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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] [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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Asano S, Ono A, Baba K, Uehara T, Sakamoto K, Hayata-Takano A, Nakazawa T, Yanamoto S, Tanimoto K, Hashimoto H, Ago Y. Blockade of vasoactive intestinal peptide receptor 2 (VIPR2) signaling suppresses cyclin D1-dependent cell-cycle progression in MCF-7 cells. J Pharmacol Sci 2024; 154:139-147. [PMID: 38395514 DOI: 10.1016/j.jphs.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/28/2023] [Accepted: 01/05/2024] [Indexed: 02/25/2024] Open
Abstract
Vasoactive intestinal peptide (VIP) receptor 2 (VIPR2) is a G protein-coupled receptor that binds to Gαs, Gαi, and Gαq proteins to regulate various downstream signaling molecules, such as protein kinase A (PKA), phosphatidylinositol 3-kinase (PI3K), and phospholipase C. In this study, we examined the role of VIPR2 in cell cycle progression. KS-133, a newly developed VIPR2-selective antagonist peptide, attenuated VIP-induced cell proliferation in MCF-7 cells. The percentage of cells in the S-M phase was decreased in MCF-7 cells treated with KS-133. KS-133 in the presence of VIP decreased the phosphorylation of extracellular signal-regulated kinase (ERK), AKT, and glycogen synthase kinase-3β (GSK3β), resulting in a decrease in cyclin D1 levels. In MCF-7 cells stably-expressing VIPR2, KS-133 decreased PI3K activity and cAMP levels. Treatment with the ERK-specific kinase (MEK) inhibitor U0126 and the class I PI3K inhibitor ZSTK474 decreased the percentage of cells in the S phase. KS-133 reduced the percentage of cells in the S phase more than treatment with U0126 or ZSTK474 alone and did not affect the effect of the mixture of these inhibitors. Our findings suggest that VIPR2 signaling regulates cyclin D1 levels through the cAMP/PKA/ERK and PI3K/AKT/GSK3β pathways, and mediates the G1/S transition to control cell proliferation.
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Affiliation(s)
- Satoshi Asano
- Department of Cellular and Molecular Pharmacology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan; School of Dentistry, Hiroshima University, Hiroshima, 734-8553, Japan.
| | - Ami Ono
- Department of Cellular and Molecular Pharmacology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan; Department of Orthodontics and Craniofacial Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Kaede Baba
- School of Dentistry, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Teru Uehara
- Department of Cellular and Molecular Pharmacology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan; Department of Oral Oncology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Kotaro Sakamoto
- Research & Development Department, Ichimaru Pharcos Company Limited, 318-1 Asagi, Motosu, Gifu, 501-0475, Japan
| | - Atsuko Hayata-Takano
- Department of Pharmacology, Graduate School of Dentistry, Osaka University, Suita, Osaka, 565-0871, Japan; Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 565-0871, Japan; Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, University of Fukui, Osaka, 565-0871, Japan
| | - Takanobu Nakazawa
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 565-0871, Japan; Laboratory of Molecular Biology, Department of Bioscience, Graduate School of Life Sciences, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Souichi Yanamoto
- School of Dentistry, Hiroshima University, Hiroshima, 734-8553, Japan; Department of Oral Oncology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Kotaro Tanimoto
- School of Dentistry, Hiroshima University, Hiroshima, 734-8553, Japan; Department of Orthodontics and Craniofacial Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Hitoshi Hashimoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 565-0871, Japan; Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, University of Fukui, Osaka, 565-0871, Japan; Division of Bioscience, Institute for Datability Science, Osaka University, Osaka, 565-0871, Japan; Transdimensional Life Imaging Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, 565-0871, Japan; Department of Molecular Pharmaceutical Science, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Yukio Ago
- Department of Cellular and Molecular Pharmacology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan; School of Dentistry, Hiroshima University, Hiroshima, 734-8553, Japan.
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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