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López-Mejía JA, Mantilla-Ollarves JC, Rocha-Zavaleta L. Modulation of JAK-STAT Signaling by LNK: A Forgotten Oncogenic Pathway in Hormone Receptor-Positive Breast Cancer. Int J Mol Sci 2023; 24:14777. [PMID: 37834225 PMCID: PMC10573125 DOI: 10.3390/ijms241914777] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Breast cancer remains the most frequently diagnosed cancer in women worldwide. Tumors that express hormone receptors account for 75% of all cases. Understanding alternative signaling cascades is important for finding new therapeutic targets for hormone receptor-positive breast cancer patients. JAK-STAT signaling is commonly activated in hormone receptor-positive breast tumors, inducing inflammation, proliferation, migration, and treatment resistance in cancer cells. In hormone receptor-positive breast cancer, the JAK-STAT cascade is stimulated by hormones and cytokines, such as prolactin and IL-6. In normal cells, JAK-STAT is inhibited by the action of the adaptor protein, LNK. However, the role of LNK in breast tumors is not fully understood. This review compiles published reports on the expression and activation of the JAK-STAT pathway by IL-6 and prolactin and potential inhibition of the cascade by LNK in hormone receptor-positive breast cancer. Additionally, it includes analyses of available datasets to determine the level of expression of LNK and various members of the JAK-STAT family for the purpose of establishing associations between expression and clinical outcomes. Together, experimental evidence and in silico studies provide a better understanding of the potential implications of the JAK-STAT-LNK loop in hormone receptor-positive breast cancer progression.
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Affiliation(s)
- José A. López-Mejía
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 03100, Mexico; (J.A.L.-M.); (J.C.M.-O.)
| | - Jessica C. Mantilla-Ollarves
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 03100, Mexico; (J.A.L.-M.); (J.C.M.-O.)
| | - Leticia Rocha-Zavaleta
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 03100, Mexico; (J.A.L.-M.); (J.C.M.-O.)
- Programa Institucional de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 03100, Mexico
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2
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Tapia JL, McDonough JC, Cauble EL, Gonzalez CG, Teteh DK, Treviño LS. Parabens Promote Protumorigenic Effects in Luminal Breast Cancer Cell Lines With Diverse Genetic Ancestry. J Endocr Soc 2023; 7:bvad080. [PMID: 37409182 PMCID: PMC10318621 DOI: 10.1210/jendso/bvad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Indexed: 07/07/2023] Open
Abstract
Context One in 8 women will develop breast cancer in their lifetime. Yet, the burden of disease is greater in Black women. Black women have a 40% higher mortality rate than White women, and a higher incidence of breast cancer at age 40 and younger. While the underlying cause of this disparity is multifactorial, exposure to endocrine disrupting chemicals (EDCs) in hair and other personal care products has been associated with an increased risk of breast cancer. Parabens are known EDCs that are commonly used as preservatives in hair and other personal care products, and Black women are disproportionately exposed to products containing parabens. Objective Studies have shown that parabens impact breast cancer cell proliferation, death, migration/invasion, and metabolism, as well as gene expression in vitro. However, these studies were conducted using cell lines of European ancestry; to date, no studies have utilized breast cancer cell lines of West African ancestry to examine the effects of parabens on breast cancer progression. Like breast cancer cell lines with European ancestry, we hypothesize that parabens promote protumorigenic effects in breast cancer cell lines of West African ancestry. Methods Luminal breast cancer cell lines with West African ancestry (HCC1500) and European ancestry (MCF-7) were treated with biologically relevant doses of methylparaben, propylparaben, and butylparaben. Results Following treatment, estrogen receptor target gene expression and cell viability were examined. We observed altered estrogen receptor target gene expression and cell viability that was paraben and cell line specific. Conclusion This study provides greater insight into the tumorigenic role of parabens in the progression of breast cancer in Black women.
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Affiliation(s)
- Jazma L Tapia
- Division of Health Equities, Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Jillian C McDonough
- Division of Health Equities, Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Emily L Cauble
- Division of Health Equities, Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Cesar G Gonzalez
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Dede K Teteh
- Department of Health Sciences, Crean College of Health and Behavioral Sciences, Chapman University, Orange, CA 92866, USA
| | - Lindsey S Treviño
- Correspondence: Lindsey S. Treviño, PhD, Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, 1500 E. Duarte Rd, Duarte, CA 91010, USA.
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3
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Porras L, Ismail H, Mader S. Positive Regulation of Estrogen Receptor Alpha in Breast Tumorigenesis. Cells 2021; 10:cells10112966. [PMID: 34831189 PMCID: PMC8616513 DOI: 10.3390/cells10112966] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/23/2021] [Accepted: 10/24/2021] [Indexed: 12/31/2022] Open
Abstract
Estrogen receptor alpha (ERα, NR3A1) contributes through its expression in different tissues to a spectrum of physiological processes, including reproductive system development and physiology, bone mass maintenance, as well as cardiovascular and central nervous system functions. It is also one of the main drivers of tumorigenesis in breast and uterine cancer and can be targeted by several types of hormonal therapies. ERα is expressed in a subset of luminal cells corresponding to less than 10% of normal mammary epithelial cells and in over 70% of breast tumors (ER+ tumors), but the basis for its selective expression in normal or cancer tissues remains incompletely understood. The mapping of alternative promoters and regulatory elements has delineated the complex genomic structure of the ESR1 gene and shed light on the mechanistic basis for the tissue-specific regulation of ESR1 expression. However, much remains to be uncovered to better understand how ESR1 expression is regulated in breast cancer. This review recapitulates the current body of knowledge on the structure of the ESR1 gene and the complex mechanisms controlling its expression in breast tumors. In particular, we discuss the impact of genetic alterations, chromatin modifications, and enhanced expression of other luminal transcription regulators on ESR1 expression in tumor cells.
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Rall-Scharpf M, Friedl TWP, Biechonski S, Denkinger M, Milyavsky M, Wiesmüller L. Sex-specific differences in DNA double-strand break repair of cycling human lymphocytes during aging. Aging (Albany NY) 2021; 13:21066-21089. [PMID: 34506302 PMCID: PMC8457596 DOI: 10.18632/aging.203519] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022]
Abstract
The gender gap in life expectancy and cancer incidence suggests differences in the aging process between the sexes. Genomic instability has been recognized as a key factor in aging, but little is known about sex-specific differences. Therefore, we analyzed DNA double-strand break (DSB) repair in cycling human peripheral blood lymphocytes (PBL) from male and female donors of different age. Reporter-based DSB repair analyses revealed differential regulation of pathway usage in PBL from male and female donors with age: Non-homologous end joining (NHEJ) was inversely regulated in men and women; the activity of pathways requiring end processing and strand annealing steps such as microhomology-mediated end joining (MMEJ) declined with age in women but not in men. Screening candidate proteins identified the NHEJ protein KU70 as well as the end resection regulatory factors ATM and BLM showing reduced expression during aging in women. Consistently, the regulatory factor BLM contributed to the MMEJ proficiency in young but not in old women as demonstrated by knockdown analysis. In conclusion, we show that DSB repair is subject to changes upon aging and age-related changes in DSB repair are distinct in men and women.
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Affiliation(s)
| | - Thomas W P Friedl
- Department of Obstetrics and Gynecology, Ulm University, Ulm, Germany
| | - Shahar Biechonski
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Michael Denkinger
- Institute for Geriatric Research Unit, Agaplesion Bethesda Hospital, Ulm University, Ulm, Germany
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm, Germany
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5
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Boudreau MW, Duraki D, Wang L, Mao C, Kim JE, Henn MA, Tang B, Fanning SW, Kiefer J, Tarasow TM, Bruckheimer EM, Moreno R, Mousses S, Greene GL, Roy EJ, Park BH, Fan TM, Nelson ER, Hergenrother PJ, Shapiro DJ. A small-molecule activator of the unfolded protein response eradicates human breast tumors in mice. Sci Transl Med 2021; 13:13/603/eabf1383. [PMID: 34290053 DOI: 10.1126/scitranslmed.abf1383] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 07/01/2021] [Indexed: 12/20/2022]
Abstract
Metastatic estrogen receptor α (ERα)-positive breast cancer is presently incurable. Seeking to target these drug-resistant cancers, we report the discovery of a compound, called ErSO, that activates the anticipatory unfolded protein response (a-UPR) and induces rapid and selective necrosis of ERα-positive breast cancer cell lines in vitro. We then tested ErSO in vivo in several preclinical orthotopic and metastasis mouse models carrying different xenografts of human breast cancer lines or patient-derived breast tumors. In multiple orthotopic models, ErSO treatment given either orally or intraperitoneally for 14 to 21 days induced tumor regression without recurrence. In a cell line tail vein metastasis model, ErSO was also effective at inducing regression of most lung, bone, and liver metastases. ErSO treatment induced almost complete regression of brain metastases in mice carrying intracranial human breast cancer cell line xenografts. Tumors that did not undergo complete regression and regrew remained sensitive to retreatment with ErSO. ErSO was well tolerated in mice, rats, and dogs at doses above those needed for therapeutic responses and had little or no effect on normal ERα-expressing murine tissues. ErSO mediated its anticancer effects through activation of the a-UPR, suggesting that activation of a tumor protective pathway could induce tumor regression.
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Affiliation(s)
- Matthew W Boudreau
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Darjan Duraki
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lawrence Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chengjian Mao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ji Eun Kim
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Madeline A Henn
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bingtao Tang
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sean W Fanning
- Ben May Department of Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | | | | | | | | | | | - Geoffrey L Greene
- Ben May Department of Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Edward J Roy
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ben Ho Park
- Department of Medicine, Division of Heme/Onc, Vanderbilt Ingram Cancer Center, Nashville, TN 37232, USA
| | - Timothy M Fan
- Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Erik R Nelson
- Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. .,Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - David J Shapiro
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. .,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Barazetti JF, Jucoski TS, Carvalho TM, Veiga RN, Kohler AF, Baig J, Al Bizri H, Gradia DF, Mader S, Carvalho de Oliveira J. From Micro to Long: Non-Coding RNAs in Tamoxifen Resistance of Breast Cancer Cells. Cancers (Basel) 2021; 13:3688. [PMID: 34359587 PMCID: PMC8345104 DOI: 10.3390/cancers13153688] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/03/2021] [Accepted: 07/15/2021] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is the most commonly diagnosed cancer and the leading cause of cancer mortality among women. Two thirds of patients are classified as hormone receptor positive, based on expression of estrogen receptor alpha (ERα), the main driver of breast cancer cell proliferation, and/or progesterone receptor, which is regulated by ERα. Despite presenting the best prognosis, these tumors can recur when patients acquire resistance to treatment by aromatase inhibitors or antiestrogen such as tamoxifen (Tam). The mechanisms that are involved in Tam resistance are complex and involve multiple signaling pathways. Recently, roles for microRNAs and lncRNAs in controlling ER expression and/or tamoxifen action have been described, but the underlying mechanisms are still little explored. In this review, we will discuss the current state of knowledge on the roles of microRNAs and lncRNAs in the main mechanisms of tamoxifen resistance in hormone receptor positive breast cancer. In the future, this knowledge can be used to identify patients at a greater risk of relapse due to the expression patterns of ncRNAs that impact response to Tam, in order to guide their treatment more efficiently and possibly to design therapeutic strategies to bypass mechanisms of resistance.
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Affiliation(s)
- Jéssica Fernanda Barazetti
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-000, Parana, Brazil; (J.F.B.); (T.S.J.); (T.M.C.); (R.N.V.); (A.F.K.); (D.F.G.)
| | - Tayana Shultz Jucoski
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-000, Parana, Brazil; (J.F.B.); (T.S.J.); (T.M.C.); (R.N.V.); (A.F.K.); (D.F.G.)
| | - Tamyres Mingorance Carvalho
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-000, Parana, Brazil; (J.F.B.); (T.S.J.); (T.M.C.); (R.N.V.); (A.F.K.); (D.F.G.)
| | - Rafaela Nasser Veiga
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-000, Parana, Brazil; (J.F.B.); (T.S.J.); (T.M.C.); (R.N.V.); (A.F.K.); (D.F.G.)
| | - Ana Flávia Kohler
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-000, Parana, Brazil; (J.F.B.); (T.S.J.); (T.M.C.); (R.N.V.); (A.F.K.); (D.F.G.)
| | - Jumanah Baig
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada; (J.B.); (H.A.B.)
