Implementation and analysis of immunogenomics and single-cell approaches to understand the evolving tumor immune microenvironment (TIME) in cancer development and immunotherapeutic resistance

The Long Lab has led or contributed to numerous computational efforts for studies examining the TIME as it relates to cancer development and/or resistance to immunotherapy-based intervention, largely stemming from a strong collaborative network within Roswell Park and with external investigators through the NCI Cancer Moonshot Immuno-oncology Translational Network (IOTN). 

As part of an analytical team, we developed a novel pipeline for the efficient identification of neoantigens from whole-genome or exome and RNA sequencing modalities that improved the identification tumor specific T-cells in advanced ovarian cancer. 

Figure from a scientific research study
Figure 1: Compiling and integrating available single-cell level data defining dendritic cell phenotypes, we applied reference based annotation to reveal the heterogeneity of iPSC derived DCs. Improving functional cDC generation from iPSCs could be a major boost for autologous DC based immunotherapy. Work in collaboration with Fumito Ito (USC). Makino K, Long MD, et. al. JITC. 2022. Click for larger image

Implementing immunogenomics approaches to map immune repertoires and TIL phenotypes at the single-cell level, we were integral in discovering the utility of a novel combination immunotherapy targeting cDC1 generation in mouse models, which is currently being developed for clinical trials. Further, using single-cell reference mapping we revealed the heterogeneity of iPSC derived DCs (Figure 1)

Leveraging multi-omics data (RNA-seq, ATAC-seq, scRNA-seq) in an integrative manner we have identified numerous tumor intrinsic mechanisms of immune suppression, for instance in triple-negative breast cancer and prostate cancer. 

Connect with the Long Lab 

Phone: 716-845-2541 

Department of Biostatistics and Bioinformatics 
Roswell Park Comprehensive Cancer Center 
Elm and Carlton Streets 
Buffalo, NY 14263