US20170313775A1 - Checkpoint Blockade and Microsatellite Instability - Google Patents

Checkpoint Blockade and Microsatellite Instability Download PDF

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US20170313775A1
US20170313775A1 US15/523,451 US201515523451A US2017313775A1 US 20170313775 A1 US20170313775 A1 US 20170313775A1 US 201515523451 A US201515523451 A US 201515523451A US 2017313775 A1 US2017313775 A1 US 2017313775A1
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Luis Diaz
Bert Vogelstein
Kenneth W. Kinzler
Nickolas Papadopoulos
Dung Le
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Definitions

  • This invention is related to the area of cancer. In particular, it relates to cancer therapy.
  • MSI Microsatellite instability
  • Lynch Syndrome is an inherited cancer syndrome that predisposes patients to colon, endometrial, gastric cancer, ovarian, small intestine, liver, hepatobiliary, upper urinary tract, brain, and prostate cancer.
  • MSI is also present in 10-20% of sporadic colorectal, gastric, prostate, lung, ampullary, and endometrial cancers. Between 0.3% and 13% of pancreatic cancers are reported to be MSI as well.
  • TILs tumor-infiltrating lymphocytes
  • CD8+ T-cells and the ratio of CD8+ effector T-cells/FoxP3+ regulatory T-cells seems to correlate with improved prognosis and long-term survival in solid malignancies such as ovarian, colorectal and pancreatic cancer, hepatocellular carcinoma, malignant MEL and RCC.
  • TILs can be expanded ex vivo and re-infused, inducing durable objective tumor responses in cancers such as melanoma.
  • the PD-1 receptor-ligand interaction is a major pathway hijacked by tumors to suppress immune control.
  • the normal function of PD-1, expressed on the cell surface of activated T-cells under healthy conditions, is to down-modulate unwanted or excessive immune responses, including autoimmune reactions.
  • the ligands for PD-1 (PD-L1 and PD-L2) are constitutively expressed or can be induced in various tumors. Binding of either PD-1 ligand to PD-1 inhibits T-cell activation triggered through the T-cell receptor.
  • PD-L1 is expressed at low levels on various non-hematopoietic tissues, most notably on vascular endothelium, whereas PD-L2 protein is only detectably expressed on antigen-presenting cells found in lymphoid tissue or chronic inflammatory environments.
  • PD-L2 is thought to control immune T-cell activation in lymphoid organs, whereas PD-L1 serves to dampen unwarranted T-cell function in peripheral tissues.
  • healthy organs express little (if any) PD-L1, a variety of cancers were demonstrated to express abundant levels of this T-cell inhibitor.
  • PD-L1 High expression of PD-L1 on tumor cells (and to a lesser extent of PD-L2) has been found to correlate with poor prognosis and survival in various cancer types, including renal cell carcinoma (RCC), pancreatic carcinoma, hepatocellular carcinoma, ovarian carcinoma and non-small cell lung cancer (NSCLC). Furthermore, PD-1 has been suggested to regulate tumor-specific T cell expansion in patients with malignant MEL. The observed correlation of clinical prognosis with PD-L1 expression in multiple cancers suggests that the PD-1/PD-L1 pathway plays a critical role in tumor immune evasion and should be considered as an attractive target for therapeutic intervention.
  • RCC renal cell carcinoma
  • NSCLC non-small cell lung cancer
  • CTLA-4 and PD-1 are upregulated on activated T cells and provide inhibitory signals to T cells undergoing activation. Inhibitory antibodies directed at these receptors have been shown to break immune tolerance and promote anti-tumor immunity.
  • MK-3475 is a humanized monoclonal IgG4 antibody against PD-1 and is showing activity in multiple tumor types including melanoma and non-small cell lung cancer (NSCLC).
  • MK-3475 (previously known as SCH 900475) is a potent and highly-selective humanized mAb of the IgG4/kappa isotype designed to directly block the interaction between PD-1 and its ligands, PD-L1 and PD-L2.
  • MK-3475 contains the S228P stabilizing mutation and has no antibody-dependent cell-mediated cytotoxicity (ADCC) or complement-dependent cytotoxicity (CDC) activity.
