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Zhang W, Cui Y, Liu B, Loza M, Park SJ, Nakai K. HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data. Brief Bioinform 2024; 25:bbae152. [PMID: 38581422 PMCID: PMC10998639 DOI: 10.1093/bib/bbae152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/19/2024] [Accepted: 03/10/2024] [Indexed: 04/08/2024] Open
Abstract
Reliable cell type annotations are crucial for investigating cellular heterogeneity in single-cell omics data. Although various computational approaches have been proposed for single-cell RNA sequencing (scRNA-seq) annotation, high-quality cell labels are still lacking in single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) data, because of extreme sparsity and inconsistent chromatin accessibility between datasets. Here, we present a novel automated cell annotation method that transfers cell type information from a well-labeled scRNA-seq reference to an unlabeled scATAC-seq target, via a parallel graph neural network, in a semi-supervised manner. Unlike existing methods that utilize only gene expression or gene activity features, HyGAnno leverages genome-wide accessibility peak features to facilitate the training process. In addition, HyGAnno reconstructs a reference-target cell graph to detect cells with low prediction reliability, according to their specific graph connectivity patterns. HyGAnno was assessed across various datasets, showcasing its strengths in precise cell annotation, generating interpretable cell embeddings, robustness to noisy reference data and adaptability to tumor tissues.
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Affiliation(s)
- Weihang Zhang
- Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Yang Cui
- Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Bowen Liu
- Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Martin Loza
- Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Sung-Joon Park
- Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Kenta Nakai
- Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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Ye M, Zhang B, Han X, Wei X, Wang Y, Cao W, Wu J, Chen C, Sun X, Sun K, Li H, Zhang Q, Liang T. Low-Pass Genomic Sequencing Reveals Novel Subtypes of Pancreatic Cystic Neoplasms. Ann Surg Oncol 2023; 30:5804-5812. [PMID: 37249723 DOI: 10.1245/s10434-023-13676-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/08/2023] [Indexed: 05/31/2023]
Abstract
BACKGROUND Over the years, the detection rate of pancreatic cystic neoplasms (PCNs) has significantly increased; however, the differential diagnosis and identification of high-risk PCNs remain challenging. We sought to investigate whether chromosomal instability (CIN) features in cell-free DNA in the cystic fluid of PCNs could help to identify high-risk PCNs. METHODS Pancreatic cystic fluid samples from 102 patients with PCNs were intraoperatively collected for detection of CIN using an ultrasensitive chromosomal aneuploidy detector. Clinical and imaging data were retrospectively collected, and statistical analysis was performed to assess the potential role of CIN in clinical practice. RESULTS CIN was investigated in a total of 100 patients. Sixteen of 26 serous cystic cystadenomas (SCAs) harbored deletions of chr3p and/or chr6p, whereas low rates of CIN were detected in mucinous cystic neoplasms. Most malignant PCNs presented with more than one type of CIN; amplification of chr1q and chr8q found in nine and seven of 11 malignant PCNs (81.8% and 63.6%), respectively, could aid in distinguishing high-risk IPMNs from low-risk ones, with a higher sensitivity than imaging. A combination of the mural nodule imaging feature and amplification of chr1q and chr8q achieved a sensitivity of 70.0% and a specificity of 82.4% in identifying high-risk IPMNs. CONCLUSIONS Our work revealed the distinct CIN signature of different types of PCNs. Deletions of chr3p and chr6p defined a subtype of SCAs. Gains of chr1q and chr8q were associated with insidious malignant PCNs and helped identify high-risk IPMNs.
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Affiliation(s)
- Mao Ye
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, China
| | - Bo Zhang
- Department of General Surgery, Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Xu Han
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaobao Wei
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yangyang Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wanyue Cao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiangchao Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Cao Chen
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xu Sun
- Department of General Surgery, Huzhou Central Hospital, Zhejiang University School of Medicine, Huzhou, China
| | - Ke Sun
- Zhejiang University Cancer Center, Hangzhou, China
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haijun Li
- Department of General Surgery, Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China.
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, China.
- Zhejiang University Cancer Center, Hangzhou, China.
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang Province, China.
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, China.
- Zhejiang University Cancer Center, Hangzhou, China.
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang Province, China.
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Tan C, Du Y, Zhu L, Jing S, Gao J, Qian Y, Yue X, Lee I. KDEL Receptor Trafficking to the Plasma Membrane Is Regulated by ACBD3 and Rab4A-GTP. Cells 2023; 12:cells12071079. [PMID: 37048152 PMCID: PMC10093020 DOI: 10.3390/cells12071079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
KDEL receptor-1 maintains homeostasis in the early secretory pathway by capturing and retrieving ER chaperones to the ER during heavy secretory activity. Unexpectedly, a fraction of the receptor is also known to reside in the plasma membrane (PM), although it is largely unknown exactly how the KDEL receptor gets exported from the Golgi and travels to the PM. We have previously shown that a Golgi scaffolding protein (ACBD3) facilitates KDEL receptor localization at the Golgi via the regulating cargo wave-induced cAMP/PKA-dependent signaling pathway. Upon endocytosis, surface-expressed KDEL receptor undergoes highly complex itineraries through the Golgi and the endo-lysosomal compartments, where the endocytosed receptor utilizes Rab14A- and Rab11A-positive recycling endosomes and clathrin-decorated tubulovesicular carriers. In this study, we sought to investigate the mechanism through which the KDEL receptor gets exported from the Golgi en route to the PM. We report here that ACBD3 depletion results in greatly increased trafficking of KDEL receptor to the PM via Rab4A-positive tubular carriers emanating from the Golgi. Expression of constitutively activated Rab4A mutant (Q72L) increases the surface expression of KDEL receptor up to 2~3-fold, whereas Rab4A knockdown or the expression of GDP-locked Rab4A mutant (S27N) inhibits KDEL receptor targeting of the PM. Importantly, KDELR trafficking from the Golgi to the PM is independent of PKA- and Src kinase-mediated mechanisms. Taken together, these results reveal that ACBD3 and Rab4A play a key role in regulating KDEL receptor trafficking to the cell surface.
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Affiliation(s)
- Chuanting Tan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yulei Du
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Lianhui Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shuaiyang Jing
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Jingkai Gao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yi Qian
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xihua Yue
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Intaek Lee
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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Effects of Human Papilloma Virus E6/E7 Oncoproteins on Genomic Structure in Head and Neck Squamous Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14246190. [PMID: 36551675 PMCID: PMC9777059 DOI: 10.3390/cancers14246190] [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: 11/26/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Human Papilloma Virus (HPV) is highly prevalent within the U.S., with studies estimating that over 80% of individuals will contract the virus in their lifetime. HPV is considered a primary risk factor for the development and progression of oropharyngeal cancers. The impact of the HPV virus's E6 and E7 oncoproteins on cellular signaling pathways and genomic integration has been extensively characterized. Indirect genomic effects; however, remain relatively unidentified. In this study, we analyzed 83 HPV+ Head and Neck Squamous Cell Carcinoma (HNSCC) patients of varying HPV types. Expression counts of the HPV E6 and E7 oncogenes were estimated across samples and correlated with genomic mutational classes. High expression of E6 and E7 oncoproteins was associated with a greater number of total point mutations, especially on chromosomes 1, 11, and 17, which have been implicated in HPV-mediated cancers in previous studies. Samples with high E6 and E7 expression also exhibited more frequent non-clustered structural variation and a lack of clustered variation altogether. Copy number segments were present with fewer number of repeats in high E6 and E7 expression samples, which is known to correlate with decreased expression of affected genes. E6 and E7 expression was associated with increased activity of several cellular pathways associated in oncogenesis and telomere maintenance. In comprehensively characterizing the effects of the HPV oncoproteins on the human genome, potential mechanisms of HNSCC pathogenesis may be further elucidated.
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ACBD3 Bioinformatic Analysis and Protein Expression in Breast Cancer Cells. Int J Mol Sci 2022; 23:ijms23168881. [PMID: 36012147 PMCID: PMC9408326 DOI: 10.3390/ijms23168881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/16/2022] Open
Abstract
ACBD3 overexpression has previously been found to correlate with worse prognosis for breast cancer patients and, as an incredibly diverse protein in both function and cellular localisation, ACBD3 may have a larger role in breast cancer than previously thought. This study further investigated ACBD3′s role in breast cancer. Bioinformatic databases were queried to characterise ACBD3 expression and mutation in breast cancer and to investigate how overexpression affects breast cancer patient outcomes. Immunohistochemistry was carried out to examine ACBD3 location within cells and tissue structures. ACBD3 was more highly expressed in breast cancer than in any other cancer or matched normal tissue, and expression over the median level resulted in reduced relapse-free, overall, and distant metastasis-free survival for breast cancer patients as a whole, with some differences observed between subtypes. IHC analysis found that ACBD3 levels varied based on hormone receptor status, indicating that ACBD3 could be a candidate biomarker for poor patient prognosis in breast cancer and may possibly be a biomarker for ER signal reprogramming of precancerous breast tissue.
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Li Z, Li Y, Wang X, Yang Q. PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer. Cancer Cell Int 2021; 21:13. [PMID: 33407498 PMCID: PMC7788839 DOI: 10.1186/s12935-020-01707-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
Background Although immune checkpoint blockade has emerged as a novel promising strategy for triple-negative breast cancer (TNBC), many patients fail response or acquire resistance to current agents. Consequently, our focus need to shift toward alternative inhibitory targets, predictor for responsiveness, and immune suppressive mechanisms. Methods In this study, we performed systematic bioinformatics analyses to identify PPP2R2B as a robust tumor suppressor in TNBC. Meanwhile, breast cancer progression cell line model was applied in our research. Quantitative real-time PCR assay (Q-PCR) was carried out to assess the role of PPP2R2B in the onset and progression of breast cancer. Furthermore, we validated the effect of PPP2R2B on immune activity via in vitro experiments based on macrophages. To further decipher the roles of PPP2R2B in TNBC, we investigated the transcriptome level, genomic profiles, and its clinical prognostic value. Results In TNBC tissues, PPP2R2B expression was significantly downregulated compared to normal breast tissues. Kaplan‐Meier survival analysis revealed that patients with low PPP2R2B expression had shorter survival time than those with high PPP2R2B expression. Q-PCR analysis suggested that PPP2R2B downregulation could play a key role in breast-cancer initiation and progression. Additionally, our findings showed that PPP2R2B was positively related with CD8 T cells, CD4 Th1 helper cells, and M1 macrophages, but negatively related with M2 macrophages. Subsequent results identified that PPP2R2B was strongly related with immune inhibitor genes (GZMA, PRF1, and IFNG), which could improve T lymphocytes antitumor function and restrict immune evasion. Meanwhile, T cell receptor signaling pathway and antigen processing and presentation signaling pathway were significantly suppressed in low PPP2R2B expression group. Afterwards, distinct subgroups based on PPP2R2B expression exhibited several unique features in somatic mutations, copy numbers alterations, extent of copy number burden, and promoter methylation level. Conclusion Our results indicated that PPP2R2B could serve as a promising biomarker for TNBC, and help predict immunotherapeutic response and guide personalized strategies in TNBC treatment.
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Affiliation(s)
- Zheng Li
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Yaming Li
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Xiaolong Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Qifeng Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China. .,Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, China. .,Research Institute of Breast Cancer, Shandong University, Jinan, Shandong, China.
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Pan-cancer driver copy number alterations identified by joint expression/CNA data analysis. Sci Rep 2020; 10:17199. [PMID: 33057153 PMCID: PMC7566486 DOI: 10.1038/s41598-020-74276-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023] Open
Abstract
AbstractAnalysis of large gene expression datasets from biopsies of cancer patients can identify co-expression signatures representing particular biomolecular events in cancer. Some of these signatures involve genomically co-localized genes resulting from the presence of copy number alterations (CNAs), for which analysis of the expression of the underlying genes provides valuable information about their combined role as oncogenes or tumor suppressor genes. Here we focus on the discovery and interpretation of such signatures that are present in multiple cancer types due to driver amplifications and deletions in particular regions of the genome after doing a comprehensive analysis combining both gene expression and CNA data from The Cancer Genome Atlas.