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Hend Al Bizri
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada; (J.B.); (H.A.B.)
| | - Daniela Fiori Gradia
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-000, Parana, Brazil; (J.F.B.); (T.S.J.); (T.M.C.); (R.N.V.); (A.F.K.); (D.F.G.)
| | - Sylvie Mader
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada; (J.B.); (H.A.B.)
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Jaqueline Carvalho de Oliveira
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-000, Parana, Brazil; (J.F.B.); (T.S.J.); (T.M.C.); (R.N.V.); (A.F.K.); (D.F.G.)
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Chic N, Schettini F, Brasó-Maristany F, Sanfeliu E, Adamo B, Vidal M, Martínez D, Galván P, González-Farré B, Cortés J, Gavilá J, Saura C, Oliveira M, Pernas S, Martínez-Sáez O, Soberino J, Ciruelos E, Carey LA, Muñoz M, Perou CM, Pascual T, Bellet M, Prat A. Oestrogen receptor activity in hormone-dependent breast cancer during chemotherapy. EBioMedicine 2021; 69:103451. [PMID: 34161883 PMCID: PMC8233691 DOI: 10.1016/j.ebiom.2021.103451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/12/2021] [Accepted: 06/04/2021] [Indexed: 12/03/2022] Open
Abstract
Background Chemotherapy efficacy in early-stage hormone receptor-positive (HR+) breast cancer (BC) according to menopausal status needs a biological explanation. Methods We compared early-stage HR+ BC biological features before and after (neo)adjuvant chemotherapy or endocrine therapy (ET), and assessed oestrogen receptor (ER) pathway activity in both pre- and post-menopausal patients. The nCounter platform was used to detect gene expression levels. Findings In 106 post-menopausal patients with HR+/HER2-negative BC randomized to neoadjuvant chemotherapy or ET (letrozole+ribociclib), a total of 19 oestrogen-regulated genes, including progesterone receptor (PGR), were found downregulated in the ET-based arm-only. We confirmed this finding in an independent dataset of 20 letrozole-treated post-menopausal patients and found, conversely, an up-regulation of the same signature in HR+/HER2-negative MCF7 cell line treated with estradiol. PGR was found down-regulated by 2 weeks of ET+anti-HER2 therapy in pre-/post-menopausal patients with HR+/HER2-positive (HER2+) BC, while anti-HER2 therapy alone increased PGR expression in HR-negative/HER2+ BC. In 88 pre- and post-menopausal patients with newly diagnosed HR+/HER2-negative BC treated with chemotherapy, the 19 oestrogen-regulated genes were found significantly downregulated only in pre-menopausal patients. In progesterone receptor (PR)+/HER2-negative BC treated with neoadjuvant chemotherapy (n=40), tumours became PR-negative in 69.2% of pre-menopausal patients and 14.8% of post-menopausal patients (p=0.001). Finally, a mean decrease in PGR levels was only observed in pre-menopausal patients undergoing anti-HER2-based multi-agent chemotherapy. Interpretation Chemotherapy reduces the expression of ER-regulated genes in pre-menopausal women suffering from hormone-dependent BC by supressing ovarian function. Further studies should test the value of chemotherapy in this patient population when ovarian function is suppressed by other methods. Funding Instituto de Salud Carlos III, Breast Cancer Now, the Breast Cancer Research Foundation, the American Association for Cancer Research, Fundació La Marató TV3, the European Union's Horizon 2020 Research and Innovation Programme, Pas a Pas, Save the Mama, Fundación Científica Asociación Española Contra el Cáncer, PhD4MDgrant of “Departament de Salut”, exp SLT008/18/00122, Fundación SEOM and ESMO. Any views, opinions, findings, conclusions, or recommendations expressed in this material are those solely of the author(s).
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Affiliation(s)
- Nuria Chic
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Department of Medical Oncology, Hospital Clinic of Barcelona, Spain; SOLTI cooperative group, Barcelona, Spain
| | - Francesco Schettini
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Department of Medical Oncology, Hospital Clinic of Barcelona, Spain; SOLTI cooperative group, Barcelona, Spain
| | - Fara Brasó-Maristany
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Department of Medical Oncology, Hospital Clinic of Barcelona, Spain; SOLTI cooperative group, Barcelona, Spain
| | - Esther Sanfeliu
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; SOLTI cooperative group, Barcelona, Spain; Department of Pathology, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Barbara Adamo
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Department of Medical Oncology, Hospital Clinic of Barcelona, Spain; SOLTI cooperative group, Barcelona, Spain
| | - Maria Vidal
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Department of Medical Oncology, Hospital Clinic of Barcelona, Spain; SOLTI cooperative group, Barcelona, Spain
| | - Débora Martínez
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Department of Medical Oncology, Hospital Clinic of Barcelona, Spain; SOLTI cooperative group, Barcelona, Spain
| | - Patricia Galván
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Department of Medical Oncology, Hospital Clinic of Barcelona, Spain; SOLTI cooperative group, Barcelona, Spain
| | - Blanca González-Farré
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; SOLTI cooperative group, Barcelona, Spain; Department of Pathology, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Javier Cortés
- Vall d´Hebron Institute of Oncology, Barcelona, Spain; Institute of Oncology (IOB)-Quiron, Madrid, Spain
| | - Joaquín Gavilá
- SOLTI cooperative group, Barcelona, Spain; Department of Medical Oncology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Cristina Saura
- SOLTI cooperative group, Barcelona, Spain; Vall d´Hebron Institute of Oncology, Barcelona, Spain
| | - Mafalda Oliveira
- SOLTI cooperative group, Barcelona, Spain; Vall d´Hebron Institute of Oncology, Barcelona, Spain
| | - Sònia Pernas
- SOLTI cooperative group, Barcelona, Spain; Department of Medical Oncology, Institut Català Oncologia, Barcelona, Spain
| | - Olga Martínez-Sáez
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Department of Medical Oncology, Hospital Clinic of Barcelona, Spain; SOLTI cooperative group, Barcelona, Spain
| | - Jesús Soberino
- Institute of Oncology (IOB)-Hospital Quirónsalud, Barcelona, Spain
| | - Eva Ciruelos
- SOLTI cooperative group, Barcelona, Spain; Department of Medical Oncology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Lisa A Carey
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, USA
| | - Montserrat Muñoz
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Department of Medical Oncology, Hospital Clinic of Barcelona, Spain; SOLTI cooperative group, Barcelona, Spain
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, USA
| | - Tomás Pascual
- SOLTI cooperative group, Barcelona, Spain; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, USA
| | - Meritxell Bellet
- SOLTI cooperative group, Barcelona, Spain; Vall d´Hebron Institute of Oncology, Barcelona, Spain
| | - Aleix Prat
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Department of Medical Oncology, Hospital Clinic of Barcelona, Spain; SOLTI cooperative group, Barcelona, Spain; Institute of Oncology (IOB)-Hospital Quirónsalud, Barcelona, Spain; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, USA; Department of Medicine, University of Barcelona, Barcelona, Spain.
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8
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Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model. Sci Rep 2021; 11:8083. [PMID: 33850167 PMCID: PMC8044218 DOI: 10.1038/s41598-021-86395-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
While transposons are generally silenced in somatic tissues, many transposons escape epigenetic repression in epithelial cancers, become transcriptionally active and contribute to the regulation of human gene expression. We have developed a bioinformatic pipeline for the integrated analysis of transcription factor binding and transcriptomic data to identify transposon-derived promoters that are activated in specific diseases and developmental states. We applied this pipeline to a breast cancer model, and found that the L1PA2 transposon subfamily contributes abundant regulatory sequences to co-ordinated transcriptional regulation in breast cancer. Transcription factor profiling demonstrates that over 27% of L1PA2 transposons harbour co-localised binding sites of functionally interacting, cancer-associated transcription factors in MCF7 cells, a cell line used to model breast cancer. Transcriptomic analysis reveals that L1PA2 transposons also contribute transcription start sites to up-regulated transcripts in MCF7 cells, including some transcripts with established oncogenic properties. In addition, we verified the utility of our pipeline on other transposon subfamilies, as well as on leukemia and lung carcinoma cell lines. We demonstrate that the normally quiescent regulatory activities of transposons can be activated and alter the cancer transcriptome. In particular, the L1PA2 subfamily contributes abundant regulatory sequences, and likely plays a global role in modulating breast cancer transcriptional regulation. Understanding the regulatory impact of L1PA2 on breast cancer genomes provides additional insights into cancer genome regulation, and may provide novel biomarkers for disease diagnosis, prognosis and therapy.
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Site-Specific Phosphorylation of Histone H1.4 Is Associated with Transcription Activation. Int J Mol Sci 2020; 21:ijms21228861. [PMID: 33238524 PMCID: PMC7700352 DOI: 10.3390/ijms21228861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 01/05/2023] Open
Abstract
Core histone variants, such as H2A.X and H3.3, serve specialized roles in chromatin processes that depend on the genomic distributions and amino acid sequence differences of the variant proteins. Modifications of these variants alter interactions with other chromatin components and thus the protein’s functions. These inferences add to the growing arsenal of evidence against the older generic view of those linker histones as redundant repressors. Furthermore, certain modifications of specific H1 variants can confer distinct roles. On the one hand, it has been reported that the phosphorylation of H1 results in its release from chromatin and the subsequent transcription of HIV-1 genes. On the other hand, recent evidence indicates that phosphorylated H1 may in fact be associated with active promoters. This conflict suggests that different H1 isoforms and modified versions of these variants are not redundant when together but may play distinct functional roles. Here, we provide the first genome-wide evidence that when phosphorylated, the H1.4 variant remains associated with active promoters and may even play a role in transcription activation. Using novel, highly specific antibodies, we generated the first genome-wide view of the H1.4 isoform phosphorylated at serine 187 (pS187-H1.4) in estradiol-inducible MCF7 cells. We observe that pS187-H1.4 is enriched primarily at the transcription start sites (TSSs) of genes activated by estradiol treatment and depleted from those that are repressed. We also show that pS187-H1.4 associates with ‘early estrogen response’ genes and stably interacts with RNAPII. Based on the observations presented here, we propose that phosphorylation at S187 by CDK9 represents an early event required for gene activation. This event may also be involved in the release of promoter-proximal polymerases to begin elongation by interacting directly with the polymerase or other parts of the transcription machinery. Although we focused on estrogen-responsive genes, taking into account previous evidence of H1.4′s enrichment of promoters of pluripotency genes, and its involvement with rDNA activation, we propose that H1.4 phosphorylation for gene activation may be a more global observation.