  • ADCC antibody-dependent cell-mediated cytotoxicity
  • CDC complement-dependent cytotoxicity
  • MK-3475 strongly enhances T lymphocyte immune responses in cultured blood cells from healthy human donors, cancer patients, and primates. In T-cell activation assays using human donor blood cells, the EC50 was in the range of 0.1 to 0.3 nM.
  • MK-3475 also modulates the level of interleukin-2 (IL-2), tumor necrosis factor alpha (TNF ⁇ ), interferon gamma (IFN ⁇ ), and other cytokines.
  • IL-2 interleukin-2
  • TNF ⁇ tumor necrosis factor alpha
  • IFN ⁇ interferon gamma
  • the antibody potentiates existing immune responses only in the presence of antigen and does not nonspecifically activate T-cells.
  • the programmed death 1 (PD-1) pathway is a negative feedback system repressing Th1 cytotoxic immune responses that, if unregulated, could damage the host 1-3 . It is upregulated in many tumors and their surrounding microenvironment. Blockade of this pathway with antibodies to PD-1 or its ligands has led to remarkable clinical responses in some patients with many different cancer types, including melanomas, non-small cell lung cancer, renal cell carcinoma, bladder cancer and Hodgkin's lymphoma 4-10 .
  • the expression of ligands to PD-1 (PD-L1 or PD-L2) on the surface of tumor cells or immune cells is important but not a definitive predictive biomarker for response to PD-1 blockade 4,6-8,11 .
  • MMR-deficient cancers contain prominent lymphocyte infiltrates, consistent with an immune response 19-22 .
  • two of the tumor types that were most responsive to PD-1 blockade in a study by Topalian et al. 10 had high numbers of somatic mutations as a result of exposure to cigarette smoke (lung cancers) or UV radiation (melanomas) 23,24 .
  • MMR-deficient tumors are more responsive to PD-1 blockade than are MMR-proficient tumors.
  • HNPCC Hereditary Non-Polyposis Colorectal Cancer
  • a method of treating a cancer patient is provided.
  • the cancer patient has a high mutational burden, such as found in microsatellite instable cancer (MSI).
  • MSI microsatellite instable cancer
  • An immune checkpoint inhibitory antibody is administered to the cancer patient.
  • a method of treating a cancer patient is provided.
  • a sample from a cancer patient is tested for one or more microsatellite markers selected from the group consisting of BAT-25, BAT-26, MON0-27, NR-21, NR-24, Penta C, and Penta D, and determined to have microsatellite instability.
  • the cancer is selected from the group consisting of: colon, gastric, endometrial, cholangiocarcinoma, pancreatic, and prostate cancers.
  • An anti-PD-1 antibody is administered to the cancer patient.
  • a method for categorizing a tumor of a human.
  • a sample from the human is tested to evaluate stability of one or more microsatellite markers. Microsatellite instability is determined in the sample.
  • the tumor is identified as a good candidate for treatment with an immune checkpoint inhibitory antibody.
  • a method for categorizing a tumor of a human.
  • a sample from the human is tested to evaluate stability of one or more microsatellite markers.
  • Microsatellite stability in the sample is determined.
  • the tumor is identified as a bad candidate for treatment with an immune checkpoint inhibitory antibody.
  • FIGS. 1A-1B Clinical Responses to pembrolizumab.
  • FIG. 1A Biochemical Responses. Serum protein biomarker levels were measured with each cycle and the values represent percent change from baseline. Patients were included if baseline tumor marker values were greater than the upper limit of normal. CA-125 was used for a patient with endometrial cancer; CA19-9 was used for one cholangiocarcinoma and one ampullary cancer; and CEA was used for all other patients. Green, red, and black lines represent patients with MMR-deficient CRCs, MMR-proficient CRCs, and MMR-deficient non-CRC, respectively.
  • FIG. 1B Radiographic responses. Tumor responses were measured at regular intervals and values show the best fractional change of the sum of longest diameters (SLD) from the baseline measurements of each measurable tumor.
  • SLD longest diameters
  • FIGS. 2A-2D Clinical benefit to pembrolizumab according to MMR status.
  • median overall survival was not reached.
  • Patients in the cohort with MMR-proficient cancers had a median PFS of 2.2 months (95% CI 1.4 to 2.8%) and a median OS of 5.0 months (95% CI 3.0 to not estimable).
