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Moore JA, Chen KT, Madison R, Newberg JY, Fleischmann Z, Wang S, Sharaf R, Murugesan K, Fendler BJ, Hughes J, Schrock AB, Hegde PS, Oxnard GR, Fabrizio D, Frampton GM, Antonarakis ES, Sokol ES, Jin DX. Pan-Cancer Analysis of Copy-Number Features Identifies Recurrent Signatures and a Homologous Recombination Deficiency Biomarker to Predict Poly (ADP-Ribose) Polymerase Inhibitor Response. JCO Precis Oncol 2023; 7:e2300093. [PMID: 37769224 DOI: 10.1200/po.23.00093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/21/2023] [Accepted: 07/21/2023] [Indexed: 09/30/2023] Open
Abstract
PURPOSE Copy-number (CN) features reveal the molecular state of cancers and may have predictive and prognostic value in the treatment of cancer. We sought to apply published CN analysis methods to a large pan-cancer data set and characterize ubiquitous CN signatures across tumor types, including potential utility for treatment selection. METHODS We analyzed the landscape of CN features in 260,333 pan-cancer samples. We examined the association of 10 signatures with genomic alterations and clinical characteristics and trained a machine learning classifier using CN and insertion and deletion features to detect homologous recombination deficiency signature (HRDsig) positivity. Clinical outcomes were assessed using a real-world clinicogenomic database (CGDB) of comprehensive genomic profiling linked to deidentified, electronic health record-derived clinical data. RESULTS CN signatures were prevalent across cancer types and associated with diverse processes including focal tandem duplications, seismic amplifications, genome-wide loss of heterozygosity (gLOH), and HRD. Our novel HRDsig outperformed gLOH in predicting BRCAness and effectively distinguished biallelic BRCA and homologous recombination-repair wild-type (HRRwt) samples pan-tumor, demonstrating high sensitivity to detect biallelic BRCA in ovarian (93%) and other HRD-associated cancers (80%-87%). Pan-tumor prevalence of HRDsig was 6.4%. HRRwt cases represented a significant fraction of the HRDsig-positive cohort, likely reflecting a population with nongenomic mechanisms of HRD. In ovarian and prostate CGDBs, HRDsig identified more patients than gLOH and had predictive value for poly (ADP-ribose) polymerase inhibitor (PARPi) benefit. CONCLUSION Tumor CN profiles are informative, revealing diverse processes active in cancer. We describe the landscape of 10 CN signatures in a large pan-cancer cohort, including two associated with HRD. We trained a machine learning-based HRDsig that robustly identified BRCAness and associated with biallelic BRCA pan-tumor, and was predictive of PARPi benefit in real-world ovarian and prostate data sets.
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Yang K, Yu W, Liu H, Lou F, Cao S, Wang H, He Z. Mutational pattern off homologous recombination repair (HRR)-related genes in upper tract urothelial carcinoma. Cancer Med 2023; 12:15304-15316. [PMID: 37387466 PMCID: PMC10417099 DOI: 10.1002/cam4.6175] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND Homologous recombination (HR) repair (HRR) has been indicated to be a biomarker for immunotherapy, chemotherapy, and poly-ADP ribose polymerase inhibitors inhibitors (PARPis). Nonetheless, their molecular correlates in upper tract urothelial carcinoma (UTUC) have not been well studied. This study aimed to explore the molecular mechanism and tumor immune profile of HRR genes and the relevance of their prognostic value in patients with UTUC. MATERIALS AND METHODS One hundred and ninety-seven tumors and matched blood samples from Chinese UTUC were subjected to next-generation sequencing. A total of 186 patients from The Cancer Genome Atlas were included. Comprehensive analysis was performed. RESULTS In Chinese patients with UTUC, 5.01% harbored germline HRR gene mutations, and 1.01% had Lynch syndrome-related genes. A total of 37.6% (74/197) of patients carried somatic or germline HRR gene mutations. There was marked discrepancy in the mutation landscapes, genetic interactions, and driver genes between the HRR-mut cohorts and HRR-wt cohorts. Aristolochic acid signatures and defective DNA mismatch repair signatures only existed in individuals in the HRR-mut cohorts. Inversely, the unknown signature (signature A) and signature SBS55 only existed in patients in the HRR-wt cohorts. HRR gene mutations regulated immune activities by NKT cells, plasmacytoid dendritic cells, hematopoietic stem cell, and M1 macrophages. In patients with local recurrence, patients with HRR gene mutations had poorer DFS rates than patients with wild-type HRR genes. CONCLUSIONS Our results imply that the detection of HRR gene mutations can predict recurrence in patients with UC. In addition, this study provides a path to explore the role of HRR-directed therapies, including PARPis, chemotherapy, and immunotherapy.
