Chowell Lab - Decoding the language of immune recognition

Cancer Cell

Artificial intelligence

Gerstung M, Liu D, Ghassemi M, Zou J, Chowell D, Teuwen J, Mahmood F, and Kather JN. 2024. Artificial intelligence. Cancer Cell. 2024

Cell Systems

The electrostatic landscape of MHC-peptide binding revealed using inception networks

Wilson EA, Cava JK, Chowell D, et al. The electrostatic landscape of MHC-peptide binding revealed using inception networks. Cell Systems. 2024.

Nature Cancer

LORIS robustly predicts patient outcomes with immune checkpoint blockade therapy using common clinical, pathologic and genomic features

Chang TG*, Cao Y*, Sfreddo HJ*, et al. LORIS robustly predicts patient outcomes with immune checkpoint blockade therapy using common clinical, pathologic and genomic features. Nature Cancer. 2024.

Science

An immunogenetic basis for lung cancer risk

Krishna C*, Tervi A*, Saffern M*, Wilson EA*, et al. An immunogenetic basis for lung cancer risk. Science. 2024.

Cancers

Validation of a Machine Learning Model to Predict Immunotherapy Response in Head and Neck Squamous Cell Carcinoma

Lee AS, Valero C, Yoo SK, et al. Validation of a Machine Learning Model to Predict Immunotherapy Response in Head and Neck Squamous Cell Carcinoma. Cancers. 2023.

The Journal of Clinical Investigation

Clinical-genomic determinants of immune checkpoint blockade response in head and neck squamous cell carcinoma

Valero C*, Golkaram M*, Vos JL*, et al. Clinical-genomic determinants of immune checkpoint blockade response in head and neck squamous cell carcinoma. JCI. 2023.

Nature Genetics

Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors

Zapata L, Caravagna G, Williams MJ, et al. Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors. Nat Genet. 2023.

Cancer Discovery

A Targetable Myeloid Inflammatory State Governs Disease Recurrence in Clear-Cell Renal Cell Carcinoma

Rappold PM*, Vuong L*, Leibold J, et al. A Targetable Myeloid Inflammatory State Governs Disease Recurrence in Clear Cell Renal Cell Carcinoma. Cancer Discov. 2022.

Cancer Cell

NKG2A and HLA-E define an alternative immune checkpoint axis in bladder cancer

Salome B, Sfakianos JP, Ranti D, et al. NKG2A and HLA-E define an alternative immune checkpoint axis in bladder cancer. Cancer Cell. 2022.

Nature Genetics

Functional landscapes of POLE and POLD1 mutations in checkpoint blockade-dependent antitumor immunity

Ma X, Riaz N, Samstein RM, et al. Functional landscapes of POLE and POLD1 mutations in checkpoint blockade-dependent antitumor immunity. Nat Genet. 2022.

Nature Biotechnology

Improved prediction of immune checkpoint blockade efficacy across multiple cancer types

Chowell D*, Yoo SK*, Valero C*, et al. Improved prediction of immune checkpoint blockade efficacy across multiple cancer types. Nat Biotechnol. 2021.

Cell

Pharmacologic modulation of RNA splicing enhances anti-tumor immunity

Lu SX*, De Neef E*, Thomas JD, et al. Pharmacologic modulation of RNA splicing enhances anti-tumor immunity. Cell. 2021;184(15): 4032-4047 e4031.

Cancer Cell

Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy

Krishna C, DiNatale RG, Kuo F, et al. Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy. Cancer Cell. 2021;39(5): 662-677 e666.

Immunity & Ageing

Genetic and environmental determinants of human TCR repertoire diversity

Krishna C*, Chowell D*, Gonen M, Elhanati Y, Chan TA. Genetic and environmental determinants of human TCR repertoire diversity. Immun Ageing. 2020;17:26.

Nature Medicine

Evolutionary divergence of HLA class I genotype impacts efficacy of cancer immunotherapy

Chowell D*, Krishna C*, Pierini F*, et al. Evolutionary divergence of HLA class I genotype impacts efficacy of cancer immunotherapy. Nat Med. 2019;25(11): 1715-1720.

Nature Medicine

Immunogenic neoantigens derived from gene fusions stimulate T cell responses

Yang W*, Lee KW*, Srivastava RM*, et al. Immunogenic neoantigens derived from gene fusions stimulate T cell responses. Nat Med. 2019;25(5): 767-775.

Nature Reviews Cancer

The evolving landscape of biomarkers for checkpoint inhibitor immunotherapy

Havel JJ*, Chowell D*, Chan TA. The evolving landscape of biomarkers for checkpoint inhibitor immunotherapy. Nat Rev Cancer. 2019;19(3): 133-150.

Cancer Research

Modeling the subclonal evolution of cancer cell populations

Chowell D, Napier J, Gupta R, Anderson KS, Maley CC, Sayres MAW. Modeling the Subclonal Evolution of Cancer Cell Populations. Cancer Res. 2018;78(3): 830-839.

Science

Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy

Chowell D, Morris LGT, Grigg CM, et al. Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy. Science. 2018;359(6375): 582-587.

Cell

Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab

Riaz N*, Havel JJ*, Makarov V*, et al. Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab. Cell. 2017;171(4): 934-949 e915.

Cancer

Diagnostic accuracy of serum antibodies to human papillomavirus type 16 early antigens in the detection of human papillomavirus-related oropharyngeal cancer

Dahlstrom KR*, Anderson KS*, Field MS, et al. Diagnostic accuracy of serum antibodies to human papillomavirus type 16 early antigens in the detection of human papillomavirus-related oropharyngeal cancer. Cancer. 2017;123(24): 4886-4894.

Genome Biology

When (distant) relatives stay too long: implications for cancer medicine

Chowell D, Boddy AM, Mallo D, Tollis M, Maley CC. When (distant) relatives stay too long: implications for cancer medicine. Genome Biology. 2016;17.

Clinical Cancer Research

HPV Serum Antibodies as Predictors of Survival and Disease Progression in Patients with HPV-Positive Squamous Cell Carcinoma of the Oropharynx

Dahlstrom KR, Anderson KS, Cheng JN, et al. HPV Serum Antibodies as Predictors of Survival and Disease Progression in Patients with HPV-Positive Squamous Cell Carcinoma of the Oropharynx. Clinical Cancer Research. 2015;21(12): 2861-2869.

PNAS

TCR contact residue hydrophobicity is a hallmark of immunogenic CD8(+) T cell epitopes

Chowell D*, Krishna S*, Becker PD, et al. TCR contact residue hydrophobicity is a hallmark of immunogenic CD8(+) T cell epitopes. Proceedings of the National Academy of Sciences of the United States of America. 2015;112(14):E1754-E1762.

Lancet Infectious Diseases

Modelling the effect of early detection of Ebola

Chowell D, Castillo-Chavez C, Krishna S, Qiu X, Anderson KS. Modelling the effect of early detection of Ebola. Lancet Infect Dis. 2015;15(2): 148-149.

Publications