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Saeed N, Mahjabeen I, Hakim F, Hussain MZ, Mehmood A, Nisar A, Ahmed MW, Kayani MA. Role of Chk1 gene in molecular classification and prognosis of gastric cancer using immunohistochemistry and LORD-Q assay. Future Oncol 2022; 18:2827-2841. [PMID: 35762179 DOI: 10.2217/fon-2021-1546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Purpose: The aim of the current study was to assess the prognostic value of the Chk1 gene in the DNA damage response pathway in gastric cancer (GC). Methods: Expression levels of the Chk1 were measured in 220 GC tumor tissues and adjacent healthy/noncancerous tissues using real-time PCR and immunohistochemical staining. Genomic instability in GC patients was measured using the long-run real-time PCR technique for DNA-damage quantification assay and comet assay. Results: Significantly downregulated expression of Chk1 was observed at the mRNA level (p < 0.0001) and protein level (p < 0.0001). Significantly increased frequency of lesions/10 kb and comets was observed in tumor tissues compared with control tissues. Conclusion: The data suggest that downregulated expression of Chk1 and positive Heliobacter pylori infection status may have prognostic significance in GC.
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Affiliation(s)
- Nadia Saeed
- Cancer genetics and epigenetic lab, Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Ishrat Mahjabeen
- Cancer genetics and epigenetic lab, Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Farzana Hakim
- Department of Biochemistry, Foundation University Medical College, Islamabad, Pakistan
| | | | - Azhar Mehmood
- Cancer genetics and epigenetic lab, Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Asif Nisar
- Cancer genetics and epigenetic lab, Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Malik Waqar Ahmed
- Cancer genetics and epigenetic lab, Department of Biosciences, COMSATS University, Islamabad, Pakistan.,Pakistan Institute of Rehabilitation Sciences (PIRS), Isra University Islamabad Campus, Islamabad, Pakistan
| | - Mahmood Akhtar Kayani
- Cancer genetics and epigenetic lab, Department of Biosciences, COMSATS University, Islamabad, Pakistan
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2
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Lopes JL, Chaudhry S, Lopes GS, Levin NK, Tainsky MA. FANCM, RAD1, CHEK1 and TP53I3 act as BRCA-like tumor suppressors and are mutated in hereditary ovarian cancer. Cancer Genet 2019; 235-236:57-64. [PMID: 31078449 DOI: 10.1016/j.cancergen.2019.04.061] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/27/2019] [Accepted: 04/18/2019] [Indexed: 11/29/2022]
Abstract
Although 25% of ovarian cancer cases are due to inherited factors, most of the genetic risk remains unexplained. We previously identified candidate genes through germline whole exome sequencing of BRCA1/BRCA2 negative ovarian cancer patients with familial risk. Here, we performed functional assessment to determine whether they act as BRCA-like tumor suppressors. Seven candidate risk genes were targeted by siRNA for mRNA depletion followed by functional assays for clonogenic survival, cytotoxicity to DNA damaging agents, and involvement in homologous recombination repair. BRCA1 and BRCA1 were targeted as standards for loss of function outcome. Knockdown of various candidate genes led to tumor suppressor phenotypes also observed in BRCA1/BRCA2 deficient cells. Deficiency of CHEK1, FANCM and TP53I3 led to reduced homologous recombination repair efficiency. Knockdown of RAD1, CHEK1 or FANCM led to a decrease in cellular viability and cells deficient in CHEK1, RAD1 or TP53I3 displayed increased sensitivity to cisplatin. Functional studies of candidate genes identified by whole exome sequencing complements bioinformatics techniques and aid the implication of novel risk loci. The results of this study suggest that genes found mutated in hereditary ovarian cancer, FANCM, RAD1, CHEK1 and TP53I3, act as BRCA-like tumor suppressors.
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Affiliation(s)
- Jaime L Lopes
- Center for Molecular Medicine and Genetics and Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Street, Suite 3126, Detroit, MI 48201, USA; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sophia Chaudhry
- Center for Molecular Medicine and Genetics and Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Street, Suite 3126, Detroit, MI 48201, USA
| | - Guilherme S Lopes
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nancy K Levin
- Center for Molecular Medicine and Genetics and Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Street, Suite 3126, Detroit, MI 48201, USA
| | - Michael A Tainsky
- Center for Molecular Medicine and Genetics and Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Street, Suite 3126, Detroit, MI 48201, USA.
