1
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Adebayo AK, Bhat-Nakshatri P, Davis C, Angus SP, Erdogan C, Gao H, Green N, Kumar B, Liu Y, Nakshatri H. Oxygen tension-dependent variability in the cancer cell kinome impacts signaling pathways and response to targeted therapies. iScience 2024; 27:110068. [PMID: 38872973 PMCID: PMC11170190 DOI: 10.1016/j.isci.2024.110068] [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: 12/15/2023] [Revised: 04/05/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024] Open
Abstract
Most cells in solid tumors are exposed to oxygen levels between 0.5% and 5%. We developed an approach that allows collection, processing, and evaluation of cancer and non-cancer cells under physioxia, while preventing exposure to ambient air. This aided comparison of baseline and drug-induced changes in signaling pathways under physioxia and ambient oxygen. Using tumor cells from transgenic models of breast cancer and cells from breast tissues of clinically breast cancer-free women, we demonstrate oxygen-dependent differences in cell preference for epidermal growth factor receptor (EGFR) or platelet-derived growth factor receptor beta (PDGFRβ) signaling. Physioxia caused PDGFRβ-mediated activation of AKT and extracellular regulated kinase (ERK) that reduced sensitivity to EGFR and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) inhibition and maintained PDGFRβ+ epithelial-mesenchymal hybrid cells with potential cancer stem cell (CSC) properties. Cells in ambient air displayed differential EGFR activation and were more sensitive to targeted therapies. Our data emphasize the importance of oxygen considerations in preclinical cancer research to identify effective drug targets and develop combination therapy regimens.
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Affiliation(s)
- Adedeji K. Adebayo
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Christopher Davis
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Steven P. Angus
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Cihat Erdogan
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hongyu Gao
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Nick Green
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Brijesh Kumar
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yunlong Liu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Roudebush VA Medical Center, Indianapolis, IN 46202, USA
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2
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Goyette MA, Stevens LE, DePinho CR, Seehawer M, Nishida J, Li Z, Wilde CM, Li R, Qiu X, Pyke AL, Zhao S, Lim K, Tender GS, Northey JJ, Riley NM, Long HW, Bertozzi CR, Weaver VM, Polyak K. Cancer-stromal cell interactions in breast cancer brain metastases induce glycocalyx-mediated resistance to HER2-targeting therapies. Proc Natl Acad Sci U S A 2024; 121:e2322688121. [PMID: 38709925 PMCID: PMC11098130 DOI: 10.1073/pnas.2322688121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/27/2024] [Indexed: 05/08/2024] Open
Abstract
Brain metastatic breast cancer is particularly lethal largely due to therapeutic resistance. Almost half of the patients with metastatic HER2-positive breast cancer develop brain metastases, representing a major clinical challenge. We previously described that cancer-associated fibroblasts are an important source of resistance in primary tumors. Here, we report that breast cancer brain metastasis stromal cell interactions in 3D cocultures induce therapeutic resistance to HER2-targeting agents, particularly to the small molecule inhibitor of HER2/EGFR neratinib. We investigated the underlying mechanisms using a synthetic Notch reporter system enabling the sorting of cancer cells that directly interact with stromal cells. We identified mucins and bulky glycoprotein synthesis as top-up-regulated genes and pathways by comparing the gene expression and chromatin profiles of stroma-contact and no-contact cancer cells before and after neratinib treatment. Glycoprotein gene signatures were also enriched in human brain metastases compared to primary tumors. We confirmed increased glycocalyx surrounding cocultures by immunofluorescence and showed that mucinase treatment increased sensitivity to neratinib by enabling a more efficient inhibition of EGFR/HER2 signaling in cancer cells. Overexpression of truncated MUC1 lacking the intracellular domain as a model of increased glycocalyx-induced resistance to neratinib both in cell culture and in experimental brain metastases in immunodeficient mice. Our results highlight the importance of glycoproteins as a resistance mechanism to HER2-targeting therapies in breast cancer brain metastases.
