Myeloid Cell-associated Resistance to PD-1/PD-L1 Blockade in Urothelial Cancer Revealed Through Bulk and Single-cell RNA Sequencing

Li Wang; John P Sfakianos; Kristin G Beaumont; Guray Akturk; Amir Horowitz; Robert P Sebra; Adam M Farkas; Sacha Gnjatic; Austin Hake; Sudeh Izadmehr; Peter Wiklund; William K Oh; Peter M Szabo; Megan Wind-Rotolo; Keziban Unsal-Kacmaz; Xin Yao; Eric Schadt; Padmanee Sharma; Nina Bhardwaj; Jun Zhu; Matthew D Galsky

doi:10.1158/1078-0432.CCR-20-4574

Myeloid Cell-associated Resistance to PD-1/PD-L1 Blockade in Urothelial Cancer Revealed Through Bulk and Single-cell RNA Sequencing

Clin Cancer Res. 2021 Aug 1;27(15):4287-4300. doi: 10.1158/1078-0432.CCR-20-4574. Epub 2021 Apr 9.

Authors

Li Wang^{1

2

3}, John P Sfakianos⁴, Kristin G Beaumont^{1

2}, Guray Akturk⁵, Amir Horowitz⁵, Robert P Sebra^{1

2

3

6}, Adam M Farkas⁵, Sacha Gnjatic⁵, Austin Hake^{1

2}, Sudeh Izadmehr⁷, Peter Wiklund⁴, William K Oh⁷, Peter M Szabo⁸, Megan Wind-Rotolo⁸, Keziban Unsal-Kacmaz⁸, Xin Yao⁹, Eric Schadt^{1

2

3}, Padmanee Sharma¹⁰, Nina Bhardwaj^{11

7}, Jun Zhu^{12

2

3}, Matthew D Galsky¹³

Affiliations

¹ Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, New York.
² Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
³ Sema4, a Mount Sinai venture, Stamford, Connecticut.
⁴ Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York.
⁵ Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York.
⁶ Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York.
⁷ Division of Hematology Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, New York.
⁸ Bristol-Myers Squibb, Princeton, New Jersey.
⁹ Department of Genitourinary Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, P.R. China.
¹⁰ Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas.
¹¹ Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York. matthew.galsky@mssm.edu jun.zhu@mssm.edu Nina.bhardwaj@mssm.edu.
¹² Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, New York. matthew.galsky@mssm.edu jun.zhu@mssm.edu Nina.bhardwaj@mssm.edu.
¹³ Division of Hematology Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, New York. matthew.galsky@mssm.edu jun.zhu@mssm.edu Nina.bhardwaj@mssm.edu.

Abstract

Purpose: To define dominant molecular and cellular features associated with PD-1/PD-L1 blockade resistance in metastatic urothelial cancer.

Experimental design: We pursued an unbiased approach using bulk RNA sequencing data from two clinical trials to discover (IMvigor 210) and validate (CheckMate 275) pretreatment molecular features associated with resistance to PD-1/PD-L1 blockade in metastatic urothelial cancer. We then generated single-cell RNA sequencing (scRNA-seq) data from muscle-invasive bladder cancer specimens to dissect the cellular composition underlying the identified gene signatures.

Results: We identified an adaptive immune response gene signature associated with response and a protumorigenic inflammation gene signature associated with resistance to PD-1/PD-L1 blockade. The adaptive immune response:protumorigenic inflammation signature expression ratio, coined the 2IR score, best correlated with clinical outcomes, and was externally validated. Mapping these bulk gene signatures onto scRNA-seq data uncovered their underlying cellular diversity, with prominent expression of the protumorigenic inflammation signature by myeloid phagocytic cells. However, heterogeneity in expression of adaptive immune and protumorigenic inflammation genes was observed among single myeloid phagocytic cells, quantified as the myeloid single cell immune:protumorigenic inflammation ratio (M_sc2IR) score. Single myeloid phagocytic cells with low M_sc2IR scores demonstrated upregulation of proinflammatory cytokines/chemokines and downregulation of antigen presentation genes, were unrelated to M1 versus M2 polarization, and were enriched in pretreatment blood samples from patients with PD-L1 blockade-resistant metastatic urothelial cancer.

Conclusions: The balance of adaptive immunity and protumorigenic inflammation in individual tumor microenvironments is associated with PD-1/PD-L1 resistance in urothelial cancer with the latter linked to a proinflammatory cellular state of myeloid phagocytic cells detectable in tumor and blood.See related commentary by Drake, p. 4139.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Carcinoma, Transitional Cell / drug therapy*
Carcinoma, Transitional Cell / genetics*
Drug Resistance, Neoplasm
Humans
Immune Checkpoint Inhibitors / therapeutic use*
Myeloid Cells / physiology*
Sequence Analysis, RNA*
Urinary Bladder Neoplasms / drug therapy*
Urinary Bladder Neoplasms / genetics*

Substances

Immune Checkpoint Inhibitors

Abstract

Publication types

MeSH terms

Substances

Grants and funding