplary treatments include a chemotherapy or chemo-immunotherapy treatment including an anthracycline and anti-CD20 antibody is R-CHOP (Rituximab, Cyclophosphamide, Hydroxydaunorubicin, Oncovin (vincristine), and Prednisone or Prednisolone), R-CHOP-14, R-CHOP-21 , DA-EPOCH-R (dose- adjusted etoposide, doxorubicin, and cyclophosphamide with vincristine, prednisone, and rituximab) or R-ACVBP (rituximab, doxorubicin, cyclophosphamide, vindesine, bleomycin, and prednisone). More preferably, the chemotherapy is R-CHOP.
  • anthracycline' refers to a class of drugs used in cancer chemotherapy derived from Streptomyces bacteria.
  • the anthracycline may be doxorubicin, daunorubicin, idarubicin or epirubicin.
  • a 'B-cell depleting antibody' is any antibody that reduces the number of clinically or biochemically detectable B-cells in a subject, preferably the number of cancerous B- cells.
  • a non-limiting example of a B-cell depleting antibody is inotuzumab or an anti- CD20 antibody.
  • 'Anti-CD20 antibody' refers to antibodies or antigen-binding fragments thereof that specifically target CD20.
  • Exemplary anti-CD20 antibodies include rituximab, obinutuzumab and ofatumumab.
  • the anti-CD20 antibody is rituximab.
  • the reference score has been predetermined or is determined from a cohort of patients with known DLBCL outcome, preferably survival (e.g. overall survival, 1 year, 2 years, 3 years or 4 years survival) after treatment with a regime that includes an anthracycline and anti-CD20 antibody.
  • survival e.g. overall survival, 1 year, 2 years, 3 years or 4 years survival
  • the reference score stratifies the subject into one of two subgroups with the following rule: if the immune score is less than the reference score, then the patient is assigned to the group with low likelihood of response (e.g.
  • the reference score stratifies subjects into a group with a high likelihood of overall survival of at least 95%, 94%, 93%, 92%, 91 %, 90%, 85%, 80%, 75% or 70%, and into a group with a low likelihood of overall survival of less than 60%, 55%, 54%, 53%, 52%, 51 %, 50%, 49%, 48%, 47%, 46%, 45% or 44%.
  • the reference score can be determined using statistical methods known in the art, for example, a tree-structure recursive partitioning statistical model or the median value. Survival analysis may be performed using Kaplan-Meier method and the two survival curves from the two subgroups can be compared using the log-rank test, such as that described in the Examples.
  • DLBCL 'Diffuse large B-cell lymphoma
  • DLBCL refers to a type of aggressive non-Hodgkin lymphoma, and includes any lymphoma diagnosed as a DLBCL by any clinical or biochemical measure.
  • DLBCL includes all four major subtypes of DLBCL: activated (ABC-DLBCL), germinal center (GCB-DLBCL), Type III (unclassified) DLBCL and primary mediastinal B-cell lymphoma (PMBL).
  • IPI International Prognostic Index
  • CHOP Cyclophosphamide, Hydroxydaunorubicin, Oncovin (vincristine), and Prednisone or Prednisolone
  • IPI International Prognostic Index
  • the biomarkers or immune markers as used herein may be related to prognosis, for example, prediction of survival, recurrence, or therapy response.
  • the ratio of differential patterns of expression of a plurality of these biomarkers may be used to predict the survival outcome of a subject with diffuse large B-cell lymphoma.
  • the unique pattern of expression of a plurality of biomarkers in a subject may be used to generate an immune score or immuno-biological score of survival using an immune ratio describe herein.
  • Any reference herein to immune score may be a reference to immuno-biological score when any aspect of the invention includes one or more of TNFa, PD-L2, LAG3, TIM3, LM02 or SCYA3.CCL3. An immuno-biological score is explained further in Example 6.
  • Subjects with a high immune score or immuno-biological score relative to a reference score of cut-off value may have, or are more likely to have, a long survival time (e.g., more than about 4 years) after a treatment regime.
  • Subjects with a low immune score or immuno-biological score relative to a reference score or cut-off value may have a short survival time (e.g., less than about 4 years) after a treatment regime.
  • reference to biomarker or immune marker refers to any one or more of CD137, CD4, CD8, CD56, TNFa (alpha), LM02, PD-1 , PD-L1 , CD163, CD68, PD-L2, LAG 3, TIM3 and SCYA3(CCL3).
