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Derks S, de Klerk LK, Xu X, Fleitas T, Liu KX, Liu Y, Dietlein F, Margolis C, Chiaravalli AM, Da Silva AC, Ogino S, Akarca FG, Freeman GJ, Rodig SJ, Hornick JL, van Allen E, Li B, Liu SX, Thorsson V, Bass AJ. Characterizing diversity in the tumor-immune microenvironment of distinct subclasses of gastroesophageal adenocarcinomas. Ann Oncol 2020; 31:1011-1020. [PMID: 32387455 PMCID: PMC7690253 DOI: 10.1016/j.annonc.2020.04.011] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/11/2020] [Accepted: 04/14/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Gastroesophageal adenocarcinomas (GEAs) are heterogeneous cancers where immune checkpoint inhibitors have robust efficacy in heavily inflamed microsatellite instability (MSI) or Epstein-Barr virus (EBV)-positive subtypes. Immune checkpoint inhibitor responses are markedly lower in diffuse/genome stable (GS) and chromosomal instable (CIN) GEAs. In contrast to EBV and MSI subtypes, the tumor microenvironment of CIN and GS GEAs have not been fully characterized to date, which limits our ability to improve immunotherapeutic strategies. PATIENTS AND METHODS Here we aimed to identify tumor-immune cell association across GEA subclasses using data from The Cancer Genome Atlas (N = 453 GEAs) and archival GEA resection specimen (N = 71). The Cancer Genome Atlas RNAseq data were used for computational inferences of immune cell subsets, which were correlated to tumor characteristics within and between subtypes. Archival tissues were used for more spatial immune characterization spanning immunohistochemistry and mRNA expression analyses. RESULTS Our results confirmed substantial heterogeneity in the tumor microenvironment between distinct subtypes. While MSI-high and EBV+ GEAs harbored most intense T cell infiltrates, the GS group showed enrichment of CD4+ T cells, macrophages and B cells and, in ∼50% of cases, evidence for tertiary lymphoid structures. In contrast, CIN cancers possessed CD8+ T cells predominantly at the invasive margin while tumor-associated macrophages showed tumor infiltrating capacity. Relatively T cell-rich 'hot' CIN GEAs were often from Western patients, while immunological 'cold' CIN GEAs showed enrichment of MYC and cell cycle pathways, including amplification of CCNE1. CONCLUSIONS These results reveal the diversity of immune phenotypes of GEA. Half of GS gastric cancers have tertiary lymphoid structures and are therefore promising candidates for immunotherapy. The majority of CIN GEAs, however, exhibit T cell exclusion and infiltrating macrophages. Associations of immune-poor CIN GEAs with MYC activity and CCNE1 amplification may enable new studies to determine precise mechanisms of immune evasion, ultimately inspiring new therapeutic modalities.
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Affiliation(s)
- S Derks
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
| | - L K de Klerk
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands; Dana-Farber Cancer Institute, Boston, USA
| | - X Xu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - T Fleitas
- Biomedical Research Institute INCLIVA, CIBERONC, University of Valencia, Valencia, Spain
| | - K X Liu
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston, USA
| | - Y Liu
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, USA
| | - F Dietlein
- Dana-Farber Cancer Institute, Boston, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, USA
| | - C Margolis
- Dana-Farber Cancer Institute, Boston, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, USA
| | | | - A C Da Silva
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - S Ogino
- Dana-Farber Cancer Institute, Boston, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, USA
| | - F G Akarca
- Dana-Farber Cancer Institute, Boston, USA
| | | | - S J Rodig
- Department of Pathology and Center for Immuno-Oncology
| | - J L Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - E van Allen
- Dana-Farber Cancer Institute, Boston, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, USA
| | - B Li
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, USA
| | - S X Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, USA
| | - V Thorsson
- Institute for Systems Biology, Seattle, USA
| | - A J Bass
- Dana-Farber Cancer Institute, Boston, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, USA.