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Affiliation(s)
- Marie-Anne Goyette
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA02115
| | - Laura E. Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA02115
| | - Carolyn R. DePinho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA02115
| | - Jun Nishida
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA02115
| | - Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA02115
| | - Callahan M. Wilde
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
| | - Rong Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA02215
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA02215
| | - Alanna L. Pyke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
| | - Stephanie Zhao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA02215
| | | | - Jason J. Northey
- Center for Bioengineering and Tissue Regeneration, University of California San Francisco, San Francisco, CA94143
| | | | - Henry W. Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA02215
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA94305
- HHMI, Stanford University, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Valerie M. Weaver
- Center for Bioengineering and Tissue Regeneration, University of California San Francisco, San Francisco, CA94143
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94143
- Department of Surgery, University of California San Francisco, San Francisco, CA94143
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA94143
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA94143
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA94143
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA02115
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3
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Ji D, Shao C, Yu J, Hou Y, Gao X, Wu Y, Wang L, Chen P. FOXA1 forms biomolecular condensates that unpack condensed chromatin to function as a pioneer factor. Mol Cell 2024; 84:244-260.e7. [PMID: 38101414 DOI: 10.1016/j.molcel.2023.11.020] [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: 06/12/2023] [Revised: 09/14/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
Eukaryotic DNA is packaged into chromatin in the nucleus, restricting the binding of transcription factors (TFs) to their target DNA sites. FOXA1 functions as a pioneer TF to bind condensed chromatin and initiate the opening of local chromatin for gene expression. However, the principles of FOXA1 recruitment and how it subsequently unpacks the condensed chromatin remain elusive. Here, we revealed that FOXA1 intrinsically forms submicron-sized condensates through its N- and C-terminal intrinsically disordered regions (IDRs). Notably, both IDRs enable FOXA1 to dissolve the condensed chromatin. In addition, the DNA-binding capacity of FOXA1 contributes to its ability to both form condensates and dissolve condensed chromatin. Further genome-wide investigation showed that IDRs enable FOXA1 to bind and unpack the condensed chromatin to regulate the proliferation and migration of breast cancer cells. This work provides a principle of how pioneer TFs function to initiate competent chromatin states using their IDRs.
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Affiliation(s)
- Dengyu Ji
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Changrong Shao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaoyao Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xiao Gao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Yichuan Wu
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Liang Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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4
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Hermawan A, Wulandari F, Yudi Utomo R, Asmah Susidarti R, Kirihata M, Meiyanto E. Transcriptomics analyses reveal the effects of Pentagamaboronon-0-ol on PI3K/Akt and cell cycle of HER2+ breast cancer cells. Saudi Pharm J 2023; 31:101847. [PMID: 38028209 PMCID: PMC10652209 DOI: 10.1016/j.jsps.2023.101847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Monoclonal antibodies and targeted therapies against HER2+ breast cancer has improved overall and disease-free survival in patients; however, encountering drug resistance causes recurrence, necessitating the development of newer HER2-targeted medications. A curcumin analog PGB-0-ol showed most cytotoxicity against HCC1954 HER2+ breast cancer cells than against other subtypes of breast cancer cells. Objective Here, we employed next-generation sequencing technology to elucidate the molecular mechanism underlying the effect of PGB-0-ol on HCC1954 HER2+ breast cancer cells. Methods The molecular mechanism underlying the action of PGB-0-ol on HCC1954 HER2+ breast cancer cells was determined using next-generation sequencing technologies. Additional bioinformatics studies were performed, including gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, disease-gene, and drug-gene associations, network topology analysis (NTA), and gene set enrichment analysis (GSEA). Results We detected 2,263 differentially expressed genes (DEGs) (1,459 upregulated and 804 downregulated) in the PGB-0-ol- and DMSO-treated HCC1954 cells. KEGG enrichment data revealed the control of phosphatidylinositol signaling system, and ErbB signaling following PGB-0-ol treatment. Gene ontology (GO) enrichment analysis demonstrated that these DEGs governed cell cycle, participated in the mitotic spindle and nuclear membrane, and controlled kinase activity at the molecular level. According to the NTA data for GO enrichment, GSEA data for KEGG, drug-gene and disease-gene, PGB-0-ol regulated PI3K/Akt signaling and cell cycle in breast cancer. Overall, our investigation revealed the transcriptomic profile of PGB-0-ol-treated HCC1954 breast cancer cells following PGB-0-ol therapy. Bioinformatics analyses showed that PI3K/Akt signaling and cell cycle was modulated. However, further studies are required to validate the findings of this study.
