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Lu Y, Oliva M, Pierce BL, Liu J, Chen LS. Integrative cross-omics and cross-context analysis elucidates molecular links underlying genetic effects on complex traits. Nat Commun 2024; 15:2383. [PMID: 38493154 PMCID: PMC10944527 DOI: 10.1038/s41467-024-46675-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/06/2022] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Genetic effects on functionally related 'omic' traits often co-occur in relevant cellular contexts, such as tissues. Motivated by the multi-tissue methylation quantitative trait loci (mQTLs) and expression QTLs (eQTLs) analysis, we propose X-ING (Cross-INtegrative Genomics) for cross-omics and cross-context integrative analysis. X-ING takes as input multiple matrices of association statistics, each obtained from different omics data types across multiple cellular contexts. It models the latent binary association status of each statistic, captures the major association patterns among omics data types and contexts, and outputs the posterior mean and probability for each input statistic. X-ING enables the integration of effects from different omics data with varying effect distributions. In the multi-tissue cis-association analysis, X-ING shows improved detection and replication of mQTLs by integrating eQTL maps. In the trans-association analysis, X-ING reveals an enrichment of trans-associations in many disease/trait-relevant tissues.
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Affiliation(s)
- Yihao Lu
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Meritxell Oliva
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
- Genomics Research Center, AbbVie, North Chicago, IL, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Jin Liu
- School of Data Science, The Chinese University of Hong Kong-Shenzhen, Shenzhen, China.
| | - Lin S Chen
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA.
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2
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Lin CC, Chang TC, Wang Y, Guo L, Gao Y, Bikorimana E, Lemoff A, Fang YV, Zhang H, Zhang Y, Ye D, Soria-Bretones I, Servetto A, Lee KM, Luo X, Otto JJ, Akamatsu H, Napolitano F, Mani R, Cescon DW, Xu L, Xie Y, Mendell JT, Hanker AB, Arteaga CL. PRMT5 is an actionable therapeutic target in CDK4/6 inhibitor-resistant ER+/RB-deficient breast cancer. Nat Commun 2024; 15:2287. [PMID: 38480701 PMCID: PMC10937713 DOI: 10.1038/s41467-024-46495-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024] Open
Abstract
CDK4/6 inhibitors (CDK4/6i) have improved survival of patients with estrogen receptor-positive (ER+) breast cancer. However, patients treated with CDK4/6i eventually develop drug resistance and progress. RB1 loss-of-function alterations confer resistance to CDK4/6i, but the optimal therapy for these patients is unclear. Through a genome-wide CRISPR screen, we identify protein arginine methyltransferase 5 (PRMT5) as a molecular vulnerability in ER+/RB1-knockout breast cancer cells. Inhibition of PRMT5 blocks the G1-to-S transition in the cell cycle independent of RB, leading to growth arrest in RB1-knockout cells. Proteomics analysis uncovers fused in sarcoma (FUS) as a downstream effector of PRMT5. Inhibition of PRMT5 results in dissociation of FUS from RNA polymerase II, leading to hyperphosphorylation of serine 2 in RNA polymerase II, intron retention, and subsequent downregulation of proteins involved in DNA synthesis. Furthermore, treatment with the PRMT5 inhibitor pemrametostat and a selective ER degrader fulvestrant synergistically inhibits growth of ER+/RB-deficient cell-derived and patient-derived xenografts. These findings highlight dual ER and PRMT5 blockade as a potential therapeutic strategy to overcome resistance to CDK4/6i in ER+/RB-deficient breast cancer.
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Affiliation(s)
- Chang-Ching Lin
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tsung-Cheng Chang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yunguan Wang
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Lei Guo
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yunpeng Gao
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Emmanuel Bikorimana
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Andrew Lemoff
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yisheng V Fang
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - He Zhang
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yanfeng Zhang
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dan Ye
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | | | - Alberto Servetto
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Kyung-Min Lee
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Life Science, Hanyang University, Seoul, South Korea
| | - Xuemei Luo
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joseph J Otto
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Hiroaki Akamatsu
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Third Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Fabiana Napolitano
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Ram Mani
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - David W Cescon
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joshua T Mendell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ariella B Hanker
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Carlos L Arteaga
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.
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3
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Pascual T, Fernandez-Martinez A, Agrawal Y, Pfefferle AD, Chic N, Brasó-Maristany F, Gonzàlez-Farré B, Paré L, Villacampa G, Saura C, Hernando C, Muñoz M, Galván P, Gonzàlez-Farré X, Oliveira M, Gil-Gil M, Ciruelos E, Villagrasa P, Gavilá J, Prat A, Perou CM. Cell-cycle inhibition and immune microenvironment in breast cancer treated with ribociclib and letrozole or chemotherapy. NPJ Breast Cancer 2024; 10:20. [PMID: 38448600 PMCID: PMC10918094 DOI: 10.1038/s41523-024-00625-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/22/2024] [Indexed: 03/08/2024] Open
Abstract
In this study, we performed genomic analyses of cell cycle and tumor microenvironment changes during and after ribociclib and letrozole or chemotherapy in the CORALLEEN trial. 106 women with untreated PAM50-defined Luminal B early breast cancers were randomly assigned to receive neoadjuvant ribociclib and letrozole or standard-of-care chemotherapy. Ki67 immunohistochemistry, tumor-infiltrating lymphocytes quantification, and RNA sequencing were obtained from tissue biopsies pre-treatment, on day 14 of treatment, and tumor specimens from surgical resection. Results showed that at surgery, Ki67 and the PAM50 proliferation scores were lower after ribociclib compared to chemotherapy. However, consistent reactivation of tumor cell proliferation from day 14 to surgery was only observed in the ribociclib arm. In tumors with complete cell cycle arrest (CCCA) at surgery, PAM50 proliferation scores were lower in the ribociclib arm compared to chemotherapy (p < 0.001), whereas the opposite was observed with tumor cellularity (p = 0.002). Gene expression signatures (GES) associated with antigen-presenting cells (APCs) and innate immune system activity showed increased expression post-chemotherapy but decreased expression post-ribociclib. Interferon-associated GES had decreased expression with CCCA and increased expression with non-CCCA. Our findings suggest that while both treatment strategies decreased proliferation, the depth and the patterns over time differed by treatment arm. Immunologically, ribociclib was associated with downregulated GES associated with APCs and the innate immune system in Luminal B tumors, contrary to existing preclinical data. Further studies are needed to understand the effect of CDK4/6 inhibition on the tumor cells and microenvironment, an effect which may vary according to tumor subtypes.
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Affiliation(s)
- Tomás Pascual
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Hospital Clinic de Barcelona, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Aranzazu Fernandez-Martinez
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Yash Agrawal
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Adam D Pfefferle
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Nuria Chic
- Medical Oncology Department, Hospital Clinic de Barcelona, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Fara Brasó-Maristany
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Blanca Gonzàlez-Farré
- SOLTI Cancer Research Group, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Pathology Department, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Laia Paré
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Hospital Clinic de Barcelona, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | | | - Cristina Saura
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Breast Cancer Program, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Cristina Hernando
- Medical Oncology Department, Hospital Clínico Universitario de Valencia, Valencia, Spain
- Breast Cancer Biology Research Group, Biomedical Research Institute INCLIVA, Valencia, Spain
| | - Montserrat Muñoz
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Hospital Clinic de Barcelona, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Patricia Galván
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Xavier Gonzàlez-Farré
- SOLTI Cancer Research Group, Barcelona, Spain
- Breast Cancer Unit, Hospital Universitari General de Catalunya, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mafalda Oliveira
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Breast Cancer Program, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Miguel Gil-Gil
- IDIBELL, L'Hospitalet, Barcelona, Spain
- Department of Medical Oncology, Multidisciplinary Breast Cancer Unit, Institut Català d'Oncologia Medical Oncology, Barcelona, Spain
| | - Eva Ciruelos
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Hospital 12 de Octubre, Madrid, Spain
- Medical Oncology Department, HM Hospitales Madrid, Madrid, Spain
| | | | - Joaquín Gavilá
- SOLTI Cancer Research Group, Barcelona, Spain
- Fundación Instituto Valenciano de Oncología, Valencia, Spain
| | - Aleix Prat
- SOLTI Cancer Research Group, Barcelona, Spain.
- Medical Oncology Department, Hospital Clinic de Barcelona, Barcelona, Spain.
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.
- Department of Medicine, University of Barcelona, Barcelona, Spain.
- Breast Cancer Unit, IOB-Quirón Salud, Barcelona, Spain.
| | - Charles M Perou
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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4
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Begg LR, Orriols AM, Zannikou M, Yeh C, Vadlamani P, Kanojia D, Bolin R, Dunne SF, Balakrishnan S, Camarda R, Roth D, Zielinski-Mozny NA, Yau C, Vassilopoulos A, Huang TH, Kim KYA, Horiuchi D. S100A8/A9 predicts response to PIM kinase and PD-1/PD-L1 inhibition in triple-negative breast cancer mouse models. Commun Med (Lond) 2024; 4:22. [PMID: 38378783 PMCID: PMC10879183 DOI: 10.1038/s43856-024-00444-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Understanding why some triple-negative breast cancer (TNBC) patients respond poorly to existing therapies while others respond well remains a challenge. This study aims to understand the potential underlying mechanisms distinguishing early-stage TNBC tumors that respond to clinical intervention from non-responders, as well as to identify clinically viable therapeutic strategies, specifically for TNBC patients who may not benefit from existing therapies. METHODS We conducted retrospective bioinformatics analysis of historical gene expression datasets to identify a group of genes whose expression levels in early-stage tumors predict poor clinical outcomes in TNBC. In vitro small-molecule screening, genetic manipulation, and drug treatment in syngeneic mouse models of TNBC were utilized to investigate potential therapeutic strategies and elucidate mechanisms of drug action. RESULTS Our bioinformatics analysis reveals a robust association between increased expression of immunosuppressive cytokine S100A8/A9 in early-stage tumors and subsequent disease progression in TNBC. A targeted small-molecule screen identifies PIM kinase inhibitors as capable of decreasing S100A8/A9 expression in multiple cell types, including TNBC and immunosuppressive myeloid cells. Combining PIM inhibition and immune checkpoint blockade induces significant antitumor responses, especially in otherwise resistant S100A8/A9-high PD-1/PD-L1-positive tumors. Notably, serum S100A8/A9 levels mirror those of tumor S100A8/A9 in a syngeneic mouse model of TNBC. CONCLUSIONS Our data propose S100A8/A9 as a potential predictive and pharmacodynamic biomarker in clinical trials evaluating combination therapy targeting PIM and immune checkpoints in TNBC. This work encourages the development of S100A8/A9-based liquid biopsy tests for treatment guidance.