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Abou Alaiwi S, Nassar A, El Bakouny Z, Berchuck JE, Nuzzo P, Flippot R, Flaifel A, Steinharter JA, Baca S, Margolis C, Vokes N, Du H, Shukla SA, Braun DA, Signoretti S, Sonpavde G, Kwiatkowski DJ, Van Allen EM, Choueiri TK. Association of polybromo-associated BAF (PBAF) complex mutations with overall survival (OS) in cancer patients (pts) treated with checkpoint inhibitors (ICIs). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
103 Background: ICIs have shown benefit across several metastatic carcinomas, yet predictive biomarkers are still lacking. 20% of malignancies harbor alterations in ≥1gene that is part of PBAF complex. With recent data suggesting an association between PBRM1 mutations (mts) and outcomes in renal cell carcinoma (RCC) pts treated with ICIs (Miao, Science, 2018), we examined the association between PBAF mts and OS in ICI-treated patients across several solid cancer (ca) types. Methods: Of 6007 pts with different ca histologies and targeted exome sequencing (Oncopanel) at Dana Farber Cancer institute (DFCI), 138 pts had truncating mts in any PBAF gene (SMARCA4, PBRM1, and ARID2) or oncogenic missense mts in SMARCA4 and were treated with ICIs. 138 histology-matched DFCI pts had none. A publicly-available cohort (2:1 histology matched) from Memorial Sloan Kettering (MSKCC) (Samstein et al., Nature Genetics, 2019) of 621 ca pts (PBAF mutant [MT] = 207, PBAF wild type [WT] = 414) treated with ICIs was analyzed for association between PBAF mts and OS. OS was defined from time from ICI initiation. OS was compared by Cox regression between PBAF MT and PBAF WT. Hazard ratio (HR) was derived using univariable and multivariable analysis (MVA) adjusted for ICI regimen (single vs combination) and age. Results: Median (Md) follow-up for the combined cohort (n = 897) was 27 months (m). Major histologies were non-small cell lung ca (268; 29.9%), melanoma (220; 24.5%), RCC (181; 20.2%), and bladder ca (65; 7.2%). Results on univariable and MVA analyses from individual and combined cohorts are presented below. Conclusions: PBAF mts are associated with survival in ICI-treated ca pts. Work in progress with non-ICI treated pts will determine if this is prognostic or predictive of response. [Table: see text]
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Affiliation(s)
| | | | | | | | - Pier Nuzzo
- Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | - Heng Du
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | | | | | | | | | | | | | - Toni K. Choueiri
- Dana-Farber Cancer Institute, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA
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3
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Vokes N, Margolis C, Liu D, Schilling B, Schadendorf D, Van Allen EM. Distinct immunogenomic properties of melanomas with stable disease as best response to immune checkpoint blockade (ICB). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.2515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2515 Background: ICB has improved survival in melanoma. Patients with stable disease (SD) as best treatment response represent an intermediate response phenotype whose biology has been incompletely characterized. Methods: Whole exome and transcriptome sequencing from pre-treatment tumors in melanoma patients treated with ICB (anti-CTLA-4 and/or anti-PD-1) were assembled and uniformly analyzed (WES n = 293; WES+RNA-seq n = 159). RECIST (v1.1) was used to determine complete or partial response (CR/PR; n = 94), SD (n = 42), or progressive disease (PD; n = 157). Gene set enrichment analysis (GSEA) was performed on 50 “hallmark” gene sets to identify pathways differentially expressed in patients with SD. CIBERSORT was used to infer relative proportions of 22 immune cell types in each sample. Mutation antigenicity was determined by calculating patient-specific mutation affinity for MHC class I peptides. Results: GSEA identified enrichment of multiple immune-related gene sets in SD tumors, including TNF-α signaling and interferon-ɣ response (FDR q < 0.1, SD vs CR/PR and SD vs PD). SD tumors had higher HLA and antigen presentation pathway expression, and increased cytolytic T cell activity compared to CR/PR and PD. CIBERSORT analysis identified higher total immune infiltrate in SD patients compared to CR/PR and PD (Mann-Whitney U p = 0.03 and p < 0.001, respectively) but not in patients with CR/PR vs PD (p = 0.124). However, checkpoint expression, including PD-1, PD-L1, and LAG3, was also higher in SD patients. Mutation load did not differ between SD and CR/PR or PD patients (SD median 2.87 vs CR/PR median 7.98, Mann-Whitney U p = 0.104; PD median 3.42, p = 0.210). However, SD patients had more antigenic passenger mutations (SD vs CR/PR, p = 0.001; vs PD, p < 0.001); there was no difference in antigenicity of driver mutations. Conclusions: Pre-treatment melanomas from patients with SD contain more antigenic passenger mutations and demonstrate a global increase in immune signaling. This may describe a subset of patients with pre-existing dysfunctional immune response that is minimally responsive to ICB. Further characterization of the tumor-immune interaction in these patients may inform improved interventions.