  • FIG. 3 ( FIG. S2 .) Spider plot of radiographic response. Tumor responses were measured at regular intervals and values show percent change of the sum of longest diameters (SLD) from the baseline measurements of each measurable tumor. Patients were only included if baseline and on study treatment scans were available. Green and red represent patients with MMR-deficient and proficient CRCs, respectively. Blue represents patients with MMR-deficient cancers other than CRC.
  • FIG. 5 ( FIG. S4 .) Waterfall plot of biochemical response. Serum protein biomarker levels were measured with each cycle and the values represent best percent change from baseline. Patients were included if baseline tumor marker values were greater than the upper limit of normal. CA-125 was used for a patient with endometrial cancer; CA19-9 was used for 1 cholangiocarcinoma and 1 ampullary cancer; and CEA was used for all other patients. Green and red represent patients with MMR-deficient and proficient CRCs, respectively. Blue represents patients with MMR-deficient cancers other than CRC.
  • FIGS. 6A-6B Somatic mutations in MMR-deficient and proficient tumors.
  • FIG. 7 ( FIG. S6 ). Immunohistochemistry of CD8 and PD-L1 Expression.
  • the invasive front (yellow dashed line) from a MMR-deficient CRC (subject #16, top) and MMR-proficient CRC (subject #3, bottom).
  • the yellow dashed line separates tumor (T) and normal (N) tissue.
  • TIL tumor infiltrating lymphocytes
  • FIG. 8 ( FIG. S7 .) CD8 and PD-L1 Expression in the MMR-deficient and MMR-proficient tumor microenvironment.
  • T cell density units are cells/mm2 of tumor.
  • Invasive front refers to the immune cells (TILs and macrophages) at the junction of the tumor and normal tissue. P-values obtained using an unpaired t-test.
  • FIG. 10 Table S1. Comparison of immune-related and RECIST response criteria (adapted from Wolchok et al. Clin Can Res 2009; 15:7412-20.)
  • FIG. 11 (Table S2.) Immune-Related response to treatment
  • FIG. 12 (Table S4.) Correlation of total somatic mutations and mutation associated neoantigens (MANA) with clinical outcomes
  • FIG. 13 (Table S5.) Correlation of immune markers with clinical outcome
  • the inventors have found that immune checkpoint inhibitors work best in tumors with high mutation burdens. Furthermore, tumors deficient in mismatch repair are particularly susceptible to a particular form of immunotherapy because this phenotype results in ongoing accumulation of mutations at a high frequency.
  • the inventors have developed a treatment for cancer patients that display the microsatellite instability phenotype or other high mutational burden.
  • the treatment involves an inhibitory antibody for an immune checkpoint.
  • checkpoints include PD-1, IDO, CTLA-4, PD-L1, and LAG-3.
  • Other immune checkpoints can be used as well.
  • Antibodies can be administered by any means that is convenient, including but not limited to intravenous infusion, oral administration, subcutaneous administration, sublingual administration, ocular administration, nasal administration, etc.
  • MSI Microsatellite instability
  • Samples may be tested for high mutational burden by identifying tumors with at least 100, at least 200, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, at least 1100, at least 1200, at least 1300, at least 1400, at least 1500, or at least 1600 mutations per tumor genome.
  • High mutational burden means a large number of somatic mutations in the tumor relative to normal tissues of the individual.
  • An average number of somatic mutations in a non-MSI tumor is about 70 somatic mutations.
  • tumors that displays the MSI phenotype or a high mutational burden may be tested and/or treated according to the invention.
  • These include without limitation cancers of the colon, gastric, endometrial, cholangiocarcinoma, pancreatic, and prostate cancer.
  • Tumors of the ampulla, biliary, brain, including glioma, breast, lung, skin, esophagus, liver, kidney, ovaries, sarcoma, uterus, cervix, bladder, testes, oral cavity, tongue, and small and large bowel may also be tested and/or treated.
  • MSI MSI monomorphic mononucleotide repeat markers
  • BAT-25, BAT-26, MON0-27, NR-21 and NR-24 markers that are highly polymorphic pentanucleotide repeat markers
  • Penta D highly polymorphic pentanucleotide repeat markers
  • fluorescently labeled primers markers are used for co-amplification of all seven of the above named markers. Fragments are detected after amplification for assignment of genotype/phenotype.
