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Minne RL, Luo NY, Traynor AM, Huang M, DeTullio L, Godden J, Stoppler M, Kimple RJ, Baschnagel AM. Genomic and Immune Landscape Comparison of MET Exon 14 Skipping and MET-Amplified Non-small Cell Lung Cancer. Clin Lung Cancer 2024:S1525-7304(24)00080-9. [PMID: 38852006 DOI: 10.1016/j.cllc.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Mutation or amplification of the mesenchymal-epithelial transition (MET) tyrosine kinase receptor causes dysregulation of receptor function and stimulates tumor growth in non-small cell lung cancer (NSCLC) with the most common mutation being MET exon 14 (METex14). We sought to compare the genomic and immune landscape of MET-altered NSCLC with MET wild-type NSCLC. METHODS 18,047 NSCLC tumors were sequenced with Tempus xT assay. Tumors were categorized based on MET exon 14 (METex14) mutations; low MET amplification defined as a copy number gain (CNG) 6-9, high MET amplification defined as CNG ≥ 10, and MET other type mutations. Immuno-oncology (IO) biomarkers and the frequency of other somatic gene alterations were compared across MET-altered and MET wild-type groups. RESULTS 276 (1.53%) METex14, 138 (0.76%) high METamp, 63 (0.35%) low METamp, 27 (0.15%) MET other, and 17,543 (97%) MET wild-type were identified. Patients with any MET mutation including METex14 were older, while patients with METex14 were more frequently female and nonsmokers. MET gene expression was highest in METamp tumors. PD-L1 positivity rates were higher in MET-altered groups than MET wild-type. METex14 exhibited the lowest tumor mutational burden (TMB) and lowest neoantigen tumor burden (NTB). METamp exhibited the lowest proportion of CD4 T cells and the highest proportion of NK cells. There were significant differences in co-alterations between METamp and METex14. CONCLUSIONS METex14 tumors exhibited differences in IO biomarkers and the somatic landscape compared to non-METex14 NSCLC tumors. Variations in immune profiles can affect immunotherapy selection in MET-altered NSCLC and require further exploration.
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Affiliation(s)
- Rachel L Minne
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Natalie Y Luo
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Anne M Traynor
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | | | | | | | | | - Randall J Kimple
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Andrew M Baschnagel
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin.
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Nayyar N, de Sauvage MA, Chuprin J, Sullivan EM, Singh M, Torrini C, Zhang BS, Bandyopadhyay S, Daniels KA, Alvarez-Breckenridge C, Dahal A, Brehm MA, Brastianos PK. CDK4/6 Inhibition Sensitizes Intracranial Tumors to PD-1 Blockade in Preclinical Models of Brain Metastasis. Clin Cancer Res 2024; 30:420-435. [PMID: 37611074 PMCID: PMC10872577 DOI: 10.1158/1078-0432.ccr-23-0433] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/15/2023] [Accepted: 08/22/2023] [Indexed: 08/25/2023]
Abstract
PURPOSE Brain metastases are associated with high morbidity and are often resistant to immune checkpoint inhibitors. We evaluated whether CDK4/6 inhibitor (CDKi) abemaciclib can sensitize intracranial tumors to programmed cell death protein 1 (PD-1) inhibition in mouse models of melanoma and breast cancer brain metastasis. EXPERIMENTAL DESIGN Treatment response was evaluated in vivo using immunocompetent mouse models of brain metastasis bearing concurrent intracranial and extracranial tumors. Treatment effect on intracranial and extracranial tumor-immune microenvironments (TIME) was evaluated using immunofluorescence, multiplex immunoassays, high-parameter flow cytometry, and T-cell receptor profiling. Mice with humanized immune systems were evaluated using flow cytometry to study the effect of CDKi on human T-cell development. RESULTS We found that combining abemaciclib with PD-1 inhibition reduced tumor burden and improved overall survival in mice. The TIME, which differed on the basis of anatomic location of tumors, was altered with CDKi and PD-1 inhibition in an organ-specific manner. Combination abemaciclib and anti-PD-1 treatment increased recruitment and expansion of CD8+ effector T-cell subsets, depleted CD4+ regulatory T (Treg) cells, and reduced levels of immunosuppressive cytokines in intracranial tumors. In immunodeficient mice engrafted with human immune systems, abemaciclib treatment supported development and maintenance of CD8+ T cells and depleted Treg cells. CONCLUSIONS Our results highlight the distinct properties of intracranial and extracranial tumors and support clinical investigation of combination CDK4/6 and PD-1 inhibition in patients with brain metastases. See related commentary by Margolin, p. 257.
