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Agrawal P, Jain N, Gopalan V, Timon A, Singh A, Rajagopal PS, Hannenhalli S. Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer. iScience 2024; 27:109752. [PMID: 38699227 PMCID: PMC11063905 DOI: 10.1016/j.isci.2024.109752] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/18/2024] [Accepted: 04/12/2024] [Indexed: 05/05/2024] Open
Abstract
Breast cancers (BRCA) exhibit substantial transcriptional heterogeneity, posing a significant clinical challenge. The global transcriptional changes in a disease context, however, are likely mediated by few key genes which reflect disease etiology better than the differentially expressed genes (DEGs). We apply our network-based tool PathExt to 1,059 BRCA tumors across 4 subtypes to identify key mediator genes in each subtype. Compared to conventional differential expression analysis, PathExt-identified genes exhibit greater concordance across tumors, revealing shared and subtype-specific biological processes; better recapitulate BRCA-associated genes in multiple benchmarks, and are more essential in BRCA subtype-specific cell lines. Single-cell transcriptomic analysis reveals a subtype-specific distribution of PathExt-identified genes in multiple cell types from the tumor microenvironment. Application of PathExt to a TNBC chemotherapy response dataset identified subtype-specific key genes and biological processes associated with resistance. We described putative drugs that target key genes potentially mediating drug resistance.
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Affiliation(s)
- Piyush Agrawal
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Vishaka Gopalan
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Annan Timon
- University of Pennsylvania, Philadelphia, PA, USA
| | - Arashdeep Singh
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Padma S. Rajagopal
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
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Agrawal P, Jain N, Gopalan V, Timon A, Singh A, Rajagopal PS, Hannenhalli S. Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in Triple Negative Breast Cancer. bioRxiv 2023:2023.05.21.541618. [PMID: 37425784 PMCID: PMC10327220 DOI: 10.1101/2023.05.21.541618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Breast cancers exhibit substantial transcriptional heterogeneity, posing a significant challenge to the prediction of treatment response and prognostication of outcomes. Especially, translation of TNBC subtypes to the clinic remains a work in progress, in part because of a lack of clear transcriptional signatures distinguishing the subtypes. Our recent network-based approach, PathExt, demonstrates that global transcriptional changes in a disease context are likely mediated by a small number of key genes, and these mediators may better reflect functional or translationally relevant heterogeneity. We apply PathExt to 1059 BRCA tumors and 112 healthy control samples across 4 subtypes to identify frequent, key-mediator genes in each BRCA subtype. Compared to conventional differential expression analysis, PathExt-identified genes (1) exhibit greater concordance across tumors, revealing shared as well as BRCA subtype-specific biological processes, (2) better recapitulate BRCA-associated genes in multiple benchmarks, and (3) exhibit greater dependency scores in BRCA subtype-specific cancer cell lines. Single cell transcriptomes of BRCA subtype tumors reveal a subtype-specific distribution of PathExt-identified genes in multiple cell types from the tumor microenvironment. Application of PathExt to a TNBC chemotherapy response dataset identified TNBC subtype-specific key genes and biological processes associated with resistance. We described putative drugs that target top novel genes potentially mediating drug resistance. Overall, PathExt applied to breast cancer refines previous views of gene expression heterogeneity and identifies potential mediators of TNBC subtypes, including potential therapeutic targets.
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Affiliation(s)
- Piyush Agrawal
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Vishaka Gopalan
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Annan Timon
- University of Pennsylvania, Philadelphia, PA, USA
| | - Arashdeep Singh
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Padma S Rajagopal
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
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Dinstag G, Shulman ED, Elis E, Ben-Zvi DS, Tirosh O, Maimon E, Meilijson I, Elalouf E, Temkin B, Vitkovsky P, Schiff E, Hoang DT, Sinha S, Nair NU, Sang-Lee J, Schäffer AA, Ronai Z, Juric D, Apolo AB, Dahut WL, Lipkowitz S, Berger R, Kurzrock R, Papanicolau-Sengos A, Karzai F, Gilbert MR, Aldape K, Rajagopal PS, Beker T, Ruppin E, Aharonov R. Abstract 957: Prediction of patient response to targeted and immunotherapies from the tumor transcriptome in a wide set of indications and clinical trials. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background: Precision oncology is gradually advancing into mainstream clinical practice, demonstrating significant survival benefits. However, eligibility and response rates remain limited in many cases, calling for better predictive biomarkers.
Methods: We present ENLIGHT, a transcriptomics-based computational approach that identifies clinically relevant genetic interactions and uses them to predict a patient’s response to a variety of therapies in multiple cancer types, importantly, without training on previous treatment response data. Consequently, in addition to its ability to predict patients' response to approved and well-studied therapies, ENLIGHT can predict the response to new treatments in early development, even before clinical data has accumulated. Accordingly, we study ENLIGHT in two translationally relevant scenarios: Personalized Oncology (PO), aimed at prioritizing approved treatments to a given patient, and Clinical Trial Design (CTD), selecting the subset of most likely responders in a patient cohort.
