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Athans SR, Krishnan N, Ramakrishnan S, Cortes Gomez E, Lage-Vickers S, Rak M, Kazmierczak ZI, Ohm JE, Attwood K, Wang J, Woloszynska A. STAG2 expression is associated with adverse survival outcomes and regulates cell phenotype in muscle-invasive bladder cancer. CANCER RESEARCH COMMUNICATIONS 2022; 2:1129-1143. [PMID: 36275363 PMCID: PMC9583756 DOI: 10.1158/2767-9764.crc-22-0155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
STAG2 (Stromal Antigen 2), in healthy somatic cells, functions in sister chromatid cohesion, DNA damage repair, and genome organization, but its role in muscle invasive bladder cancer (MIBC) remains unknown. Here, using whole-exome and targeted sequencing (n=119 bladder cancer clinical samples), we found several STAG2 mutations in MIBC that correlate with loss of protein expression. The analysis of a bladder cancer tissue microarray (n=346) revealed that decreased STAG2 protein expression is associated with improved overall and progression-free survival for MIBC patients. In mouse xenograft studies, STAG2 knockdown (KD) decelerated MIBC tumor growth, whereas STAG2 overexpression accelerated tumor growth. In cell line studies, STAG2 loss augmented treatment with cisplatin, a first-line therapy for MIBC. STAG2 KD or overexpression did not alter degree of aneuploidy, copy number variations, or cell cycle distribution. However, unbiased RNA sequencing analysis revealed that STAG2 KD altered gene expression. STAG2 KD led to significant downregulation of several gene sets, such as collagen containing extracellular matrix, external encapsulating structure organization, and regulation of chemotaxis. Therefore, we investigated the effect of STAG2 KD on cell migration and invasion in vitro. We found that STAG2 KD minimized cell speed, displacement, and invasion. Altogether, our results present a non-canonical function of STAG2 in promoting cell motility and invasion of MIBC cells. This work forms the basis for additional investigation into the role of STAG2 in transcriptional regulation and how it becomes dysregulated in STAG2-mutant MIBC.
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Affiliation(s)
- Sarah R. Athans
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Nithya Krishnan
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Swathi Ramakrishnan
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Eduardo Cortes Gomez
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | | | - Monika Rak
- Department of Cell Biology, Jagiellonian University, 31-007, Krakow, Poland
| | - Zara I. Kazmierczak
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Joyce Ellen Ohm
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Kristopher Attwood
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Jianmin Wang
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Anna Woloszynska
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
- Corresponding Author: Anna Woloszynska, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203. Phone: 716-845-8495; E-mail:
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Kiang KMY, Chan AA, Leung GKK. Secondary gliosarcoma: the clinicopathological features and the development of a patient-derived xenograft model of gliosarcoma. BMC Cancer 2021; 21:265. [PMID: 33706745 PMCID: PMC7948380 DOI: 10.1186/s12885-021-08008-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/02/2021] [Indexed: 12/03/2022] Open
Abstract
Background Gliosarcoma (GSM) is a distinct and aggressive variant of glioblastoma multiforme (GBM) with worse prognosis and few treatment options. It is often managed with the same treatment modalities with temozolomide (TMZ) as in GBM. However, the therapeutic benefits on GSM from such treatment regimen is largely unknown. Patient-derived xenograft (PDX) models have been used widely to model tumor progression, and subsequently to validate biomarkers and inform potential therapeutic regimens. Here, we report for the first time the successful development of a PDX model of secondary GSM. Methods Tissue obtained from a tumor resection revealed a secondary GSM arising from GBM. The clinical, radiological, and histopathological records of the patient were retrospectively reviewed. Samples obtained from surgery were cultured ex vivo and/or implanted subcutaneously in immunocompromised mice. Histopathological features between the primary GBM, secondary GSM, and GSM PDX are compared. Results In explant culture, the cells displayed a spindle-shaped morphology under phase contrast microscopy, consistent with the sarcomatous component. GSM samples were subcutaneously engrafted into immunocompromised mice after single-cell suspension. Xenografts of serial passages showed enhanced growth rate with increased in vivo passage. We did not observe any histopathological differences between the secondary GSM and its serial in vivo passages of PDX tumors. Conclusions Our PDX model for GSM retained the histopathological characteristics of the engrafted tumor from the patient. It may provide valuable information to facilitate molecular and histopathological modelling of GSM and be of significant implication in future research to establish precise cancer medicine for this highly malignant tumor.
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Affiliation(s)
- Karrie Mei-Yee Kiang
- Division of Neurosurgery, Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Andrian A Chan
- Division of Neurosurgery, Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Gilberto Ka-Kit Leung
- Division of Neurosurgery, Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China.