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Affiliation(s)
- Naema Nayyar
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA
| | | | - Jane Chuprin
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA
| | - Emily M Sullivan
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA
| | - Mohini Singh
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA
| | - Consuelo Torrini
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA
| | - Britney S Zhang
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA
| | - Sushobhana Bandyopadhyay
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania
| | - Keith A Daniels
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA
| | - Christopher Alvarez-Breckenridge
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ashish Dahal
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA
| | - Michael A Brehm
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA
| | - Priscilla K Brastianos
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
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Hanna GJ, Villa A, Nandi SP, Shi R, ONeill A, Liu M, Quinn CT, Treister NS, Sroussi HY, Vacharotayangul P, Goguen LA, Annino DJ, Rettig EM, Jo VY, Wong KS, Lizotte P, Paweletz CP, Uppaluri R, Haddad RI, Cohen EEW, Alexandrov LB, William WN, Lippman SM, Woo SB. Nivolumab for Patients With High-Risk Oral Leukoplakia: A Nonrandomized Controlled Trial. JAMA Oncol 2024; 10:32-41. [PMID: 37971722 PMCID: PMC10654930 DOI: 10.1001/jamaoncol.2023.4853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/07/2023] [Indexed: 11/19/2023]
Abstract
Importance Proliferative verrucous leukoplakia (PVL) is an aggressive oral precancerous disease characterized by a high risk of transformation to invasive oral squamous cell carcinoma (OSCC), and no therapies have been shown to affect its natural history. A recent study of the PVL immune landscape revealed a cytotoxic T-cell-rich microenvironment, providing strong rationale to investigate immune checkpoint therapy. Objective To determine the safety and clinical activity of anti-programmed cell death 1 protein (PD-1) therapy to treat high-risk PVL. Design, Setting, and Participants This nonrandomized, open-label, phase 2 clinical trial was conducted from January 2019 to December 2021 at a single academic medical center; median (range) follow-up was 21.1 (5.4-43.6) months. Participants were a population-based sample of patients with PVL (multifocal, contiguous, or a single lesion ≥4 cm with any degree of dysplasia). Intervention Patients underwent pretreatment biopsy (1-3 sites) and then received 4 doses of nivolumab (480 mg intravenously) every 28 days, followed by rebiopsy and intraoral photographs at each visit. Main Outcomes and Measures The primary end point was the change in composite score (size and degree of dysplasia) from before to after treatment (major response [MR]: >80% decrease in score; partial response: 40%-80% decrease). Secondary analyses included immune-related adverse events, cancer-free survival (CFS), PD-1 ligand 1 (PD-L1) expression, 9p21.3 deletion, and other exploratory immunologic and genomic associations of response. Results A total of 33 patients were enrolled (median [range] age, 63 [32-80] years; 18 [55%] were female), including 8 (24%) with previously resected early-stage OSCC. Twelve patients (36%) (95% CI, 20.4%-54.8%) had a response by composite score (3 MRs [9%]), 4 had progressive disease (>10% composite score increase, or cancer). Nine patients (27%) developed OSCC during the trial, with a 2-year CFS of 73% (95% CI, 53%-86%). Two patients (6%) discontinued because of toxic effects; 7 (21%) experienced grade 3 to 4 immune-related adverse events. PD-L1 combined positive scores were not associated with response or CFS. Of 20 whole-exome sequenced patients, all 6 patients who had progression to OSCC after nivolumab treatment exhibited 9p21.3 somatic copy-number loss on pretreatment biopsy, while only 4 of the 14 patients (29%) who did not develop OSCC had 9p21.3 loss. Conclusions and Relevance This immune checkpoint therapy precancer nonrandomized clinical trial met its prespecified response end point, suggesting potential clinical activity for nivolumab in high-risk PVL. Findings identified immunogenomic associations to inform future trials in this precancerous disease with unmet medical need that has been difficult to study. Trial Registration ClinicalTrials.gov Identifier: NCT03692325.