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Affiliation(s)
| | | | - David Liu
- Dana-Farber Cancer Institute, Boston, MA
| | - Bastian Schilling
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Dirk Schadendorf
- Universitaetsklinikum Essen & German Cancer Consortium, Essen, Germany
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Rodrigues DN, Rescigno P, Liu D, Yuan W, Carreira S, Lambros MB, Seed G, Mateo J, Riisnaes R, Mullane S, Margolis C, Miao D, Miranda S, Dolling D, Clarke M, Bertan C, Crespo M, Boysen G, Ferreira A, Sharp A, Figueiredo I, Keliher D, Aldubayan S, Burke KP, Sumanasuriya S, Fontes MS, Bianchini D, Zafeiriou Z, Mendes LST, Mouw K, Schweizer MT, Pritchard CC, Salipante S, Taplin ME, Beltran H, Rubin MA, Cieslik M, Robinson D, Heath E, Schultz N, Armenia J, Abida W, Scher H, Lord C, D'Andrea A, Sawyers CL, Chinnaiyan AM, Alimonti A, Nelson PS, Drake CG, Van Allen EM, de Bono JS. Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer. J Clin Invest 2018; 128:5185. [PMID: 30382943 DOI: 10.1172/jci125184] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Nava Rodrigues D, Rescigno P, Liu D, Yuan W, Carreira S, Lambros MB, Seed G, Mateo J, Riisnaes R, Mullane S, Margolis C, Miao D, Miranda S, Dolling D, Clarke M, Bertan C, Crespo M, Boysen G, Ferreira A, Sharp A, Figueiredo I, Keliher D, Aldubayan S, Burke KP, Sumanasuriya S, Fontes MS, Bianchini D, Zafeiriou Z, Teixeira Mendes LS, Mouw K, Schweizer MT, Pritchard CC, Salipante S, Taplin ME, Beltran H, Rubin MA, Cieslik M, Robinson D, Heath E, Schultz N, Armenia J, Abida W, Scher H, Lord C, D'Andrea A, Sawyers CL, Chinnaiyan AM, Alimonti A, Nelson PS, Drake CG, Van Allen EM, de Bono JS. Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer. J Clin Invest 2018; 128:4441-4453. [PMID: 30179225 PMCID: PMC6159966 DOI: 10.1172/jci121924] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND. Understanding the integrated immunogenomic landscape of advanced prostate cancer (APC) could impact stratified treatment selection. METHODS. Defective mismatch repair (dMMR) status was determined by either loss of mismatch repair protein expression on IHC or microsatellite instability (MSI) by PCR in 127 APC biopsies from 124 patients (Royal Marsden [RMH] cohort); MSI by targeted panel next-generation sequencing (MSINGS) was then evaluated in the same cohort and in 254 APC samples from the Stand Up To Cancer/Prostate Cancer Foundation (SU2C/PCF). Whole exome sequencing (WES) data from this latter cohort were analyzed for pathogenic MMR gene variants, mutational load, and mutational signatures. Transcriptomic data, available for 168 samples, was also performed. RESULTS. Overall, 8.1% of patients in the RMH cohort had some evidence of dMMR, which associated with decreased overall survival. Higher MSINGS scores associated with dMMR, and these APCs were enriched for higher T cell infiltration and PD-L1 protein expression. Exome MSINGS scores strongly correlated with targeted panel MSINGS scores (r = 0.73, P < 0.0001), and higher MSINGS scores associated with dMMR mutational signatures in APC exomes. dMMR mutational signatures also associated with MMR gene mutations and increased immune cell, immune checkpoint, and T cell–associated transcripts. APC with dMMR mutational signatures overexpressed a variety of immune transcripts, including CD200R1, BTLA, PD-L1, PD-L2, ADORA2A, PIK3CG, and TIGIT. CONCLUSION. These data could impact immune target selection, combination therapeutic strategy selection, and selection of predictive biomarkers for immunotherapy in APC. FUNDING. We acknowledge funding support from Movember, Prostate Cancer UK, The Prostate Cancer Foundation, SU2C, and Cancer Research UK.
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Affiliation(s)
- Daniel Nava Rodrigues
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden, London, United Kingdom
| | - Pasquale Rescigno
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden, London, United Kingdom.,Department of Clinical Medicine and Surgery, Department of Translational Medical Sciences, Azienda Ospedaliera Universitaria (AOU) Federico II, Naples, Italy
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,The Broad Institute, Cambridge, Massachusetts, USA
| | - Wei Yuan
- The Institute of Cancer Research, London, United Kingdom
| | | | | | - George Seed
- The Institute of Cancer Research, London, United Kingdom
| | - Joaquin Mateo
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden, London, United Kingdom
| | - Ruth Riisnaes
- The Institute of Cancer Research, London, United Kingdom
| | - Stephanie Mullane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,The Broad Institute, Cambridge, Massachusetts, USA
| | - Claire Margolis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,The Broad Institute, Cambridge, Massachusetts, USA
| | - Diana Miao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,The Broad Institute, Cambridge, Massachusetts, USA
| | - Susana Miranda
- The Institute of Cancer Research, London, United Kingdom
| | - David Dolling
- The Institute of Cancer Research, London, United Kingdom
| | - Matthew Clarke
- The Institute of Cancer Research, London, United Kingdom
| | - Claudia Bertan
- The Institute of Cancer Research, London, United Kingdom
| | - Mateus Crespo
- The Institute of Cancer Research, London, United Kingdom
| | - Gunther Boysen
- The Institute of Cancer Research, London, United Kingdom
| | - Ana Ferreira
- The Institute of Cancer Research, London, United Kingdom
| | - Adam Sharp
