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Shahrouzi P, Forouz F, Mathelier A, Kristensen VN, Duijf PHG. Copy number alterations: a catastrophic orchestration of the breast cancer genome. Trends Mol Med 2024:S1471-4914(24)00120-5. [PMID: 38772764 DOI: 10.1016/j.molmed.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/23/2024]
Abstract
Breast cancer (BCa) is a prevalent malignancy that predominantly affects women around the world. Somatic copy number alterations (CNAs) are tumor-specific amplifications or deletions of DNA segments that often drive BCa development and therapy resistance. Hence, the complex patterns of CNAs complement BCa classification systems. In addition, understanding the precise contributions of CNAs is essential for tailoring personalized treatment approaches. This review highlights how tumor evolution drives the acquisition of CNAs, which in turn shape the genomic landscapes of BCas. It also discusses advanced methodologies for identifying recurrent CNAs, studying CNAs in BCa and their clinical impact.
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Affiliation(s)
- Parastoo Shahrouzi
- Department of Medical Genetics, Institute of Basic Medical Science, Faculty of Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Farzaneh Forouz
- School of Pharmacy, University of Queensland, Woolloongabba, Brisbane, Australia
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway; Center for Bioinformatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway; Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Vessela N Kristensen
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway; Division of Medicine, Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University Hospital, Lørenskog, Norway; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Pascal H G Duijf
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway; Centre for Cancer Biology, UniSA Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide, Australia.
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2
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Zara Rozalen A, Martin JM, Rajendran R, Jain M, Nava VE. Ductal Adenocarcinoma of the Prostate with Novel Genetic Alterations Characterized by Next-Generation Sequencing. Curr Oncol 2024; 31:1556-1561. [PMID: 38534951 PMCID: PMC10968787 DOI: 10.3390/curroncol31030118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/23/2023] [Accepted: 03/17/2024] [Indexed: 05/26/2024] Open
Abstract
Ductal adenocarcinoma of the prostate (DAP) is an uncommon variant of prostate cancer associated with aggressive disease and poor outcome. It presents most frequently as a mixed tumor combined with acinar adenocarcinoma. Although the histopathological features of DAP are well known, its genomic characteristics are still evolving, prompting the suggestion that all DAP would benefit from molecular analysis with the purpose of improving tumor recognition, genetic classification, and, ultimately, personalized therapy. Herein, we report a case of DAP with novel genetic alterations (BCOR P1153S, ERG M219I, KDR A750E, POLE S1896P, and RAD21 T461del).
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Affiliation(s)
- Alexandra Zara Rozalen
- Department of Pathology, Veterans Affairs Medical Center, Washington, DC 20422, USA; (A.Z.R.); (J.M.M.); (R.R.)
- Department of Pathology, Mount Sinai Morningside and West Hospitals, New York, NY 10019, USA
| | - Jose Manuel Martin
- Department of Pathology, Veterans Affairs Medical Center, Washington, DC 20422, USA; (A.Z.R.); (J.M.M.); (R.R.)
| | - Rithika Rajendran
- Department of Pathology, Veterans Affairs Medical Center, Washington, DC 20422, USA; (A.Z.R.); (J.M.M.); (R.R.)
| | - Maneesh Jain
- Section of Hematology & Oncology, Veterans Affairs Medical Center, Washington, DC 20422, USA;
- Department of Medicine, The George Washington University Hospital, Washington, DC 20037, USA
| | - Victor E. Nava
- Department of Pathology, Veterans Affairs Medical Center, Washington, DC 20422, USA; (A.Z.R.); (J.M.M.); (R.R.)
- Department of Pathology, The George Washington University Hospital, Washington, DC 20037, USA
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3
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Jurenaite N, León-Periñán D, Donath V, Torge S, Jäkel R. SetQuence & SetOmic: Deep set transformers for whole genome and exome tumour analysis. Biosystems 2024; 235:105095. [PMID: 38065399 DOI: 10.1016/j.biosystems.2023.105095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 10/17/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023]
Abstract
In oncology, Deep Learning has shown great potential to personalise tasks such as tumour type classification, based on per-patient omics data-sets. Being high dimensional, incorporation of such data in one model is a challenge, often leading to one-dimensional studies and, therefore, information loss. Instead, we first propose relying on non-fixed sets of whole genome or whole exome variant-associated sequences, which can be used for supervised learning of oncology-relevant tasks by our Set Transformer based Deep Neural Network, SetQuence. We optimise this architecture to improve its efficiency. This allows for exploration of not just coding but also non-coding variants, from large datasets. Second, we extend the model to incorporate these representations together with multiple other sources of omics data in a flexible way with SetOmic. Evaluation, using these representations, shows improved robustness and reduced information loss compared to previous approaches, while still being computationally tractable. By means of Explainable Artificial Intelligence methods, our models are able to recapitulate the biological contribution of highly attributed features in the tumours studied. This validation opens the door to novel directions in multi-faceted genome and exome wide biomarker discovery and personalised treatment among other presently clinically relevant tasks.
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Affiliation(s)
- Neringa Jurenaite
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), TU Dresden, Chemnitzer Str 46b, Dresden, 01187, Saxony, Germany.
| | - Daniel León-Periñán
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), TU Dresden, Chemnitzer Str 46b, Dresden, 01187, Saxony, Germany; Max-Delbrück-Centrum für Molekulare Medizin, Hannoversche Str. 28, Berlin, 10115, Germany.
| | - Veronika Donath
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), TU Dresden, Chemnitzer Str 46b, Dresden, 01187, Saxony, Germany.
| | - Sunna Torge
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), TU Dresden, Chemnitzer Str 46b, Dresden, 01187, Saxony, Germany.
| | - René Jäkel
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), TU Dresden, Chemnitzer Str 46b, Dresden, 01187, Saxony, Germany.
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Zhang S, Bai X, Li F, Ni C, Li Y, Che N, Zhao N, Zhao X, Liu T. UTP23 Functions in Breast Cancer Progression and Predicts Poor Prognosis of Luminal a Breast Cancer. Clin Breast Cancer 2024; 24:e20-e30.e6. [PMID: 37880005 DOI: 10.1016/j.clbc.2023.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND Luminal A breast cancer is the most common molecular subtype of breast cancer. Exploring biomarkers to identify luminal A breast cancer patients at high risk of recurrence and metastasis has important clinical significance. UTP23 is a component of ribosomal small-subunit processome, which is involved in ribosome synthesis and RNA maturation. The role of UTP23 in breast cancer has not been reported. METHODS TCGA-BRCA data, LinkedOmics, STRING, Metascape and ssGSEA were used to analyze UTP23 expression in breast cancer and evaluate prognosis. Quantitative real-time PCR, western blot and in vitro cell experiment were used to demonstrate the role of UTP23 in breast cancer. RESULTS UTP23 showed abnormally high expression in multiple cancers and was associated with poor prognosis. UTP23 was associated with T stage, lymph node metastasis, race, histological type, molecular subtypes and survival status in breast cancer. Importantly, UTP23 was significantly associated with poor OS in luminal A or early breast cancer, not in non-luminal A or advanced breast cancer. UTP23 expression was significantly correlated with immune cells infiltration. Enrichment analysis suggested that UTP23 might regulate cell cycle and cell division. Bioinformatics analysis showed DCAF13 might be downstream factor of UTP23. UTP23 expression promoted MCF-7 cells proliferation, migration and invasion possibly through regulating DCAF13 expression. CONCLUSIONS UTP23 may function in breast cancer progression. The elevated UTP23 may be a potential prognostic biomarker for luminal A or early breast cancer.
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Affiliation(s)
- Sida Zhang
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Xiaoyu Bai
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Fan Li
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Chunsheng Ni
- Department of Pathology, Tianjin Medical University, Tianjin, China; Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Yanlei Li
- Department of Pathology, Tianjin Medical University, Tianjin, China; Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Na Che
- Department of Pathology, Tianjin Medical University, Tianjin, China; Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Nan Zhao
- Department of Pathology, Tianjin Medical University, Tianjin, China; Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Xiulan Zhao
- Department of Pathology, Tianjin Medical University, Tianjin, China; Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China.
| | - Tieju Liu
- Department of Pathology, Tianjin Medical University, Tianjin, China; Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China.
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Høland M, Berg KCG, Eilertsen IA, Bjerkehagen B, Kolberg M, Boye K, Lingjærde OC, Guren TK, Mandahl N, van den Berg E, Palmerini E, Smeland S, Picci P, Mertens F, Sveen A, Lothe RA. Transcriptomic subtyping of malignant peripheral nerve sheath tumours highlights immune signatures, genomic profiles, patient survival and therapeutic targets. EBioMedicine 2023; 97:104829. [PMID: 37837931 PMCID: PMC10585232 DOI: 10.1016/j.ebiom.2023.104829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND Malignant peripheral nerve sheath tumour (MPNST) is an aggressive orphan disease commonly affecting adolescents or young adults. Current knowledge of molecular tumour biology has been insufficient for development of rational treatment strategies. We aimed to discover molecular subtypes of potential clinical relevance. METHODS Fresh frozen samples of MPNSTs (n = 94) and benign neurofibromas (n = 28) from 115 patients in a European multicentre study were analysed by DNA copy number and/or transcriptomic profiling. Unsupervised transcriptomic subtyping was performed and the subtypes characterized for genomic aberrations, clinicopathological associations and patient survival. FINDINGS MPNSTs were classified into two transcriptomic subtypes defined primarily by immune signatures and proliferative processes. "Immune active" MPNSTs (44%) had sustained immune signals relative to neurofibromas, were more frequently low-grade (P = 0.01) and had favourable prognostic associations in a multivariable model of disease-specific survival with clinicopathological factors (hazard ratio 0.25, P = 0.003). "Immune deficient" MPNSTs were more aggressive and characterized by proliferative signatures, high genomic complexity, aberrant TP53 and PRC2 loss, as well as high relative expression of several potential actionable targets (EGFR, ERBB2, EZH2, KIF11, PLK1, RRM2). Integrated gene-wise analyses suggested a DNA copy number-basis for proliferative transcriptomic signatures in particular, and the tumour copy number burden further stratified the transcriptomic subtypes according to patient prognosis (P < 0.01). INTERPRETATION Approximately half of MPNSTs belong to an "immune deficient" transcriptomic subtype associated with an aggressive disease course, PRC2 loss and expression of several potential therapeutic targets, providing a rationale for molecularly-guided intervention trials. FUNDING Research grants from non-profit organizations, as stated in the Acknowledgements.
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Affiliation(s)
- Maren Høland
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kaja C G Berg
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Bodil Bjerkehagen
- Institute for Clinical Medicine, University of Oslo, Oslo, Norway; Division of Laboratory Medicine, Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Matthias Kolberg
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Kjetil Boye
- Division of Cancer Medicine, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Ole Christian Lingjærde
- Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Tormod K Guren
- Division of Cancer Medicine, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Nils Mandahl
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Eva van den Berg
- Department of Genetics, The University Medical Center Groningen, the Netherlands
| | - Emanuela Palmerini
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Sigbjørn Smeland
- Institute for Clinical Medicine, University of Oslo, Oslo, Norway; Division of Cancer Medicine, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Piero Picci
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Fredrik Mertens
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Institute for Clinical Medicine, University of Oslo, Oslo, Norway.
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Albarakati N, Al-Ghamdi H, Al-Sowayan B, Alshareeda A. Homologous recombination mRNAs (RAD21, RAD50 and BARD1) have a potentially poor prognostic role in ERBB2-low bladder cancer patients. Sci Rep 2023; 13:11738. [PMID: 37474724 PMCID: PMC10359419 DOI: 10.1038/s41598-023-38923-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023] Open
Abstract
Human epidermal growth factor receptor 2 (HER2/ERBB2) factor is known to be implicated in many malignancies and the potential of it as a prognostic biomarker was reported years ago. Molecular subtypes of HER2/ERBB2 negative and positive with distinct clinical outcomes have been identified in recent years; however, it is still under investigation for bladder cancer. This study evaluates the biological and prognostic significance of RAD21, RAD50 and BARD1 (homologous recombination biomarkers) mRNA levels with ERBB2 low and high expression to explore their impact on bladder cancer patient survival and cancer aggressiveness. The expression of ERBB2, RAD21, RAD50 and BARD1 mRNA levels was assessed in The Cancer Genome Atlas (TCGA) bladder cancer dataset along with four validation cohorts. Outcome analysis was evaluated using disease-free survival (DFS) and overall survival (OS). Univariate and multivariate analysis were used to evaluate the relationship between RAD21, RAD50, BARD1 and ERBB2 expression and clinicopathological variables. A significant increase in mRNA expression levels of RAD21, RAD50 and BARD1 was noticed in ERBB2-low patients compared to ERBB2-high patients. This overexpression of the homologous recombination repair transcripts was associated with poor outcome in ERBB2-low tumors, not in ERBB2-high tumors. Furthermore, the combined expression of high RAD21/RAD50, high RAD21/BARD1 or high RAD50/BARD1 were significantly associated with worse DFS and a better outcome for those with low co-expression in the ERBB2-low cohort. High expression of either RAD21/RAD50 or RAD21/BARD1 in ERBB2-low cohort associated with higher chance of metastasis. In addition, gene expression of BARD1 alone or in combination with RAD50 acted as an independent prognostic factor for worst survival. The data presented in this study reveal a connection between RAD21, RAD50, BARD1 and ERBB2 and patient survival. Importantly, it provided novel findings and potential prognostic markers, particularly in ERBB2-low bladder cancer.