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Affiliation(s)
- Glenn J. Hanna
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alessandro Villa
- Miami Cancer Institute and Herbert Wertheim College of Medicine, Florida International University, Miami
| | - Shuvro P. Nandi
- Moores Cancer Center, UC San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, California
| | - Ruichao Shi
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Anne ONeill
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mofei Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Charles T. Quinn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nathaniel S. Treister
- Division of Oral Medicine and Dentistry, Dana-Farber Cancer Institute and Brigham & Women’s Hospital, Boston, Massachusetts
| | - Herve Y. Sroussi
- Division of Oral Medicine and Dentistry, Dana-Farber Cancer Institute and Brigham & Women’s Hospital, Boston, Massachusetts
| | - Piamkamon Vacharotayangul
- Division of Oral Medicine and Dentistry, Dana-Farber Cancer Institute and Brigham & Women’s Hospital, Boston, Massachusetts
| | - Laura A. Goguen
- Division of Otolaryngology–Head and Neck Surgery, Brigham & Women’s Hospital and Head and Neck Surgical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Donald J. Annino
- Division of Otolaryngology–Head and Neck Surgery, Brigham & Women’s Hospital and Head and Neck Surgical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eleni M. Rettig
- Division of Otolaryngology–Head and Neck Surgery, Brigham & Women’s Hospital and Head and Neck Surgical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Vickie Y. Jo
- Department of Pathology, Brigham & Women’s Hospital, Boston, Massachusetts
| | - Kristine S. Wong
- Department of Pathology, Brigham & Women’s Hospital, Boston, Massachusetts
| | - Patrick Lizotte
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cloud P. Paweletz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ravindra Uppaluri
- Division of Otolaryngology–Head and Neck Surgery, Brigham & Women’s Hospital and Head and Neck Surgical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Robert I. Haddad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Ludmil B. Alexandrov
- Moores Cancer Center, UC San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, California
- Department of Bioengineering, UC San Diego, La Jolla, California
| | - William N. William
- Oncology Center, Hospital BP, a Beneficência Portuguesa de São Paulo, São Paulo, Brazil
| | | | - Sook-bin Woo
- Division of Oral Medicine and Dentistry, Dana-Farber Cancer Institute and Brigham & Women’s Hospital, Boston, Massachusetts
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Jiang Y, Wu Y, Zhang L, Wang Y, Xu G, Deng Y, Han L, Li E, Ma Q, Xu M, Wu Z, Wang Z. Loss of chromosome 9p21 is associated with a poor prognosis in adenosquamous carcinoma of the pancreas. PRECISION CLINICAL MEDICINE 2023; 6:pbad030. [PMID: 38024139 PMCID: PMC10681361 DOI: 10.1093/pcmedi/pbad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Adenosquamous carcinoma of the pancreas (ASCP) is a rare histological subtype of pancreatic cancer with a poor prognosis and a high metastasis rate. However, little is known about its genomic landscape and prognostic biomarkers. A total of 48 ASCP specimens and 98 pancreatic ductal adenocarcinoma (PDAC) tumour specimens were sequenced to explore the genomic landscape and prognostic biomarkers. The homozygous deletion of the 9p21.3 region (including CDKN2A, CDKN2B, and MTAP) (9p21 loss) occurred in both ASCP and PDAC, and a higher frequency of 9p21 loss was observed in ASCP (12.5% vs 2.0%, P = 0.022). Notably, 9p21 loss was significantly associated with poor disease-free survival (DFS) in ASCP patients (mDFS (Median DFS) = 4.17 vs 7.33 months, HR (Hazard Ratio) = 3.70, P = 0.009). The most common gene alterations in patients with ASCP were KRAS (96%), TP53 (81%), CDKN2A (42%), SMAD4 (21%), CDKN2B (13%), and FAT3 (13%). The mutation rates of ACVR2A (6.25% vs 0%), FANCA (6.25% vs 0%), RBM10 (6.25% vs 0%), and SPTA1 (8.33% vs 1.02%) were significantly higher in ASCP than in PDAC. In conclusion, we have comprehensively described the genomic landscape of the largest cohort of ASCP patients to date and highlight that 9p21 loss may be a promising prognostic biomarker for ASCP, which provides a molecular basis for prognosis prediction and new therapeutic strategies for ASCP.