Results: Evaluating ENLIGHT’s performance on 21 blinded clinical trial datasets spanning 11 indications and 15 different drugs in the PO setting, we show that it can effectively predict a patient’s treatment response across multiple therapies and cancer types, with an overall odds ratio of 2.59 (p=3.41e-8), and a 36% increase in response rate over the baseline (p=3.30e-13). Its prediction accuracy is better than other state-of-the-art transcriptomics-based signatures. Unlike most signatures that are prognostic or provide insights for only very few, specific treatments, ENLIGHT provides matching scores to a broad range of treatments. Quite strikingly, its performance is comparable to that of supervised predictors developed for specific indications and drugs. In combination with the IFN-γ signature, ENLIGHT achieves an odds ratio larger than 4 in predicting response to immune checkpoint therapy. In the CTD scenario, our results show that by excluding non-responders ENLIGHT can enhance clinical trial success for immunotherapies and other monoclonal antibodies, achieving > 90% of the response rate attainable under an optimal exclusion strategy.
Conclusion: ENLIGHT is a powerful transcriptomics-based precision oncology pipeline developed by Pangea Biomed that broadly predicts response to both extant and novel targeted and immune therapies, going beyond context-specific biomarkers.
Citation Format: Gal Dinstag, Eldad D. Shulman, Efrat Elis, Doreen S. Ben-Zvi, Omer Tirosh, Eden Maimon, Isaac Meilijson, Emmanuel Elalouf, Boris Temkin, Philipp Vitkovsky, Eyal Schiff, Danh-Tai Hoang, Sanju Sinha, Nishanth Ulhas Nair, Joo Sang-Lee, Alejandro A. Schäffer, Ze'ev Ronai, Dejan Juric, Andrea B. Apolo, William L. Dahut, Stanley Lipkowitz, Raanan Berger, Razelle Kurzrock, Antonios Papanicolau-Sengos, Fatima Karzai, Mark R. Gilbert, Kenneth Aldape, Padma S. Rajagopal, Tuvik Beker, Eytan Ruppin, Ranit Aharonov. Prediction of patient response to targeted and immunotherapies from the tumor transcriptome in a wide set of indications and clinical trials [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 957.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Danh-Tai Hoang
- 2The Australian National University, Canberra, Australia
| | | | | | - Joo Sang-Lee
- 4Sungkyunkwan University, Suwon, Republic of Korea
| | | | - Ze'ev Ronai
- 5Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Dejan Juric
- 6Massachusetts General Hospital Cancer Center, Boston, MA
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Dinstag G, Shulman ED, Elis E, Ben-Zvi DS, Tirosh O, Maimon E, Meilijson I, Elalouf E, Temkin B, Vitkovsky P, Schiff E, Hoang DT, Sinha S, Nair NU, Lee JS, Schäffer AA, Ronai Z, Juric D, Apolo AB, Dahut WL, Lipkowitz S, Berger R, Kurzrock R, Papanicolau-Sengos A, Karzai F, Gilbert MR, Aldape K, Rajagopal PS, Beker T, Ruppin E, Aharonov R. Clinically oriented prediction of patient response to targeted and immunotherapies from the tumor transcriptome. Med (N Y) 2023; 4:15-30.e8. [PMID: 36513065 PMCID: PMC10029756 DOI: 10.1016/j.medj.2022.11.001] [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: 04/11/2022] [Revised: 08/30/2022] [Accepted: 10/31/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Precision oncology is gradually advancing into mainstream clinical practice, demonstrating significant survival benefits. However, eligibility and response rates remain limited in many cases, calling for better predictive biomarkers. METHODS We present ENLIGHT, a transcriptomics-based computational approach that identifies clinically relevant genetic interactions and uses them to predict a patient's response to a variety of therapies in multiple cancer types without training on previous treatment response data. We study ENLIGHT in two translationally oriented scenarios: personalized oncology (PO), aimed at prioritizing treatments for a single patient, and clinical trial design (CTD), selecting the most likely responders in a patient cohort. FINDINGS Evaluating ENLIGHT's performance on 21 blinded clinical trial datasets in the PO setting, we show that it can effectively predict a patient's treatment response across multiple therapies and cancer types. Its prediction accuracy is better than previously published transcriptomics-based signatures and is comparable with that of supervised predictors developed for specific indications and drugs. In combination with the interferon-γ signature, ENLIGHT achieves an odds ratio larger than 4 in predicting response to immune checkpoint therapy. In the CTD scenario, ENLIGHT can potentially enhance clinical trial success for immunotherapies and other monoclonal antibodies by excluding non-responders while overall achieving more than 90% of the response rate attainable under an optimal exclusion strategy. CONCLUSIONS ENLIGHT demonstrably enhances the ability to predict therapeutic response across multiple cancer types from the bulk tumor transcriptome. FUNDING This research was supported in part by the Intramural Research Program, NIH and by the Israeli Innovation Authority.