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Li Q, Liang J, Chen B. Identification of CDCA8, DSN1 and BIRC5 in Regulating Cell Cycle and Apoptosis in Osteosarcoma Using Bioinformatics and Cell Biology. Technol Cancer Res Treat 2020; 19:1533033820965605. [PMID: 33153400 PMCID: PMC7673055 DOI: 10.1177/1533033820965605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Introduction: Osteosarcoma is the most common primary tumor of bone, although some molecular markers have been identified, the detailed molecular mechanisms underlying osteosarcoma are currently not fully understood. In the present study, we attempted to identify the potential key genes and pathways in osteosarcoma using bioinformatics analysis. Methods: GSE14359 was downloaded from the GEO database, and analyzed using Limma package. Gene Ontology and pathway enrichment analyses of the DEGs were performed in the DAVID database, followed by the construction of a protein–protein interaction (PPI) network with software Cytoscape, subnetwork modules were subsequently identified and analyzed, and further validation in human osteosarcoma tissues and osteosarcoma cells line was performed. Results: 964 Differentially expressed genes (DEGs) identified, of which 222 were up-regulated and 742 were down-regulated. Among them, 10 genes (including BIRC5, MAD2L1, Bub1, DSN1, SPC24, CDCA8, STAG2, CENPA, MLF1IP and Mis12) were identified as hub genes and they were mainly enriched in pathways, including mRNA surveillance, RNA transport and PI3K-Akt signaling pathways. Further validation indicated 6 gene (DSN1, BIRC5, CDCA8, MLF1IP, MAD2L1 and SPC24) is highly expressed in osteosarcoma tissues. Among them, CDCA8, DSN1 and BIRC5 significantly promoted the proliferation of osteosarcoma cells in vitro. In terms of mechanism, DSN1 and CDCA8 were mainly involved in cell cycle regulation, while BIRC5 was mainly involved in the regulation of apoptosis pathway. Conclusions: We identified some key genes and pathways in osteosarcoma, which might be used as molecular targets or diagnostic biomarker for the diagnosis and therapy of osteosarcoma.
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Affiliation(s)
- Qinwen Li
- Department of Orthopedics, 117899The People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang City, Hubei, China
| | - Jie Liang
- Department of Orthopedics, 117899The People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang City, Hubei, China
| | - Bo Chen
- Department of Orthopedics, 117899The People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang City, Hubei, China
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4
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The meiosis-specific cohesin component stromal antigen 3 promotes cell migration and chemotherapeutic resistance in colorectal cancer. Cancer Lett 2020; 497:112-122. [PMID: 33039558 DOI: 10.1016/j.canlet.2020.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/24/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022]
Abstract
Chromosome instability is one of the hallmarks of cancer. Stromal antigen (STAG) 3 is a core component of the meiosis-specific cohesin complex, which regulates sister chromatid cohesion. Although aberrantly activated genes encoding the cohesin complex have been identified in cancers, little is known about the role of STAG3 in colorectal cancer (CRC). Here, we evaluated the prognostic impact and role of STAG3 in CRC. Analysis of 172 CRC surgical specimens revealed that high STAG3 expression was associated with poor prognosis. STAG3 knockdown inhibited cell migration and increased drug sensitivity to oxaliplatin, 5-fluorouracil, irinotecan hydrochloride hydrate, and BRAF inhibitor in CRC cell lines. The enhanced drug sensitivity was also confirmed in a human organoid established from a CRC specimen. Moreover, suppression of STAG3 increased γH2AX foci. Particularly, in BRAF-mutant CRC cells, STAG3 silencing suppressed the expression of snail family transcriptional repressor 1 and phosphorylation of extracellular signal-regulated kinase via upregulation of dual-specificity phosphatase 6. Our findings suggest that STAG3 is related to poor clinical outcomes and promotes metastasis and chemotherapeutic resistance in CRC. STAG3 may be a novel prognostic marker and potential therapeutic target for CRC.
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Huang L, Chen S, Fan H, Ai F, Sheng W. BZW2 promotes the malignant progression of colorectal cancer via activating the ERK/MAPK pathway. J Cell Physiol 2019; 235:4834-4842. [PMID: 31643092 DOI: 10.1002/jcp.29361] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/07/2019] [Indexed: 01/21/2023]
Abstract
Colorectal cancer (CRC) is one of the most prevalent malignant solid cancers worldwide involving the dysregulation of multiple signaling molecules. However, the role and corresponding mechanism of basic leucine zipper and W2 domains 2 (BZW2) in CRC development, to our knowledge, has not been reported. We found BZW2 was overexpressed in human CRC tissues compared with that in paired adjacent colorectal samples. BZW2 overexpression was closely associated with tumor T stage (p = .030), metastatic lymph nodes (p = .037), TNM stage (p = .018) and the worse prognosis of CRC patients (p = .009). Moreover, BZW2 was an independent disadvantage prognostic factor (p = .031). BZW2 also showed an increased expression in different invasive CRC cell lines. Its silencing and overexpression diminished and increased cell proliferation, invasion, and migration in Colo205 and HCT116 cells via specifically activating of extracellular-signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) signaling. Moreover, ERK/MAPK inhibitor PD98059 reverse the enhancement of cell proliferation, invasion, and migration in BZW2 overexpressing HCT116 cells. BZW2 silencing also inhibited subcutaneous tumors growth and p-ERK expression in vivo. BZW2 promotes the malignant progression of CRC via activating ERK/MAPK signaling, which provided a promising gene target therapy for CRC.