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10
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Gaynor SM, Sun R, Lin X, Quackenbush J. Identification of differentially expressed gene sets using the Generalized Berk-Jones statistic. Bioinformatics 2020; 35:4568-4576. [PMID: 31062858 DOI: 10.1093/bioinformatics/btz277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/14/2019] [Accepted: 04/23/2019] [Indexed: 01/09/2023] Open
Abstract
MOTIVATION Cancer genomics studies frequently aim to identify genes that are differentially expressed between clinically distinct patient subgroups, generally by testing single genes one at a time. However, the results of any individual transcriptomic study are often not fully reproducible. A particular challenge impeding statistical analysis is the difficulty of distinguishing between differential expression comprising part of the genomic disease etiology and that induced by downstream effects. More robust analytical approaches that are well-powered to detect potentially causative genes, are less prone to discovering spurious associations, and can deliver reproducible findings across different studies are needed. RESULTS We propose a set-based procedure for testing of differential expression and show that this set-based approach can produce more robust results by aggregating information across multiple, correlated genomic markers. Specifically, we adapt the Generalized Berk-Jones statistic to test for the transcription factors that may contribute to the progression of estrogen receptor positive breast cancer. We demonstrate the ability of our method to produce reproducible findings by applying the same analysis to 21 publicly available datasets, producing a similar list of significant transcription factors across most studies. Our Generalized Berk-Jones approach produces results that show improved consistency over three set-based testing algorithms: Generalized Higher Criticism, Gene Set Analysis and Gene Set Enrichment Analysis. AVAILABILITY AND IMPLEMENTATION Data are in the MetaGxBreast R package. Code is available at github.com/ryanrsun/gaynor_sun_GBJ_breast_cancer. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sheila M Gaynor
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA.,Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ryan Sun
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA.,Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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11
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McCartney A, Malorni L. Thymidine kinase-1 as a biomarker in breast cancer: estimating prognosis and early recognition of treatment resistance. Biomark Med 2020; 14:495-498. [PMID: 32378432 DOI: 10.2217/bmm-2020-0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Amelia McCartney
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, Prato, Italy
| | - Luca Malorni
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, Prato, Italy.,"Sandro Pitigliani" Translational Research Unit, Hospital of Prato, Prato, Italy
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12
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Revelation of Proteomic Indicators for Colorectal Cancer in Initial Stages of Development. Molecules 2020; 25:molecules25030619. [PMID: 32023884 PMCID: PMC7036866 DOI: 10.3390/molecules25030619] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
Background: Colorectal cancer (CRC) at a current clinical level is still hardly diagnosed, especially with regard to nascent tumors, which are typically asymptotic. Searching for reliable biomarkers of early diagnosis is an extremely essential task. Identification of specific post-translational modifications (PTM) may also significantly improve net benefits and tailor the process of CRC recognition. We examined depleted plasma samples obtained from 41 healthy volunteers and 28 patients with CRC at different stages to conduct comparative proteome-scaled analysis. The main goal of the study was to establish a constellation of protein markers in combination with their PTMs and semi-quantitative ratios that may support and realize the distinction of CRC until the disease has a poor clinical manifestation. Results: Proteomic analysis revealed 119 and 166 proteins for patients in stages I–II and III–IV, correspondingly. Plenty of proteins (44 proteins) reflected conditions of the immune response, lipid metabolism, and response to stress, but only a small portion of them were significant (p < 0.01) for distinguishing stages I–II of CRC. Among them, some cytokines (Clusterin (CLU), C4b-binding protein (C4BP), and CD59 glycoprotein (CD59), etc.) were the most prominent and the lectin pathway was specifically enhanced in patients with CRC. Significant alterations in Inter-alpha-trypsin inhibitor heavy chains (ITIH1, ITIH2, ITIH3, and ITIH4) levels were also observed due to their implication in tumor growth and the malignancy process. Other markers (Alpha-1-acid glycoprotein 2 (ORM2), Alpha-1B-glycoprotein (A1BG), Haptoglobin (HP), and Leucine-rich alpha-2-glycoprotein (LRG1), etc.) were found to create an ambiguous core involved in cancer development but also to exactly promote tumor progression in the early stages. Additionally, we identified post-translational modifications, which according to the literature are associated with the development of colorectal cancer, including kininogen 1 protein (T327-p), alpha-2-HS-glycoprotein (S138-p) and newly identified PTMs, i.e., vitamin D-binding protein (K75-ac and K370-ac) and plasma protease C1 inhibitor (Y294-p), which may also contribute and negatively impact on CRC progression. Conclusions: The contribution of cytokines and proteins of the extracellular matrix is the most significant factor in CRC development in the early stages. This can be concluded since tumor growth is tightly associated with chronic aseptic inflammation and concatenated malignancy related to loss of extracellular matrix stability. Due attention should be paid to Apolipoprotein E (APOE), Apolipoprotein C1 (APOC1), and Apolipoprotein B-100 (APOB) because of their impact on the malfunction of DNA repair and their capability to regulate mTOR and PI3K pathways. The contribution of the observed PTMs is still equivocal, but a significant decrease in the likelihood between modified and native proteins was not detected confidently.
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13
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Parsons J, Francavilla C. 'Omics Approaches to Explore the Breast Cancer Landscape. Front Cell Dev Biol 2020; 7:395. [PMID: 32039208 PMCID: PMC6987401 DOI: 10.3389/fcell.2019.00395] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/30/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer incidence is increasing worldwide with more than 600,000 deaths reported in 2018 alone. In current practice treatment options for breast cancer patients consists of surgery, chemotherapy, radiotherapy or targeting of classical markers of breast cancer subtype: estrogen receptor (ER) and HER2. However, these treatments fail to prevent recurrence and metastasis. Improved understanding of breast cancer and metastasis biology will help uncover novel biomarkers and therapeutic opportunities to improve patient stratification and treatment. We will first provide an overview of current methods and models used to study breast cancer biology, focusing on 2D and 3D cell culture, including organoids, and on in vivo models such as the MMTV mouse model and patient-derived xenografts (PDX). Next, genomic, transcriptomic, and proteomic approaches and their integration will be considered in the context of breast cancer susceptibility, breast cancer drivers, and therapeutic response and resistance to treatment. Finally, we will discuss how 'Omics datasets in combination with traditional breast cancer models are useful for generating insights into breast cancer biology, for suggesting individual treatments in precision oncology, and for creating data repositories to undergo further meta-analysis. System biology has the potential to catalyze the next great leap forward in treatment options for breast cancer patients.
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Affiliation(s)
- Joseph Parsons
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Chiara Francavilla
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
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14
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Zimta AA, Tigu AB, Muntean M, Cenariu D, Slaby O, Berindan-Neagoe I. Molecular Links between Central Obesity and Breast Cancer. Int J Mol Sci 2019; 20:ijms20215364. [PMID: 31661891 PMCID: PMC6862548 DOI: 10.3390/ijms20215364] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/21/2019] [Accepted: 10/25/2019] [Indexed: 02/07/2023] Open
Abstract
Worldwide, breast cancer (BC) is the most common malignancy in women, in regard to incidence and mortality. In recent years, the negative role of obesity during BC development and progression has been made abundantly clear in several studies. However, the distribution of body fat may be more important to analyze than the overall body weight. In our review of literature, we reported some key findings regarding the role of obesity in BC development, but focused more on central adiposity. Firstly, the adipose microenvironment in obese people bears many similarities with the tumor microenvironment, in respect to associated cellular composition, chronic low-grade inflammation, and high ratio of reactive oxygen species to antioxidants. Secondly, the adipose tissue functions as an endocrine organ, which in obese people produces a high level of tumor-promoting hormones, such as leptin and estrogen, and a low level of the tumor suppressor hormone, adiponectin. As follows, in BC this leads to the activation of oncogenic signaling pathways: NFκB, JAK, STAT3, AKT. Moreover, overall obesity, but especially central obesity, promotes a systemic and local low grade chronic inflammation that further stimulates the increase of tumor-promoting oxidative stress. Lastly, there is a constant exchange of information between BC cells and adipocytes, mediated especially by extracellular vesicles, and which changes the transcription profile of both cell types to an oncogenic one with the help of regulatory non-coding RNAs.
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Affiliation(s)
- Alina-Andreea Zimta
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine, and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 400337 Cluj-Napoca, Romania.
| | - Adrian Bogdan Tigu
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine, and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 400337 Cluj-Napoca, Romania.
- Babeș-Bolyai University, Faculty of Biology, and Geology, 42 Republicii Street, 400015 Cluj-Napoca, Romania.
| | - Maximilian Muntean
- Department of Plastic Surgery, University of Medicine and Pharmacy "Iuliu Hatieganu", 400337 Cluj-Napoca, Romania.
| | - Diana Cenariu
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine, and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 400337 Cluj-Napoca, Romania.
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, 62100 Brno, Czech Republic.
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, 60200 Brno, Czech Republic.
| | - Ioana Berindan-Neagoe
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine, and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 400337 Cluj-Napoca, Romania.
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine, and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania.
- Department of Functional Genomics, and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Republicii 34th street, 400015 Cluj-Napoca, Romania.
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15
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Keratin 19 regulates cell cycle pathway and sensitivity of breast cancer cells to CDK inhibitors. Sci Rep 2019; 9:14650. [PMID: 31601969 PMCID: PMC6787034 DOI: 10.1038/s41598-019-51195-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/20/2019] [Indexed: 01/05/2023] Open
Abstract
Keratin 19 (K19) belongs to the keratin family of proteins, which maintains structural integrity of epithelia. In cancer, K19 is highly expressed in several types where it serves as a diagnostic marker. Despite the positive correlation between higher expression of K19 in tumor and worse patient survival, the role of K19 in breast cancer remains unclear. Therefore, we ablated K19 expression in MCF7 breast cancer cells and found that K19 was required for cell proliferation. Transcriptome analyses of KRT19 knockout cells identified defects in cell cycle progression and levels of target genes of E2F1, a key transcriptional factor for the transition into S phase. Furthermore, proper levels of cyclin dependent kinases (CDKs) and cyclins, including D-type cyclins critical for E2F1 activation, were dependent on K19 expression, and K19-cyclin D co-expression was observed in human breast cancer tissues. Importantly, K19 interacts with cyclin D3, and a loss of K19 resulted in decreased protein stability of cyclin D3 and sensitivity of cells towards CDK inhibitor-induced cell death. Overall, these findings reveal a novel function of K19 in the regulation of cell cycle program and suggest that K19 may be used to predict the efficacy of CDK inhibitors for treatments of breast cancer.
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16
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Babu RL, Naveen Kumar M, Patil RH, Kiran Kumar KM, Devaraju KS, Ramesh GT, Sharma SC. Forskolin and Phorbol 12-myristate 13-acetate modulates the expression pattern of AP-1 factors and cell cycle regulators in estrogen-responsive MCF-7 cells. Genes Dis 2018; 6:159-166. [PMID: 31194000 PMCID: PMC6545452 DOI: 10.1016/j.gendis.2018.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/05/2018] [Indexed: 12/12/2022] Open
Abstract
Activator protein-1 (AP-1) transcription factor is a key component of many signal transduction pathways involved in the regulation of cellular processes and controls rapid responses of mammalian cells when exposed to the variety of stimulus. The phorbol 12-myristate 13-acetate and Forskolin (Fo) are well-known kinase activators/stimulators of Protein Kinase C (PKC) and Protein Kinase A (PKA) respectively. Importantly, these kinases are found to be present in transitional points of many cell signaling pathways, especially those involved in proliferation. The stimulating effect of PKC and PKA on the expression of AP-1 factors in MCF-7 breast cell proliferation is not well characterized. Hence, the role of PKC by PMA treatment and the role of PKA by using Fo in MCF-7 cells is investigated. Where, cells treated with PMA showed increased cell proliferation, while Fo had no effect, but inhibited the PMA induced proliferation. The RT-PCR results showed the PMA induced c-Jun, c-Fos and Fra-1 expressions compared to control and Fo. However, Fo in combination with PMA, inhibit the PMA induced above mRNA expressions where Fo alone has no effect. Western blot studies validated the c-Jun expressions in PMA treated MCF-7 cells. Further, PMA increases the mRNA expression of Cyclin-E1, Cyclin-D1, and CDK-4, whereas Fo decreases their expressions. Thus, mitogenic effect of PMA and inhibitory action of Fo on MCF-7 cells is probably enhanced via activation of AP-1 factors and concomitant action of cell cycle regulators in the downstream singling cascade.
