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Singh P, Rathi A, Minocha R, Sinha A, Haque MM, Hassan MI, Dohare R. Breast Cancer Prognostic Hub Genes Identified by Integrated Transcriptomic and Weighted Network Analysis: A Road Toward Personalized Medicine. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:227-236. [PMID: 37155625 DOI: 10.1089/omi.2023.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Breast cancer (BC) is the second-most common type and among the leading causes of worldwide cancer-related deaths. There is marked person-to-person variability in susceptibility to, and phenotypic expression and prognosis of BC, a predicament that calls for personalized medicine and individually tailored therapeutics. In this study, we report new observations on prognostic hub genes and key pathways involved in BC. We used the data set GSE109169, comprising 25 pairs of BC and adjacent normal tissues. Using a high-throughput transcriptomic approach, we selected data on 293 differentially expressed genes to establish a weighted gene coexpression network. We identified three age-linked modules where the light-gray module strongly correlated with BC. Based on the gene significance and module membership features, peptidase inhibitor 15 (PI15) and KRT5 were identified as our hub genes from the light-gray module. These genes were further verified at transcriptional and translational levels across 25 pairs of BC and adjacent normal tissues. Their promoter methylation profiles were assessed based on various clinical parameters. In addition, these hub genes were used for Kaplan-Meier survival analysis, and their correlation with tumor-infiltrating immune cells was investigated. We found that PI15 and KRT5 may be potential biomarkers and potential drug targets. These findings call for future research in a larger sample size, which could inform diagnosis and clinical management of BC, thus paving the way toward personalized medicine.
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Affiliation(s)
- Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Aanchal Rathi
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Rashmi Minocha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Anuradha Sinha
- Department of Preventive Oncology, Homi Bhabha Cancer Hospital and Research Centre, Muzaffarpur, India
| | - Mohammad Mahfuzul Haque
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Clemenceau A, Lacouture A, Bherer J, Ouellette G, Michaud A, Audet-Walsh É, Diorio C, Durocher F. Role of Secreted Frizzled-Related Protein 1 in Early Breast Carcinogenesis and Breast Cancer Aggressiveness. Cancers (Basel) 2023; 15:cancers15082251. [PMID: 37190179 DOI: 10.3390/cancers15082251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 03/30/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
A human transcriptome array on ERα-positive breast cancer continuum of risk identified Secreted Frizzled-Related Protein 1 (SFRP1) as decreased during breast cancer progression. In addition, SFRP1 was inversely associated with breast tissue age-related lobular involution, and differentially regulated in women with regard to their parity status and the presence of microcalcifications. The causal role of SFRP1 in breast carcinogenesis remains, nevertheless, not well understood. In this study, we characterized mammary epithelial cells from both nulliparous and multiparous mice in organoid culture ex vivo, in the presence of estradiol (E2) and/or hydroxyapatite microcalcifications (HA). Furthermore, we have modulated SFRP1 expression in breast cancer cell lines, including the MCF10A series, and investigated their tumoral properties. We observed that organoids obtained from multiparous mice were resistant to E2 treatment, while organoids obtained from nulliparous mice developed the luminal phenotype associated with a lower ratio between Sfrp1 and Esr1 expression. The decrease in SFRP1 expression in MCF10A and MCF10AT1 cell lines increased their tumorigenic properties in vitro. On the other hand, the overexpression of SFRP1 in MCF10DCIS, MCF10CA1a, and MCF7 reduced their aggressiveness. Our results support the hypothesis that a lack of SFRP1 could have a causal role in early breast carcinogenesis.
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Affiliation(s)
- Alisson Clemenceau
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, QC G1V 0A6, Canada
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada
| | - Aurélie Lacouture
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, QC G1V 0A6, Canada
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada
| | - Juliette Bherer
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, QC G1V 0A6, Canada
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada
| | - Geneviève Ouellette
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, QC G1V 0A6, Canada
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada
| | - Annick Michaud
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada
- Department of Social and Preventive Medicine, Faculty of Medicine, Laval University, Quebec, QC G1V 0A6, Canada
| | - Étienne Audet-Walsh
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, QC G1V 0A6, Canada
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada
| | - Caroline Diorio
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada
- Department of Social and Preventive Medicine, Faculty of Medicine, Laval University, Quebec, QC G1V 0A6, Canada
| | - Francine Durocher
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, QC G1V 0A6, Canada
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada
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3
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Zhao M, Wu J, Xu J, Li A, Mei Y, Ge X, Yin G, Liu X, Wei L, Xu Q. Association of environmental exposure to chromium with differential DNA methylation: An epigenome-wide study. Front Genet 2023; 13:1043486. [PMID: 36685967 PMCID: PMC9845398 DOI: 10.3389/fgene.2022.1043486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction: Previous studies have reported that chromium (Cr)-induced epigenetic alterations and DNA methylation play a vital role in the pathogenesis of diseases induced by chromium exposure. Epigenomic analyses have been limited and mainly focused on occupational chromium exposure; their findings are not generalizable to populations with environmental Cr exposure. Methods: We identified the differential methylation of genes and regions to elucidate the mechanisms of toxicity related to environmental chromium exposure. DNA methylation was measured in blood samples collected from individuals in Cr-contaminated (n = 10) and unexposed areas (n = 10) by using the Illumina Infinium HumanMethylation850K array. To evaluate the relationship between chromium levels in urine and CpG methylation at 850 thousand sites, we investigated differentially methylated positions (DMPs) and differentially methylated regions (DMRs) by using linear models and DMRcate method, respectively. The model was adjusted for biologically relevant variables and estimated cell-type compositions. Results: At the epigenome-wide level, we identified five CpGs [cg20690919 (p FDR =0.006), cg00704664 (p FDR =0.024), cg10809143 (p FDR =0.043), cg27057652 (p FDR =0.047), cg05390480 (p FDR =0.024)] and one DMR (chr17: 19,648,718-19,648,972), annotated to ALDH3A1 genes (p < 0.05) as being significantly associated with log2 transformed urinary chromium levels. Discussion: Environmental chromium exposure is associated with DNA methylation, and the significant DMPs and DMR being annotated to cause DNA damage and genomic instability were found in this work. Research involving larger samples is required to further explore the epigenetic effect of environmental chromium exposure on health outcomes through DNA methylation.