- The Institute of Cancer Research, London, United Kingdom
| | | | - Daniel Keliher
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,The Broad Institute, Cambridge, Massachusetts, USA
| | - Saud Aldubayan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,The Broad Institute, Cambridge, Massachusetts, USA
| | - Kelly P Burke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Mariane Sousa Fontes
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden, London, United Kingdom
| | - Diletta Bianchini
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden, London, United Kingdom
| | - Zafeiris Zafeiriou
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden, London, United Kingdom
| | | | - Kent Mouw
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Michael T Schweizer
- University of Washington, Seattle, Washington, USA.,Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Mary-Ellen Taplin
- Department of Clinical Medicine and Surgery, Department of Translational Medical Sciences, Azienda Ospedaliera Universitaria (AOU) Federico II, Naples, Italy
| | - Himisha Beltran
- Weill Medical College of Cornell University, New York, New York, USA
| | - Mark A Rubin
- Weill Medical College of Cornell University, New York, New York, USA
| | - Marcin Cieslik
- University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Dan Robinson
- University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | | | - Joshua Armenia
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Wassim Abida
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Howard Scher
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Alan D'Andrea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | | | - Andrea Alimonti
- Institute of Oncology Research (IOR), Bellinzona and Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Peter S Nelson
- University of Washington, Seattle, Washington, USA.,Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,The Broad Institute, Cambridge, Massachusetts, USA
| | - Johann S de Bono
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden, London, United Kingdom
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Wankowicz SA, Bowden M, Lis R, Margolis C, Livitz D, Leshchiner I, Liu D, He MX, Zhang Z, Getz G, Taplin ME, Allen EV. Abstract 4350: Integrative and multiregional molecular analysis of localized, high grade prostate cancer treated with neoadjuvant androgen deprivation treatment. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Neoadjuvant intense androgen deprivation treatment (ADT) in localized, high risk prostate cancer (HG PCa) has varied degrees of response. While some patients have an outstanding response with minimal residual disease [MRD; ≤0.5mm of tumor at radical prostatectomy (RP)], others have no response but delay potential curative treatment. Previous studies have demonstrated that HG PCa is heterogenous, however previous studies have not investigated whether heterogeneity itself or specific genetic molecular features correlate with response to intense neoadjuvant ADT. Herein, we provide an integrated molecular analysis of the spatial heterogeneity of HG PCa treated with neoadjuvant ADT. We examined 53 pre-treatment biopsy samples (n=35 biopsies containing tumor, n=18 normal prostate tissue) from 14 patients with matched blood normals who were treated with an intense neoadjuvant regimen of lupron plus abiraterone/enzalutamide. Patients were stratified as exceptional responders (n=8; MRD at RP) or non-responders (n=6; pT3 or lymph node positive at RP). We performed whole exome and whole transcriptome sequencing on multiple, spatially heterogeneous biopsies within each patient to examine the role of heterogeneity in response to therapy. We called somatic and germline variants, inferred mutational clonality, phylogenetic relationships, called genetic fusion, and analyzed differentially expressed genes. After QC, we observed well known prostate driver mutations (SPOP, ATM, TP53, FOXA1, PTEN, and APC) across the entire cohort (n=14 patients). Within each individual, all driver mutations were clonal across tumor cores, but the proportion of all mutations that were always clonal varied widely (0.08-0.57), median 0.3). Among known drivers, SPOP mutations were only observed in exceptional responders (4/8 v. 0/6), and TP53 and PTEN mutations were only observed in non-responders (4/6 v. 0/8). Responders and non-responders did not differ by mutational or copy number burden. Mutational heterogeneity varied greatly between samples, however this did not split between responders and non-responders. In terms of gene expression, exceptional responders showed upregulation of androgen and estrogen response pathways, while non-responders had increased expression of E2F targets and cell cycle pathways. We confirmed that a subset of localized, HG PCa are molecularly heterogeneous in terms of mutations and expression. We are presently underpowered to explain the genomic differences between excpetional responders and non-responders. However, molecular heterogeneous and homogenous HG PCa tumors can respond to intense neoadjuvant ADT therapy. We are currently analyzing a larger cohort.
Citation Format: Stephanie A. Wankowicz, Michaela Bowden, Rosina Lis, Claire Margolis, Dimitri Livitz, Ignaty Leshchiner, David Liu, Meng Xiao He, Zhenwei Zhang, Gad Getz, Mary-Ellen Taplin, Eliezer Van Allen. Integrative and multiregional molecular analysis of localized, high grade prostate cancer treated with neoadjuvant androgen deprivation treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4350.