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Gjerstorff MF. Novel Insights Into Epigenetic Reprogramming and Destabilization of Pericentromeric Heterochromatin in Cancer. Front Oncol 2020; 10:594163. [PMID: 33251148 PMCID: PMC7674669 DOI: 10.3389/fonc.2020.594163] [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: 08/12/2020] [Accepted: 10/15/2020] [Indexed: 12/17/2022] Open
Abstract
Pericentromeric heterochromatin is maintained in a condensed structure by repressive epigenetic control mechanisms and perturbation of these may cause diseases. The chromosome 1q12 region harbors the largest pericentromeric heterochromatin domain in the genome and is among the most common breakpoints in both solid and hematopoietic cancers. Furthermore, the 1q arm is frequently amplified in cancer and this may support tumorigenesis by increasing the dosage of the many oncogenes of this genomic region. Recent studies have provided insight into the mechanisms leading to loss of 1q12 stability and 1q amplification and DNA hypomethylation seems to play a prominent role. This may be the result of decreased activity of DNA methyltransferases and instrumental for 1q12 destabilization or arise secondary to perturbation of other important epigenetic mechanisms that control repression of pericentromeric heterochromatin. Polycomb proteins were recently demonstrated to epigenetically reprogram demethylated 1q12 pericentromeric heterochromatin in premalignant and malignant cells to form large subnuclear structures known as polycomb bodies. This may influence the regulation and stability of 1q12 pericentromeric heterochromatin and/or the distribution of polycomb factors to support tumorigenesis. This review will discuss recent insight into the epigenetic perturbations causing the destabilization of 1q12 pericentromeric heterochromatin and its possible implications for tumor biology.
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Affiliation(s)
- Morten Frier Gjerstorff
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Odense, Denmark.,Academy of Geriatric Cancer Research (AgeCare), Odense University Hospital, Odense, Denmark
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Dessources K, Da Cruz Paula A, Pareja F, Stylianou A, Cybulska P, Farmanbar A, Chandarlapaty S, Abu-Rustum NR, Reis-Filho JS, Weigelt B, Mueller JJ. Acquisition of APOBEC Mutagenesis and Microsatellite Instability Signatures in the Development of Brain Metastases in Low-Grade, Early-Stage Endometrioid Endometrial Carcinoma. JCO Precis Oncol 2020; 4:PO.20.00044. [PMID: 33163849 PMCID: PMC7608574 DOI: 10.1200/po.20.00044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2020] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anthe Stylianou
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paulina Cybulska
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Amir Farmanbar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
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Rossi T, Gallerani G, Angeli D, Cocchi C, Bandini E, Fici P, Gaudio M, Martinelli G, Rocca A, Maltoni R, Fabbri F. Single-Cell NGS-Based Analysis of Copy Number Alterations Reveals New Insights in Circulating Tumor Cells Persistence in Early-Stage Breast Cancer. Cancers (Basel) 2020; 12:cancers12092490. [PMID: 32887501 PMCID: PMC7565733 DOI: 10.3390/cancers12092490] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Circulating tumor cells (CTCs) are crucial for the identification of patients with a higher risk of relapse, including those diagnosed with breast cancer (BC). The aim of this study was to explore their molecular aspects in 11 early-stage BC patients during patient management, focusing on copy number alterations (CNAs) and exploiting a single-CTC next-generation sequencing approach. CTCs showed different degrees of aberration based on access time. Moreover, CTCs, in particular those persisting even months after tumor resection, shared CNAs with matched tumor tissue. Enrichment analyses of CNAs on CTCs highlighted peculiar aberrations, especially associated with interferon (IFN)-associated terms. The study of CTCs CNAs can provide information about the molecular mechanisms involving CTC-related processes and their survival ability in occult niches, supporting the goal of exploiting their application in patients’ surveillance and follow-up. Abstract Circulating tumor cells (CTCs) are a rare population of cells representing a key player in the metastatic cascade. They are recognized as a validated tool for the identification of patients with a higher risk of relapse, including those diagnosed with breast cancer (BC). However, CTCs are characterized by high levels of heterogeneity that also involve copy number alterations (CNAs), structural variations associated with gene dosage changes. In this study, single CTCs were isolated from the peripheral blood of 11 early-stage BC patients at different time points. A label-free enrichment of CTCs was performed using OncoQuick, and single CTCs were isolated using DEPArray. Libraries were prepared from single CTCs and DNA extracted from matched tumor tissues for a whole-genome low-coverage next-generation sequencing (NGS) analysis using the Ion Torrent S5 System. The analysis of the CNA burden highlighted that CTCs had different degrees of aberration based on the time point and subtype. CTCs were found even six months after surgery and shared CNAs with matched tumor tissue. Tumor-associated CNAs that were recurrent in CTCs were patient-specific, and some alterations involved regions associated with BC and survival (i.e., gains at 1q21-23 and 5p15.33). The enrichment analysis emphasized the involvement of aberrations of terms, associated in particular with interferon (IFN) signaling. Collectively, our findings reveal that these aberrations may contribute to understanding the molecular mechanisms involving CTC-related processes and their survival ability in occult niches, supporting the goal of exploiting their application in patients’ surveillance and follow-up.
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Affiliation(s)
- Tania Rossi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (G.G.); (C.C.); (E.B.); (P.F.); (F.F.)
- Correspondence: ; Tel.: +39-05-4373-9982
| | - Giulia Gallerani
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (G.G.); (C.C.); (E.B.); (P.F.); (F.F.)
| | - Davide Angeli
- Unit of Biostatistics and Clinical Trials, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy;
| | - Claudia Cocchi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (G.G.); (C.C.); (E.B.); (P.F.); (F.F.)
| | - Erika Bandini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (G.G.); (C.C.); (E.B.); (P.F.); (F.F.)
| | - Pietro Fici
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (G.G.); (C.C.); (E.B.); (P.F.); (F.F.)
| | - Michele Gaudio
- Pathology Unit, AUSL Romagna, Morgagni-Pierantoni Hospital, 47121 Forlì, Italy;
| | - Giovanni Martinelli
- Scientific Directorate, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy;
| | - Andrea Rocca
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (A.R.); (R.M.)
| | - Roberta Maltoni
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (A.R.); (R.M.)
| | - Francesco Fabbri
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (G.G.); (C.C.); (E.B.); (P.F.); (F.F.)
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Saxena M, Kalathur RKR, Rubinstein N, Vettiger A, Sugiyama N, Neutzner M, Coto-Llerena M, Kancherla V, Ercan C, Piscuoglio S, Fischer J, Fagiani E, Cantù C, Basler K, Christofori G. A Pygopus 2-Histone Interaction Is Critical for Cancer Cell Dedifferentiation and Progression in Malignant Breast Cancer. Cancer Res 2020; 80:3631-3648. [PMID: 32586983 DOI: 10.1158/0008-5472.can-19-2910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/19/2020] [Accepted: 06/22/2020] [Indexed: 11/16/2022]
Abstract
Pygopus 2 (Pygo2) is a coactivator of Wnt/β-catenin signaling that can bind bi- or trimethylated lysine 4 of histone-3 (H3K4me2/3) and participate in chromatin reading and writing. It remains unknown whether the Pygo2-H3K4me2/3 association has a functional relevance in breast cancer progression in vivo. To investigate the functional relevance of histone-binding activity of Pygo2 in malignant progression of breast cancer, we generated a knock-in mouse model where binding of Pygo2 to H3K4me2/3 was rendered ineffective. Loss of Pygo2-histone interaction resulted in smaller, differentiated, and less metastatic tumors, due, in part, to decreased canonical Wnt/β-catenin signaling. RNA- and ATAC-sequencing analyses of tumor-derived cell lines revealed downregulation of TGFβ signaling and upregulation of differentiation pathways such as PDGFR signaling. Increased differentiation correlated with a luminal cell fate that could be reversed by inhibition of PDGFR activity. Mechanistically, the Pygo2-histone interaction potentiated Wnt/β-catenin signaling, in part, by repressing the expression of Wnt signaling antagonists. Furthermore, Pygo2 and β-catenin regulated the expression of miR-29 family members, which, in turn, repressed PDGFR expression to promote dedifferentiation of wild-type Pygo2 mammary epithelial tumor cells. Collectively, these results demonstrate that the histone binding function of Pygo2 is important for driving dedifferentiation and malignancy of breast tumors, and loss of this binding activates various differentiation pathways that attenuate primary tumor growth and metastasis formation. Interfering with the Pygo2-H3K4me2/3 interaction may therefore serve as an attractive therapeutic target for metastatic breast cancer. SIGNIFICANCE: Pygo2 represents a potential therapeutic target in metastatic breast cancer, as its histone-binding capability promotes β-catenin-mediated Wnt signaling and transcriptional control in breast cancer cell dedifferentiation, EMT, and metastasis.
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Affiliation(s)
- Meera Saxena
- Department of Biomedicine, University of Basel, Basel, Switzerland.
| | | | | | - Andrea Vettiger
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Nami Sugiyama
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Melanie Neutzner
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | | | - Caner Ercan
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Jonas Fischer
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Ernesta Fagiani
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Claudio Cantù
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Wallenberg Centre for Molecular Medicine Linköping; Department of Biomedical and Clinical Sciences, Faculty of Health Science, Linköping University, Linköping, Sweden
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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12
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Elsarraj HS, Hong Y, Limback D, Zhao R, Berger J, Bishop SC, Sabbagh A, Oppenheimer L, Harper HE, Tsimelzon A, Huang S, Hilsenbeck SG, Edwards DP, Fontes J, Fan F, Madan R, Fangman B, Ellis A, Tawfik O, Persons DL, Fields T, Godwin AK, Hagan CR, Swenson-Fields K, Coarfa C, Thompson J, Behbod F. BCL9/STAT3 regulation of transcriptional enhancer networks promote DCIS progression. NPJ Breast Cancer 2020; 6:12. [PMID: 32352029 PMCID: PMC7181646 DOI: 10.1038/s41523-020-0157-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/04/2020] [Indexed: 12/21/2022] Open
Abstract
The molecular processes by which some human ductal carcinoma in situ (DCIS) lesions advance to the more aggressive form, while others remain indolent, are largely unknown. Experiments utilizing a patient-derived (PDX) DCIS Mouse INtraDuctal (MIND) animal model combined with ChIP-exo and RNA sequencing revealed that the formation of protein complexes between B Cell Lymphoma-9 (BCL9), phosphoserine 727 STAT3 (PS-727-STAT3) and non-STAT3 transcription factors on chromatin enhancers lead to subsequent transcription of key drivers of DCIS malignancy. Downregulation of two such targets, integrin β3 and its associated metalloproteinase, MMP16, resulted in a significant inhibition of DCIS invasive progression. Finally, in vivo targeting of BCL9, using rosemary extract, resulted in significant inhibition of DCIS malignancy in both cell line and PDX DCIS MIND animal models. As such, our studies provide compelling evidence for future testing of rosemary extract as a chemopreventive agent in breast cancer.