  • nucleotide sequence of the gene and mRNA, and the polypeptide sequence of the gene product that is translated can be identified by a person skilled in the art by accessing any one of a number of publicly accessible databases such as GenBank or EMBL or as shown in Table 6 herein.
  • the level of each biomarker may be converted into an immune score using a ratio as outlined in Table 3 or 5.
  • a 'ratio' or 'immune ratio' as used herein refers to the relationship between two or more biomarkers.
  • the ratio or immune ratio is the relationship between one or more of CD137, CD4, CD8, CD56, TNFa (alpha) and LM02 to one or more of PD-1 , PD-L1 , CD163, CD68, PD-L2, LAG 3, TIM3 and SCYA3(CCL3).
  • the ratio or immune ratio is the relationship between one or more of CD137, CD4, CD4 and CD56 to one or more of PD-1 , PD-L1 , CD163 and CD68.
  • the ratio or immune ratio is one of those listed in Table 3 or 5.
  • the ratio or immune ratio may also be expressed herein as an immune-effector: checkpoint ratio.
  • the immune scores generated may be used to classify patients into high or low immune score based on a comparison with a survival cut-off value.
  • An immune score that is higher than the survival cut-off is associated with a good prognosis, such as a long survival time or a better survival or more positive response to a treatment regime, and an immune score that is lower than the survival cut-off is associated with a poor prognosis, such as a short survival time or a poor survival or less positive response to a treatment regime.
  • a survival cut-off value may be derived from a control group of patients of known outcome after treatment with a particular regime, for example a treatment regime including an anthracycline and anti-CD20 antibody, using standard statistical techniques, for example, using a permutation test.
  • the method further comprises the step of treating the DLBCL by administering one or more therapeutic agents.
  • the therapeutic agents may be an anthracycline and anti-CD20 antibody, or any regime including anthracycline and anti-CD20 antibody as described herein.
  • the method may include treating the subjects identified with a high immune score with a treatment regime including an anthracycline and anti-CD20 antibody, such as R-CHOP or other regime described herein.
  • the method further comprises the step of enrolling the subject identified as having a low immune score in a clinical trial for treatment of DLBCL.
  • the method may further comprise the step of administering a compound that binds to and inhibits PD-1 to a subject identified as having a low immune score.
  • a biological sample such as a tissue or cell sample, may be collected from a subject with a lymphoma, for example diffuse large B-cell lymphoma.
  • the collection step may comprise surgical resection.
  • the sample of tissue may be stored in RNAIater or flash frozen, such that RNA may be isolated at a later date.
  • RNA may be isolated from the tissue and used to generate labeled probes for a nucleic acid microarray analysis.
  • the RNA may also be used as a template for a method described herein in which the expression or level of a plurality of biomarkers is analyzed (e.g. microarray, qRT-PCR).
  • the expression data generated may be used to derive an immune score, e.g., using a ratio as described in Table 3 or 5.
  • the method further comprises a step of providing a biological sample from the subject or obtaining a biological sample from the subject.
  • the methods comprise surgically removing a biological sample, preferably a tumour sample, from the subject.
  • the biological sample may be further treated before analysis.
  • the biological sample may be selected from the group consisting of formalin fixed embedded tissue or cells, processed tissue, frozen tissue, and a biopsy. Preferably, at least 40%, 50%, 60%, 70%, 80% or 90% of the cells in the sample are tumour cells.
  • the invention described herein involves measuring expression of one or more biomarkers in a biological sample of cells or tissue from a subject with diffuse large B-cell lymphoma.
  • the expression information may be obtained by testing biological samples by a lab, a technician, a device, or a clinician.
  • determining the level (or obtaining an expression level or profile) of one or more biomarkers in a biological sample from the subject comprises extracting nucleic acids from the sample from the subject.
  • the nucleic acid sample is an RNA sample, preferably an mRNA sample.
  • the expression level of the nucleic acid is determined by any method described herein, such as by hybridizing the nucleic acid, or amplification products thereof, to a DNA microarray or by using RNA-sequencing.
  • Amplification products may be generated, for example, with reverse transcription, optionally followed by PCR amplification of the products.
  • the pattern or signature of expression in each biological sample may then be used to generate an immune score for prognosis or classification, such as predicting overall survival, disease recurrence or response to therapy.