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Affiliation(s)
- Meiduo Zhao
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China,Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jingtao Wu
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China,Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jing Xu
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China,Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Ang Li
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China,Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yayuan Mei
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China,Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xiaoyu Ge
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China,Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Guohuan Yin
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China,Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xiaolin Liu
- Department of Epidemiology and Biostatistics, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Lanping Wei
- Jinzhou Central Hospital, Jinzhou, Liaoning, China
| | - Qun Xu
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China,Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,*Correspondence: Qun Xu,
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Sadovska L, Zayakin P, Eglītis K, Endzeliņš E, Radoviča-Spalviņa I, Avotiņa E, Auders J, Keiša L, Liepniece-Karele I, Leja M, Eglītis J, Linē A. Comprehensive characterization of RNA cargo of extracellular vesicles in breast cancer patients undergoing neoadjuvant chemotherapy. Front Oncol 2022; 12:1005812. [PMID: 36387168 PMCID: PMC9644097 DOI: 10.3389/fonc.2022.1005812] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/10/2022] [Indexed: 08/30/2023] Open
Abstract
Extracellular vesicles (EVs) are g7aining increased attention as carriers of cancer-derived molecules for liquid biopsies. Here, we studied the dynamics of EV levels in the plasma of breast cancer (BC) patients undergoing neoadjuvant chemotherapy (NAC) and explored the relevance of their RNA cargo for the prediction of patients' response to the therapy. EVs were isolated from serial blood samples collected at the time of diagnosis, at the end of NAC, and 7 days, 6, and 12 months after the surgery from 32 patients with locally advanced BC, and 30 cancer-free healthy controls (HCs) and quantified by nanoparticle tracking analysis. The pre-treatment levels of EVs in BC patients were higher than in HCs, significantly increased during the NAC and surgery, and decreased to the levels found in HCs 6 months after surgery, thus showing that a substantial fraction of plasma EVs in BC patients are produced due to the disease processes and treatment. RNA sequencing analysis revealed that the changes in the EV levels were associated with the alterations in the proportions of various RNA biotypes in EVs. To search for RNA biomarkers that predict response to the NAC, patients were dichotomized as responders and non-responders based on Miller-Payne grades and differential expression analyses were carried out between responders and non-responders, and HCs. This resulted in the identification of 6 miRNAs, 4 lncRNAs, and 1 snoRNA that had significantly higher levels in EVs from non-responders than responders at the time of diagnosis and throughout the NAC, and significantly lower levels in HCs, thus representing biomarkers for the prediction of response to NAC at the time of diagnosis. In addition, we found 14 RNAs representing piRNA, miRNA, lncRNA, snoRNA, and snRNA biotypes that were induced by NAC in non-responders and 2 snoRNAs and 1 piRNA that were induced by NAC in patients with early disease progression, thus warranting further functional studies on their role in chemoresistance and metastasis.
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Affiliation(s)
- Lilite Sadovska
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Pawel Zayakin
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Kristaps Eglītis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, Riga, Latvia
| | - Edgars Endzeliņš
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Elīza Avotiņa
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
| | - Jānis Auders
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Laura Keiša
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Inta Liepniece-Karele
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, Riga, Latvia
- Department of Pathology, Riga Stradins University, Riga, Latvia
| | - Mārcis Leja
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
| | - Jānis Eglītis
- Latvian Oncology Center, Riga Eastern Clinical University Hospital, Riga, Latvia
- University of Latvia, Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Aija Linē
- Cancer Biomarker group, Latvian Biomedical Research and Study Centre, Riga, Latvia
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5
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Song J, Zheng A, Li S, Zhang W, Zhang M, Li X, Jin F, Ji Z. Clinical significance and prognostic value of small nucleolar RNA SNORA38 in breast cancer. Front Oncol 2022; 12:930024. [PMID: 36158687 PMCID: PMC9500313 DOI: 10.3389/fonc.2022.930024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022] Open
Abstract
BackgroundBreast cancer is the most common malignant tumor among women worldwide, and breast cancer stem cells (BCSCs) are believed to be the source of tumorigenesis. New findings suggest that small nucleolar RNAs (snoRNAs) play a significant role in tumor development.MethodsThe Cancer Genome Atlas (TCGA) and Kaplan–Meier survival analysis were used to demonstrate expression and survival of SNORA38 signature. In situ hybridization (ISH) and immunohistochemical (IHC) were conducted to analyze the correlation between SNORA38 and stemness biomarker in 77 BC samples. Gene Set Enrichment Analysis (GSEA) was performed to investigate the mechanisms related to SNORA38 expression in BC. Real-time qPCR was employed to evaluate the expression of SNORA38 in breast cancer cell lines.ResultsIn the public database and patients’ biopsies, SNORA38 was significantly up-regulated in breast cancer. Furthermore, the expression of SNORA38 was significantly correlated with tumor size, lymph node metastasis, and TNM stage, among which tumor size was an independent factor for SNORA38 expression. Higher SNORA38 expression was associated with shorter overall survival (OS). Meanwhile, SNORA38 was positively associated with the stem cell marker OCT-4, which suggested that SNORA38 might be related to breast cancer stemness.ConclusionsSNORA38 is an important carcinogenic snoRNA in breast cancer and might be a prognostic biomarker for breast cancer.
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Affiliation(s)
- Jian Song
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Ang Zheng
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Shan Li
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Wenrong Zhang
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Meilin Zhang
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Xingzhe Li
- Department of Ultrasound, The First Hospital of China Medical University, Shenyang, China
| | - Feng Jin
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
- *Correspondence: Feng Jin, ; Ziyao Ji,
| | - Ziyao Ji
- Department of Ultrasound, The First Hospital of China Medical University, Shenyang, China
- *Correspondence: Feng Jin, ; Ziyao Ji,
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6
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dos Santos A, Ouellete G, Diorio C, Elowe S, Durocher F. Knockdown of CKAP2 Inhibits Proliferation, Migration, and Aggregate Formation in Aggressive Breast Cancer. Cancers (Basel) 2022; 14:cancers14153759. [PMID: 35954424 PMCID: PMC9367390 DOI: 10.3390/cancers14153759] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/26/2022] Open
Abstract
Simple Summary Cancer is a complex disease where cells grow and divide in an uncontrolled manner. It is well established that its development and progression involve major alterations in the activity of mitotic regulators. In order to improve our understanding of the contribution of cell-cycle progression defects to the development of disease, the aim of this study is to identify genes relevant to the proper progression of mitosis that are deregulated in breast cancer. Our findings identified CKAP2 as an important mitotic regulator in BC tumors. Moreover, in vitro experiments showed that gene silencing of CKAP2 blocked cell growth, cell migration, and formation of cell aggregates. These results demonstrated the important role of CKAP2 in breast cancer tumor formation. Abstract Loss of mitotic regulation is commonly observed in cancer and is a major cause of whole-chromosome aneuploidy. The identification of genes that play a role in the proper progression of mitosis can help us to understand the development and evolution of this disease. Here, we generated a list of proteins implicated in mitosis that we used to probe a patient-derived breast cancer (BC) continuum gene-expression dataset generated by our group by human transcriptome analysis of breast lesions of varying aggressiveness (from normal to invasive). We identified cytoskeleton-associated protein 2 (CKAP2) as an important mitotic regulator in invasive BC. The results showed that CKAP2 is overexpressed in invasive BC tumors when compared with normal tissues, and highly expressed in all BC subtypes. Higher expression of CKAP2 is also related to a worse prognosis in overall survival and relapse-free survival in estrogen receptor (ER)-positive and human epidermal growth factor receptor type 2 (HER2)-negative BC patients. Knockdown of CKAP2 in SKBR3 cells impaired cell proliferation and cell migration and reduced aggregate formation in a 3D culture. Our results show the important role of CKAP2 in BC tumorigenesis, and its potential utility as a prognostic marker in BC.
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Affiliation(s)
- Alexsandro dos Santos
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec City, QC G1V 0A6, Canada; (A.d.S.); (G.O.)
- Centre de Recherche sur le Cancer, CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada;
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, L’ingénierie et les Applications des Protéines, Québec City, QC G1V 0A6, Canada
| | - Geneviève Ouellete
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec City, QC G1V 0A6, Canada; (A.d.S.); (G.O.)
- Centre de Recherche sur le Cancer, CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada;
| | - Caroline Diorio
- Centre de Recherche sur le Cancer, CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada;
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Sabine Elowe
- Centre de Recherche sur le Cancer, CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada;
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, L’ingénierie et les Applications des Protéines, Québec City, QC G1V 0A6, Canada
- Département de Pédiatrie, Faculté de Médecine, Université Laval et le Centre de recherche sur le Cancer de l’Université Laval, Québec City, QC G1R 2J6, Canada
- Correspondence: (S.E.); (F.D.)
| | - Francine Durocher
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec City, QC G1V 0A6, Canada; (A.d.S.); (G.O.)
- Centre de Recherche sur le Cancer, CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada;
- Correspondence: (S.E.); (F.D.)
