9p21 loss confers a cold tumor immune microenvironment and primary resistance to immune checkpoint therapy

Guangchun Han, Guoliang Yang, Dapeng Hao, Yang Lu, Kyaw Thein, Benjamin S. Simpson, Jianfeng Chen, Ryan Sun, Omar Alhalabi, Ruiping Wang, Minghao Dang, Enyu Dai, Shaojun Zhang, Fengqi Nie, Shuangtao Zhao, Charles Guo, Ameer Hamza, Bogdan Czerniak, Chao Cheng, Arlene Siefker-Radtke, Krishna Bhat, Andrew Futreal, Guang Peng, Jennifer Wargo, Weiyi Peng, Humam Kadara, Jaffer Ajani, Charles Swanton, Kevin Litchfield, Jordi Rodon Ahnert, Jianjun Gao () and Linghua Wang ()
Additional contact information
Guangchun Han: The University of Texas MD Anderson Cancer Center
Guoliang Yang: The University of Texas MD Anderson Cancer Center
Dapeng Hao: The University of Texas MD Anderson Cancer Center
Yang Lu: The University of Texas MD Anderson Cancer Center
Kyaw Thein: The University of Texas MD Anderson Cancer Center
Benjamin S. Simpson: University College London Cancer Institute
Jianfeng Chen: The University of Texas MD Anderson Cancer Center
Ryan Sun: The University of Texas MD Anderson Cancer Center
Omar Alhalabi: The University of Texas MD Anderson Cancer Center
Ruiping Wang: The University of Texas MD Anderson Cancer Center
Minghao Dang: The University of Texas MD Anderson Cancer Center
Enyu Dai: The University of Texas MD Anderson Cancer Center
Shaojun Zhang: The University of Texas MD Anderson Cancer Center
Fengqi Nie: The University of Texas MD Anderson Cancer Center
Shuangtao Zhao: The University of Texas MD Anderson Cancer Center
Charles Guo: The University of Texas MD Anderson Cancer Center
Ameer Hamza: The University of Texas MD Anderson Cancer Center
Bogdan Czerniak: The University of Texas MD Anderson Cancer Center
Chao Cheng: Epidemiology and Population Science, Baylor College of Medicine
Arlene Siefker-Radtke: The University of Texas MD Anderson Cancer Center
Krishna Bhat: The University of Texas MD Anderson Cancer Center
Andrew Futreal: The University of Texas MD Anderson Cancer Center
Guang Peng: The University of Texas MD Anderson Cancer Center
Jennifer Wargo: The University of Texas MD Anderson Cancer Center
Weiyi Peng: University of Houston
Humam Kadara: The University of Texas MD Anderson Cancer Center
Jaffer Ajani: The University of Texas MD Anderson Cancer Center
Charles Swanton: The Francis Crick Institute
Kevin Litchfield: University College London Cancer Institute
Jordi Rodon Ahnert: The University of Texas MD Anderson Cancer Center
Jianjun Gao: The University of Texas MD Anderson Cancer Center
Linghua Wang: The University of Texas MD Anderson Cancer Center

Nature Communications, 2021, vol. 12, issue 1, 1-19

Abstract: Abstract Immune checkpoint therapy (ICT) provides substantial clinical benefits to cancer patients, but a large proportion of cancers do not respond to ICT. To date, the genomic underpinnings of primary resistance to ICT remain elusive. Here, we performed immunogenomic analysis of data from TCGA and clinical trials of anti-PD-1/PD-L1 therapy, with a particular focus on homozygous deletion of 9p21.3 (9p21 loss), one of the most frequent genomic defects occurring in ~13% of all cancers. We demonstrate that 9p21 loss confers “cold” tumor-immune phenotypes, characterized by reduced abundance of tumor-infiltrating leukocytes (TILs), particularly, T/B/NK cells, altered spatial TILs patterns, diminished immune cell trafficking/activation, decreased rate of PD-L1 positivity, along with activation of immunosuppressive signaling. Notably, patients with 9p21 loss exhibited significantly lower response rates to ICT and worse outcomes, which were corroborated in eight ICT trials of >1,000 patients. Further, 9p21 loss synergizes with PD-L1/TMB for patient stratification. A “response score” was derived by incorporating 9p21 loss, PD-L1 expression and TMB levels in pre-treatment tumors, which outperforms PD-L1, TMB, and their combination in identifying patients with high likelihood of achieving sustained response from otherwise non-responders. Moreover, we describe potential druggable targets in 9p21-loss tumors, which could be exploited to design rational therapeutic interventions.

Date: 2021
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DOI: 10.1038/s41467-021-25894-9

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