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Affiliation(s)
- Nada Albarakati
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Jeddah, Kingdom of Saudi Arabia.
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh, Saudi Arabia.
| | - Hanin Al-Ghamdi
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Jeddah, Kingdom of Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Batla Al-Sowayan
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Alaa Alshareeda
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh, Saudi Arabia
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Sun Y, Xu X, Zhao W, Zhang Y, Chen K, Li Y, Wang X, Zhang M, Xue B, Yu W, Hou Y, Wang C, Xie W, Li C, Kong D, Wang S, Sun Y. RAD21 is the core subunit of the cohesin complex involved in directing genome organization. Genome Biol 2023; 24:155. [PMID: 37381036 DOI: 10.1186/s13059-023-02982-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/07/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND The ring-shaped cohesin complex is an important factor for the formation of chromatin loops and topologically associating domains (TADs) by loop extrusion. However, the regulation of association between cohesin and chromatin is poorly understood. In this study, we use super-resolution imaging to reveal the unique role of cohesin subunit RAD21 in cohesin loading and chromatin structure regulation. RESULTS We directly visualize that up-regulation of RAD21 leads to excessive chromatin loop extrusion into a vermicelli-like morphology with RAD21 clustered into foci and excessively loaded cohesin bow-tying a TAD to form a beads-on-a-string-type pattern. In contrast, up-regulation of the other four cohesin subunits results in even distributions. Mechanistically, we identify that the essential role of RAD21 is attributed to the RAD21-loader interaction, which facilitates the cohesin loading process rather than increasing the abundance of cohesin complex upon up-regulation of RAD21. Furthermore, Hi-C and genomic analysis reveal how RAD21 up-regulation affects genome-wide higher-order chromatin structure. Accumulated contacts are shown at TAD corners while inter-TAD interactions increase after vermicelli formation. Importantly, we find that in breast cancer cells, the expression of RAD21 is aberrantly high with poor patient survival and RAD21 forms beads in the nucleus. Up-regulated RAD21 in HeLa cells leads to compartment switching and up-regulation of cancer-related genes. CONCLUSIONS Our results provide key insights into the molecular mechanism by which RAD21 facilitates the cohesin loading process and provide an explanation to how cohesin and loader work cooperatively to promote chromatin extrusion, which has important implications in construction of three-dimensional genome organization.
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Affiliation(s)
- Yuao Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Xin Xu
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Wenxue Zhao
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing, 100871, China
| | - Yu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing, 100084, China
| | - Keyang Chen
- Yuanpei College, Peking University, Beijing, 100871, China
| | - Yongzheng Li
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Xiaotian Wang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Mengling Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Wanting Yu
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Yingping Hou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Chaobin Wang
- Breast Center, Peking University People's Hospital, Beijing, 100044, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing, 100084, China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing, 100871, China
| | - Daochun Kong
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Shu Wang
- Breast Center, Peking University People's Hospital, Beijing, 100044, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.
- Breast Center, Peking University People's Hospital, Beijing, 100044, China.
- National Biomedical Imaging Center, College of Future Technology, Peking University, Beijing, 100871, China.
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8
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Wang J, Nakato R. Comprehensive multiomics analyses reveal pervasive involvement of aberrant cohesin binding in transcriptional and chromosomal disorder of cancer cells. iScience 2023; 26:106908. [PMID: 37283809 PMCID: PMC10239702 DOI: 10.1016/j.isci.2023.106908] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 02/27/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023] Open
Abstract
Chromatin organization, whose malfunction causes various diseases including cancer, is fundamentally controlled by cohesin. While cancer cells have been found with mutated or misexpressed cohesin genes, there is no comprehensive survey about the presence and role of abnormal cohesin binding in cancer cells. Here, we systematically identified ∼1% of cohesin-binding sites (701-2,633) as cancer-aberrant binding sites of cohesin (CASs). We integrated CASs with large-scale transcriptomics, epigenomics, 3D genomics, and clinical information. CASs represent tissue-specific epigenomic signatures enriched for cancer-dysregulated genes with functional and clinical significance. CASs exhibited alterations in chromatin compartments, loops within topologically associated domains, and cis-regulatory elements, indicating that CASs induce dysregulated genes through misguided chromatin structure. Cohesin depletion data suggested that cohesin binding at CASs actively regulates cancer-dysregulated genes. Overall, our comprehensive investigation suggests that aberrant cohesin binding is an essential epigenomic signature responsible for dysregulated chromatin structure and transcription in cancer cells.
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Affiliation(s)
- Jiankang Wang
- School of Biomedical Sciences, Hunan University, Changsha, China
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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9
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Sustained activation of non-canonical NF-κB signalling drives glycolytic reprogramming in doxorubicin-resistant DLBCL. Leukemia 2023; 37:441-452. [PMID: 36446947 DOI: 10.1038/s41375-022-01769-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
Abstract
DLBCL is the most common lymphoma with high tumor heterogeneity. Treatment refractoriness and relapse from R-CHOP therapy in patients remain a clinical problem. Activation of the non-canonical NF-κB pathway is associated with R-CHOP resistance. However, downstream targets of non-canonical NF-κB mediating R-CHOP-induced resistance remains uncharacterized. Here, we identify the common mechanisms underlying both intrinsic and acquired resistance that are induced by doxorubicin, the main cytotoxic component of R-CHOP. We performed global transcriptomic analysis of (1) a panel of resistant versus sensitive and (2) isogenic acquired doxorubicin-resistant DLBCL cell lines following short and chronic exposure to doxorubicin respectively. Doxorubicin-induced stress in resistant cells activates a distinct transcriptional signature that is enriched in metabolic reprogramming and oncogenic signalling. Selective and sustained activation of non-canonical NF-κB signalling in these resistant cells exacerbated their survival by augmenting glycolysis. In response to doxorubicin, p52-RelB complexes transcriptionally activated multiple glycolytic regulators with prognostic significance through increased recruitment at their gene promoters. Targeting p52-RelB and their targets in resistant cells increased doxorubicin sensitivity in vitro and in vivo. Collectively, our study uncovered novel molecular drivers of doxorubicin-induced resistance that are regulated by non-canonical NF-κB pathway. We reveal new avenues of therapeutic targeting for R-CHOP-treated refractory/relapsed DLBCL patients.
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10
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Balaji AK, Saha S, Deshpande S, Poola D, Sengupta K. Nuclear envelope, chromatin organizers, histones, and DNA: The many achilles heels exploited across cancers. Front Cell Dev Biol 2022; 10:1068347. [PMID: 36589746 PMCID: PMC9800887 DOI: 10.3389/fcell.2022.1068347] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
In eukaryotic cells, the genome is organized in the form of chromatin composed of DNA and histones that organize and regulate gene expression. The dysregulation of chromatin remodeling, including the aberrant incorporation of histone variants and their consequent post-translational modifications, is prevalent across cancers. Additionally, nuclear envelope proteins are often deregulated in cancers, which impacts the 3D organization of the genome. Altered nuclear morphology, genome organization, and gene expression are defining features of cancers. With advances in single-cell sequencing, imaging technologies, and high-end data mining approaches, we are now at the forefront of designing appropriate small molecules to selectively inhibit the growth and proliferation of cancer cells in a genome- and epigenome-specific manner. Here, we review recent advances and the emerging significance of aberrations in nuclear envelope proteins, histone variants, and oncohistones in deregulating chromatin organization and gene expression in oncogenesis.
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11
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Gou R, Li X, Dong H, Hu Y, Liu O, Liu J, Lin B. RAD21 Confers Poor Prognosis and Affects Ovarian Cancer Sensitivity to Poly(ADP-Ribose)Polymerase Inhibitors Through DNA Damage Repair. Front Oncol 2022; 12:936550. [PMID: 35860572 PMCID: PMC9289200 DOI: 10.3389/fonc.2022.936550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022] Open
Abstract
Background Poly(ADP-ribose)polymerase (PARP) inhibitors are a class of molecular-targeted cancer drugs. Synthetic lethality is a phenomenon that renders homologous recombination repair defective cells more sensitive to PARP inhibitors. As a component of the cohesin complex, RAD21 regulates DNA damage repair. However, the biological roles of RAD21 in ovarian cancer and their underlying mechanisms remain unclear. Methods An immunohistochemical assay was used to validate the expression of RAD21 in ovarian cancer and its correlation with prognosis. The effects of RAD21 were evaluated through Cell Counting Kit-8 (CCK8), wound-healing, and invasion assays in vitro and the tumor growth in vivo. Furthermore, CCK8 assay and immunofluorescence assay were used to detect the effect of RAD21 on cell sensitivity to PARP inhibitors and their mechanism. The pathway changes were detected by Western blotting. Results RAD21 was markedly upregulated in ovarian cancer samples. High RAD21 expression was correlated with poor differentiation and poor prognosis in patients with ovarian cancer. Functionally, RAD21 overexpression promoted cancer cell proliferation, migration, and invasion. Moreover, RAD21 knockdown increased the sensitivity of ovarian cancer cells to three kinds of PARP inhibitors by affecting DNA damage repair. In vivo experiments indicated that RAD21 promoted tumor growth. Mechanistically, the overexpression of RAD21 led to increased phosphorylation levels of Akt and mTOR. Blocking the Akt/mTOR signaling pathway reversed RAD21 overexpression-induced cancer progression and drug resistance. Conclusions RAD21 can serve as a valuable prognostic marker for ovarian cancer and has the potential as a therapeutic target that can expand the utility of PARP inhibitors.
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Affiliation(s)
- Rui Gou
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Xiao Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Hui Dong
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Yuexin Hu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Ouxuan Liu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Juanjuan Liu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Bei Lin
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
- *Correspondence: Bei Lin,
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12
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Segeren HA, Westendorp B. Mechanisms used by cancer cells to tolerate drug-induced replication stress. Cancer Lett 2022; 544:215804. [PMID: 35750276 DOI: 10.1016/j.canlet.2022.215804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/15/2022] [Accepted: 06/19/2022] [Indexed: 11/02/2022]
Abstract
Activation of oncogenes in cancer cells forces cell proliferation, leading to DNA replication stress (RS). As a consequence, cancer cells heavily rely on the intra S-phase checkpoint for survival. This fundamental principle formed the basis for the development of inhibitors against key players of the intra S-phase checkpoint, ATR and CHK1. These drugs are often combined with chemotherapeutic drugs that interfere with DNA replication to exacerbate RS and exhaust the intra S-phase checkpoint in cancer cells. However, drug resistance impedes efficient clinical use, suggesting that some cancer cells tolerate severe RS. In this review, we describe how an increased nucleotide pool, boosted stabilization and repair of stalled forks and firing of dormant origins fortify the RS response in cancer cells. Notably, the vast majority of the genes that confer RS tolerance are regulated by the E2F and NRF2 transcription factors. These transcriptional programs are frequently activated in cancer cells, allowing simultaneous activation of multiple tolerance avenues. We propose that the E2F and NRF2 transcriptional programs can be used as biomarker to select patients for treatment with RS-inducing drugs and as novel targets to kill RS-tolerant cancer cells. Together, this review aims to provide a framework to maximally exploit RS as an Achilles' heel of cancer cells.
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Affiliation(s)
- Hendrika A Segeren
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Bart Westendorp
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
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13
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Xu T, Wu K, Shi J, Ji L, Song X, Tao G, Zheng S, Zhang L, Jiang B. LINC00858 promotes colon cancer progression through activation of STAT3/5 signaling by recruiting transcription factor RAD21 to upregulate PCNP. Cell Death Dis 2022; 8:228. [PMID: 35468892 PMCID: PMC9038718 DOI: 10.1038/s41420-022-00832-w] [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: 07/23/2021] [Revised: 12/22/2021] [Accepted: 01/11/2022] [Indexed: 12/02/2022]
Abstract
The purpose of our investigation is to explore the putative molecular mechanisms underpinning LINC00858 involvement in colon cancer. The expression of LINC00858 in TCGA data was identified using the GEPIA website. Colon cancer cancerous tissues were clinically collected. The expression of LINC00858, RAD21, and PCNP in colon tissues or cells was determined using RT-qPCR. The interactions among LINC00858, RAD21, and PCNP promoter region were determined by means of RNA pull down, RIP, and ChIP assays. Cell proliferative, apoptotic, invasive, and migrated capabilities were evaluated. Western blot was conducted to determine RAD21, PCNP, phosphorylated (p)-STAT3, STAT3, p-STAT5 and STAT5 and apoptosis related proteins. A nude mouse model of colon cancer was constructed and tumorigenesis of colon cancer cells was observed. LINC00858 was upregulated in cancerous tissues and cells. LINC00858 recruited the transcription factor RAD21. Overexpression of LINC00858 promoted the binding of RAD21 and PCNP promoter region, which increased the expression of PCNP. Silencing of RAD21 or PCNP reversed the promoting effect of LINC00858 on the disease initiation and development. PCNP silencing inhibited proliferative ability and promoted apoptotic ability of cancerous cells via STAT3/5 inhibition, which was reversed by colivelin-activated STAT3. In vivo experiments further verified that LINC00858 enhanced the tumorigenicity of colon cancer cells in vivo by regulating the RAD21/PCNP/STAT3/5 axis. It indicated the promoting role of LINC00858 in colon cancer progression though activating PCNP-mediated STAT3/5 pathway by recruiting RAD21.