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Affiliation(s)
- Longping Huang
- Department of General and Hepatobiliary Surgery, The Fourth People's Hospital of Shenyang city, Shenyang, China
| | - Si Chen
- Department of Anesthesiology, The Fourth People's Hospital of Shenyang city, Shenyang, China
| | - Haijun Fan
- Department of General and Hepatobiliary Surgery, The Fourth People's Hospital of Shenyang city, Shenyang, China
| | - Fan Ai
- Department of General and Hepatobiliary Surgery, The Fourth People's Hospital of Shenyang city, Shenyang, China
| | - Weiwei Sheng
- Department of Gastrointestinal Surgery, The First Hospital, China Medical University, Shenyang, China
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Clonal analyses of refractory testicular germ cell tumors. PLoS One 2019; 14:e0213815. [PMID: 30870501 PMCID: PMC6417677 DOI: 10.1371/journal.pone.0213815] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 02/28/2019] [Indexed: 12/15/2022] Open
Abstract
Testicular germ cell tumors (TGCTs) are unique amongst solid tumors in terms of the high cure rates using chemotherapy for metastatic disease. Nevertheless, TGCTs still kill approximately 400 men per year, at a median age of 30 years, in the United States. This young age of mortality dramatically amplifies the impact of these deaths for the patients and their often young families. Furthermore the high cure rate makes it difficult to conduct further clinical trials of non curable disease. TGCTs are characterized by a marked aneuploidy and the presence of gain of chromosomal region 12p. Genomic testing may offer the ability to identify potentially lethal TGCTs at the time of initial diagnosis. However sequencing based studies have shown a paucity of somatic mutations in TGCT genomes including those that drive refractory disease. Furthermore these studies may be limited by genetic heterogeneity in primary tumors and the evolution of sub populations during disease progression. Herein we applied a systematic approach combining DNA content flow cytometry, whole genome copy number and whole exome sequence analyses to interrogate tumor heterogeneity in primary and metastatic refractory TGCTs. We identified both known and novel somatic copy number aberrations (12p, MDM2, and RHBDD1) and mutations (XRCC2, PIK3CA, RITA1) including candidate markers for platinum resistance that were present in a primary tumor of mixed histology and that remained after tandem autologous stem cell transplant.
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Gupta P, Totti S, Pérez-Mancera PA, Dyke E, Nisbet A, Schettino G, Webb R, Velliou EG. Chemoradiotherapy screening in a novel biomimetic polymer based pancreatic cancer model. RSC Adv 2019; 9:41649-41663. [PMID: 35541584 PMCID: PMC9076463 DOI: 10.1039/c9ra09123h] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/09/2019] [Indexed: 11/21/2022] Open
Abstract
Pancreatic Ductal Adenocarcinoma (PDAC) is a deadly and aggressive disease with a very low survival rate. This is partly due to the resistance of the disease to currently available treatment options. Herein, we report for the first time the use of a novel polyurethane scaffold based PDAC model for screening the short and relatively long term (1 and 17 days post-treatment) responses of chemotherapy, radiotherapy and their combination. We show a dose dependent cell viability reduction and apoptosis induction for both chemotherapy and radiotherapy. Furthermore, we observe a change in the impact of the treatment depending on the time-frame, especially for radiation for which the PDAC scaffolds showed resistance after 1 day but responded more 17 days post-treatment. This is the first study to report a viable PDAC culture in a scaffold for more than 2 months and the first to perform long-term (17 days) post-treatment observations in vitro. This is particularly important as a longer time-frame is much closer to animal studies and to patient treatment regimes, highlighting that our scaffold system has great potential to be used as an animal free model for screening of PDAC. Poly-urethane scaffold based 3D pancreatic cancer model enables realistic long term chemotherapy and radiotherapy screening. This model can be used for personalised treatment screening.![]()
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Affiliation(s)
- Priyanka Gupta
- Bioprocess and Biochemical Engineering Group (BioProChem)
- Department of Chemical and Process Engineering
- University of Surrey
- Guildford
- UK
| | - Stella Totti
- Bioprocess and Biochemical Engineering Group (BioProChem)
- Department of Chemical and Process Engineering
- University of Surrey
- Guildford
- UK
| | | | - Eleanor Dyke
- Department of Medical Physics
- The Royal Surrey County Hospital
- NHS Foundation Trust
- Guildford
- UK
| | - Andrew Nisbet
- Department of Medical Physics
- The Royal Surrey County Hospital
- NHS Foundation Trust
- Guildford
- UK
| | - Giuseppe Schettino
- Department of Physics
- University of Surrey
- Guildford GU2 7XH
- UK
- Medical Radiation Science Group
| | - Roger Webb
- The Ion Beam Centre
- University of Surrey
- Guildford
- UK
| | - Eirini G. Velliou
- Bioprocess and Biochemical Engineering Group (BioProChem)
- Department of Chemical and Process Engineering
- University of Surrey
- Guildford
- UK
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8