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Affiliation(s)
- R L Babu
- Department of Bioinformatics and Biotechnology, Akkamahadevi Women's University, Jnanashakthi Campus, Vijayapura, 586 108, Karnataka, India.,Department of Biology, Center for Biotechnology and Biomedical Sciences, Norfolk State University, Norfolk, VA, USA
| | - M Naveen Kumar
- Department of Microbiology and Biotechnology, Bangalore University, Jnana Bharathi, Bengaluru, 560 056, Karnataka, India
| | - Rajeshwari H Patil
- Department of Microbiology and Biotechnology, Bangalore University, Jnana Bharathi, Bengaluru, 560 056, Karnataka, India
| | - K M Kiran Kumar
- Department of Microbiology and Biotechnology, Bangalore University, Jnana Bharathi, Bengaluru, 560 056, Karnataka, India
| | - K S Devaraju
- Department of Biochemistry, Karnatak University, Dharwad, 580003, Karnataka, India
| | - Govindarajan T Ramesh
- Department of Biology, Center for Biotechnology and Biomedical Sciences, Norfolk State University, Norfolk, VA, USA
| | - S Chidananda Sharma
- Department of Microbiology and Biotechnology, Bangalore University, Jnana Bharathi, Bengaluru, 560 056, Karnataka, India
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17
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Expression of calcium pumps is differentially regulated by histone deacetylase inhibitors and estrogen receptor alpha in breast cancer cells. BMC Cancer 2018; 18:1029. [PMID: 30352569 PMCID: PMC6199715 DOI: 10.1186/s12885-018-4945-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/12/2018] [Indexed: 12/24/2022] Open
Abstract
Background Remodeling of Ca2+ signaling is an important step in cancer progression, and altered expression of members of the Ca2+ signaling toolkit including the plasma membrane Ca2+ ATPases (PMCA proteins encoded by ATP2B genes) is common in tumors. Methods In this study PMCAs were examined in breast cancer datasets and in a variety of breast cancer cell lines representing different subtypes. We investigated how estrogen receptor alpha (ER-α) and histone deacetylase (HDAC) inhibitors regulate the expression of these pumps. Results Three distinct datasets displayed significantly lower ATP2B4 mRNA expression in invasive breast cancer tissue samples compared to normal breast tissue, whereas the expression of ATP2B1 and ATP2B2 was not altered. Studying the protein expression profiles of Ca2+ pumps in a variety of breast cancer cell lines revealed low PMCA4b expression in the ER-α positive cells, and its marked upregulation upon HDAC inhibitor treatments. PMCA4b expression was also positively regulated by the ER-α pathway in MCF-7 cells that led to enhanced Ca2+ extrusion capacity in response to 17β-estradiol (E2) treatment. E2-induced PMCA4b expression was further augmented by HDAC inhibitors. Surprisingly, E2 did not affect the expression of PMCA4b in other ER-α positive cells ZR-75-1, T-47D and BT-474. These findings were in good accordance with ChIP-seq data analysis that revealed an ER-α binding site in the ATP2B4 gene in MCF-7 cells but not in other ER-α positive tumor cells. In the triple negative cells PMCA4b expression was relatively high, and the effect of HDAC inhibitor treatment was less pronounced as compared to that of the ER-α positive cells. Although, the expression of PMCA4b was relatively high in the triple negative cells, a fraction of the protein was found in intracellular compartments that could interfere with the cellular function of the protein. Conclusions Our results suggest that the expression of Ca2+ pumps is highly regulated in breast cancer cells in a subtype specific manner. Our results suggest that hormonal imbalances, epigenetic modifications and impaired protein trafficking could interfere with the expression and cellular function of PMCA4b in the course of breast cancer progression. Electronic supplementary material The online version of this article (10.1186/s12885-018-4945-x) contains supplementary material, which is available to authorized users.
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18
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Wang S, Li X, Zhang W, Gao Y, Zhang K, Hao Q, Li W, Wang Z, Li M, Zhang W, Zhang Y, Zhang C. Genome-Wide Investigation of Genes Regulated by ERα in Breast Cancer Cells. Molecules 2018; 23:molecules23102543. [PMID: 30301189 PMCID: PMC6222792 DOI: 10.3390/molecules23102543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/26/2018] [Accepted: 10/03/2018] [Indexed: 01/13/2023] Open
Abstract
Estrogen receptor alpha (ERα), which has been detected in over 70% of breast cancer cases, is a driving factor for breast cancer growth. For investigating the underlying genes and networks regulated by ERα in breast cancer, RNA-seq was performed between ERα transgenic MDA-MB-231 cells and wild type MDA-MB-231 cells. A total of 267 differentially expressed genes (DEGs) were identified. Then bioinformatics analyses were performed to illustrate the mechanism of ERα. Besides, by comparison of RNA-seq data obtained from MDA-MB-231 cells and microarray dataset obtained from estrogen (E2) stimulated MCF-7 cells, an overlap of 126 DEGs was screened. The expression level of ERα was negatively associated with metastasis and EMT in breast cancer. We further verified that ERα might inhibit metastasis by regulating of VCL and TNFRSF12A, and suppress EMT by the regulating of JUNB and ID3. And the relationship between ERα and these genes were validated by RT-PCR and correlation analysis based on TCGA database. By PPI network analysis, we identified TOP5 hub genes, FOS, SP1, CDKN1A, CALCR and JUNB, which were involved in cell proliferation and invasion. Taken together, the whole-genome insights carried in this work can help fully understanding biological roles of ERα in breast cancer.
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Affiliation(s)
- Shuning Wang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Xiaoju Li
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Wangqian Zhang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Yuan Gao
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Kuo Zhang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Qiang Hao
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Weina Li
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Zhaowei Wang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Meng Li
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Wei Zhang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Yingqi Zhang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Cun Zhang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
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19
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Xu Z, Yang Y, Li B, Li Y, Xia K, Yang Y, Li X, Wang M, Li S, Wu H. Checkpoint suppressor 1 suppresses transcriptional activity of ERα and breast cancer cell proliferation via deacetylase SIRT1. Cell Death Dis 2018; 9:559. [PMID: 29752474 PMCID: PMC5948204 DOI: 10.1038/s41419-018-0629-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/13/2018] [Accepted: 04/18/2018] [Indexed: 02/08/2023]
Abstract
Breast cancer is a highly heterogeneous carcinoma in women worldwide, but the underlying mechanisms that account for breast cancer initiation and development have not been fully established. Mounting evidence indicates that Checkpoint suppressor 1 (CHES1) is tightly associated with tumorigenesis and prognosis in many types of cancer. However, the definitive function of CHES1 in breast cancer remains to be explored. Here we showed that CHES1 had a physical interaction with estrogen receptor-α (ERα) and repressed the transactivation of ERα in breast cancer cells. Mechanistically, the interaction between CHES1 and ERα enhanced the recruitment of nicotinamide adenine dinucleotide (NAD+) deacetylase Sirtuin 1 (SIRT1), and it further induced SIRT1-mediated ERα deacetylation and repression on the promoter-binding enrichment of ERα. In addition, we also found that the expression of CHES1 was repressed by estrogen-ERα signaling and the expression level of CHES1 was significantly downregulated in ERα-positive breast cancer. The detailed mechanism was that ERα may directly bind to CHES1 potential promoter via recognizing the conserved estrogen response element (ERE) motif in response to estrogen stimulation. Functionally, CHES1 inhibited ERα-mediated proliferation and tumorigenesis of breast cancer cells in vivo and in vitro. Totally, these results identified a negative cross-regulatory loop between ERα and CHES1 that was required for growth of breast cancer cells, it might uncover novel insight into molecular mechanism of CHES1 involved in breast cancer and provide new avenues for molecular-targeted therapy in hormone-regulated breast cancer.
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Affiliation(s)
- Zhaowei Xu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Yangyang Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Bowen Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Yanan Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Kangkai Xia
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Yuxi Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Xiahui Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Miao Wang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Shujing Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Huijian Wu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China.
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20
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Hunter I, Hay CW, Esswein B, Watt K, McEwan IJ. Tissue control of androgen action: The ups and downs of androgen receptor expression. Mol Cell Endocrinol 2018; 465:27-35. [PMID: 28789969 DOI: 10.1016/j.mce.2017.08.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/28/2017] [Accepted: 08/03/2017] [Indexed: 12/17/2022]
Abstract
The hormone testosterone plays crucial roles during male development and puberty and throughout life, as an anabolic regulator of muscle and bone structure and function. The actions of testosterone are mediated, primarily, through the androgen receptor, a member of the nuclear receptor superfamily. The androgen receptor gene is located on the X-chromosome and receptor levels are tightly controlled both at the level of transcription of the gene and post-translationally at the protein level. Sp1 has emerged as the major driver of expression of the androgen receptor gene, while auto-regulation by androgens is associated with both positive and negative regulation in a possible cell-selective manner. Research into the networks of positive and negative regulators of the androgen receptor gene are vital in order to understand the temporal and spatial control of receptor levels and the consequences for healthy aging and disease. A clear understanding of the multiple transcription factors participating in regulation of the androgen receptor gene will likely aid in the development and application of hormone therapies to boast or curb receptor activity.
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Affiliation(s)
- Irene Hunter
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Colin W Hay
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Bianca Esswein
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK; Friedrich-Schiller-Universitat, Jena, Germany
| | - Kate Watt
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Iain J McEwan
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK.
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21
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Pirsko V, Cakstina I, Priedite M, Dortane R, Feldmane L, Nakazawa-Miklasevica M, Daneberga Z, Gardovskis J, Miklasevics E. An Effect of Culture Media on Epithelial Differentiation Markers in Breast Cancer Cell Lines MCF7, MDA-MB-436 and SkBr3. MEDICINA (KAUNAS, LITHUANIA) 2018; 54:E11. [PMID: 30344242 PMCID: PMC6037242 DOI: 10.3390/medicina54020011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/19/2018] [Accepted: 03/27/2018] [Indexed: 12/19/2022]
Abstract
Background and objectives: Cell culture is one of the mainstays in the research of breast cancer biology, although the extent to which this approach allows to preserve the original characteristics of originating tumor and implications of cell culture findings to real life situations have been widely debated in the literature. The aim of this study was to determine the role of three cell culture media on transcriptional expression of breast cancer markers in three breast cancer reference cell lines (MCF7, SkBr3 and MDA-MB-436). Materials and methods: Cell lines were conditioned in three studied media (all containing 5% fetal bovine serum (FBS) + hormones/growth factors; different composition of basal media) for four passages. Population growth was characterized by cumulative population doubling levels, average generation time, cell yield and viability at the fourth passage. Transcriptional expression of breast cancer differentiation markers and regulatory transcriptional programs was measured by qPCR. Results: Differences in the composition of growth media significantly influenced the growth of studied cell lines and the expression of mammary lineage governing transcriptional programs and luminal/basal markers. Effects of media on transcriptional expression were more pronounced in luminal cell lines (MCF7, SkBr3), than in the basal cell line (MDA-MB-436). Changes in growth media in terms of supplementation and basal medium delayed growth of cells, but improved cell yields. Conclusions: The expression of breast cancer cell differentiation phenotypic markers depends on the composition of cell growth medium, therefore cell culture as a tool in phenotypic studies should be used considering this effect. The findings of such studies should always be interpreted with caution. The formulation of cell growth media has greater effect on the expression of phenotypic markers in luminal, rather than basal cell lines. Media containing mitogens and higher vitamin content improved efficacy of cell culture in terms of cell yields, although greatly increased growth times.
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Affiliation(s)
- Valdis Pirsko
- Institute of Oncology, Riga Stradins University, LV1086 Riga, Latvia.
| | - Inese Cakstina
- Institute of Oncology, Riga Stradins University, LV1086 Riga, Latvia.
| | - Marta Priedite
- Institute of Oncology, Riga Stradins University, LV1086 Riga, Latvia.
| | - Rasma Dortane
- Institute of Oncology, Riga Stradins University, LV1086 Riga, Latvia.
| | - Linda Feldmane
- Institute of Oncology, Riga Stradins University, LV1086 Riga, Latvia.
| | | | - Zanda Daneberga
- Institute of Oncology, Riga Stradins University, LV1086 Riga, Latvia.
| | - Janis Gardovskis
- Institute of Oncology, Riga Stradins University, LV1086 Riga, Latvia.