  • Samples that can be tested for MSI include tumor tissue as well as body fluids that contain nucleic acids shed from tumors. Testing for tumor DNA in such tissues and body fluids is well known.
  • Types of antibodies which can be used include any that are developed for the immune checkpoint inhibitors. These can be monoclonal or polyclonal. They may be single chain fragments or other fragments of full antibodies, including those made by enzymatic cleavage or recombinant DNA techniques. They may be of any isotype, including but not limited to IgG, IgM, IgE.
  • the antibodies may be of any species source, including human, goat, rabbit, mouse, cow, chimpanzee.
  • the antibodies may be humanized or chimeric.
  • the antibodies may be conjugated or engineered to be attached to another moiety, whether a therapeutic molecule or a tracer molecule.
  • the therapeutic molecule may be a toxin, for example.
  • MMR-deficiency occurs in many cancers, including those of the colorectum, uterus, stomach, biliary tract, pancreas, ovary, prostate and small intestine 18,34-42 .
  • Patients with MMR-deficient tumors of these types also benefit from anti-PD-1 therapy, as may patients whose tumors contain other DNA repair deficiencies, such as those with mutations in POLD, POLE, or MYH. 18,43,44
  • MMR-deficient tumors stimulate the immune system is not a new idea 45 , and has been supported by the dense immune infiltration and Th1-associated cytokine-rich environment observed in MMR-deficient tumors. 19-22,46 A recent study refined these classic observations by showing that the MMR-deficient tumor microenvironment strongly expressed several immune checkpoint ligands including PD-1, PD-L1, CTLA-4, LAG-3 and IDO, indicating that their active immune microenvironment is counterbalanced by immune inhibitory signals that resists tumor elimination 47 . That the immune infiltrate associated with MMR-deficient carcinomas was directed at neoantigens was the most likely explanation for both the old and new findings. The correlation of higher mutational load and higher response rate to anti-CTLA-4 in melanoma 41 and anti-PD-1 in lung cancer 48 provide further support for the idea that MANA recognition is an important component of the endogenous anti-tumor immune response.
  • MMR-deficient and MMR-proficient tumors may result in differences in secretion of soluble factors that could result in differential activation of the PD-1 pathway within the tumor microenvironment 26-28 .
  • Genetic differences could effect epigenetic differences that alter the expression of tumor-associated self-antigens that in turn could alter the antigenicity of the tumor.
  • Experimental analyses of antigen-specific immune responses as well as changes in immune microenvironments should help to define the relative contribution of these factors to the striking responsiveness of MMR-deficient tumors to PD-1 antibodies.
  • MSI testing is already standardized and performed in CLIA-certified laboratories without need for assay development. Archived tumor samples or newly obtained biopsies will be used for determining MSI. MSI status will be performed locally by CLIA certified immunohistochemistry (IHC) or PCR based tests for eligibility. Evaluable patients will be confirmed using the MSI Analysis System from Promega at Johns Hopkins. This test will determine MSI status through the insertion or deletion of repeating units in the five nearly monomorphic mononucleotide repeat markers (BAT-25, BAT-26, MON0-27, NR-21 and NR-24). At least 2 MSI loci are required to be evaluable in Cohorts A and C. Patients may be assigned to a new cohort and/or replaced based on the Promega test results.
  • Cohort A was composed of patients with MMR-deficient colorectal adenocarcinomas
  • Cohort B was composed of patients with MMR-proficient colorectal adenocarcinomas
  • Cohort C was composed of patients with MMR-deficient cancers of types other than colorectal.
  • the protocol which can be found at NEJM.org, was approved by each site's institutional review boards, and the study was conducted in accordance with the Declaration of Helsinki and the International Conference on Harmonization Guidelines for Good Clinical Practice. All the patients provided written informed consent before study entry. The principal investigator (D.L.) and study sponsor (L.A.D.) were responsible for oversight of the study. Merck donated the study drug, reviewed the final drafts of the protocol and of this manuscript. The clinical study was primarily funded through philanthropic support.
  • Pembrolizumab is a humanized monoclonal anti-PD-1 antibody of the IgG4/kappa isotype that blocks the interaction between PD-1 and its ligands, PD-L1 and PD-L2.