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Lelo A, Prip F, Harris BT, Solomon D, Berry DL, Chaldekas K, Kumar A, Simko J, Jensen JB, Bhattacharyya P, Mannion C, Kim JS, Philips G, Dyrskjøt L, Waldman T. STAG2 Is a Biomarker for Prediction of Recurrence and Progression in Papillary Non-Muscle-Invasive Bladder Cancer. Clin Cancer Res 2018; 24:4145-4153. [PMID: 29954776 PMCID: PMC6125225 DOI: 10.1158/1078-0432.ccr-17-3244] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/27/2018] [Accepted: 05/23/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Most bladder cancers are early-stage tumors known as papillary non-muscle-invasive bladder cancer (NMIBC). After resection, up to 70% of NMIBCs recur locally, and up to 20% of these recurrences progress to muscle invasion. There is an unmet need for additional biomarkers for stratifying tumors based on their risk of recurrence and progression. We previously identified STAG2 as among the most commonly mutated genes in NMIBC and provided initial evidence in a pilot cohort that STAG2-mutant tumors recurred less frequently than STAG2 wild-type tumors. Here, we report a STAG2 biomarker validation study using two independent cohorts of clinically annotated papillary NMIBC tumors from the United States and Europe.Experimental Design: The value of STAG2 immunostaining for prediction of recurrence was initially evaluated in a cohort of 82 patients with papillary NMIBC ("Georgetown cohort"). Next, the value of STAG2 immunostaining for prediction of progression to muscle invasion was evaluated in a progressor-enriched cohort of 253 patients with papillary NMIBC ("Aarhus cohort").Results: In the Georgetown cohort, 52% of NMIBC tumors with intact STAG2 expression recurred, whereas 25% of STAG2-deficient tumors recurred (P = 0.02). Multivariable analysis identified intact STAG2 expression as an independent predictor of recurrence (HR = 2.4; P = 0.05). In the progressor-enriched Aarhus cohort, 38% of tumors with intact STAG2 expression progressed within 5 years, versus 16% of STAG2-deficient tumors (P < 0.01). Multivariable analysis identified intact STAG2 expression as an independent predictor of progression (HR = 1.86; P = 0.05).Conclusions: STAG2 IHC is a simple, binary, new assay for risk stratification in papillary NMIBC. Clin Cancer Res; 24(17); 4145-53. ©2018 AACR.
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Affiliation(s)
- Alana Lelo
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
- Tumor Biology Training Program, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
| | - Frederik Prip
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Brent T Harris
- Department of Pathology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
- Histopathology and Tissue Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
| | - David Solomon
- Department of Pathology, University of California San Francisco School of Medicine, San Francisco, California
| | - Deborah L Berry
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
- Histopathology and Tissue Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
| | - Krysta Chaldekas
- Histopathology and Tissue Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
| | - Anagha Kumar
- Department of Biostatistics, MedStar Health Research Institute, Washington, District of Columbia
| | - Jeffry Simko
- Department of Pathology, University of California San Francisco School of Medicine, San Francisco, California
| | | | - Pritish Bhattacharyya
- Department of Pathology, Hackensack University Medical Center, Hackensack, New Jersey
| | - Ciaran Mannion
- Department of Pathology, Hackensack University Medical Center, Hackensack, New Jersey
| | - Jung-Sik Kim
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
| | - George Philips
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia
- MedStar Washington Hospital Center, Washington, District of Columbia
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Todd Waldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia.
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Low expression of CD40L in tumor-free lymph node of oral cavity cancer related with poor prognosis. Int J Clin Oncol 2018; 23:851-859. [DOI: 10.1007/s10147-018-1294-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 04/23/2018] [Indexed: 01/04/2023]
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10
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Ho J, Li X, Zhang L, Liang Y, Hu W, Yau JCW, Chan H, Gin T, Chan MTV, Tse G, Wu WKK. Translational genomics in pancreatic ductal adenocarcinoma: A review with re-analysis of TCGA dataset. Semin Cancer Biol 2018; 55:70-77. [PMID: 29705685 DOI: 10.1016/j.semcancer.2018.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/16/2018] [Accepted: 04/16/2018] [Indexed: 12/19/2022]
Abstract
Malignancy of the pancreas is a leading cause of cancer-related mortality, with the highest case-fatality of all cancers. Nevertheless, the lack of sensitive biomarkers and presence of biological heterogeneity precludes its early detection and effective treatment. The recent introduction of next-generation sequencing allows characterization of multiple driver mutations at genome- and exome-wide levels. Sequencing of DNA and RNA from circulating tumour cells has also opened an exciting era of non-invasive procedures for tumour detection and prognostication. This massively-parallel sequencing technology has uncovered the previously obscure molecular mechanisms, providing clues for better stratification of patients and identification of druggable targets for the disease. Identification of active oncogenic pathways and gene-gene interactions may reveal oncogene addiction and synthetic lethality. Relevant findings can be extrapolated to develop targeted and personalized therapeutic interventions. In addition to known mutational events, the role of chromosomal rearrangements in pancreatic neoplasms is gradually uncovered. Coupled with bioinformatics pipelines and epidemiological analyses, a better framework for risk stratification and prognostication of pancreatic cancer will be possible in the near future. In this review, we discuss how translational genomic studies facilitate our understanding of pathobiology, and development of novel diagnostics and therapeutics for pancreatic ductal adenocarcinoma with emphases on whole genome sequencing, whole exome sequencing, and liquid biopsies. We have also re-analyzed The Cancer Genome Atlas (TCGA) dataset to look for genetic features associated with altered survival in patients with pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Jeffery Ho
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Xianchun Li
- State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 00060, China
| | - Lin Zhang
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Yonghao Liang
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Wei Hu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Johnny C W Yau
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Hung Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Tony Gin
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China.