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Affiliation(s)
| | | | | | | | | | | | - Isaac Meilijson
- Pangea Biomed Ltd., Tel Aviv, Israel; Tel Aviv University, Tel Aviv, Israel
| | | | | | | | | | - Danh-Tai Hoang
- Biological Data Science Institute, College of Science, The Australian National University, Canberra, ACT, Australia
| | - Sanju Sinha
- Cancer Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nishanth Ulhas Nair
- Cancer Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joo Sang Lee
- Department of Precision Medicine, School of Medicine & Department of Artificial Intelligence, Sungkyunkwan University, Suwon, Republic of Korea
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ze'ev Ronai
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Dejan Juric
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andrea B Apolo
- Genitourinary Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - William L Dahut
- Genitourinary Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stanley Lipkowitz
- Women's Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raanan Berger
- Cancer Center, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Razelle Kurzrock
- Worldwide Innovative Network (WIN) for Personalized Cancer Therapy, Chevilly-Larue, France
| | | | - Fatima Karzai
- Genitourinary Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Padma S Rajagopal
- Cancer Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Women's Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Eytan Ruppin
- Cancer Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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Nair NU, Cheng K, Naddaf L, Sharon E, Pal LR, Rajagopal PS, Unterman I, Aldape K, Hannenhalli S, Day CP, Tabach Y, Ruppin E. Cross-species identification of cancer resistance-associated genes that may mediate human cancer risk. Sci Adv 2022; 8:eabj7176. [PMID: 35921407 PMCID: PMC9348801 DOI: 10.1126/sciadv.abj7176] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Cancer is a predominant disease across animals. We applied a comparative genomics approach to systematically characterize genes whose conservation levels correlate positively (PC) or negatively (NC) with cancer resistance estimates across 193 vertebrates. Pathway analysis reveals that NC genes are enriched for metabolic functions and PC genes in cell cycle regulation, DNA repair, and immune response, pointing to their corresponding roles in mediating cancer risk. We find that PC genes are less tolerant to loss-of-function (LoF) mutations, are enriched in cancer driver genes, and are associated with germline mutations that increase human cancer risk. Their relevance to cancer risk is further supported via the analysis of mouse functional genomics and cancer mortality of zoo mammals' data. In sum, our study describes a cross-species genomic analysis pointing to candidate genes that may mediate human cancer risk.
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Affiliation(s)
- Nishanth Ulhas Nair
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Corresponding author. (N.U.N.); (K.C.); (Y.T.); (E.R.)
| | - Kuoyuan Cheng
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
- Corresponding author. (N.U.N.); (K.C.); (Y.T.); (E.R.)
| | - Lamis Naddaf
- Department of Developmental Biology and Cancer Research, Institute of Medical Research–Israel-Canada, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Elad Sharon
- Department of Developmental Biology and Cancer Research, Institute of Medical Research–Israel-Canada, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Lipika R. Pal
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Padma S. Rajagopal
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Irene Unterman
- Department of Developmental Biology and Cancer Research, Institute of Medical Research–Israel-Canada, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, Institute of Medical Research–Israel-Canada, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Corresponding author. (N.U.N.); (K.C.); (Y.T.); (E.R.)
| | - Eytan Ruppin
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Corresponding author. (N.U.N.); (K.C.); (Y.T.); (E.R.)
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Crawford DR, Sinha S, Nair NU, Ryan BM, Barnholtz-Sloan J, Mount SM, Erez A, Adalpe K, Castle PE, Rajagopal PS, Day CP, Schäffer AA, Ruppin E. Abstract 27: Sex biases in cancer and autoimmune disease incidence are strongly positively correlated with mitochondrial gene expression across human tissues. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer occurs more frequently in men while autoimmune diseases (AIDs) occur more frequently in women. To explore whether these sex biases have a common basis, we collected 170 AID incidence studies from many countries for tissues that have both a cancer type and an AID that arise from that tissue. Analyzing a total of 182 country-specific, tissue-matched cancer-AID incidence rate sex bias data pairs, we find that the sex biases observed in the incidence of AIDs and cancers that occur in the same tissue are positively correlated across human tissues. Second, we find that the sex bias in the expression of the 37 genes encoded in the mitochondrial genome stands out as the common key factor whose levels across human tissues are most strongly and positively associated with these incidence rate sex biases.
Citation Format: David Robert Crawford, Sanju Sinha, Nishanth U. Nair, Bríd M. Ryan, Jill Barnholtz-Sloan, Stephen M. Mount, Ayelet Erez, Kenneth Adalpe, Philip E. Castle, Padma S. Rajagopal, Chi-Ping Day, Alejandro A. Schäffer, Eytan Ruppin. Sex biases in cancer and autoimmune disease incidence are strongly positively correlated with mitochondrial gene expression across human tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 27.