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Affiliation(s)
- Hanan S. Elsarraj
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Yan Hong
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Darlene Limback
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Ruonan Zhao
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Jenna Berger
- Warren Alpert Medical School of Brown University, Providence, RI 02912 USA
| | - Stephanie C. Bishop
- Department of Pharmaceutical Sciences, South University, 709 Mall Blvd, Savannah, GA 31406 USA
| | - Aria Sabbagh
- McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030 USA
| | - Linzi Oppenheimer
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Haleigh E. Harper
- University of Kansas School of Medicine, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Anna Tsimelzon
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Shixia Huang
- Dan L. Duncan Cancer Center and Department of Molecular & Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Susan G. Hilsenbeck
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX C30 USA
| | - Dean P. Edwards
- Dan L. Duncan Cancer Center and Department of Molecular & Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Joseph Fontes
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Fang Fan
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Rashna Madan
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Ben Fangman
- University of Kansas School of Medicine, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Ashley Ellis
- University of Kansas School of Medicine, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Ossama Tawfik
- MAWD Pathology Group, St Luke’s Health System of Kansas City, 2750 Clay Edwards Dr, Kansas City, MO 64116 USA
| | - Diane L. Persons
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Timothy Fields
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Christy R. Hagan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Katherine Swenson-Fields
- Department of Anatomy and Cell Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Cristian Coarfa
- Dan L. Duncan Cancer Center and Department of Molecular & Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Jeffrey Thompson
- Department of Biostatistics, The University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160 USA
| | - Fariba Behbod
- Department of Pathology and Laboratory Medicine, MS 3045, The University of Kansas Medical Center, Kansas City, KS 66160 USA
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13
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Denomy C, Germain S, Haave B, Vizeacoumar FS, Freywald A, Weaver BA, Vizeacoumar FJ. Banding Together: A Systematic Comparison of The Cancer Genome Atlas and the Mitelman Databases. Cancer Res 2019; 79:5181-5190. [PMID: 31416843 DOI: 10.1158/0008-5472.can-19-0585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/22/2019] [Accepted: 08/09/2019] [Indexed: 11/16/2022]
Abstract
Cytogenetic aberrations at the single-cell level represent an important characteristic of cancer cells relevant to tumor evolution and prognosis. However, with the advent of The Cancer Genome Atlas (TCGA), there has been a major shift in cancer research to the use of data from aggregate cell populations. Given that tumor cells harbor hundreds to thousands of biologically relevant genetic alterations that manifest as intratumor heterogeneity, these aggregate analyses may miss alterations readily observable at single-cell resolution. Using the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer, we developed an algorithm to parse International System for Cytogenetic Nomenclature notation for quantitative abnormalities. Comparison of the Mitelman database and TCGA demonstrated that the Mitelman database is a powerful resource, and that cytogenetic aberrations captured by traditional approaches used in Mitelman database are on par with population-based genomic analyses used in TCGA. This algorithm will help nonspecialists to overcome the challenges associated with the format and syntax of the Mitelman database. SIGNIFICANCE: A novel in silico approach compares cytogenetic data between the Mitelman database and TCGA, highlighting the advantages and limitations of both datasets.
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Affiliation(s)
- Connor Denomy
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Samuel Germain
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Bjorn Haave
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Beth A Weaver
- Department of Cell and Regenerative Biology, Department of Oncology/McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Franco J Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Canada. .,Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Canada
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14
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The Great Escape: how phosphatidylinositol 4-kinases and PI4P promote vesicle exit from the Golgi (and drive cancer). Biochem J 2019; 476:2321-2346. [DOI: 10.1042/bcj20180622] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/06/2019] [Accepted: 08/12/2019] [Indexed: 12/13/2022]
Abstract
Abstract
Phosphatidylinositol 4-phosphate (PI4P) is a membrane glycerophospholipid and a major regulator of the characteristic appearance of the Golgi complex as well as its vesicular trafficking, signalling and metabolic functions. Phosphatidylinositol 4-kinases, and in particular the PI4KIIIβ isoform, act in concert with PI4P to recruit macromolecular complexes to initiate the biogenesis of trafficking vesicles for several Golgi exit routes. Dysregulation of Golgi PI4P metabolism and the PI4P protein interactome features in many cancers and is often associated with tumour progression and a poor prognosis. Increased expression of PI4P-binding proteins, such as GOLPH3 or PITPNC1, induces a malignant secretory phenotype and the release of proteins that can remodel the extracellular matrix, promote angiogenesis and enhance cell motility. Aberrant Golgi PI4P metabolism can also result in the impaired post-translational modification of proteins required for focal adhesion formation and cell–matrix interactions, thereby potentiating the development of aggressive metastatic and invasive tumours. Altered expression of the Golgi-targeted PI 4-kinases, PI4KIIIβ, PI4KIIα and PI4KIIβ, or the PI4P phosphate Sac1, can also modulate oncogenic signalling through effects on TGN-endosomal trafficking. A Golgi trafficking role for a PIP 5-kinase has been recently described, which indicates that PI4P is not the only functionally important phosphoinositide at this subcellular location. This review charts new developments in our understanding of phosphatidylinositol 4-kinase function at the Golgi and how PI4P-dependent trafficking can be deregulated in malignant disease.
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15
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Rodrigues-Peres RM, de S Carvalho B, Anurag M, Lei JT, Conz L, Gonçalves R, Cardoso Filho C, Ramalho S, de Paiva GR, Derchain SFM, Lopes-Cendes I, Ellis MJ, Sarian LO. Copy number alterations associated with clinical features in an underrepresented population with breast cancer. Mol Genet Genomic Med 2019; 7:e00750. [PMID: 31099189 PMCID: PMC6625096 DOI: 10.1002/mgg3.750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/22/2019] [Accepted: 04/26/2019] [Indexed: 12/14/2022] Open
Abstract
Background As the most incident tumor among women worldwide, breast cancer is a heterogeneous disease. Tremendous efforts have been made to understand how tumor characteristics as histological type, molecular subtype, and tumor microenvironment collectively influence disease diagnosis to treatment, which impact outcomes. Differences between populations and environmental and cultural factors have impacts on the origin and evolution of the disease, as well as the therapeutic challenges that arise due to these factors. We, then, compared copy number variations (CNVs) in mucinous and nonmucinous luminal breast tumors from a Brazilian cohort to investigate major CNV imbalances in mucinous tumors versus non‐mucinous luminal tumors, taking into account their clinical and pathological features. Methods 48 breast tumor samples and 48 matched control blood samples from Brazilian women were assessed for CNVs by chromosome microarray. Logistic regression and random forest models were used in order to assess CNVs in chromosomal regions from tumors. Results CNVs that were identified in chromosomes 1, 5, 8, 17, 19, and 21 classify tumors according to their histological type, ethnicity, disease stage, and familial history. Conclusion Copy number alterations described in this study provide a better understanding of the landscape of genomic aberrations in mucinous breast cancers that are associated with clinical features.
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Affiliation(s)
- Raquel M Rodrigues-Peres
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Benilton de S Carvalho
- Department of Statistics, Institute of Mathematics, Statistics and Scientific Computing, State University of Campinas-UNICAMP, Campinas, Brazil.,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Meenakshi Anurag
- Department of Medicine, Baylor College of Medicine, Houston, TX.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX
| | - Jonathan T Lei
- Department of Medicine, Baylor College of Medicine, Houston, TX.,Interdepartmental Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX
| | - Livia Conz
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Rodrigo Gonçalves
- Department of Mastology, Hospital das Clínicas, Discipline of Gynecology, Department of Obstetrics and Gynecology, Faculty of Medicine, University of São Paulo, Brazil
| | - Cássio Cardoso Filho
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Susana Ramalho
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Geisilene R de Paiva
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Sophie F M Derchain
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Iscia Lopes-Cendes
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil.,Department of Medical Genetics, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Matthew J Ellis
- Department of Medicine, Baylor College of Medicine, Houston, TX.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX.,Interdepartmental Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | - Luis O Sarian
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
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16
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Zhang Y, Chen Y, You F, Li W, Lang Z, Zou Z. Prognostic and clinicopathological significance of Cks1 in cancer: Evidence from a meta-analysis. J Cell Physiol 2019; 234:13423-13430. [PMID: 30605238 DOI: 10.1002/jcp.28021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/30/2018] [Indexed: 01/11/2023]
Abstract
BACKGROUND Cyclin-dependent kinase subunit 1 (Cks1), as a highly conserved regulatory protein, has pleiotropic roles in cell cycle progression. As research progresses, increasingly more statistics show that Cks1 may be involved in the occurrence, development, and prognosis of a variety of tumors but the conclusions remain controversial. In addition, there has been no meta-analysis demonstrating the correlation between Cks1 and cancer. Therefore, this meta-analysis was performed to determine the prognostic and clinicopathological significance of Cks1 in various cancers. METHODS Systematic computer literature retrieval was conducted on the Web of Science, Embase, PubMed, CNKI, and Wanfang databases. Stata SE12.0 software was used in the quantitative meta-analysis. The hazard ratio (HR) and relative risk (RR) were pooled to assess the relationship between Cks1 expression and overall survival (OS), disease-free survival (DFS), and clinicopathological parameters. RESULTS Nineteen studies were included, totaling 2,224 participants. High expression of Cks1 was significantly correlated with worse OS (HR, 2.62; 95% confidence interval [CI], 2.18-3.14; p < 0.001) and poorer DFS (HR, 2.73; 95% CI, 1.83-4.08; p < 0.001). In addition, high expression of Cks1 was related to lymph node metastasis (RR, 1.59; 95% CI, 1.22-2.07; p = 0.001) and advanced T stage (RR, 1.14; 95% CI, 1.04-1.25; p = 0.005). CONCLUSIONS High Cks1 expression predicted poorer prognosis and worse clinicopathological parameters in various cancers. Increased Cks1 could be a significant prognostic biomarker for poor survival in patients with various cancers.
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Affiliation(s)
- Yi Zhang
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P. R. China.,Nanchang University, Nanchang, Jiangxi, P. R. China
| | - Yuting Chen
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P. R. China.,Nanchang University, Nanchang, Jiangxi, P. R. China
| | - Fan You
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P. R. China.,Nanchang University, Nanchang, Jiangxi, P. R. China
| | - Wang Li
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P. R. China.,Nanchang University, Nanchang, Jiangxi, P. R. China
| | - Zhiquan Lang
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P. R. China.,Nanchang University, Nanchang, Jiangxi, P. R. China
| | - Zhenhong Zou
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P. R. China
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17
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Thomas A, Routh ED, Pullikuth A, Jin G, Su J, Chou JW, Hoadley KA, Print C, Knowlton N, Black MA, Demaria S, Wang E, Bedognetti D, Jones WD, Mehta GA, Gatza ML, Perou CM, Page DB, Triozzi P, Miller LD. Tumor mutational burden is a determinant of immune-mediated survival in breast cancer. Oncoimmunology 2018; 7:e1490854. [PMID: 30386679 PMCID: PMC6207420 DOI: 10.1080/2162402x.2018.1490854] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 12/19/2022] Open
Abstract
Mounting evidence supports a role for the immune system in breast cancer outcomes. The ability to distinguish highly immunogenic tumors susceptible to anti-tumor immunity from weakly immunogenic or inherently immune-resistant tumors would guide development of therapeutic strategies in breast cancer. Genomic, transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) breast cancer cohorts were used to examine statistical associations between tumor mutational burden (TMB) and the survival of patients whose tumors were assigned to previously-described prognostic immune subclasses reflecting favorable, weak or poor immune-infiltrate dispositions (FID, WID or PID, respectively). Tumor immune subclasses were associated with survival in patients with high TMB (TMB-Hi, P < 0.001) but not in those with low TMB (TMB-Lo, P = 0.44). This statistical relationship was confirmed in the METABRIC cohort (TMB-Hi, P = 0.047; TMB-Lo, P = 0.39), and also found to hold true in the more-indolent Luminal A tumor subtype (TMB-Hi, P = 0.011; TMB-Lo, P = 0.91). In TMB-Hi tumors, the FID subclass was associated with prolonged survival independent of tumor stage, molecular subtype, age and treatment. Copy number analysis revealed the reproducible, preferential amplification of chromosome 1q immune-regulatory genes in the PID immune subclass. These findings demonstrate a previously unappreciated role for TMB as a determinant of immune-mediated survival of breast cancer patients and identify candidate immune-regulatory mechanisms associated with immunologically cold tumors. Immune subtyping of breast cancers may offer opportunities for therapeutic stratification.