| | - Gary Tse
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - William K K Wu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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11
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Clinical study of genomic drivers in pancreatic ductal adenocarcinoma. Br J Cancer 2017; 117:572-582. [PMID: 28720843 PMCID: PMC5558689 DOI: 10.1038/bjc.2017.209] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/18/2017] [Accepted: 06/12/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDA) is a lethal cancer with complex genomes and dense fibrotic stroma. This study was designed to identify clinically relevant somatic aberrations in pancreatic cancer genomes of patients with primary and metastatic disease enrolled and treated in two clinical trials. METHODS Tumour nuclei were flow sorted prior to whole genome copy number variant (CNV) analysis. Targeted or whole exome sequencing was performed on most samples. We profiled biopsies from 68 patients enrolled in two Stand Up to Cancer (SU2C)-sponsored clinical trials. These included 38 resected chemoradiation naïve tumours (SU2C 20206-003) and metastases from 30 patients who progressed on prior therapies (SU2C 20206-001). Patient outcomes including progression-free survival (PFS) and overall survival (OS) were observed. RESULTS We defined: (a) CDKN2A homozygous deletions that included the adjacent MTAP gene, only its' 3' region, or excluded MTAP; (b) SMAD4 homozygous deletions that included ME2; (c) a pancreas-specific MYC super-enhancer region; (d) DNA repair-deficient genomes; and (e) copy number aberrations present in PDA patients with long-term (⩾ 40 months) and short-term (⩽ 12 months) survival after surgical resection. CONCLUSIONS We provide a clinically relevant framework for genomic drivers of PDA and for advancing novel treatments.
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12
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Chang JTH, Wang F, Chapin W, Huang RS. Identification of MicroRNAs as Breast Cancer Prognosis Markers through the Cancer Genome Atlas. PLoS One 2016; 11:e0168284. [PMID: 27959953 PMCID: PMC5154569 DOI: 10.1371/journal.pone.0168284] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/29/2016] [Indexed: 12/21/2022] Open
Abstract
Breast cancer is the second-most common cancer and second-leading cause of cancer mortality in American women. The dysregulation of microRNAs (miRNAs) plays a key role in almost all cancers, including breast cancer. We comprehensively analyzed miRNA expression, global gene expression, and patient survival from the Cancer Genomes Atlas (TCGA) to identify clinically relevant miRNAs and their potential gene targets in breast tumors. In our analysis, we found that increased expression of 12 mature miRNAs-hsa-miR-320a, hsa-miR-361-5p, hsa-miR-103a-3p, hsa-miR-21-5p, hsa-miR-374b-5p, hsa-miR-140-3p, hsa-miR-25-3p, hsa-miR-651-5p, hsa-miR-200c-3p, hsa-miR-30a-5p, hsa-miR-30c-5p, and hsa-let-7i-5p -each predicted improved breast cancer survival. Of the 12 miRNAs, miR-320a, miR-361-5p, miR-21-5p, miR-103a-3p were selected for further analysis. By correlating global gene expression with miRNA expression and then employing miRNA target prediction analysis, we suggest that the four miRNAs may exert protective phenotypes by targeting breast oncogenes that contribute to patient survival. We propose that miR-320a targets the survival-associated genes RAD51, RRP1B, and TDG; miR-361-5p targets ARCN1; and miR-21-5p targets MSH2, RMND5A, STAG2, and UBE2D3. The results of our stringent bioinformatics approach for identifying clinically relevant miRNAs and their targets indicate that miR-320a, miR-361-5p, and miR-21-5p may contribute to breast cancer survival.