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Affiliation(s)
| | | | - Rosina Lis
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | - David Liu
- 1Dana-Farber Cancer Institute, Boston, MA
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Voss MH, Buros Novik J, Hellmann MD, Ball M, Hakimi AA, Miao D, Margolis C, Horak C, Wind-Rotolo M, De Velasco G, Tannir NM, Tamboli P, Appleman LJ, Rathmell K, Hsieh JJ, Allaf M, Choueiri TK, VanAllen E, Snyder A, Motzer RJ. Correlation of degree of tumor immune infiltration and insertion-and-deletion (indel) burden with outcome on programmed death 1 (PD1) therapy in advanced renal cell cancer (RCC). J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.4518] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | - Mark Ball
- National Cancer Institute, Bethesda, MD
| | - A. Ari Hakimi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diana Miao
- Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | - Nizar M. Tannir
- The University of Texas MD Anderson Cancer Center, Houston, TX
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8
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Vokes N, Miao D, Margolis C, Liu D, Wankowicz S, Schilling B, Sholl LM, Getz G, Janne PA, Haddad RI, Choueiri TK, Barbie DA, Haq R, Awad MM, Schadendorf D, Hodi FS, Bellmunt J, Wong KK, Hammerman PS, Van Allen EM. Genomic correlates of response to immune checkpoint blockade in microsatellite stable solid tumors. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.3036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Diana Miao
- Dana-Farber Cancer Institute, Boston, MA
| | | | - David Liu
- Dana-Farber Cancer Institute, Boston, MA
| | | | - Bastian Schilling
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | | | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | - Rizwan Haq
- Massachusetts General Hospital, Boston, MA
| | | | - Dirk Schadendorf
- Department of Dermatology, University of Duisburg-Essen, Essen, Germany
| | | | | | | | - Peter S. Hammerman
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
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Kamran SC, Lennerz JK, Margolis C, Liu D, Reardon B, Wankowicz SA, Wo JYL, Willers H, Corcoran RB, Van Allen EM, Hong TS. Genomic evolution and acquired resistance to preoperative chemoradiation therapy (CRT) in rectal cancer. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.4_suppl.613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
613 Background: Following pre-operative CRT for locally advanced rectal cancer, ~20% of patients achieve a pathologic complete response and 20-40% have little to no response (NR) at time of surgery. Pathologic downstaging after CRT is associated with improved outcomes but molecular predictors of response are poorly understood. The objective of this study was to characterize somatic mutations and derive genomic biomarkers distinguishing complete and excellent partial responders (R) vs NR through whole exome sequencing (WES) in pre- and post-CRT tumor samples. Methods: Rectal cancer patients treated with pre-operative CRT and having either a R or NR were identified. DNA extraction from clinical FFPE samples and WES were performed on pre/post-CRT tumor and matched germline DNA followed by genomic analysis to identify somatic mutations, insertion/deletions, and clonal/subclonal mutational evolution. RNA extraction/sequencing and GSEA was performed in parallel. Results: We identified 34 pre- and post-CRT matched tumor samples from 17 patients treated with pre-operative fluoropyrimidine-based CRT (50.4 Gy) followed by surgery within 8-10 weeks. Nine and 8 patients were classified as NR and R, respectively. All FFPE passed quality control metrics and were successfully sequenced. Mean somatic mutational burden pre-CRT was 3.78 mutations/Mb (rg, 2.25-8.43), which, unexpectedly, was not significantly increased in the post-CRT samples (4.23 mutations/Mb; rg, 1.74-8.96). NR cases had more concurrent KRAS/TP53 (KP) mutations than R cases (67% vs 13%, p < 0.05). Related to this finding, NR was associated with epithelial-to-mesenchymal transition (p < 0.001) and potentially linked to high intra-tumoral heterogeneity pre-CRT (p = 0.08). Conclusions: We have established feasibility and a pipeline for performing WES on pre- and post-CRT FFPE tumor samples. Our data suggest that evolution of CRT resistance is not through hypermutation. In conjunction with recent observations from our group (Hong, JNCI 2017; Wang, Cancer Res 2017), our findings strongly support the clinical utility of the KP genotype as a biomarker of CRT resistance and begin to offer insight into the underlying mechanisms on a genomic level.
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Affiliation(s)
| | - Jochen K Lennerz
- Massachusetts General Hospital/ Harvard Medical School, Boston, MA
| | | | - David Liu
- Dana-Farber Cancer Institute, Boston, MA
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Miao D, Liu D, Keliher D, Shukla S, Schilling B, Margolis C, Smart A, Garraway L, Hodi S, Schadendorf D, Allen EMV. Abstract 571: Meta-analysis of genomic predictors of response to immune checkpoint therapy in metastatic melanoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Immune checkpoint therapies benefit a subset of patients with metastatic melanoma, but ability to predict clinical outcomes is limited. This meta-analysis of genomic predictors of outcomes to aPD1 and aCTLA4 in melanoma combines 220 sequenced tumors from 3 published cohorts, aiming to validate existing hypotheses regarding response to immune checkpoint therapies and discover new relationships with greater power.