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Affiliation(s)
| | - Sanju Sinha
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Nishanth U. Nair
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Bríd M. Ryan
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | | | - Ayelet Erez
- 3Weizmann Institute of Science, Rehovot, Israel
| | - Kenneth Adalpe
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Philip E. Castle
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Chi-Ping Day
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Eytan Ruppin
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
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Calvo-Alcañiz C, Rajagopal PS, Sinha S, Schischlik F, Papanicolau-Sengos A, Nair NU, Ruppin E. Abstract 985: Is the transcriptome of primary and metastatic cancers closer to their origin or target tissues. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Most cancer deaths are caused by metastasis, yet understanding how metastatic cancers adapt from their origin tissues to their target tissues remains a fundamental scientific and clinical challenge. To date, no studies have systematically analyzed the transcriptomic similarity of metastatic cancers to their target tissues in a genome wide manner. Here, we ask if the overall gene expression of primary and metastatic tumors is closer to their tissue of origin or closer to their target tissue? Next, we aim to identify the key pathways in metastatic tumors whose gene expression becomes markedly closer to their target than primary tissue of origin.
Methods: We analyzed the expression profiles of: (a) primary tumors of 9 cancer types, which have metastasized to the liver, lung, or brain (TCGA data, n = 306), (b) metastatic tumors of 12 cancer types (MET500 collection, n = 194) and (c) their origin and target normal tissue samples (GTEx, n = 5,663). We computed the similarity (Euclidean distance) between the expression profiles of the tumors (either primary or metastasis) to the mean expression of their corresponding normal tissue of origin and target tissues, termed their transcriptomic distance (TD). For each tumor sample’s expression profile (either primary tumor or metastasis), we compute the ratio of its TD to the tissue of origin over its TD to the target tissue to get its TD ratio.
Results: 1) We find that while most primary tumors are more similar to the tissue of origin than to the target tissues, there is a shift in expression patterns in metastatic tumors towards their target.
2) Across cancer types that metastasize to the liver, cell cycle and growth pathways are significantly transcriptomically closer to the tissue of origin; while the expression of pathways related to more specialized liver cellular functions, such as coagulation and bile acid metabolism are becoming significantly closer to the liver.
3) We tested our key findings by analyzing a matched cohort of primary breast cancers and metastasis samples, reassuringly finding that they overall recapitulate the key results emerging from the non-matched analysis. The key pathways altered when metastasizing to four target tissues (liver, lung, ovary, skin) are adipogenesis, fatty acid metabolism, coagulation, xenobiotic metabolism, and bile acid metabolism.
Conclusions: Quite surprisingly, this the first systematic analysis comparing the landscape of primary and metastatic transcriptional alterations of the same cancer type, providing a genome wide view of how cancers adapt to new environments during metastasis. The systematic identification of the specific pathways whose expression shifts towards the target tissues in metastatic tumors provides important leads to their potential targeting.
Citation Format: Camilo Calvo-Alcañiz, Padma S. Rajagopal, Sanju Sinha, Fiorella Schischlik, Antonios Papanicolau-Sengos, Nishanth Ulhas Nair, Eytan Ruppin. Is the transcriptome of primary and metastatic cancers closer to their origin or target tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 985.
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Kar SP, Considine DP, Tyrer JP, Plummer JT, Chen S, Dezem FS, Barbeira AN, Rajagopal PS, Rosenow WT, Moreno F, Bodelon C, Chang-Claude J, Chenevix-Trench G, deFazio A, Dörk T, Ekici AB, Ewing A, Fountzilas G, Goode EL, Hartman M, Heitz F, Hillemanns P, Høgdall E, Høgdall CK, Huzarski T, Jensen A, Karlan BY, Khusnutdinova E, Kiemeney LA, Kjaer SK, Klapdor R, Köbel M, Li J, Liebrich C, May T, Olsson H, Permuth JB, Peterlongo P, Radice P, Ramus SJ, Riggan MJ, Risch HA, Saloustros E, Simard J, Szafron LM, Titus L, Thompson CL, Vierkant RA, Winham SJ, Zheng W, Doherty JA, Berchuck A, Lawrenson K, Im HK, Manichaikul AW, Pharoah PD, Gayther SA, Schildkraut JM. Pleiotropy-guided transcriptome imputation from normal and tumor tissues identifies candidate susceptibility genes for breast and ovarian cancer. HGG Adv 2021; 2:100042. [PMID: 34317694 PMCID: PMC8312632 DOI: 10.1016/j.xhgg.2021.100042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 01/03/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Familial, sequencing, and genome-wide association studies (GWASs) and genetic correlation analyses have progressively unraveled the shared or pleiotropic germline genetics of breast and ovarian cancer. In this study, we aimed to leverage this shared germline genetics to improve the power of transcriptome-wide association studies (TWASs) to identify candidate breast cancer and ovarian cancer susceptibility genes. We built gene expression prediction models using the PrediXcan method in 681 breast and 295 ovarian tumors from The Cancer Genome Atlas and 211 breast and 99 ovarian normal tissue samples from the Genotype-Tissue Expression project and integrated these with GWAS meta-analysis data from the Breast Cancer Association Consortium (122,977 cases/105,974 controls) and the Ovarian Cancer Association Consortium (22,406 cases/40,941 controls). The integration was achieved through application of a pleiotropy-guided conditional/conjunction false discovery rate (FDR) approach in the setting of a TWASs. This identified 14 candidate breast cancer susceptibility genes spanning 11 genomic regions and 8 candidate ovarian cancer susceptibility genes spanning 5 genomic regions at conjunction FDR < 0.05 that were >1 Mb away from known breast and/or ovarian cancer susceptibility loci. We also identified 38 candidate breast cancer susceptibility genes and 17 candidate ovarian cancer susceptibility genes at conjunction FDR < 0.05 at known breast and/or ovarian susceptibility loci. The 22 genes identified by our cross-cancer analysis represent promising candidates that further elucidate the role of the transcriptome in mediating germline breast and ovarian cancer risk.