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22
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Lemieux S, Sargeant T, Laperrière D, Ismail H, Boucher G, Rozendaal M, Lavallée VP, Ashton-Beaucage D, Wilhelm B, Hébert J, Hilton DJ, Mader S, Sauvageau G. MiSTIC, an integrated platform for the analysis of heterogeneity in large tumour transcriptome datasets. Nucleic Acids Res 2017; 45:e122. [PMID: 28472340 PMCID: PMC5570030 DOI: 10.1093/nar/gkx338] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 04/21/2017] [Indexed: 01/22/2023] Open
Abstract
Genome-wide transcriptome profiling has enabled non-supervised classification of tumours, revealing different sub-groups characterized by specific gene expression features. However, the biological significance of these subtypes remains for the most part unclear. We describe herein an interactive platform, Minimum Spanning Trees Inferred Clustering (MiSTIC), that integrates the direct visualization and comparison of the gene correlation structure between datasets, the analysis of the molecular causes underlying co-variations in gene expression in cancer samples, and the clinical annotation of tumour sets defined by the combined expression of selected biomarkers. We have used MiSTIC to highlight the roles of specific transcription factors in breast cancer subtype specification, to compare the aspects of tumour heterogeneity targeted by different prognostic signatures, and to highlight biomarker interactions in AML. A version of MiSTIC preloaded with datasets described herein can be accessed through a public web server (http://mistic.iric.ca); in addition, the MiSTIC software package can be obtained (github.com/iric-soft/MiSTIC) for local use with personalized datasets.
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Affiliation(s)
- Sebastien Lemieux
- The Leucegene project, Université de Montréal, Montréal, QC H3C 3J7, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada.,Computer science and operation research, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Tobias Sargeant
- The Leucegene project, Université de Montréal, Montréal, QC H3C 3J7, Canada.,Division of Molecular Medicine, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - David Laperrière
- The Leucegene project, Université de Montréal, Montréal, QC H3C 3J7, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Houssam Ismail
- The Leucegene project, Université de Montréal, Montréal, QC H3C 3J7, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Geneviève Boucher
- The Leucegene project, Université de Montréal, Montréal, QC H3C 3J7, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Marieke Rozendaal
- The Leucegene project, Université de Montréal, Montréal, QC H3C 3J7, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Vincent-Philippe Lavallée
- The Leucegene project, Université de Montréal, Montréal, QC H3C 3J7, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Dariel Ashton-Beaucage
- The Leucegene project, Université de Montréal, Montréal, QC H3C 3J7, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Brian Wilhelm
- The Leucegene project, Université de Montréal, Montréal, QC H3C 3J7, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Josée Hébert
- The Leucegene project, Université de Montréal, Montréal, QC H3C 3J7, Canada.,Division of Hematology, Maisonneuve-Rosemont Hospital, Montréal, QC H1T 2M4, Canada.,Leukemia Cell Bank of Quebec, Maisonneuve-Rosemont Hospital, Montréal, QC H1T 2M4, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Douglas J Hilton
- Division of Molecular Medicine, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sylvie Mader
- The Leucegene project, Université de Montréal, Montréal, QC H3C 3J7, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada.,Department of Biochemistry, Université de Montréal, Montréal, QC H3C 3J7, Canada, and Centre de Recherche du Centre Hospitalier Universitaire de l'Université de Montréal, Montréal, QC H2X 0A9, Canada
| | - Guy Sauvageau
- The Leucegene project, Université de Montréal, Montréal, QC H3C 3J7, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada.,Division of Hematology, Maisonneuve-Rosemont Hospital, Montréal, QC H1T 2M4, Canada.,Leukemia Cell Bank of Quebec, Maisonneuve-Rosemont Hospital, Montréal, QC H1T 2M4, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
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23
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Sheldon LA. Inhibition of E2F1 activity and cell cycle progression by arsenic via retinoblastoma protein. Cell Cycle 2017; 16:2058-2072. [PMID: 28880708 DOI: 10.1080/15384101.2017.1338221] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The regulation of cell cycle progression by steroid hormones and growth factors is important for maintaining normal cellular processes including development and cell proliferation. Deregulated progression through the G1/S and G2/M cell cycle transitions can lead to uncontrolled cell proliferation and cancer. The transcription factor E2F1, a key cell cycle regulator, targets genes encoding proteins that regulate cell cycle progression through the G1/S transition as well as proteins important in DNA repair and apoptosis. E2F1 expression and activity is inhibited by inorganic arsenic (iAs) that has a dual role as a cancer therapeutic and as a toxin that leads to diseases including cancer. An understanding of what underlies this dichotomy will contribute to understanding how to use iAs as a more effective therapeutic and also how to treat cancers that iAs promotes. Here, we show that quiescent breast adenocarcinoma MCF-7 cells treated with 17-β estradiol (E2) progress through the cell cycle, but few cells treated with E2 + iAs progress from G1 into S-phase due to a block in cell cycle progression. Our data support a model in which iAs inhibits the dissociation of E2F1 from the tumor suppressor, retinoblastoma protein (pRB) due to changes in pRB phosphorylation which leads to decreased E2F1 transcriptional activity. These findings present an explanation for how iAs can disrupt cell cycle progression through E2F1-pRB and has implications for how iAs acts as a cancer therapeutic as well as how it may promote tumorigenesis through decreased DNA repair.
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Affiliation(s)
- Lynn A Sheldon
- a Geisel School of Medicine at Dartmouth, Department of Molecular and Systems Biology , Hanover , NH , USA
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24
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Stender JD, Nwachukwu JC, Kastrati I, Kim Y, Strid T, Yakir M, Srinivasan S, Nowak J, Izard T, Rangarajan ES, Carlson KE, Katzenellenbogen JA, Yao XQ, Grant BJ, Leong HS, Lin CY, Frasor J, Nettles KW, Glass CK. Structural and Molecular Mechanisms of Cytokine-Mediated Endocrine Resistance in Human Breast Cancer Cells. Mol Cell 2017; 65:1122-1135.e5. [PMID: 28306507 PMCID: PMC5546241 DOI: 10.1016/j.molcel.2017.02.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/02/2017] [Accepted: 02/09/2017] [Indexed: 02/07/2023]
Abstract
Human breast cancers that exhibit high proportions of immune cells and elevated levels of pro-inflammatory cytokines predict poor prognosis. Here, we demonstrate that treatment of human MCF-7 breast cancer cells with pro-inflammatory cytokines results in ERα-dependent activation of gene expression and proliferation, in the absence of ligand or presence of 4OH-tamoxifen (TOT). Cytokine activation of ERα and endocrine resistance is dependent on phosphorylation of ERα at S305 in the hinge domain. Phosphorylation of S305 by IKKβ establishes an ERα cistrome that substantially overlaps with the estradiol (E2)-dependent ERα cistrome. Structural analyses suggest that S305-P forms a charge-linked bridge with the C-terminal F domain of ERα that enables inter-domain communication and constitutive activity from the N-terminal coactivator-binding site, revealing the structural basis of endocrine resistance. ERα therefore functions as a transcriptional effector of cytokine-induced IKKβ signaling, suggesting a mechanism through which the tumor microenvironment controls tumor progression and endocrine resistance.
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Affiliation(s)
- Joshua D Stender
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jerome C Nwachukwu
- Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Irida Kastrati
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Yohan Kim
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Tobias Strid
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maayan Yakir
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sathish Srinivasan
- Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Jason Nowak
- Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Tina Izard
- Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Erumbi S Rangarajan
- Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Kathryn E Carlson
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - John A Katzenellenbogen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Xin-Qiu Yao
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Barry J Grant
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Hon S Leong
- Department of Surgery, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Chin-Yo Lin
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Jonna Frasor
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Kendall W Nettles
- Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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25
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Targeting the CDK4/6 Pathway in Breast Cancer. Breast Cancer 2017. [DOI: 10.1007/978-3-319-48848-6_69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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Zeng H, Lu L, Chan NT, Horswill M, Ahlquist P, Zhong X, Xu W. Systematic identification of Ctr9 regulome in ERα-positive breast cancer. BMC Genomics 2016; 17:902. [PMID: 27829357 PMCID: PMC5103509 DOI: 10.1186/s12864-016-3248-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 11/02/2016] [Indexed: 02/08/2023] Open
Abstract
Background We had previously identified Ctr9, the key scaffold subunit of the human RNA polymerase II (RNAPII) associated factor complex (PAFc), as a key factor regulating a massive ERα target gene expression and ERα-positive breast cancer growth. Furthermore, we have shown that knockdown of Ctr9 reduces ERα protein stability and decreases the occupancy of ERα and RNAPII at a few ERα-target loci. However, it remains to be determined whether Ctr9 controls ERα-target gene expression by regulating the global chromatin occupancy of ERα and RNAPII in the presence of estrogen. Results In this study, we determined the genome-wide ERα and RNAPII occupancy in response to estrogen treatment and/or Ctr9 knockdown by performing chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq). We found that loss of Ctr9 dramatically decreases the global occupancy of ERα and RNAPII, highlighting the significance of Ctr9 in regulating estrogen signaling in ERα-positive breast cancer cells. Combining this resource with previously published genomic data sets, we identified a unique subset of ERα and Ctr9 target genes, and further delineated the independent function of Ctr9 from other subunits in PAFc when regulating transcription. Conclusions Our data demonstrated that Ctr9, independent of other PAFc subunits, controls ERα-target gene expression by regulating global chromatin occupancies of ERα and RNAPII. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3248-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Zeng
- McArdle Laboratory for Cancer Research, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Present address: Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Li Lu
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ngai Ting Chan
- McArdle Laboratory for Cancer Research, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Mark Horswill
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Paul Ahlquist
- McArdle Laboratory for Cancer Research, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Wei Xu
- McArdle Laboratory for Cancer Research, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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27
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Critical re-evaluation of neuroglobin expression reveals conserved patterns among mammals. Neuroscience 2016; 337:339-354. [DOI: 10.1016/j.neuroscience.2016.07.042] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/26/2016] [Accepted: 07/26/2016] [Indexed: 01/08/2023]
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28
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Mao C, Livezey M, Kim JE, Shapiro DJ. Antiestrogen Resistant Cell Lines Expressing Estrogen Receptor α Mutations Upregulate the Unfolded Protein Response and are Killed by BHPI. Sci Rep 2016; 6:34753. [PMID: 27713477 PMCID: PMC5054422 DOI: 10.1038/srep34753] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 09/15/2016] [Indexed: 12/13/2022] Open
Abstract
Outgrowth of metastases expressing ERα mutations Y537S and D538G is common after endocrine therapy for estrogen receptor α (ERα) positive breast cancer. The effect of replacing wild type ERα in breast cancer cells with these mutations was unclear. We used the CRISPR-Cas9 genome editing system and homology directed repair to isolate and characterize 14 T47D cell lines in which ERαY537S or ERαD538G replace one or both wild-type ERα genes. In 2-dimensional, and in quantitative anchorage-independent 3-dimensional cell culture, ERαY537S and ERαD538G cells exhibited estrogen-independent growth. A progestin further increased their already substantial proliferation in micromolar 4-hydroxytamoxifen and fulvestrant/ICI 182,780 (ICI). Our recently described ERα biomodulator, BHPI, which hyperactivates the unfolded protein response (UPR), completely blocked proliferation. In ERαY537S and ERαD538G cells, estrogen-ERα target genes were constitutively active and partially antiestrogen resistant. The UPR marker sp-XBP1 was constitutively activated in ERαY537S cells and further induced by progesterone in both cell lines. UPR-regulated genes associated with tamoxifen resistance, including the oncogenic chaperone BiP/GRP78, were upregulated. ICI displayed a greater than 2 fold reduction in its ability to induce ERαY537S and ERαD538G degradation. Progestins, UPR activation and perhaps reduced ICI-stimulated ERα degradation likely contribute to antiestrogen resistance seen in ERαY537S and ERαD538G cells.