  • the expression of one or more biomarkers may be measured by a variety of techniques that are well known in the art. Quantifying the levels of the RNA (e.g. mRNA) of a biomarker may be used to measure the level or expression of the biomarker. Alternatively, quantifying the levels of the protein product of a biomarker may be used to measure the expression of the biomarker. Additional information regarding the methods discussed below may be found in Ausubel et al. (2003) or Sambrook et al. (1989). As would be recognized by one of skill in the art, various parameters may be manipulated to optimize detection of the mRNA or protein of interest.
  • a nucleic acid microarray may be used to quantify the differential expression of a plurality of biomarkers.
  • Microarray analysis may be performed using commercially available equipment, following manufacturer's protocols, such as by using the Affymetrix GeneChip® technology (Santa Clara, CA) or the Microarray System from Incyte (Fremont, CA).
  • single-stranded nucleic acids e.g., cDNAs or oligonucleotides
  • the arrayed sequences are then hybridized with specific nucleic acid probes from the cells of interest.
  • Fluorescently labeled cDNA probes may be generated through incorporation of fluorescently labeled deoxynucleotides by reverse transcription of RNA extracted from the cells of interest.
  • the RNA may be amplified by in vitro transcription and labeled with a marker, such as biotin.
  • the labeled probes are then hybridized to the immobilized nucleic acids on the microchip under highly stringent conditions. After stringent washing to remove the non-specifically bound probes, the chip is scanned by confocal laser microscopy or by another detection method, such as a CCD camera.
  • the raw fluorescence intensity data in the hybridization files are generally preprocessed with the robust multichip average (RMA) algorithm to generate expression values.
  • RMA robust multichip average
  • Quantitative real-time PCR may also be used to measure the differential expression of a plurality of biomarkers.
  • the RNA template is generally reverse transcribed into cDNA, which is then amplified via a PCR reaction.
  • the amount of PCR product is followed cycle-by-cycle in real time, which allows for determination of the initial concentrations of mRNA.
  • the reaction may be performed in the presence of a fluorescent dye, such as SYBR Green, which binds to double-stranded DNA.
  • the reaction may also be performed with a fluorescent reporter probe that is specific for the DNA being amplified.
  • a non-limiting example of a fluorescent reporter probe is a TaqMan® probe (Applied Biosystems, Foster City, CA).
  • the fluorescent reporter probe fluoresces when the quencher is removed during the PCR extension cycle.
  • Multiplex qRT-PCR may be performed by using multiple gene-specific reporter probes, each of which contains a different fluorophore. Fluorescence values are recorded during each cycle and represent the amount of product amplified to that point in the amplification reaction. To minimize errors and reduce any sample-to-sample variation, qRT-PCR may be performed using a reference standard. The ideal reference standard is expressed at a constant level among different tissues, and is unaffected by the experimental treatment.
  • Suitable reference standards include, but are not limited to, mRNAs for the housekeeping genes glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) and ⁇ - actin.
  • GPDH glyceraldehyde-3-phosphate-dehydrogenase
  • ⁇ - actin The level of mRNA in the original sample or the fold change in expression of each biomarker may be determined using calculations well known in the art.
  • RNA quantification may be by the NanoString Gene Expression Assay as described herein, specifically in Example 1.
  • the level of a biomarker may be detected using Northern blot analysis.
  • total cellular RNA can be purified from cells by homogenization in the presence of nucleic acid extraction buffer, followed by centrifugation. Nucleic acids are precipitated, and DNA is removed by treatment with DNase and precipitation. The RNA molecules are then separated by gel electrophoresis on agarose gels according to standard techniques, and transferred to nitrocellulose filters. The RNA is then immobilized on the filters by heating. Detection and quantification of specific RNA is accomplished using appropriately labelled DNA or RNA probes complementary to the RNA in question.
  • the nucleic acid probe can be labelled with, e.g., a radionuclide, such as 3H, 32P, 33P, 14C, or 35S; a heavy metal; or a ligand capable of functioning as a specific binding pair member for a labelled ligand (e.g., biotin, avidin or an antibody), a fluorescent molecule, a chemiluminescent molecule, or an enzyme.