Methods: Genomic data and clinical annotations from published cohorts were analyzed with standardized pipelines for somatic variant calling, mutational signature deconvolution, and neoantigen prediction. Patients were stratified into clinical benefit (CB) and no clinical benefit (NCB) as described in Van Allen et al. 2015. Analyses were repeated using two other published response metrics (CB=PFS>6 months; CB=CR or PR).
Results: Nonsynonymous mutational burden was significantly higher in CB vs. NCB using all 3 response metrics, though significance was less pronounced using PFS alone (p<0.01 vs. p<0.0001; Wilcoxon rank sum), partially due to 3 patients with high mutational burden who experienced PR for <6 months, potentially representing early acquired rather than intrinsic resistance. To assess the impact of mutational processes contributing to overall mutational burden, we used a non-negative matrix factorization framework to infer mutational activity in tumors from 6 signatures previously seen in melanoma: aging (S1), T>C substitutions (S5), mismatch repair (S6), alkylating agents (S11), UV (S7), and T>G substitutions (S17). The proportion of mutations in S7 or S11 was positively correlated with mutational burden (Spearman’s rho=0.66), while S5 and S1 were anti-correlated (rho=-0.62). In a multivariate logistic model, S7 and S11 activity were independent predictors of CB adjusting for mutational load (p<0.05), with the sum of S7 and S11 activity being a strong predictor (p<0.001). Of the patients with low mutational burden (<median) with CB, a large majority (23/29) had >1/2 of mutations in S7 or S11, compared to only 36/71 of low-mutation NCB (p<0.01; Pearson’s chi-squared). Neoantigen burden was strongly correlated with mutational burden, and did not improve ability to predict CB. In examining mutations in specific genes, >500 genes were mutated more frequently in either CB or NCB (p<0.05, Fisher’s exact). Restricting analysis to genes recurrently mutated in cancer and correcting for patient mutational burden by permutation, nonsynonymous mutations in ACSL3 and MET and truncating alterations in ARID2 were significantly enriched in CB.
Conclusions: In this meta-analysis of 220 patients, harmonized clinical and whole exome analysis confirmed that mutational burden correlates with CB from aPD1 and aCTLA4 therapy, while mutational signatures and alterations in specific genes potentially provide additional predictive power.
Citation Format: Diana Miao, David Liu, Daniel Keliher, Sachet Shukla, Bastian Schilling, Claire Margolis, Alicia Smart, Levi Garraway, Stephen Hodi, Dirk Schadendorf, Eliezer M. Van Allen. Meta-analysis of genomic predictors of response to immune checkpoint therapy in metastatic melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 571. doi:10.1158/1538-7445.AM2017-571
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Affiliation(s)
- Diana Miao
- 1Dana-Farber Cancer Institute, Boston, MA
| | - David Liu
- 1Dana-Farber Cancer Institute, Boston, MA
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Smart AC, Margolis C, Miao D, Liu D, Park J, He MX, Reardon B, Mullane S, Schilling B, Garraway LA, Schadendorf D, Allen EMV. Abstract 5647: Intron retention as a novel source of tumor neoantigens associated with response to checkpoint inhibitor therapy. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Development of immune checkpoint inhibitors has substantially improved outcomes in patients diagnosed with metastatic melanoma. However, only a minority of patients treated experience long-term clinical benefit, and clinicians have limited ability to predict which patients will respond. Recent studies have demonstrated that the burden of tumor neoantigens generated by expressed somatic mutations is predictive of response to immunotherapy. Intron retention, which is widespread in cancer transcriptomes, represents a putative source of tumor neoantigens by generating peptides that are available for presentation through the MHC I pathway.
Methods: We developed a neoantigen prediction pipeline to identify patient-specific neoantigens from transcriptome sequencing data, which enables identification of retained intron neoantigens from clinical cohorts receiving checkpoint inhibitor therapy. This pipeline incorporates published methods for detecting intron retention events from transcriptome data, detects open reading frames that extend from normal transcripts into intronic sequences, and identifies neoepitopes predicted as strong binders based on the patient’s HLA molecules. We applied this pipeline to a cohort of 41 melanoma patients receiving checkpoint inhibitor therapy and classified patient outcomes as receiving clinical benefit (CB) (n=14), no clinical benefit (NCB) (n=22), or long-term survival without clinical benefit (LS) (n=5).