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Affiliation(s)
- Chengjian Mao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mara Livezey
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ji Eun Kim
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - David J Shapiro
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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29
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Pendse SN, Maertens A, Rosenberg M, Roy D, Fasani RA, Vantangoli MM, Madnick SJ, Boekelheide K, Fornace AJ, Odwin SA, Yager JD, Hartung T, Andersen ME, McMullen PD. Information-dependent enrichment analysis reveals time-dependent transcriptional regulation of the estrogen pathway of toxicity. Arch Toxicol 2016; 91:1749-1762. [PMID: 27592001 PMCID: PMC5364265 DOI: 10.1007/s00204-016-1824-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/22/2016] [Indexed: 02/06/2023]
Abstract
The twenty-first century vision for toxicology involves a transition away from high-dose animal studies to in vitro and computational models (NRC in Toxicity testing in the 21st century: a vision and a strategy, The National Academies Press, Washington, DC, 2007). This transition requires mapping pathways of toxicity by understanding how in vitro systems respond to chemical perturbation. Uncovering transcription factors/signaling networks responsible for gene expression patterns is essential for defining pathways of toxicity, and ultimately, for determining the chemical modes of action through which a toxicant acts. Traditionally, transcription factor identification is achieved via chromatin immunoprecipitation studies and summarized by calculating which transcription factors are statistically associated with up- and downregulated genes. These lists are commonly determined via statistical or fold-change cutoffs, a procedure that is sensitive to statistical power and may not be as useful for determining transcription factor associations. To move away from an arbitrary statistical or fold-change-based cutoff, we developed, in the context of the Mapping the Human Toxome project, an enrichment paradigm called information-dependent enrichment analysis (IDEA) to guide identification of the transcription factor network. We used a test case of activation in MCF-7 cells by 17β estradiol (E2). Using this new approach, we established a time course for transcriptional and functional responses to E2. ERα and ERβ were associated with short-term transcriptional changes in response to E2. Sustained exposure led to recruitment of additional transcription factors and alteration of cell cycle machinery. TFAP2C and SOX2 were the transcription factors most highly correlated with dose. E2F7, E2F1, and Foxm1, which are involved in cell proliferation, were enriched only at 24 h. IDEA should be useful for identifying candidate pathways of toxicity. IDEA outperforms gene set enrichment analysis (GSEA) and provides similar results to weighted gene correlation network analysis, a platform that helps to identify genes not annotated to pathways.
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Affiliation(s)
- Salil N Pendse
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC, USA.,ScitoVation, LLC, 6 Davis Drive, PO Box 110566, Research Triangle Park, NC, 27709, USA
| | - Alexandra Maertens
- Center for Alternatives to Animal Testing (CAAT), Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | | | | | | | | | - Samantha J Madnick
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Kim Boekelheide
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Albert J Fornace
- Department of Biochemistry and Molecular and Cellular Biology, and Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Shelly-Ann Odwin
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - James D Yager
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Thomas Hartung
- Center for Alternatives to Animal Testing (CAAT), Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Center for Alternatives to Animal Testing-Europe, University of Konstanz, Constance, Germany
| | - Melvin E Andersen
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC, USA.,ScitoVation, LLC, 6 Davis Drive, PO Box 110566, Research Triangle Park, NC, 27709, USA
| | - Patrick D McMullen
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC, USA. .,ScitoVation, LLC, 6 Davis Drive, PO Box 110566, Research Triangle Park, NC, 27709, USA.
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30
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Rondón-Lagos M, Rangel N, Di Cantogno LV, Annaratone L, Castellano I, Russo R, Manetta T, Marchiò C, Sapino A. Effect of low doses of estradiol and tamoxifen on breast cancer cell karyotypes. Endocr Relat Cancer 2016; 23:635-50. [PMID: 27357940 PMCID: PMC5064758 DOI: 10.1530/erc-16-0078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 06/29/2016] [Indexed: 12/21/2022]
Abstract
Evidence supports a role of 17&-estradiol (E2) in carcinogenesis and the large majority of breast carcinomas are dependent on estrogen. The anti-estrogen tamoxifen (TAM) is widely used for both treatment and prevention of breast cancer; however, it is also carcinogenic in human uterus and rat liver, highlighting the profound complexity of its actions. The nature of E2- or TAM-induced chromosomal damage has been explored using relatively high concentrations of these agents, and only some numerical aberrations and chromosomal breaks have been analyzed. This study aimed to determine the effects of low doses of E2 and TAM (10(&8 )mol L(&1) and 10(&6 )mol L(&1) respectively) on karyotypes of MCF7, T47D, BT474, and SKBR3 breast cancer cells by comparing the results of conventional karyotyping and multi-FISH painting with cell proliferation. Estrogen receptor (ER)-positive (+) cells showed an increase in cell proliferation after E2 treatment (MCF7, T47D, and BT474) and a decrease after TAM treatment (MCF7 and T47D), whereas in ER& cells (SKBR3), no alterations in cell proliferation were observed, except for a small increase at 96 h. Karyotypes of both ER+ and ER& breast cancer cells increased in complexity after treatments with E2 and TAM leading to specific chromosomal abnormalities, some of which were consistent throughout the treatment duration. This genotoxic effect was higher in HER2+ cells. The ER&/HER2+ SKBR3 cells were found to be sensitive to TAM, exhibiting an increase in chromosomal aberrations. These in vitro results provide insights into the potential role of low doses of E2 and TAM in inducing chromosomal rearrangements in breast cancer cells.
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Affiliation(s)
| | - Nelson Rangel
- Department of Medical SciencesUniversity of Turin, Turin, Italy Natural and Mathematical Sciences FacultyUniversidad del Rosario, Bogotá, Colombia
| | | | | | | | - Rosalia Russo
- Department of Medical SciencesUniversity of Turin, Turin, Italy
| | - Tilde Manetta
- Department of Public Health and PediatricsUniversity of Turin, Turin, Italy
| | | | - Anna Sapino
- Department of Medical SciencesUniversity of Turin, Turin, Italy Candiolo Cancer InstituteFPO-IRCCS, Candiolo, Italy
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Cheraghi S, Razi M, Malekinejad H. Involvement of cyclin D1 and E2f1 in zearalenone-induced DNA damage in testis of rats. Toxicon 2015; 106:108-16. [DOI: 10.1016/j.toxicon.2015.09.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 09/09/2015] [Accepted: 09/15/2015] [Indexed: 11/16/2022]
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Yuchi Y, Cai Y, Legein B, De Groef S, Leuckx G, Coppens V, Van Overmeire E, Staels W, De Leu N, Martens G, Van Ginderachter JA, Heimberg H, Van de Casteele M. Estrogen Receptor α Regulates β-Cell Formation During Pancreas Development and Following Injury. Diabetes 2015; 64:3218-28. [PMID: 26015547 DOI: 10.2337/db14-1798] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 05/16/2015] [Indexed: 11/13/2022]
Abstract
Identifying pathways for β-cell generation is essential for cell therapy in diabetes. We investigated the potential of 17β-estradiol (E2) and estrogen receptor (ER) signaling for stimulating β-cell generation during embryonic development and in the severely injured adult pancreas. E2 concentration, ER activity, and number of ERα transcripts were enhanced in the pancreas injured by partial duct ligation (PDL) along with nuclear localization of ERα in β-cells. PDL-induced proliferation of β-cells depended on aromatase activity. The activation of Neurogenin3 (Ngn3) gene expression and β-cell growth in PDL pancreas were impaired when ERα was turned off chemically or genetically (ERα(-/-)), whereas in situ delivery of E2 promoted β-cell formation. In the embryonic pancreas, β-cell replication, number of Ngn3(+) progenitor cells, and expression of key transcription factors of the endocrine lineage were decreased by ERα inactivation. The current study reveals that E2 and ERα signaling can drive β-cell replication and formation in mouse pancreas.
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Affiliation(s)
- Yixing Yuchi
- Diabetes Research Center, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ying Cai
- Diabetes Research Center, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bart Legein
- Diabetes Research Center, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sofie De Groef
- Diabetes Research Center, Vrije Universiteit Brussel, Brussels, Belgium
| | - Gunter Leuckx
- Diabetes Research Center, Vrije Universiteit Brussel, Brussels, Belgium
| | - Violette Coppens
- Diabetes Research Center, Vrije Universiteit Brussel, Brussels, Belgium
| | - Eva Van Overmeire
- Myeloid Cell Immunology Laboratory, Vlaams Instituut voor Biotechnologie, Brussels, Belgium Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Willem Staels
- Diabetes Research Center, Vrije Universiteit Brussel, Brussels, Belgium Department of Pediatrics, Division of Pediatric Endocrinology, Ghent University Hospital, and Department of Pediatrics and Medical Genetics, Ghent University, Ghent, Belgium
| | - Nico De Leu
- Diabetes Research Center, Vrije Universiteit Brussel, Brussels, Belgium Department of Endocrinology, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Geert Martens
- Diabetes Research Center, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jo A Van Ginderachter
- Myeloid Cell Immunology Laboratory, Vlaams Instituut voor Biotechnologie, Brussels, Belgium Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Harry Heimberg
- Diabetes Research Center, Vrije Universiteit Brussel, Brussels, Belgium
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Ma Q, Hu QS, Xu RJ, Zhen XC, Wang GH. Protease Omi facilitates neurite outgrowth in mouse neuroblastoma N2a cells by cleaving transcription factor E2F1. Acta Pharmacol Sin 2015; 36:966-75. [PMID: 26238290 DOI: 10.1038/aps.2015.48] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 04/28/2015] [Indexed: 12/13/2022] Open
Abstract
AIM Omi is an ATP-independent serine protease that is necessary for neuronal function and survival. The aim of this study was to investigate the role of protease Omi in regulating differentiation of mouse neuroblastoma cells and to identify the substrate of Omi involved in this process. METHODS Mouse neuroblastoma N2a cells and Omi protease-deficient mnd2 mice were used in this study. To modulate Omi and E2F1 expression, N2a cells were transfected with expression plasmids, shRNA plasmids or siRNA. Protein levels were detected using immunoblot assays. The interaction between Omi and E2F1 was studied using immunoprecipitation, GST pulldown and in vitro cleavage assays. N2a cells were treated with 20 μmol/L retinoic acid (RA) and 1% fetal bovine serum to induce neurite outgrowth, which was measured using Image J software. RESULTS E2F1 was significantly increased in Omi knockdown cells and in brain lysates of mnd2 mice, and was decreased in cells overexpressing wild-type Omi, but not inactive Omi S276C. In brain lysates of mnd2 mice, endogenous E2F1 was co-immunoprecipitated with endogenous Omi. In vitro cleavage assay demonstrated that Omi directly cleaved E2F1. Treatment of N2a cells with RA induced marked differentiation and neurite outgrowth accompanied by significantly increased Omi and decreased E2F1 levels, which were suppressed by pretreatment with the specific Omi inhibitor UCF-101. Knockdown of Omi in N2a cells suppressed RA-induced neurite outgrowth, which was partially restored by knockdown of E2F1. CONCLUSION Protease Omi facilitates neurite outgrowth by cleaving the transcription factor E2F1 in differentiated neuroblastoma cells; E2F1 is a substrate of Omi.
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Abstract
PURPOSE OF REVIEW To review the latest preclinical and clinical findings on the role of cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors in breast cancer and update on the studies investigating the predictive biomarkers of response to CDK4/6 inhibitors. RECENT FINDINGS The retinoblastoma tumor suppressor (Rb) pathway is frequently deregulated in breast cancer and strategies to target this pathway have recently been proven to be effective in breast cancer patients. Preclinical and clinical data suggest that CDK4/6 inhibitors might be particularly useful in patients with hormone-receptor-positive or HER2-positive tumors, whereas the role of such inhibitors in triple-negative breast cancer is still controversial. Clinical trials are now investigating the safety and efficacy of different CDK4/6 inhibitors, mostly in breast cancer patients with hormone-receptor-positive tumors. Recent studies demonstrated that alterations in the cyclin D-CDK4-Rb pathway may have a role in primary resistance to CDK4/6 inhibitors. SUMMARY Target therapies have brought great improvements in the management of breast cancer patients. CDK4/6 inhibitors look promising in the treatment of patients with hormone-receptor-positive breast cancer, but it is of pivotal importance to identify which subgroup of patients would mostly benefit from CDK4/6 inhibition with biomarker-driven clinical trials.