  • MMR-status was assessed using the MSI Analysis System from Promega in tumors, through the evaluation of selected microsatellite sequences particularly prone to copying errors when MMR is compromised 26-28 . See Supplementary Appendix for additional details.
  • the primary endpoints for Cohorts A and B were immune-related objective response rate (irORR) and immune-related progression-free survival (irPFS) rate at 20 weeks assessed using immune-related response criteria (irRC) 33 .
  • the primary endpoint for Cohort C was irPFS rate at 20 weeks.
  • Immune-related criteria i.e, criteria used to evaluate immune-based therapies
  • RECIST criteria capture extent of disease after disease progression; these criteria are defined and compared to RECIST v1.1 in FIG. 10 (Table S1).
  • Response rate and PFS rate at 20 weeks were evaluated and reported in this study using RECIST v1.1 and irRC ( FIG. 10 (Table S1)).
  • PFS and overall survival was summarized by Kaplan-Meier method. Details of the hypothesis, the decision rules to reject the null hypotheses and early-stopping rules for efficacy and futility, and statistical methods are provided in the Supplementary Appendix.
  • patients had to be at least 18 years of age, have histologically confirmed evidence of previously-treated, progressive carcinoma. All patients underwent MMR status testing prior to enrollment. All patients had at least one measurable lesion as defined by the Response Evaluation Criteria in Solid Tumors (RECIST), version 1.1, an Eastern Cooperative Oncology Group (ECOG) performance-status score of 0 or 1, and adequate hematologic, hepatic, and renal function. Eligible patients with CRC must have received at least 2 prior cancer therapies and patients with other cancer types must have received at least 1 prior cancer therapy. Patients with untreated brain metastases, history of HIV, hepatitis B, hepatitis C, clinically significant ascites/effusions, or autoimmune disease were excluded.
  • RECIST Solid Tumors
  • Eligible patients with CRC must have received at least 2 prior cancer therapies and patients with other cancer types must have received at least 1 prior cancer therapy.
  • HLA-A, HLA-B and HLA-C Sequence Based Typing can be divided into three distinct steps, as described below.
  • a generic, A*02 specific, B generic, B group specific, C generic and C*07 specific PCR and sequencing mixes were made in the JHU core facility.
  • Celera's AlleleSEQR HLA-B Sequence Based Typing kit was used for B generic SBT.
  • the HLA-A typing scheme is composed of two PCR reactions, A generic and A*02 specific.
  • a generic amplicon encompasses partial exon 1—partial exon 5.
  • A*02 amplicon encompasses partial intron 1—partial exon 5.
  • HLA-B typing scheme is composed of two PCR reactions, B generic and B group specific.
  • the B generic PCR is a multiplexed reaction containing two PCR amplicons encompassing exon 2—exon 3 and exon 4—exon 7.
  • B group specific amplicon encompasses partial intron 1—partial exon 5.
  • HLA-C typing scheme is composed of two PCR reactions, C generic and C*07 specific.
  • C generic and C*07 specific amplicons encompasses exons 1-7.
  • the specificity of the HLA-A and B PCR employed AmpliTaq Gold DNA polymerase.
  • the GeneAmp High Fidelity enzyme is used for the HLA-C and C*07 PCR mixes. This enzyme is a mix of two polymerases: AmpliTaq DNA polymerase (non-proofreading polymerase) and a proofreading polymerase. This enzyme mix is necessary to produce efficient and robust amplification of the larger full length HLA-C amplicon.
  • PCR product purification was performed using Exonuclease I and Shrimp Alkaline Phosphatase
  • the A generic and B generic amplicons were bi-directionally sequenced for exons 2,3,4.
  • the C generic amplicon was bi-directionally sequenced for exons 2,3 and sequenced in a single direction for exons 1,4,5,6,7.
  • A*02 specific, B group specific and C*07 specific amplicons were sequenced in a single direction for exons 2,3. All sequencing reactions were performed with Big Dye Terminator V1.1 from Applied Biosystems and sequenced with an ABI Prism 3500XL Genetic Analyzer. Conexio Genomic's “Assign SBT” allele assignment software was used to process the data files.