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Affiliation(s)
- Jeremy T-H. Chang
- Biological Sciences Collegiate Division, University of Chicago, Chicago, Illinois, United States of America
| | - Fan Wang
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - William Chapin
- Pritzker School of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - R. Stephanie Huang
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
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13
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Witkiewicz AK, Balaji U, Eslinger C, McMillan E, Conway W, Posner B, Mills GB, O'Reilly EM, Knudsen ES. Integrated Patient-Derived Models Delineate Individualized Therapeutic Vulnerabilities of Pancreatic Cancer. Cell Rep 2016; 16:2017-31. [PMID: 27498862 DOI: 10.1016/j.celrep.2016.07.023] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/28/2016] [Accepted: 07/09/2016] [Indexed: 12/20/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) harbors the worst prognosis of any common solid tumor, and multiple failed clinical trials indicate therapeutic recalcitrance. Here, we use exome sequencing of patient tumors and find multiple conserved genetic alterations. However, the majority of tumors exhibit no clearly defined therapeutic target. High-throughput drug screens using patient-derived cell lines found rare examples of sensitivity to monotherapy, with most models requiring combination therapy. Using PDX models, we confirmed the effectiveness and selectivity of the identified treatment responses. Out of more than 500 single and combination drug regimens tested, no single treatment was effective for the majority of PDAC tumors, and each case had unique sensitivity profiles that could not be predicted using genetic analyses. These data indicate a shortcoming of reliance on genetic analysis to predict efficacy of currently available agents against PDAC and suggest that sensitivity profiling of patient-derived models could inform personalized therapy design for PDAC.
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Affiliation(s)
- Agnieszka K Witkiewicz
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA; Department of Pathology, University of Arizona, 1501 N. Campbell Street, Tucson, AZ 85724, USA; University of Arizona Cancer Center, University of Arizona, 1515 N. Campbell Street, Tucson, AZ 85724, USA.
| | - Uthra Balaji
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Cody Eslinger
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Elizabeth McMillan
- Department of Cell Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - William Conway
- Department of Surgery, Ochsner Medical Center, 1514 Jefferson Highway, Jefferson, LA 70121, USA
| | - Bruce Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Eileen M O'Reilly
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, 1275 York Street, New York, NY 10065, USA
| | - Erik S Knudsen
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA; University of Arizona Cancer Center, University of Arizona, 1515 N. Campbell Street, Tucson, AZ 85724, USA; Department of Medicine, University of Arizona, 1515 N. Campbell Street, Tucson, AZ 85724, USA.
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14
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Hill VK, Kim JS, Waldman T. Cohesin mutations in human cancer. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1866:1-11. [PMID: 27207471 PMCID: PMC4980180 DOI: 10.1016/j.bbcan.2016.05.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/12/2016] [Accepted: 05/14/2016] [Indexed: 12/19/2022]
Abstract
Cohesin is a highly-conserved protein complex that plays important roles in sister chromatid cohesion, chromatin structure, gene expression, and DNA repair. In humans, cohesin is a ubiquitously expressed, multi-subunit protein complex composed of core subunits SMC1A, SMC3, RAD21, STAG1/2 and regulatory subunits WAPL, PDS5A/B, CDCA5, NIPBL, and MAU2. Recent studies have demonstrated that genes encoding cohesin subunits are somatically mutated in a wide range of human cancers. STAG2 is the most commonly mutated subunit, and in a recent analysis was identified as one of only 12 genes that are significantly mutated in four or more cancer types. In this review we summarize the findings reported to date and comment on potential functional implications of cohesin mutation in the pathogenesis of human cancer.
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Affiliation(s)
- Victoria K Hill
- Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, 3970 Reservoir Road, NW, NRB E304, Washington, DC 20057, USA
| | - Jung-Sik Kim
- Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, 3970 Reservoir Road, NW, NRB E304, Washington, DC 20057, USA
| | - Todd Waldman
- Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, 3970 Reservoir Road, NW, NRB E304, Washington, DC 20057, USA
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15
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Genomic amplification of 9p24.1 targeting JAK2, PD-L1, and PD-L2 is enriched in high-risk triple negative breast cancer. Oncotarget 2016; 6:26483-93. [PMID: 26317899 PMCID: PMC4694916 DOI: 10.18632/oncotarget.4494] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/22/2015] [Indexed: 12/16/2022] Open
Abstract
We used DNA content flow cytometry followed by oligonucleotide array based comparative genomic hybridization to survey the genomes of 326 tumors, including 41 untreated surgically resected triple negative breast cancers (TNBC). A high level (log2ratio ≥ 1) 9p24 amplicon was found in TNBC (12/41), glioblastomas (2/44), and colon carcinomas (2/68). The shortest region of overlap for the amplicon targets 9p24.1 and includes the loci for PD-L1, PD-L2, and JAK2 (PDJ amplicon). In contrast this amplicon was absent in ER+ (0/8) and HER2+ (0/15) breast tumors, and in pancreatic ductal adenocarcinomas (0/150). The PDJ amplicon in TNBCs was correlated with clinical outcomes in group comparisons by two-sample t-tests for continuous variables and chi-squared tests for categorical variables. TNBC patients with the PDJ amplicon had a worse outcome with worse disease-free and overall survival. Quantitative RT-PCR confirmed that the PDJ amplicon in TNBC is associated with elevated expression of JAK2 and of the PD-1 ligands. These initial findings demonstrate that the PDJ amplicon is enriched in TNBC, targets signaling pathways that activate the PD-1 mediated immune checkpoint, and identifies patients with a poor prognosis.