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H19 lncRNA mediates 17β-estradiol-induced cell proliferation in MCF-7 breast cancer cells. Oncol Rep 2015; 33:3045-52. [DOI: 10.3892/or.2015.3899] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/10/2015] [Indexed: 11/05/2022] Open
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Bisphenol-A induces expression of HOXC6, an estrogen-regulated homeobox-containing gene associated with breast cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:697-708. [PMID: 25725483 DOI: 10.1016/j.bbagrm.2015.02.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 02/13/2015] [Accepted: 02/17/2015] [Indexed: 12/31/2022]
Abstract
HOXC6 is a homeobox-containing gene associated with mammary gland development and is overexpressed in variety of cancers including breast and prostate cancers. Here, we have examined the expression of HOXC6 in breast cancer tissue, investigated its transcriptional regulation via estradiol (E2) and bisphenol-A (BPA, an estrogenic endocrine disruptor) in vitro and in vivo. We observed that HOXC6 is differentially over-expressed in breast cancer tissue. E2 induces HOXC6 expression in cultured breast cancer cells and in mammary glands of Sprague Dawley rats. HOXC6 expression is also induced upon exposure to BPA both in vitro and in vivo. Estrogen-receptor-alpha (ERα) and ER-coregulators such as MLL-histone methylases are bound to the HOXC6 promoter upon exposure to E2 or BPA and that resulted in increased histone H3K4-trimethylation, histone acetylation, and recruitment of RNA polymerase II at the HOXC6 promoter. HOXC6 overexpression induces expression of tumor growth factors and facilitates growth 3D-colony formation, indicating its potential roles in tumor growth. Our studies demonstrate that HOXC6, which is a critical player in mammary gland development, is upregulated in multiple cases of breast cancer, and is transcriptionally regulated by E2 and BPA, in vitro and in vivo.
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Yang ZH, Zhou CL, Zhu H, Li JH, He CD. A functional SNP in the MDM2 promoter mediates E2F1 affinity to modulate cyclin D1 expression in tumor cell proliferation. Asian Pac J Cancer Prev 2015; 15:3817-23. [PMID: 24870800 DOI: 10.7314/apjcp.2014.15.8.3817] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The MDM2 oncogene, a negative regulator of p53, has a functional polymorphism in the promoter region (SNP309) that is associated with multiple kinds of cancers including non-melanoma skin cancer. SNP309 has been shown to associate with accelerated tumor formation by increasing the affinity of the transcriptional activator Sp1. It remains unknown whether there are other factors involved in the regulation of MDM2 transcription through a trans-regulatory mechanism. METHODS In this study, SNP309 was verified to be associated with overexpression of MDM2 in tumor cells. Bioinformatics predicts that the T to G substitution at SNP309 generates a stronger E2F1 binding site, which was confirmed by ChIP and luciferase assays. RESULTS E2F1 knockdown downregulates the expression of MDM2, which confirms that E2F1 is a functional upstream regulator. Furthermore, tumor cells with the GG genotype exhibited a higher proliferation rate than TT, correlating with cyclin D1 expression. E2F1 depletion significantly inhibits the proliferation capacity and downregulates cyclin D1 expression, especially in GG genotype skin fibroblasts. Notably, E2F1 siRNA effects could be rescued by cyclin D1 overexpression. CONCLUSION Taken together, a novel modulator E2F1 was identified as regulating MDM2 expression dependent on SNP309 and further mediates cyclin D1 expression and tumor cell proliferation. E2F1 might act as an important factor for SNP309 serving as a rate-limiting event in carcinogenesis.
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Affiliation(s)
- Zhen-Hai Yang
- Department of Dermatology, No.1 Hospital of China Medical University, Shenyang, China E-mail :
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HSP90 empowers evolution of resistance to hormonal therapy in human breast cancer models. Proc Natl Acad Sci U S A 2014; 111:18297-302. [PMID: 25489079 DOI: 10.1073/pnas.1421323111] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The efficacy of hormonal therapies for advanced estrogen receptor-positive breast cancers is limited by the nearly inevitable development of acquired resistance. Efforts to block the emergence of resistance have met with limited success, largely because the mechanisms underlying it are so varied and complex. Here, we investigate a new strategy aimed at the very processes by which cancers evolve resistance. From yeast to vertebrates, heat shock protein 90 (HSP90) plays a unique role among molecular chaperones by promoting the evolution of heritable new traits. It does so by regulating the folding of a diverse portfolio of metastable client proteins, many of which mediate adaptive responses that allow organisms to adapt and thrive in the face of diverse challenges, including those posed by drugs. Guided by our previous work in pathogenic fungi, in which very modest HSP90 inhibition impairs resistance to mechanistically diverse antifungals, we examined the effect of similarly modest HSP90 inhibition on the emergence of resistance to antiestrogens in breast cancer models. Even though this degree of inhibition fell below the threshold for proteotoxic activation of the heat-shock response and had no overt anticancer activity on its own, it dramatically impaired the emergence of resistance to hormone antagonists both in cell culture and in mice. Our findings strongly support the clinical testing of combined hormone antagonist-low-level HSP90 inhibitor regimens in the treatment of metastatic estrogen receptor-positive breast cancer. At a broader level, they also provide promising proof of principle for a generalizable strategy to combat the pervasive problem of rapidly emerging resistance to molecularly targeted therapeutics.
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Abstract
Sustained estrogenic exposure increases the risk and/or the progression of various cancers, including those of the breast, endometrium and ovary. Unexpectedly, physiological level of estrogen together with a novel IKKα inhibitor BAY11-7082 could effectively induce cell apoptosis in ER-positive breast cancer cells, suggesting combining estrogen with IKKα inhibition may be beneficial for breast cancer patients. This opinion article touches upon the dual role estrogen played in inducing cancer cell death and asks whether use of estrogen in combination with IKKα-targeted therapy would be possible reconsider the newly identified crosstalk between ER and NFκB pathway which can be utilized to switch the effects of estrogen on cell death.
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Affiliation(s)
- Wen Zhou
- Braman Family Breast Cancer Institute, University of Miami Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Fl 33136, USA ; Department of Biological Sciences, Columbia University, New York, 10027, USA
| | - Xiaoxia Zhu
- Molecular Oncology Program, Division of Surgical Oncology, Dewitt Daughtry Family of Surgery, University of Miami Miller School of Medicine, Miami, Fl 33136, USA
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Jonsson P, Katchy A, Williams C. Support of a bi-faceted role of estrogen receptor β (ERβ) in ERα-positive breast cancer cells. Endocr Relat Cancer 2014; 21:143-60. [PMID: 24192230 PMCID: PMC3946733 DOI: 10.1530/erc-13-0444] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The expression of estrogen receptor α (ERα) in breast cancer identifies patients most likely to respond to endocrine treatment. The second ER, ERβ, is also expressed in breast tumors, but its function and therapeutic potential need further study. Although in vitro studies have established that ERβ opposes transcriptional and proliferative functions of ERα, several clinical studies report its correlation with proliferative markers and poorer prognosis. The data demonstrate that ERβ opposes ERα are primarily based on transient expression of ERβ. Here, we explored the functions of constitutively expressed ERβ in ERα-positive breast cancer lines MCF7 and T47D. We found that ERβ, under these conditions heterodimerized with ERα in the presence and absence of 17β-estradiol, and induced genome-wide transcriptional changes. Widespread anti-ERα signaling was, however, not observed and ERβ was not antiproliferative. Tamoxifen antagonized proliferation and ER-mediated gene regulation both in the presence and absence of ERβ. In conclusion, ERβ's role in cells adapted to its expression appears to differ from its role in cells with transient expression. Our study is important because it provides a deeper understanding of ERβ's role in breast tumors that coexpress both receptors and supports an emerging bi-faceted role of ERβ.
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Affiliation(s)
| | | | - Cecilia Williams
- To whom correspondence should be addressed:, Postal address: Center for Nuclear Receptors and Cell Signaling, 3605 Cullen Blvd., SERC Bldg. 545, Houston, TX 77204-5056,
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Zhang L, Zhou Q, Zhang N, Li W, Ying M, Ding W, Yang B, He Q. E2F1 impairs all-trans retinoic acid-induced osteogenic differentiation of osteosarcoma via promoting ubiquitination-mediated degradation of RARα. Cell Cycle 2014; 13:1277-87. [PMID: 24608861 DOI: 10.4161/cc.28190] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
All-trans retinoic acid (ATRA) is a widely used differentiation drug that can effectively induce osteogenic differentiation of osteosarcoma cells, but the underlying mechanism remains elusive, which limits the clinical application for ATRA in osteosarcoma patients. In this study, we identified E2F1 as a novel regulator involved in ATRA-induced osteogenic differentiation of osteosarcoma cells. We observed that osteosarcoma cells are coupled with individual differences in the expression levels of E2F1 in patients, and E2F1 impairs ATRA-induced differentiation of osteosarcoma cells. Moreover, remarkable anti-proliferative and differentiation-inducing effects of ATRA treatment are only observed in E2F1 low to negative expressed primary osteosarcoma cultures. These results strongly suggested that E2F1 may serve as a potent indicator for the effectiveness of ATRA treatment in osteosarcoma. Interestingly, E2F1 is found to downregulate retinoic acid receptor α (RARα), a key factor determines the effectiveness of ATRA. E2F1 specifically binds to RARα and promotes its ubiquitination-mediated degradation; as a consequence, RARα-mediated differentiation is inhibited in osteosarcoma. Therefore, our studies present E2F1 as a potent biomarker, as well as a therapeutic target for ATRA-based differentiation therapeutics, and raise the hope of using differentiation-based approaches for osteosarcoma patients.
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Affiliation(s)
- Lei Zhang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; College of Pharmaceutical Sciences; Zhejiang University; Hangzhou, China
| | - Qian Zhou
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; College of Pharmaceutical Sciences; Zhejiang University; Hangzhou, China
| | - Ning Zhang
- Department of Orthopedics; The Second Affiliated Hospital of Zhejiang University; Zhejiang University; Hangzhou, China
| | - Weixu Li
- Department of Orthopedics; The Second Affiliated Hospital of Zhejiang University; Zhejiang University; Hangzhou, China
| | - Meidan Ying
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; College of Pharmaceutical Sciences; Zhejiang University; Hangzhou, China
| | - Wanjing Ding
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; College of Pharmaceutical Sciences; Zhejiang University; Hangzhou, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; College of Pharmaceutical Sciences; Zhejiang University; Hangzhou, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; College of Pharmaceutical Sciences; Zhejiang University; Hangzhou, China
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Liao XH, Lu DL, Wang N, Liu LY, Wang Y, Li YQ, Yan TB, Sun XG, Hu P, Zhang TC. Estrogen receptor α mediates proliferation of breast cancer MCF-7 cells via a p21/PCNA/E2F1-dependent pathway. FEBS J 2014; 281:927-42. [DOI: 10.1111/febs.12658] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/09/2013] [Accepted: 11/20/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Xing-Hua Liao
- Key Laboratory of Industrial Fermentation Microbiology; Ministry of Education and Tianjin; College of Biotechnology; Tianjin University of Science and Technology; China
- Institute of Biology and Medicine; Wuhan University of Science and Technology; China
| | - Da-Lin Lu
- Institute of Biology and Medicine; Wuhan University of Science and Technology; China
| | - Nan Wang
- Key Laboratory of Industrial Fermentation Microbiology; Ministry of Education and Tianjin; College of Biotechnology; Tianjin University of Science and Technology; China
| | - Long-Yue Liu
- Key Laboratory of Industrial Fermentation Microbiology; Ministry of Education and Tianjin; College of Biotechnology; Tianjin University of Science and Technology; China
| | - Yue Wang
- Key Laboratory of Industrial Fermentation Microbiology; Ministry of Education and Tianjin; College of Biotechnology; Tianjin University of Science and Technology; China
| | - Yan-Qi Li
- Key Laboratory of Industrial Fermentation Microbiology; Ministry of Education and Tianjin; College of Biotechnology; Tianjin University of Science and Technology; China
| | - Ting-Bao Yan
- Key Laboratory of Industrial Fermentation Microbiology; Ministry of Education and Tianjin; College of Biotechnology; Tianjin University of Science and Technology; China
| | - Xue-Guang Sun
- Key Laboratory of Industrial Fermentation Microbiology; Ministry of Education and Tianjin; College of Biotechnology; Tianjin University of Science and Technology; China
| | - Peng Hu
- Institute of Biology and Medicine; Wuhan University of Science and Technology; China
| | - Tong-Cun Zhang
- Key Laboratory of Industrial Fermentation Microbiology; Ministry of Education and Tianjin; College of Biotechnology; Tianjin University of Science and Technology; China
- Institute of Biology and Medicine; Wuhan University of Science and Technology; China
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The estrogen receptor joins other cancer biomarkers as a predictor of outcome. Obstet Gynecol Int 2013; 2013:479541. [PMID: 24223042 PMCID: PMC3816067 DOI: 10.1155/2013/479541] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/10/2013] [Indexed: 11/17/2022] Open
Abstract
Endometrial cancer, the most common gynecologic malignancy in the United States, is on the rise, and survival is worse today than 40 years ago. In order to improve the outcomes, better biomarkers that direct the choice of therapy are urgently needed. In this review, we explore the estrogen receptor as the most studied biomarker and the best predictor for response for endometrial cancer reported to date.