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7
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Rebbeck CA, Xian J, Bornelöv S, Geradts J, Hobeika A, Geiger H, Alvarez JF, Rozhkova E, Nicholls A, Robine N, Lyerly HK, Hannon GJ. Gene expression signatures of individual ductal carcinoma in situ lesions identify processes and biomarkers associated with progression towards invasive ductal carcinoma. Nat Commun 2022; 13:3399. [PMID: 35697697 PMCID: PMC9192778 DOI: 10.1038/s41467-022-30573-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/06/2022] [Indexed: 12/27/2022] Open
Abstract
Ductal carcinoma in situ (DCIS) is considered a non-invasive precursor to breast cancer, and although associated with an increased risk of developing invasive disease, many women with DCIS will never progress beyond their in situ diagnosis. The path from normal duct to invasive ductal carcinoma (IDC) is not well understood, and efforts to do so are hampered by the substantial heterogeneity that exists between patients, and even within patients. Here we show gene expression analysis from > 2,000 individually micro-dissected ductal lesions representing 145 patients. Combining all samples into one continuous trajectory we show there is a progressive loss in basal layer integrity heading towards IDC, coupled with two epithelial to mesenchymal transitions, one early and a second coinciding with the convergence of DCIS and IDC expression profiles. We identify early processes and potential biomarkers, including CAMK2N1, MNX1, ADCY5, HOXC11 and ANKRD22, whose reduced expression is associated with the progression of DCIS to invasive breast cancer.
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Affiliation(s)
- Clare A Rebbeck
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
| | - Jian Xian
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Susanne Bornelöv
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Joseph Geradts
- Department of Pathology & Laboratory Medicine, East Carolina University Brody School of Medicine, Greenville, NC, USA
| | - Amy Hobeika
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | | | - Jose Franco Alvarez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Elena Rozhkova
- Department of Dermatology, Boston University School of Medicine, Boston, MA, USA
| | - Ashley Nicholls
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Herbert K Lyerly
- Department of Surgery, Duke University Medical Center, Durham, NC, USA.
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
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8
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Marino N, German R, Podicheti R, Rusch DB, Rockey P, Huang J, Sandusky GE, Temm CJ, Althouse S, Nephew KP, Nakshatri H, Liu J, Vode A, Cao S, Storniolo AMV. Aberrant epigenetic and transcriptional events associated with breast cancer risk. Clin Epigenetics 2022; 14:21. [PMID: 35139887 PMCID: PMC8830042 DOI: 10.1186/s13148-022-01239-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/25/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Genome-wide association studies have identified several breast cancer susceptibility loci. However, biomarkers for risk assessment are still missing. Here, we investigated cancer-related molecular changes detected in tissues from women at high risk for breast cancer prior to disease manifestation. Disease-free breast tissue cores donated by healthy women (N = 146, median age = 39 years) were processed for both methylome (MethylCap) and transcriptome (Illumina's HiSeq4000) sequencing. Analysis of tissue microarray and primary breast epithelial cells was used to confirm gene expression dysregulation. RESULTS Transcriptomic analysis identified 69 differentially expressed genes between women at high and those at average risk of breast cancer (Tyrer-Cuzick model) at FDR < 0.05 and fold change ≥ 2. Majority of the identified genes were involved in DNA damage checkpoint, cell cycle, and cell adhesion. Two genes, FAM83A and NEK2, were overexpressed in tissue sections (FDR < 0.01) and primary epithelial cells (p < 0.05) from high-risk breasts. Moreover, 1698 DNA methylation changes were identified in high-risk breast tissues (FDR < 0.05), partially overlapped with cancer-related signatures, and correlated with transcriptional changes (p < 0.05, r ≤ 0.5). Finally, among the participants, 35 women donated breast biopsies at two time points, and age-related molecular alterations enhanced in high-risk subjects were identified. CONCLUSIONS Normal breast tissue from women at high risk of breast cancer bears molecular aberrations that may contribute to breast cancer susceptibility. This study is the first molecular characterization of the true normal breast tissues, and provides an opportunity to investigate molecular markers of breast cancer risk, which may lead to new preventive approaches.
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Affiliation(s)
- Natascia Marino
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA. .,Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Rana German
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA
| | - Ram Podicheti
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Pam Rockey
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA
| | - Jie Huang
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - George E Sandusky
- Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Constance J Temm
- Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sandra Althouse
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kenneth P Nephew
- Department of Anatomy, Cell Biology, & Physiology, Indiana University, Bloomington, IN, 47405, USA
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jun Liu
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Ashley Vode
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA
| | - Sha Cao
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Anna Maria V Storniolo
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA.,Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
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Barone I, Caruso A, Gelsomino L, Giordano C, Bonofiglio D, Catalano S, Andò S. Obesity and endocrine therapy resistance in breast cancer: Mechanistic insights and perspectives. Obes Rev 2022; 23:e13358. [PMID: 34559450 PMCID: PMC9285685 DOI: 10.1111/obr.13358] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/07/2021] [Accepted: 08/13/2021] [Indexed: 12/24/2022]
Abstract
The incidence of obesity, a recognized risk factor for various metabolic and chronic diseases, including numerous types of cancers, has risen dramatically over the recent decades worldwide. To date, convincing research in this area has painted a complex picture about the adverse impact of high body adiposity on breast cancer onset and progression. However, an emerging but overlooked issue of clinical significance is the limited efficacy of the conventional endocrine therapies with selective estrogen receptor modulators (SERMs) or degraders (SERDs) and aromatase inhibitors (AIs) in patients affected by breast cancer and obesity. The mechanisms behind the interplay between obesity and endocrine therapy resistance are likely to be multifactorial. Therefore, what have we actually learned during these years and which are the main challenges in the field? In this review, we will critically discuss the epidemiological evidence linking obesity to endocrine therapeutic responses and we will outline the molecular players involved in this harmful connection. Given the escalating global epidemic of obesity, advances in understanding this critical node will offer new precision medicine-based therapeutic interventions and more appropriate dosing schedule for treating patients affected by obesity and with breast tumors resistant to endocrine therapies.
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Affiliation(s)
- Ines Barone
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza, Italy
| | - Amanda Caruso
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza, Italy
| | - Luca Gelsomino
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza, Italy
| | - Cinzia Giordano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza, Italy
| | - Daniela Bonofiglio
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza, Italy
| | - Stefania Catalano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza, Italy
| | - Sebastiano Andò
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza, Italy
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10
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Kumari K, Groza P, Aguilo F. Regulatory roles of RNA modifications in breast cancer. NAR Cancer 2021; 3:zcab036. [PMID: 34541538 PMCID: PMC8445368 DOI: 10.1093/narcan/zcab036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/07/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
Collectively referred to as the epitranscriptome, RNA modifications play important roles in gene expression control regulating relevant cellular processes. In the last few decades, growing numbers of RNA modifications have been identified not only in abundant ribosomal (rRNA) and transfer RNA (tRNA) but also in messenger RNA (mRNA). In addition, many writers, erasers and readers that dynamically regulate the chemical marks have also been characterized. Correct deposition of RNA modifications is prerequisite for cellular homeostasis, and its alteration results in aberrant transcriptional programs that dictate human disease, including breast cancer, the most frequent female malignancy, and the leading cause of cancer-related death in women. In this review, we emphasize the major RNA modifications that are present in tRNA, rRNA and mRNA. We have categorized breast cancer-associated chemical marks and summarize their contribution to breast tumorigenesis. In addition, we describe less abundant tRNA modifications with related pathways implicated in breast cancer. Finally, we discuss current limitations and perspectives on epitranscriptomics for use in therapeutic strategies against breast and other cancers.