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16
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França JA, Diniz MG, Bernardes VF, Costa-Silva RC, Souza RP, Gomez RS, Gomes CC. Cohesin subunits, STAG1 and STAG2, and cohesin regulatory factor, PDS5b, in oral squamous cells carcinomas. J Oral Pathol Med 2016; 46:188-193. [PMID: 27341316 DOI: 10.1111/jop.12474] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Cohesin complex is responsible for sister chromatid cohesion. STAG1/STAG2 is part of the complex, which is regulated by PDS5B. Alterations in these genes were described in tumors. PDS5B is a negative regulator of cell proliferation. We aimed to assess molecular alterations in these genes in oral squamous cell carcinoma (OSCC) and predict their expression by the expression of 84 cell cycle genes. In addition, we investigated whether pds5b protein expression impacted ki-67 and p53 immunopositivity. METHODS We assessed loss of heterozygosity (LOH) at STAG1 and STAG2 loci in 15 OSCC using three polymorphic markers. Associations between the immunoexpression of pds5b and ki-67 and p53 were tested in 62 samples. Differences between transcriptional levels of STAG1, STAG2, and PDS5B between OSCC and normal oral mucosa (NM) were evaluated by qPCR. An 84 cell cycle genes qPCR array was carried with OSCC samples, and STAG1, STAG2, and PDS5B were independently used as response variables in multiple linear regression models. RESULTS Loss of heterozygosity in at least one marker was observed in three samples. pds5b, p53, and ki-67 were highly expressed, and no association was found between pds5b immunoexpression and ki-67 or p53 (P > 0.05). OSCC and NM showed similar transcriptional levels of STAG1, STAG2, and PDS5B. STAG1 and CUL3 expression seem to be related (P = 0.004). CONCLUSIONS There is LOH at STAG1 and STAG2 loci in OSCC, but OSCC and NM showed similar transcriptional levels of STAG1, STAG2, and PDS5B. pds5b immunoexpression in OSCC was high, but it was not associated with proliferation cell index.
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Affiliation(s)
- Josiane Alves França
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Brazil
| | - Marina Gonçalves Diniz
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Brazil
| | - Vanessa Fátima Bernardes
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Brazil
| | - Raíssa Cristina Costa-Silva
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Brazil
| | - Renan Pedra Souza
- Department of General Biology, Biological Sciences Institute, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Brazil
| | - Ricardo Santiago Gomez
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Brazil
| | - Carolina Cavaliéri Gomes
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Brazil
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17
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Guo J, Jing R, Lv X, Wang X, Li J, Li L, Li C, Wang D, Bi B, Chen X, Yang JH. H2A/K pseudogene mutation may promote cell proliferation. Mutat Res 2016; 787:32-42. [PMID: 26953487 DOI: 10.1016/j.mrfmmm.2016.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 01/01/2016] [Accepted: 02/28/2016] [Indexed: 11/16/2022]
Abstract
Little attention has been paid to the histone H2A/K pseudogene. Results from our laboratory showed that 7 of 10 kidney cancer patients carried a mutant H2A/K pseudogene; therefore, we were interested in determining the relationship between mutant H2A/K and cell proliferation. We used shotgun and label-free proteomics methods to study whether mutant H2A/K lncRNAs affected cell proliferation. Quantitative proteomic analysis indicated that the expression of mutant H2A/K lncRNAs resulted in the upregulation of many oncogenes, which promoted cell proliferation. Further interaction analyses revealed that a proliferating cell nuclear antigen (PCNA)-protein interaction network, with PCNA in the center, contributes to cell proliferation in cells expressing the mutant H2A/K lncRNAs. Western blotting confirmed the critical upregulation of PCNA by mutant H2A/K lncRNA expression. Finally, the promotion of cell proliferation by mutant H2A/K lncRNAs (C290T, C228A and A45G) was confirmed using cell proliferation assays. Although we did not determine the exact mechanism by which the oncogenes were upregulated by the mutant H2A/K lncRNAs, we confirmed that the mutant H2A/K lncRNAs promoted cell proliferation by upregulating PCNA and other oncogenes. The hypothesis that cell proliferation is promoted by the mutant H2A/K lncRNAs was supported by the protein expression and cell proliferation assay results. Therefore, mutant H2A/K lncRNAs may be a new factor in renal carcinogenesis.
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Affiliation(s)
- Jisheng Guo
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Ruirui Jing
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Xin Lv
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Xiaoyue Wang
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Junqiang Li
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Lin Li
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Cuiling Li
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Daoguang Wang
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Baibing Bi
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Xinjun Chen
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Jing-Hua Yang
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China; Department of Surgery, VA Boston Healthcare System, Boston University School of Medicine, Boston 510660, MA, USA.