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Affiliation(s)
- Ting Xu
- The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, P. R. China
| | - Kun Wu
- Department of Gastrointestinal Surgery, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, P. R. China
| | - Jin Shi
- Department of Gastrointestinal Surgery, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, P. R. China
| | - Lindong Ji
- Department of Gastrointestinal Surgery, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, P. R. China
| | - Xudong Song
- Department of Gastrointestinal Surgery, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, P. R. China
| | - Guoquan Tao
- Department of Gastrointestinal Surgery, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, P. R. China.
| | - Shutao Zheng
- Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, P. R. China
| | - Li Zhang
- VIP Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, P. R. China
| | - Baofei Jiang
- Department of Gastrointestinal Surgery, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, 223300, P. R. China.
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14
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Di Nardo M, Pallotta MM, Musio A. The multifaceted roles of cohesin in cancer. J Exp Clin Cancer Res 2022; 41:96. [PMID: 35287703 PMCID: PMC8919599 DOI: 10.1186/s13046-022-02321-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
The cohesin complex controls faithful chromosome segregation by pairing sister chromatids after DNA replication until mitosis. In addition, it is crucial for hierarchal three-dimensional organization of the genome, transcription regulation and maintaining DNA integrity. The core complex subunits SMC1A, SMC3, STAG1/2, and RAD21 as well as its modulators, have been found to be recurrently mutated in human cancers. The mechanisms by which cohesin mutations trigger cancer development and disease progression are still poorly understood. Since cohesin is involved in a range of chromosome-related processes, the outcome of cohesin mutations in cancer is complex. Herein, we discuss recent discoveries regarding cohesin that provide new insight into its role in tumorigenesis.
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Affiliation(s)
- Maddalena Di Nardo
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
| | - Maria M. Pallotta
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
| | - Antonio Musio
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
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15
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Sharaf R, Montesion M, Hopkins JF, Song J, Frampton GM, Albacker LA. A pan-cancer landscape of telomeric content shows that RAD21 and HGF alterations are associated with longer telomeres. Genome Med 2022; 14:25. [PMID: 35227290 PMCID: PMC8883689 DOI: 10.1186/s13073-022-01029-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/11/2022] [Indexed: 01/02/2023] Open
Abstract
Background Cancer cells can proliferate indefinitely through telomere maintenance mechanisms. These mechanisms include telomerase-dependent elongation, mediated by TERT activation, and alternative lengthening of telomeres (ALT), linked to loss of ATRX or DAXX. Methods We analyzed the telomeric content of 89,959 tumor samples within the Foundation Medicine dataset and investigated the genomic determinants of high telomeric content, linking them to clinical outcomes, when available. Results Telomeric content varied widely by disease type with leiomyosarcoma having the highest and Merkel cell carcinoma having the lowest telomeric content. In agreement with previous studies, telomeric content was significantly higher in samples with alterations in TERC, ATRX, and DAXX. We further identified that amplifications in two genes, RAD21 and HGF, were enriched in samples with high telomeric content, which was confirmed using the PCAWG/ICGC dataset. We identified the minimal amplified region associated with high telomeric content for RAD21 (8q23.1–8q24.12), which excludes MYC, and for HGF (7q21.11). Our results demonstrated that RAD21 and HGF exerted an additive telomere lengthening effect on samples with existing alterations in canonical genes previously associated with telomere elongation. Furthermore, patients with breast cancer who harbor RAD21 alterations had poor median overall survival and trended towards higher levels of Ki-67 staining. Conclusions This study highlights the importance of the role played by RAD21 (8q23.1–8q24.12) and HGF (7q21.11) in the lengthening of telomeres, supporting unlimited replication in tumors. These findings open avenues for work aimed at targeting this crucial pathway in tumorigenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01029-7.
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Affiliation(s)
- Radwa Sharaf
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA
| | - Meagan Montesion
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA
| | - Julia F Hopkins
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA
| | - Jiarong Song
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA
| | | | - Lee A Albacker
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA.
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16
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Rasool R, Ullah I, Mubeen B, Alshehri S, Imam SS, Ghoneim MM, Alzarea SI, Al-Abbasi FA, Murtaza BN, Kazmi I, Nadeem MS. Theranostic Interpolation of Genomic Instability in Breast Cancer. Int J Mol Sci 2022; 23:ijms23031861. [PMID: 35163783 PMCID: PMC8836911 DOI: 10.3390/ijms23031861] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is a diverse disease caused by mutations in multiple genes accompanying epigenetic aberrations of hazardous genes and protein pathways, which distress tumor-suppressor genes and the expression of oncogenes. Alteration in any of the several physiological mechanisms such as cell cycle checkpoints, DNA repair machinery, mitotic checkpoints, and telomere maintenance results in genomic instability. Theranostic has the potential to foretell and estimate therapy response, contributing a valuable opportunity to modify the ongoing treatments and has developed new treatment strategies in a personalized manner. “Omics” technologies play a key role while studying genomic instability in breast cancer, and broadly include various aspects of proteomics, genomics, metabolomics, and tumor grading. Certain computational techniques have been designed to facilitate the early diagnosis of cancer and predict disease-specific therapies, which can produce many effective results. Several diverse tools are used to investigate genomic instability and underlying mechanisms. The current review aimed to explore the genomic landscape, tumor heterogeneity, and possible mechanisms of genomic instability involved in initiating breast cancer. We also discuss the implications of computational biology regarding mutational and pathway analyses, identification of prognostic markers, and the development of strategies for precision medicine. We also review different technologies required for the investigation of genomic instability in breast cancer cells, including recent therapeutic and preventive advances in breast cancer.
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Affiliation(s)
- Rabia Rasool
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan; (R.R.); (I.U.); (B.M.)
| | - Inam Ullah
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan; (R.R.); (I.U.); (B.M.)
| | - Bismillah Mubeen
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan; (R.R.); (I.U.); (B.M.)
| | - Sultan Alshehri
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.A.); (S.S.I.)
| | - Syed Sarim Imam
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.A.); (S.S.I.)
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia;
| | - Sami I. Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia;
| | - Fahad A. Al-Abbasi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Bibi Nazia Murtaza
- Department of Zoology, Abbottabad University of Science and Technology (AUST), Abbottabad 22310, Pakistan;
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Correspondence: (I.K.); (M.S.N.)
| | - Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Correspondence: (I.K.); (M.S.N.)
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17
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Mfarej MG, Skibbens RV. Genetically induced redox stress occurs in a yeast model for Roberts syndrome. G3 (BETHESDA, MD.) 2022; 12:6460337. [PMID: 34897432 PMCID: PMC9210317 DOI: 10.1093/g3journal/jkab426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/01/2021] [Indexed: 12/31/2022]
Abstract
Roberts syndrome (RBS) is a multispectrum developmental disorder characterized by severe limb, craniofacial, and organ abnormalities and often intellectual disabilities. The genetic basis of RBS is rooted in loss-of-function mutations in the essential N-acetyltransferase ESCO2 which is conserved from yeast (Eco1/Ctf7) to humans. ESCO2/Eco1 regulate many cellular processes that impact chromatin structure, chromosome transmission, gene expression, and repair of the genome. The etiology of RBS remains contentious with current models that include transcriptional dysregulation or mitotic failure. Here, we report evidence that supports an emerging model rooted in defective DNA damage responses. First, the results reveal that redox stress is elevated in both eco1 and cohesion factor Saccharomyces cerevisiae mutant cells. Second, we provide evidence that Eco1 and cohesion factors are required for the repair of oxidative DNA damage such that ECO1 and cohesin gene mutations result in reduced cell viability and hyperactivation of DNA damage checkpoints that occur in response to oxidative stress. Moreover, we show that mutation of ECO1 is solely sufficient to induce endogenous redox stress and sensitizes mutant cells to exogenous genotoxic challenges. Remarkably, antioxidant treatment desensitizes eco1 mutant cells to a range of DNA damaging agents, raising the possibility that modulating the cellular redox state may represent an important avenue of treatment for RBS and tumors that bear ESCO2 mutations.
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Affiliation(s)
- Michael G Mfarej
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Robert V Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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18
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Prakadan SM, Alvarez-Breckenridge CA, Markson SC, Kim AE, Klein RH, Nayyar N, Navia AW, Kuter BM, Kolb KE, Bihun I, Mora JL, Bertalan MS, Shaw B, White M, Kaplan A, Stocking JH, Wadsworth MH, Lee EQ, Chukwueke U, Wang N, Subramanian M, Rotem D, Cahill DP, Adalsteinsson VA, Miller JW, Sullivan RJ, Carter SL, Brastianos PK, Shalek AK. Genomic and transcriptomic correlates of immunotherapy response within the tumor microenvironment of leptomeningeal metastases. Nat Commun 2021; 12:5955. [PMID: 34642316 PMCID: PMC8511044 DOI: 10.1038/s41467-021-25860-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 08/25/2021] [Indexed: 12/30/2022] Open
Abstract
Leptomeningeal disease (LMD) is a devastating complication of solid tumor malignancies, with dire prognosis and no effective systemic treatment options. Over the past decade, the incidence of LMD has steadily increased due to therapeutics that have extended the survival of cancer patients, highlighting the need for new interventions. To examine the efficacy of immune checkpoint inhibitors (ICI) in patients with LMD, we completed two phase II clinical trials. Here, we investigate the cellular and molecular features underpinning observed patient trajectories in these trials by applying single-cell RNA and cell-free DNA profiling to longitudinal cerebrospinal fluid (CSF) draws from enrolled patients. We recover immune and malignant cell types in the CSF, characterize cell behavior changes following ICI, and identify genomic features associated with relevant clinical phenomena. Overall, our study describes the liquid LMD tumor microenvironment prior to and following ICI treatment and demonstrates clinical utility of cell-free and single-cell genomic measurements for LMD research.
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Affiliation(s)
- Sanjay M Prakadan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA
| | - Christopher A Alvarez-Breckenridge
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Neurosurgery, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Samuel C Markson
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Albert E Kim
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Robert H Klein
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Naema Nayyar
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Andrew W Navia
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA
| | - Benjamin M Kuter
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Kellie E Kolb
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA
| | - Ivanna Bihun
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Joana L Mora
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Mia Solana Bertalan
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Brian Shaw
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Michael White
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Alexander Kaplan
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Jackson H Stocking
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Marc H Wadsworth
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA
| | - Eudocia Q Lee
- Division of Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ugonma Chukwueke
- Division of Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nancy Wang
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Megha Subramanian
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Denisse Rotem
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
| | - Viktor A Adalsteinsson
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeffrey W Miller
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Ryan J Sullivan
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Scott L Carter
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA.
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA.
| | - Priscilla K Brastianos
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, MA, USA.
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.
| | - Alex K Shalek
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute, Harvard University & Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital, Cambridge, MA, USA.
- Division of Health Science & Technology, Harvard Medical School, Cambridge, MA, USA.
- Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Nies HW, Mohamad MS, Zakaria Z, Chan WH, Remli MA, Nies YH. Enhanced Directed Random Walk for the Identification of Breast Cancer Prognostic Markers from Multiclass Expression Data. ENTROPY (BASEL, SWITZERLAND) 2021; 23:1232. [PMID: 34573857 PMCID: PMC8472068 DOI: 10.3390/e23091232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/12/2022]
Abstract
Artificial intelligence in healthcare can potentially identify the probability of contracting a particular disease more accurately. There are five common molecular subtypes of breast cancer: luminal A, luminal B, basal, ERBB2, and normal-like. Previous investigations showed that pathway-based microarray analysis could help in the identification of prognostic markers from gene expressions. For example, directed random walk (DRW) can infer a greater reproducibility power of the pathway activity between two classes of samples with a higher classification accuracy. However, most of the existing methods (including DRW) ignored the characteristics of different cancer subtypes and considered all of the pathways to contribute equally to the analysis. Therefore, an enhanced DRW (eDRW+) is proposed to identify breast cancer prognostic markers from multiclass expression data. An improved weight strategy using one-way ANOVA (F-test) and pathway selection based on the greatest reproducibility power is proposed in eDRW+. The experimental results show that the eDRW+ exceeds other methods in terms of AUC. Besides this, the eDRW+ identifies 294 gene markers and 45 pathway markers from the breast cancer datasets with better AUC. Therefore, the prognostic markers (pathway markers and gene markers) can identify drug targets and look for cancer subtypes with clinically distinct outcomes.