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Affiliation(s)
- Yina Jiang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 70061, China
- Pancreatic disease treatment center, Xi'an Jiaotong University, Xi'an 70061, China
| | - Yinying Wu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 70061, China
- Pancreatic disease treatment center, Xi'an Jiaotong University, Xi'an 70061, China
| | | | - Yan Wang
- OrigiMed Co. Ltd, Shanghai 201114, China
| | - Guiping Xu
- Department of Radiology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 70061, China
- Pancreatic disease treatment center, Xi'an Jiaotong University, Xi'an 70061, China
| | - Yuan Deng
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 70061, China
- Pancreatic disease treatment center, Xi'an Jiaotong University, Xi'an 70061, China
| | - Liang Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 70061, China
- Pancreatic disease treatment center, Xi'an Jiaotong University, Xi'an 70061, China
| | - Enxiao Li
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 70061, China
- Pancreatic disease treatment center, Xi'an Jiaotong University, Xi'an 70061, China
| | - Qingyong Ma
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 70061, China
- Pancreatic disease treatment center, Xi'an Jiaotong University, Xi'an 70061, China
| | - Mian Xu
- OrigiMed Co. Ltd, Shanghai 201114, China
| | - Zheng Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 70061, China
- Pancreatic disease treatment center, Xi'an Jiaotong University, Xi'an 70061, China
| | - Zheng Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 70061, China
- Pancreatic disease treatment center, Xi'an Jiaotong University, Xi'an 70061, China
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5
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Alessi JV, Wang X, Elkrief A, Ricciuti B, Li YY, Gupta H, Spurr LF, Rizvi H, Luo J, Pecci F, Lamberti G, Recondo G, Venkatraman D, Di Federico A, Gandhi MM, Vaz VR, Nishino M, Sholl LM, Cherniack AD, Ladanyi M, Price A, Richards AL, Donoghue M, Lindsay J, Sharma B, Turner MM, Pfaff KL, Felt KD, Rodig SJ, Lin X, Meyerson ML, Johnson BE, Christiani DC, Schoenfeld AJ, Awad MM. Impact of Aneuploidy and Chromosome 9p Loss on Tumor Immune Microenvironment and Immune Checkpoint Inhibitor Efficacy in NSCLC. J Thorac Oncol 2023; 18:1524-1537. [PMID: 37247843 PMCID: PMC10913104 DOI: 10.1016/j.jtho.2023.05.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/28/2023] [Accepted: 05/13/2023] [Indexed: 05/31/2023]
Abstract
INTRODUCTION Although gene-level copy number alterations have been studied as a potential biomarker of immunotherapy efficacy in NSCLC, the impact of aneuploidy burden and chromosomal arm-level events on immune checkpoint inhibitor (ICI) efficacy in NSCLC is uncertain. METHODS Patients who received programmed cell death protein 1 or programmed death-ligand 1 (PD-L1) inhibitor at two academic centers were included. Across all 22 chromosomes analyzed, an arm was considered altered if at least 70% of its territory was either gained or deleted. Among nonsquamous NSCLCs which underwent targeted next-generation sequencing, we retrospectively quantified aneuploidy using the adjusted fraction of chromosomal arm alterations (FAA), defined as the number of altered chromosome arms divided by the number of chromosome arms assessed, adjusted for tumor purity. RESULTS Among 2293 nonsquamous NSCLCs identified, the median FAA increased with more advanced cancer stage and decreased with higher PD-L1 tumor proportion score (TPS) levels (median FAA in TPS < 1%: 0.09, TPS 1%-49%: 0.08, TPS ≥ 50%: 0.05, p < 0.0001). There was a very weak correlation between FAA and tumor mutational burden when taken as continuous variables (R: 0.07, p = 0.0005). A total of 765 advanced nonsquamous NSCLCs with available FAA values were treated with ICIs. With decreasing FAA tertiles, there was a progressive improvement in objective response rate (ORR 15.1% in upper tertile versus 23.2% in middle tertile versus 28.4% in lowest tertile, p = 0.001), median progression-free survival (mPFS 2.5 versus 3.3 versus 4.1 mo, p < 0.0001), and median overall survival (mOS 12.5 versus 13.9 versus 16.4 mo, p = 0.006), respectively. In the arm-level enrichment analysis, chromosome 9p loss (OR = 0.22, Q = 0.0002) and chromosome 1q gain (OR = 0.43, Q = 0.002) were significantly enriched in ICI nonresponders after false discovery rate adjustment. Compared with NSCLCs without chromosome 9p loss (n = 452), those with 9p loss (n = 154) had a lower ORR (28.1% versus 7.8%, p < 0.0001), a shorter mPFS (4.1 versus 2.3 mo, p < 0.0001), and a shorter mOS (18.0 versus 9.6 mo, p < 0.0001) to immunotherapy. In addition, among NSCLCs with high PD-L1 expression (TPS ≥ 50%), chromosome 9p loss was associated with lower ORR (43% versus 6%, p < 0.0001), shorter mPFS (6.4 versus 2.6 mo, p = 0.0006), and shorter mOS (30.2 versus 14.3 mo, p = 0.0008) to immunotherapy compared with NSCLCs without 9p loss. In multivariable analysis, adjusting for key variables including FAA, chromosome 9p loss, but not 1q gain, retained a significant impact on ORR (hazard ratio [HR] = 0.25, p < 0.001), mPFS (HR = 1.49, p = 0.001), and mOS (HR = 1.47, p = 0.003). Multiplexed immunofluorescence and computational deconvolution of RNA sequencing data revealed that tumors with either high FAA levels or chromosome 9p loss had significantly fewer tumor-associated cytotoxic immune cells. CONCLUSIONS Nonsquamous NSCLCs with high aneuploidy and chromosome 9p loss have a distinct tumor immune microenvironment and less favorable outcomes to ICIs.