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Affiliation(s)
- Adam Hermawan
- Laboratory of Macromolecular Engineering, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia
- Cancer Chemoprevention Research Center, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia
- Laboratory of Advanced Pharmaceutical Sciences. APSLC Building, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia
| | - Febri Wulandari
- Cancer Chemoprevention Research Center, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia
| | - Rohmad Yudi Utomo
- Cancer Chemoprevention Research Center, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia
| | - Ratna Asmah Susidarti
- Cancer Chemoprevention Research Center, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia
| | - Mitsunori Kirihata
- Research Center for BNCT, Osaka Metropolitan University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka 599-8570, Japan
| | - Edy Meiyanto
- Laboratory of Macromolecular Engineering, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia
- Cancer Chemoprevention Research Center, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia
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5
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Flint AC, Mitchell DK, Angus SP, Smith AE, Bessler W, Jiang L, Mang H, Li X, Lu Q, Rodriguez B, Sandusky GE, Masters AR, Zhang C, Dang P, Koenig J, Johnson GL, Shen W, Liu J, Aggarwal A, Donoho GP, Willard MD, Bhagwat SV, Wade Clapp D, Rhodes SD. Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma. Clin Cancer Res 2023; 29:3438-3456. [PMID: 37406085 PMCID: PMC11060649 DOI: 10.1158/1078-0432.ccr-22-2854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/06/2023] [Accepted: 06/29/2023] [Indexed: 07/07/2023]
Abstract
PURPOSE Plexiform neurofibromas (PNF) are peripheral nerve sheath tumors that cause significant morbidity in persons with neurofibromatosis type 1 (NF1), yet treatment options remain limited. To identify novel therapeutic targets for PNF, we applied an integrated multi-omic approach to quantitatively profile kinome enrichment in a mouse model that has predicted therapeutic responses in clinical trials for NF1-associated PNF with high fidelity. EXPERIMENTAL DESIGN Utilizing RNA sequencing combined with chemical proteomic profiling of the functionally enriched kinome using multiplexed inhibitor beads coupled with mass spectrometry, we identified molecular signatures predictive of response to CDK4/6 and RAS/MAPK pathway inhibition in PNF. Informed by these results, we evaluated the efficacy of the CDK4/6 inhibitor, abemaciclib, and the ERK1/2 inhibitor, LY3214996, alone and in combination in reducing PNF tumor burden in Nf1flox/flox;PostnCre mice. RESULTS Converging signatures of CDK4/6 and RAS/MAPK pathway activation were identified within the transcriptome and kinome that were conserved in both murine and human PNF. We observed robust additivity of the CDK4/6 inhibitor, abemaciclib, in combination with the ERK1/2 inhibitor, LY3214996, in murine and human NF1(Nf1) mutant Schwann cells. Consistent with these findings, the combination of abemaciclib (CDK4/6i) and LY3214996 (ERK1/2i) synergized to suppress molecular signatures of MAPK activation and exhibited enhanced antitumor activity in Nf1flox/flox;PostnCre mice in vivo. CONCLUSIONS These findings provide rationale for the clinical translation of CDK4/6 inhibitors alone and in combination with therapies targeting the RAS/MAPK pathway for the treatment of PNF and other peripheral nerve sheath tumors in persons with NF1.