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3
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Ortiz AB, Garcia D, Vicente Y, Palka M, Bellas C, Martin P. Prognostic significance of cyclin D1 protein expression and gene amplification in invasive breast carcinoma. PLoS One 2017; 12:e0188068. [PMID: 29140993 PMCID: PMC5687747 DOI: 10.1371/journal.pone.0188068] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/31/2017] [Indexed: 02/07/2023] Open
Abstract
The oncogenic capacity of cyclin D1 has long been established in breast cancer. CCND1 amplification has been identified in a subset of patients with poor prognosis, but there are conflicting data regarding the predictive value of cyclin D1 protein overexpression. This study was designed to analyze the expression of cyclin D1 and its correlation with CCND1 amplification and their prognostic implications in invasive breast cancer. By using the tissue microarray technique, we performed an immunohistochemical study of ER, PR, HER2, p53, cyclin D1, Ki67 and p16 in 179 invasive breast carcinoma cases. The FISH method was performed to detect HER2/Neu and CCND1 amplification. High cyclin D1 expression was identified in 94/179 (52%) of invasive breast cancers. Cyclin D1 overexpression and CCND1 amplification were significantly associated (p = 0.010). Overexpression of cyclin D1 correlated with ER expression, PR expression and Luminal subtypes (p<0.001), with a favorable impact on overall survival in the whole series. However, in the Luminal A group, high expression of cyclin D1 correlated with shorter disease-free survival, suggesting that the prognostic role of cyclin D1 depends on the molecular subtype. CCND1 gene amplification was detected in 17 cases (9%) and correlated significantly with high tumor grade (p = 0.038), high Ki-67 protein expression (p = 0.002), and the Luminal B subtype (p = 0.002). Patients with tumors with high amplification of CCND1 had an increased risk of recurrence (HR = 2.5; 95% CI, 1.2-4.9, p = 0.01). These findings suggest that CCND1 amplification could be useful for predicting recurrence in invasive breast cancer.
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Affiliation(s)
- Angela B. Ortiz
- Pathology Department, Instituto de Investigación Sanitaria Puerta de Hierro-Majadahonda (IDIPHIM) Majadahonda, Madrid, Spain
| | - Diego Garcia
- Pathology Department, Instituto de Investigación Sanitaria Puerta de Hierro-Majadahonda (IDIPHIM) Majadahonda, Madrid, Spain
| | - Yolanda Vicente
- Pathology Department, Instituto de Investigación Sanitaria Puerta de Hierro-Majadahonda (IDIPHIM) Majadahonda, Madrid, Spain
| | - Magda Palka
- Medical Oncology Department, Instituto de Investigación Sanitaria Puerta de Hierro-Majadahonda (IDIPHIM) Majadahonda, Madrid, Spain
| | - Carmen Bellas
- Pathology Department, Instituto de Investigación Sanitaria Puerta de Hierro-Majadahonda (IDIPHIM) Majadahonda, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Paloma Martin
- Pathology Department, Instituto de Investigación Sanitaria Puerta de Hierro-Majadahonda (IDIPHIM) Majadahonda, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- * E-mail:
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4
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Abstract
Cancer is characterized by uncontrolled tumour cell proliferation resulting from aberrant activity of various cell cycle proteins. Therefore, cell cycle regulators are considered attractive targets in cancer therapy. Intriguingly, animal models demonstrate that some of these proteins are not essential for proliferation of non-transformed cells and development of most tissues. By contrast, many cancers are uniquely dependent on these proteins and hence are selectively sensitive to their inhibition. After decades of research on the physiological functions of cell cycle proteins and their relevance for cancer, this knowledge recently translated into the first approved cancer therapeutic targeting of a direct regulator of the cell cycle. In this Review, we focus on proteins that directly regulate cell cycle progression (such as cyclin-dependent kinases (CDKs)), as well as checkpoint kinases, Aurora kinases and Polo-like kinases (PLKs). We discuss the role of cell cycle proteins in cancer, the rationale for targeting them in cancer treatment and results of clinical trials, as well as the future therapeutic potential of various cell cycle inhibitors.
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Affiliation(s)
- Tobias Otto
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
- Department of Internal Medicine III, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
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5
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Personalised Medicine: Genome Maintenance Lessons Learned from Studies in Yeast as a Model Organism. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1007:157-178. [PMID: 28840557 DOI: 10.1007/978-3-319-60733-7_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Yeast research has been tremendously contributing to the understanding of a variety of molecular pathways due to the ease of its genetic manipulation, fast doubling time as well as being cost-effective. The understanding of these pathways did not only help scientists learn more about the cellular functions but also assisted in deciphering the genetic and cellular defects behind multiple diseases. Hence, yeast research not only opened the doors for transforming basic research into applied research, but also paved the roads for improving diagnosis and innovating personalized therapy of different diseases. In this chapter, we discuss how yeast research has contributed to understanding major genome maintenance pathways such as the S-phase checkpoint activation pathways, repair via homologous recombination and non-homologous end joining as well as topoisomerases-induced protein linked DNA breaks repair. Defects in these pathways lead to neurodegenerative diseases and cancer. Thus, the understanding of the exact genetic defects underlying these diseases allowed the development of personalized medicine, improving the diagnosis and treatment and overcoming the detriments of current conventional therapies such as the side effects, toxicity as well as drug resistance.