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Affiliation(s)
- Kanchan Kumari
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
| | - Paula Groza
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
| | - Francesca Aguilo
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
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11
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Penalty term based suitable fuzzy intuitionistic possibilistic clustering: analyzing high dimensional gene expression cancer database. Soft comput 2021. [DOI: 10.1007/s00500-020-05321-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Kothari C, Clemenceau A, Ouellette G, Ennour-Idrissi K, Michaud A, C.-Gaudreault R, Diorio C, Durocher F. TBC1D9: An Important Modulator of Tumorigenesis in Breast Cancer. Cancers (Basel) 2021; 13:3557. [PMID: 34298771 PMCID: PMC8304074 DOI: 10.3390/cancers13143557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/05/2021] [Accepted: 07/12/2021] [Indexed: 01/02/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a major concern among the different subtypes of breast cancer (BC) due to the lack of effective treatment. In a previous study by our group aimed at understanding the difference between TNBC and non-TNBC tumors, we identified the gene TBC1 domain family member 9 (TBC1D9), the expression of which was lower in TNBC as compared to non-TNBC tumors. In the present study, analysis of TBC1D9 expression in TNBC (n = 58) and non-TNBC (n = 25) patient tumor samples validated that TBC1D9 expression can differentiate TNBC (low) from non-TNBC (high) samples and that expression of TBC1D9 was inversely correlated with grade and proliferative index. Moreover, we found that downregulation of the TBC1D9 gene decreases the proliferation marginally in non-TNBC and was associated with increased migratory and tumorigenic potential in both TNBC and luminal BC cell lines. This increase was mediated by the upregulation of ARL8A, ARL8B, PLK1, HIF1α, STAT3, and SPP1 expression in TBC1D9 knockdown cells. Our results suggest that TBC1D9 expression might limit tumor aggressiveness and that it has a differential expression in TNBC vs. non-TNBC tumors.
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Affiliation(s)
- Charu Kothari
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec City, QC G1T 1C2, Canada; (C.K.); (A.C.); (G.O.); (R.C.-G.)
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada; (K.E.-I.); (A.M.); (C.D.)
| | - Alisson Clemenceau
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec City, QC G1T 1C2, Canada; (C.K.); (A.C.); (G.O.); (R.C.-G.)
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada; (K.E.-I.); (A.M.); (C.D.)
| | - Geneviève Ouellette
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec City, QC G1T 1C2, Canada; (C.K.); (A.C.); (G.O.); (R.C.-G.)
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada; (K.E.-I.); (A.M.); (C.D.)
| | - Kaoutar Ennour-Idrissi
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada; (K.E.-I.); (A.M.); (C.D.)
- Département de Biologie Moléculaire, de Biochimie Médicale et de Pathologie, Faculté de Médecine, Université Laval, Québec City, QC G1T 1C2, Canada
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec City, QC G1T 1C2, Canada
| | - Annick Michaud
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada; (K.E.-I.); (A.M.); (C.D.)
| | - René C.-Gaudreault
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec City, QC G1T 1C2, Canada; (C.K.); (A.C.); (G.O.); (R.C.-G.)
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada; (K.E.-I.); (A.M.); (C.D.)
- Laboratoire de Chimie Médicinale, l’Hôpital Saint-François d’Assise, Université Laval, Québec City, QC G1L 3L5, Canada
| | - Caroline Diorio
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada; (K.E.-I.); (A.M.); (C.D.)
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec City, QC G1T 1C2, Canada
- Centre des Maladies du Sein, Hôpital du Saint-Sacrement, Québec City, QC G1S 4L8, Canada
| | - Francine Durocher
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec City, QC G1T 1C2, Canada; (C.K.); (A.C.); (G.O.); (R.C.-G.)
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada; (K.E.-I.); (A.M.); (C.D.)
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13
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Santana-Codina N, Muixí L, Foj R, Sanz-Pamplona R, Badia-Villanueva M, Abramowicz A, Marcé-Grau A, Cosialls AM, Gil J, Archilla I, Pedrosa L, Gonzalez J, Aldecoa I, Sierra A. GRP94 promotes brain metastasis by engaging pro-survival autophagy. Neuro Oncol 2021; 22:652-664. [PMID: 31637425 DOI: 10.1093/neuonc/noz198] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND GRP94 is a glucose-regulated protein critical for survival in endoplasmic reticulum stress. Expression of GRP94 is associated with cellular transformation and increased tumorigenicity in breast cancer. Specifically, overexpression of GRP94 predicts brain metastasis (BM) in breast carcinoma patients with either triple negative or ErbB2 positive tumors. The aim of this study was to understand if microenvironmental regulation of GRP94 expression might be a hinge orchestrating BM progression. METHODS GRP94 ablation was performed in a BM model BR-eGFP-CMV/Luc-V5CA1 (BRV5CA1) of breast cancer. In vitro results were validated in a dataset of 29 metastases in diverse organs from human breast carcinomas and in BM tissue from tumors of different primary origin. BM patient-derived xenografts (PDXs) were used to test sensitivity to the therapeutic approach. RESULTS BMs that overexpress GRP94 as well as tumor necrosis factor receptor-associated factor 2 are more resistant to glucose deprivation by induction of anti-apoptotic proteins (B-cell lymphoma 2 and inhibitors of apoptosis proteins) and engagement of pro-survival autophagy. GRP94 ablation downregulated autophagy in tumor cells, resulting in increased BM survival in vivo. These results were validated in a metastasis dataset from human patients, suggesting that targeting autophagy might be strategic for BM prevention. Indeed, hydroxychloroquine treatment of preclinical models of BM from PDX exerts preventive inhibition of tumor growth (P < 0.001). CONCLUSIONS We show that GRP94 is directly implicated in BM establishment by activating pro-survival autophagy. Disruption of this compensatory fueling route might prevent metastatic growth.