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Affiliation(s)
- Alyssa C. Flint
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dana K. Mitchell
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Steven P. Angus
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center
| | - Abbi E. Smith
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Waylan Bessler
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Li Jiang
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Henry Mang
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xiaohong Li
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Qingbo Lu
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Brooke Rodriguez
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - George E. Sandusky
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andi R. Masters
- Clinical Pharmacology Analytical Core, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chi Zhang
- Center for Computational Biology and Bioinformatics and Department of Medical and Molecular Genetics, Indiana University School of Medicine
| | - Pengtao Dang
- Center for Computational Biology and Bioinformatics and Department of Medical and Molecular Genetics, Indiana University School of Medicine
| | - Jenna Koenig
- Medical Scientist Training Program, Indiana University School of Medicine, Indianapolis, IN USA
| | - Gary L. Johnson
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Weihua Shen
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Jiangang Liu
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Amit Aggarwal
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Gregory P. Donoho
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Melinda D. Willard
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Shripad V. Bhagwat
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - D. Wade Clapp
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center
| | - Steven D. Rhodes
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center
- Division of Pediatric Hematology-Oncology, Indiana University School of Medicine, Indianapolis, IN, USA
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6
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Lin D, Xu W, Hong P, Wu C, Zhang Z, Zhang S, Xing L, Yang B, Zhou W, Xiao Q, Wang J, Wang C, He Y, Chen X, Cao X, Man J, Reheman A, Wu X, Hao X, Hu Z, Chen C, Cao Z, Yin R, Fu ZF, Zhou R, Teng Z, Li G, Cao G. Decoding the spatial chromatin organization and dynamic epigenetic landscapes of macrophage cells during differentiation and immune activation. Nat Commun 2022; 13:5857. [PMID: 36195603 PMCID: PMC9532393 DOI: 10.1038/s41467-022-33558-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 09/22/2022] [Indexed: 11/09/2022] Open
Abstract
Immunocytes dynamically reprogram their gene expression profiles during differentiation and immunoresponse. However, the underlying mechanism remains elusive. Here, we develop a single-cell Hi-C method and systematically delineate the 3D genome and dynamic epigenetic atlas of macrophages during these processes. We propose "degree of disorder" to measure genome organizational patterns inside topologically-associated domains, which is correlated with the chromatin epigenetic states, gene expression, and chromatin structure variability in individual cells. Furthermore, we identify that NF-κB initiates systematic chromatin conformation reorganization upon Mycobacterium tuberculosis infection. The integrated Hi-C, eQTL, and GWAS analysis depicts the atlas of the long-range target genes of mycobacterial disease susceptible loci. Among these, the SNP rs1873613 is located in the anchor of a dynamic chromatin loop with LRRK2, whose inhibitor AdoCbl could be an anti-tuberculosis drug candidate. Our study provides comprehensive resources for the 3D genome structure of immunocytes and sheds insights into the order of genome organization and the coordinated gene transcription during immunoresponse.
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Affiliation(s)
- Da Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Weize Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Ping Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, China.,College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Chengchao Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhihui Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Siheng Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lingyu Xing
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Bing Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wei Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Qin Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Jinyue Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Cong Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yu He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xi Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaojian Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jiangwei Man
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Aikebaier Reheman
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,College of Animal Science and Technology, Tarim University, Alar, China
| | - Xiaofeng Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xingjie Hao
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhe Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Chunli Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Guizhou University, Guiyang, China
| | - Zimeng Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China.,College of Animal Sciences, Yangtze River University, Jingzhou, China
| | - Rong Yin
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhen F Fu
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Rong Zhou
- Dapartment of Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhaowei Teng
- The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. .,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, China. .,College of Informatics, Huazhong Agricultural University, Wuhan, China.
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China. .,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. .,College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China.
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7
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Ayipo YO, Ajiboye AT, Osunniran WA, Jimoh AA, Mordi MN. Epigenetic oncogenesis, biomarkers and emerging chemotherapeutics for breast cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194873. [PMID: 36064110 DOI: 10.1016/j.bbagrm.2022.194873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/20/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Breast cancer remains one of the leading causes of cancer-related deaths globally and the most prominent among females, yet with limited effective therapeutic options. Most of the current medications are challenged by various factors including low efficacy, incessant resistance, immune evasion and frequent recurrence of the disease. Further understanding of the prognosis and identification of plausible therapeutic channels thus requires multimodal approaches. In this review, epigenetics studies of several pathways to BC oncogenesis via the inducement of oncogenic changes on relevant markers have been overviewed. Similarly, the counter-epigenetic mechanisms to reverse such changes as effective therapeutic strategies were surveyed. The epigenetic oncogenesis occurs through several pathways, notably, DNMT-mediated hypermethylation of DNA, dysregulated expression for ERα, HER2/ERBB and PR, histone modification, overexpression of transcription factors including the CDK9-cyclin T1 complex and suppression of tumour suppressor genes. Scientifically, the regulatory reversal of the mechanisms constitutes effective epigenetic approaches for mitigating BC initiation, progression and metastasis. These were exhibited at various experimental levels by classical chemotherapeutic agents including some repurposable drugs, endocrine inhibitors, monoclonal antibodies and miRNAs, natural products, metal complexes and nanoparticles. Dozens of the potential candidates are currently in clinical trials while others are still at preclinical experimental stages showing promising anti-BC efficacy. The review presents a model for a wider understanding of epigenetic oncogenic pathways to BC and reveals plausible channels for reversing the unpleasant changes through epigenetic modifications. It advances the science of therapeutic designs for ameliorating the global burden of BC upon further translational studies.