  • a tumor area containing at least 20% neoplastic cells, designated by a board-certified Anatomic Pathologist was macrodissected using the Pinpoint DNA isolation system (Zymo Research, Irvine, Calif.), digested in proteinase K for 8 hours and DNA was isolated using a QIAamp DNA Mini Kit (Qiagen, Valencia, Calif.).
  • MSI was assessed using the MSI Analysis System (Promega, Madison, Wis.), composed of 5 pseudomonomorphic mononucleotide repeats (BAT-25, BAT-26, NR-21, NR-24 and MONO-27) to detect MSI and 2-pentanucleotide repeat loci (PentaC and PentaD) to confirm identity between normal and tumor samples, per manufacturer's instructions.
  • MSI Analysis System Promega, Madison, Wis.
  • PentaC and PentaD 2-pentanucleotide repeat loci
  • the fluorescent PCR products were sized on an Applied Biosystems 3130xl capillary electrophoresis instrument (Invitrogen, Calsbad, Calif.). Pentanucleotide loci confirmed identity in all cases.
  • Controls included water as a negative control and a mixture of 80% germline DNA with 20% MSI cancer DNA as a positive control.
  • the size in bases was determined for each microsatellite locus and tumors were designated as MSI if two or more mononucleotide loci varied in length compared to the germline DNA.
  • Sample preparation, library construction, exome capture, next generation sequencing, and bioinformatics analyses of tumor and normal samples were performed at Personal Genome Diagnostics, Inc. (Baltimore, Md.).
  • DNA was extracted from frozen or formalin-fixed paraffin embedded (FFPE) tissue, along with matched blood or saliva samples using the Qiagen DNA FFPE tissue kit or Qiagen DNA blood mini kit (Qiagen, CA).
  • FFPE formalin-fixed paraffin embedded
  • Qiagen DNA blood mini kit Qiagen, CA
  • Genomic DNA from tumor and normal samples were fragmented and used for Rumina TruSeq library construction (Illumina, San Diego, Calif.) according to the manufacturer's instructions or as previously described4.
  • DNA was purified using Agencourt AMPure XP beads (Beckman Coulter, IN) in a ratio of 1.0 to 0.9 of PCR product to beads twice and washed using 70% ethanol per the manufacturer's instructions.
  • PCRs of 25 ⁇ l each were set up, each including 15.5 ⁇ l of H2O, 5 ⁇ l of 5 ⁇ Phusion HF buffer, 0.5 ⁇ l of a dNTP mix containing 10 mM of each dNTP, 1.25 ⁇ l of DMSO, 0.25 ⁇ l of Illumina PE primer #1, 0.25 ⁇ l of Illumina PE primer #2, 0.25 ⁇ l of Hotstart Phusion polymerase, and 2 ⁇ l of the DNA.
  • the PCR program used was: 98° C. for 2 minutes; 12 cycles of 98° C. for 15 seconds, 65° C. for 30 seconds, 72° C. for 30 seconds; and 72° C. for 5 min.
  • DNA was purified using Agencourt AMPure XP beads (Beckman Coulter, IN) in a ratio of 1.0 to 1.0 of PCR product to beads and washed using 70% ethanol per the manufacturer's instructions. Exonic or targeted regions were captured in solution using the Agilent SureSelect v.4 kit according to the manufacturer's instructions (Agilent, Santa Clara, Calif.). The captured library was then purified with a Qiagen MinElute column purification kit and eluted in 17 ⁇ l of 70° C. EB to obtain 15 ⁇ l of captured DNA library.
  • the captured DNA library was amplified in the following way: Eight 30 uL PCR reactions each containing 19 ⁇ l of H2O, 6 ⁇ l of 5 ⁇ Phusion HF buffer, 0.6 ⁇ l of 10 mM dNTP, 1.5 ⁇ l of DMSO, 0.30 ⁇ l of Illumina PE primer #1, 0.30 ⁇ l of Illumina PE primer #2, 0.30 ⁇ l of Hotstart Phusion polymerase, and 2 ⁇ l of captured exome library were set up.
  • the PCR program used was: 98° C. for 30 seconds; 14 cycles (exome) or 16 cycles (targeted) of 98° C. for 10 seconds, 65° C. for 30 seconds, 72° C. for 30 seconds; and 72° C. for 5 min.