Results: Our initial analysis identified a mean retained intron neoantigen burden of 7709 per sample, without significant difference between response groups. In one patient who derived clinical benefit from checkpoint inhibition, neoantigen load from nonsynonymous mutations was low (407, 0.34 standard deviations (SD) below a mean of 1,015 among CB patients), while retained intron neoantigen load was high (14579, 1.7 SDs above a mean of 7517 among CB patients), suggesting that retained intron neoantigen load may explain response in some patients with low mutational burden. Preliminary analysis of specific neoantigens suggests that a retained intron in ZNF880 identified in patients expressing HLA-A01:01 is present in 6 of 6 patients experiencing clinical benefit, but only 2 of 7 patients not experiencing clinical benefit. The same analysis was performed on two additional cohorts of melanoma tumor samples to assess whether a larger sample size could aid in the identification of recurrent neoepitopes generated by retained introns.
Conclusions: Application of this approach to data from patients receiving checkpoint blockade with selective response identifies response-associated neoantigens that may warrant further investigation. Identification of a novel source of neoantigens associated with immunotherapy response will provide valuable prognostic information to patients and inform the development of next generation immunotherapeutics.
Citation Format: Alicia C. Smart, Claire Margolis, Diana Miao, David Liu, Jihye Park, Meng Xiao He, Brendan Reardon, Stephanie Mullane, Bastian Schilling, Levi A. Garraway, Dirk Schadendorf, Eliezer M. Van Allen. Intron retention as a novel source of tumor neoantigens associated with response to checkpoint inhibitor therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5647. doi:10.1158/1538-7445.AM2017-5647
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Affiliation(s)
| | | | - Diana Miao
- 1Dana Farber Cancer Institute, Boston, MA
| | - David Liu
- 1Dana Farber Cancer Institute, Boston, MA
| | - Jihye Park
- 1Dana Farber Cancer Institute, Boston, MA
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Miao D, Margolis C, Martini D, Mullane SA, Cullen D, Horak C, Wind-Rotolo M, Hellmann MD, Voss MH, Motzer RJ, Norton C, Signoretti S, Snyder Charen A, Van Allen EM, Choueiri TK. Loss-of-function of PBRM1 to predict response to anti-PD-1/PD-L1 therapy in metastatic renal cell carcinoma. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.3016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3016 Background: Immune checkpoint inhibitors targeting programmed cell death-1 (PD-1) substantially improve patient survival in clear-cell renal cell carcinoma (ccRCC), but predictive biomarkers for efficacy have not yet been identified. Methods: We analyzed whole exome sequencing (WES) from a clinical trial of anti-PD-1 monotherapy (nivolumab) for ccRCC (N = 34) to discover genomic predictors of response to immune checkpoint therapy, and validated our findings in 28 ccRCC patients from 2 institutions treated with anti-PD-1 or anti-PD-L1 therapies. We defined 3 response groups: clinical benefit (CB) – complete or partial response by RECIST or stable disease with objective decrease in tumor burden and progression free survival (PFS) > 6 months - and no clinical benefit (NCB) – progressive disease with PFS < 3 months, with all other patients in intermediate benefit (IB). We further validated our findings in WES from 212 melanoma patients treated with immune checkpoint therapies in 3 published cohorts. Results: Biallelic loss of the chromatin remodeling subunit PBRM1, mutated in 34/62 (55%) patients across both cohorts and up to 41% of ccRCC overall, was the only gene mutation associated with CB in both the training (p = 0.0064; Pearson’s chi-squared) and validation cohorts (p = 0.043), and predicted both PFS and overall survival (OS) (p = 0.042 and 0.014, respectively; Kaplan-Meier). In 212 melanomas, truncating alterations in ARID2 – a closely related chromatin remodeler - were also enriched in responders after correcting for tumor mutational burden (p = 0.036), and having a truncating alteration in either PBRM1 or ARID2 significantly predicted overall survival (p = 0.022). In this ccRCC cohort, tumor mutational burden and loss of antigen presentation machinery were not associated with CB or NCB. Conclusions: Loss of chromatin remodeling subunits may impact response to immune checkpoint therapy in both ccRCC and melanoma. Further study in larger cohorts of immunotherapy-treated patients and functional characterization of ARID2 and PBRM1 in the context of the tumor-immune microenvironment will help to determine potential for further biomarker development.
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Affiliation(s)
- Diana Miao
- Dana-Farber Cancer Institute, Boston, MA
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Margolis C, Jotkowitz A, Sitter H. A problem solving and decision making toolbox for approaching clinical problems and decisions. Inflamm Res 2004; 53 Suppl 2:S179-83. [PMID: 15338073 DOI: 10.1007/s00011-004-0354-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In this paper, we begin by presenting three real patients and then review all the practical conceptual tools that have been suggested for systematically analyzing clinical problems. Each of these conceptual tools (e.g. Evidence-Based Medicine, Clinical Practice Guidelines, Decision Analysis) deals mainly with a different type or aspect of clinical problems. We suggest that all of these conceptual tools can be thought of as belonging in the clinician's toolbox for solving clinical problems and making clinical decisions. A heuristic for guiding the clinician in using the tools is proposed. The heuristic is then used to analyze management of the three patients presented at the outset.