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Affiliation(s)
- Lauren R Begg
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Adrienne M Orriols
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- University of Florida College of Medicine, Gainesville, FL, USA
| | - Markella Zannikou
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chen Yeh
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Biostatistics Collaboration Center, Northwestern University, Chicago, IL, USA
- Rush University Medical Center, Chicago, IL, USA
| | | | - Deepak Kanojia
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Mythic Therapeutics, Waltham, MA, USA
| | - Rosemary Bolin
- Center for Comparative Medicine, Northwestern University, Chicago, IL, USA
- Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Sara F Dunne
- High Throughput Analysis Laboratory, Northwestern University, Evanston, IL, USA
| | - Sanjeev Balakrishnan
- University of California, San Francisco, San Francisco, CA, USA
- Pulze.ai, San Francisco, CA, USA
| | - Roman Camarda
- University of California, San Francisco, San Francisco, CA, USA
- Novo Ventures US, Inc., San Francisco, CA, USA
| | - Diane Roth
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nicolette A Zielinski-Mozny
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Comparative Medicine, Northwestern University, Chicago, IL, USA
| | - Christina Yau
- University of California, San Francisco, San Francisco, CA, USA
| | - Athanassios Vassilopoulos
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
- AbbVie, Inc., North Chicago, IL, USA
| | - Tzu-Hsuan Huang
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kwang-Youn A Kim
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Biostatistics Collaboration Center, Northwestern University, Chicago, IL, USA
| | - Dai Horiuchi
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
- Center for Human Immunobiology, Northwestern University, Chicago, IL, USA.
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5
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Zaikova E, Cheng BYC, Cerda V, Kong E, Lai D, Lum A, Bates C, den Brok W, Kono T, Bourque S, Chan A, Feng X, Fenton D, Gurjal A, Levasseur N, Lohrisch C, Roberts S, Shenkier T, Simmons C, Taylor S, Villa D, Miller R, Aguirre-Hernandez R, Aparicio S, Gelmon K. Circulating tumour mutation detection in triple-negative breast cancer as an adjunct to tissue response assessment. NPJ Breast Cancer 2024; 10:3. [PMID: 38182588 PMCID: PMC10770342 DOI: 10.1038/s41523-023-00607-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 12/02/2023] [Indexed: 01/07/2024] Open
Abstract
Circulating tumour DNA (ctDNA) detection via liquid biopsy is an emerging alternative to tissue biopsy, but its potential in treatment response monitoring and prognosis in triple negative breast cancer (TNBC) is not yet well understood. Here we determined the prevalence of actionable mutations detectable in ctDNA using a clinically validated cancer gene panel assay in patients with TNBC, without recurrence at the time of study entry. Sequencing of plasma DNA and validation of variants from 130 TNBC patients collected within 7 months of primary treatment completion revealed that 7.7% had detectable residual disease with a hotspot panel. Among neoadjuvant treated patients, we observed a trend where patients with incomplete pathologic response and positive ctDNA within 7 months of treatment completion were at much higher risk of reduced progression free survival. We propose that a high risk subset of early TNBC patients treated in neoadjuvant therapy protocols may be identifiable by combining tissue response and sensitive ctDNA detection.
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Affiliation(s)
- Elena Zaikova
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Brian Y C Cheng
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Viviana Cerda
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Esther Kong
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Daniel Lai
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Amy Lum
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Cherie Bates
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Wendie den Brok
- Medical Oncology, BC Cancer, 600 W10th Avenue, Vancouver, Canada
| | - Takako Kono
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada
| | - Sylvie Bourque
- Medical Oncology, BC Cancer, 13750 96 Ave, Surrey, Canada
| | - Angela Chan
- Medical Oncology, BC Cancer, 13750 96 Ave, Surrey, Canada
| | - Xioalan Feng
- Medical Oncology, BC Cancer, 2410 Lee Ave, Victoria, Canada
| | - David Fenton
- Medical Oncology, BC Cancer, 2410 Lee Ave, Victoria, Canada
| | - Anagha Gurjal
- Medical Oncology, BC Cancer, 32900 Marshall Rd, Abbotsford, Canada
| | | | | | - Sarah Roberts
- Medical Oncology, BC Cancer, 1215 Lethbridge St, Prince George, Canada
| | - Tamara Shenkier
- Medical Oncology, BC Cancer, 600 W10th Avenue, Vancouver, Canada
| | | | - Sara Taylor
- Medical Oncology, BC Cancer, 399 Royal Ave, Kelowna, Canada
| | - Diego Villa
- Medical Oncology, BC Cancer, 600 W10th Avenue, Vancouver, Canada
| | - Ruth Miller
- Imagia Canexia Health, 204-2389 Health Sciences Mall, Vancouver, Canada
| | | | - Samuel Aparicio
- Molecular Oncology, BC Cancer, 675 W10th Avenue, Vancouver, Canada.
| | - Karen Gelmon
- Medical Oncology, BC Cancer, 600 W10th Avenue, Vancouver, Canada.
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6
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Guerriero JL, Lin JR, Pastorello RG, Du Z, Chen YA, Townsend MG, Shimada K, Hughes ME, Ren S, Tayob N, Zheng K, Mei S, Patterson A, Taneja KL, Metzger O, Tolaney SM, Lin NU, Dillon DA, Schnitt SJ, Sorger PK, Mittendorf EA, Santagata S. Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer. NPJ Breast Cancer 2024; 10:2. [PMID: 38167908 PMCID: PMC10761880 DOI: 10.1038/s41523-023-00605-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 12/02/2023] [Indexed: 01/05/2024] Open
Abstract
Emerging data suggests that HER2 intratumoral heterogeneity (ITH) is associated with therapy resistance, highlighting the need for new strategies to assess HER2 ITH. A promising approach is leveraging multiplexed tissue analysis techniques such as cyclic immunofluorescence (CyCIF), which enable visualization and quantification of 10-60 antigens at single-cell resolution from individual tissue sections. In this study, we qualified a breast cancer-specific antibody panel, including HER2, ER, and PR, for multiplexed tissue imaging. We then compared the performance of these antibodies against established clinical standards using pixel-, cell- and tissue-level analyses, utilizing 866 tissue cores (representing 294 patients). To ensure reliability, the CyCIF antibodies were qualified against HER2 immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) data from the same samples. Our findings demonstrate the successful qualification of a breast cancer antibody panel for CyCIF, showing high concordance with established clinical antibodies. Subsequently, we employed the qualified antibodies, along with antibodies for CD45, CD68, PD-L1, p53, Ki67, pRB, and AR, to characterize 567 HER2+ invasive breast cancer samples from 189 patients. Through single-cell analysis, we identified four distinct cell clusters within HER2+ breast cancer exhibiting heterogeneous HER2 expression. Furthermore, these clusters displayed variations in ER, PR, p53, AR, and PD-L1 expression. To quantify the extent of heterogeneity, we calculated heterogeneity scores based on the diversity among these clusters. Our analysis revealed expression patterns that are relevant to breast cancer biology, with correlations to HER2 ITH and potential relevance to clinical outcomes.
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Affiliation(s)
- Jennifer L Guerriero
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, 02215, USA.
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA.
| | - Jia-Ren Lin
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, 02215, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
| | - Ricardo G Pastorello
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Pathology, Hospital Sírio Libanês, São Paulo, SP, 01308-050, Brazil
| | - Ziming Du
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yu-An Chen
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
| | - Madeline G Townsend
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kenichi Shimada
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, 02215, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
| | - Melissa E Hughes
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, 02215, USA
| | - Siyang Ren
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Nabihah Tayob
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kelly Zheng
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Shaolin Mei
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
| | - Alyssa Patterson
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, 02215, USA
| | - Krishan L Taneja
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Otto Metzger
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, 02215, USA
| | - Sara M Tolaney
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, 02215, USA
| | - Nancy U Lin
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, 02215, USA
| | - Deborah A Dillon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Stuart J Schnitt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Peter K Sorger
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, 02215, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
| | - Elizabeth A Mittendorf
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, 02215, USA
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, 02215, USA
| | - Sandro Santagata
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, 02215, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
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7
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Shi Y, Olsson LT, Hoadley KA, Calhoun BC, Marron JS, Geradts J, Niethammer M, Troester MA. Predicting early breast cancer recurrence from histopathological images in the Carolina Breast Cancer Study. NPJ Breast Cancer 2023; 9:92. [PMID: 37952058 PMCID: PMC10640636 DOI: 10.1038/s41523-023-00597-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Approaches for rapidly identifying patients at high risk of early breast cancer recurrence are needed. Image-based methods for prescreening hematoxylin and eosin (H&E) stained tumor slides could offer temporal and financial efficiency. We evaluated a data set of 704 1-mm tumor core H&E images (2-4 cores per case), corresponding to 202 participants (101 who recurred; 101 non-recurrent matched on age and follow-up time) from breast cancers diagnosed between 2008-2012 in the Carolina Breast Cancer Study. We leveraged deep learning to extract image information and trained a model to identify recurrence. Cross-validation accuracy for predicting recurrence was 62.4% [95% CI: 55.7, 69.1], similar to grade (65.8% [95% CI: 59.3, 72.3]) and ER status (66.3% [95% CI: 59.8, 72.8]). Interestingly, 70% (19/27) of early-recurrent low-intermediate grade tumors were identified by our image model. Relative to existing markers, image-based analyses provide complementary information for predicting early recurrence.