  • NucleoSpin Extract II purification kit (Macherey-Nagel, PA) was used following the manufacturer's instructions. Paired-end sequencing, resulting in 100 bases from each end of the fragments for exome libraries and 150 bases from each end of the fragment for targeted libraries, was performed using Illumina HiSeq 2000/2500 and IIlumina MiSeq instrumentation (Ilumina, San Diego, Calif.).
  • Somatic mutations were identified using VariantDx custom software (Personal Genome Diagnostics, Baltimore, Md.) for identifying mutations in matched tumor and normal samples. Prior to mutation calling, primary processing of sequence data for both tumor and normal samples were performed using Illumina CASAVA software (v1.8), including masking of adapter sequences. Sequence reads were aligned against the human reference genome (version hg18) using ELAND with additional realignment of select regions using the Needleman-Wunsch method 5.
  • Candidate somatic mutations, consisting of point mutations, insertions, and deletions were then identified using VariantDx across the either the whole exome or regions of interest.
  • VariantDx examines sequence alignments of tumor samples against a matched normal while applying filters to exclude alignment and sequencing artifacts.
  • an alignment filter was applied to exclude quality failed reads, unpaired reads, and poorly mapped reads in the tumor.
  • a base quality filter was applied to limit inclusion of bases with reported phred quality score >30 for the tumor and >20 for the normal.
  • a mutation in the tumor was identified as a candidate somatic mutation only when (i) distinct paired reads contained the mutation in the tumor; (ii) the number of distinct paired reads containing a particular mutation in the tumor was at least 10% of read pairs; (iii) the mismatched base was not present in >1% of the reads in the matched normal sample as well as not present in a custom database of common germline variants derived from dbSNP; and (iv) the position was covered in both the tumor and normal at >150 ⁇ . Mutations arising from misplaced genome alignments, including paralogous sequences, were identified and excluded by searching the reference genome.
  • Candidate somatic mutations were further filtered based on gene annotation to identify those occurring in protein-coding regions. Functional consequences were predicted using snpEff and a custom database of CCDS, RefSeq and Ensembl annotations using the latest transcript versions available on hg18 from UCSC (https://genome.ucsc.edu/). Predictions were ordered to prefer transcripts with canonical start and stop codons and CCDS or Refseq transcripts over Ensembl when available. Finally mutations were filtered to exclude intronic and silent changes, while retaining mutations resulting in missense mutations, nonsense mutations, frameshifts, or splice site alterations. A manual visual inspection step was used to further remove artifactual changes.
  • Somatic frameshift, insertions, deletions, and missense mutations predicted to result in an amino acid change were analyzed for potential MHC class I binding based on the individual patient's HLA haplotype.
  • Amino acid mutations were linked to their corresponding CCDS accession number and in instances where this was unavailable, either a Refseq or ensemble transcript was used to extract the protein sequence. To identify 8mer, 9mer, and 10mer epitopes, amino acid fragments surrounding each mutation were identified.
  • mutant peptides that were strong potential binders when the complementary wild-type peptide was predicted a weak potential binder. These mutant peptides are referred to as mutation-associated neoantigens (MANA).
  • MANA mutation-associated neoantigens
  • This trial was conducted using a parallel two-stage design to simultaneously evaluate the efficacy of MK-3475 and MSI as a treatment selection marker for anti-PD-1 therapy. It consisted of two-stage phase 2 studies in parallel in the three cohorts of patients described in the text. The study agent, MK-3475, was administered at 10 mg/kg intravenously every 14 days.
  • the co-primary endpoints were progression-free-survival (irPFS) at 20 weeks and objective response (irOR) assessed using immune related criteria.
  • irPFS progression-free-survival
  • irOR objective response
  • a step-down gatekeeping procedure was used to preserve the overall type I error.
  • a two-stage Green-Dahlberg design was used to evaluate irPFS, with interim and final analysis after 15 and 25 patients, respectively.
  • ⁇ 1 of 15 free-of-progression at 20 weeks were required to proceed to the second stage, and ⁇ 4 of 25 free-of-progression at 20 weeks were then required to proceed to test for irOR, with ⁇ 4 of 25 responders (irCR or irPR) indicating promising efficacy in that cohort.