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Affiliation(s)
- Naiara Santana-Codina
- Biological Clues of the Invasive and Metastatic Phenotype Group, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,Autonomous University of Barcelona, Campus Bellaterra, Cerdanyola del Vallés, Barcelona, Spain
| | - Laia Muixí
- Biological Clues of the Invasive and Metastatic Phenotype Group, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ruben Foj
- Biological Clues of the Invasive and Metastatic Phenotype Group, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Madrid, Spain
| | - Miriam Badia-Villanueva
- Laboratory of Molecular and Translational Oncology, Center of Biomedical Research-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Agata Abramowicz
- Maria Sklodowska-Curie Institute-Oncology Center, Gliwice, Poland
| | - Anna Marcé-Grau
- Biological Clues of the Invasive and Metastatic Phenotype Group, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ana María Cosialls
- Department of Physiological Sciences, School of Medicine and Health Sciences, Campus Bellvitge, Universitat de Barcelona, Oncobell, Bellvitge Medical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Joan Gil
- Department of Physiological Sciences, School of Medicine and Health Sciences, Campus Bellvitge, Universitat de Barcelona, Oncobell, Bellvitge Medical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ivan Archilla
- Pathology Department, Center of Biomedical Diagnosis, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Leire Pedrosa
- Hematology and Oncology Department, Hospital Clinic Barcelona, IDIBAPS, Barcelona, Spain
| | - Josep Gonzalez
- Department of Neurosurgery Hospital Clinic Barcelona, IDIBAPS Advances in Neurosurgery Research Group, Barcelona, Spain
| | - Iban Aldecoa
- Pathology Department, Center of Biomedical Diagnosis, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Angels Sierra
- Biological Clues of the Invasive and Metastatic Phenotype Group, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,Laboratory of Molecular and Translational Oncology, Center of Biomedical Research-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Health and Social Studies Center (CESS), University of Vic‒Central University of Catalonia, Vic, Spain
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14
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Is Carboxypeptidase B1 a Prognostic Marker for Ductal Carcinoma In Situ? Cancers (Basel) 2021; 13:cancers13071726. [PMID: 33917306 PMCID: PMC8038727 DOI: 10.3390/cancers13071726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Ductal carcinoma in situ (DCIS) is an early-stage breast cancer (BC), in which tumor cells are growing in a localized duct of the mammary gland. DCIS is considered a precursor disease for invasive BC and, therefore, treated as soon as it is identified. However, low-grade DCIS can be confused with atypical ductal hyperplasia, which is not a malignant lesion, leading to unnecessary surgery in around 70% of women with suspected DCIS. On the other hand, if left untreated, a DCIS has the potential to progress to IDC. In this retrospective study, we identified a gene signature, carboxypeptidase B1 (CPB1), the expression of which could help differentiate DCIS from an ADH lesion and DCIS that may progress to an invasive BC. Abstract Ductal carcinoma in situ (DCIS) is considered a non-obligatory precursor for invasive ductal carcinoma (IDC). Around 70% of women with atypical ductal hyperplasia (ADH) undergo unnecessary surgery due to the difficulty in differentiating ADH from low-grade DCIS. If untreated, 14–60% of DCIS progress to IDC, highlighting the importance of identifying a DCIS gene signature. Human transcriptome data of breast tissue samples representing each step of BC progression were analyzed and high expression of carboxypeptidase B1 (CPB1) expression strongly correlated with DCIS. This was confirmed by quantitative PCR in breast tissue samples and cell lines model. High CPB1 expression correlated with better survival outcome, and mRNA level was highest in DCIS than DCIS adjacent to IDC and IDC. Moreover, loss of CPB1 in a DCIS cell line led to invasive properties associated with activation of HIF1α, FN1, STAT3 and SPP1 and downregulation of SFRP1 and OS9. The expression of CPB1 could predict 90.1% of DCIS in a cohort consisting of DCIS and IDC. We identified CPB1, a biomarker that helps differentiate DCIS from ADH or IDC and in predicting if a DCIS is likely to progress to IDC, thereby helping clinicians in their decisions.
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15
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Kothari C, Diorio C, Durocher F. Gene signatures of breast cancer development and the potential for novel targeted treatments. Pharmacogenomics 2021; 21:157-161. [PMID: 31967517 DOI: 10.2217/pgs-2019-0158] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Charu Kothari
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada.,Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 0A6, Canada
| | - Caroline Diorio
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 0A6, Canada.,Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Francine Durocher
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada.,Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 0A6, Canada
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16
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Dsouza VL, Adiga D, Sriharikrishnaa S, Suresh PS, Chatterjee A, Kabekkodu SP. Small nucleolar RNA and its potential role in breast cancer - A comprehensive review. Biochim Biophys Acta Rev Cancer 2021; 1875:188501. [PMID: 33400969 DOI: 10.1016/j.bbcan.2020.188501] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/07/2020] [Accepted: 12/28/2020] [Indexed: 02/07/2023]
Abstract
Small Nucleolar RNAs (snoRNAs) are known for their canonical functions, including ribosome biogenesis and RNA modification. snoRNAs act as endogenous sponges that regulate miRNA expression. Thus, precise snoRNA expression is critical for fine-tuning miRNA expression. snoRNAs processed into miRNA-like sequences play a crucial role in regulating the expression of protein-coding genes similar to that of miRNAs. Recent studies have linked snoRNA deregulation to breast cancer (BC). Inappropriate snoRNA expression contributes to BC pathology by facilitating breast cells to acquire cancer hallmarks. Since snoRNAs show significant differential expression in normal and cancer conditions, measuring snoRNA levels could be useful for BC prognosis and diagnosis. The present article provides a comprehensive overview of the role of snoRNAs in breast cancer pathology. More specifically, we have discussed the regulation, biological function, signaling pathways, and clinical utility of abnormally expressed snoRNAs in BC. Besides, we have also discussed the role of snoRNA host genes in breast tumorigenesis and emerging and future research directions in the field of snoRNA and cancer.
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Affiliation(s)
- Venzil Lavie Dsouza
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - S Sriharikrishnaa
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Padmanaban S Suresh
- School of Biotechnology, National Institute of Technology, Calicut, Kerala 673601, India
| | - Aniruddha Chatterjee
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin, New Zealand
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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17
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Breast Cancer and Microcalcifications: An Osteoimmunological Disorder? Int J Mol Sci 2020; 21:ijms21228613. [PMID: 33203195 PMCID: PMC7696282 DOI: 10.3390/ijms21228613] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022] Open
Abstract
The presence of microcalcifications in the breast microenvironment, combined with the growing evidences of the possible presence of osteoblast-like or osteoclast-like cells in the breast, suggest the existence of active processes of calcification in the breast tissue during a woman’s life. Furthermore, much evidence that osteoimmunological disorders, such as osteoarthritis, rheumatoid arthritis, or periodontitis influence the risk of developing breast cancer in women exists and vice versa. Antiresorptive drugs benefits on breast cancer incidence and progression have been reported in the past decades. More recently, biological agents targeting pro-inflammatory cytokines used against rheumatoid arthritis also demonstrated benefits against breast cancer cell lines proliferation, viability, and migratory abilities, both in vitro and in vivo in xenografted mice. Hence, it is tempting to hypothesize that breast carcinogenesis should be considered as a potential osteoimmunological disorder. In this review, we compare microenvironments and molecular characteristics in the most frequent osteoimmunological disorders with major events occurring in a woman’s breast during her lifetime. We also highlight what the use of bone anabolic drugs, antiresorptive, and biological agents targeting pro-inflammatory cytokines against breast cancer can teach us.
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18
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Clemenceau A, Hanna M, Ennour-Idrissi K, Burguin A, Diorio C, Durocher F. Secreted Frizzled-Related Protein 1 as a Biomarker against Incomplete Age-Related Lobular Involution and Microcalcifications' Development. Cancers (Basel) 2020; 12:cancers12092693. [PMID: 32967276 PMCID: PMC7565692 DOI: 10.3390/cancers12092693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/11/2020] [Accepted: 09/16/2020] [Indexed: 12/21/2022] Open
Abstract
As a downregulator of the Wnt signaling pathway, SFRP1 is involved in several components of the age-related lobular involution process such as inflammation, apoptosis, and adipogenesis. Because microcalcifications are associated with inflammation, we aimed to demystify the cross talk between SFRP1, inflammatory markers, and microcalcifications by assessing SFRP1 expression (immunohistochemistry) in a cohort of 162 women with different degrees of lobular involution. SFRP1 expression was inversely associated with the degree of lobular involution (OR = 0.84; p-value < 0.01). SFRP1 expression, age at mastectomy, and waist circumference taken together predicted the degree of lobular involution (AUC = 78.1). This predictive model was best in patients with microcalcifications (AUC = 81.1) and in parous women (AUC = 87.8). SFRP1 expression was correlated with leptin (rho = 0.32), TNF-α (rho = 0.21), and IL-6 (rho = 0.21) expression by epithelial cells (all p-values <0.001). SFRP1 expression was lower in nulliparous women with involuted breast tissue compared with parous women with involuted breast tissue (Δmean = -2.31; p-value < 0.01) and was higher in nulliparous women with microcalcifications compared with nulliparous women without microcalcifications (Δmean = 2.4; p-value < 0.05). In this study, we highlighted two SFRP1-based predictive models for incomplete lobular involution and the development of microcalcifications and identified two distinct inflammatory profiles associated with age-related lobular involution in parous and nulliparous women.