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Affiliation(s)
- Kaiwei Yang
- Department of urologyPeking University First HospitalBeijingChina
| | - Wei Yu
- Department of urologyPeking University First HospitalBeijingChina
| | | | - Feng Lou
- AcornMed Biotechnology Co., Ltd.BeijingChina
| | - Shanbo Cao
- AcornMed Biotechnology Co., Ltd.BeijingChina
| | - Huina Wang
- AcornMed Biotechnology Co., Ltd.BeijingChina
| | - Zhisong He
- Department of urologyPeking University First HospitalBeijingChina
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Wang P, Shi Y, Zhang J, Shou J, Zhang M, Zou D, Liang Y, Li J, Tan Y, Zhang M, Bi X, Zhou L, Ci W, Li X. UCseek: ultrasensitive early detection and recurrence monitoring of urothelial carcinoma by shallow-depth genome-wide bisulfite sequencing of urinary sediment DNA. EBioMedicine 2023; 89:104437. [PMID: 36758479 PMCID: PMC9941055 DOI: 10.1016/j.ebiom.2023.104437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Current methods for the detection and surveillance of urothelial carcinomas (UCs) are often invasive, costly, and not effective for low-grade, early-stage, and minimal residual disease (MRD) tumors. We aimed to develop and validate a model from urine sediments to predict different grade and stage UCs with low cost and high accuracy. METHODS We collected 167 samples, including 90 tumors and 77 individuals without tumors, as a discovery cohort. We assessed copy number variations and methylation values for them and constructed a diagnostic classifier to detect UC, UCseek, by using an individual read-based method and support vector machine. The performance of UCseek was validated in an independent cohort derived from three hospitals (n = 206) and a relapse cohort (n = 42) for monitoring recurrence. FINDINGS We constructed UCseek, which could predict UCs with high sensitivity (92.7%), high specificity (90.7%), and high accuracy (91.7%) in the independent validation set. The accuracy of UCseek in low-grade and early-stage patients reached 91.8% and 94.3%, respectively. Notably, UCseek retained great performance at ultralow sequencing depths (0.3X-0.5X). It also demonstrated a powerful ability to monitor recurrence in a surveillance cohort compared with cystoscopy (90.91% vs. 59.09%). INTERPRETATION We optimized an improved approach named UCseek for the noninvasive diagnosis and monitoring of UCs in both low- and high-grade tumors and in early- and advanced-stage tumors, even at ultralow sequencing depths, which may reduce the burden of cystoscopy and blind second surgery. FUNDING A full list of funding bodies that contributed to this study can be found in the Acknowledgments section.
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Affiliation(s)
- Ping Wang
- Department of Urology, Peking University First Hospital, Beijing, 100034, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Shi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Jianye Zhang
- Department of Urology, Peking University First Hospital, Beijing, 100034, China; Institute of Urology, Peking University, Beijing, 100034, China
| | - Jianzhong Shou
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Mingxin Zhang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Daojia Zou
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Liang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Juan Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yezhen Tan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mei Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Xingang Bi
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, 100034, China; Institute of Urology, Peking University, Beijing, 100034, China; National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China.
| | - Weimin Ci
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing, 100034, China; Institute of Urology, Peking University, Beijing, 100034, China; National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China.