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Affiliation(s)
- Hui Wen Nies
- School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (Z.Z.); (W.H.C.)
| | - Mohd Saberi Mohamad
- Health Data Science Lab, Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Al Ain 17666, United Arab Emirates;
| | - Zalmiyah Zakaria
- School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (Z.Z.); (W.H.C.)
| | - Weng Howe Chan
- School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (Z.Z.); (W.H.C.)
| | - Muhammad Akmal Remli
- Institute for Artificial Intelligence and Big Data, Universiti Malaysia Kelantan, Kota Bharu 16100, Malaysia;
| | - Yong Hui Nies
- Department of Anatomy, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Cheras, Kuala Lumpur 56000, Malaysia;
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20
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Jann JC, Tothova Z. Cohesin mutations in myeloid malignancies. Blood 2021; 138:649-661. [PMID: 34157074 PMCID: PMC8394903 DOI: 10.1182/blood.2019004259] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022] Open
Abstract
Cohesin is a multisubunit protein complex that forms a ring-like structure around DNA. It is essential for sister chromatid cohesion, chromatin organization, transcriptional regulation, and DNA damage repair and plays a major role in dynamically shaping the genome architecture and maintaining DNA integrity. The core complex subunits STAG2, RAD21, SMC1, and SMC3, as well as its modulators PDS5A/B, WAPL, and NIPBL, have been found to be recurrently mutated in hematologic and solid malignancies. These mutations are found across the full spectrum of myeloid neoplasia, including pediatric Down syndrome-associated acute megakaryoblastic leukemia, myelodysplastic syndromes, chronic myelomonocytic leukemia, and de novo and secondary acute myeloid leukemias. The mechanisms by which cohesin mutations act as drivers of clonal expansion and disease progression are still poorly understood. Recent studies have described the impact of cohesin alterations on self-renewal and differentiation of hematopoietic stem and progenitor cells, which are associated with changes in chromatin and epigenetic state directing lineage commitment, as well as genomic integrity. Herein, we review the role of the cohesin complex in healthy and malignant hematopoiesis. We discuss clinical implications of cohesin mutations in myeloid malignancies and discuss opportunities for therapeutic targeting.
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Affiliation(s)
- Johann-Christoph Jann
- Department of Hematology and Oncology, University of Heidelberg, Mannheim, Germany; and
| | - Zuzana Tothova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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21
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Antony J, Chin CV, Horsfield JA. Cohesin Mutations in Cancer: Emerging Therapeutic Targets. Int J Mol Sci 2021; 22:6788. [PMID: 34202641 PMCID: PMC8269296 DOI: 10.3390/ijms22136788] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/08/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
The cohesin complex is crucial for mediating sister chromatid cohesion and for hierarchal three-dimensional organization of the genome. Mutations in cohesin genes are present in a range of cancers. Extensive research over the last few years has shown that cohesin mutations are key events that contribute to neoplastic transformation. Cohesin is involved in a range of cellular processes; therefore, the impact of cohesin mutations in cancer is complex and can be cell context dependent. Candidate targets with therapeutic potential in cohesin mutant cells are emerging from functional studies. Here, we review emerging targets and pharmacological agents that have therapeutic potential in cohesin mutant cells.
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Affiliation(s)
- Jisha Antony
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - Chue Vin Chin
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
| | - Julia A. Horsfield
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
- Genetics Otago Research Centre, University of Otago, Dunedin 9016, New Zealand
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22
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Huang RSP, Haberberger J, McGregor K, Mata DA, Decker B, Hiemenz MC, Lechpammer M, Danziger N, Schiavone K, Creeden J, Graf RP, Strowd R, Lesser GJ, Razis ED, Bartsch R, Giannoudis A, Bhogal T, Lin NU, Pusztai L, Ross JS, Palmieri C, Ramkissoon SH. Clinicopathologic and Genomic Landscape of Breast Carcinoma Brain Metastases. Oncologist 2021; 26:835-844. [PMID: 34105210 DOI: 10.1002/onco.13855] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 05/28/2021] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Among patients with breast carcinoma who have metastatic disease, 15%-30% will eventually develop brain metastases. We examined the genomic landscape of a large cohort of patients with breast carcinoma brain metastases (BCBMs) and compared it with a cohort of patients with primary breast carcinomas (BCs). MATERIAL AND METHODS We retrospectively analyzed 733 BCBMs tested with comprehensive genomic profiling (CGP) and compared them with 10,772 primary breast carcinomas (not-paired) specimens. For a subset of 16 triple-negative breast carcinoma (TNBC)-brain metastasis samples, programmed death-ligand 1 (PD-L1) immunohistochemistry (IHC) was performed concurrently. RESULTS A total of 733 consecutive BCBMs were analyzed. Compared with primary BCs, BCBMs were enriched for genomic alterations in TP53 (72.0%, 528/733), ERBB2 (25.6%, 188/733), RAD21 (14.1%, 103/733), NF1 (9.0%, 66/733), BRCA1 (7.8%, 57/733), and ESR1 (6.3%,46/733) (p < .05 for all comparisons). Immune checkpoint inhibitor biomarkers such as high tumor mutational burden (TMB-high; 16.2%, 119/733); high microsatellite instability (1.9%, 14/733); CD274 amplification (3.6%, 27/733); and apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like mutational signature (5.9%, 43/733) were significantly higher in the BCBM cohort compared with the primary BC cohort (p < .05 for all comparisons). When using both CGP and PD-L1 IHC, 37.5% (6/16) of patients with TNBC brain metastasis were eligible for atezolizumab based on PD-L1 IHC, and 18.8% (3/16) were eligible for pembrolizumab based on TMB-high status. CONCLUSION We found a high prevalence of clinically relevant genomic alterations in patients with BCBM, suggesting that tissue acquisition (surgery) and/or cerebrospinal fluid for CGP in addition to CGP of the primary tumor may be clinically warranted. IMPLICATIONS FOR PRACTICE This study found a high prevalence of clinically relevant genomic alterations in patients with breast carcinoma brain metastasis (BCBM), suggesting that tissue acquisition (surgery) and/or cerebrospinal fluid for comprehensive genomic profiling (CGP) in addition to CGP of the primary tumor may be clinically warranted. In addition, this study identified higher positive rates for FDA-approved immunotherapy biomarkers detected by CGP in patients with BCBM, opening a possibility of new on-label treatments. Last, this study noted limited correlation between tumor mutational burden and PD-L1 immunohistochemistry (IHC), which shows the importance of testing patients with triple-negative BCBM for immune checkpoint inhibitor eligibility with both PD-L1 IHC and CGP.
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Affiliation(s)
| | | | | | - Douglas A Mata
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Brennan Decker
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | | | | | | | | | - James Creeden
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Ryon P Graf
- Foundation Medicine, Inc., San Diego, California, USA
| | - Roy Strowd
- Section on Hematology and Oncology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Glenn J Lesser
- Section on Hematology and Oncology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | | | | | - Athina Giannoudis
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Talvinder Bhogal
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom.,The Clatterbridge Cancer Centre National Health Service (NHS) Foundation Trust, Liverpool, United Kingdom
| | - Nancy U Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Lajos Pusztai
- Yale School of Medicine, New Haven, Connecticut, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA.,Department of Pathology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA
| | - Carlo Palmieri
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom.,The Clatterbridge Cancer Centre National Health Service (NHS) Foundation Trust, Liverpool, United Kingdom
| | - Shakti H Ramkissoon
- Foundation Medicine, Inc., Morrisville, North Carolina, USA.,Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.,Department of Pathology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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23
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Wang J, Zhao H, Yu J, Xu X, Jing H, Li N, Tang Y, Wang S, Li Y, Cai J, Jin J. MiR-320b/RAD21 axis affects hepatocellular carcinoma radiosensitivity to ionizing radiation treatment through DNA damage repair signaling. Cancer Sci 2020; 112:575-588. [PMID: 33251678 PMCID: PMC7894001 DOI: 10.1111/cas.14751] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/12/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancies in the world and is associated with high mortality. Ionizing radiation (IR)-based therapy causes DNA damage, exerting a curative effect; however, DNA damage repair signaling pathways lead to HCC resistance to IR-based therapy. RAD21 is a component of the cohesion complex, crucial for chromosome segregation and DNA damage repair, while it is still unclear whether RAD21 is implicated in DNA damage and influences IR sensitivity in HCC. The current research explores the effect and upstream regulatory mechanism of RAD21 on IR sensitivity in HCC. In the present study, RAD21 mRNA and protein expression were increased within HCC tissue samples, particularly within IR-insensitive HCC tissues. The overexpression of RAD21 partially attenuated the roles of IR in HCC by promoting the viability and suppressing the apoptosis of HCC cells. RAD21 overexpression reduced the culture medium 8-hydroxy-2-deoxyguanosine concentration and decreased the protein levels of γH2AX and ATM, suggesting that RAD21 overexpression attenuated IR treatment-induced DNA damage to HCC cells. miR-320b targeted RAD21 3'-UTR to inhibit RAD21 expression. In HCC tissues, particularly in IR-insensitive HCC tissues, miR-320b expression was significantly downregulated. miR-320b inhibition also attenuated IR treatment-induced DNA damage to HCC cells; more importantly, RAD21 silencing significantly attenuated the effects of miR-320b inhibition on IR treatment-induced DNA damage, suggesting that miR-320b plays a role through targeting RAD21. In conclusion, an miR-320b/RAD21 axis modulating HCC sensitivity to IR treatment through acting on IR-induced DNA damage was demonstrated. The miR-320b/RAD21 axis could be a novel therapeutic target for further study of HCC sensitivity to IR treatment.
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Affiliation(s)
- Jianyang Wang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hong Zhao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Yu
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xin Xu
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Jing
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ning Li
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Tang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shulian Wang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yexiong Li
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianqiang Cai
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Jin
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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24
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Garrido-Castro AC, Spurr LF, Hughes ME, Li YY, Cherniack AD, Kumari P, Lloyd MR, Bychkovsky B, Barroso-Sousa R, Di Lascio S, Jain E, Files J, Mohammed-Abreu A, Krevalin M, MacKichan C, Barry WT, Guo H, Xia D, Cerami E, Rollins BJ, MacConaill LE, Lindeman NI, Krop IE, Johnson BE, Wagle N, Winer EP, Dillon DA, Lin NU. Genomic Characterization of de novo Metastatic Breast Cancer. Clin Cancer Res 2020; 27:1105-1118. [PMID: 33293374 DOI: 10.1158/1078-0432.ccr-20-1720] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/05/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE In contrast to recurrence after initial diagnosis of stage I-III breast cancer [recurrent metastatic breast cancer (rMBC)], de novo metastatic breast cancer (dnMBC) represents a unique setting to elucidate metastatic drivers in the absence of treatment selection. We present the genomic landscape of dnMBC and association with overall survival (OS). EXPERIMENTAL DESIGN Targeted DNA sequencing (OncoPanel) was prospectively performed on either primary or metastatic tumors from 926 patients (212 dnMBC and 714 rMBC). Single-nucleotide variants, copy-number variations, and tumor mutational burden (TMB) in treatment-naïve dnMBC primary tumors were compared with primary tumors in patients who ultimately developed rMBC, and correlated with OS across all dnMBC. RESULTS When comparing primary tumors by subtype, MYB amplification was enriched in triple-negative dnMBC versus rMBC (21.1% vs. 0%, P = 0.0005, q = 0.111). Mutations in KMTD2, SETD2, and PIK3CA were more prevalent, and TP53 and BRCA1 less prevalent, in primary HR+/HER2- tumors of dnMBC versus rMBC, though not significant after multiple comparison adjustment. Alterations associated with shorter OS in dnMBC included TP53 (wild-type: 79.7 months; altered: 44.2 months; P = 0.008, q = 0.107), MYC (79.7 vs. 23.3 months; P = 0.0003, q = 0.011), and cell-cycle (122.7 vs. 54.9 months; P = 0.034, q = 0.245) pathway genes. High TMB correlated with better OS in triple-negative dnMBC (P = 0.041). CONCLUSIONS Genomic differences between treatment-naïve dnMBC and primary tumors of patients who developed rMBC may provide insight into mechanisms underlying metastatic potential and differential therapeutic sensitivity in dnMBC. Alterations associated with poor OS in dnMBC highlight the need for novel approaches to overcome potential intrinsic resistance to current treatments.