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Affiliation(s)
- Yifeng Shi
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Linnea T Olsson
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Benjamin C Calhoun
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J S Marron
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joseph Geradts
- Department of Pathology, East Carolina University, Greenville, NC, USA
| | - Marc Niethammer
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa A Troester
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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8
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Saatci O, Cetin M, Uner M, Tokat UM, Chatzistamou I, Ersan PG, Montaudon E, Akyol A, Aksoy S, Uner A, Marangoni E, Sajish M, Sahin O. Toxic PARP trapping upon cAMP-induced DNA damage reinstates the efficacy of endocrine therapy and CDK4/6 inhibitors in treatment-refractory ER+ breast cancer. Nat Commun 2023; 14:6997. [PMID: 37914699 PMCID: PMC10620179 DOI: 10.1038/s41467-023-42736-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 02/28/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023] Open
Abstract
Resistance to endocrine therapy and CDK4/6 inhibitors, the standard of care (SOC) in estrogen receptor-positive (ER+) breast cancer, greatly reduces patient survival. Therefore, elucidating the mechanisms of sensitivity and resistance to SOC therapy and identifying actionable targets are urgently needed. Here, we show that SOC therapy causes DNA damage and toxic PARP1 trapping upon generation of a functional BRCAness (i.e., BRCA1/2 deficiency) phenotype, leading to increased histone parylation and reduced H3K9 acetylation, resulting in transcriptional blockage and cell death. Mechanistically, SOC therapy downregulates phosphodiesterase 4D (PDE4D), a novel ER target gene in a feedforward loop with ER, resulting in increased cAMP, PKA-dependent phosphorylation of mitochondrial COXIV-I, ROS generation and DNA damage. However, during SOC resistance, an ER-to-EGFR switch induces PDE4D overexpression via c-Jun. Notably, combining SOC with inhibitors of PDE4D, EGFR or PARP1 overcomes SOC resistance irrespective of the BRCA1/2 status, providing actionable targets for restoring SOC efficacy.
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Affiliation(s)
- Ozge Saatci
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Metin Cetin
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Meral Uner
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, Turkey
| | - Unal Metin Tokat
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06800, Turkey
| | - Ioulia Chatzistamou
- Department of Pathology, Microbiology & Immunology, University of South Carolina, Columbia, SC, 29208, USA
| | - Pelin Gulizar Ersan
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Elodie Montaudon
- Translational Research Department, Institut Curie, PSL Research University, Paris, 75005, France
| | - Aytekin Akyol
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, Turkey
| | - Sercan Aksoy
- Department of Medical Oncology, Hacettepe University Cancer Institute, 06100, Ankara, Turkey
| | - Aysegul Uner
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, Turkey
| | - Elisabetta Marangoni
- Translational Research Department, Institut Curie, PSL Research University, Paris, 75005, France
| | - Mathew Sajish
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Ozgur Sahin
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA.
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA.
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9
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Puthanmadhom Narayanan S, Ren D, Oesterreich S, Lee AV, Rosenzweig MQ, Brufsky AM. Effects of socioeconomic status and race on survival and treatment in metastatic breast cancer. NPJ Breast Cancer 2023; 9:90. [PMID: 37914742 PMCID: PMC10620133 DOI: 10.1038/s41523-023-00595-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023] Open
Abstract
Race and socioeconomic factors affect outcomes in breast cancer. We aimed to assess the effect of race and neighborhood socioeconomic status (SES) on overall survival and treatment patterns in patients with metastatic breast cancer (MBC). This is a retrospective cohort study involving patients (N = 1246) with distant breast cancer metastases diagnosed at UPMC Magee Women's Breast Cancer Clinic from 2000-2017. Overall survival and treatment patterns were compared between races (Blacks and whites) and SES groups (defined using Area Deprivation Index). Low SES, but not tumor characteristics, was associated with Black race (P < 0.001) in the study population. Low SES (Median [Interquartile Range, IQR] survival 2.3[2.2-2.5] years vs high SES 2.7[2.5-3.1] years, P = 0.01) and Black race (Median [IQR] survival 1.8[1.3-2.3] years, vs white 2.5[2.3-2.7] years P = 0.008) separately were associated with worse overall survival in patients with MBC. In the Cox Proportional Hazard model with SES, race, age, subtype, number of metastases, visceral metastasis, and year of diagnosis as covariates, low SES (Hazard ratio 1.19[1.04-1.35], P = 0.01), but not Black race (Hazard ratio 1.19[0.96-1.49], P = 0.12), independently predicted overall survival in MBC. Moreover, patients from low SES neighborhoods and Black race received fewer lines of chemotherapy than high SES and whites. In conclusion, low neighborhood SES is associated with worse outcomes in patients with MBC. Poor outcomes in Black patients with MBC, at least in part is driven by socioeconomic factors. Future studies should delineate the interplay between neighborhood SES, race, and their effects on tumor biology in MBC.
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Affiliation(s)
| | - Dianxu Ren
- University of Pittsburgh, Pittsburgh, PA, USA
| | - Steffi Oesterreich
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Women's Cancer Research Center (WCRC), UPMC, Pittsburgh, PA, USA
- University of Pittsburgh, Pittsburgh, PA, USA
- Magee-Womens Research Institute, Pittsburgh, PA, USA
| | - Adrian V Lee
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Women's Cancer Research Center (WCRC), UPMC, Pittsburgh, PA, USA
- University of Pittsburgh, Pittsburgh, PA, USA
- Magee-Womens Research Institute, Pittsburgh, PA, USA
| | - Margaret Q Rosenzweig
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- University of Pittsburgh, Pittsburgh, PA, USA
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10
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Tripathi S, Shirnekhi HK, Gorman SD, Chandra B, Baggett DW, Park CG, Somjee R, Lang B, Hosseini SMH, Pioso BJ, Li Y, Iacobucci I, Gao Q, Edmonson MN, Rice SV, Zhou X, Bollinger J, Mitrea DM, White MR, McGrail DJ, Jarosz DF, Yi SS, Babu MM, Mullighan CG, Zhang J, Sahni N, Kriwacki RW. Defining the condensate landscape of fusion oncoproteins. Nat Commun 2023; 14:6008. [PMID: 37770423 PMCID: PMC10539325 DOI: 10.1038/s41467-023-41655-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/10/2022] [Accepted: 09/13/2023] [Indexed: 09/30/2023] Open
Abstract
Fusion oncoproteins (FOs) arise from chromosomal translocations in ~17% of cancers and are often oncogenic drivers. Although some FOs can promote oncogenesis by undergoing liquid-liquid phase separation (LLPS) to form aberrant biomolecular condensates, the generality of this phenomenon is unknown. We explored this question by testing 166 FOs in HeLa cells and found that 58% formed condensates. The condensate-forming FOs displayed physicochemical features distinct from those of condensate-negative FOs and segregated into distinct feature-based groups that aligned with their sub-cellular localization and biological function. Using Machine Learning, we developed a predictor of FO condensation behavior, and discovered that 67% of ~3000 additional FOs likely form condensates, with 35% of those predicted to function by altering gene expression. 47% of the predicted condensate-negative FOs were associated with cell signaling functions, suggesting a functional dichotomy between condensate-positive and -negative FOs. Our Datasets and reagents are rich resources to interrogate FO condensation in the future.
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Affiliation(s)
- Swarnendu Tripathi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hazheen K Shirnekhi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott D Gorman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Arrakis Therapeutics, 830 Winter St, Waltham, MA, 02451, USA
| | - Bappaditya Chandra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David W Baggett
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ramiz Somjee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Rhodes College, Memphis, TN, USA
- Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Benjamin Lang
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Seyed Mohammad Hadi Hosseini
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brittany J Pioso
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yongsheng Li
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qingsong Gao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael N Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen V Rice
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John Bollinger
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Dewpoint Therapeutics, 451 D Street, Suite 104, Boston, MA, 02210, USA
| | - Michael R White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- IDEXX Laboratories, Inc., One IDEXX Drive, Westbrook, ME, 04092, USA
| | - Daniel J McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Biomedical Engineering, and Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA
| | - M Madan Babu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, USA.
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11
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Chitty JL, Yam M, Perryman L, Parker AL, Skhinas JN, Setargew YFI, Mok ETY, Tran E, Grant RD, Latham SL, Pereira BA, Ritchie SC, Murphy KJ, Trpceski M, Findlay AD, Melenec P, Filipe EC, Nadalini A, Velayuthar S, Major G, Wyllie K, Papanicolaou M, Ratnaseelan S, Phillips PA, Sharbeen G, Youkhana J, Russo A, Blackwell A, Hastings JF, Lucas MC, Chambers CR, Reed DA, Stoehr J, Vennin C, Pidsley R, Zaratzian A, Da Silva AM, Tayao M, Charlton B, Herrmann D, Nobis M, Clark SJ, Biankin AV, Johns AL, Croucher DR, Nagrial A, Gill AJ, Grimmond SM, Pajic M, Timpson P, Jarolimek W, Cox TR. A first-in-class pan-lysyl oxidase inhibitor impairs stromal remodeling and enhances gemcitabine response and survival in pancreatic cancer. Nat Cancer 2023; 4:1326-1344. [PMID: 37640930 PMCID: PMC10518255 DOI: 10.1038/s43018-023-00614-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 07/07/2023] [Indexed: 08/31/2023]
Abstract
The lysyl oxidase family represents a promising target in stromal targeting of solid tumors due to the importance of this family in crosslinking and stabilizing fibrillar collagens and its known role in tumor desmoplasia. Using small-molecule drug-design approaches, we generated and validated PXS-5505, a first-in-class highly selective and potent pan-lysyl oxidase inhibitor. We demonstrate in vitro and in vivo that pan-lysyl oxidase inhibition decreases chemotherapy-induced pancreatic tumor desmoplasia and stiffness, reduces cancer cell invasion and metastasis, improves tumor perfusion and enhances the efficacy of chemotherapy in the autochthonous genetically engineered KPC model, while also demonstrating antifibrotic effects in human patient-derived xenograft models of pancreatic cancer. PXS-5505 is orally bioavailable, safe and effective at inhibiting lysyl oxidase activity in tissues. Our findings present the rationale for progression of a pan-lysyl oxidase inhibitor aimed at eliciting a reduction in stromal matrix to potentiate chemotherapy in pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Jessica L Chitty
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Michelle Yam
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Lara Perryman
- Pharmaxis, Frenchs Forest, New South Wales, Australia
| | - Amelia L Parker
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Joanna N Skhinas
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Yordanos F I Setargew
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Ellie T Y Mok
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Emmi Tran
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Rhiannon D Grant
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Sharissa L Latham
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Brooke A Pereira
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Shona C Ritchie
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Kendelle J Murphy
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Michael Trpceski
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | | | - Pauline Melenec
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Elysse C Filipe
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Audrey Nadalini
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Sipiththa Velayuthar
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Gretel Major
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Kaitlin Wyllie
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Michael Papanicolaou
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Shivanjali Ratnaseelan
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Phoebe A Phillips
- School of Biomedical Sciences, Faculty of Medicine, Lowy Cancer Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - George Sharbeen
- School of Biomedical Sciences, Faculty of Medicine, Lowy Cancer Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Janet Youkhana
- School of Biomedical Sciences, Faculty of Medicine, Lowy Cancer Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Alice Russo
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Antonia Blackwell
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Jordan F Hastings
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Morghan C Lucas
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Cecilia R Chambers
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Daniel A Reed
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Janett Stoehr
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Claire Vennin
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Ruth Pidsley
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Anaiis Zaratzian
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Andrew M Da Silva
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Michael Tayao
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | | | - David Herrmann
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Max Nobis
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- Intravital Imaging Expertise Center, VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Susan J Clark
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - Amber L Johns
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - David R Croucher
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Adnan Nagrial
- Department of Medical Oncology, Westmead Hospital, Sydney, New South Wales, Australia
| | - Anthony J Gill
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, New South Wales, Australia
- Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, Sydney, New South Wales, Australia
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, VCCC, Melbourne, Victoria, Australia
| | - Marina Pajic
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Paul Timpson
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | | | - Thomas R Cox
- Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia.