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18
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Complete loss of STAG2 expression is an indicator of good prognosis in patients with bladder cancer. Tumour Biol 2016; 37:10279-86. [PMID: 26838030 DOI: 10.1007/s13277-016-4894-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/20/2016] [Indexed: 10/22/2022] Open
Abstract
Stromal antigen 2 (STAG2) is an important member of cohesin, a conserved complex holding the sister chromatid together. Recent whole-genome sequencing studies have identified that genetic alterations of stag2 are common in bladder cancer (BC). The prognostic implications of STAG2 expression in BC remain unclear; we therefore analyzed its associations with the histopathological characteristics and clinical outcome in a Chinese population. We used immunohistochemistry assay to determine STAG2 protein expression in tumor tissues from 125 BC patients. STAG2 expression was analyzed according to clinicopathological features and patients' survival. Univariable and multivariable analyses were performed to identify predictors for recurrence-free survival (RFS) and cancer-specific survival (CSS). STAG2 expression was detected in 79.2 % of BC tissues, and 20.8 % of the tumor tissues had a complete loss of STAG2 protein expression. This STAG2-negative result was associated with a lower tumor histological grade with P = 0.009. The log-rank analysis revealed that the complete loss of STAG2 expression was associated with a lower risk of recurrence (P = 0.023) and a diminished risk of death (P = 0.034), especially in the subgroup of muscle-invasive BC (P = 0.043 for RFS and P = 0.087 for CSS). In multivariable Cox regression models, the loss of STAG2 expression remained a beneficial factor for RFS and CSS of BC patients. Univariate and multivariate analyses' results indicated that the complete loss of STAG2 expression was predictive for better RFS and CSS, suggesting its potential value as a prognostic biomarker.
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19
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Corces MR, Corces VG. The three-dimensional cancer genome. Curr Opin Genet Dev 2016; 36:1-7. [PMID: 26855137 PMCID: PMC4880523 DOI: 10.1016/j.gde.2016.01.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 01/06/2016] [Accepted: 01/13/2016] [Indexed: 10/22/2022]
Abstract
The past decade of cancer research has ushered in a comprehensive understanding of the way that the sequence of the genome can be co-opted during the process of tumorigenesis. However, only recently has the epigenome, and in particular the three-dimensional topology of chromatin, been implicated in cancer progression. Here we review recent findings of how the cancer genome is regulated and dysregulated to effect changes in 3D genome topology. We discuss the impact of the spatial organization of the genome on the frequency of tumorigenic chromosomal translocations and the effects of disruption of the proteins responsible for the establishment of chromatin loops. Alteration of the three-dimensional cancer genome is a rapidly emerging hallmark of multiple cancer subtypes.
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Affiliation(s)
- M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Victor G Corces
- Department of Biology, Emory University, 1510 Clifton Rd NE, Atlanta, GA 30322, USA.
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20
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Crompton BD, Stewart C, Taylor-Weiner A, Alexe G, Kurek KC, Calicchio ML, Kiezun A, Carter SL, Shukla SA, Mehta SS, Thorner AR, de Torres C, Lavarino C, Suñol M, McKenna A, Sivachenko A, Cibulskis K, Lawrence MS, Stojanov P, Rosenberg M, Ambrogio L, Auclair D, Seepo S, Blumenstiel B, DeFelice M, Imaz-Rosshandler I, Schwarz-Cruz y Celis A, Rivera MN, Rodriguez-Galindo C, Fleming MD, Golub TR, Getz G, Mora J, Stegmaier K. The Genomic Landscape of Pediatric Ewing Sarcoma. Cancer Discov 2014; 4:1326-41. [DOI: 10.1158/2159-8290.cd-13-1037] [Citation(s) in RCA: 342] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Solomon DA, Kim JS, Waldman T. Cohesin gene mutations in tumorigenesis: from discovery to clinical significance. BMB Rep 2014; 47:299-310. [PMID: 24856830 PMCID: PMC4163871 DOI: 10.5483/bmbrep.2014.47.6.092] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Indexed: 12/30/2022] Open
Abstract
Cohesin is a multi-protein complex composed of four core subunits (SMC1A, SMC3, RAD21, and either STAG1 or STAG2) that is responsible for the cohesion of sister chromatids following DNA replication until its cleavage during mitosis thereby enabling faithful segregation of sister chromatids into two daughter cells. Recent cancer genomics analyses have discovered a high frequency of somatic mutations in the genes encoding the core cohesin subunits as well as cohesin regulatory factors (e.g. NIPBL, PDS5B, ESPL1) in a select subset of human tumors including glioblastoma, Ewing sarcoma, urothelial carcinoma, acute myeloid leukemia, and acute megakaryoblastic leukemia. Herein we review these studies including discussion of the functional significance of cohesin inactivation in tumorigenesis and potential therapeutic mechanisms to selectively target cancers harboring cohesin mutations.
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MESH Headings
- Carcinogenesis
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Humans
- Leukemia, Megakaryoblastic, Acute/genetics
- Leukemia, Megakaryoblastic, Acute/metabolism
- Leukemia, Megakaryoblastic, Acute/pathology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mutation
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Protein Subunits/genetics
- Protein Subunits/metabolism
- Urologic Neoplasms/genetics
- Urologic Neoplasms/metabolism
- Urologic Neoplasms/pathology
- Cohesins
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Affiliation(s)
- David A. Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, United States
| | - Jung-Sik Kim
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057, United States
| | - Todd Waldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057, United States
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