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Affiliation(s)
- Joao V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xinan Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Arielle Elkrief
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yvonne Y Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Hersh Gupta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Liam F Spurr
- Pritzker School of Medicine, The University of Chicago, Chicago, Illinois
| | - Hira Rizvi
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jia Luo
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Federica Pecci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Giuseppe Lamberti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gonzalo Recondo
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Deepti Venkatraman
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Malini M Gandhi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Victor R Vaz
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women's Hospital and Department of Imaging, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Adam Price
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Allison L Richards
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James Lindsay
- Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Bijaya Sharma
- ImmunoProfile, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Madison M Turner
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kathleen L Pfaff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kristen D Felt
- ImmunoProfile, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Matthew L Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Bruce E Johnson
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Adam J Schoenfeld
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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Tuna M, Mills GB, Amos CI. Common and distinct patterns of acquired uniparental disomy and homozygous deletions between lung squamous cell carcinomas and lung adenocarcinoma. Neoplasia 2023; 45:100932. [PMID: 37801862 PMCID: PMC10562662 DOI: 10.1016/j.neo.2023.100932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 08/19/2023] [Accepted: 08/31/2023] [Indexed: 10/08/2023]
Abstract
Acquired uniparental disomy (aUPD) is a chromosomal alteration that can lead to homozygosity of existing aberrations. We used data from The Cancer Genome Atlas SNP-based arrays to identify distinct and common aUPD profiles in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Moreover, we tested relevance of aUPD for homozygous deletion (HMD), overall survival (OS), and recurrence-free survival (RFS). Overall, we found significantly higher aUPD (q = 5.34E-09) in LUSC than in LUAD. A significant portion of HMD was associated with aUPD in LUSC (24.9%) and LUAD (19.7%). We identified segmental, whole-chromosome arm and whole-chromosome aUPD, in which whole 7p arm aUPD was restricted to LUSC, while whole-chromosome 3 aUPD was observed only in LUAD, and whole-chromosome 21 aUPD was common to both LUSC and LUAD. The most frequent aUPD and HMD were observed at CDKN2A/B region in both LUAD and LUSC. In LUAD, aUPD and HMD at CDKN2A/B region were associated with shorter OS (q < 0.021 and q < 0.005), and RFS (q < 0.005 and q < 0.005), while heterozygous deletion was not associated with OS and RFS. In contrast, no association was found between aUPD at CDKN2A/B region and survival in LUSC. In LUAD, CTLA expression was significantly lower in samples with aUPD at CDKN2A/B regions than in samples without copy number and allele-based changes. Immune infiltration correlated with aUPD or HMD at CDKN2A/B, gain at HLA class I region, and aUPD at whole-chromosome q-arm or whole chromosome in LUAD, but not in LUSC. Both LUSC and LUAD have common and distinct patterns of aUPD regions with differing frequencies of occurrence and associations with outcome.