  • a radionuclide such as 3H, 32P, 33P, 14C, or 35S
  • a heavy metal e.g., a ligand capable of functioning as a specific binding pair member for a labelled ligand (e.g., biotin, avidin or an antibody), a fluorescent molecule, a chemiluminescent molecule, or an enzyme.
  • Probes can be labelled to high specific activity by nick translation, random priming, or other methods known to one of skill in the art.
  • RNA gene transcript levels can be quantified by computerized imaging systems, such the Molecular P-71519-PC Dynamics 400-B 2D Phosphorimager available from Amersham Biosciences, Piscataway, NJ.
  • determining the levels of an RNA expression can be accomplished using the technique of in situ hybridization.
  • This technique requires fewer cells than the Northern blotting technique, and involves depositing whole cells onto a microscope cover slip and probing the nucleic acid content of the cell with a solution containing radioactive or otherwise labelled nucleic acid (e.g., cDNA or RNA) probes.
  • This technique is particularly well-suited for analyzing tissue biopsy samples from subjects.
  • the practice of the in situ hybridization technique is described in more detail in U.S. Pat. No. 5,427,916, the disclosure of which is incorporated herein by reference.
  • the Kaplan-Meier method (also known as the product limit estimator) estimates the survival function from life-time data. In medical research, it can be used to measure the fraction of patients living for a certain amount of time after treatment.
  • a plot of the Kaplan-Meier method of the survival function is a series of horizontal steps of declining magnitude which, when a large enough sample is taken, approaches the true survival function for that population.
  • the value of the survival function between successive distinct sampled observations ("clicks") is assumed to be constant.
  • Kaplan-Meier curve An important advantage of the Kaplan-Meier curve is that the method can take into account "censored" data— losses from the sample before the final outcome is observed (for instance, if a patient withdraws from a study). On the plot, small vertical tick-marks indicate losses, where patient data has been censored. When no truncation or censoring occurs, the Kaplan-Meier curve is equivalent to the empirical distribution. Survival analysis can be performed using the Kaplan-Meier method (as described in the Examples herein and shown in Figure 1 ).
  • the log-rank test (also known as the Mantel-Cox test) is a hypothesis test to compare the survival distributions of two groups of patients. It is a nonparametric test and appropriate to use when the data are right censored. It is widely used in clinical trials to establish the efficacy of new drugs compared to a control group when the measurement is the time to event.
  • the log-rank test statistic compares estimates of the hazard functions of the two groups at each observed event time. It is constructed by computing the observed and expected number of events in one of the groups at each observed event time and then adding these to obtain an overall summary across all time points where there is an event.
  • the log-rank statistic can be derived as the score test for the Cox proportional hazards model comparing two groups. It is therefore asymptotically equivalent to the likelihood ratio test statistic based from that model.
  • the invention also provides a device, system, kit or article of manufacture for use in implementing the above described methods.
  • the device, system, kit or article of manufacture may include a nucleic acid for hybridising to any one or more of the biomarkers useful to determine an immune score by Watson-Crick base pairing.
  • the nucleic acid may be an oligonucleotide or like probe having from about 8 to 100 or more nucleotides.
  • the nucleic acid has a sequence sharing at least 70% nucleotide sequence identity, preferably 75% identity, preferably 80% identity, preferably 85% identity, preferably 90% identity, preferably 95% identity, preferably 98 or 99 % identity with the sequence of the relevant nucleic acid encoding, or complementary to a nucleic acid encoding, a biomarker as described herein.
  • Percent sequence identity is determined by conventional methods, by means of computer programs known in the art such as GAP provided in the GCG program package (Program Manual for the Wisconsin Package, Version 8, August 1994, Genetics Computer Group, 575 Science Drive, Madison, Wisconsin, USA 5371 1 ) as disclosed in Needleman, S.B. and Wunsch, CD., (1970), Journal of Molecular Biology, 48, 443-453, which is hereby incorporated by reference in its entirety.
  • GAP is used with the following settings for DNA sequence comparison: GAP creation penalty of 5.0 and GAP extension penalty of 0.3.
  • the device, system, kit or article of manufacture may include reagents for use in the amplification or digestion or other manipulation of nucleic acids including an enzyme, such as a polymerase or a restriction endonuclease.
  • the device, system, kit or article of manufacture may include reagents for quantitative Northern and Southern blotting, and microarray and PCR, preferably realtime or quantitative PCR.