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Affiliation(s)
- Alexandra Thomas
- Section of Hematology and Oncology, Department of Internal Medicine, Wake Forest Baptist Medical Center, Winston-Salem, NC, USA.,Wake Forest Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Eric D Routh
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Ashok Pullikuth
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Guangxu Jin
- Wake Forest Comprehensive Cancer Center, Winston-Salem, NC, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jing Su
- Division of Radiologic Sciences and Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
| | - Jeff W Chou
- Wake Forest Comprehensive Cancer Center, Winston-Salem, NC, USA.,Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Katherine A Hoadley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cristin Print
- Department of Molecular Medicine and Pathology and Maurice Wilkins Institute, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Nick Knowlton
- Department of Molecular Medicine and Pathology and Maurice Wilkins Institute, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Michael A Black
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Sandra Demaria
- Department of Radiation Oncology and Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Ena Wang
- Department of Tumor Biology, Immunology and Therapy, Division of Translational Medicine, Sidra Medical and Research Center, Doha, Qatar
| | - Davide Bedognetti
- Department of Tumor Biology, Immunology and Therapy, Division of Translational Medicine, Sidra Medical and Research Center, Doha, Qatar
| | | | - Gaurav A Mehta
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Michael L Gatza
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Charles M Perou
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David B Page
- Department of Medicine, Providence Cancer Center, Earle A. Chiles Research Institute, Portland, OR, USA
| | - Pierre Triozzi
- Section of Hematology and Oncology, Department of Internal Medicine, Wake Forest Baptist Medical Center, Winston-Salem, NC, USA.,Wake Forest Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Lance D Miller
- Wake Forest Comprehensive Cancer Center, Winston-Salem, NC, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
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18
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Circulating tumor cells: potential markers of minimal residual disease in ovarian cancer? a study of the OVCAD consortium. Oncotarget 2017; 8:106415-106428. [PMID: 29290959 PMCID: PMC5739744 DOI: 10.18632/oncotarget.22468] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 10/11/2017] [Indexed: 11/25/2022] Open
Abstract
Purpose In 75% of ovarian cancer patients the tumor mass is completely eradicated by established surgical and cytotoxic treatment; however, the majority of the tumors recur within 24 months. Here we investigated the role of circulating tumor cells (CTCs) indicating occult tumor load, which remains inaccessible by established diagnostics. Experimental design Blood was taken at diagnosis (baseline samples, n = 102) and six months after completion of adjuvant first-line chemotherapy (follow-up samples; n = 78). CTCs were enriched by density gradient centrifugation. A multi-marker immunostaining was established and further complemented by FISH on CTCs and tumor/metastasis tissues using probes for stem-cell like fusion genes MECOM and HHLA1. Results CTCs were observed in 26.5% baseline and 7.7% follow-up blood samples at a mean number of 12.4 and 2.8 CTCs per ml blood, respectively. Baseline CTCs indicated a higher risk of death in R0 patients with complete gross resection (univariate: HR 2.158, 95% CI 1.111–4.191, p = 0.023; multivariate: HR 2.720, 95% CI 1.340–5.522, p = 0.006). At follow-up, the presence of CTCs was associated with response to primary treatment as assessed using RECIST criteria. Chromosomal gains at MECOM and HHLA1 loci suggest that the observed cells were cancer cells and reflect pathophysiological decisive chromosomal aberrations of the primary and metastatic tumors. Conclusions Our data suggest that CTCs detected by the multi-marker protein panel and/or MECOM/HHLA1 FISH represent minimal residual disease in optimally debulked ovarian cancer patients. The role of CTCs cells especially for clinical therapy stratification of the patients has to be validated in consecutive larger studies applying standardized treatment schemes.
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19
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Gu X, Liu CJ, Wei JJ. Predicting pathway cross-talks in ankylosing spondylitis through investigating the interactions among pathways. ACTA ACUST UNITED AC 2017; 51:e6698. [PMID: 29160414 PMCID: PMC5685062 DOI: 10.1590/1414-431x20176698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 09/06/2017] [Indexed: 11/22/2022]
Abstract
Given that the pathogenesis of ankylosing spondylitis (AS) remains unclear, the aim of this study was to detect the potentially functional pathway cross-talk in AS to further reveal the pathogenesis of this disease. Using microarray profile of AS and biological pathways as study objects, Monte Carlo cross-validation method was used to identify the significant pathway cross-talks. In the process of Monte Carlo cross-validation, all steps were iterated 50 times. For each run, detection of differentially expressed genes (DEGs) between two groups was conducted. The extraction of the potential disrupted pathways enriched by DEGs was then implemented. Subsequently, we established a discriminating score (DS) for each pathway pair according to the distribution of gene expression levels. After that, we utilized random forest (RF) classification model to screen out the top 10 paired pathways with the highest area under the curve (AUCs), which was computed using 10-fold cross-validation approach. After 50 bootstrap, the best pairs of pathways were identified. According to their AUC values, the pair of pathways, antigen presentation pathway and fMLP signaling in neutrophils, achieved the best AUC value of 1.000, which indicated that this pathway cross-talk could distinguish AS patients from normal subjects. Moreover, the paired pathways of SAPK/JNK signaling and mitochondrial dysfunction were involved in 5 bootstraps. Two paired pathways (antigen presentation pathway and fMLP signaling in neutrophil, as well as SAPK/JNK signaling and mitochondrial dysfunction) can accurately distinguish AS and control samples. These paired pathways may be helpful to identify patients with AS for early intervention.
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Affiliation(s)
- Xiang Gu
- Department of Orthopedics, People's Hospital of Ri Zhao, Ri Zhao, Shandong, China
| | - Cong-Jian Liu
- Department of Orthopedics, People's Hospital of Ri Zhao, Ri Zhao, Shandong, China
| | - Jian-Jie Wei
- Department of Orthopedics, Weihaiwei People's Hospital, Weihai, Shandong, China
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20
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Joshi PS, Modur V, Cheng J, Robinson K, Rao K. Characterization of immortalized human mammary epithelial cell line HMEC 2.6. Tumour Biol 2017; 39:1010428317724283. [PMID: 29022488 DOI: 10.1177/1010428317724283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Primary human mammary epithelial cells have a limited life span which makes it difficult to study them in vitro for most purposes. To overcome this problem, we have developed a cell line that was immortalized using defined genetic elements, and we have characterized this immortalized non-tumorigenic human mammary epithelial cell line to establish it as a potential model system. human mammary epithelial cells were obtained from a healthy individual undergoing reduction mammoplasty at SIU School of Medicine. The cells were transduced with CDK4R24C followed by transduction with human telomerase reverse transcriptase. Post all manipulation, the cells displayed a normal cell cycle phase distribution and were near diploid in nature, which was confirmed by flow cytometry and karyotyping. In vitro studies showed that the cells were anchorage dependent and were non-invasive in nature. The cell line expressed basal epithelial markers such as cytokeratin 7, CD10, and p63 and was negative for the expression of estrogen receptor and progesterone receptor. Upon G-band karyotyping, the cell line displayed the presence of a few cytogenic abnormalities, including trisomy 20 and trisomy 7, which are also commonly present in other immortalized mammary cell lines. Furthermore, the benign nature of these cells was confirmed by multiple in vitro and in vivo experiments. Therefore, we think that this cell line could serve as a good model to understand the molecular mechanisms involved in the development and progression of breast cancer and to also assess the effect of novel therapeutics on human mammary epithelial cells.
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Affiliation(s)
- Pooja S Joshi
- 1 Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Vishnu Modur
- 2 Department of Pediatrics and Cincinnati Children's Hospital, University of Cincinnati, Cincinnati, OH, USA
| | - JiMing Cheng
- 3 For You Dentistry, 477 Union Ave., Bridgewater, NJ
| | - Kathy Robinson
- 4 Division of Hematology/Oncology, Department of Internal Medicine, Southern Illinois University School of Medicine, USA.,5 Simmons Cancer Institute at Southern Illinois University, Springfield, IL, USA
| | - Krishna Rao
- 1 Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL, USA.,4 Division of Hematology/Oncology, Department of Internal Medicine, Southern Illinois University School of Medicine, USA.,5 Simmons Cancer Institute at Southern Illinois University, Springfield, IL, USA
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21
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Depreeuw J, Stelloo E, Osse EM, Creutzberg CL, Nout RA, Moisse M, Garcia-Dios DA, Dewaele M, Willekens K, Marine JC, Matias-Guiu X, Amant F, Lambrechts D, Bosse T. Amplification of 1q32.1 Refines the Molecular Classification of Endometrial Carcinoma. Clin Cancer Res 2017; 23:7232-7241. [PMID: 28939739 DOI: 10.1158/1078-0432.ccr-17-0566] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 07/13/2017] [Accepted: 09/15/2017] [Indexed: 01/02/2023]
Abstract
Purpose: Molecular classification of endometrial cancer identified distinct molecular subgroups. However, the largest subset of endometrial cancers remains poorly characterized and is referred to as the "nonspecific molecular profile" (NSMP) subgroup. Here, we aimed at refining the classification of this subgroup by profiling somatic copy-number aberrations (SCNAs).Experimental Design: SCNAs were analyzed in 141 endometrial cancers using whole-genome SNP arrays and pooled with 361 endometrial cancers from The Cancer Genome Atlas. Genomic Identification of Significant Targets in Cancer (GISTIC) identified statistically enriched SCNAs and penalized Cox regression assessed survival effects. The prognostic significance of relevant SCNAs was validated using multiplex ligation-dependent probe amplification in 840 endometrial cancers from the PORTEC-1/2 trials. Copy-number status of genes was correlated with gene expression to identify potential cancer drivers. One plausible oncogene was validated in vitro using antisense oligonucleotide-based strategy.Results: SCNAs affecting chromosome 1q32.1 significantly correlated with worse relapse-free survival (RFS) in the NSMP subgroup (HR, 2.12; 95% CI, 1.26-3.59; P = 0.005). This effect was replicated in NSMP endometrial cancers from PORTEC-1/2 (HR, 2.34; 95% CI, 1.17-4.70; P = 0.017). A new molecular classification including the 1q32.1 amplification improved risk prediction of recurrence. MDM4 gene expression strongly correlated with 1q32.1 amplification. Silencing MDM4 inhibited cell growth in cell lines carrying 1q32.1 amplification, but not in those without MDM4 amplification. Vice versa, increasing MDM4 expression in nonamplified cell lines stimulated cell proliferation.Conclusions: 1q32.1 amplification was identified as a prognostic marker for poorly characterized NSMP endometrial cancers, refining the molecular classification of this subgroup. We functionally validated MDM4 as a potential oncogenic driver in the 1q32.1 region. Clin Cancer Res; 23(23); 7232-41. ©2017 AACR.
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Affiliation(s)
- Jeroen Depreeuw
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, KU Leuven (University of Leuven), University Hospitals Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Laboratory for Translational Genetics, Leuven, Belgium.,VIB, VIB Center for Cancer Biology, Laboratory for Translational Genetics, Leuven, Belgium
| | - Ellen Stelloo
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Elisabeth M Osse
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Carien L Creutzberg
- Department of Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Remi A Nout
- Department of Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Matthieu Moisse
- Department of Human Genetics, KU Leuven, Laboratory for Translational Genetics, Leuven, Belgium.,VIB, VIB Center for Cancer Biology, Laboratory for Translational Genetics, Leuven, Belgium
| | - Diego A Garcia-Dios
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, KU Leuven (University of Leuven), University Hospitals Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Laboratory for Translational Genetics, Leuven, Belgium.,VIB, VIB Center for Cancer Biology, Laboratory for Translational Genetics, Leuven, Belgium
| | - Michael Dewaele
- Department of Oncology, KU Leuven, Laboratory for Molecular Cancer Biology, Leuven, Belgium.,VIB, VIB Center for Cancer Biology, Laboratory for Molecular Cancer Biology, Leuven, Belgium
| | - Karen Willekens
- Department of Oncology, KU Leuven, Laboratory for Molecular Cancer Biology, Leuven, Belgium.,VIB, VIB Center for Cancer Biology, Laboratory for Molecular Cancer Biology, Leuven, Belgium
| | - Jean-Christophe Marine
- Department of Oncology, KU Leuven, Laboratory for Molecular Cancer Biology, Leuven, Belgium.,VIB, VIB Center for Cancer Biology, Laboratory for Molecular Cancer Biology, Leuven, Belgium
| | - Xavier Matias-Guiu
- Pathology and Molecular Genetics, Institut de Recerca Biomedica de Lleida, Lleida, Spain
| | - Frédéric Amant
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, KU Leuven (University of Leuven), University Hospitals Leuven, Leuven, Belgium.,Center for Gynaecologic Oncology Amsterdam (CGOA), Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Diether Lambrechts
- Department of Human Genetics, KU Leuven, Laboratory for Translational Genetics, Leuven, Belgium.,VIB, VIB Center for Cancer Biology, Laboratory for Translational Genetics, Leuven, Belgium
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
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22
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Deconvolution of DNA methylation identifies differentially methylated gene regions on 1p36 across breast cancer subtypes. Sci Rep 2017; 7:11594. [PMID: 28912426 PMCID: PMC5599639 DOI: 10.1038/s41598-017-10199-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/04/2017] [Indexed: 12/31/2022] Open
Abstract
Breast cancer is a complex disease consisting of four distinct molecular subtypes. DNA methylation-based (DNAm) studies in tumors are complicated further by disease heterogeneity. In the present study, we compared DNAm in breast tumors with normal-adjacent breast samples from The Cancer Genome Atlas (TCGA). We constructed models stratified by tumor stage and PAM50 molecular subtype and performed cell-type reference-free deconvolution to control for cellular heterogeneity. We identified nineteen differentially methylated gene regions (DMGRs) in early stage tumors across eleven genes (AGRN, C1orf170, FAM41C, FLJ39609, HES4, ISG15, KLHL17, NOC2L, PLEKHN1, SAMD11, WASH5P). These regions were consistently differentially methylated in every subtype and all implicated genes are localized to the chromosomal cytoband 1p36.3. Seventeen of these DMGRs were independently validated in a similar analysis of an external data set. The identification and validation of shared DNAm alterations across tumor subtypes in early stage tumors advances our understanding of common biology underlying breast carcinogenesis and may contribute to biomarker development. We also discuss evidence of the specific importance and potential function of 1p36 in cancer.