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia.
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12
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Kim HJ, Rames MJ, Goncalves F, Kirschbaum CW, Roskams-Hieter B, Spiliotopoulos E, Briand J, Doe A, Estabrook J, Wagner JT, Demir E, Mills G, Ngo TTM. Selective enrichment of plasma cell-free messenger RNA in cancer-associated extracellular vesicles. Commun Biol 2023; 6:885. [PMID: 37644220 PMCID: PMC10465482 DOI: 10.1038/s42003-023-05232-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/05/2022] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Extracellular vesicles (EVs) have been shown as key mediators of extracellular small RNA transport. However, carriers of cell-free messenger RNA (cf-mRNA) in human biofluids and their association with cancer remain poorly understood. Here, we performed a transcriptomic analysis of size-fractionated plasma from lung cancer, liver cancer, multiple myeloma, and healthy donors. Morphology and size distribution analysis showed the successful separation of large and medium particles from other soluble plasma protein fractions. We developed a strategy to purify and sequence ultra-low amounts of cf-mRNA from particle and protein enriched subpopulations with the implementation of RNA spike-ins to control for technical variability and to normalize for intrinsic drastic differences in cf-mRNA amount carried in each plasma fraction. We found that the majority of cf-mRNA was enriched and protected in EVs with remarkable stability in RNase-rich environments. We observed specific enrichment patterns of cancer-associated cf-mRNA in each particle and protein enriched subpopulation. The EV-enriched differentiating genes were associated with specific biological pathways, such as immune systems, liver function, and toxic substance regulation in lung cancer, liver cancer, and multiple myeloma, respectively. Our results suggest that dissecting the complexity of EV subpopulations illuminates their biological significance and offers a promising liquid biopsy approach.
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Affiliation(s)
- Hyun Ji Kim
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Matthew J Rames
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Florian Goncalves
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - C Ward Kirschbaum
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Breeshey Roskams-Hieter
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Elias Spiliotopoulos
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Josephine Briand
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Aaron Doe
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Joseph Estabrook
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA
| | - Josiah T Wagner
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Molecular Genomics Laboratory, Providence Health and Services, Portland, OR, USA
| | - Emek Demir
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Gordon Mills
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Thuy T M Ngo
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.
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13
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Li X, Poire A, Jeong KJ, Zhang D, Chen G, Sun C, Mills GB. Single-cell trajectory analysis reveals a CD9 positive state to contribute to exit from stem cell-like and embryonic diapause states and transit to drug-resistant states. Cell Death Discov 2023; 9:285. [PMID: 37542044 PMCID: PMC10403509 DOI: 10.1038/s41420-023-01586-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023] Open
Abstract
Bromo- and extra-terminal domain (BET) inhibitors (BETi) have been shown to decrease tumor growth in preclinical models and clinical trials. However, toxicity and rapid emergence of resistance have limited their clinical implementation. To identify state changes underlying acquisition of resistance to the JQ1 BETi, we reanalyzed single-cell RNAseq data from JQ1 sensitive and resistant SUM149 and SUM159 triple-negative breast cancer cell lines. Parental and JQ1-resistant SUM149 and SUM159 exhibited a stem cell-like and embryonic diapause (SCLED) cell state as well as a transitional cell state between the SCLED state that is present in both treatment naïve and JQ1 treated cells, and a number of JQ1 resistant cell states. A transitional cell state transcriptional signature but not a SCLED state transcriptional signature predicted worsened outcomes in basal-like breast cancer patients suggesting that transit from the SCLED state to drug-resistant states contributes to patient outcomes. Entry of SUM149 and SUM159 into the transitional cell state was characterized by elevated expression of the CD9 tetraspanin. Knockdown or inhibition of CD9-sensitized cells to multiple targeted and cytotoxic drugs in vitro. Importantly, CD9 knockdown or blockade sensitized SUM149 to JQ1 in vivo by trapping cells in the SCLED state and limiting transit to resistant cell states. Thus, CD9 appears to be critical for the transition from a SCLED state into treatment-resistant cell states and warrants exploration as a therapeutic target in basal-like breast cancer.
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Affiliation(s)
- Xi Li
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA.
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China.
| | - Alfonso Poire
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Kang Jin Jeong
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Dong Zhang
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Gordon B Mills
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
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14
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Fanucci KA, Bai Y, Pelekanou V, Nahleh ZA, Shafi S, Burela S, Barlow WE, Sharma P, Thompson AM, Godwin AK, Rimm DL, Hortobagyi GN, Liu Y, Wang L, Wei W, Pusztai L, Blenman KRM. Image analysis-based tumor infiltrating lymphocytes measurement predicts breast cancer pathologic complete response in SWOG S0800 neoadjuvant chemotherapy trial. NPJ Breast Cancer 2023; 9:38. [PMID: 37179362 PMCID: PMC10182981 DOI: 10.1038/s41523-023-00535-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
We assessed the predictive value of an image analysis-based tumor-infiltrating lymphocytes (TILs) score for pathologic complete response (pCR) and event-free survival in breast cancer (BC). About 113 pretreatment samples were analyzed from patients with stage IIB-IIIC HER-2-negative BC randomized to neoadjuvant chemotherapy ± bevacizumab. TILs quantification was performed on full sections using QuPath open-source software with a convolutional neural network cell classifier (CNN11). We used easTILs% as a digital metric of TILs score defined as [sum of lymphocytes area (mm2)/stromal area(mm2)] × 100. Pathologist-read stromal TILs score (sTILs%) was determined following published guidelines. Mean pretreatment easTILs% was significantly higher in cases with pCR compared to residual disease (median 36.1 vs.14.8%, p < 0.001). We observed a strong positive correlation (r = 0.606, p < 0.0001) between easTILs% and sTILs%. The area under the prediction curve (AUC) was higher for easTILs% than sTILs%, 0.709 and 0.627, respectively. Image analysis-based TILs quantification is predictive of pCR in BC and had better response discrimination than pathologist-read sTILs%.
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Affiliation(s)
- Kristina A Fanucci
- Department of Internal Medicine Section of Medical Oncology and Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06520, USA
| | - Yalai Bai
- Department of Pathology, Yale School of Medicine, 310 Cedar St, New Haven, CT, 06520, USA
| | - Vasiliki Pelekanou
- Department of Pathology, Yale School of Medicine, 310 Cedar St, New Haven, CT, 06520, USA
- Bayer Pharmaceuticals, 245 First St Cambridge Science Center 100 and 200 Floors 1 and 2, Cambridge, MA, 02142, USA
| | - Zeina A Nahleh
- Department of Hematology/Oncology, Cleveland Clinic Florida, Maroone Cancer Center, 2950 Cleveland Clinic Blvd, Weston, FL, 33331, USA
| | - Saba Shafi
- Department of Pathology, Yale School of Medicine, 310 Cedar St, New Haven, CT, 06520, USA
- Department of Pathology, Ohio State University, 6100 Optometry Clinic & Health Sciences Faculty Office Building, 1664 Neil Avenue, Columbus, OH, 43210, USA
| | - Sneha Burela
- Department of Pathology, Yale School of Medicine, 310 Cedar St, New Haven, CT, 06520, USA
| | - William E Barlow
- SWOG Statistics and Data Management Center, 1730 Minor Avenue Suite 1900, Seattle, WA, 98101, USA
| | - Priyanka Sharma
- Department of Medical Oncology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - Alastair M Thompson
- Section of Breast Surgery, 1 Baylor Plaza, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Andrew K Godwin
- Department of Medical Oncology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, 310 Cedar St, New Haven, CT, 06520, USA
| | - Gabriel N Hortobagyi
- Department of Breast Medical Oncology, MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Yihan Liu
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Leona Wang
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Wei Wei
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Lajos Pusztai
- Department of Internal Medicine Section of Medical Oncology and Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06520, USA
| | - Kim R M Blenman
- Department of Internal Medicine Section of Medical Oncology and Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06520, USA.
- Department of Computer Science, Yale School of Engineering and Applied Science, 17 Hillhouse Avenue, New Haven, CT, 06520, USA.
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15
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Freeman JQ, Shubeck S, Howard FM, Chen N, Nanda R, Huo D. Evaluation of multigene assays as predictors for response to neoadjuvant chemotherapy in early-stage breast cancer patients. NPJ Breast Cancer 2023; 9:33. [PMID: 37149628 PMCID: PMC10164191 DOI: 10.1038/s41523-023-00536-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/20/2023] [Indexed: 05/08/2023] Open
Abstract
OncotypeDX and MammaPrint assays have not been validated to predict pathologic complete response (pCR) to neoadjuvant chemotherapy (NACT) in early-stage breast cancer patients. We analyzed the 2010-2019 National Cancer Database and found that high OncotypeDX recurrence scores or high MammaPrint scores were associated with greater odds of pCR. Our findings suggest that OncotypeDX and MammaPrint testing predict pCR after NACT and could facilitate clinical decision-making between clinicians and patients.
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Affiliation(s)
- Jincong Q Freeman
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Sarah Shubeck
- Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Frederick M Howard
- Department of Medicine, Section of Hematology & Oncology, University of Chicago, Chicago, IL, USA
| | - Nan Chen
- Department of Medicine, Section of Hematology & Oncology, University of Chicago, Chicago, IL, USA
| | - Rita Nanda
- Department of Medicine, Section of Hematology & Oncology, University of Chicago, Chicago, IL, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
- Department of Medicine, Section of Hematology & Oncology, University of Chicago, Chicago, IL, USA.