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Affiliation(s)
- Siddhartha P. Kar
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Daniel P.C. Considine
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan P. Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Jasmine T. Plummer
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Stephanie Chen
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Felipe S. Dezem
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Alvaro N. Barbeira
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Padma S. Rajagopal
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Will T. Rosenow
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Fernando Moreno
- Department of Oncology, Hospital Clínico San Carlos, Madrid, Spain
| | - Clara Bodelon
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Anna deFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, Australia
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Erlangen, Germany
- Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen, Erlangen, Germany
| | - Ailith Ewing
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Ellen L. Goode
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Mikael Hartman
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/Evang., Essen, Germany
- Department of Gynecology, Center for Oncologic Surgery, Charité Campus Virchow-Klinikum, Berlin, Germany
| | - Peter Hillemanns
- Department of Gynecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Estrid Høgdall
- Department of Virus, Lifestyle, and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Claus K. Høgdall
- The Juliane Marie Centre, Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Tomasz Huzarski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
- Department of Genetics and Pathology, University of Zielona Góra, Zielona Góra, Poland
| | - Allan Jensen
- Department of Lifestyle, Reproduction, and Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Beth Y. Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Lambertus A. Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne K. Kjaer
- Department of Virus, Lifestyle, and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Rüdiger Klapdor
- Department of Gynecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Foothills Medical Center, Calgary, AB, Canada
| | - Jingmei Li
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Human Genetics, Singapore, Singapore
| | - Clemens Liebrich
- Department of Obstetrics and Gynecology, Klinikum Wolfsburg, Wolfsburg, Germany
| | - Taymaa May
- Division of Gynecologic Oncology, University Health Network, Princess Margaret Hospital, Toronto, ON, Canada
| | - Håkan Olsson
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Jennifer B. Permuth
- Departments of Cancer Epidemiology and Gastrointestinal Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM-The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Susan J. Ramus
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Marjorie J. Riggan
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Harvey A. Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | | | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Lukasz M. Szafron
- Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Linda Titus
- Muskie School of Public Service, University of Southern Maine, Portland, ME, USA
| | - Cheryl L. Thompson
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - Robert A. Vierkant
- Department of Quantitative Health Sciences, Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Stacey J. Winham
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jennifer A. Doherty
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Andrew Berchuck
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Kate Lawrenson
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Ani W. Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Paul D.P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joellen M. Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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Pividori M, Rajagopal PS, Barbeira A, Liang Y, Melia O, Bastarache L, Park Y, Consortium GTE, Wen X, Im HK. PhenomeXcan: Mapping the genome to the phenome through the transcriptome. Sci Adv 2020; 6:6/37/eaba2083. [PMID: 32917697 DOI: 10.1126/sciadv.aba2083] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 07/29/2020] [Indexed: 05/02/2023]
Abstract
Large-scale genomic and transcriptomic initiatives offer unprecedented insight into complex traits, but clinical translation remains limited by variant-level associations without biological context and lack of analytic resources. Our resource, PhenomeXcan, synthesizes 8.87 million variants from genome-wide association study summary statistics on 4091 traits with transcriptomic data from 49 tissues in Genotype-Tissue Expression v8 into a gene-based, queryable platform including 22,515 genes. We developed a novel Bayesian colocalization method, fast enrichment estimation aided colocalization analysis (fastENLOC), to prioritize likely causal gene-trait associations. We successfully replicate associations from the phenome-wide association studies (PheWAS) catalog Online Mendelian Inheritance in Man, and an evidence-based curated gene list. Using PhenomeXcan results, we provide examples of novel and underreported genome-to-phenome associations, complex gene-trait clusters, shared causal genes between common and rare diseases via further integration of PhenomeXcan with ClinVar, and potential therapeutic targets. PhenomeXcan (phenomexcan.org) provides broad, user-friendly access to complex data for translational researchers.