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Affiliation(s)
- Alisson Clemenceau
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, QC G1V 0A6, Canada; (A.C.); (A.B.)
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada; (M.H.); (K.E.-I.); (C.D.)
| | - Mirette Hanna
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada; (M.H.); (K.E.-I.); (C.D.)
- Department of Preventive and Social Medicine, Faculty of Medicine, Laval University, Quebec, QC G1V 0A6, Canada
| | - Kaoutar Ennour-Idrissi
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada; (M.H.); (K.E.-I.); (C.D.)
- Department of Preventive and Social Medicine, Faculty of Medicine, Laval University, Quebec, QC G1V 0A6, Canada
| | - Anna Burguin
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, QC G1V 0A6, Canada; (A.C.); (A.B.)
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada; (M.H.); (K.E.-I.); (C.D.)
| | - Caroline Diorio
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada; (M.H.); (K.E.-I.); (C.D.)
- Department of Preventive and Social Medicine, Faculty of Medicine, Laval University, Quebec, QC G1V 0A6, Canada
| | - Francine Durocher
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, QC G1V 0A6, Canada; (A.C.); (A.B.)
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada; (M.H.); (K.E.-I.); (C.D.)
- Correspondence:
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19
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Kothari C, Diorio C, Durocher F. The Importance of Breast Adipose Tissue in Breast Cancer. Int J Mol Sci 2020; 21:ijms21165760. [PMID: 32796696 PMCID: PMC7460846 DOI: 10.3390/ijms21165760] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
Adipose tissue is a complex endocrine organ, with a role in obesity and cancer. Adipose tissue is generally linked to excessive body fat, and it is well known that the female breast is rich in adipose tissue. Hence, one can wonder: what is the role of adipose tissue in the breast and why is it required? Adipose tissue as an organ consists of adipocytes, an extracellular matrix (ECM) and immune cells, with a significant role in the dynamics of breast changes throughout the life span of a female breast from puberty, pregnancy, lactation and involution. In this review, we will discuss the importance of breast adipose tissue in breast development and its involvement in breast changes happening during pregnancy, lactation and involution. We will focus on understanding the biology of breast adipose tissue, with an overview on its involvement in the various steps of breast cancer development and progression. The interaction between the breast adipose tissue surrounding cancer cells and vice-versa modifies the tumor microenvironment in favor of cancer. Understanding this mutual interaction and the role of breast adipose tissue in the tumor microenvironment could potentially raise the possibility of overcoming breast adipose tissue mediated resistance to therapies and finding novel candidates to target breast cancer.
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Affiliation(s)
- Charu Kothari
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, QC G1T 1C2, Canada;
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada;
| | - Caroline Diorio
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada;
- Department of Preventive and Social Medicine, Faculty of Medicine, Laval University, Quebec, QC G1T 1C2, Canada
| | - Francine Durocher
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, QC G1T 1C2, Canada;
- Cancer Research Centre, CHU de Quebec Research Centre, Quebec, QC G1V 4G2, Canada;
- Correspondence: ; Tel.: +1-(418)-525-4444 (ext. 48508)
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20
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Kothari C, Osseni MA, Agbo L, Ouellette G, Déraspe M, Laviolette F, Corbeil J, Lambert JP, Diorio C, Durocher F. Machine learning analysis identifies genes differentiating triple negative breast cancers. Sci Rep 2020; 10:10464. [PMID: 32591639 PMCID: PMC7320018 DOI: 10.1038/s41598-020-67525-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/02/2020] [Indexed: 02/07/2023] Open
Abstract
Triple negative breast cancer (TNBC) is one of the most aggressive form of breast cancer (BC) with the highest mortality due to high rate of relapse, resistance, and lack of an effective treatment. Various molecular approaches have been used to target TNBC but with little success. Here, using machine learning algorithms, we analyzed the available BC data from the Cancer Genome Atlas Network (TCGA) and have identified two potential genes, TBC1D9 (TBC1 domain family member 9) and MFGE8 (Milk Fat Globule-EGF Factor 8 Protein), that could successfully differentiate TNBC from non-TNBC, irrespective of their heterogeneity. TBC1D9 is under-expressed in TNBC as compared to non-TNBC patients, while MFGE8 is over-expressed. Overexpression of TBC1D9 has a better prognosis whereas overexpression of MFGE8 correlates with a poor prognosis. Protein-protein interaction analysis by affinity purification mass spectrometry (AP-MS) and proximity biotinylation (BioID) experiments identified a role for TBC1D9 in maintaining cellular integrity, whereas MFGE8 would be involved in various tumor survival processes. These promising genes could serve as biomarkers for TNBC and deserve further investigation as they have the potential to be developed as therapeutic targets for TNBC.
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Affiliation(s)
- Charu Kothari
- Département de Médecine Moléculaire, Faculté de médecine, Université Laval, Québec City, QC, Canada
- Centre de Recherche Sur Le Cancer, Centre de Recherche du CHU de Québec-Université Laval, 2705 Laurier Blvd, Bloc R4778, Québec, G1V4G2, Canada
| | - Mazid Abiodoun Osseni
- Département de Médecine Moléculaire, Faculté de médecine, Université Laval, Québec City, QC, Canada
- Big Data Research Centre, CHU de Québec-Université Laval, Quebec City, QC, Canada
| | - Lynda Agbo
- Département de Médecine Moléculaire, Faculté de médecine, Université Laval, Québec City, QC, Canada
- Centre de Recherche Sur Le Cancer, Centre de Recherche du CHU de Québec-Université Laval, 2705 Laurier Blvd, Bloc R4778, Québec, G1V4G2, Canada
| | - Geneviève Ouellette
- Département de Médecine Moléculaire, Faculté de médecine, Université Laval, Québec City, QC, Canada
- Centre de Recherche Sur Le Cancer, Centre de Recherche du CHU de Québec-Université Laval, 2705 Laurier Blvd, Bloc R4778, Québec, G1V4G2, Canada
| | - Maxime Déraspe
- Département de Médecine Moléculaire, Faculté de médecine, Université Laval, Québec City, QC, Canada
- Big Data Research Centre, CHU de Québec-Université Laval, Quebec City, QC, Canada
| | - François Laviolette
- Big Data Research Centre, CHU de Québec-Université Laval, Quebec City, QC, Canada
- Département D'informatique Et de génie Logiciel, Faculté des sciences et de génie, Université Laval, Québec City, QC, Canada
| | - Jacques Corbeil
- Département de Médecine Moléculaire, Faculté de médecine, Université Laval, Québec City, QC, Canada
- Big Data Research Centre, CHU de Québec-Université Laval, Quebec City, QC, Canada
| | - Jean-Philippe Lambert
- Département de Médecine Moléculaire, Faculté de médecine, Université Laval, Québec City, QC, Canada
- Centre de Recherche Sur Le Cancer, Centre de Recherche du CHU de Québec-Université Laval, 2705 Laurier Blvd, Bloc R4778, Québec, G1V4G2, Canada
| | - Caroline Diorio
- Centre de Recherche Sur Le Cancer, Centre de Recherche du CHU de Québec-Université Laval, 2705 Laurier Blvd, Bloc R4778, Québec, G1V4G2, Canada
- Département de Médecine Sociale Et Préventive, Faculté de Médecine, Université Laval, Québec City, QC, Canada
| | - Francine Durocher
- Département de Médecine Moléculaire, Faculté de médecine, Université Laval, Québec City, QC, Canada.
- Centre de Recherche Sur Le Cancer, Centre de Recherche du CHU de Québec-Université Laval, 2705 Laurier Blvd, Bloc R4778, Québec, G1V4G2, Canada.
