Pooled Mutant KRAS-Targeted Long Peptide Vaccine Combined with Nivolumab and Ipilimumab for Patients with Resected MMR-p Colorectal and Pancreatic Cancer

We developed INtraCEllular Reverse Transcription with Sorting and sequencing (INCERTS), an approach to combine molecular indexing of receptor repertoires within intact cells and fluorescence-activated cell sorting (FACS). We demonstrate that INCERTS enables efficient processing of millions of cells from pooled human peripheral blood mononuclear cell (PBMC) samples while retaining robust association between T cell receptor (TCR) sequences and cellular phenotypes. We used INCERTS to discover antigen-specific TCRs from patients with cancer immunized with a novel mutant KRAS peptide vaccine. After ex vivo stimulation, 28 uniquely barcoded samples were pooled prior to FACS into peptide-reactive and non-reactive CD4+ and CD8+ populations. Combining complementary patient-matched single-cell RNA sequencing (scRNA-seq) data enabled retrieval of full-length, paired TCR alpha and beta chain sequences for future validation of therapeutic utility. Data available through dbGaP include scRNA-seq with matched TCR-seq.]]>
Inclusion Criteria:Age ≥18 years.Have histologically or cytologically-proven cancer of the pancreas (PDA) or MSS colorectal (CRC) in one of the following categories: 1) PDAC must have no evidence of disease and last dose of neoadjuvant and/or adjuvant chemotherapy/radiation therapy/or surgery must be < 6 months from study entry 2) Metastatic MSS CRC after exposure to 2 more lines of chemotherapy in the metastatic setting including 5-flurouracil, irinotecan, and oxaliplatin exposure. Patients treated with FOLFOXIRI may enroll after progression or intolerance to that regimen.For metastatic MSS CRC cohort, must have tumor lesions amenable to repeated biopsy, and patient's acceptance to have a tumor biopsy of an accessible lesion at baseline and on treatment if the lesion can be biopsied with acceptable clinical risk (as judged by the Principal Investigator).For metastatic MSS CRC patients, must have measurable disease per RECIST 1.1.Have sufficient archival tumor tissue for next-generation sequencing (NGS) and immune-phenotyping.Have one of the KRAS mutations included in the vaccine at the time of vaccination expressed in tumor.Eastern Cooperative Oncology Group (ECOG) performance status 0 or 1Life expectancy of greater than 6 months.Patients must have adequate organ and marrow function defined by study-specified laboratory tests prior to initial study drug.Woman of childbearing potential must have a negative pregnancy test and follow contraceptive guidelines as defined per protocol.Men must use acceptable form of birth control while on study.Ability to understand and willingness to sign a written informed consent document.Exclusion CriteriaIf expected to require any other form of systemic or localized antineoplastic therapy while on study.Within 2 weeks prior to first dose of study drug: 1) Systemic or topical steroids corticosteroids at immunosuppressive doses (> 10 mg/day of prednisone or equivalent). Inhaled or topical steroids, and adrenal replacement steroid doses ≤ 10 mg daily prednisone equivalent, are permitted in the absence of active autoimmune disease. 2) Any palliative or adjuvant radiation or gamma knife radiosurgery. 3) Any chemotherapy.Within 4 weeks prior to first dose of study drug: 1) Any investigational cytotoxic drug. 2) Any investigational device. 3) Has received a live vaccine. 4) Received any allergen hyposensitization therapy. 5) Received any growth factors, e.g. granulocyte-colony stimulating factor (G-CSF), granulocyte macrophage-colony stimulating factor (GM-CSF), erythropoietin. 6) Any major surgery.Prior treatment with immunotherapy agents (including, anti-PD-1, anti-PD-L1, anti-PD-L2, anti-cytotoxic T-lymphocyte-associated protein 4 (CTLA4), etc.).Hypersensitivity reaction to any monoclonal antibody.Known history or evidence of brain metastases.Has active autoimmune disease that has required systemic treatment in the past 2 years, or a documented history of clinically severe autoimmune disease, or a syndrome that requires systemic steroids or immunosuppressive agents.Known history or concurrent interstitial lung disease.Has a pulse oximetry < 92% on room air.Requires the use of home oxygen.Infection with HIV or hepatitis B or C.Uncontrolled intercurrent illness including, but not limited to, uncontrolled infection, symptomatic congestive heart failure, unstable angina, cardiac arrhythmia, metastatic cancer, or psychiatric illness/social situations that would limit compliance with study requirements.Has been diagnosed with another cancer or myeloproliferative disorder within the past 5 year.Has a diagnosis of immunodeficiency.Presence of any tissue or organ allograft, regardless of need for immunosuppression, including corneal allograft. Patients with a history of allogeneic hematopoietic stem cell transplant will be excluded.Any other sound medical, psychiatric, and/or social reason as determined by the Investigator.Unwilling or unable to follow the study schedule for any reason.Are pregnant or breastfeeding.For metastatic MSS CRC cohort, any peritoneal involvement by the tumor.For metastatic MSS CRC cohort, any radiological or clinical pleural effusions or ascites.For metastatic MSS CRC cohort, patients on parenteral nutrition.For metastatic MSS CRC cohort, patients with any single liver metastases greater than 5 cm or greater > 50% liver involvement.For metastatic MSS CRC cohort, history of malignant bowel obstruction.]]>