  • Each cohort could be terminated for efficacy as soon as ⁇ 4 free-of-progression at 20 weeks and ⁇ 4 responses were confirmed, or be terminated for futility as soon as 0 of 15 in stage 1 were free-of-progression at 20 weeks or ⁇ 22 subjects had disease progression by 20 weeks.
  • This design achieves 90% power to detect a 20-week irPFS rate of 25% and 80% power to detect an irOR rate (irORR) of 21%, with an overall type I error of 0.05 at the null hypothesis of 20-week irPFS rate of 5% and irORR of 5%.
  • the primary endpoint was irPFS at 20 weeks.
  • a two-stage Green-Dahlberg two-stage design was used, with an interim and final analysis after 14 and 21 patients; at stage 1, ⁇ 1 of 14 free-of-progression at 20 weeks were required to proceed to the second stage, with ⁇ 4 of 21 free-of-progression at 20 weeks at the end indicating adequate efficacy in Cohort C.
  • the cohort could be terminated as soon as ⁇ 4 free-of-progression at 20 weeks were confirmed.
  • the design has 81% power to detect a 20-week irPFS rate of 25% with a 5% type I error at the null hypothesis of 20-week irPFS rate of 5%.
  • PFS progression-free survival
  • irPFS immune-related response criteria
  • ORR was the proportion of patients who achieved best overall response of CR or PR (irCR or irPR). Patients who were in the study long enough to have tumor response evaluations were included in the analysis for estimating response rates. Among those who responded (CR or PR), duration of response was the time of first RECIST response to the time of disease progression, and was censored at the last evaluable tumor assessment for responders who had not progressed.
  • PFS and irPFS were defined as the time from the date of initial dose to the date of disease progression or the date of death due to any cause, whichever occurred first. PFS and irPFS were censored on the date of the last evaluable tumor assessment documenting absence of progressive disease for patients who were alive and progression-free. Overall survival (OS) was defined as the time from the date of initial dose to death due to any cause. For patients who were still alive at the time of analysis, the OS time was censored on the last date the patients were known to be alive. Survival times were summarized by the Kaplan-Meier method. As a post hoc analysis, log-rank tests were used to compare Cohort A and B and hazard ratios were estimated based on Cox models.
  • the fraction of malignant cells exhibiting a membranous pattern of B7-H1 expression and the percentage at the invasive front were quantified by three pathologists (R.A.A., F.B., and J.M.T.) as previously reported9,10.
  • Image analysis was used to determine the number of CD8 diaminobenzidine (DAB)-stained cells.
  • DAB diaminobenzidine
  • the CD8-stained slides were scanned at 20 ⁇ equivalent magnification (0.49 micrometers per pixel) on an Aperio ScanScope AT. Regions corresponding to tumor, invasive front and normal tissue (above, from the H&E) were annotated on separate layers using Aperio ImageScope v12.1.0.5029.
  • CD8-positive lymphocyte density was calculated in each of the above regions using a custom algorithm implemented in PIP11. Results were converted to Deepzoom images using the VIPS libraryl2 and visualized using the OpenSeadragon viewer (http://openseadragon.github.io).
  • Cohort B comprised of patients with MMR-proficient CRCs, irORR and 20-week irPFS were 0% (95% CI, 0 to 20%) and 11% (2 of 18 patients; 95% CI, 1 to 35%).
  • the median time of follow-up for patients was 32 weeks (range, 5-51 weeks) for patients with MMR-deficient CRC (Cohort A), 12 weeks (range, 2-56 weeks) for patients with MMR-proficient CRC (Cohort B) and 12 weeks (range, 4-42 weeks) for patients with MMR-deficient non-CRC tumors (Cohort C). All patients evaluable for 20-week irPFS were followed for at least 20 weeks.
  • HR hazard ratios
  • the CEA response occurred well in advance of radiographic confirmation of disease control (range, 10 to 35 weeks).
  • patients who progressed showed rapid biomarker elevation within 30 days of initiating therapy.
  • changes in CEA levels significantly preceded and correlated with ultimate radiographic changes.
  • FIGS. 6A-6B S 5 ; see also Table S3 which is available on-line at New England Journal of Medicine; incorporated by reference herein). Most (63%) of these mutations are predicted to alter amino acids.
  • TILs tumor infiltrating lymphocytes

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