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Affiliation(s)
- C Margolis
- Faculty of Health Sciences, Health Economics and Administration, Ben Gurion Univ. of the Negev, 84105, Beer Sheva, Israel.
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Stinner B, Bauhofer A, Lorenz W, Rothmund M, Plaul U, Torossian A, Celik I, Sitter H, Koller M, Black A, Duda D, Encke A, Greger B, van Goor H, Hanisch E, Hesterberg R, Klose KJ, Lacaine F, Lorijn RH, Margolis C, Neugebauer E, Nyström PO, Reemst PH, Schein M, Solovera J. Granulocyte-colony stimulating factor in the prevention of postoperative infectious complications and sub-optimal recovery from operation in patients with colorectal cancer and increased preoperative risk (ASA 3 and 4). Protocol of a controlled clinical trial developed by consensus of an international study group. Part three: individual patient, complication algorithm and quality manage. Inflamm Res 2001; 50:233-48. [PMID: 11409486 DOI: 10.1007/s000110050749] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
GENERAL DESIGN Presentation of a new type of a study protocol for evaluation of the effectiveness of an immune modifier (rhG-CSF, filgrastim): prevention of postoperative infectious complications and of sub-optimal recovery from operation in patients with colorectal cancer and increased preoperative risk (ASA 3 and 4). A randomised, placebo controlled, double-blinded, single-centre study is performed at an University Hospital (n = 40 patients for each group). This part presents the course of the individual patient and a complication algorithm for the management of anastomotic leakage and quality management. OBJECTIVE In part three of the protocol, the three major sections include: The course of the individual patient using a comprehensive graphic display, including the perioperative period, hospital stay and post discharge outcome. A center based clinical practice guideline for the management of the most important postoperative complication--anastomotic leakage--including evidence based support for each step of the algorithm. Data management, ethics and organisational structure. CONCLUSIONS Future studies with immune modifiers will also fail if not better structured (reduction of variance) to achieve uniform patient management in a complex clinical scenario. This new type of a single-centre trial aims to reduce the gap between animal experiments and clinical trials or--if it fails--at least demonstrates new ways for explaining the failures.
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Affiliation(s)
- B Stinner
- Department of General Surgery, Philipps-University Marburg, Germany
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Encke A, Hanisch E, Sitter H, Greger B, Bauhofer A, Margolis C, Lorenz W. [Evaluation models for therapy planning/standardization exemplified by infection]. Langenbecks Arch Chir Suppl Kongressbd 1997; 114:323-329. [PMID: 9574147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Models of evaluation in therapeutic management pathways (practice guidelines, clinical algorithms) are demanded today, both by public health research and health policy. However, practical achievements are lacking. To overcome this controversy, the Lucerne Study Group on Sepsis Research was founded to develop guidelines in accordance with a series of official groups. It was shown that there was no agreement between the providers and the daily users. However, every surgeon has a firm, personal view about sepsis.
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Affiliation(s)
- A Encke
- Klinik für Allgemeinchirurgie, J. W.-Goethe-Universität, Frankfurt/Main
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Margolis C, Barak N, Dagan R. [Clinical algorithms]. Harefuah 1989; 116:233-6. [PMID: 2659451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Abstract
The present study was designed to assess evaluations of physicians interacting with patients via the telephone. Observers used ten adjective scales which resulted in three variables: empathic, dominant, and calm. Thirty doctor-patient interactions were presented in two different communication modes: audio-only and typed transcript-only. As predicted, female listeners rated doctors as more empathic, dominant, and calm, and communication modes were significantly different with audio segments rated as more empathic, dominant and calm. Middle phases of the conversation also were evaluated more positively than greeting phases. Significant interactions between temporal phase and mode indicated that audio segments were interpreted more positively during middle phases. Also, female listeners were more sensitive to audio segments. Physicians' amplitude and speech rate were positively correlated with dominance.
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Affiliation(s)
- J A Harrigan
- University of Cincinnati, College of Medicine, OH 45267
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Armstrong DM, Viola HJ, Margolis C. Magnificent Voyagers. Evolution 1986. [DOI: 10.2307/2408771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Eldar R, Ronen D, Margolis C. Development of city health services by an academic department. World Hosp 1984; 20:40-1. [PMID: 10265638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Evans FJ, Finer B, Perry C, Evans BJ, Margolis C. Hypnosis in the treatment of chronic pain. Pain 1984. [DOI: 10.1016/0304-3959(84)90276-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Jacobus D, Grenan M, Wagner B, Margolis C, Jaffe I. Osteolathyrogenic effect of penicillamine. Am J Pathol 1969; 54:21-32. [PMID: 5772907 PMCID: PMC2013355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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