  • arrays and microarrays which contain probes specific for the biomarkers, and determining an immune or immuno-biological score, as disclosed herein are also encompassed within the scope of this invention. Methods of making arrays are well- known in the art and as such do not need to be described in detail.
  • Arrays of the invention can contain the profiles of one or more genes as disclosed in Table 3 or 5. Accordingly, arrays for detection of recurrence can be customized for determining response to therapy or overall survival of a subject with diffuse large B-cell lymphoma.
  • the array can be packaged as part of kit comprising the customized array itself and a set of instructions for how to use the array to determine an subject's likelihood of responding to a treatment regime.
  • kits of the invention further include instructions for practicing the methods of the invention.
  • These instructions may be present in the kits in a variety of forms, one or more of which may be present in the kit.
  • One form in which these instructions may be present is as printed information on a suitable medium or substrate, e.g., a piece or pieces of paper on which the information is printed, in the packaging of the kit, in a package insert, etc.
  • Yet another means would be a computer readable medium, e.g., diskette, CD, etc., on which the information has been recorded.
  • Yet another means that may be present is a website address which may be used via the internet to access the information at a remote site. Any convenient means of conveying instructions may be present in the kits.
  • One aspect of the invention provides a kit comprising: (a) any of the gene chips described herein; and (b) one of the computer-readable mediums described herein.
  • the invention also includes computer readable media that comprises reference gene expression profiles.
  • Such media can contain all or part of the gene expression profiles of the biomarkers described herein that can be used to determine an immune score.
  • the media can be a list of the genes or contain the raw data for running a user's own statistical calculation, such as the methods disclosed herein.
  • Another aspect of the invention provides a program product (i.e., software product) for use in a computer device that executes program instructions recorded in a computer-readable medium to perform one or more steps of the methods described herein, such as for estimating the likelihood of a subject with diffuse large B-cell lymphoma responding to a treatment regime including an anthracycline and anti-CD20 antibody.
  • a program product i.e., software product
  • the initial tissue cohort comprised 252 patients with histologically confirmed DLBCL. All patients received R-CHOP, and were otherwise selected solely on the basis of FFPE tissue availability. Only de-novo cases of DLBCL were included. Grade 1MB or transformed follicular lymphoma, HIV-positive and post -transplant patients were excluded. Survival data was available in 158 patients.
  • Affymetix platform Liffymetix platform
  • RNA samples were chosen to permit COO categorization (Wright et al. Proc Natl Acad Sci U S A 2003; 100(17): 9991 -6.), and analysis of immune effectors and immune- checkpoints.
  • Hybridizations were carried out according to the NanoString Gene Expression Assay Manual. Five microliter of each RNA sample (100ng) was mixed with 20 ⁇ of nCounter Reporter probes in hybridization buffer and 5 ⁇ of nCounter Capture probes for a total reaction volume of 30 ⁇ . The hybridizations incubated at 65°C for approximately 16-20 hours. Three separate runs were performed requiring the production of three identical codesets.
  • Tree-based recursive portioning analysis A survival analysis based on the tree-structured recursive partitioning model was applied to stratify patients into two survival subgroups (low or high-risk) based on a single marker or ratio (Hothorn T, Hornik K, Zeileis A. Unbiased recursive partitioning: A conditional inference framework. Journal of Computational and Graphical Statistics 2006; 15(3): 651 -74.) .
  • the survival tree determines the best optimal cutoff for each single marker or ratio based on a permutation test.
  • Example 3 Immune-effector homepoint ratios as a measure of net anti- tumoural immunity within the TME.
  • the denominators were the checkpoints PD-1 , PD-L1 , CD163, CD68 and ' ⁇ 2' (defined as the ratio of CD163.div.CD68 checkpoint molecules).
  • the rationale for including M2 was that the combination of CD68 and CD163 was likely to be more informative than either checkpoint alone.
  • the tree-structured model identified a number of prognostic immune molecule combinations (Table 3 or 5).
  • CD4xCD8.div.M2xPD-L1 This was selected for further testing.
  • the CD4 * CD8 * :M2 * PD-L1 ratio separated patients into disparate high and low-ratio 4 year survivals that differed by 45% ( Figure 1A, P ⁇ 0.0001 ).
  • the proportion of patients in high and low-ratio groups were 59% and 41 %.
  • * or x refers to the product or multiplication of, and 'div' refers to a division or ratio.