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Affiliation(s)
- Musaffe Tuna
- Department of Medicine, Institute of Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
| | - Gordon B Mills
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health Science University, Portland, OR 97239, USA
| | - Christopher I Amos
- Department of Medicine, Institute of Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Hong TH, Bang YH, Joe C, Choi YL, Lee SH. Comment on "Leveraging NGS Data to Refine Immunotherapy Response Prediction in NSCLC: PD-L1 Copy Number, Tumor Mutation Burden, and Beyond". J Thorac Oncol 2023; 18:e88-e90. [PMID: 37599051 DOI: 10.1016/j.jtho.2023.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 05/30/2023] [Indexed: 08/22/2023]
Affiliation(s)
- Tae Hee Hong
- Department of Digital Health, Samsung Advanced Institute for Health Science & Technology (SAIHST), Sungkyunkwan University, Seoul, Republic of Korea; Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Yeong Hak Bang
- Department of Digital Health, Samsung Advanced Institute for Health Science & Technology (SAIHST), Sungkyunkwan University, Seoul, Republic of Korea; Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - CheolYong Joe
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea; Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Yoon-La Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Se-Hoon Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea; Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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Tu Z, Wang X, Cai H, Sheng Y, Wu L, Huang K, Zhu X. The cell senescence regulator p16 is a promising cancer prognostic and immune check-point inhibitor (ICI) therapy biomarker. Aging (Albany NY) 2023; 15:2136-2157. [PMID: 36961395 PMCID: PMC10085592 DOI: 10.18632/aging.204601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/01/2023] [Indexed: 03/25/2023]
Abstract
Cyclin-dependent kinase inhibitor 2A (CDKN2A) encodes the cell senescence regulator protein p16. The expression of p16 raises in cell senescence and has a nuclear regulation in cell aging. Meanwhile, it's also reported to inhibit the aggression of several cancers. But its clinical application and role in cancer immunotherapy needs further investigation. We collected the transcriptional data of pan-cancer and normal human tissues from The Cancer Genome Atlas and the Genotype-Tissue Expression databases. CBioPortal webtool was employed to mine the genomic alteration status of CDKN2A across cancers. Kaplan-Meier method and univariate Cox regression were performed for prognostic assessments across cancers, respectively. Gene Set Enrichment Analysis is the main method used to search the associated cancer hallmarks associated with CDKN2A. TIMER2.0 was used to analyze the immune cell infiltration relevance with CDKN2A in pan-cancer. The associations between CDKN2A and immunotherapy biomarkers or regulators were performed by spearman correlation analysis. We found CDKN2A is overexpressed in most cancers and exhibits prognosis predictive ability in various cancers. In addition, it is significantly correlated with immune-activated hallmarks, cancer immune cell infiltrations and immunoregulators. The most interesting finding is that CDKN2A can significantly predict anti-PDL1 therapy response. Finally, specific inhibitors which correlated with CDKN2A expression in different cancer types were also screened by using Connectivity Map (CMap) tool. The results revealed that CDKN2A acts as a robust cancer prognostic and immunotherapy biomarker. Its function in the regulation of cancer cell senescence might shape the tumor microenvironment and contribute to its predictive ability of immunotherapy.
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Affiliation(s)
- Zewei Tu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, P.R. China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- JXHC Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, P.R. China
| | - Xiaolin Wang
- The Second Clinical Medical College of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Huan Cai
- Department of Medical Ultrasonics, Integrated Chinese and Western Medicine Hospital of Jiangxi Province, Nanchang 330006, Jiangxi, P.R. China
| | - Yilei Sheng
- The HuanKui Medical College of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
| | - Lei Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, P.R. China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- JXHC Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, P.R. China
| | - Kai Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, P.R. China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- JXHC Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, P.R. China
| | - Xingen Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, P.R. China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, P.R. China
- JXHC Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, P.R. China