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Affiliation(s)
- Yusuf Oloruntoyin Ayipo
- Centre for Drug Research, Universiti Sains Malaysia, USM, 11800 Pulau Pinang, Malaysia; Department of Chemistry and Industrial Chemistry, Kwara State University, P.M.B., Malete, 1530 Ilorin, Nigeria.
| | - Abdulfatai Temitope Ajiboye
- Department of Chemistry and Industrial Chemistry, Kwara State University, P.M.B., Malete, 1530 Ilorin, Nigeria
| | - Wahab Adesina Osunniran
- Department of Chemistry and Industrial Chemistry, Kwara State University, P.M.B., Malete, 1530 Ilorin, Nigeria
| | - Akeem Adebayo Jimoh
- Department of Chemistry and Industrial Chemistry, Kwara State University, P.M.B., Malete, 1530 Ilorin, Nigeria
| | - Mohd Nizam Mordi
- Centre for Drug Research, Universiti Sains Malaysia, USM, 11800 Pulau Pinang, Malaysia
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8
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FOXA1 in Breast Cancer: A Luminal Marker with Promising Prognostic and Predictive Impact. Cancers (Basel) 2022; 14:cancers14194699. [PMID: 36230619 PMCID: PMC9564251 DOI: 10.3390/cancers14194699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
The present review focuses on the function of the forkhead protein FOXA1 in breast cancer (BC) in relation to steroid hormone receptors. We explored the currently available analytic approaches for FOXA1 assessment both at gene and protein levels, comparing the differences between the available techniques used for its diagnostic assessment. In addition, we elaborated on data regarding the prognostic and predictive role of this marker in BC based on several studies that evaluated its expression in relation to the outcome and/or response to therapy. FOXA1, similar to the androgen receptor (AR), may have a dual role in BC according to hormonal status. In luminal cancers, its expression contributes to a better prognosis, while in triple-negative breast cancers (TNBC), it implies an adverse outcome. Consequently, we observed that FOXA1-positive expression in a neoadjuvant setting may predict a lack of response in luminal BC as opposed to TNBC, in which FOXA1 allegedly increases its chemosensitivity. In conclusion, considering its accessible and convenient identification by immunohistochemistry, its important impact on prognosis, and its suitability to identify patients with different responses to chemotherapy, we propose that FOXA1 could be tested in routine diagnostics as an additional prognostic and predictive marker in BC.
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9
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East MP, Johnson GL. Adaptive chromatin remodeling and transcriptional changes of the functional kinome in tumor cells in response to targeted kinase inhibition. J Biol Chem 2021; 298:101525. [PMID: 34958800 PMCID: PMC8888345 DOI: 10.1016/j.jbc.2021.101525] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Pharmacological inhibition of protein kinases induces adaptive reprogramming of tumor cell regulatory networks by altering expression of genes that regulate signaling, including protein kinases. Adaptive responses are dependent on transcriptional changes resulting from remodeling of enhancer and promoter landscapes. Enhancer and promoter remodeling in response to targeted kinase inhibition is controlled by changes in open chromatin state and by activity of specific transcription factors, such as c-MYC. This review focuses on the dynamic plasticity of protein kinase expression of the tumor cell kinome and the resulting adaptive resistance to targeted kinase inhibition. Plasticity of the functional kinome has been shown in patient window trials where triple-negative and human epidermal growth factor receptor 2–positive breast cancer patient tumors were characterized by RNAseq after biopsies before and after 1 week of therapy. The expressed kinome changed dramatically during drug treatment, and these changes in kinase expression were shown in cell lines and xenografts in mice to be correlated with adaptive tumor cell drug resistance. The dynamic transcriptional nature of the kinome also differs for inhibitors targeting different kinase signaling pathways (e.g., BRAF-MEK-ERK versus PI3K-AKT) that are commonly activated in cancers. Heterogeneity arising from differences in gene regulation and mutations represents a challenge to therapeutic durability and prevention of clinical drug resistance with drug-tolerant tumor cell populations developing and persisting through treatment. We conclude that understanding the heterogeneity of kinase expression at baseline and in response to therapy is imperative for development of combinations and timing intervals of therapies making interventions durable.
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Affiliation(s)
- Michael P East
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Gary L Johnson
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.