  • the cutoff for each single marker or ratio was determined by the tree-structured survival model to divide the patients into two subgroups.
  • a immune score that is above the cut-off stratifies the patient into a high immune score or high ratio group with a high likelihood of response or overall survival, whereas an immune score that is below the cut-off stratifies the patient into a low immune score or low ratio group with a low likelihood of response or survival.
  • the likelihood of survival for the high and low groups are shown below.
  • subject with an immune score above -0.278958829 when using the immune ratio CD4xCD8.div.M2xPD-L1 would be stratified into the high immune score group.
  • a subject from the cohort with an immune score of 0.541762908 what stratified into the high immune score group. That subject had a 4.13 year survival time.
  • Another subject from the cohort had an immune score of - 1.186672016 that stratified that subject into the low immune score group. That subject had a 0.56 year survival time.
  • the difference between survival curves as shown here as adjusted P-values is a measure of the prognostic value of each marker/ratio to separate the two subgroups based on their survival.
  • the greater the difference between the survival curves for a ratio i.e. the lower the P value) the greater the prognostic value.
  • the values above correlate with the likelihood of survival of a patient with an immune score that, when compared with the cut-off value, stratifies them into a low immune score or low ratio group. For example, a patient that has a low immune score or low ratio when using the immune ratio CD4xCD8.div.M2xPD-L1 , has a 47% likelihood of survival after 4 years.
  • the values above correlate with the likelihood of survival of a patient with an immune score that, when compared with the cut-off value, stratifies them into a high immune score or high ratio group. For example, a patient that has a high immune score or high ratio when using the immune ratio CD4xCD8.div.M2xPD-L1 , has a 92% likelihood of survival after 4 years.
  • Example 4 Immune-effectorxheckpoint ratios adds to conventional prognosticators.
  • Table 4 4-year survival stratified by high vs low immune-ratios in the Australian- tissue cohort.
  • R-IPI * There were 152 patients with R-IPI data.
  • R-IPI with the immune-ratio gave the following proportions: VG/G-high 37%; VG/G-low 21 %; poor-high 22%; poor-low 21 %.
  • proportions were GCB-high 43%; GCB-low 23%; non-GCB-high 16%; non- GCB-low 18%.
  • Example 5 External validation of immune-ratios using the Affymetrix platform on frozen tissue.
  • the immune-ratio CD4*CD8:M2*PD-L1 was then applied to the independent cohort of R-CHOP-like treated patients in which gene expression was quantified on fresh-frozen samples using an Affymetrix platform. 7
  • the immune-ratio (CD4*CD8:[CD163.div.CD68]*PD-L1 ) was identified for further evaluation. Notably, the denominator itself also included a ratio (CD163.div.CD68).
  • TAMs are either 'Ml ' (CD68 hi CD163 l0 ) or ' ⁇ 2' (CD68 hi CD163 hi ), but only M2 TAMs that are tumour promoting.
  • the CD163.div.CD68 ratio (as a measure of M2-TAMs) was more informative than either marker alone.
  • the CD4*CD8:M2*PD-L1 immune-ratio high and low survival curves were distinct, and the ratio was independent of COO and R-IPI.
  • a new prognosticator must segregate patients into distinct categories containing a high proportion of patients, and enhance the discriminatory ability of R-IPI and COO.
  • R-IPI is influenced by patient fitness, age and tumour burden, whereas COO reflects B-cell differentiation.
  • the combination of net anti- tumoural immunity using the immune-ratio with either COO or R-IPI better distinguished patients than R-IPI or COO alone.
  • therapeutic PD-1 blockade is more effective in cancers enriched with immune- effectors that are negatively regulated by PD-1 /PD-L1 -axis mediated inhibition (Tumeh PC et al. Nature 2014; 515(7528): 568-71 ).
  • levels of PD-1 on tumour-infiltrating lymphocytes is less predictive of response to PD-1 blockade than PD-L1 expression (Ansell SM et al. N Engl J Med 2015; 372(4): 31 1 -9; Taube JM et al. Clin Cancer Res 2014; 20(19): 5064-74).
  • Immune-ratios measured by digital hybridization technologies applicable to FFPE may permit rational selection of patients in whom checkpoint- blockade should be tested.
  • the values in the fair right column in Table 5 correlate with the likelihood of survival of a patient with an immune score that, when compared with the cut-off value, stratifies them into a high immune score or high ratio group.