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Development and validation of an integrative pan-solid tumor predictor of PD-1/PD-L1 blockade benefit. COMMUNICATIONS MEDICINE 2023; 3:14. [PMID: 36750617 PMCID: PMC9905474 DOI: 10.1038/s43856-023-00243-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 01/12/2023] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Anti-PD-1 and PD-L1 (collectively PD-[L]1) therapies are approved for many advanced solid tumors. Biomarkers beyond PD-L1 immunohistochemistry, microsatellite instability, and tumor mutation burden (TMB) may improve benefit prediction. METHODS Using treatment data and genomic and transcriptomic tumor tissue profiling from an observational trial (NCT03061305), we developed Immunotherapy Response Score (IRS), a pan-tumor predictive model of PD-(L)1 benefit. IRS real-world progression free survival (rwPFS) and overall survival (OS) prediction was validated in an independent cohort of trial patients. RESULTS Here, by Cox modeling, we develop IRS-which combines TMB with CD274, PDCD1, ADAM12 and TOP2A quantitative expression-to predict pembrolizumab rwPFS (648 patients; 26 tumor types; IRS-High or -Low groups). In the 248 patient validation cohort (248 patients; 24 tumor types; non-pembrolizumab PD-[L]1 monotherapy treatment), median rwPFS and OS are significantly longer in IRS-High vs. IRS-Low patients (rwPFS adjusted hazard ratio [aHR] 0.52, p = 0.003; OS aHR 0.49, p = 0.005); TMB alone does not significantly predict PD-(L)1 rwPFS nor OS. In 146 patients treated with systemic therapy prior to pembrolizumab monotherapy, pembrolizumab rwPFS is only significantly longer than immediately preceding therapy rwPFS in IRS-High patients (interaction test p = 0.001). In propensity matched lung cancer patients treated with first-line pembrolizumab monotherapy or pembrolizumab+chemotherapy, monotherapy rwPFS is significantly shorter in IRS-Low patients, but is not significantly different in IRS-High patients. Across 24,463 molecularly-evaluable trial patients, 7.6% of patients outside of monotherapy PD-(L)1 approved tumor types are IRS-High/TMB-Low. CONCLUSIONS The validated, predictive, pan-tumor IRS model can expand PD-(L)1 monotherapy benefit outside currently approved indications.
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Thol K, Pawlik P, McGranahan N. Therapy sculpts the complex interplay between cancer and the immune system during tumour evolution. Genome Med 2022; 14:137. [PMID: 36476325 PMCID: PMC9730559 DOI: 10.1186/s13073-022-01138-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Cancer development is an evolutionary process. A key selection pressure is exerted by therapy, one of the few players in cancer evolution that can be controlled. As such, an understanding of how treatment acts to sculpt the tumour and its microenvironment and how this influences a tumour's subsequent evolutionary trajectory is critical. In this review, we examine cancer evolution and intra-tumour heterogeneity in the context of therapy. We focus on how radiotherapy, chemotherapy and immunotherapy shape both tumour development and the environment in which tumours evolve and how resistance can develop or be selected for during treatment.
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Affiliation(s)
- Kerstin Thol
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
| | - Piotr Pawlik
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK.
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Somatic 9p24.1 alterations in HPV - head and neck squamous cancer dictate immune microenvironment and anti-PD-1 checkpoint inhibitor activity. Proc Natl Acad Sci U S A 2022; 119:e2213835119. [PMID: 36395141 PMCID: PMC9704728 DOI: 10.1073/pnas.2213835119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Somatic copy number alterations (SCNAs), generally (1) losses containing interferons and interferon-pathway genes, many on chromosome 9p, predict immune-cold, immune checkpoint therapy (ICT)-resistant tumors (2); however, genomic regions mediating these effects are unclear and probably tissue specific. Previously, 9p21.3 loss was found to be an early genetic driver of human papillomavirus-negative (HPV-) head and neck squamous cancer (HNSC), associated with an immune-cold tumor microenvironment (TME) signal, and recent evidence suggested that this TME-cold phenotype was greatly enhanced with 9p21 deletion size, notably encompassing band 9p24.1 (3). Here, we report multi-omic, -threshold and continuous-variable dissection of 9p21 and 9p24 loci (including depth and degree of somatic alteration of each band at each locus, and each gene at each band) and TME of four HPV- HNSC cohorts. Preferential 9p24 deletion, CD8 T-cell immune-cold associations were observed, driven by 9p24.1 loss, and in turn by an essential telomeric regulatory gene element, JAK2-CD274. Surprisingly, same genetic region gains were immune hot. Related 9p21-TME analyses were less evident. Inherent 9p-band-level influences on anti-PD1 ICT survival rates, coincident with TME patterns, were also observed. At a 9p24.1 whole-transcriptome expression threshold of 60th percentile, ICT survival rate exceeded that of lower expression percentiles and of chemotherapy; below this transcript threshold, ICT survival was inferior to chemotherapy, the latter unaffected by 9p24.1 expression level (P-values < 0.01, including in a PD-L1 immunohistochemistry-positive patient subgroup). Whole-exome analyses of 10 solid-tumor types suggest that these 9p-related ICT findings could be relevant to squamous cancers, in which 9p24.1 gain/immune-hot associations exist.
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