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16
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Sella T, Zheng Y, Rosenberg SM, Ruddy KJ, Gelber SI, Tamimi RM, Peppercorn JM, Schapira L, Borges VF, Come SE, Carey LA, Winer EP, Partridge AH. Extended adjuvant endocrine therapy in a longitudinal cohort of young breast cancer survivors. NPJ Breast Cancer 2023; 9:31. [PMID: 37185922 PMCID: PMC10130172 DOI: 10.1038/s41523-023-00529-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 03/30/2023] [Indexed: 05/17/2023] Open
Abstract
Extended adjuvant endocrine therapy (eET) improves outcomes in breast cancer survivors. Most studies however have been limited to postmenopausal women, and optimal eET for young survivors is uncertain. We report eET use among participants in the Young Women's Breast Cancer Study (YWS), a multicenter prospective cohort of women age ≤40 newly diagnosed with breast cancer enrolled between 2006-2016. Women with stage I-III hormone receptor-positive breast cancer, ≥6 years from diagnosis without recurrence were considered eET candidates. Use of eET was elicited from annual surveys sent years 6-8 after diagnosis, censoring for recurrence/death. 663 women were identified as eET candidates with 73.9% (490/663) having surveys eligible for analysis. Among eligible participants, mean age was 35.5 (±3.9), 85.9% were non-Hispanic white, and 59.6% reported eET use. Tamoxifen monotherapy was the most reported eET (77.4%), followed by aromatase inhibitor (AI) monotherapy (21.9%), AI-ovarian function suppression (AI-OFS) (6.8%) and tamoxifen-OFS (3.1%). In multivariable analysis, increasing age (per year odds ratio [OR]: 1.10, 95% confidence interval [CI]: 1.04-1.16), stage (II v. I: OR: 2.86, 95% CI: 1.81-4.51; III v. I: OR: 3.73, 95%CI: 1.87-7.44) and receipt of chemotherapy (OR: 3.66, 95% CI: 2.16-6.21) were significantly associated with eET use. Many young breast cancer survivors receive eET despite limited data regarding utility in this population. While some factors associated with eET use reflect appropriate risk-based care, potential sociodemographic disparities in uptake warrants further investigation in more diverse populations.
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Affiliation(s)
- Tal Sella
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Sheba Medical Center, Tel HaShomer, Israel
| | - Yue Zheng
- Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shoshana M Rosenberg
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | | | - Shari I Gelber
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rulla M Tamimi
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Jeffrey M Peppercorn
- Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Steven E Come
- Harvard Medical School, Boston, MA, USA
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Lisa A Carey
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
| | - Eric P Winer
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Yale Cancer Center, New Haven, CT, USA
| | - Ann H Partridge
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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17
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Carter JM, Chumsri S, Hinerfeld DA, Ma Y, Wang X, Zahrieh D, Hillman DW, Tenner KS, Kachergus JM, Brauer HA, Warren SE, Henderson D, Shi J, Liu Y, Joensuu H, Lindman H, Leon-Ferre RA, Boughey JC, Liu MC, Ingle JN, Kalari KR, Couch FJ, Knutson KL, Goetz MP, Perez EA, Thompson EA. Distinct spatial immune microlandscapes are independently associated with outcomes in triple-negative breast cancer. Nat Commun 2023; 14:2215. [PMID: 37072398 PMCID: PMC10113250 DOI: 10.1038/s41467-023-37806-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 05/27/2021] [Accepted: 03/30/2023] [Indexed: 04/20/2023] Open
Abstract
The utility of spatial immunobiomarker quantitation in prognostication and therapeutic prediction is actively being investigated in triple-negative breast cancer (TNBC). Here, with high-plex quantitative digital spatial profiling, we map and quantitate intraepithelial and adjacent stromal tumor immune protein microenvironments in systemic treatment-naïve (female only) TNBC to assess the spatial context in immunobiomarker-based prediction of outcome. Immune protein profiles of CD45-rich and CD68-rich stromal microenvironments differ significantly. While they typically mirror adjacent, intraepithelial microenvironments, this is not uniformly true. In two TNBC cohorts, intraepithelial CD40 or HLA-DR enrichment associates with better outcomes, independently of stromal immune protein profiles or stromal TILs and other established prognostic variables. In contrast, intraepithelial or stromal microenvironment enrichment with IDO1 associates with improved survival irrespective of its spatial location. Antigen-presenting and T-cell activation states are inferred from eigenprotein scores. Such scores within the intraepithelial compartment interact with PD-L1 and IDO1 in ways that suggest prognostic and/or therapeutic potential. This characterization of the intrinsic spatial immunobiology of treatment-naïve TNBC highlights the importance of spatial microenvironments for biomarker quantitation to resolve intrinsic prognostic and predictive immune features and ultimately inform therapeutic strategies for clinically actionable immune biomarkers.
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Affiliation(s)
- Jodi M Carter
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Saranya Chumsri
- Department of Medicine, Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Yaohua Ma
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL, USA
| | - Xue Wang
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL, USA
| | - David Zahrieh
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - David W Hillman
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Kathleen S Tenner
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | - Ji Shi
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Yi Liu
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Heikki Joensuu
- Department of Oncology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Henrik Lindman
- Department of Oncology, University of Uppsala, Uppsala, Sweden
| | - Roberto A Leon-Ferre
- Department of Oncology, Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | | | | | - James N Ingle
- Department of Oncology, Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Krishna R Kalari
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Keith L Knutson
- Department of Immunology, Mayo Clinic, Jacksonville, FL, USA
| | - Matthew P Goetz
- Department of Oncology, Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Edith A Perez
- Department of Medicine, Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, USA
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18
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Howard FM, Dolezal J, Kochanny S, Khramtsova G, Vickery J, Srisuwananukorn A, Woodard A, Chen N, Nanda R, Perou CM, Olopade OI, Huo D, Pearson AT. Integration of clinical features and deep learning on pathology for the prediction of breast cancer recurrence assays and risk of recurrence. NPJ Breast Cancer 2023; 9:25. [PMID: 37059742 PMCID: PMC10104799 DOI: 10.1038/s41523-023-00530-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 03/30/2023] [Indexed: 04/16/2023] Open
Abstract
Gene expression-based recurrence assays are strongly recommended to guide the use of chemotherapy in hormone receptor-positive, HER2-negative breast cancer, but such testing is expensive, can contribute to delays in care, and may not be available in low-resource settings. Here, we describe the training and independent validation of a deep learning model that predicts recurrence assay result and risk of recurrence using both digital histology and clinical risk factors. We demonstrate that this approach outperforms an established clinical nomogram (area under the receiver operating characteristic curve of 0.83 versus 0.76 in an external validation cohort, p = 0.0005) and can identify a subset of patients with excellent prognoses who may not need further genomic testing.
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Affiliation(s)
| | - James Dolezal
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sara Kochanny
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Jasmine Vickery
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | | | - Anna Woodard
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Department of Computer Science, University of Chicago, Chicago, IL, USA
| | - Nan Chen
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Rita Nanda
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles M Perou
- Department of Genetics, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
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19
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Amici DR, Cingoz H, Alasady MJ, Alhayek S, Phoumyvong CM, Sahni N, Yi SS, Mendillo ML. The HAPSTR2 retrogene buffers stress signaling and resilience in mammals. Nat Commun 2023; 14:152. [PMID: 36631436 PMCID: PMC9834230 DOI: 10.1038/s41467-022-35697-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
We recently identified HAPSTR1 (C16orf72) as a key component in a novel pathway which regulates the cellular response to molecular stressors, such as DNA damage, nutrient scarcity, and protein misfolding. Here, we identify a functional paralog to HAPSTR1: HAPSTR2. HAPSTR2 formed early in mammalian evolution, via genomic integration of a reverse transcribed HAPSTR1 transcript, and has since been preserved under purifying selection. HAPSTR2, expressed primarily in neural and germline tissues and a subset of cancers, retains established biochemical features of HAPSTR1 to achieve two functions. In normal physiology, HAPSTR2 directly interacts with HAPSTR1, markedly augmenting HAPSTR1 protein stability in a manner independent from HAPSTR1's canonical E3 ligase, HUWE1. Alternatively, in the context of HAPSTR1 loss, HAPSTR2 expression is sufficient to buffer stress signaling and resilience. Thus, we discover a mammalian retrogene which safeguards fitness.
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Affiliation(s)
- David R Amici
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Harun Cingoz
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Milad J Alasady
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Sammy Alhayek
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Claire M Phoumyvong
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, and Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, and Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
- Interdisciplinary Life Sciences Graduate Programs (ILSGP), and Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, 78712, USA
| | - Marc L Mendillo
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA.
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20
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Mandelker D, Marra A, Mehta N, Selenica P, Yelskaya Z, Yang C, Somar J, Mehine M, Misyura M, Basturk O, Latham A, Carlo M, Walsh M, Stadler ZK, Offit K, Bandlamudi C, Hameed M, Chi P, Reis-Filho JS, Ceyhan-Birsoy O. Expanded genetic testing of GIST patients identifies high proportion of non-syndromic patients with germline alterations. NPJ Precis Oncol 2023; 7:1. [PMID: 36593350 PMCID: PMC9807588 DOI: 10.1038/s41698-022-00342-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/14/2022] [Indexed: 01/03/2023] Open
Abstract
Traditional genetic testing for patients with gastrointestinal stromal tumors (GISTs) focus on those with syndromic features. To assess whether expanded genetic testing of GIST patients could identify hereditary cancer predisposition, we analyzed matched tumor-germline sequencing results from 103 patients with GISTs over a 6-year period. Germline pathogenic/likely pathogenic (P/LP) variants in GIST-associated genes (SDHA, SDHB, SDHC, NF1, KIT) were identified in 69% of patients with KIT/PDGFRA-wildtype GISTs, 63% of whom did not have any personal or family history of syndromic features. To evaluate the frequency of somatic versus germline variants identified in tumor-only sequencing of GISTs, we analyzed 499 de-identified tumor-normal pairs. P/LP variants in certain genes (e.g., BRCA1/2, SDHB) identified in tumor-only sequencing of GISTs were almost exclusively germline in origin. Our results provide guidance for genetic testing of GIST patients and indicate that germline testing should be offered to all patients with KIT/PDGFRA-wildtype GISTs regardless of their history of syndromic features.