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Affiliation(s)
- Ana C Garrido-Castro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Harvard Medical School, Boston, Massachusetts
| | - Liam F Spurr
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Melissa E Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yvonne Y Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Priti Kumari
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Maxwell R Lloyd
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Brittany Bychkovsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | | | - Simona Di Lascio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Esha Jain
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Janet Files
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Max Krevalin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Colin MacKichan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - William T Barry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Hao Guo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Daniel Xia
- Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women' Hospital, Boston, Massachusetts
| | - Ethan Cerami
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Barrett J Rollins
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Laura E MacConaill
- Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women' Hospital, Boston, Massachusetts.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Neal I Lindeman
- Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women' Hospital, Boston, Massachusetts.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ian E Krop
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Bruce E Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Eric P Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Deborah A Dillon
- Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women' Hospital, Boston, Massachusetts
| | - Nancy U Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
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25
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Cheng H, Zhang N, Pati D. Cohesin subunit RAD21: From biology to disease. Gene 2020; 758:144966. [PMID: 32687945 PMCID: PMC7949736 DOI: 10.1016/j.gene.2020.144966] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023]
Abstract
RAD21 (also known as KIAA0078, NXP1, HR21, Mcd1, Scc1, and hereafter called RAD21), an essential gene, encodes a DNA double-strand break (DSB) repair protein that is evolutionarily conserved in all eukaryotes from budding yeast to humans. RAD21 protein is a structural component of the highly conserved cohesin complex consisting of RAD21, SMC1a, SMC3, and SCC3 [STAG1 (SA1) and STAG2 (SA2) in metazoans] proteins, involved in sister chromatid cohesion. This function is essential for proper chromosome segregation, post-replicative DNA repair, and prevention of inappropriate recombination between repetitive regions. In interphase, cohesin also functions in the control of gene expression by binding to numerous sites within the genome. In addition to playing roles in the normal cell cycle and DNA DSB repair, RAD21 is also linked to the apoptotic pathways. Germline heterozygous or homozygous missense mutations in RAD21 have been associated with human genetic disorders, including developmental diseases such as Cornelia de Lange syndrome (CdLS) and chronic intestinal pseudo-obstruction (CIPO) called Mungan syndrome, respectively, and collectively termed as cohesinopathies. Somatic mutations and amplification of the RAD21 have also been widely reported in both human solid and hematopoietic tumors. Considering the role of RAD21 in a broad range of cellular processes that are hot spots in neoplasm, it is not surprising that the deregulation of RAD21 has been increasingly evident in human cancers. Herein, we review the biology of RAD21 and the cellular processes that this important protein regulates and discuss the significance of RAD21 deregulation in cancer and cohesinopathies.
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Affiliation(s)
- Haizi Cheng
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, United States; Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Nenggang Zhang
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, United States; Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Debananda Pati
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, United States; Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States; Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States.
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26
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SNAI1-Driven Sequential EMT Changes Attributed by Selective Chromatin Enrichment of RAD21 and GRHL2. Cancers (Basel) 2020; 12:cancers12051140. [PMID: 32370157 PMCID: PMC7281482 DOI: 10.3390/cancers12051140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 01/06/2023] Open
Abstract
Over two decades of research on cancer-associated epithelial-mesenchymal transition (EMT) led us to ascertain the occurrence of transitional intermediate states (collectively referred to as the EMT spectrum). Among the molecular factors that drive EMT, SNAI1 plays an indispensable role in regulating other core transcription factors, and this regulation is highly context-dependent. However, molecular investigation on this context-dependent regulation is still lacking. Using two ovarian cancer cell lines, we show that SNAI1 regulation on other core EMT-TFs switches from a repressive control in highly epithelial cells to an activation signaling in intermediate epithelial cells. Upon further scrutiny, we identify that the expression of early epithelial genes PERP and ERBB3 are differentially regulated in SNAI1-induced sequential EMT changes. Mechanistically, we show that changes in PERP and ERBB3 transcript levels could be correlated to the selective enrichment loss of RAD21, a cohesin component, at the distal enhancer sites of PERP and ERBB3, which precedes that of the proximal promoter-associated sites. Furthermore, the RAD21 enrichment at the distal enhancer sites is dependent on GRHL2 expression. In a nutshell, the alteration of GRHL2-associated RAD21 enrichment in epithelial genes is crucial to redefine the transition of cellular states along the EMT spectrum.
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27
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Zhu T, Gao Z, Yuan K, Wang Y. High expression of RAD21 predicts poor survival in patients with operated non-small-cell lung cancer. TUMORI JOURNAL 2020; 106:300891620910805. [PMID: 32178590 DOI: 10.1177/0300891620910805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
PURPOSE To investigate the expression profile and prognostic value of RAD21 in patients with non-small cell lung cancer (NSCLC). METHODS A tissue microarray (TMA) containing 60 paired NSCLC tissues and peritumor tissues was purchased and another TMA containing 140 NSCLC tissues was constructed. Then, immunohistochemical staining was performed and scored. Finally, the expression profile and prognostic value of RAD21 were evaluated. RESULTS RAD21 was predominantly detected in the nucleus of tumor and peritumor cells. RAD21 was more highly expressed in tumor tissues compared to peritumor tissues. High RAD21 expression was correlated with more lymph node metastases and advanced pathological stage, but not with any other clinicopathological features. High RAD21 expression led to worsened overall survival (OS) and was an independent prognostic factor for worsened OS in NSCLC, especially in stage II-III. CONCLUSION High RAD21 expression indicates poor survival in patients with NSCLC. RAD21 may become a novel prognostic biomarker and therapeutic target in patients with NSCLC.
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Affiliation(s)
- Tao Zhu
- Division of Thoracic Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu Province, China
| | - Zhaojia Gao
- Division of Thoracic Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu Province, China
- Heart and Lung Disease Laboratory, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu Province, China
| | - Kai Yuan
- Division of Thoracic Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu Province, China
- Heart and Lung Disease Laboratory, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu Province, China
| | - Yong Wang
- Division of Thoracic Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu Province, China
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28
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Fumasoni M, Murray AW. The evolutionary plasticity of chromosome metabolism allows adaptation to constitutive DNA replication stress. eLife 2020; 9:e51963. [PMID: 32043971 PMCID: PMC7069727 DOI: 10.7554/elife.51963] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/11/2020] [Indexed: 01/22/2023] Open
Abstract
Many biological features are conserved and thus considered to be resistant to evolutionary change. While rapid genetic adaptation following the removal of conserved genes has been observed, we often lack a mechanistic understanding of how adaptation happens. We used the budding yeast, Saccharomyces cerevisiae, to investigate the evolutionary plasticity of chromosome metabolism, a network of evolutionary conserved modules. We experimentally evolved cells constitutively experiencing DNA replication stress caused by the absence of Ctf4, a protein that coordinates the enzymatic activities at replication forks. Parallel populations adapted to replication stress, over 1000 generations, by acquiring multiple, concerted mutations. These mutations altered conserved features of two chromosome metabolism modules, DNA replication and sister chromatid cohesion, and inactivated a third, the DNA damage checkpoint. The selected mutations define a functionally reproducible evolutionary trajectory. We suggest that the evolutionary plasticity of chromosome metabolism has implications for genome evolution in natural populations and cancer.
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Affiliation(s)
- Marco Fumasoni
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
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29
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Leylek TR, Jeusset LM, Lichtensztejn Z, McManus KJ. Reduced Expression of Genes Regulating Cohesion Induces Chromosome Instability that May Promote Cancer and Impact Patient Outcomes. Sci Rep 2020; 10:592. [PMID: 31953484 PMCID: PMC6969069 DOI: 10.1038/s41598-020-57530-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/03/2020] [Indexed: 12/15/2022] Open
Abstract
Chromosome instability (CIN), or continual changes in chromosome complements, is an enabling feature of cancer; however, the molecular determinants of CIN remain largely unknown. Emerging data now suggest that aberrant sister chromatid cohesion may induce CIN and contribute to cancer. To explore this possibility, we employed clinical and fundamental approaches to systematically assess the impact reduced cohesion gene expression has on CIN and cancer. Ten genes encoding critical functions in cohesion were evaluated and remarkably, each exhibits copy number losses in 12 common cancer types, and reduced expression is associated with worse patient survival. To gain mechanistic insight, we combined siRNA-based silencing with single cell quantitative imaging microscopy to comprehensively assess the impact reduced expression has on CIN in two karyotypically stable cell lines. We show that reduced expression induces CIN phenotypes, namely increases in micronucleus formation and nuclear areas. Subsequent direct tests involving a subset of prioritized genes also revealed significant changes in chromosome numbers with corresponding increases in moderate and severe cohesion defects within mitotic chromosome spreads. Collectively, our clinical and fundamental findings implicate reduced sister chromatid cohesion, resulting from gene copy number losses, as a key pathogenic event in the development and progression of many cancer types.
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Affiliation(s)
- Tarik R Leylek
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Lucile M Jeusset
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Zelda Lichtensztejn
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Kirk J McManus
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada.
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada.
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30
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Nacht AS, Ferrari R, Zaurin R, Scabia V, Carbonell-Caballero J, Le Dily F, Quilez J, Leopoldi A, Brisken C, Beato M, Vicent GP. C/EBPα mediates the growth inhibitory effect of progestins on breast cancer cells. EMBO J 2019; 38:e101426. [PMID: 31373033 DOI: 10.15252/embj.2018101426] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 01/19/2023] Open
Abstract
Steroid hormones are key gene regulators in breast cancer cells. While estrogens stimulate cell proliferation, progestins activate a single cell cycle followed by proliferation arrest. Here, we use biochemical and genome-wide approaches to show that progestins achieve this effect via a functional crosstalk with C/EBPα. Using ChIP-seq, we identify around 1,000 sites where C/EBPα binding precedes and helps binding of progesterone receptor (PR) in response to hormone. These regions exhibit epigenetic marks of active enhancers, and C/EBPα maintains an open chromatin conformation that facilitates loading of ligand-activated PR. Prior to hormone exposure, C/EBPα favors promoter-enhancer contacts that assure hormonal regulation of key genes involved in cell proliferation by facilitating binding of RAD21, YY1, and the Mediator complex. Knockdown of C/EBPα disrupts enhancer-promoter contacts and decreases the presence of these architectural proteins, highlighting its key role in 3D chromatin looping. Thus, C/EBPα fulfills a previously unknown function as a potential growth modulator in hormone-dependent breast cancer.
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Affiliation(s)
- A Silvina Nacht
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Roberto Ferrari
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Roser Zaurin
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Valentina Scabia
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - José Carbonell-Caballero
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Francois Le Dily
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Javier Quilez
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Alexandra Leopoldi
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Cathrin Brisken
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guillermo P Vicent
- Center for Genomic Regulation (CRG), Barcelona, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
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31
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Mintzas K, Heuser M. Emerging strategies to target the dysfunctional cohesin complex in cancer. Expert Opin Ther Targets 2019; 23:525-537. [PMID: 31020869 DOI: 10.1080/14728222.2019.1609943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 04/17/2019] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Mutations in cohesin genes have been described in numerous solid cancers and hematologic malignancies; subsequent experimental evidence has linked these mutations with carcinogenesis. Areas covered: In this review, we present current information about the physiological role of the cohesin complex in normal and malignant cells and describe current therapeutic strategies that are being explored in cohesin-mutated cancers. We discuss a range of targets and strategies that should be explored to develop targeted therapies for patients with aberrant cohesin. Expert opinion: Targeting of the cohesin complex is an underexplored area of drug development. There is a high frequency of cohesin mutations in multiple cancers, hence specific targeting strategies should be explored. Cohesins play a crucial role in cellular organization; therefore, we expect a narrow therapeutic window of direct inhibitors of cohesin components. Exploiting experimental approaches that correct dysfunctional cohesins and coupling them with current therapeutic strategies can provide novel, innovative and more effective treatment regimens.
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Affiliation(s)
- Konstantinos Mintzas
- a Department of Hematology , Oncology, Hemostasis and Stem Cell Transplantation, Hannover Medical School , Hannover , Germany
| | - Michael Heuser
- a Department of Hematology , Oncology, Hemostasis and Stem Cell Transplantation, Hannover Medical School , Hannover , Germany
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32
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Koosha S, Mohamed Z, Sinniah A, Alshawsh MA. Investigation into the Molecular Mechanisms underlying the Anti-proliferative and Anti-tumorigenesis activities of Diosmetin against HCT-116 Human Colorectal Cancer. Sci Rep 2019; 9:5148. [PMID: 30914796 PMCID: PMC6435658 DOI: 10.1038/s41598-019-41685-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 03/08/2019] [Indexed: 01/06/2023] Open
Abstract
Diosmetin (Dis) is a bioflavonoid with cytotoxicity properties against variety of cancer cells including hepatocarcinoma, breast and colorectal (CRC) cancer. The exact mechanism by which Dis acts against CRC however, still remains unclear, hence in this study, we investigated the possible molecular mechanisms of Dis in CRC cell line, HCT-116. Here, we monitored the viability of HCT-116 cells in the presence of Dis and investigated the underlying mechanism of Dis against HCT-116 cells at the gene and protein levels using NanoString and proteome profiler array technologies. Findings demonstrated that Dis exhibits greater cytotoxic effects towards HCT-116 CRC cells (IC50 = 3.58 ± 0.58 µg/ml) as compared to the normal colon CCD-841 cells (IC50 = 51.95 ± 0.11 µg/ml). Arrests of the cells in G2/M phase confirms the occurrence of mitotic disruption via Dis. Activation of apoptosis factors such as Fas and Bax at the gene and protein levels along with the release of Cytochrome C from mitochondria and cleavage of Caspase cascades indicate the presence of turbulence as a result of apoptosis induction in Dis-treated cells. Moreover, NF-ƙB translocation was inhibited in Dis-treated cells. Our results indicate that Dis can target HCT-116 cells through the mitotic disruption and apoptosis induction.