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Liang Y, Tan Y, Guan B, Guo B, Xia M, Li J, Shi Y, Yu Z, Zhang Q, Liu D, Yang X, Hao J, Gong Y, Shakeel M, Zhou L, Ci W, Li X. Single-cell atlases link macrophages and CD8 + T-cell subpopulations to disease progression and immunotherapy response in urothelial carcinoma. Am J Cancer Res 2022; 12:7745-7759. [PMID: 36451860 PMCID: PMC9706581 DOI: 10.7150/thno.77281] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/30/2022] [Indexed: 12/03/2022] Open
Abstract
Rationale: Immune checkpoint inhibitors (ICIs) have revolutionized the management of locally advanced or metastatic urothelial carcinoma. Strikingly, compared to urothelial carcinoma of the bladder (UCB), upper tract urothelial carcinoma (UTUC) has a higher response rate to ICIs. The stratification of patients most likely to benefit from ICI therapy remains a major clinical challenge. Methods: In this study, we performed the first single-cell RNA sequencing (scRNA-seq) study of 13 surgical tissue specimens from 12 patients with UTUC. The key results were validated by the analysis of two independent cohorts with bulk RNA-seq data for UCB (n = 404) and UTUC (n = 158) and one cohort of patients with metastatic urothelial carcinoma (mUC) who were treated with atezolizumab (n = 348). Results: Using scRNA-seq, we observed a higher proportion of tumor-infiltrating immune cells in locally advanced UTUC. Similar prognostically relevant intrinsic basal and luminal-like epithelial subtypes were found in both UTUC and UCB, although UTUC is predominantly of the luminal subtype. We also discovered that immunosuppressive macrophages and exhausted T-cell subpopulations were enriched in the basal subtype and showed enhanced interactions. Furthermore, we developed a gene expression signature (Macro-C3 score) capturing the immunosuppressive macrophages that better predicts outcomes than the currently established subtypes. We also developed a computational method to model immune evasion, and the Macro-C3 score predicted therapeutic response of mUC treated with first-line anti-PD-L1 inhibitors in patients with lower basal scores. Conclusions: Overall, the distinct microenvironment and Macro-C3 score provide an explanation for ICI efficacy in urothelial carcinoma and reveal new candidate regulators of immune evasion, suggesting potential therapeutic targets for improving antitumor immunity in the basal subtype.
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Affiliation(s)
- Yuan Liang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Yezhen Tan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bao Guan
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China
| | - Bin Guo
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mancheng Xia
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China
| | - Juan Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Shi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zihui Yu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Liu
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Xiaopeng Yang
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Junfeng Hao
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China
| | - Muhammad Shakeel
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China.,✉ Corresponding authors: Department of Urology, Peking University First Hospital; Institute of Urology, Peking University. No.8, Street Xishiku, District Xicheng, Beijing 100034, China. Tel: +86-10-8357-2211. E-mail addresses: (X. Li); (L. Zhou); Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China. Tel. +86-10-8409-7318. E-mail address: (W. Ci)
| | - Weimin Ci
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,✉ Corresponding authors: Department of Urology, Peking University First Hospital; Institute of Urology, Peking University. No.8, Street Xishiku, District Xicheng, Beijing 100034, China. Tel: +86-10-8357-2211. E-mail addresses: (X. Li); (L. Zhou); Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China. Tel. +86-10-8409-7318. E-mail address: (W. Ci)
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China.,✉ Corresponding authors: Department of Urology, Peking University First Hospital; Institute of Urology, Peking University. No.8, Street Xishiku, District Xicheng, Beijing 100034, China. Tel: +86-10-8357-2211. E-mail addresses: (X. Li); (L. Zhou); Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China. Tel. +86-10-8409-7318. E-mail address: (W. Ci)
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