One of the critical steps to developing curative and tumor-specific immunotherapy is the identification and selection of antigens with tumor-restricted expression in order to avoid undesirable immune responses against normal tissues. Proteins with tumor-specific mutations have the potential to be the most restricted of all tumor antigens. However, the comprehensive identification of such 'neoantigens'has only become feasible recently using next-generation massively parallel sequencing technologies, providing unprecedented genetic information about cancer cells. The current project seeks to apply tumor sequence information to study this under-evaluated class of tumor-specific antigens. We hypothesize that immune responses against chronic lymphocytic leukemia (CLL) - observed in patients treated with hematopeotic stem cell transplant (HSCT), donor lymphocyte infusion (DLI) and leukemia whole cell vaccination - are often targeted against neoantigens generated from somatic tumor mutations. We have recently completed whole genome or exome sequencing of paired leukemia and normal tissue from 7 individuals with CLL, and have discovered many missense mutations, splice-site changes and gene fusions per individual. The current proposal focuses on defining the immunologic consequence of these genetic changes. We propose to systematically identify mutated peptides that are expressed, processed and presented by MHC molecules on CLL tumor cells (Aims 1-2). We will then test whether CD8+ T cells targeting these mutated peptides show selective lysis of CLL cells ex vivo and expand in number in HSCT/DLI-treated or vaccinated patients concurrent with the anti-leukemia response (Aim 3). The identification of tumor-specific neoantigens and T cell responses against them would help explain the success of HSCT/DLI in CLL and provide a motivation for the development of individualized, highly-specific and safer tumor vaccines.

Public Health Relevance

A great hope for cancer therapy is to vaccinate patients and induce a strong immune response that eradicates the tumor, but most immunotherapies vaccinate with molecules that are present on both tumors and normal cells, making it likely that the immune response will also cause damage to normal tissues. Here we propose to test a new strategy for vaccine design in which the immune system recognizes tumor-derived proteins - called mutated peptides -- that are only present on tumors, and hence is expected to be safer and more effective. With novel high-throughput sequencing technologies, we will comprehensively identify these mutated peptides in patients with chronic lymphocytic leukemia (CLL) and test whether their immune responses can target leukemia cells via these peptides;if so, then these data would supply proof-of-concept that personalized immunotherapy can be generated.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project (R01)
Project #
Application #
Study Section
Transplantation, Tolerance, and Tumor Immunology Study Section (TTT)
Program Officer
Mccarthy, Susan A
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Dana-Farber Cancer Institute
United States
Zip Code
Giannakis, Marios; Mu, Xinmeng Jasmine; Shukla, Sachet A et al. (2016) Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Cell Rep :
Bachireddy, Pavan; Wu, Catherine J (2016) Arresting the Inflammatory Drive of Chronic Lymphocytic Leukemia with Ibrutinib. Clin Cancer Res 22:1547-9
Wang, Lili; Brooks, Angela N; Fan, Jean et al. (2016) Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia. Cancer Cell 30:750-763
McGranahan, Nicholas; Furness, Andrew J S; Rosenthal, Rachel et al. (2016) Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science 351:1463-9
Strickland, Kyle C; Howitt, Brooke E; Shukla, Sachet A et al. (2016) Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer. Oncotarget 7:13587-98
Howitt, Brooke E; Shukla, Sachet A; Sholl, Lynette M et al. (2015) Association of Polymerase e-Mutated and Microsatellite-Instable Endometrial Cancers With Neoantigen Load, Number of Tumor-Infiltrating Lymphocytes, and Expression of PD-1 and PD-L1. JAMA Oncol 1:1319-23
Bachireddy, Pavan; Burkhardt, Ute E; Rajasagi, Mohini et al. (2015) Haematological malignancies: at the forefront of immunotherapeutic innovation. Nat Rev Cancer 15:201-15
Guièze, Romain; Wu, Catherine J (2015) Genomic and epigenomic heterogeneity in chronic lymphocytic leukemia. Blood 126:445-53
Rooney, Michael S; Shukla, Sachet A; Wu, Catherine J et al. (2015) Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell 160:48-61
Shukla, Sachet A; Rooney, Michael S; Rajasagi, Mohini et al. (2015) Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat Biotechnol 33:1152-8

Showing the most recent 10 out of 31 publications