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Affiliation(s)
- Sanaz Koosha
- Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Zahurin Mohamed
- Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ajantha Sinniah
- Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Mohammed A Alshawsh
- Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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33
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Perez S, Gevor M, Davidovich A, Kaspi A, Yamin K, Domovich T, Meirson T, Matityahu A, Brody Y, Stemmer SM, El-Osta A, Haviv I, Onn I, Gal-Tanamy M. Dysregulation of the cohesin subunit RAD21 by Hepatitis C virus mediates host-virus interactions. Nucleic Acids Res 2019; 47:2455-2471. [PMID: 30698808 PMCID: PMC6412124 DOI: 10.1093/nar/gkz052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 12/30/2018] [Accepted: 01/24/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) infection is the leading cause of chronic hepatitis, which often results in liver fibrosis, cirrhosis and hepatocellular carcinoma (HCC). HCV possesses an RNA genome and its replication is confined to the cytoplasm. Yet, infection with HCV leads to global changes in gene expression, and chromosomal instability (CIN) in the host cell. The mechanisms by which the cytoplasmic virus affects these nuclear processes are elusive. Here, we show that HCV modulates the function of the Structural Maintenance of Chromosome (SMC) protein complex, cohesin, which tethers remote regions of chromatin. We demonstrate that infection of hepatoma cells with HCV leads to up regulation of the expression of the RAD21 cohesin subunit and changes cohesin residency on the chromatin. These changes regulate the expression of genes associated with virus-induced pathways. Furthermore, siRNA downregulation of viral-induced RAD21 reduces HCV infection. During mitosis, HCV infection induces hypercondensation of chromosomes and the appearance of multi-centrosomes. We provide evidence that the underlying mechanism involves the viral NS3/4 protease and the cohesin regulator, WAPL. Altogether, our results provide the first evidence that HCV induces changes in gene expression and chromosome structure of infected cells by modulating cohesin.
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Affiliation(s)
- Shira Perez
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Cancer Personalized Medicine and Diagnostic Genomics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Michael Gevor
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ateret Davidovich
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
| | - Katreena Yamin
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Tom Domovich
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Tomer Meirson
- Cell Migration and Invasion Laboratory, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Avi Matityahu
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Yehuda Brody
- The Broad institute of Harvard and MIT, Cambridge, MA, USA
| | - Salomon M Stemmer
- Davidoff Center, Rabin Medical Center, Beilinson Campus, Petach Tikva, and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR
| | - Izhak Haviv
- Cancer Personalized Medicine and Diagnostic Genomics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Itay Onn
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Meital Gal-Tanamy
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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34
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Bianco F, Eisenman ST, Colmenares Aguilar MG, Bonora E, Clavenzani P, Linden DR, De Giorgio R, Farrugia G, Gibbons SJ. Expression of RAD21 immunoreactivity in myenteric neurons of the human and mouse small intestine. Neurogastroenterol Motil 2018; 30:e13429. [PMID: 30069982 PMCID: PMC6150808 DOI: 10.1111/nmo.13429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/20/2018] [Accepted: 06/22/2018] [Indexed: 12/23/2022]
Abstract
BACKGROUND RAD21 is a double-strand-break repair protein and component of the cohesin complex with key roles in cellular functions. A RAD21 loss-of-function mutation was found in cases of chronic intestinal pseudo-obstruction (CIPO) with associated enteric neuronal loss. Analysis of RAD21 expression in the enteric nervous system is lacking, thus we aimed to characterize RAD21 immunoreactivity (IR) in myenteric ganglia. METHODS Double labeling immunofluorescence in mouse and human jejunum was used to determine colocalization of RAD21 with HuC/D, PGP9.5, neuronal nitric oxide synthase (nNOS), neuropeptide Y (NPY), choline acetyl transferase (ChAT), Kit, platelet-derived growth factor receptor-α (PDGFRα), and glial fibrillary acid protein (GFAP) IRs. RESULTS A subset of PGP9.5- and HuC/D-IR neuronal cell bodies and nerve fibers in the myenteric plexus of human and mouse small intestine also displayed cytoplasmic RAD21-IR Cytoplasmic RAD21-IR was found in 43% of HuC/D-IR neurons in adult and neonatal mice but did not colocalize with nNOS. A subset of ChAT-positive neurons had cytoplasmic RAD21-IR Punctate RAD21-IR was restricted to the nucleus in most cell types consistent with labeling of the cohesin complex. Cytoplasmic RAD21-IR was not detected in interstitial cells of Cajal, fibroblast-like cells or glia. Subsets of neurons in primary culture exhibited cytoplasmic RAD21-IR Suppression of RAD21 expression by shRNA knockdown abolished RAD21-IR in cultured neurons. CONCLUSIONS Our data showing cytoplasmic RAD21 expression in enteric neurons provide a basis toward understanding how mutations of this gene may contribute to altered neuronal function/survival thus leading to gut-motor abnormalities.
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Affiliation(s)
- F Bianco
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, Bologna, Italy
| | - S T Eisenman
- Enteric NeuroScience Program, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - M G Colmenares Aguilar
- Enteric NeuroScience Program, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - E Bonora
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - P Clavenzani
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, Bologna, Italy
| | - D R Linden
- Enteric NeuroScience Program, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - R De Giorgio
- Department of Medical Sciences, Nuovo Arcispedale S.Anna, University of Ferrara, Ferrara, Italy
| | - G Farrugia
- Enteric NeuroScience Program, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - S J Gibbons
- Enteric NeuroScience Program, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
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35
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Pottier C, Kriegsmann M, Alberts D, Smargiasso N, Baiwir D, Mazzucchelli G, Herfs M, Fresnais M, Casadonte R, Delvenne P, Pauw E, Longuespée R. Microproteomic Profiling of High‐Grade Squamous Intraepithelial Lesion of the Cervix: Insight into Biological Mechanisms of Dysplasia and New Potential Diagnostic Markers. Proteomics Clin Appl 2018; 13:e1800052. [DOI: 10.1002/prca.201800052] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/06/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Charles Pottier
- Mass Spectrometry LaboratoryGIGA‐ResearchDepartment of ChemistryUniversity of Liège Liège Belgium
- Department of Medical OncologyUniversity of Liège Liège Belgium
| | - Mark Kriegsmann
- Institute of pathologyUniversity of Heidelberg Heidelberg Germany
| | - Deborah Alberts
- Mass Spectrometry LaboratoryGIGA‐ResearchDepartment of ChemistryUniversity of Liège Liège Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry LaboratoryGIGA‐ResearchDepartment of ChemistryUniversity of Liège Liège Belgium
| | | | - Gabriel Mazzucchelli
- Mass Spectrometry LaboratoryGIGA‐ResearchDepartment of ChemistryUniversity of Liège Liège Belgium
| | - Michael Herfs
- Laboratory of Experimental PathologyGIGA‐CancerDepartment of PathologyUniversity of Liège Liège Belgium
| | - Margaux Fresnais
- Department of Clinical Pharmacology and PharmacoepidemiologyUniversity of Heidelberg Heidelberg Germany
- German Cancer Consortium (DKTK)‐German Cancer Research Center (DKFZ) Heidelberg Germany
| | | | - Philippe Delvenne
- Laboratory of Experimental PathologyGIGA‐CancerDepartment of PathologyUniversity of Liège Liège Belgium
| | - Edwin Pauw
- Mass Spectrometry LaboratoryGIGA‐ResearchDepartment of ChemistryUniversity of Liège Liège Belgium
| | - Rémi Longuespée
- Mass Spectrometry LaboratoryGIGA‐ResearchDepartment of ChemistryUniversity of Liège Liège Belgium
- Institute of pathologyUniversity of Heidelberg Heidelberg Germany
- Proteopath GmbH Trier Germany
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36
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Xia L, Wang M, Li H, Tang X, Chen F, Cui J. The effect of aberrant expression and genetic polymorphisms of Rad21 on cervical cancer biology. Cancer Med 2018; 7:3393-3405. [PMID: 29797792 PMCID: PMC6051231 DOI: 10.1002/cam4.1592] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/08/2018] [Accepted: 05/10/2018] [Indexed: 12/18/2022] Open
Abstract
The therapeutic challenge of advanced, recurrent, and refractory cervical cancer (CC) needs to develop new molecularly targeted drugs. Rad21 is an important regulatory gene that maintains the correct dissociation of sister chromatids during cell mitosis. The aim of this study was to investigate the effect of Rad21 on CC. Rad21 expression in CC and cervical intraepithelial neoplasia III was significantly increased. Women with the rs2289937 C genotype (CC+CT) of rs4570 and rs4579555 genotypes and haplotype 1 (TTTCAGGCGC) were significantly associated with CC risk, while women with low frequencies of haplotype 6 (TTTTAGGCGC) also increased the risk of CC.Rad21‐specific shRNA decreased cancerous cell proliferation, migration, and invasion and increased the proportion of cells in G2/M phase as well as sensitivity to radiation. The Rad21 influenced the expression of XPO1, CyclinB1, CDK1, P21, P27, and P53 through up‐and downregulating the Rad21 expression. The TCGA database of CC also showed that Rad21 expression was associated with poor disease survival and XPO1 expression. Moreover, the KEGG pathway indicated that Rad21 is broadly involved in the cell cycle and RNA transportation via XPO1. This suggests that Rad21 involves the development of cervical cancer possibly by participating in the regulation of cell cycle and the nuclear output of the tumor suppressor gene via XPO1.
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Affiliation(s)
- Li Xia
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Minjie Wang
- Department of Obstetrics and Gynecology, People's Hospital of Linying, Luohe, China
| | - Hongying Li
- Department of Obstetrics and Gynecology, Pingdingshan First People's Hospital of Henan Province, Pingdingshan, China
| | - Xiangjing Tang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fei Chen
- Department of Gynaecology and Obstetrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinquan Cui
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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37
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Anticancer drugs and the regulation of Hedgehog genes GLI1 and PTCH1, a comparative study in nonmelanoma skin cancer cell lines. Anticancer Drugs 2017; 28:1106-1117. [DOI: 10.1097/cad.0000000000000551] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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38
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Increased LOH due to Defective Sister Chromatid Cohesion Is due Primarily to Chromosomal Aneuploidy and not Recombination. G3-GENES GENOMES GENETICS 2017; 7:3305-3315. [PMID: 28983067 PMCID: PMC5633381 DOI: 10.1534/g3.117.300091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Loss of heterozygosity (LOH) is an important factor in cancer, pathogenic fungi, and adaptation to changing environments. The sister chromatid cohesion process (SCC) suppresses aneuploidy and therefore whole chromosome LOH. SCC is also important to channel recombinational repair to sister chromatids, thereby preventing LOH mediated by allelic recombination. There is, however, insufficient information about the relative roles that the SCC pathway plays in the different modes of LOH. Here, we found that the cohesin mutation mcd1-1, and other mutations in SCC, differentially affect the various types of LOH. The greatest effect, by three orders of magnitude, was on whole chromosome loss (CL). In contrast, there was little increase in recombination-mediated LOH, even for telomeric markers. Some of the LOH events that were increased by SCC mutations were complex, i.e., they were the result of several chromosome transactions. Although these events were independent of POL32, the most parsimonious way to explain the formation of at least some of them was break-induced replication through the centromere. Interestingly, the mcd1-1 pol32Δ double mutant showed a significant reduction in the rate of CL in comparison with the mcd1-1 single mutant. Our results show that defects in SCC allow the formation of complex LOH events that, in turn, can promote drug or pesticide resistance in diploid microbes that are pathogenic to humans or plants.