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23
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Liu C, Gu X, Jiang Z. Identification of novel targets for multiple myeloma through integrative approach with Monte Carlo cross-validation analysis. J Bone Oncol 2017; 8:8-12. [PMID: 28856086 PMCID: PMC5565744 DOI: 10.1016/j.jbo.2017.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/01/2017] [Accepted: 08/10/2017] [Indexed: 11/20/2022] Open
Abstract
More than one pathway is involved in disease development and progression, and two or more pathways may be interconnected to further affect the disease onset, as functional proteins participate in multiple pathways. Thus, identifying cross-talk among pathways is necessary to understand the molecular mechanisms of multiple myeloma (MM). Based on this, this paper looked at extracting potential pathway cross-talk in MM through an integrative approach using Monte Carlo cross-validation analysis. The gene expression library of MM (accession number: GSE6477) was downloaded from the Gene Expression Omnibus (GEO) database. The integrative approach was then used to identify potential pathway cross-talk, and included four steps: Firstly, differential expression analysis was conducted to identify differentially expressed genes (DEGs). Secondly, the DEGs obtained were mapped to the pathways downloaded from an ingenuity pathways analysis (IPA), to reveal the underlying relationship between the DEGs and pathways enriched by these DEGs. A subset of pathways enriched by the DEGs was then obtained. Thirdly, a discriminating score (DS) value for each paired pathway was computed. Lastly, random forest (RF) classification was used to identify the paired pathways based on area under the curve (AUC) and Monte Carlo cross-validation, which was repeated 50 times to explore the best paired pathways. These paired pathways were tested with another independently published MM microarray data (GSE85837), using in silico validation. Overall, 60 DEGs and 19 differential pathways enriched by DEGs were extracted. Each pathway was sorted based on their AUC values. The paired pathways, inhibition of matrix metalloproteases and EIF2 signaling pathway, indicated the best AUC value of 1.000. Paired pathways consisting of IL-8 and EIF2 signaling pathways with higher AUC of 0.975, were involved in 7 runs. Furthermore, it was validated consistently in separate microarray data sets (GSE85837). Paired pathways (inhibition of matrix metalloproteases and EIF2 signaling, IL-8 signaling and EIF2 signaling) exhibited the best AUC values and higher frequency of validation. Two paired pathways (inhibition of matrix metalloproteases and EIF2 signaling, IL-8 signaling and EIF2 signaling) were used to accurately classify MM and control samples. These paired pathways may be potential bio-signatures for diagnosis and management of MM.
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24
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Zhao SN, Liu LL, Lv ZP, Wang XH, Wang CH. Network analysis of HBV‑ and HCV‑induced hepatocellular carcinoma based on Random Forest and Monte Carlo cross‑validation. Mol Med Rep 2017; 16:2411-2416. [PMID: 28656273 DOI: 10.3892/mmr.2017.6861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 03/28/2017] [Indexed: 11/06/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer‑associated mortality worldwide. Hepatitis B virus (HBV) and hepatitis C virus (HCV) are two common risk factors for HCC. The majority of patients with HCC present at an advanced stage and are refractory to therapy. It is important to identify a method for efficient diagnosis at early stage. In the present study gene expression profile data, generated from microarray data, were pretreated according to the annotation files. The genes were mapped to pathways of Ingenuity Pathways Analysis. Dysregulated pathways and dysregulated pathway pairs were identified and constructed into individual networks, and a main network was constructed from individual networks with several edges. Random Forest (RF) classification was introduced to calculate the area under the curve (AUC) value of this network. Subsequently, 50 runs of Monte Carlo cross‑validation were used to screen the optimal main network. The results indicated that a total of 4,929 genes were identified in the pathways and gene expression profile. By combining dysregulated pathways with Z<0.05 and dysregulated pathway pairs with Z<0.2, individual networks were constructed. The optimal main network with the highest AUC value was identified. In the HCV group, the network was identified with an AUC value of 0.98, including 41 pairs of pathways, and in the HBV group, the network was identified with an AUC value of 0.94, including eight pairs of pathways. In addition, four pairs were identified in both groups. In conclusion, the optimal networks of HCV and HBV groups were identified with the highest AUC values. The use of these networks is expected to assist in diagnosing patients effectively at an early stage.
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Affiliation(s)
- Shan-Na Zhao
- Department of Clinical Laboratory, Yantaishan Hospital, Yantai, Shandong 264008, P.R. China
| | - Ling-Ling Liu
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated Shandong University, Jinan, Shandong 250021, P.R. China
| | - Zhi-Ping Lv
- Department of Clinical Laboratory, Yantaishan Hospital, Yantai, Shandong 264008, P.R. China
| | - Xiao-Hua Wang
- Department of Clinical Laboratory, Yantaishan Hospital, Yantai, Shandong 264008, P.R. China
| | - Cheng-Hong Wang
- Department of Clinical Laboratory, Yantaishan Hospital, Yantai, Shandong 264008, P.R. China
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25
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Lin S, Wang Y, Mu S, Zhang J, Yuan F, Sun K. Pathway analysis based on Monte Carlo Cross-Validation in polyarticular juvenile idiopathic arthritis. Pathol Res Pract 2016; 213:7-12. [PMID: 27894617 DOI: 10.1016/j.prp.2016.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/28/2016] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Juvenile idiopathic arthritis (JIA) is a common chronic disease with onset before the 16 years old in a child. Polyarticular JIA has been reported as the main form of JIA in several locations. Until now, understanding of the genetic basis of JIA is incomplete. The purpose of this study was to identify pathway pairs of great potential functional relevance in the progression of polyarticular JIA. MATERIALS AND METHODS Microarray data of 59 peripheral blood samples from healthy children and 61 samples from polyarticular JIA were transformed to gene expression data. Differential expressed genes (DEG) between patients and normal controls were identified using Linear Models for Microarray Analysis. After performed enrichment of DEG, differential pathways were identified with Fisher's test and false discovery rate. Differential pathway pairs were constructed with random two differential pathways, and were evaluated by Random Forest classification. Monte Carlo Cross-Validation was introduced to screen the best pathway pair. RESULTS 42 DEG with P-values<0.01 were identified. 19 differential pathways with P-values<0.01 were identified. Area under the curve (AUC) of pathway pairs was generated with RF classification. After 50 bootstraps of Monte Carlo Cross-Validation, the best pathway pair with the highest AUC value was identified, and it was the pair of tumoricidal function of hepatic natural killer cells pathway and erythropoietin signaling pathway. CONCLUSION These identified pathway pairs may play pivotal roles in the progress of polyarticular JIA and can be applied for diagnosis. Particular attention can be focused on them for further research.
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Affiliation(s)
- Shunhua Lin
- Department of Orthopaedics, The People's Hopital of Rizhao, Rizhao 276800, Shandong, PR China
| | - Yuanji Wang
- Department of Orthopaedics, The People's Hopital of Rizhao, Rizhao 276800, Shandong, PR China
| | - Shunmei Mu
- Department of Ophthalmology, The People's Hopital of Donggang District, Rizhao 276800, Shandong, PR China
| | - Junxi Zhang
- Department of Orthopaedics, The People's Hopital of Rizhao, Rizhao 276800, Shandong, PR China
| | - Fangchang Yuan
- Department of Orthopaedics, The People's Hopital of Rizhao, Rizhao 276800, Shandong, PR China
| | - Kang Sun
- Department of Orthopaedics, The Affiliated Hopital of Qingdao University, Qingdao 266000, Shandong, PR China.
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26
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Falasca M, Hamilton JR, Selvadurai M, Sundaram K, Adamska A, Thompson PE. Class II Phosphoinositide 3-Kinases as Novel Drug Targets. J Med Chem 2016; 60:47-65. [DOI: 10.1021/acs.jmedchem.6b00963] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Marco Falasca
- Metabolic
Signalling Group, School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, Western Australia 6845, Australia
| | - Justin R. Hamilton
- Australian
Centre for Blood Diseases and Department of Clinical Haematology, Monash University, 99 Commercial Road, Melbourne, Victoria 3004, Australia
| | - Maria Selvadurai
- Australian
Centre for Blood Diseases and Department of Clinical Haematology, Monash University, 99 Commercial Road, Melbourne, Victoria 3004, Australia
| | - Krithika Sundaram
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Aleksandra Adamska
- Metabolic
Signalling Group, School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, Western Australia 6845, Australia
| | - Philip E. Thompson
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052, Australia
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27
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Sun G, Luan B, Zhao R, Li Z, Xing Z. Characterizing Dysregulated Networks in Individual Patients with Ischemic Stroke Based on Monte Carlo Cross-Validation. DNA Cell Biol 2016; 35:795-801. [PMID: 27726417 DOI: 10.1089/dna.2016.3453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The purpose of this study was to introduce a new method to elucidating the molecular mechanisms in ischemic stroke. Genes from microarray data were performed enrichment to biological pathways. Dysregulated pathways and dysregulated pathway pairs were identified and constructed into networks. After Random Forest classification was performed, area under the curve (AUC) value of main network was calculated. After 50 bootstraps of Monte Carlo Cross-Validation, six pairs of pathways were found for >40 times. The best main network with AUC value = 0.735 was identified, including 14 pairs of pathways. Compared with the traditional method (gene set enrichment analysis), although a small part of pathways were shared, most of the pathways were closely related with ischemic stroke. The best network may give new insights into the underlying molecular mechanisms in ischemic stroke. It may play pivotal roles in the progression of ischemic stroke and particular attention should be focused on them for further research.