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Lu Y, You M, Ghazoui Z, Liu P, Vedell PT, Wen W, Bode AM, Grubbs CJ, Lubet RA. Concordant effects of aromatase inhibitors on gene expression in ER+ Rat and human mammary cancers and modulation of the proteins coded by these genes. Cancer Prev Res (Phila) 2013; 6:1151-61. [PMID: 24067424 DOI: 10.1158/1940-6207.capr-13-0126] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Aromatase inhibitors are effective in therapy/prevention of estrogen receptor-positive (ER⁺) breast cancers. Rats bearing methylnitrosourea (MNU)-induced ER⁺ mammary cancers were treated with the aromatase inhibitor vorozole (1.25 mg/kg BW/day) for five days. RNA expression showed 162 downregulated and 180 upregulated (P < 0.05 and fold change >1.5) genes. Genes modulated by vorozole were compared with published data from four clinical neoadjuvant trials using aromatase inhibitors (anastrozole or letrozole). More than 30 genes and multiple pathways exhibited synchronous changes in animal and human datasets. Cell-cycle genes related to chromosome condensation in prometaphase [anaphase-prometaphase complex (APC) pathway, including Aurora-A kinase, BUBR1B, TOP2, cyclin A, cyclin B CDC2, and TPX-2)] were downregulated in animal and human studies reflecting the strong antiproliferative effects of aromatase inhibitors. Comparisons of rat arrays with a cell culture study where estrogen was removed from MCF-7 cells showed decreased expression of E2F1-modulated genes as a major altered pathway. Alterations of the cell cycle and E2F-related genes were confirmed in a large independent set of human samples (81 pairs baseline and two weeks anastrozole treatment). Decreases in proliferation-related genes were confirmed at the protein level for cyclin A2, BuRB1, cdc2, Pttg, and TPX-2. Interestingly, the proteins downregulated in tumors were similarly downregulated in vorozole-treated normal rat mammary epithelium. Finally, decreased expression of known estrogen-responsive genes (including TFF, 1,3, progesterone receptor, etc.) were decreased in the animal model. These studies demonstrate that gene expression changes (pathways and individual genes) are similar in humans and the rat model.
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Affiliation(s)
- Yan Lu
- University of Alabama at Birmingham, 1670 University Boulevard, Volker Hall G-78-D Box 800, Birmingham, AL 35294.
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Madak-Erdogan Z, Charn TH, Jiang Y, Liu ET, Katzenellenbogen JA, Katzenellenbogen BS. Integrative genomics of gene and metabolic regulation by estrogen receptors α and β, and their coregulators. Mol Syst Biol 2013; 9:676. [PMID: 23774759 PMCID: PMC3964312 DOI: 10.1038/msb.2013.28] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 05/03/2013] [Indexed: 02/06/2023] Open
Abstract
The closely related transcription factors (TFs), estrogen receptors ERα and ERβ, regulate divergent gene expression programs and proliferative outcomes in breast cancer. Utilizing breast cancer cells with ERα, ERβ, or both receptors as a model system to define the basis for differing response specification by related TFs, we show that these TFs and their key coregulators, SRC3 and RIP140, generate overlapping as well as unique chromatin-binding and transcription-regulating modules. Cistrome and transcriptome analyses and the use of clustering algorithms delineated 11 clusters representing different chromatin-bound receptor and coregulator assemblies that could be functionally associated through enrichment analysis with distinct patterns of gene regulation and preferential coregulator usage, RIP140 with ERβ and SRC3 with ERα. The receptors modified each other's transcriptional effect, and ERβ countered the proliferative drive of ERα through several novel mechanisms associated with specific binding-site clusters. Our findings delineate distinct TF-coregulator assemblies that function as control nodes, specifying precise patterns of gene regulation, proliferation, and metabolism, as exemplified by two of the most important nuclear hormone receptors in human breast cancer.
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Affiliation(s)
- Zeynep Madak-Erdogan
- Department of Molecular and Integrative Physiology, and Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tze-Howe Charn
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yan Jiang
- Department of Molecular and Integrative Physiology, and Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Edison T Liu
- The Genome Institute of Singapore, Singapore, Singapore
| | | | - Benita S Katzenellenbogen
- Department of Molecular and Integrative Physiology, and Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Effect of estrogen and tamoxifen on the expression pattern of AP-1 factors in MCF-7 cells: role of c-Jun, c-Fos, and Fra-1 in cell cycle regulation. Mol Cell Biochem 2013; 380:143-51. [DOI: 10.1007/s11010-013-1667-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Accepted: 04/17/2013] [Indexed: 10/26/2022]
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Wu M, Liu L, Hijazi H, Chan C. A multi-layer inference approach to reconstruct condition-specific genes and their regulation. ACTA ACUST UNITED AC 2013; 29:1541-52. [PMID: 23610368 DOI: 10.1093/bioinformatics/btt186] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
UNLABELLED An important topic in systems biology is the reverse engineering of regulatory mechanisms through reconstruction of context-dependent gene networks. A major challenge is to identify the genes and the regulations specific to a condition or phenotype, given that regulatory processes are highly connected such that a specific response is typically accompanied by numerous collateral effects. In this study, we design a multi-layer approach that is able to reconstruct condition-specific genes and their regulation through an integrative analysis of large-scale information of gene expression, protein interaction and transcriptional regulation (transcription factor-target gene relationships). We establish the accuracy of our methodology against synthetic datasets, as well as a yeast dataset. We then extend the framework to the application of higher eukaryotic systems, including human breast cancer and Arabidopsis thaliana cold acclimation. Our study identified TACSTD2 (TROP2) as a target gene for human breast cancer and discovered its regulation by transcription factors CREB, as well as NFkB. We also predict KIF2C is a target gene for ER-/HER2- breast cancer and is positively regulated by E2F1. The predictions were further confirmed through experimental studies. AVAILABILITY The implementation and detailed protocol of the layer approach is available at http://www.egr.msu.edu/changroup/Protocols/Three-layer%20approach%20 to % 20reconstruct%20condition.html.
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Affiliation(s)
- Ming Wu
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
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Bhar A, Haubrock M, Mukhopadhyay A, Maulik U, Bandyopadhyay S, Wingender E. Coexpression and coregulation analysis of time-series gene expression data in estrogen-induced breast cancer cell. Algorithms Mol Biol 2013; 8:9. [PMID: 23521829 PMCID: PMC3827943 DOI: 10.1186/1748-7188-8-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/07/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Estrogen is a chemical messenger that has an influence on many breast cancers as it helps cells to grow and divide. These cancers are often known as estrogen responsive cancers in which estrogen receptor occupies the surface of the cells. The successful treatment of breast cancers requires understanding gene expression, identifying of tumor markers, acquiring knowledge of cellular pathways, etc. In this paper we introduce our proposed triclustering algorithm δ-TRIMAX that aims to find genes that are coexpressed over subset of samples across a subset of time points. Here we introduce a novel mean-squared residue for such 3D dataset. Our proposed algorithm yields triclusters that have a mean-squared residue score below a threshold δ. RESULTS We have applied our algorithm on one simulated dataset and one real-life dataset. The real-life dataset is a time-series dataset in estrogen induced breast cancer cell line. To establish the biological significance of genes belonging to resultant triclusters we have performed gene ontology, KEGG pathway and transcription factor binding site enrichment analysis. Additionally, we represent each resultant tricluster by computing its eigengene and verify whether its eigengene is also differentially expressed at early, middle and late estrogen responsive stages. We also identified hub-genes for each resultant triclusters and verified whether the hub-genes are found to be associated with breast cancer. Through our analysis CCL2, CD47, NFIB, BRD4, HPGD, CSNK1E, NPC1L1, PTEN, PTPN2 and ADAM9 are identified as hub-genes which are already known to be associated with breast cancer. The other genes that have also been identified as hub-genes might be associated with breast cancer or estrogen responsive elements. The TFBS enrichment analysis also reveals that transcription factor POU2F1 binds to the promoter region of ESR1 that encodes estrogen receptor α. Transcription factor E2F1 binds to the promoter regions of coexpressed genes MCM7, ANAPC1 and WEE1. CONCLUSIONS Thus our integrative approach provides insights into breast cancer prognosis.
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Xu F, You X, Liu F, Shen X, Yao Y, Ye L, Zhang X. The oncoprotein HBXIP up-regulates Skp2 via activating transcription factor E2F1 to promote proliferation of breast cancer cells. Cancer Lett 2013; 333:124-32. [PMID: 23352642 DOI: 10.1016/j.canlet.2013.01.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 01/07/2013] [Accepted: 01/15/2013] [Indexed: 02/08/2023]
Abstract
Hepatitis B X-interacting protein (HBXIP) is a novel oncoprotein. In this study, we found that the expression levels of HBXIP were positively associated with those of S-phase kinase-associated protein 2 (Skp2) in clinical breast cancer tissues and cell lines. Moreover, we found that HBXIP was able to stimulate the promoter of Skp2 through binding to the -640/-443 region in Skp2 promoter involving activating E2F transcription factor 1 (E2F1). Skp2 plays crucial roles in HBXIP-enhanced proliferation of breast cancer cells in vitro and in vivo. We conclude that HBXIP up-regulates Skp2 via activating E2F1 to promote proliferation of breast cancer cells.
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Affiliation(s)
- Fuqiang Xu
- Department of Cancer Research, Key Laboratory of Molecular Microbiology and Technology of Ministry of Education, Institute for Molecular Biology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
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Cui J, Shen Y, Li R. Estrogen synthesis and signaling pathways during aging: from periphery to brain. Trends Mol Med 2013; 19:197-209. [PMID: 23348042 DOI: 10.1016/j.molmed.2012.12.007] [Citation(s) in RCA: 431] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 12/18/2012] [Accepted: 12/27/2012] [Indexed: 01/05/2023]
Abstract
Estrogens are the primary female sex hormones and play important roles in both reproductive and non-reproductive systems. Estrogens can be synthesized in non-reproductive tissues such as liver, heart, muscle, bone and brain, and tissue-specific estrogen synthesis is consistent with a diversity of estrogen actions. In this article we review tissue and cell-specific estrogen synthesis and estrogen receptor signaling in three parts: (i) synthesis and metabolism, (ii) the distribution of estrogen receptors and signaling, and (iii) estrogen functions and related disorders, including cardiovascular diseases, osteoporosis, Alzheimer's disease (AD), and Parkinson disease (PD). This comprehensive review provides new insights into estrogens by giving a better understanding of the tissue-specific estrogen effects and their roles in various diseases.
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Affiliation(s)
- Jie Cui
- Center for Hormone Advanced Science and Education (CHASE), Roskamp Institute, Sarasota, FL 34243, USA
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