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Polymorphisms in mitotic checkpoint-related genes can influence survival outcomes of early-stage non-small cell lung cancer. Oncotarget 2017; 8:61777-61785. [PMID: 28977903 PMCID: PMC5617463 DOI: 10.18632/oncotarget.18693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/22/2017] [Indexed: 12/22/2022] Open
Abstract
This study was conducted to investigate the association between variants in mitotic checkpoint-related genes and clinical outcomes of non-small cell lung cancer (NSCLC). A total of 766 patients with NSCLC who underwent curative surgery were enrolled. Among the 73 variants evaluated, 4 variants were related with survival outcomes. BUB3 rs7897156C>T was associated with worse overall survival under a recessive model (adjusted hazard ratio = 1.58, 95% confidence interval = 1.07–2.33, P = 0.02). AURKB rs1059476G>A was associated with better overall survival under a recessive model (adjusted hazard ratio = 0.64, 95% confidence interval = 0.41–0.99, P = 0.05). PTTG1 rs1895320T>C and RAD21 rs1374297C>G were associated with worse disease-free survival. In the functional study, relative luciferase activity was higher at the BUB3 rs7897156T allele compared to that at the C allele. Western blot showed that the phosphorylation of AKT and mTOR in the AURKB variant-type (M298) was significantly lower than in the AURKB wild-type (T298). We found that 4 variants of mitotic checkpoint-related genes were associated with survival outcomes in patients with surgically resected NSCLC. Particularly, our results suggest that BUB3 rs7897156C>T and AURKB rs1059476G>A are functional variants.
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Cai J, Li B, Zhu Y, Fang X, Zhu M, Wang M, Liu S, Jiang X, Zheng J, Zhang X, Chen P. Prognostic Biomarker Identification Through Integrating the Gene Signatures of Hepatocellular Carcinoma Properties. EBioMedicine 2017; 19:18-30. [PMID: 28434945 PMCID: PMC5440601 DOI: 10.1016/j.ebiom.2017.04.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 02/06/2023] Open
Abstract
Many molecular classification and prognostic gene signatures for hepatocellular carcinoma (HCC) patients have been established based on genome-wide gene expression profiling; however, their generalizability is unclear. Herein, we systematically assessed the prognostic effects of these gene signatures and identified valuable prognostic biomarkers by integrating these gene signatures. With two independent HCC datasets (GSE14520, N = 242 and GSE54236, N = 78), 30 published gene signatures were evaluated, and 11 were significantly associated with the overall survival (OS) of postoperative HCC patients in both datasets. The random survival forest models suggested that the gene signatures were superior to clinical characteristics for predicting the prognosis of the patients. Based on the 11 gene signatures, a functional protein-protein interaction (PPI) network with 1406 nodes and 10,135 edges was established. With tissue microarrays of HCC patients (N = 60), we determined the prognostic values of the core genes in the network and found that RAD21, CDK1, and HDAC2 expression levels were negatively associated with OS for HCC patients. The multivariate Cox regression analyses suggested that CDK1 was an independent prognostic factor, which was validated in an independent case cohort (N = 78). In cellular models, inhibition of CDK1 by siRNA or a specific inhibitor, RO-3306, reduced cellular proliferation and viability for HCC cells. These results suggest that the prognostic predictive capacities of these gene signatures are reproducible and that CDK1 is a potential prognostic biomarker or therapeutic target for HCC patients. Eleven gene signatures have promising values for the OS prediction of HCC patients who undergo the surgical treatments. Prediction results for the 11 gene signatures were in moderate concordance, and genes included were functionally linked. CDK1 is an independent prognostic biomarker and a potential therapeutic target for HCC patients.
Various gene signatures for hepatocellular carcinoma (HCC) patients have been reported; however, their generalizability is unclear. Using two HCC patient datasets, we assessed the prognostic values of these gene signatures and identified 11 gene signatures that were associated with overall survival for postoperative HCC patients in both cohorts. Genes derived from these signatures formed a functional protein-protein interaction network with 1,406 nodes and 10,135 edges, and the expression levels of three core genes, RAD21, CDK1, and HDAC2, in the network were negatively associated with the overall survival of HCC patients. Further studies suggested that CDK1 is an independent prognostic factor and that it is a potential therapeutic target for HCC patients.
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Affiliation(s)
- Jialin Cai
- Translational Medicine Research Center, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, PR China
| | - Bin Li
- Biliary Tract Surgery Department I, Eastern Hepatobiliary Surgery Hospital, Secondary Military Medical University, Shanghai 200433, PR China; Diagnosis and Treatment Center of Malignant Biliary Tract Diseases, Secondary Military Medical University, Shanghai 200433, PR China
| | - Yan Zhu
- Department of Pathology, Changhai Hospital, Secondary Military Medical University, Shanghai 200433, PR China
| | - Xuqian Fang
- Translational Medicine Research Center, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, PR China
| | - Mingyu Zhu
- Department of Infectious Diseases, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, PR China
| | - Mingjie Wang
- Department of Infectious Diseases, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, PR China
| | - Shupeng Liu
- Department of Pathology, Changhai Hospital, Secondary Military Medical University, Shanghai 200433, PR China
| | - Xiaoqing Jiang
- Biliary Tract Surgery Department I, Eastern Hepatobiliary Surgery Hospital, Secondary Military Medical University, Shanghai 200433, PR China; Diagnosis and Treatment Center of Malignant Biliary Tract Diseases, Secondary Military Medical University, Shanghai 200433, PR China
| | - Jianming Zheng
- Department of Pathology, Changhai Hospital, Secondary Military Medical University, Shanghai 200433, PR China.
| | - XinXin Zhang
- Translational Medicine Research Center, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, PR China; Department of Infectious Diseases, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, PR China.
| | - Peizhan Chen
- Translational Medicine Research Center, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, PR China.
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Abstract
Acute Myeloid Leukemia (AML) is a hematologic malignancy with a poor prognosis. Recent genome-wide sequencing studies have identified frequent mutations in genes encoding members of the cohesin complex. Mutations in cohesin contribute to myeloid malignancies by conferring enhanced self-renewal of hematopoietic stem and progenitor cells but the mechanisms behind this phenotype have not been fully elucidated. Of note, cohesin mutations are highly prevalent in acute megakaryocytic leukemia associated with Down syndrome (DS-AMKL), where they occur in over half of patients. Evidence suggests that cohesin mutations alter gene expression through changes in chromatin accessibility and/or aberrant targeting of epigenetic complexes. In this review we discuss the pathogenic mechanisms by which cohesin mutations contribute to myeloid malignancies.
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Affiliation(s)
- Joseph B. Fisher
- Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI, USA
| | - Maureen McNulty
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Michael J. Burke
- Department of Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplantation, Medical College of Wisconsin, Milwaukee, WI, USA
| | - John D. Crispino
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Sridhar Rao
- Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI, USA
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplantation, Medical College of Wisconsin, Milwaukee, WI, USA
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Rooney N, Riggio AI, Mendoza-Villanueva D, Shore P, Cameron ER, Blyth K. Runx Genes in Breast Cancer and the Mammary Lineage. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 962:353-368. [PMID: 28299668 DOI: 10.1007/978-981-10-3233-2_22] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A full understanding of RUNX gene function in different epithelial lineages has been thwarted by the lethal phenotypes observed when constitutively knocking out these mammalian genes. However temporal expression of the Runx genes throughout the different phases of mammary gland development is indicative of a functional role in this tissue. A few studies have emerged describing how these genes impact on the fate of mammary epithelial cells by regulating lineage differentiation and stem/progenitor cell potential, with implications for the transformed state. The importance of the RUNX/CBFβ core factor binding complex in breast cancer has very recently been highlighted with both RUNX1 and CBFβ appearing in a comprehensive gene list of predicted breast cancer driver mutations. Nonetheless, the evidence to date shows that the RUNX genes can have dualistic outputs with respect to promoting or constraining breast cancer phenotypes, and that this may be aligned to individual subtypes of the clinical disease. We take this opportunity to review the current literature on RUNX and CBFβ in the normal and neoplastic mammary lineage while appreciating that this is likely to be the tip of the iceberg in our knowledge.
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Affiliation(s)
- Nicholas Rooney
- Beatson Institute for Cancer Research, Bearsden, Glasgow, G61 1BD, UK
| | | | | | - Paul Shore
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Ewan R Cameron
- School of Veterinary Medicine, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
| | - Karen Blyth
- Beatson Institute for Cancer Research, Bearsden, Glasgow, G61 1BD, UK.
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Repo H, Löyttyniemi E, Nykänen M, Lintunen M, Karra H, Pitkänen R, Söderström M, Kuopio T, Kronqvist P. The Expression of Cohesin Subunit SA2 Predicts Breast Cancer Survival. Appl Immunohistochem Mol Morphol 2016; 24:615-621. [PMID: 26447899 DOI: 10.1097/pai.0000000000000240] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cohesin is one of the main regulators of sister chromatid separation during the metaphase/anaphase transition. It is a multiprotein complex consisting of 4 core subunits, one of those being the SA2 subunit. SA2 plays the final role in dismantling the cohesion complex from the sister chromatids and also functions in DNA double-strand break repair and gene regulation. There is increasing evidence regarding the involvement of both overexpression and underexpression of cohesin in cancer. Here, we present expression patterns of SA2 in different types of human breast tissue, and the prognostic analysis in the material from breast cancer patients with long-term follow-up. SA2 immunoexpression was evaluated in benign, precancerous, and malignant breast tissue, and was classified into low-intensity or high-intensity groups. The DNA content was determined by image cytometry on breast cancer cell imprints. Prognostic analyses were based on 445 breast cancer patients with upto 20 years' follow-up. SA2 immunoexpression was equally high in both benign and precancerous breast tissue. Instead, 72% of the invasive breast cancers showed deficient SA2 expression. These patients were also associated with an unfavorable outcome as indicated by a 1.6-fold risk of breast cancer death (P=0.0208). The majority (75%) of the patients with low SA2 expression were alive 6.0 years after the diagnosis, whereas the majority of the patients with high SA2 expression survived 17.6 years after the diagnosis. No statistically significant association could be detected between SA2 immunoexpression and DNA aneuploidy. Our results and previous literature indicate that decreased SA2 immunoexpression is associated with malignant breast disease and a particularly unfavorable course of disease.
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Affiliation(s)
- Heli Repo
- *Department of Pathology, University of Turku and Turku University Hospital †Department of Medical Statistics, Medical Faculty, University of Turku, Turku ‡Department of Pathology, Jyväskylä Central Hospital, Jyväskylä §Department of Pathology, Pori Central Hospital, Pori, Finland
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44
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Pan XW, Gan SS, Ye JQ, Fan YH, Hong Υ, Chu CM, Gao Y, Li L, Liu X, Chen L, Huang Y, Xu H, Ren JZ, Yin L, Qu FJ, Huang H, Cui XG, Xu DF. SMC1A promotes growth and migration of prostate cancer in vitro and in vivo. Int J Oncol 2016; 49:1963-1972. [PMID: 27667360 DOI: 10.3892/ijo.2016.3697] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/31/2016] [Indexed: 11/05/2022] Open
Abstract
Structural maintenance of chromosome 1 alpha (SMC1A) gene has been reported to be related to tumor development in some types of human cancers. However, the misregulation of SMC1A and its functions in castration-resistant prostate cancer (CRPC) have not been well understood. In the present study, we found that SMC1A was elevated in androgen-independent PCa cell lines PC-3 and DU-145 compared to androgen sensitive LNCap and 22RV1 cells by qPCR and western blot assay. Knockdown of SMC1A inhibited cell growth, colony formation and cell migration abilities of PC-3 and DU145 cells by MTT, colony formation and transwell assays, and affected cell cycle progression in PC-3 and DU145 cells by flow cytometry. Moreover, SMC1A knockdown significantly reduced tumor growth in vivo in a nude mouse model. Additionally, we also found that the expression of SMC1A gene was higher in prostate cancer tissues than in the adjacent normal tissues by immunohistochemical staining, and was positively correlated to tumor metastasis and recurrence by Oncomine database mining. Taken together, the present study indicates that SMC1A may play an important role in malignant transformation of PCa under conditions of androgen deprivation and act as a new target for PCa diagnosis and treatment.