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Affiliation(s)
- Milton Pividori
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Padma S Rajagopal
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Alvaro Barbeira
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Yanyu Liang
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Owen Melia
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Department of Medicine, Vanderbilt University, Nashville, TN, USA
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - YoSon Park
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.
| | - Hae K Im
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA.
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Scheunemann LP, Khalil R, Rajagopal PS, Arnold RM. Development and Pilot Testing of a Simulation to Study How Physicians Facilitate Surrogate Decision Making Based on Critically Ill Patients' Values and Preferences. J Pain Symptom Manage 2019; 57:216-223.e8. [PMID: 30408496 PMCID: PMC6348012 DOI: 10.1016/j.jpainsymman.2018.10.513] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 11/22/2022]
Abstract
CONTEXT There are no evidence-based programs to train physicians to facilitate shared decision making based on incapacitated intensive care unit patients' values and preferences. OBJECTIVES The objective of this study was to develop a high-fidelity simulation to fill this gap. METHODS Case development involved six steps: 1) drafting a case about an elderly patient receiving prolonged mechanical ventilation; 2) engaging an expert advisory board to optimize case content; 3) revising the case based on advisory board input; 4) training actors to portray the case patient's daughter; 5) obtaining physician feedback on the simulation; and 6) revising the case based on their feedback. We conducted a cross-sectional pilot study with 50 physicians to assess feasibility and acceptability, defined a priori as an enrollment rate >40 physicians/year, study procedures <75 minutes/participant, >95% actor adherence to standardization rules, and high physician ratings of realism and acceptability. RESULTS Advisory panel feedback yielded two modifications: 1) refocusing the case on decision making about tracheostomy and percutaneous gastrostomy and 2) making the patient's values more authentic. Physician feedback yielded two additional modifications: 1) reducing how readily the actor divulged the patient's values and 2) making her more emotional. All 50 physicians enrolled in the pilot study over 11 months completed study procedures in <75 minutes. Actor adherence to standardization rules was 95.8%. Physicians' mean ratings of realism and acceptability were 8.4 and 9.1, respectively, on a 10-point scale. CONCLUSION Simulation is feasible, is acceptable, and can be adequately standardized to study physicians' skills for facilitating surrogate decision making based on an incapacitated intensive care unit patient's values and preferences.
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Affiliation(s)
- Leslie P Scheunemann
- Division of Geriatric Medicine and Gerontology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
| | - Ramy Khalil
- St. Clair Hospital, Pittsburgh, Pennsylvania, USA
| | - Padma S Rajagopal
- Division of Hematology/Oncology, University of Chicago, Chicago, Illinois, USA
| | - Robert M Arnold
- Section of Palliative Care and Medical Ethics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Palliative and Supportive Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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Mathew A, Rajagopal PS, Villgran V, Sandhu GS, Jankowitz RC, Jacob M, Rosenzweig M, Oesterreich S, Brufsky A. Distinct Pattern of Metastases in Patients with Invasive Lobular Carcinoma of the Breast. Geburtshilfe Frauenheilkd 2017; 77:660-666. [PMID: 28757653 DOI: 10.1055/s-0043-109374] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/12/2017] [Accepted: 04/20/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Invasive lobular carcinoma (ILC) comprises around 10 - 15% of invasive breast cancers. Few prior studies have demonstrated a unique pattern of metastases between ILC and the more common invasive ductal carcinoma (IDC). To our knowledge, such data is limited to first sites of distant recurrence. We aimed to perform a comparison of the metastatic pattern of ILC and IDC at first distant recurrence as well as over the entire course of metastatic disease. METHODS We used a prospectively collated database of patients with metastatic breast cancer. Breast cancer recurrence or metastases were classified into various sites and a descriptive analysis was performed. RESULTS Among 761 patients, 88 (11.6%) were diagnosed with ILC and 673 (88.4%) with IDC. Patients with ILC showed more frequent metastases to the bone (56.8 vs. 37.7%, p = 0.001) and gastrointestinal (GI) tract (5.7 vs. 0.3%, p < 0.001) as first site of distant recurrence, and less to organs such as lung (5.7 vs. 24.2%, p < 0.001) and liver (4.6 vs. 11.4%, p = 0.049). Over the entire course of metastatic disease, more patients with ILC had ovarian (5.7 vs. 2.1%, p = 0.042) and GI tract metastases (8.0 vs. 0.6%, p < 0.001), also demonstrating reduced tendency to metastasize to the liver (20.5 vs. 49.0%, p < 0.001) and lung (23.9 vs. 51.9%, p < 0.001). All associations but bone held after sensitivity analysis on hormonal status. Although patients presenting with ILC were noted to have more advanced stage at presentation, recurrence-free survival in these patients was increased (4.8 years vs. 3.2 years, p = 0.017). However, overall survival was not (2.5 vs. 2.0 years, p = 0.75). CONCLUSION After accounting for hormone receptor status, patients with IDC had greater lung/pleura and liver involvement, while patients with ILC had a greater propensity to develop ovarian and GI metastases both at first site and overall. Clinicians can use this information to provide more directed screening for metastases; it also adds to the argument that these two variants of breast cancer should be managed as unique diseases.