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21
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Shan NL, Minden A, Furmanski P, Bak MJ, Cai L, Wernyj R, Sargsyan D, Cheng D, Wu R, Kuo HCD, Li SN, Fang M, Maehr H, Kong AN, Suh N. Analysis of the Transcriptome: Regulation of Cancer Stemness in Breast Ductal Carcinoma In Situ by Vitamin D Compounds. Cancer Prev Res (Phila) 2020; 13:673-686. [PMID: 32467291 DOI: 10.1158/1940-6207.capr-19-0566] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 04/01/2020] [Accepted: 05/20/2020] [Indexed: 12/21/2022]
Abstract
Ductal carcinoma in situ (DCIS), which accounts for one out of every five new breast cancer diagnoses, will progress to potentially lethal invasive ductal carcinoma (IDC) in about 50% of cases. Vitamin D compounds have been shown to inhibit progression to IDC in the MCF10DCIS model. This inhibition appears to involve a reduction in the cancer stem cell-like population in MCF10DCIS tumors. To identify genes that are involved in the vitamin D effects, a global transcriptomic analysis was undertaken of MCF10DCIS cells grown in mammosphere cultures, in which cancer stem-like cells grow preferentially and produce colonies by self-renewal and maturation, in the presence and absence of 1α25(OH)2D3 and a vitamin D analog, BXL0124. Using next-generation RNA-sequencing, we found that vitamin D compounds downregulated genes involved in maintenance of breast cancer stem-like cells (e.g., GDF15), epithelial-mesenchymal transition, invasion, and metastasis (e.g., LCN2 and S100A4), and chemoresistance (e.g., NGFR, PPP1R1B, and AGR2), while upregulating genes associated with a basal-like phenotype (e.g., KRT6A and KRT5) and negative regulators of breast tumorigenesis (e.g., EMP1). Gene methylation status was analyzed to determine whether the changes in expression induced by vitamin D compounds occurred via this mechanism. Ingenuity pathway analysis was performed to identify upstream regulators and downstream signaling pathway genes differentially regulated by vitamin D, including TP63 and vitamin D receptor -mediated canonical pathways in particular. This study provides a global profiling of changes in the gene signature of DCIS regulated by vitamin D compounds and possible targets for chemoprevention of DCIS progression to IDC in patients.
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Affiliation(s)
- Naing Lin Shan
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Audrey Minden
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, New Jersey.,Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Philip Furmanski
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, New Jersey.,Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Min Ji Bak
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Li Cai
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey.,Department of Biomedical Engineering, School of Engineering, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Roman Wernyj
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Davit Sargsyan
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - David Cheng
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Hsiao-Chen D Kuo
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Shanyi N Li
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Mingzhu Fang
- Environmental and Occupational Health Sciences Institute and School of Public Health, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Hubert Maehr
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Ah-Ng Kong
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Nanjoo Suh
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, New Jersey. .,Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
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22
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Role of Secreted Frizzled-Related Protein 1 in Early Mammary Gland Tumorigenesis and Its Regulation in Breast Microenvironment. Cells 2020; 9:cells9010208. [PMID: 31947616 PMCID: PMC7017175 DOI: 10.3390/cells9010208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/09/2020] [Accepted: 01/12/2020] [Indexed: 12/11/2022] Open
Abstract
In mice, the lack of secreted frizzled-related protein 1 (SFRP1) is responsible for mammogenesis and hyperplasia, while, in bovines, its overexpression is associated with post-lactational mammary gland involution. Interestingly, there are no reports dealing with the role of SFRP1 in female involution. However, SFRP1 dysregulation is largely associated with human tumorigenesis in the literature. Indeed, the lack of SFRP1 is associated with both tumor development and patient prognosis. Considering the increased risk of breast tumor development associated with incomplete mammary gland involution, it is crucial to demystify the "grey zone" between physiological age-related involution and tumorigenesis. In this review, we explore the functions of SFRP1 involved in the breast involution processes to understand the perturbations driven by the disappearance of SFRP1 in mammary tissue. Moreover, we question the presence of recurrent microcalcifications identified by mammography. In bone metastases from prostate primary tumor, overexpression of SFRP1 results in an osteolytic response of the tumor cells. Hence, we explore the hypothesis of an osteoblastic differentiation of mammary cells induced by the lack of SFRP1 during lobular involution, resulting in a new accumulation of hydroxyapatite crystals in the breast tissue.
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23
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Sultan G, Zubair S, Tayubi IA, Dahms HU, Madar IH. Towards the early detection of ductal carcinoma (a common type of breast cancer) using biomarkers linked to the PPAR(γ) signaling pathway. Bioinformation 2019; 15:799-805. [PMID: 31902979 PMCID: PMC6936658 DOI: 10.6026/97320630015799] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 11/28/2019] [Accepted: 12/07/2019] [Indexed: 02/08/2023] Open
Abstract
Breast cancer is a leading cause of morbidity and mortality among women comprising about 12% females worldwide. The underlying alteration in the gene expression, molecular mechanism and metabolic pathways responsible for incidence and progression of breast tumorigenesis are yet not completely understood. In the present study, potential biomarker genes involved in the early progression for early diagnosis of breast cancer has been detailed. Regulation and Gene profiling of Ductal Carcinoma In-situ (DCIS), Invasive Ductal Carcinoma (IDC) and healthy samples have been analyzed to follow their expression pattern employing normalization, statistical calculation, DEGs annotation and Protein-Protein Interaction (PPI) network. We have performed a comparative study on differentially expressed genes among Healthy vs DCIS, Healthy vsIDC and DCIS vs IDC. We found MCM102 and SLC12A8as consistently over-expressed and LEP, SORBS1, SFRP1, PLIN1, FABP4, RBP4, CD300LG, ID4, CRYAB, ECRG4, G0S2, FMO2, ADAMTS5, CAV1, CAV2, ABCA8, MAMDC2, IGFBP6, CLDN11, TGFBR3as under-expressed genes in all the 3 conditions categorized for pre-invasive and invasive ductal breast carcinoma. These genes were further studied for the active pathways where PPAR(γ) signaling pathway was found to be significantly involved. The gene expression profile database can be a potential tool in the early diagnosis of breast cancer.
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Affiliation(s)
- Ghazala Sultan
- Department of Computer Science, Aligarh Muslim University, Aligarh, Uttar Pradesh 202001, India
| | - Swaleha Zubair
- Department of Computer Science, Aligarh Muslim University, Aligarh, Uttar Pradesh 202001, India
| | - Iftikhar Aslam Tayubi
- Faculty of Computing and Information Technology, Rabigh, King Abdulaziz University, Jeddah 21911, Saudi Arabia
| | - Hans-Uwe Dahms
- Department of Computer Science, Aligarh Muslim University, Aligarh, Uttar Pradesh 202001, India
| | - Inamul Hasan Madar
- Department of Biomedical Science and Environmental Biology, KMU-Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Biotechnology, School of Biotechnology and Genetic Engineering, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
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24
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Toss MS, Miligy IM, Gorringe KL, AlKawaz A, Mittal K, Aneja R, Ellis IO, Green AR, Roxanis I, Rakha EA. Geometric characteristics of collagen have independent prognostic significance in breast ductal carcinoma in situ: an image analysis study. Mod Pathol 2019; 32:1473-1485. [PMID: 31175326 DOI: 10.1038/s41379-019-0296-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/01/2019] [Accepted: 05/02/2019] [Indexed: 12/30/2022]
Abstract
Collagen plays a key role in normal and malignant tissue homeostasis. While the prognostic significance of collagen fiber remodeling in invasive breast cancer has been studied, its role in ductal carcinoma in situ (DCIS) remains poorly defined. Using image analysis, we aimed to evaluate the prognostic significance of the geometric characteristics of collagen surrounding DCIS. A large well-characterized cohort of DCIS comprising pure DCIS (n = 610) and DCIS coexisting with invasive carcinoma (n = 180) were histochemically stained for collagen using picrosirius red. ImageJ software was used to assess collagen density, degree of collagen fiber dispersion and directionality in relation to DCIS ducts' boundary. We developed a collagen prognostic index and evaluated its prognostic significance. A poor index was observed in 24% of the pure DCIS and was associated with determinants of high-risk DCIS including higher nuclear grade, comedo type necrosis, hormonal receptor negativity, HER2 positivity and high proliferation index. High collagen prognostic index was associated with the collagen remodeling protein prolyl-4-hydroxlase alpha subunit 2 and the hypoxia-related protein hypoxia inducible factor 1α. DCIS coexisting with invasive breast cancer had a higher collagen prognostic index than pure DCIS ( p < 0.0001). High index was an independent poor prognostic factor for DCIS recurrence for all recurrences (HR = 2.3, p = 0.005) and just invasive recurrences (HR = 3.4, p = 0.003). Interaction between collagen prognostic index and radiotherapy showed that the index was associated with poor outcome even with adjuvant radiotherapy ( p = 0.0001). Collagen reorganization around DCIS is associated with poor outcome and provides a potential predictor for disease progression and resistance to radiotherapy. Mechanistic studies are warranted to decipher the underlying mechanisms.