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Affiliation(s)
- Xiu-Wu Pan
- Department of Urinary Surgery, Third Affiliated Hospital, Second Military Medical University, Shanghai 201805, P.R. China
| | - Si-Shun Gan
- Department of Urinary Surgery, Third Affiliated Hospital, Second Military Medical University, Shanghai 201805, P.R. China
| | - Jian-Qing Ye
- Department of Urinary Surgery, Third Affiliated Hospital, Second Military Medical University, Shanghai 201805, P.R. China
| | - Ying-Hui Fan
- Department of Anesthesiology, Renji Hospital, Shanghai Jiaotong University, Shanghai 200127, P.R. China
| | - Υi Hong
- Department of Urinary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Chuan-Min Chu
- Department of Urinary Surgery, Third Affiliated Hospital, Second Military Medical University, Shanghai 201805, P.R. China
| | - Yi Gao
- Department of Urinary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Lin Li
- Department of Urinary Surgery, Third Affiliated Hospital, Second Military Medical University, Shanghai 201805, P.R. China
| | - Xi Liu
- Department of Urinary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Lu Chen
- Department of Urinary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Yi Huang
- Department of Urinary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Hong Xu
- Department of Urinary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Ji-Zhong Ren
- Department of Urinary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Lei Yin
- Department of Urinary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Fa-Jun Qu
- Department of Urinary Surgery, Third Affiliated Hospital, Second Military Medical University, Shanghai 201805, P.R. China
| | - Hai Huang
- Department of Urinary Surgery, Third Affiliated Hospital, Second Military Medical University, Shanghai 201805, P.R. China
| | - Xin-Gang Cui
- Department of Urinary Surgery, Third Affiliated Hospital, Second Military Medical University, Shanghai 201805, P.R. China
| | - Dan-Feng Xu
- Department of Urinary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
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Yun J, Song SH, Kim HP, Han SW, Yi EC, Kim TY. Dynamic cohesin-mediated chromatin architecture controls epithelial-mesenchymal plasticity in cancer. EMBO Rep 2016; 17:1343-59. [PMID: 27466323 PMCID: PMC5007572 DOI: 10.15252/embr.201541852] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 06/03/2016] [Accepted: 06/22/2016] [Indexed: 01/26/2023] Open
Abstract
Epithelial to mesenchymal transition (EMT) and mesenchymal to epithelial transition (MET) are important interconnected events in tumorigenesis controlled by complex genetic networks. However, the cues that activate EMT-initiating factors and the mechanisms that reversibly connect EMT/MET are not well understood. Here, we show that cohesin-mediated chromatin organization coordinates EMT/MET by regulating mesenchymal genes. We report that RAD21, a subunit of the cohesin complex, is expressed in epithelial breast cancer cells, whereas its expression is decreased in mesenchymal cancer. Depletion of RAD21 in epithelial cancer cells causes transcriptional activation of TGFB1 and ITGA5, inducing EMT. Reduced binding of RAD21 changes intrachromosomal chromatin interactions within the TGFB1 and ITGA5 loci, creating an active transcriptional environment. Similarly, stem cell-like cancer cells also show an open chromatin structure at both genes, which correlates with high expression levels and mesenchymal fate characteristics. Conversely, overexpression of RAD21 in mesenchymal cancer cells induces MET-specific expression patterns. These findings indicate that dynamic cohesin-mediated chromatin structures are responsible for the initiation and regulation of essential EMT-related cell fate changes in cancer.
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Affiliation(s)
- Jiyeon Yun
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology Seoul National University College of Medicine, Seoul, Korea
| | - Sang-Hyun Song
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hwang-Phill Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Sae-Won Han
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Eugene C Yi
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology Seoul National University College of Medicine, Seoul, Korea
| | - Tae-You Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology Seoul National University College of Medicine, Seoul, Korea Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
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46
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Dasgupta T, Antony J, Braithwaite AW, Horsfield JA. HDAC8 Inhibition Blocks SMC3 Deacetylation and Delays Cell Cycle Progression without Affecting Cohesin-dependent Transcription in MCF7 Cancer Cells. J Biol Chem 2016; 291:12761-12770. [PMID: 27072133 PMCID: PMC4933439 DOI: 10.1074/jbc.m115.704627] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/11/2016] [Indexed: 12/19/2022] Open
Abstract
Cohesin, a multi-subunit protein complex involved in chromosome organization, is frequently mutated or aberrantly expressed in cancer. Multiple functions of cohesin, including cell division and gene expression, highlight its potential as a novel therapeutic target. The SMC3 subunit of cohesin is acetylated (ac) during S phase to establish cohesion between replicated chromosomes. Following anaphase, ac-SMC3 is deacetylated by HDAC8. Reversal of SMC3 acetylation is imperative for recycling cohesin so that it can be reloaded in interphase for both non-mitotic and mitotic functions. We blocked deacetylation of ac-SMC3 using an HDAC8-specific inhibitor PCI-34051 in MCF7 breast cancer cells, and examined the effects on transcription of cohesin-dependent genes that respond to estrogen. HDAC8 inhibition led to accumulation of ac-SMC3 as expected, but surprisingly, had no influence on the transcription of estrogen-responsive genes that are altered by siRNA targeting of RAD21 or SMC3. Knockdown of RAD21 altered estrogen receptor α (ER) recruitment at SOX4 and IL20, and affected transcription of these genes, while HDAC8 inhibition did not. Rather, inhibition of HDAC8 delayed cell cycle progression, suppressed proliferation and induced apoptosis in a concentration-dependent manner. We conclude that HDAC8 inhibition does not change the estrogen-specific transcriptional role of cohesin in MCF7 cells, but instead, compromises cell cycle progression and cell survival. Our results argue that candidate inhibitors of cohesin function may differ in their effects depending on the cellular genotype and should be thoroughly tested for predicted effects on cohesin's mechanistic roles.
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Affiliation(s)
- Tanushree Dasgupta
- From the Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, and
| | - Jisha Antony
- From the Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, and
| | - Antony W Braithwaite
- From the Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, and; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Julia A Horsfield
- From the Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, and; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand.
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47
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Zhu S, Zhao L, Li Y, Hou P, Yao R, Tan J, Liu D, Han L, Huang B, Lu J, Zhang Y. Suppression of RAD21 Induces Senescence of MDA‐MB‐231 Human Breast Cancer Cells Through RB1 Pathway Activation Via c‐Myc Downregulation. J Cell Biochem 2015; 117:1359-69. [DOI: 10.1002/jcb.25426] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 10/30/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Shan Zhu
- The Institute of Genetics and CytologyNortheast Normal UniversityChangchun130024China
- The First Affiliated HospitalJilin UniversityChangchun130012China
| | - Li Zhao
- The Key Laboratory of Molecular Epigenetics of the Ministry of EducationNortheast Normal UniversityChangchun130020China
| | - Yueyang Li
- The Institute of Genetics and CytologyNortheast Normal UniversityChangchun130024China
| | - Pingfu Hou
- The Institute of Genetics and CytologyNortheast Normal UniversityChangchun130024China
| | - Ruosi Yao
- The Institute of Genetics and CytologyNortheast Normal UniversityChangchun130024China
| | - Jiang Tan
- The Institute of Genetics and CytologyNortheast Normal UniversityChangchun130024China
| | - Dongxu Liu
- The University of AucklandGraftonAuckland1023New Zealand
| | - Liping Han
- School of Life SciencesChangchun Normal UniversityChangchun130032China
| | - Baiqu Huang
- The Institute of Genetics and CytologyNortheast Normal UniversityChangchun130024China
| | - Jun Lu
- The First Affiliated HospitalJilin UniversityChangchun130012China
| | - Yu Zhang
- The Institute of Genetics and CytologyNortheast Normal UniversityChangchun130024China
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48
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Yao F, Zhang C, Du W, Liu C, Xu Y. Identification of Gene-Expression Signatures and Protein Markers for Breast Cancer Grading and Staging. PLoS One 2015; 10:e0138213. [PMID: 26375396 PMCID: PMC4573873 DOI: 10.1371/journal.pone.0138213] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/27/2015] [Indexed: 12/13/2022] Open
Abstract
The grade of a cancer is a measure of the cancer's malignancy level, and the stage of a cancer refers to the size and the extent that the cancer has spread. Here we present a computational method for prediction of gene signatures and blood/urine protein markers for breast cancer grades and stages based on RNA-seq data, which are retrieved from the TCGA breast cancer dataset and cover 111 pairs of disease and matching adjacent noncancerous tissues with pathologists-assigned stages and grades. By applying a differential expression and an SVM-based classification approach, we found that 324 and 227 genes in cancer have their expression levels consistently up-regulated vs. their matching controls in a grade- and stage-dependent manner, respectively. By using these genes, we predicted a 9-gene panel as a gene signature for distinguishing poorly differentiated from moderately and well differentiated breast cancers, and a 19-gene panel as a gene signature for discriminating between the moderately and well differentiated breast cancers. Similarly, a 30-gene panel and a 21-gene panel are predicted as gene signatures for distinguishing advanced stage (stages III-IV) from early stage (stages I-II) cancer samples and for distinguishing stage II from stage I samples, respectively. We expect these gene panels can be used as gene-expression signatures for cancer grade and stage classification. In addition, of the 324 grade-dependent genes, 188 and 66 encode proteins that are predicted to be blood-secretory and urine-excretory, respectively; and of the 227 stage-dependent genes, 123 and 51 encode proteins predicted to be blood-secretory and urine-excretory, respectively. We anticipate that some combinations of these blood and urine proteins could serve as markers for monitoring breast cancer at specific grades and stages through blood and urine tests.
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Affiliation(s)
- Fang Yao
- Key Laboratory for Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, United States of America
- Jilin Teachers’ Institute of Engineering and Technology, Changchun, China
| | - Chi Zhang
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, United States of America
| | - Wei Du
- Key Laboratory for Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, United States of America
- * E-mail: (WD); (YX)
| | - Chao Liu
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, United States of America
- Department of Oral and Maxillofacial Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Ying Xu
- Key Laboratory for Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, United States of America
- * E-mail: (WD); (YX)
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Abstract
Despite the rapid accumulation of tumor-profiling data and transcription factor (TF) ChIP-seq profiles, efforts integrating TF binding with the tumor-profiling data to understand how TFs regulate tumor gene expression are still limited. To systematically search for cancer-associated TFs, we comprehensively integrated 686 ENCODE ChIP-seq profiles representing 150 TFs with 7484 TCGA tumor data in 18 cancer types. For efficient and accurate inference on gene regulatory rules across a large number and variety of datasets, we developed an algorithm, RABIT (regression analysis with background integration). In each tumor sample, RABIT tests whether the TF target genes from ChIP-seq show strong differential regulation after controlling for background effect from copy number alteration and DNA methylation. When multiple ChIP-seq profiles are available for a TF, RABIT prioritizes the most relevant ChIP-seq profile in each tumor. In each cancer type, RABIT further tests whether the TF expression and somatic mutation variations are correlated with differential expression patterns of its target genes across tumors. Our predicted TF impact on tumor gene expression is highly consistent with the knowledge from cancer-related gene databases and reveals many previously unidentified aspects of transcriptional regulation in tumor progression. We also applied RABIT on RNA-binding protein motifs and found that some alternative splicing factors could affect tumor-specific gene expression by binding to target gene 3'UTR regions. Thus, RABIT (rabit.dfci.harvard.edu) is a general platform for predicting the oncogenic role of gene expression regulators.
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50
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Xu W, Ying Y, Shan L, Feng J, Zhang S, Gao Y, Xu X, Yao Y, Zhu C, Mao W. Enhanced expression of cohesin loading factor NIPBL confers poor prognosis and chemotherapy resistance in non-small cell lung cancer. J Transl Med 2015; 13:153. [PMID: 25963978 PMCID: PMC4438579 DOI: 10.1186/s12967-015-0503-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/22/2015] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND NIPBL, the sister chromatid cohesion 2 (SCC2) human homolog, is a cohesin loading factor which is essential for deposition of cohesin onto the sister chromatid. Recent studies have shown that NIPBL contribute to sister chromatid cohesion and plays a critical role in development, DNA repair, and gene regulation. In this study, we measured the expression of NIPBL in clinical non-small cell lung cancer specimens, and determined its effects on cellular processes and chemosensitivity in vitro. METHODS NIPBL immunohistochemistry was performed on 123 lung adenocarcinoma samples. Through knockdown of NIPBL protein expression, non-small cell lung cancer cell lines were used to test the potential involvement of NIPBL silencing on cell proliferation, migration, invasion, and apoptosis. Chemosensitivity was assessed with clonogenic assays, and chromatin immunoprecipitation assays were performed to analyze the relationship between NIPBL and signal transducers and activators of transcription 3 (STAT3). RESULTS Immunohistochemical analysis showed that high expression of NIPBL was strongly correlated with poor prognosis, tumor differentiation, and lymph node metastasis. Survival analysis further indicated that NIPBL expression was a potential prognostic factor for non-small cell lung cancer. Knockdown of NIPBL in non-small cell lung cancer cell lines significantly reduced cellular proliferation, migration, and invasion, and enhanced cellular apoptosis and sensitivity to cisplatin, paclitaxel, and gemcitabine hydrochloride. NIPBL bound to the promoter region of the STAT3 gene, directly regulating the expression of STAT3. CONCLUSIONS These data suggested that NIPBL played a significant role in lung carcinogenesis. NIPBL expression conferred poor prognosis and resistance to chemotherapy in non-small cell lung cancer, suggesting that NIPBL may be a novel therapeutic target.
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Affiliation(s)
- Weizhen Xu
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Cancer Research Institute, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Yinyin Ying
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Lihong Shan
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Jianguo Feng
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Cancer Research Institute, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Shengjie Zhang
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Cancer Research Institute, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Yun Gao
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Cancer Research Institute, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Xiaoling Xu
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Yinli Yao
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Chihong Zhu
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Cancer Research Institute, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Weimin Mao
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Cancer Research Institute, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
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