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Affiliation(s)
- Guojian Sun
- 1 Department of Rehabilitation Medicine, The People's Hospital of Liaocheng , Liaocheng, People's Republic of China
| | - Bin Luan
- 1 Department of Rehabilitation Medicine, The People's Hospital of Liaocheng , Liaocheng, People's Republic of China
| | - Ruiying Zhao
- 2 The Blood Center of Liaocheng , Liaocheng, People's Republic of China
| | - Zhanbiao Li
- 1 Department of Rehabilitation Medicine, The People's Hospital of Liaocheng , Liaocheng, People's Republic of China
| | - Zhangmin Xing
- 1 Department of Rehabilitation Medicine, The People's Hospital of Liaocheng , Liaocheng, People's Republic of China
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28
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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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29
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Hibsh D, Buetow KH, Yaari G, Efroni S. Quantification of read species behavior within whole genome sequencing of cancer genomes for the stratification and visualization of genomic variation. Nucleic Acids Res 2016; 44:e81. [PMID: 26809676 PMCID: PMC4872078 DOI: 10.1093/nar/gkw031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 01/11/2016] [Indexed: 11/13/2022] Open
Abstract
The cancer genome is abnormal genome, and the ability to monitor its sequence had undergone a technological revolution. Yet prognosis and diagnosis remain an expert-based decision, with only limited abilities to provide machine-based decisions. We introduce a heterogeneity-based method for stratifying and visualizing whole-genome sequencing (WGS) reads. This method uses the heterogeneity within WGS reads to markedly reduce the dimensionality of next-generation sequencing data; it is available through the tool HiBS (Heterogeneity-Based Subclassification) that allows cancer sample classification. We validated HiBS using >200 WGS samples from nine different cancer types from The Cancer Genome Atlas (TCGA). With HiBS, we show progress with two WGS related issues: (i) differentiation between normal (NB) and tumor (TP) samples based solely on the information structure of their WGS data, and (ii) identification of specific regions of chromosomal amplification/deletion and their association with tumor stage. By comparing results to those obtained through available WGS analyses tools, we demonstrate some of the novelties obtained by the approach implemented in HiBS and also show nearly perfect normal/tumor classification, used to identify known and unknown chromosomal aberrations. Finally, the HiBS index has been associated with breast cancer tumor stage.
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Affiliation(s)
- Dror Hibsh
- Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Kenneth H Buetow
- Computational Sciences and Informatics Program, Complex Adaptive Systems Initiative, Arizona State University, Tempe AZ 85281, USA
| | - Gur Yaari
- Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Sol Efroni
- Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
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30
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Monte Carlo cross-validation analysis screens pathway cross-talk associated with Parkinson’s disease. Neurol Sci 2016; 37:1327-33. [DOI: 10.1007/s10072-016-2595-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/27/2016] [Indexed: 10/21/2022]
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31
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Liu L, Kimball S, Liu H, Holowatyj A, Yang ZQ. Genetic alterations of histone lysine methyltransferases and their significance in breast cancer. Oncotarget 2016; 6:2466-82. [PMID: 25537518 PMCID: PMC4385864 DOI: 10.18632/oncotarget.2967] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 12/10/2015] [Indexed: 12/27/2022] Open
Abstract
Histone lysine methyltransferases (HMTs), a large class of enzymes that catalyze site-specific methylation of lysine residues on histones and other proteins, play critical roles in controlling transcription, chromatin architecture, and cellular differentiation. However, the genomic landscape and clinical significance of HMTs in breast cancer remain poorly characterized. Here, we conducted a meta-analysis of approximately 50 HMTs in breast cancer and identified associations among recurrent copy number alterations, mutations, gene expression, and clinical outcome. We identified 12 HMTs with the highest frequency of genetic alterations, including 8 with high-level amplification, 2 with putative homozygous deletion, and 2 with somatic mutation. Different subtypes of breast cancer have different patterns of copy number and expression for each HMT gene. In addition, chromosome 1q contains four HMTs that are concurrently or independently amplified or overexpressed in breast cancer. Copy number or mRNA expression of several HMTs was significantly associated with basal-like breast cancer and shorter patient survival. Integrative analysis identified 8 HMTs (SETDB1, SMYD3, ASH1L, SMYD2, WHSC1L1, SUV420H1, SETDB2, and KMT2C) that are dysregulated by genetic alterations, classifying them as candidate therapeutic targets. Together, our findings provide a strong foundation for further mechanistic research and therapeutic options using HMTs to treat breast cancer.
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Affiliation(s)
- Lanxin Liu
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Sarah Kimball
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Hui Liu
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Andreana Holowatyj
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Zeng-Quan Yang
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
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Cava C, Bertoli G, Castiglioni I. Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential. BMC SYSTEMS BIOLOGY 2015; 9:62. [PMID: 26391647 PMCID: PMC4578257 DOI: 10.1186/s12918-015-0211-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/15/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Development of human cancer can proceed through the accumulation of different genetic changes affecting the structure and function of the genome. Combined analyses of molecular data at multiple levels, such as DNA copy-number alteration, mRNA and miRNA expression, can clarify biological functions and pathways deregulated in cancer. The integrative methods that are used to investigate these data involve different fields, including biology, bioinformatics, and statistics. RESULTS These methodologies are presented in this review, and their implementation in breast cancer is discussed with a focus on integration strategies. We report current applications, recent studies and interesting results leading to the identification of candidate biomarkers for diagnosis, prognosis, and therapy in breast cancer by using both individual and combined analyses. CONCLUSION This review presents a state of art of the role of different technologies in breast cancer based on the integration of genetics and epigenetics, and shares some issues related to the new opportunities and challenges offered by the application of such integrative approaches.
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Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
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Elsarraj HS, Hong Y, Valdez KE, Michaels W, Hook M, Smith WP, Chien J, Herschkowitz JI, Troester MA, Beck M, Inciardi M, Gatewood J, May L, Cusick T, McGinness M, Ricci L, Fan F, Tawfik O, Marks JR, Knapp JR, Yeh HW, Thomas P, Carrasco DR, Fields TA, Godwin AK, Behbod F. Expression profiling of in vivo ductal carcinoma in situ progression models identified B cell lymphoma-9 as a molecular driver of breast cancer invasion. Breast Cancer Res 2015; 17:128. [PMID: 26384318 PMCID: PMC4574212 DOI: 10.1186/s13058-015-0630-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/11/2015] [Indexed: 11/29/2022] Open
Abstract
Introduction There are an estimated 60,000 new cases of ductal carcinoma in situ (DCIS) each year. A lack of understanding in DCIS pathobiology has led to overtreatment of more than half of patients. We profiled the temporal molecular changes during DCIS transition to invasive ductal carcinoma (IDC) using in vivo DCIS progression models. These studies identified B cell lymphoma-9 (BCL9) as a potential molecular driver of early invasion. BCL9 is a newly found co-activator of Wnt-stimulated β-catenin-mediated transcription. BCL9 has been shown to promote progression of multiple myeloma and colon carcinoma. However BCL9 role in breast cancer had not been previously recognized. Methods Microarray and RNA sequencing were utilized to characterize the sequential changes in mRNA expression during DCIS invasive transition. BCL9-shRNA knockdown was performed to assess the role of BCL9 in in vivo invasion, epithelial-mesenchymal transition (EMT) and canonical Wnt-signaling. Immunofluorescence of 28 patient samples was used to assess a correlation between the expression of BCL9 and biomarkers of high risk DCIS. The cancer genome atlas data were analyzed to assess the status of BCL9 gene alterations in breast cancers. Results Analysis of BCL9, by RNA and protein showed BCL9 up-regulation to be associated with DCIS transition to IDC. Analysis of patient DCIS revealed a significant correlation between high nuclear BCL9 and pathologic characteristics associated with DCIS recurrence: Estrogen receptor (ER) and progesterone receptor (PR) negative, high nuclear grade, and high human epidermal growth factor receptor2 (HER2). In vivo silencing of BCL9 resulted in the inhibition of DCIS invasion and reversal of EMT. Analysis of the TCGA data showed BCL9 to be altered in 26 % of breast cancers. This is a significant alteration when compared to HER2 (ERBB2) gene (19 %) and estrogen receptor (ESR1) gene (8 %). A significantly higher proportion of basal like invasive breast cancers compared to luminal breast cancers showed BCL9 amplification. Conclusion BCL9 is a molecular driver of DCIS invasive progression and may predispose to the development of basal like invasive breast cancers. As such, BCL9 has the potential to serve as a biomarker of high risk DCIS and as a therapeutic target for prevention of IDC. Electronic supplementary material The online version of this article (doi:10.1186/s13058-015-0630-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hanan S Elsarraj
- Department of Pathology, University of Kansas Medical Center, 3901 Rainbow Blvd, Mail Stop 3003, Kansas City, KS, 66160, USA.
| | - Yan Hong
- Department of Pathology, University of Kansas Medical Center, 3901 Rainbow Blvd, Mail Stop 3003, Kansas City, KS, 66160, USA.
| | - Kelli E Valdez
- Department of Pathology, University of Kansas Medical Center, 3901 Rainbow Blvd, Mail Stop 3003, Kansas City, KS, 66160, USA.
| | - Whitney Michaels
- School of Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Marcus Hook
- School of Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - William P Smith
- Department of Radiology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Jeremy Chien
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Jason I Herschkowitz
- Department of Biomedical Sciences, University at Albany-SUNY, Rensselaer, NY, 12144, USA.
| | - Melissa A Troester
- School of Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | - Moriah Beck
- Department of Chemistry, Wichita State University, Wichita, KS, 67260, USA.
| | - Marc Inciardi
- Department of Radiology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Jason Gatewood
- Department of Radiology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Lisa May
- School of Medicine, University of Kansas, Wichita, KS, 67214, USA.
| | - Therese Cusick
- School of Medicine, University of Kansas, Wichita, KS, 67214, USA.
| | - Marilee McGinness
- Department of Surgery, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Lawrence Ricci
- Department of Radiology, Truman Medical Center, Kansas City, MO, 64108, USA.
| | - Fang Fan
- Department of Pathology, University of Kansas Medical Center, 3901 Rainbow Blvd, Mail Stop 3003, Kansas City, KS, 66160, USA.
| | - Ossama Tawfik
- Department of Pathology, University of Kansas Medical Center, 3901 Rainbow Blvd, Mail Stop 3003, Kansas City, KS, 66160, USA.
| | - Jeffrey R Marks
- Department of Surgery, Duke University, Durham, NC, 27710, USA.
| | - Jennifer R Knapp
- Kansas Intellectual and Developmental Disabilities Research Center, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Hung-Wen Yeh
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Patricia Thomas
- Department of Pathology, University of Kansas Medical Center, 3901 Rainbow Blvd, Mail Stop 3003, Kansas City, KS, 66160, USA.
| | - D R Carrasco
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115-5450, USA.
| | - Timothy A Fields
- Department of Pathology, University of Kansas Medical Center, 3901 Rainbow Blvd, Mail Stop 3003, Kansas City, KS, 66160, USA.
| | - Andrew K Godwin
- Department of Pathology, University of Kansas Medical Center, 3901 Rainbow Blvd, Mail Stop 3003, Kansas City, KS, 66160, USA.
| | - Fariba Behbod
- Department of Pathology, University of Kansas Medical Center, 3901 Rainbow Blvd, Mail Stop 3003, Kansas City, KS, 66160, USA.
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Integrative Analysis with Monte Carlo Cross-Validation Reveals miRNAs Regulating Pathways Cross-Talk in Aggressive Breast Cancer. BIOMED RESEARCH INTERNATIONAL 2015; 2015:831314. [PMID: 26240829 PMCID: PMC4512830 DOI: 10.1155/2015/831314] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/31/2015] [Accepted: 06/08/2015] [Indexed: 12/11/2022]
Abstract
In this work an integrated approach was used to identify functional miRNAs regulating gene pathway cross-talk in breast cancer (BC). We first integrated gene expression profiles and biological pathway information to explore the underlying associations between genes differently expressed among normal and BC samples and pathways enriched from these genes. For each pair of pathways, a score was derived from the distribution of gene expression levels by quantifying their pathway cross-talk. Random forest classification allowed the identification of pairs of pathways with high cross-talk. We assessed miRNAs regulating the identified gene pathways by a mutual information analysis. A Fisher test was applied to demonstrate their significance in the regulated pathways. Our results suggest interesting networks of pathways that could be key regulatory of target genes in BC, including stem cell pluripotency, coagulation, and hypoxia pathways and miRNAs that control these networks could be potential biomarkers for diagnostic, prognostic, and therapeutic development in BC. This work shows that standard methods of predicting normal and tumor classes such as differentially expressed miRNAs or transcription factors could lose intrinsic features; instead our approach revealed the responsible molecules of the disease.