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Affiliation(s)
- Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikita Mehta
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zarina Yelskaya
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ciyu Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joshua Somar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Miika Mehine
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maksym Misyura
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olca Basturk
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alicia Latham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaitanya Bandlamudi
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meera Hameed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ping Chi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Ozge Ceyhan-Birsoy
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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21
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Doebley AL, Ko M, Liao H, Cruikshank AE, Santos K, Kikawa C, Hiatt JB, Patton RD, De Sarkar N, Collier KA, Hoge ACH, Chen K, Zimmer A, Weber ZT, Adil M, Reichel JB, Polak P, Adalsteinsson VA, Nelson PS, MacPherson D, Parsons HA, Stover DG, Ha G. A framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA. Nat Commun 2022; 13:7475. [PMID: 36463275 PMCID: PMC9719521 DOI: 10.1038/s41467-022-35076-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Cell-free DNA (cfDNA) has the potential to inform tumor subtype classification and help guide clinical precision oncology. Here we develop Griffin, a framework for profiling nucleosome protection and accessibility from cfDNA to study the phenotype of tumors using as low as 0.1x coverage whole genome sequencing data. Griffin employs a GC correction procedure tailored to variable cfDNA fragment sizes, which generates a better representation of chromatin accessibility and improves the accuracy of cancer detection and tumor subtype classification. We demonstrate estrogen receptor subtyping from cfDNA in metastatic breast cancer. We predict estrogen receptor subtype in 139 patients with at least 5% detectable circulating tumor DNA with an area under the receive operator characteristic curve (AUC) of 0.89 and validate performance in independent cohorts (AUC = 0.96). In summary, Griffin is a framework for accurate tumor subtyping and can be generalizable to other cancer types for precision oncology applications.
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Affiliation(s)
- Anna-Lisa Doebley
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Minjeong Ko
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hanna Liao
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - A Eden Cruikshank
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | | | - Caroline Kikawa
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Joseph B Hiatt
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Robert D Patton
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Navonil De Sarkar
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Anna C H Hoge
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Katharine Chen
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | - Anat Zimmer
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Zachary T Weber
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Mohamed Adil
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jonathan B Reichel
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Paz Polak
- Department of Oncological Sciences, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | | | - Peter S Nelson
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - David MacPherson
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Daniel G Stover
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Gavin Ha
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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22
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Tatarova Z, Blumberg DC, Korkola JE, Heiser LM, Muschler JL, Schedin PJ, Ahn SW, Mills GB, Coussens LM, Jonas O, Gray JW. A multiplex implantable microdevice assay identifies synergistic combinations of cancer immunotherapies and conventional drugs. Nat Biotechnol 2022; 40:1823-1833. [PMID: 35788566 PMCID: PMC9750874 DOI: 10.1038/s41587-022-01379-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/31/2022] [Indexed: 01/14/2023]
Abstract
Systematically identifying synergistic combinations of targeted agents and immunotherapies for cancer treatments remains difficult. In this study, we integrated high-throughput and high-content techniques-an implantable microdevice to administer multiple drugs into different sites in tumors at nanodoses and multiplexed imaging of tumor microenvironmental states-to investigate the tumor cell and immunological response signatures to different treatment regimens. Using a mouse model of breast cancer, we identified effective combinations from among numerous agents within days. In vivo studies in three immunocompetent mammary carcinoma models demonstrated that the predicted combinations synergistically increased therapeutic efficacy. We identified at least five promising treatment strategies, of which the panobinostat, venetoclax and anti-CD40 triple therapy was the most effective in inducing complete tumor remission across models. Successful drug combinations increased spatial association of cancer stem cells with dendritic cells during immunogenic cell death, suggesting this as an important mechanism of action in long-term breast cancer control.
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Affiliation(s)
- Zuzana Tatarova
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Radiology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dylan C Blumberg
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, Portland, OR, USA
| | - James E Korkola
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Laura M Heiser
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - John L Muschler
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Pepper J Schedin
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Sebastian W Ahn
- Department of Radiology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gordon B Mills
- Division of Oncologic Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Lisa M Coussens
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Oliver Jonas
- Department of Radiology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Joe W Gray
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, Portland, OR, USA.
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
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23
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Qing T, Karn T, Rozenblit M, Foldi J, Marczyk M, Shan NL, Blenman K, Holtrich U, Kalinsky K, Meric-Bernstam F, Pusztai L. Molecular differences between younger versus older ER-positive and HER2-negative breast cancers. NPJ Breast Cancer 2022; 8:119. [PMID: 36344517 PMCID: PMC9640562 DOI: 10.1038/s41523-022-00492-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022] Open
Abstract
The RxPONDER and TAILORx trials demonstrated benefit from adjuvant chemotherapy in patients age ≤ 50 with node-positive breast cancer and Recurrence Score (RS) 0-26, and in node-negative disease with RS 16-25, respectively, but no benefit in older women with the same clinical features. We analyzed transcriptomic and genomic data of ER+/HER2- breast cancers with in silico RS < 26 from TCGA (n = 530), two microarray cohorts (A: n = 865; B: n = 609), the METABRIC (n = 867), and the SCAN-B (n = 1636) datasets. There was no difference in proliferation-related gene expression between age groups. Older patients had higher mutation burden and more frequent ESR1 copy number gain, but lower frequency of GATA3 mutations. Younger patients had higher rate of ESR1 copy number loss. In all datasets, younger patients had significantly lower mRNA expression of ESR1 and ER-associated genes, and higher expression of immune-related genes. The ER- and immune-related gene signatures showed negative correlation and defined three subpopulations in younger women: immune-high/ER-low, immune-intermediate/ER-intermediate, and immune-low/ER-intermediate. We hypothesize that in immune-high cancers, the cytotoxic effect of chemotherapy may drive the benefit, whereas in immune-low/ER-intermediate cancers chemotherapy induced ovarian suppression may play important role.
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Affiliation(s)
- Tao Qing
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Thomas Karn
- Department of Gynecology and Obstetrics, Goethe-University Frankfurt, Frankfurt, Germany
| | - Mariya Rozenblit
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Julia Foldi
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Michal Marczyk
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Naing Lin Shan
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Kim Blenman
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Uwe Holtrich
- Department of Gynecology and Obstetrics, Goethe-University Frankfurt, Frankfurt, Germany
| | - Kevin Kalinsky
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lajos Pusztai
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA.
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24
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Gruber JJ, Afghahi A, Timms K, DeWees A, Gross W, Aushev VN, Wu HT, Balcioglu M, Sethi H, Scott D, Foran J, McMillan A, Ford JM, Telli ML. A phase II study of talazoparib monotherapy in patients with wild-type BRCA1 and BRCA2 with a mutation in other homologous recombination genes. Nat Cancer 2022; 3:1181-1191. [PMID: 36253484 PMCID: PMC9586861 DOI: 10.1038/s43018-022-00439-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 08/29/2022] [Indexed: 11/09/2022]
Abstract
Talazoparib, a PARP inhibitor, is active in germline BRCA1 and BRCA2 (gBRCA1/2)-mutant advanced breast cancer, but its activity beyond gBRCA1/2 is poorly understood. We conducted Talazoparib Beyond BRCA ( NCT02401347 ), an open-label phase II trial, to evaluate talazoparib in patients with pretreated advanced HER2-negative breast cancer (n = 13) or other solid tumors (n = 7) with mutations in homologous recombination (HR) pathway genes other than BRCA1 and BRCA2. In patients with breast cancer, four patients had a Response Evaluation Criteria in Solid Tumors (RECIST) partial response (overall response rate, 31%), and three additional patients had stable disease of ≥6 months (clinical benefit rate, 54%). All patients with germline mutations in PALB2 (gPALB2; encoding partner and localizer of BRCA2) had treatment-associated tumor regression. Tumor or plasma circulating tumor DNA (ctDNA) HR deficiency (HRD) scores were correlated with treatment outcomes and were increased in all gPALB2 tumors. In addition, a gPALB2-associated mutational signature was associated with tumor response. Thus, talazoparib has been demonstrated to have efficacy in patients with advanced breast cancer who have gPALB2 mutations, showing activity in the context of HR pathway gene mutations beyond gBRCA1/2.
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Affiliation(s)
- Joshua J Gruber
- Department of Internal Medicine and Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Anosheh Afghahi
- Department of Medicine, University of Colorado, Aurora, CO, USA
| | | | - Alyssa DeWees
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Wyatt Gross
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | | | - Danika Scott
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Jessica Foran
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Alex McMillan
- Department of Statistics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - James M Ford
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Melinda L Telli
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, USA.
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25
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Kelly MR, Wisniewska K, Regner MJ, Lewis MW, Perreault AA, Davis ES, Phanstiel DH, Parker JS, Franco HL. A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer. Nat Commun 2022; 13:4247. [PMID: 35869079 PMCID: PMC9307778 DOI: 10.1038/s41467-022-31919-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/08/2022] [Indexed: 01/14/2023] Open
Abstract
The human genome contains regulatory elements, such as enhancers, that are often rewired by cancer cells for the activation of genes that promote tumorigenesis and resistance to therapy. This is especially true for cancers that have little or no known driver mutations within protein coding genes, such as ovarian cancer. Herein, we utilize an integrated set of genomic and epigenomic datasets to identify clinically relevant super-enhancers that are preferentially amplified in ovarian cancer patients. We systematically probe the top 86 super-enhancers, using CRISPR-interference and CRISPR-deletion assays coupled to RNA-sequencing, to nominate two salient super-enhancers that drive proliferation and migration of cancer cells. Utilizing Hi-C, we construct chromatin interaction maps that enable the annotation of direct target genes for these super-enhancers and confirm their activity specifically within the cancer cell compartment of human tumors using single-cell genomics data. Together, our multi-omic approach examines a number of fundamental questions about how regulatory information encoded into super-enhancers drives gene expression networks that underlie the biology of ovarian cancer.
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Affiliation(s)
- Michael R Kelly
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kamila Wisniewska
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Matthew J Regner
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Michael W Lewis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Andrea A Perreault
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Eric S Davis
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Douglas H Phanstiel
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Hector L Franco
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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26
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Marczyk M, Qing T, O'Meara T, Yagahoobi V, Pelekanou V, Bai Y, Reisenbichler E, Cole KS, Li X, Gunasekharan V, Ibrahim E, Fanucci K, Wei W, Rimm DL, Pusztai L, Blenman KRM. Tumor immune microenvironment of self-identified African American and non-African American triple negative breast cancer. NPJ Breast Cancer 2022; 8:88. [PMID: 35869114 PMCID: PMC9307813 DOI: 10.1038/s41523-022-00449-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 06/20/2022] [Indexed: 02/06/2023] Open
Abstract
Differences in the tumor immune microenvironment may result in differences in prognosis and response to treatment in cancer patients. We hypothesized that differences in the tumor immune microenvironment may exist between African American (AA) and NonAA patients, due to ancestry-related or socioeconomic factors, that may partially explain differences in clinical outcomes. We analyzed clinically matched triple-negative breast cancer (TNBC) tissues from self-identified AA and NonAA patients and found that stromal TILs, PD-L1 IHC-positivity, mRNA expression of immune-related pathways, and immunotherapy response predictive signatures were significantly higher in AA samples (p < 0.05; Fisher's Exact Test, Mann-Whitney Test, Permutation Test). Cancer biology and metabolism pathways, TAM-M2, and Immune Exclusion were significantly higher in NonAA samples (p < 0.05; Permutation Test, Mann-Whitney Test). There were no differences in somatic tumor mutation burden. Overall, there is greater immune infiltration and inflammation in AA TNBC and these differences may impact response to immune checkpoint inhibitors and other therapeutic agents that modulate the immune microenvironment.