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Affiliation(s)
- Michael S Toss
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham City Hospital, Nottingham, UK.,Histopathology Department, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Islam M Miligy
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham City Hospital, Nottingham, UK.,Histopathology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Kylie L Gorringe
- Cancer Genomics Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Abdulbaqi AlKawaz
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham City Hospital, Nottingham, UK.,College of Dentistry, Al Mustansiriya University, Baghdad, Iraq
| | | | - Ritu Aneja
- Georgia State University, Atlanta, GA, USA
| | - Ian O Ellis
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Andrew R Green
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Ioannis Roxanis
- Institute of Cancer Research, London, UK.,Royal Free London NHS Foundation Trust, London, UK
| | - Emad A Rakha
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham City Hospital, Nottingham, UK. .,Histopathology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt.
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25
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Gene expression signature of atypical breast hyperplasia and regulation by SFRP1. Breast Cancer Res 2019; 21:76. [PMID: 31248446 PMCID: PMC6598287 DOI: 10.1186/s13058-019-1157-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 05/28/2019] [Indexed: 02/06/2023] Open
Abstract
Background Atypical breast hyperplasias (AH) have a 10-year risk of progression to invasive cancer estimated at 4–7%, with the overall risk of developing breast cancer increased by ~ 4-fold. AH lesions are estrogen receptor alpha positive (ERα+) and represent risk indicators and/or precursor lesions to low grade ERα+ tumors. Therefore, molecular profiles of AH lesions offer insights into the earliest changes in the breast epithelium, rendering it susceptible to oncogenic transformation. Methods In this study, women were selected who were diagnosed with ductal or lobular AH, but no breast cancer prior to or within the 2-year follow-up. Paired AH and histologically normal benign (HNB) tissues from patients were microdissected. RNA was isolated, amplified linearly, labeled, and hybridized to whole transcriptome microarrays to determine gene expression profiles. Genes that were differentially expressed between AH and HNB were identified using a paired analysis. Gene expression signatures distinguishing AH and HNB were defined using AGNES and PAM methods. Regulation of gene networks was investigated using breast epithelial cell lines, explant cultures of normal breast tissue and mouse tissues. Results A 99-gene signature discriminated the histologically normal and AH tissues in 81% of the cases. Network analysis identified coordinated alterations in signaling through ERα, epidermal growth factor receptors, and androgen receptor which were associated with the development of both lobular and ductal AH. Decreased expression of SFRP1 was also consistently lower in AH. Knockdown of SFRP1 in 76N-Tert cells resulted altered expression of 13 genes similarly to that observed in AH. An SFRP1-regulated network was also observed in tissues from mice lacking Sfrp1. Re-expression of SFRP1 in MCF7 cells provided further support for the SFRP1-regulated network. Treatment of breast explant cultures with rSFRP1 dampened estrogen-induced progesterone receptor levels. Conclusions The alterations in gene expression were observed in both ductal and lobular AH suggesting shared underlying mechanisms predisposing to AH. Loss of SFRP1 expression is a significant regulator of AH transcriptional profiles driving previously unidentified changes affecting responses to estrogen and possibly other pathways. The gene signature and pathways provide insights into alterations contributing to AH breast lesions. Electronic supplementary material The online version of this article (10.1186/s13058-019-1157-5) contains supplementary material, which is available to authorized users.
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26
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Lessi F, Scatena C, Aretini P, Menicagli M, Franceschi S, Naccarato AG, Mazzanti CM. Molecular profiling of microinvasive breast cancer microenvironment progression. J Transl Med 2019; 17:187. [PMID: 31159827 PMCID: PMC6547528 DOI: 10.1186/s12967-019-1936-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 05/24/2019] [Indexed: 12/15/2022] Open
Abstract
Background Tumors develop by progression through a series of stages. Every cell of the tumor microenvironment is constantly changing in the flow of the cancer progression. It has become clear in recent years that stroma is essential for tumor maintenance and growth. Here, we aimed to give a chronological order of gene expression changes given in the dynamical framework of microinvasive breast cancer microenvironment. Methods RNA-seq was performed on seven microinvasive breast cancers. For each of them we microdissected seven different portions of the tumor, four related to the breast epithelium and three to the stroma. Breast epithelium was chronologically subdivided in normal breast epithelium (NBE), carcinoma in situ (CIS), emerging invasive fingers (EIF) and invasive breast cancer (IBC). For each of the breast epithelium subdivisions we collected the adjacent stroma (S): S-NBE, S-EIF and S-IBC. Results The overall differentially expressed genes (DEGs) in all the compartments were analysed and evaluated to understand the pathways involved in tumor progression. Then we analysed the DEGs of the epithelial and stromal portions in comparison with the normal portions. We observed that the stromal cells are necessary for the development and the maintenance of the tumor, especially in tumor progression. Moreover the most important genes involved in the main metabolic pathways were analysed and the communications within the different cell compartments were highlighted. Conclusions As a future perspective, a deeply study of the identified key genes, particularly in the stromal cells, will be crucial to develop an anticancer therapy that is undergoing a conversion from a cancer cell-centric strategy to a stroma-centric strategy, more genomically stable. Electronic supplementary material The online version of this article (10.1186/s12967-019-1936-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- F Lessi
- Genomic Section, Fondazione Pisana per la Scienza ONLUS, via Ferruccio Giovannini, 13, S. Giuliano Terme (PI), 56017, Pisa, Italy.
| | - C Scatena
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - P Aretini
- Genomic Section, Fondazione Pisana per la Scienza ONLUS, via Ferruccio Giovannini, 13, S. Giuliano Terme (PI), 56017, Pisa, Italy
| | - M Menicagli
- Genomic Section, Fondazione Pisana per la Scienza ONLUS, via Ferruccio Giovannini, 13, S. Giuliano Terme (PI), 56017, Pisa, Italy
| | - S Franceschi
- Genomic Section, Fondazione Pisana per la Scienza ONLUS, via Ferruccio Giovannini, 13, S. Giuliano Terme (PI), 56017, Pisa, Italy
| | - A G Naccarato
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - C M Mazzanti
- Genomic Section, Fondazione Pisana per la Scienza ONLUS, via Ferruccio Giovannini, 13, S. Giuliano Terme (PI), 56017, Pisa, Italy
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