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Waugh MG. Amplification of Chromosome 1q Genes Encoding the Phosphoinositide Signalling Enzymes PI4KB, AKT3, PIP5K1A and PI3KC2B in Breast Cancer. J Cancer 2014; 5:790-6. [PMID: 25368680 PMCID: PMC4216804 DOI: 10.7150/jca.9794] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/11/2014] [Indexed: 01/08/2023] Open
Abstract
Little is known about the possible oncogenic roles of genes encoding for the phosphatidylinositol 4-kinases, a family of enzymes that regulate an early step in phosphoinositide signalling. To address this issue, the mutational status of all four human phosphatidylinositol 4-kinases genes was analyzed across 852 breast cancer samples using the COSMIC data resource. Point mutations in the phosphatidylinositol 4-kinase genes were uncommon and appeared in less than 1% of the patient samples however, 62% of the tumours had increases in gene copy number for PI4KB which encodes the phosphatidylinositol 4-kinase IIIbeta isozyme. Extending this analysis to subsequent enzymes in the phosphoinositide signalling cascades revealed that the only PIP5K1A, PI3KC2B and AKT3 genes exhibited similar patterns of gene copy number variation. By comparison, gene copy number increases for established oncogenes such as EGFR and HER2/Neu were only evident in 20% of the samples. The PI4KB, PIP5K1A, PI3KC2B and AKT3 genes are related in that they all localize to chromosome 1q which is often structurally and numerically abnormal in breast cancer. These results demonstrate that a gene quartet encoding a potential phosphoinositide signalling pathway is amplified in a subset of breast cancers.
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Affiliation(s)
- Mark G Waugh
- Lipid and Membrane Biology Group, Institute for Liver and Digestive Health, UCL, Royal Free Campus, Rowland Hill Street, London, NW3 2PF United Kingdom
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Pérez-Tenorio G, Karlsson E, Stål O. Clinical value of isoform-specific detection and targeting of AKT1, AKT2 and AKT3 in breast cancer. BREAST CANCER MANAGEMENT 2014. [DOI: 10.2217/bmt.14.35] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
SUMMARY Overactivation of the PI3K/AKT signaling pathway is frequently reported in breast cancer, consequently inhibitors targeting this pathway are clinically useful. AKT constitutes a hub in the regulation of several cancer hallmarks, such as proliferation, survival and migration. Three AKT isoforms, named AKT1, AKT2 and AKT3, are identified in humans. AKT alterations, mainly upregulation of phosphorylated AKT in tumors may have prognostic and predictive value. Moreover, the AKT isoforms may possess partly divergent cellular functions and be upregulated in certain breast cancer subtypes, suggesting the importance of isoform-specific analyses. In conclusion, AKT isoform-specific detection and targeting in different tumor subtypes will hopefully result into a further developed personalized medicine.
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Affiliation(s)
- Gizeh Pérez-Tenorio
- Department of Clinical & Experimental Medicine & Department of Oncology, Linköping University, Linköping, SE-58185, Sweden
| | - Elin Karlsson
- Department of Clinical & Experimental Medicine & Department of Oncology, Linköping University, Linköping, SE-58185, Sweden
| | - Olle Stål
- Department of Clinical & Experimental Medicine & Department of Oncology, Linköping University, Linköping, SE-58185, Sweden
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Cava C, Bertoli G, Ripamonti M, Mauri G, Zoppis I, Rosa PAD, Gilardi MC, Castiglioni I. Integration of mRNA expression profile, copy number alterations, and microRNA expression levels in breast cancer to improve grade definition. PLoS One 2014; 9:e97681. [PMID: 24866763 PMCID: PMC4035288 DOI: 10.1371/journal.pone.0097681] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 04/23/2014] [Indexed: 12/20/2022] Open
Abstract
Defining the aggressiveness and growth rate of a malignant cell population is a key step in the clinical approach to treating tumor disease. The correct grading of breast cancer (BC) is a fundamental part in determining the appropriate treatment. Biological variables can make it difficult to elucidate the mechanisms underlying BC development. To identify potential markers that can be used for BC classification, we analyzed mRNAs expression profiles, gene copy numbers, microRNAs expression and their association with tumor grade in BC microarray-derived datasets. From mRNA expression results, we found that grade 2 BC is most likely a mixture of grade 1 and grade 3 that have been misclassified, being described by the gene signature of either grade 1 or grade 3. We assessed the potential of the new approach of integrating mRNA expression profile, copy number alterations, and microRNA expression levels to select a limited number of genomic BC biomarkers. The combination of mRNA profile analysis and copy number data with microRNA expression levels led to the identification of two gene signatures of 42 and 4 altered genes (FOXM1, KPNA4, H2AFV and DDX19A) respectively, the latter obtained through a meta-analytical procedure. The 42-based gene signature identifies 4 classes of up- or down-regulated microRNAs (17 microRNAs) and of their 17 target mRNA, and the 4-based genes signature identified 4 microRNAs (Hsa-miR-320d, Hsa-miR-139-5p, Hsa-miR-567 and Hsa-let-7c). These results are discussed from a biological point of view with respect to pathological features of BC. Our identified mRNAs and microRNAs were validated as prognostic factors of BC disease progression, and could potentially facilitate the implementation of assays for laboratory validation, due to their reduced number.
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Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
| | - Marilena Ripamonti
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
| | - Giancarlo Mauri
- Department of Informatics, Systems and Communications, University of Milan–Bicocca, Milan, Italy
| | - Italo Zoppis
- Department of Informatics, Systems and Communications, University of Milan–Bicocca, Milan, Italy
| | | | - Maria Carla Gilardi
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
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Tan WJ, Lai JC, Thike AA, Lim JCT, Tan SY, Koh VCY, Lim TH, Bay BH, Tan MH, Tan PH. Novel genetic aberrations in breast phyllodes tumours: comparison between prognostically distinct groups. Breast Cancer Res Treat 2014; 145:635-45. [PMID: 24831776 DOI: 10.1007/s10549-014-2982-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/23/2014] [Indexed: 11/24/2022]
Abstract
Phyllodes tumours of the breast are uncommon fibroepithelial neoplasms which pose management challenges due to difficulties in accurate prediction of clinical behaviour, as histological assessment has its limitations. Molecular studies have improved the understanding of these rare tumours but such findings are scant. We aimed to investigate genetic aberrations in phyllodes tumours stratified according to clinical behaviour, to identify potential genes contributing to disease progression. Twenty phyllodes tumours were separated into prognostically distinct categories depending on whether they had recurred/metastasized within the follow-up period. DNA extracted from FFPE materials was subjected to Affymetrix OncoScan™ FFPE Express molecular inversion probe microarray platform for analysis of copy number changes and mutational status. Results were cross validated with Sanger sequencing, FISH and immunohistochemistry. A higher number of chromosomal aberrations were observed in cases which recurred/metastasized, with median events of 19 compared to 3.5 in cases which did not recur/metastasize. High-level amplification and homozygous deletions were detected exclusively in the former group. Regions of high-level amplification included MDM4 (1q32.1), RAF1 (3p25), EGFR (7p12) and PDZD2 (5p13.3). EGFR amplification was confirmed on FISH and accompanied by intense EGFR immunostaining. Regions of homozygous deletion included CDKN2A (9p21) and MACROD2 (20p12.1). Homozygous deletion of 9p21 which involved CDKN2A was accompanied by loss of protein expression. No mutations were identified in all samples. These findings provide insights into identifying target genes and pathways exploited by phyllodes tumours, which would aid future development of individualised therapy.
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Affiliation(s)
- Wai Jin Tan
- Department of Pathology, Singapore General Hospital, 20 College Road, Academia, Diagnostics Tower, Singapore, 169856, Singapore
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Orsetti B, Selves J, Bascoul-Mollevi C, Lasorsa L, Gordien K, Bibeau F, Massemin B, Paraf F, Soubeyran I, Hostein I, Dapremont V, Guimbaud R, Cazaux C, Longy M, Theillet C. Impact of chromosomal instability on colorectal cancer progression and outcome. BMC Cancer 2014; 14:121. [PMID: 24559140 PMCID: PMC4233623 DOI: 10.1186/1471-2407-14-121] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 02/07/2014] [Indexed: 01/16/2023] Open
Abstract
Background It remains presently unclear whether disease progression in colorectal carcinoma (CRC), from early, to invasive and metastatic forms, is associated to a gradual increase in genetic instability and to a scheme of sequentially occurring Copy Number Alterations (CNAs). Methods In this work we set to determine the existence of such links between CRC progression and genetic instability and searched for associations with patient outcome. To this aim we analyzed a set of 162 Chromosomal Instable (CIN) CRCs comprising 131 primary carcinomas evenly distributed through stage 1 to 4, 31 metastases and 14 adenomas by array-CGH. CNA profiles were established according to disease stage and compared. We, also, asked whether the level of genomic instability was correlated to disease outcome in stage 2 and 3 CRCs. Two metrics of chromosomal instability were used; (i) Global Genomic Index (GGI), corresponding to the fraction of the genome involved in CNA, (ii) number of breakpoints (nbBP). Results Stage 1, 2, 3 and 4 tumors did not differ significantly at the level of their CNA profiles precluding the conventional definition of a progression scheme based on increasing levels of genetic instability. Combining GGI and nbBP,we classified genomic profiles into 5 groups presenting distinct patterns of chromosomal instability and defined two risk classes of tumors, showing strong differences in outcome and hazard risk (RFS: p = 0.012, HR = 3; OS: p < 0.001, HR = 9.7). While tumors of the high risk group were characterized by frequent fractional CNAs, low risk tumors presented predominantly whole chromosomal arm CNAs. Searching for CNAs correlating with negative outcome we found that losses at 16p13.3 and 19q13.3 observed in 10% (7/72) of stage 2–3 tumors showed strong association with early relapse (p < 0.001) and death (p < 0.007, p < 0.016). Both events showed frequent co-occurrence (p < 1x10-8) and could, therefore, mark for stage 2–3 CRC susceptible to negative outcome. Conclusions Our data show that CRC disease progression from stage 1 to stage 4 is not paralleled by increased levels of genetic instability. However, they suggest that stage 2–3 CRC with elevated genetic instability and particularly profiles with fractional CNA represent a subset of aggressive tumors.
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Sarajlić A, Filipović A, Janjić V, Coombes RC, Pržulj N. The role of genes co-amplified with nicastrin in breast invasive carcinoma. Breast Cancer Res Treat 2013; 143:393-401. [DOI: 10.1007/s10549-013-2805-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 12/03/2013] [Indexed: 12/21/2022]
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Muthuswami M, Ramesh V, Banerjee S, Viveka Thangaraj S, Periasamy J, Bhaskar Rao D, Barnabas GD, Raghavan S, Ganesan K. Breast tumors with elevated expression of 1q candidate genes confer poor clinical outcome and sensitivity to Ras/PI3K inhibition. PLoS One 2013; 8:e77553. [PMID: 24147022 PMCID: PMC3798322 DOI: 10.1371/journal.pone.0077553] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 09/03/2013] [Indexed: 12/15/2022] Open
Abstract
Genomic aberrations are common in cancers and the long arm of chromosome 1 is known for its frequent amplifications in breast cancer. However, the key candidate genes of 1q, and their contribution in breast cancer pathogenesis remain unexplored. We have analyzed the gene expression profiles of 1635 breast tumor samples using meta-analysis based approach and identified clinically significant candidates from chromosome 1q. Seven candidate genes including exonuclease 1 (EXO1) are consistently over expressed in breast tumors, specifically in high grade and aggressive breast tumors with poor clinical outcome. We derived a EXO1 co-expression module from the mRNA profiles of breast tumors which comprises 1q candidate genes and their co-expressed genes. By integrative functional genomics investigation, we identified the involvement of EGFR, RAS, PI3K / AKT, MYC, E2F signaling in the regulation of these selected 1q genes in breast tumors and breast cancer cell lines. Expression of EXO1 module was found as indicative of elevated cell proliferation, genomic instability, activated RAS/AKT/MYC/E2F1 signaling pathways and loss of p53 activity in breast tumors. mRNA-drug connectivity analysis indicates inhibition of RAS/PI3K as a possible targeted therapeutic approach for the patients with activated EXO1 module in breast tumors. Thus, we identified seven 1q candidate genes strongly associated with the poor survival of breast cancer patients and identified the possibility of targeting them with EGFR/RAS/PI3K inhibitors.