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Affiliation(s)
- Michal Marczyk
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
- Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Tao Qing
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
| | - Tess O'Meara
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
- Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Vesal Yagahoobi
- Department of Pathology, Yale University, New Haven, CT, USA
| | - Vasiliki Pelekanou
- Department of Pathology, Yale University, New Haven, CT, USA
- Precision Medicine - Oncology, Translational Medical Oncology, Translational Medicine Early Development, Sanofi, Cambridge, MA, USA
| | - Yalai Bai
- Department of Pathology, Yale University, New Haven, CT, USA
| | | | - Kimberly S Cole
- Department of Pathology, Yale University, New Haven, CT, USA
- Sema4 Genomics, Branford, CT, USA
| | - Xiaotong Li
- Department of Computational Biology & Bioinformatics, Biological & Biomedical Sciences, Yale University, New Haven, CT, USA
| | - Vignesh Gunasekharan
- Yale Cancer Center, Yale University, New Haven, CT, USA
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
| | - Eiman Ibrahim
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | | | - Wei Wei
- Yale Cancer Center, Yale University, New Haven, CT, USA
- Department of Biostatistics, Yale University, New Haven, CT, USA
| | - David L Rimm
- Yale Cancer Center, Yale University, New Haven, CT, USA
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
- Department of Pathology, Yale University, New Haven, CT, USA
| | - Lajos Pusztai
- Yale Cancer Center, Yale University, New Haven, CT, USA.
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA.
| | - Kim R M Blenman
- Yale Cancer Center, Yale University, New Haven, CT, USA.
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA.
- Department of Computer Science, Yale University, New Haven, CT, USA.
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27
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Hurson AN, Abubakar M, Hamilton AM, Conway K, Hoadley KA, Love MI, Olshan AF, Perou CM, Garcia-Closas M, Troester MA. Prognostic significance of RNA-based TP53 pathway function among estrogen receptor positive and negative breast cancer cases. NPJ Breast Cancer 2022; 8:74. [PMID: 35701440 PMCID: PMC9198049 DOI: 10.1038/s41523-022-00437-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/04/2022] [Indexed: 11/20/2022] Open
Abstract
TP53 and estrogen receptor (ER) are essential in breast cancer development and progression, but TP53 status (by DNA sequencing or protein expression) has been inconsistently associated with survival. We evaluated whether RNA-based TP53 classifiers are related to survival. Participants included 3213 women in the Carolina Breast Cancer Study (CBCS) with invasive breast cancer (stages I-III). Tumors were classified for TP53 status (mutant-like/wildtype-like) using an RNA signature. We used Cox proportional hazards models to estimate covariate-adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) for breast cancer-specific survival (BCSS) among ER- and TP53-defined subtypes. RNA-based results were compared to DNA- and IHC-based TP53 classification, as well as Basal-like versus non-Basal-like subtype. Findings from the diverse (50% Black), population-based CBCS were compared to those from the largely white METABRIC study. RNA-based TP53 mutant-like was associated with BCSS among both ER-negatives and ER-positives (HR (95% CI) = 5.38 (1.84-15.78) and 4.66 (1.79-12.15), respectively). Associations were attenuated when using DNA- or IHC-based TP53 classification. In METABRIC, few ER-negative tumors were TP53-wildtype-like, but TP53 status was a strong predictor of BCSS among ER-positives. In both populations, the effect of TP53 mutant-like status was similar to that for Basal-like subtype. RNA-based measures of TP53 status are strongly associated with BCSS and may have value among ER-negative cancers where few prognostic markers have been robustly validated. Given the role of TP53 in chemotherapeutic response, RNA-based TP53 as a prognostic biomarker could address an unmet need in breast cancer.
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Affiliation(s)
- Amber N Hurson
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Mustapha Abubakar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Alina M Hamilton
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kathleen Conway
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew F Olshan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Charles M Perou
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Melissa A Troester
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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28
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Li Z, Spoelstra NS, Sikora MJ, Sams SB, Elias A, Richer JK, Lee AV, Oesterreich S. Mutual exclusivity of ESR1 and TP53 mutations in endocrine resistant metastatic breast cancer. NPJ Breast Cancer 2022; 8:62. [PMID: 35538119 PMCID: PMC9090919 DOI: 10.1038/s41523-022-00426-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/31/2022] [Indexed: 12/12/2022] Open
Abstract
Both TP53 and ESR1 mutations occur frequently in estrogen receptor positive (ER+) metastatic breast cancers (MBC) and their distinct roles in breast cancer tumorigenesis and progression are well appreciated. Recent clinical studies discovered mutual exclusivity between TP53 and ESR1 mutations in metastatic breast cancers; however, mechanisms underlying this intriguing clinical observation remain largely understudied and unknown. Here, we explored the interplay between TP53 and ESR1 mutations using publicly available clinical and experimental data sets. We first confirmed the robust mutational exclusivity using six independent cohorts with 1,056 ER+ MBC samples and found that the exclusivity broadly applies to all ER+ breast tumors regardless of their clinical and distinct mutational features. ESR1 mutant tumors do not exhibit differential p53 pathway activity, whereas we identified attenuated ER activity and expression in TP53 mutant tumors, driven by a p53-associated E2 response gene signature. Further, 81% of these p53-associated E2 response genes are either direct targets of wild-type (WT) p53-regulated transactivation or are mutant p53-associated microRNAs, representing bimodal mechanisms of ER suppression. Lastly, we analyzed the very rare cases with co-occurrences of TP53 and ESR1 mutations and found that their simultaneous presence was also associated with reduced ER activity. In addition, tumors with dual mutations showed higher levels of total and PD-L1 positive macrophages. In summary, our study utilized multiple publicly available sources to explore the mechanism underlying the mutual exclusivity between ESR1 and TP53 mutations, providing further insights and testable hypotheses of the molecular interplay between these two pivotal genes in ER+ MBC.
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Affiliation(s)
- Zheqi Li
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Women's Cancer Research Center, Magee Women's Research Institute, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Nicole S Spoelstra
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew J Sikora
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sharon B Sams
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Anthony Elias
- School of Medicine, Division of Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jennifer K Richer
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Adrian V Lee
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Women's Cancer Research Center, Magee Women's Research Institute, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Steffi Oesterreich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.
- Women's Cancer Research Center, Magee Women's Research Institute, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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29
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Prakadan SM, Alvarez-Breckenridge CA, Markson SC, Kim AE, Klein RH, Nayyar N, Navia AW, Kuter BM, Kolb KE, Bihun I, Mora JL, Bertalan MS, Shaw B, White M, Kaplan A, Stocking JH, Wadsworth MH, Lee EQ, Chukwueke U, Wang N, Subramanian M, Rotem D, Cahill DP, Adalsteinsson VA, Miller JW, Sullivan RJ, Carter SL, Brastianos PK, Shalek AK. Genomic and transcriptomic correlates of immunotherapy response within the tumor microenvironment of leptomeningeal metastases. Nat Commun 2021; 12:5955. [PMID: 34642316 PMCID: PMC8511044 DOI: 10.1038/s41467-021-25860-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 08/25/2021] [Indexed: 12/30/2022] Open
Abstract
Leptomeningeal disease (LMD) is a devastating complication of solid tumor malignancies, with dire prognosis and no effective systemic treatment options. Over the past decade, the incidence of LMD has steadily increased due to therapeutics that have extended the survival of cancer patients, highlighting the need for new interventions. To examine the efficacy of immune checkpoint inhibitors (ICI) in patients with LMD, we completed two phase II clinical trials. Here, we investigate the cellular and molecular features underpinning observed patient trajectories in these trials by applying single-cell RNA and cell-free DNA profiling to longitudinal cerebrospinal fluid (CSF) draws from enrolled patients. We recover immune and malignant cell types in the CSF, characterize cell behavior changes following ICI, and identify genomic features associated with relevant clinical phenomena. Overall, our study describes the liquid LMD tumor microenvironment prior to and following ICI treatment and demonstrates clinical utility of cell-free and single-cell genomic measurements for LMD research.
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Affiliation(s)
- Sanjay M Prakadan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA
| | - Christopher A Alvarez-Breckenridge
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Neurosurgery, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Samuel C Markson
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Albert E Kim
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Robert H Klein
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Naema Nayyar
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Andrew W Navia
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA
| | - Benjamin M Kuter
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Kellie E Kolb
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA
| | - Ivanna Bihun
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Joana L Mora
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Mia Solana Bertalan
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Brian Shaw
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Michael White
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Alexander Kaplan
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Jackson H Stocking
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Marc H Wadsworth
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA
| | - Eudocia Q Lee
- Division of Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ugonma Chukwueke
- Division of Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nancy Wang
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Megha Subramanian
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Denisse Rotem
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Viktor A Adalsteinsson
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeffrey W Miller
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Ryan J Sullivan
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Scott L Carter
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA.
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA.
| | - Priscilla K Brastianos
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA.
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.
| | - Alex K Shalek
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA.
- Division of Health Science & Technology, Harvard Medical School, Cambridge, MA, USA.
- Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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30
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Ahuno ST, Doebley AL, Ahearn TU, Yarney J, Titiloye N, Hamel N, Adjei E, Clegg-Lamptey JN, Edusei L, Awuah B, Song X, Vanderpuye V, Abubakar M, Duggan M, Stover DG, Nyarko K, Bartlett JMS, Aitpillah F, Ansong D, Gardner KL, Boateng FA, Bowcock AM, Caldas C, Foulkes WD, Wiafe S, Wiafe-Addai B, Garcia-Closas M, Kwarteng A, Ha G, Figueroa JD, Polak P. Circulating tumor DNA is readily detectable among Ghanaian breast cancer patients supporting non-invasive cancer genomic studies in Africa. NPJ Precis Oncol 2021; 5:83. [PMID: 34535742 PMCID: PMC8448727 DOI: 10.1038/s41698-021-00219-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 07/21/2021] [Indexed: 12/20/2022] Open
Abstract
Circulating tumor DNA (ctDNA) sequencing studies could provide novel insights into the molecular pathology of cancer in sub-Saharan Africa. In 15 patient plasma samples collected at the time of diagnosis as part of the Ghana Breast Health Study and unselected for tumor grade and subtype, ctDNA was detected in a majority of patients based on whole- genome sequencing at high (30×) and low (0.1×) depths. Breast cancer driver copy number alterations were observed in the majority of patients.