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10
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Seachrist DD, Anstine LJ, Keri RA. FOXA1: A Pioneer of Nuclear Receptor Action in Breast Cancer. Cancers (Basel) 2021; 13:cancers13205205. [PMID: 34680352 PMCID: PMC8533709 DOI: 10.3390/cancers13205205] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 12/26/2022] Open
Abstract
The pioneering function of FOXA1 establishes estrogen-responsive transcriptomes in luminal breast cancer. Dysregulated FOXA1 chromatin occupancy through focal amplification, mutation, or cofactor recruitment modulates estrogen receptor (ER) transcriptional programs and drives endocrine-resistant disease. However, ER is not the sole nuclear receptor (NR) expressed in breast cancers, nor is it the only NR for which FOXA1 serves as a licensing factor. Receptors for androgens, glucocorticoids, and progesterone are also found in the majority of breast cancers, and their functions are also impacted by FOXA1. These NRs interface with ER transcriptional programs and, depending on their activation level, can reprogram FOXA1-ER cistromes. Thus, NR interplay contributes to endocrine therapy response and resistance and may provide a vulnerability for future therapeutic benefit in patients. Herein, we review what is known regarding FOXA1 regulation of NR function in breast cancer in the context of cell identity, endocrine resistance, and NR crosstalk in breast cancer progression and treatment.
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Affiliation(s)
- Darcie D. Seachrist
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
| | - Lindsey J. Anstine
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ruth A. Keri
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
- Department of Cancer Biology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence:
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FOXA1 of regulatory variant associated with risk of breast cancer through allele-specific enhancer in the Chinese population. Breast Cancer 2021; 29:247-259. [PMID: 34635981 DOI: 10.1007/s12282-021-01305-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/07/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND FOXA1 is a pioneer transcription factor which has been established as a carcinogenic factor and can regulate the expression of downstream target genes in breast cancer. We hypothesized that genetic variants modulating FOXA1 expression might play a role in the risk of breast cancer. METHODS Physical interaction predicted by PreSTIGE analysis and CHIA-PET data integration with cis-expression quantitative trait loci (cis-eQTL) based SNP-FOXA1 analysis were used to identify potentially regulatory variants modulating the expression of FOXA1. Then, we utilized a case-control study consisting of 855 new diagnosed breast cancer cases and 920 controls in the Chinese population to identify breast cancer associated variants. Biological assays were conducted in breast cancer cell lines to illustrate the effects of associated variants on breast cancer risk. RESULTS We identified that rs7160774 G > A variant was associated with lower risk of breast cancer (OR = 0.77, 95% confidence interval = 0.62-0.96, P = 0.022). Biological experiments indicated that rs7160774[A] allele down-regulated the expression of FOXA1 compared to the G allele by influencing transcription factor binding affinity, thus playing an important role in the development of breast cancer. CONCLUSION Our study suggested that the regulatory variant rs7160774 was associated with risk of breast cancer by long-range modulating FOXA1 expression and provided critical insights into pinpoint causal genetic variants.
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12
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New strategies for targeting kinase networks in cancer. J Biol Chem 2021; 297:101128. [PMID: 34461089 PMCID: PMC8449055 DOI: 10.1016/j.jbc.2021.101128] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 12/18/2022] Open
Abstract
Targeted strategies against specific driver molecules of cancer have brought about many advances in cancer treatment since the early success of the first small-molecule inhibitor Gleevec. Today, there are a multitude of targeted therapies approved by the Food and Drug Administration for the treatment of cancer. However, the initial efficacy of virtually every targeted treatment is often reversed by tumor resistance to the inhibitor through acquisition of new mutations in the target molecule, or reprogramming of the epigenome, transcriptome, or kinome of the tumor cells. At the core of this clinical problem lies the assumption that targeted treatments will only be efficacious if the inhibitors are used at their maximum tolerated doses. Such aggressive regimens create strong selective pressure on the evolutionary progression of the tumor, resulting in resistant cells. High-dose single agent treatments activate alternative mechanisms that bypass the inhibitor, while high-dose combinatorial treatments suffer from increased toxicity resulting in treatment cessation. Although there is an arsenal of targeted agents being tested clinically and preclinically, identifying the most effective combination treatment plan remains a challenge. In this review, we discuss novel targeted strategies with an emphasis on the recent cross-disciplinary studies demonstrating that it is possible to achieve antitumor efficacy without increasing toxicity by adopting low-dose multitarget approaches to treatment of cancer and metastasis.
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