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Affiliation(s)
- Aju Mathew
- University of Kentucky Markey Cancer Center, Lexington, KY, USA
| | - Padma S Rajagopal
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | | | - Gurprataap S Sandhu
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | | | - Mini Jacob
- Department of Physical Medicine & Rehabilitation, Harvard Medical School, Boston, MA, USA
| | | | | | - Adam Brufsky
- University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
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Partridge AH, Rosenberg SM, Rajagopal PS, Ruddy KJ, Tamimi RM, Schapira L, Come S, Borges V, Gelber S. Abstract P4-10-04: Employment trends in young women following a breast cancer diagnosis. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p4-10-04] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Workplace concerns are particularly salient for young women with breast cancer (BC), and a cancer diagnosis (dx) and treatment may affect their careers. We sought to evaluate the perceived impact of dx on employment, describe job changes, and identify factors associated with transition out of the workforce after dx of BC at a young age.
Methods: As part of an ongoing, multi-center cohort of young women diagnosed with BC at age ≤ 40, we surveyed women with early-stage BC about their pre- and post-dx employment status. Additional items assessed socio-demographic and treatment information; tumor characteristics were ascertained via pathology and medical record review. We used logistic regression to identify predictors of transitioning from pre-dx employment to unemployment at 1 year after dx. Among women employed 1 year after dx, we evaluated job satisfaction, perceived impact of dx on job performance, accommodations made by employers, and perceived likelihood of employment in the future.
Results: 76% of women (555/730) were employed both before dx and at 1 year; 13% were not employed at either time point; 7% were employed pre-dx but unemployed at 1 year; 4% were not employed prior to dx but reported employment at 1 year. Among women employed 1 year after dx, 74% (427/581) were somewhat or completely satisfied with their job. Only 6% said cancer or treatment limited their ability to perform their job quite a bit or very much; 38% said their ability was affected a little bit. Most (63%) said their employers had made accommodations for them, and almost all women (93%) said it was very likely they would be working in 1 year. In multivariable analyses (Table 1), women with stage 3 disease (vs. stage 1), were more likely to transition out of the workforce following dx, while women with a college or graduate degree (vs. no college degree) were less likely to transition out.
Conclusion: Most young women with early stage BC remain employed and report a willingness by their employer to make accommodations following a breast cancer dx. While few women reported that their dx or treatment limited their job performance, the finding that women with more advanced disease were more likely to transition out of the workforce suggests an impact of dx/treatment burden on employment. Women without a college degree were also at risk for unemployment post-dx, suggesting that job type, socioeconomic status, and environment affect employment outcomes. Attention to these subgroups of women is warranted to ensure that they are sufficiently supported given the potential adverse psychosocial and financial impacts of unemployment on patients, families, communities, and society.
Table 1. Multivariable analysis of factors associated with transition out of workforce 1year post-dx (N=634) OR (95% CI)Stage (ref=1) 04.52 (0.60-33.85)21.11 (0.48-2.58)34.05 (1.53-10.72)*White non-Hispanic (ref=non-WNH)1.47 (0.56-3.81)College graduate (ref=no college degree)0.44 (0.22-0.90)*Married/Living as married (ref=unmarried)0.95 (0.43-2.08)Parous (ref=nulliparous)1.75 (0.83-3.69)Age at diagnosis (years)0.98 (0.90-1.06)Mastectomy (ref=lumpectomy)1.74 (0.75-4.05)Endocrine therapy (ref=none)0.75 (0.41-1.39)Chemotherapy (ref=none)5.20 (0.93-29.22)Radiation (ref=none)1.38 (0.64-2.96)*p<0.05
Citation Format: Partridge AH, Rosenberg SM, Rajagopal PS, Ruddy KJ, Tamimi RM, Schapira L, Come S, Borges V, Gelber S. Employment trends in young women following a breast cancer diagnosis. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-10-04.