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Affiliation(s)
- Samuel Terkper Ahuno
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Anna-Lisa Doebley
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Nancy Hamel
- Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | | | | | | | | | - Xiaoyu Song
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | | | - Mustapha Abubakar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Maire Duggan
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Daniel G Stover
- Stefanie Spielman Comprehensive Breast Cancer, The Ohio State University, Columbus, OH, USA
- Division of Medical Oncology, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | | | - John M S Bartlett
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Edinburgh Cancer Research Centre, Edinburgh, United Kingdom
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Francis Aitpillah
- Komfo Anokye Teaching Hospital, Kumasi, Ghana
- School of Medicine & Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Daniel Ansong
- Department of Child Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Kevin L Gardner
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | | | - Anne M Bowcock
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | | | - William D Foulkes
- Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montréal, QC, Canada
- Program in Cancer Genetics, Departments of Oncology and Human Genetics, McGill University, Montréal, QC, Canada
| | - Seth Wiafe
- School of Public Health, Loma Linda University, Loma Linda, CA, USA
| | | | | | - Alexander Kwarteng
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Kumasi Center for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Gavin Ha
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Jonine D Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
- CRUK Edinburgh Centre, University of Edinburgh, Edinburgh, UK.
| | - Paz Polak
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.
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31
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Grible JM, Zot P, Olex AL, Hedrick SE, Harrell JC, Woock AE, Idowu MO, Clevenger CV. The human intermediate prolactin receptor is a mammary proto-oncogene. NPJ Breast Cancer 2021; 7:37. [PMID: 33772010 PMCID: PMC7997966 DOI: 10.1038/s41523-021-00243-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 03/05/2021] [Indexed: 12/16/2022] Open
Abstract
The hormone prolactin (PRL) and its receptor (hPRLr) are significantly involved in breast cancer pathogenesis. The intermediate hPRLr (hPRLrI) is an alternatively-spliced isoform, capable of stimulating cellular viability and proliferation. An analogous truncated mouse PRLr (mPRLr) was recently found to be oncogenic when co-expressed with wild-type mPRLr. The goal of this study was to determine if a similar transforming event occurs with the hPRLr in human breast epithelial cells and to better understand the mechanism behind such transformation. hPRLrL+I co-expression in MCF10AT cells resulted in robust in vivo and in vitro transformation, while hPRLrI knock-down in MCF7 cells significantly decreased in vitro malignant potential. hPRLrL+I heterodimers displayed greater stability than hPRLrL homodimers, and while being capable of activating Jak2, Ras, and MAPK, they were unable to induce Stat5a tyrosine phosphorylation. Both immunohistochemical breast cancer tissue microarray data and RNA sequencing analyses using The Cancer Genome Atlas (TCGA) identified that higher hPRLrI expression associates with triple-negative breast cancer. These studies indicate the hPRLrI, when expressed alongside hPRLrL, participates in mammary transformation, and represents a novel oncogenic mechanism.
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Affiliation(s)
- Jacqueline M Grible
- Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Patricija Zot
- Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Amy L Olex
- Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA, USA
| | - Shannon E Hedrick
- Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - J Chuck Harrell
- Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Alicia E Woock
- Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
- Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA, USA
| | - Michael O Idowu
- Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Charles V Clevenger
- Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA.
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32
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Ge JY, Shu S, Kwon M, Jovanović B, Murphy K, Gulvady A, Fassl A, Trinh A, Kuang Y, Heavey GA, Luoma A, Paweletz C, Thorner AR, Wucherpfennig KW, Qi J, Brown M, Sicinski P, McDonald TO, Pellman D, Michor F, Polyak K. Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer. Nat Commun 2020; 11:2350. [PMID: 32393766 PMCID: PMC7214447 DOI: 10.1038/s41467-020-16170-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
BET inhibitors are promising therapeutic agents for the treatment of triple-negative breast cancer (TNBC), but the rapid emergence of resistance necessitates investigation of combination therapies and their effects on tumor evolution. Here, we show that palbociclib, a CDK4/6 inhibitor, and paclitaxel, a microtubule inhibitor, synergize with the BET inhibitor JQ1 in TNBC lines. High-complexity DNA barcoding and mathematical modeling indicate a high rate of de novo acquired resistance to these drugs relative to pre-existing resistance. We demonstrate that the combination of JQ1 and palbociclib induces cell division errors, which can increase the chance of developing aneuploidy. Characterizing acquired resistance to combination treatment at a single cell level shows heterogeneous mechanisms including activation of G1-S and senescence pathways. Our results establish a rationale for further investigation of combined BET and CDK4/6 inhibition in TNBC and suggest novel mechanisms of action for these drugs and new vulnerabilities in cells after emergence of resistance.
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Affiliation(s)
- Jennifer Y Ge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, 02115, USA
| | - Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Mijung Kwon
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, 120-750, Korea
| | - Bojana Jovanović
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Katherine Murphy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Anushree Gulvady
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Anne Trinh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Yanan Kuang
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Grace A Heavey
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Adrienne Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Cloud Paweletz
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Aaron R Thorner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, 02115, USA
| | - Jun Qi
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Thomas O McDonald
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Franziska Michor
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, 02115, USA.
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
- Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, 02115, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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33
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Mazumdar A, Tahaney WM, Reddy Bollu L, Poage G, Hill J, Zhang Y, Mills GB, Brown PH. The phosphatase PPM1A inhibits triple negative breast cancer growth by blocking cell cycle progression. NPJ Breast Cancer 2019; 5:22. [PMID: 31372497 PMCID: PMC6659706 DOI: 10.1038/s41523-019-0118-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 06/26/2019] [Indexed: 12/31/2022] Open
Abstract
Estrogen receptor (ER)-negative, progesterone receptor (PR)-negative and HER2-negative, or "triple negative," breast cancer (TNBC) is a poor prognosis clinical subtype that occurs more frequently in younger women and is commonly treated with toxic chemotherapy. Effective targeted therapy for TNBC is urgently needed. Our previous studies have identified several kinases critical for TNBC growth. Since phosphatases regulate the function of kinase signaling pathways, we sought to identify critical growth-regulatory phosphatases that are expressed differentially in ER-negative, as compared to ER-positive, breast cancers. In this study, we examined the role of one of these differentially expressed phosphatases, the protein phosphatase Mg + 2/Mn + 2 dependent 1A (PPM1A) which is underexpressed in ER-negative breast cancer as compared to ER-positive breast cancers, in regulating TNBC growth. We found that PPM1A is deleted in ~40% of ER-negative breast cancers, and that induced expression of PPM1A suppresses in vitro and in vivo growth of TNBC cells. This study demonstrates that induction of PPM1A expression blocks the cell cycle and reduces CDK and Rb phosphorylation. These results suggest PPM1A is a crucial regulator of cell cycle progression in triple negative breast cancer. Our results also suggest that PPM1A loss should be explored as a predictive biomarker of CDK inhibitor sensitivity.
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Affiliation(s)
- Abhijit Mazumdar
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Texas, USA
| | - William M. Tahaney
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Texas, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Lakshmi Reddy Bollu
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Texas, USA
| | | | - Jamal Hill
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Texas, USA
| | - Yun Zhang
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Texas, USA
| | - Gordon B. Mills
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Oregon, USA
| | - Powel H. Brown
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Texas, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030 USA
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34
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Levine KM, Priedigkeit N, Basudan A, Tasdemir N, Sikora MJ, Sokol ES, Hartmaier RJ, Ding K, Ahmad NZ, Watters RJ, Weiss KR, Blohmer JU, Denkert C, Machleidt A, Karsten MM, Boisen MM, Elishaev E, Lucas PC, Lee AV, Oesterreich S. FGFR4 overexpression and hotspot mutations in metastatic ER+ breast cancer are enriched in the lobular subtype. NPJ Breast Cancer 2019; 5:19. [PMID: 31263748 PMCID: PMC6597581 DOI: 10.1038/s41523-019-0114-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 05/30/2019] [Indexed: 12/16/2022] Open
Abstract
Invasive lobular carcinoma (ILC) is an understudied subtype of breast cancer that requires novel therapies in the advanced setting. To study acquired resistance to endocrine therapy in ILC, we have recently performed RNA-Sequencing on long-term estrogen deprived cell lines and identified FGFR4 overexpression as a top druggable target. Here, we show that FGFR4 expression also increases dramatically in endocrine-treated distant metastases, with an average fold change of 4.8 relative to the paired primary breast tumor for ILC, and 2.4-fold for invasive ductal carcinoma (IDC). In addition, we now report that FGFR4 hotspot mutations are enriched in metastatic breast cancer, with an additional enrichment for ILC, suggesting a multimodal selection of FGFR4 activation. These data collectively support the notion that FGFR4 is an important mediator of endocrine resistance in ILC, warranting future mechanistic studies on downstream signaling of overexpressed wild-type and mutant FGFR4.
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Affiliation(s)
- Kevin M. Levine
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh, PA USA
- Magee-Women’s Research Institute, Magee-Women’s Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA USA
| | - Nolan Priedigkeit
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh, PA USA
- Magee-Women’s Research Institute, Magee-Women’s Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA USA
| | - Ahmed Basudan
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh, PA USA
- Magee-Women’s Research Institute, Magee-Women’s Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA USA
- Present Address: Department of Clinical Laboratory Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nilgun Tasdemir
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh, PA USA
- Magee-Women’s Research Institute, Magee-Women’s Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA USA
| | - Matthew J. Sikora
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | | | | | - Kai Ding
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh, PA USA
- Magee-Women’s Research Institute, Magee-Women’s Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA USA
| | - Nedah Z. Ahmad
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh, PA USA
| | - Rebecca J. Watters
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA USA
- Department of Orthopedic Surgery, University of Pittsburgh, Pittsburgh, PA USA
| | - Kurt R. Weiss
- Department of Orthopedic Surgery, University of Pittsburgh, Pittsburgh, PA USA
| | | | | | | | | | - Michelle M. Boisen
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA USA
| | - Esther Elishaev
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA USA
| | - Peter C. Lucas
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA USA
| | - Adrian V. Lee
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh, PA USA
- Magee-Women’s Research Institute, Magee-Women’s Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA USA
| | - Steffi Oesterreich
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh, PA USA
- Magee-Women’s Research Institute, Magee-Women’s Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA USA
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