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Affiliation(s)
- Muthulakshmi Muthuswami
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Vignesh Ramesh
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Saikat Banerjee
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Soundara Viveka Thangaraj
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Jayaprakash Periasamy
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Divya Bhaskar Rao
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Georgina D. Barnabas
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Swetha Raghavan
- Department of Biotechnology, Indian Institute of Technology Madras, Chenna, India
| | - Kumaresan Ganesan
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
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Vlug E, Ercan C, van der Wall E, van Diest PJ, Derksen PWB. Lobular Breast Cancer: Pathology, Biology, and Options for Clinical Intervention. Arch Immunol Ther Exp (Warsz) 2013; 62:7-21. [DOI: 10.1007/s00005-013-0251-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 08/05/2013] [Indexed: 12/13/2022]
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Soloviev M, Esteves MP, Amiri F, Crompton MR, Rider CC. Elevated transcription of the gene QSOX1 encoding quiescin Q6 sulfhydryl oxidase 1 in breast cancer. PLoS One 2013; 8:e57327. [PMID: 23460839 PMCID: PMC3583868 DOI: 10.1371/journal.pone.0057327] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 01/21/2013] [Indexed: 11/18/2022] Open
Abstract
The q arm of chromosome 1 is frequently amplified at the gene level in breast cancer. Since the significance of this is unclear we investigated whether 1q genes are overexpressed in this disease. The cDNA levels of 1q-located genes were analysed in a search for overexpressed genes. 26 genes mapping to the 1q arm show highly significant (P≤0.01) overexpression of transcripts in breast cancer compared to normal breast tissue. Amongst those showing the highest levels of overexpression in both expressed sequence tag (EST) and serial analysis of gene expression (SAGE) databases was enzyme quiescin Q6 sulfhydryl oxidase 1 (QSOX1). We investigated QSOX1 cDNA derived from T47D breast carcinoma cells by RT-PCR and 3′-RACE PCR and identified a novel extended form of QSOX1 transcript, containing a long 3′UTR, nearly double the size of the previously reported QSOX1 cDNA, and confirmed its 3′ end nucleotide sequence using RACE-PCR. We also used quantitative real-time PCR to analyse a panel of cDNAs derived from 50 clinically-graded normal and malignant breast tissue samples for the expression of QSOX1 mRNAs. QSOX1 transcription was elevated in an increasing proportion in the grade 2 and grade 3 tumours (graded according to the Nottingham prognostic index), with 10 of the 15 grade 3 tumours (67%) examined exceeding the normal range. There was a significant correlation between relative transcript level and clinical grade (P≤0.01) for all qPCR primer sets tested. QSOX1 mRNA levels, based on SAGE expression data, did not correlate with either Estrogen Receptor (ER) or Epidermal Growth Factor Receptor 2 (ErbB-2 or HER2/neu) expression. Our data indicate that QSOX1 is a potential new prognostic marker which may prove of use in the staging of breast tumours and the stratification of breast cancer patients.
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MESH Headings
- Alternative Splicing/genetics
- Base Sequence
- Breast Neoplasms/enzymology
- Breast Neoplasms/genetics
- Carcinoma, Ductal, Breast/enzymology
- Carcinoma, Ductal, Breast/genetics
- Cell Line, Tumor
- DNA, Complementary/genetics
- Expressed Sequence Tags
- Female
- Gene Expression Regulation, Neoplastic
- Genes, Neoplasm/genetics
- Humans
- Molecular Sequence Data
- Open Reading Frames/genetics
- Oxidoreductases Acting on Sulfur Group Donors/genetics
- Oxidoreductases Acting on Sulfur Group Donors/metabolism
- Protein Biosynthesis/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Real-Time Polymerase Chain Reaction
- Transcription, Genetic
- Up-Regulation/genetics
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Affiliation(s)
- Mikhail Soloviev
- School of Biological Sciences, Centre for Biomedical Sciences, Royal Holloway University of London, London, United Kingdom.
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Mesquita B, Lopes P, Rodrigues A, Pereira D, Afonso M, Leal C, Henrique R, Lind GE, Jerónimo C, Lothe RA, Teixeira MR. Frequent copy number gains at 1q21 and 1q32 are associated with overexpression of the ETS transcription factors ETV3 and ELF3 in breast cancer irrespective of molecular subtypes. Breast Cancer Res Treat 2013; 138:37-45. [PMID: 23329352 DOI: 10.1007/s10549-013-2408-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 01/07/2013] [Indexed: 01/03/2023]
Abstract
Several ETS transcription factors are involved in the pathogenesis of human cancers by different mechanisms. As gene copy number gain/amplification is an alternative mechanism of oncogenic activation and 1q gain is the most common copy number change in breast carcinoma, we investigated how that genomic change impacts in the expression of the three 1q ETS family members ETV3, ELK4, and ELF3. We have first evaluated 141 breast carcinomas for genome-wide copy number changes by chromosomal CGH and showed that 1q21 and 1q32 were the two chromosome bands with most frequent genomic copy number gains. Second, we confirmed by FISH with locus-specific BAC clones that cases showing 1q gain/amplification by CGH showed copy number increase of the ETS genes ETV3 (located in 1q21~23), ELF3, and ELK4 (both in 1q32). Third, gene expression levels of the three 1q ETS genes, as well as their potential targets MYC and CRISP3, were evaluated by quantitative real-time PCR. We here show for the first time that the most common genomic copy number gains in breast cancer, 1q21 and 1q32, are associated with overexpression of the ETS transcription factors ETV3 and ELF3 (but not ELK4) at these loci irrespective of molecular subtypes. Among the three 1q ETS genes, ELF3 has a relevant role in breast carcinogenesis and is also the most likely target of the 1q copy number increase. The basal-like molecular subtype presented the worst prognosis regarding disease-specific survival, but no additional prognostic value was found for 1q copy number status or ELF3 expression. In addition, we show that there is a correlation between the expression of the oncogene MYC, irrespectively of copy number gain at its loci in 8q24, and the expression of both the transcriptional repressor ETV3 and the androgen respondent ELK4.
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Affiliation(s)
- Bárbara Mesquita
- Department of Genetics, Portuguese Oncology Institute, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
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45
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Wiechec E, Overgaard J, Kjeldsen E, Hansen LL. Chromosome 1q25.3 copy number alterations in primary breast cancers detected by multiplex ligation-dependent probe amplification and allelic imbalance assays and its comparison with fluorescent in situ hybridization assays. Cell Oncol (Dordr) 2012; 36:113-20. [DOI: 10.1007/s13402-012-0117-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2012] [Indexed: 11/28/2022] Open
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46
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The Non-Crosslinking Fixative RCL2®-CS100 is Compatible with Both Pathology Diagnosis and Molecular Analyses. Pathol Oncol Res 2012; 19:41-53. [DOI: 10.1007/s12253-012-9556-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 07/10/2012] [Indexed: 12/16/2022]
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47
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Significance of Loss of Heterozygosity in Predicting Axillary Lymph Node Metastasis of Invasive Ductal Carcinoma of the Breast. Appl Immunohistochem Mol Morphol 2012; 20:116-23. [DOI: 10.1097/pai.0b013e31822afce2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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48
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Abstract
Once stimulated, the epidermal growth factor receptor (EGFR) undergoes self-phosphorylation, which, on the one hand, instigates signaling cascades, and on the other hand, recruits CBL ubiquitin ligases, which mark EGFRs for degradation. Using RNA interference screens, we identified a deubiquitinating enzyme, Cezanne-1, that opposes receptor degradation and enhances EGFR signaling. These functions require the catalytic and ubiquitin-binding domains of Cezanne-1, and they involve physical interactions and trans-phosphorylaton of Cezanne-1 by EGFR. In line with the ability of Cezanne-1 to augment EGF-induced growth and migration signals, the enzyme is overexpressed in breast cancer. Congruently, the corresponding gene is amplified in approximately one third of mammary tumors, and high transcript levels predict an aggressive disease course. In conclusion, deubiquitination by Cezanne-1 curtails degradation of growth factor receptors, thereby promotes oncogenic growth signals.
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49
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Cho SG, Wang Y, Rodriguez M, Tan K, Zhang W, Luo J, Li D, Liu M. Haploinsufficiency in the prometastasis Kiss1 receptor Gpr54 delays breast tumor initiation, progression, and lung metastasis. Cancer Res 2011; 71:6535-46. [PMID: 21852382 DOI: 10.1158/0008-5472.can-11-0329] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Activation of KISS1 receptor (KISS1R or GPR54) by its ligands (Kisspeptins) regulates a diverse function both in normal physiology and pathophysiology. In cancer, KISS1R has been implicated in tumor angiogenesis and metastasis, but a broader evaluation of KISS1R in tumorigenesis and tumor progression is yet to be conducted. In this study, we used mouse models of Kiss1r gene knockout and mouse mammary tumor virus-polyoma virus middle T antigen (MMTV-PyMT)-induced breast cancer to conduct such an evaluation. Kiss1r heterozygosity in MMTV-PyMT mice was sufficient to attenuate breast cancer initiation, growth, latency, multiplicity, and lung metastasis. To confirm these effects and assess possible contributions of endogenous ligands, we isolated primary tumor cells from PyMT/Kiss1r(+/+) and PyMT/Kiss1r(+/-) mice and compared their phenotypes by in vitro and in vivo assays. Kiss1r loss attenuated in vitro tumorigenic properties as well as tumor growth in vivo in immunocompromised NOD.SCID/NCr mice. Kiss1r activation in these cells, resulting from the addition of its ligand Kisspeptin-10, resulted in RhoA activation and RhoA-dependent gene expression through the Gαq-p63RhoGEF signaling pathway. Anchorage-independent growth was tightly linked to dose-dependent regulation of RhoA by Kiss1r. In support of these results, siRNA-mediated knockdown of KISS1R or inactivation of RhoA in human MCF10A breast epithelial cells overexpressing H-RasV12 was sufficient to reduce Ras-induced anchorage-independent growth. In summary, we concluded that Kiss1r attenuation was sufficient to delay breast tumor initiation, progression, and metastasis through inhibitory effects on the downstream Gαq-p63RhoGEF-RhoA signaling pathway.
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Affiliation(s)
- Sung-Gook Cho
- Center for Cancer and Stem Cell Biology, Institute of Bioscience and Technology, Texas A&M System Health Science Center, Houston, Texas 77030, USA
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50
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Prognostic significance of TRIM24/TIF-1α gene expression in breast cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 178:1461-9. [PMID: 21435435 DOI: 10.1016/j.ajpath.2010.12.026] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 12/07/2010] [Accepted: 12/10/2010] [Indexed: 11/22/2022]
Abstract
In this study, we have analyzed the expression of TRIM24/TIF-1α, a negative regulator of various transcription factors (including nuclear receptors and p53) at the genomic, mRNA, and protein levels in human breast tumors. In breast cancer biopsy specimens, TRIM24/TIF-1α mRNA levels (assessed by Real-Time Quantitative PCR or microarray expression profiling) were increased as compared to normal breast tissues. At the genomic level, array comparative genomic hybridization analysis showed that the TRIM24/TIF-1α locus (7q34) exhibited both gains and losses that correlated with mRNA levels. By re-analyzing a series of 238 tumors, high levels of TRIM24/TIF-1α mRNA significantly correlated with various markers of poor prognosis (such as the molecular subtype) and were associated with worse overall survival. By using a rabbit polyclonal antibody for immunochemistry, the TRIM24/TIF-1α protein was detected in nuclei of normal luminal epithelial breast cells, but not in myoepithelial cells. Tissue microarray analysis confirmed that its expression was increased in epithelial cells from normal to breast infiltrating duct carcinoma and correlated with worse overall survival. Altogether, this work is the first study that shows that overexpression of the TRIM24/TIF-1α gene in breast cancer is associated with poor prognosis and worse survival, and it suggests that this transcription coregulator may play a role in mammary carcinogenesis and represent a novel prognostic marker.
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