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Affiliation(s)
- AH Partridge
- Dana-Farber Cancer Institute; University of Pittsburgh Medical Center; Mayo Clinic; Channing Division of Network Medicine, Brigham and Women's Hospital; Massachusetts General Hospital; Beth Israel Deaconess Medical Center; University of Colorado Cancer Center
| | - SM Rosenberg
- Dana-Farber Cancer Institute; University of Pittsburgh Medical Center; Mayo Clinic; Channing Division of Network Medicine, Brigham and Women's Hospital; Massachusetts General Hospital; Beth Israel Deaconess Medical Center; University of Colorado Cancer Center
| | - PS Rajagopal
- Dana-Farber Cancer Institute; University of Pittsburgh Medical Center; Mayo Clinic; Channing Division of Network Medicine, Brigham and Women's Hospital; Massachusetts General Hospital; Beth Israel Deaconess Medical Center; University of Colorado Cancer Center
| | - KJ Ruddy
- Dana-Farber Cancer Institute; University of Pittsburgh Medical Center; Mayo Clinic; Channing Division of Network Medicine, Brigham and Women's Hospital; Massachusetts General Hospital; Beth Israel Deaconess Medical Center; University of Colorado Cancer Center
| | - RM Tamimi
- Dana-Farber Cancer Institute; University of Pittsburgh Medical Center; Mayo Clinic; Channing Division of Network Medicine, Brigham and Women's Hospital; Massachusetts General Hospital; Beth Israel Deaconess Medical Center; University of Colorado Cancer Center
| | - L Schapira
- Dana-Farber Cancer Institute; University of Pittsburgh Medical Center; Mayo Clinic; Channing Division of Network Medicine, Brigham and Women's Hospital; Massachusetts General Hospital; Beth Israel Deaconess Medical Center; University of Colorado Cancer Center
| | - S Come
- Dana-Farber Cancer Institute; University of Pittsburgh Medical Center; Mayo Clinic; Channing Division of Network Medicine, Brigham and Women's Hospital; Massachusetts General Hospital; Beth Israel Deaconess Medical Center; University of Colorado Cancer Center
| | - V Borges
- Dana-Farber Cancer Institute; University of Pittsburgh Medical Center; Mayo Clinic; Channing Division of Network Medicine, Brigham and Women's Hospital; Massachusetts General Hospital; Beth Israel Deaconess Medical Center; University of Colorado Cancer Center
| | - S Gelber
- Dana-Farber Cancer Institute; University of Pittsburgh Medical Center; Mayo Clinic; Channing Division of Network Medicine, Brigham and Women's Hospital; Massachusetts General Hospital; Beth Israel Deaconess Medical Center; University of Colorado Cancer Center
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Leow JJ, Martin-Doyle W, Rajagopal PS, Patel CG, Anderson EM, Rothman AT, Cote RJ, Urun Y, Chang SL, Choueiri TK, Bellmunt J. Adjuvant chemotherapy for invasive bladder cancer: a 2013 updated systematic review and meta-analysis of randomized trials. Eur Urol 2013; 66:42-54. [PMID: 24018020 DOI: 10.1016/j.eururo.2013.08.033] [Citation(s) in RCA: 254] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/13/2013] [Indexed: 12/21/2022]
Abstract
CONTEXT The role of adjuvant chemotherapy remains poorly defined for the management of muscle-invasive bladder cancer (MIBC). The last meta-analysis evaluating adjuvant chemotherapy, conducted in 2005, had limited power to fully support its use. OBJECTIVE To update the current evidence of the benefit of postoperative adjuvant cisplatin-based chemotherapy compared with control (ie, surgery alone) in patients with MIBC. EVIDENCE ACQUISITION A comprehensive literature review was performed to identify all randomized controlled trials (RCTs) comparing adjuvant cisplatin-based chemotherapy with control for patients with MIBC. The search included the Medline, Embase, Cochrane Central Register of Controlled Trials databases, and abstracts from the American Society of Clinical Oncology meetings up to May 2013. An updated systematic review and meta-analysis was performed. EVIDENCE SYNTHESIS A total of 945 patients included in nine RCTs (five previously analyzed, one updated, and three new) were examined. For overall survival, the pooled hazard ratio (HR) across all nine trials was 0.77 (95% confidence interval [CI], 0.59-0.99; p=0.049). For disease-free survival, the pooled HR across seven trials reporting this outcome was 0.66 (95% CI, 0.45-0.91; p=0.014). This disease-free survival benefit was more apparent among those with positive nodal involvement (p=0.010). CONCLUSIONS This updated and improved meta-analysis of randomized trials provides further evidence of an overall survival and disease-free survival benefit in patients with MIBC receiving adjuvant cisplatin-based chemotherapy after radical cystectomy.
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Affiliation(s)
- Jeffrey J Leow
- Harvard School of Public Health, Harvard University, Boston, MA, USA; Center for Surgery and Public Health, Brigham and Women's Hospital, Boston, MA, USA; Division of Urology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Padma S Rajagopal
- Harvard School of Public Health, Harvard University, Boston, MA, USA
| | - Chirayu G Patel
- Harvard School of Public Health, Harvard University, Boston, MA, USA
| | - Erin M Anderson
- Harvard School of Public Health, Harvard University, Boston, MA, USA
| | - Andrew T Rothman
- Harvard School of Public Health, Harvard University, Boston, MA, USA
| | - Richard J Cote
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Yuksel Urun
- Bladder Cancer Center, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - Steven L Chang
- Center for Surgery and Public Health, Brigham and Women's Hospital, Boston, MA, USA; Division of Urology, Brigham and Women's Hospital, Boston, MA, USA
| | - Toni K Choueiri
- Bladder Cancer Center, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - Joaquim Bellmunt
- Bladder Cancer Center, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA; University Hospital del Mar-IMIM, Barcelona, Spain.
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