  • a patient that has a high immune score or high ratio when using the immune ratio CD4xCD8xCD137.TNFR9xTNF.AIphaxLM02.div.M2xSCYA3..CCL3xPD.1xPD.L1 has a 90% likelihood of survival after 4 years.
  • the immune score could be extended to include combinations that include the additional markers TNFa (alpha) (numerator) and PD-L2, LAG3, TIM3 (denominators), and this combined with the biological markers LM02 (numerator) and SCYA3.CCL3 (denominator), as an 'immuno-biological score' (any reference herein to immune score may be a reference to immuno-biological score when any aspect of the invention includes one or more of TNFa, PD-L2, LAG 3, TIM3, LM02 or SCYA3.CCL3).
  • Table 5 Results of tree-structured survival analysis described in Example 6. The cutoff for each single marker or ratio was determined by the tree- structured survival model to divide the patients into two subgroups. Adjusted P-values (Bonferroni multiple correction procedure) of the survival curve difference test was used to assess the prognostic value of each marker/ratio together with the 4-year survival proportion in each survival group. Other statistical models can be used to calculate the cutoff, for example the median value. The results are shown to 9 decimal places however the cutoff values still apply when only 2 decimal places are used.
  • Table 6 List of the NCBI reference sequences or accession numbers from the GenBank database including version numbers for each gene sequence referred to herein. Exemplary probes that target the relevant gene sequences are listed (NSID: unique identifier used by NanoString to track and identify probes comprised of the accession number and the nucleotide position immediately prior to the target region, i.e. target region for CD4 probe is 976-1075).

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Abstract

L'invention concerne des méthodes, des dispositifs et des kits permettant d'obtenir le pronostic de sujets atteints d'un lymphome. En particulier, lesdites méthodes consistent à déterminer la probabilité de survie, la récurrence ou l'issue d'un traitement chez des patients atteints d'un lymphome d'immunotype B qui suivent et/ou qui ont suivi une chimiothérapie. En particulier, la présente invention concerne une méthode permettant d'obtenir un pronostic d'un sujet atteint d'un lymphome diffus à grandes cellules d'immunotype B répondant à un schéma thérapeutique comprenant une anthracycline et un anticorps appauvri en lymphocytes B, tel qu'un anticorps anti-CD20, ladite méthode consistant à : déterminer un score immunitaire pour le sujet sur la base du rapport d'un taux d'un ou plusieurs éléments quelconques parmi CD137, CD4, CD8, CD56, TNFα (alpha) et LMO2 chez le sujet à un taux d'un ou plusieurs éléments quelconques parmi PD-1, PD-L1, CD163, CD68, PD-L2, LAG3, TIM3 et SCYA3 (CCL3) chez le sujet, et comparer le score immunitaire à un score de référence ; le score immunitaire en comparaison avec le score de référence indiquant le pronostic du sujet à répondre à un schéma thérapeutique comprenant une anthracycline et un anticorps appauvri en lymphocytes B.
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JP7206203B2 (ja) 2017-02-07 2023-01-17 アンスティチュ ナショナル ドゥ ラ サンテ エ ドゥ ラ ルシェルシュ メディカル がんの重症度を評価するためのｔｉｍ－３
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CN111909999A (zh) * 2019-05-07 2020-11-10 上海交通大学医学院附属瑞金医院 miRNA组合及其在制备DLBCL预后的标记物中的应用
CN111909999B (zh) * 2019-05-07 2023-03-07 上海交通大学医学院附属瑞金医院 miRNA组合及其在制备DLBCL预后的标记物中的应用
CN110687281A (zh) * 2019-08-26 2020-01-14 中国医学科学院肿瘤医院 Pd-l1自身抗体在肿瘤预后评估中的应用
CN110687281B (zh) * 2019-08-26 2023-05-23 中国医学科学院肿瘤医院 Pd-l1自身抗体在肿瘤预后评估中的应用
WO2022093910A1 (fr) * 2020-10-27 2022-05-05 The Children’S Mercy Hospital Signature du gène pronostique et procédé de pronostic et de traitement du lymphome diffus à grandes cellules b
WO2022197236A1 (fr) * 2021-03-19 2022-09-22 Mezheyeuski Artur Nouveau biomarqueur

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