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6
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Pang JMB, Gorringe KL, Fox SB. Ductal carcinoma in situ - update on risk assessment and management. Histopathology 2016; 68:96-109. [PMID: 26768032 DOI: 10.1111/his.12796] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 07/31/2015] [Indexed: 12/20/2022]
Abstract
Ductal carcinoma in situ (DCIS) accounts for ~20-25% of breast cancers. While DCIS is not life-threatening, it may progress to invasive carcinoma over time, and treatment intended to prevent invasive progression may itself cause significant morbidity. Accurate risk assessment is therefore necessary to avoid over- or undertreatment of an individual patient. In this review we will outline the evidence for current management of DCIS, discuss approaches to DCIS risk assessment and challenges facing identification of novel DCIS biomarkers.
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Affiliation(s)
- Jia-Min B Pang
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, Vic., Australia.,Department of Pathology, University of Melbourne, Melbourne, Vic., Australia
| | - Kylie L Gorringe
- Department of Pathology, University of Melbourne, Melbourne, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic., Australia.,Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Vic., Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, Vic., Australia.,Department of Pathology, University of Melbourne, Melbourne, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic., Australia
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7
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Manic G, Obrist F, Sistigu A, Vitale I. Trial Watch: Targeting ATM-CHK2 and ATR-CHK1 pathways for anticancer therapy. Mol Cell Oncol 2015; 2:e1012976. [PMID: 27308506 PMCID: PMC4905354 DOI: 10.1080/23723556.2015.1012976] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/25/2015] [Accepted: 01/26/2015] [Indexed: 02/08/2023]
Abstract
The ataxia telangiectasia mutated serine/threonine kinase (ATM)/checkpoint kinase 2 (CHEK2, best known as CHK2) and the ATM and Rad3-related serine/threonine kinase (ATR)/CHEK1 (best known as CHK1) cascades are the 2 major signaling pathways driving the DNA damage response (DDR), a network of processes crucial for the preservation of genomic stability that act as a barrier against tumorigenesis and tumor progression. Mutations and/or deletions of ATM and/or CHK2 are frequently found in tumors and predispose to cancer development. In contrast, the ATR-CHK1 pathway is often upregulated in neoplasms and is believed to promote tumor growth, although some evidence indicates that ATR and CHK1 may also behave as haploinsufficient oncosuppressors, at least in a specific genetic background. Inactivation of the ATM-CHK2 and ATR-CHK1 pathways efficiently sensitizes malignant cells to radiotherapy and chemotherapy. Moreover, ATR and CHK1 inhibitors selectively kill tumor cells that present high levels of replication stress, have a deficiency in p53 (or other DDR players), or upregulate the ATR-CHK1 module. Despite promising preclinical results, the clinical activity of ATM, ATR, CHK1, and CHK2 inhibitors, alone or in combination with other therapeutics, has not yet been fully demonstrated. In this Trial Watch, we give an overview of the roles of the ATM-CHK2 and ATR-CHK1 pathways in cancer initiation and progression, and summarize the results of clinical studies aimed at assessing the safety and therapeutic profile of regimens based on inhibitors of ATR and CHK1, the only 2 classes of compounds that have so far entered clinics.
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Affiliation(s)
| | - Florine Obrist
- Université Paris-Sud/Paris XI; Le Kremlin-Bicêtre, France
- INSERM, UMRS1138; Paris, France
- Equipe 11 labelisée par la Ligue Nationale contre le Cancer; Centre de Recherche des Cordeliers; Paris, France
- Gustave Roussy Cancer Campus; Villejuif, France
| | | | - Ilio Vitale
- Regina Elena National Cancer Institute; Rome, Italy
- Department of Biology, University of Rome “TorVergata”; Rome, Italy
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8
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Pang JMB, Gorringe KL, Wong SQ, Dobrovic A, Campbell IG, Fox SB. Appraisal of the technologies and review of the genomic landscape of ductal carcinoma in situ of the breast. Breast Cancer Res 2015; 17:80. [PMID: 26078038 PMCID: PMC4469314 DOI: 10.1186/s13058-015-0586-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ductal carcinoma in situ is a biologically diverse entity. Whereas some lesions are cured by local surgical excision, others recur as in situ disease or progress to invasive carcinoma with subsequent potential for metastatic spread. Reliable prognostic biomarkers are therefore desirable for appropriate clinical management but remain elusive. In common with invasive breast cancer, ductal carcinoma in situ exhibits many genomic changes, predominantly copy number alterations. Although studies have revealed the genomic heterogeneity within individual ductal carcinoma in situ lesions and the association of certain copy number alterations with nuclear grade, none of the genomic changes defined so far is consistently associated with invasive transformation or recurrence risk in pure ductal carcinoma in situ. This article will review the current landscape of genomic alterations in ductal carcinoma in situ and their potential as prognostic biomarkers together with the technologies used to define these.
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Affiliation(s)
- Jia-Min B Pang
- Department of Pathology, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia. .,Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia.
| | - Kylie L Gorringe
- Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Stephen Q Wong
- Department of Pathology, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia. .,Translational Research Laboratory, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Alexander Dobrovic
- Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Translational Genomics & Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Studley Road, Heidelberg, VIC, 3084, Australia.
| | - Ian G Campbell
- Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia. .,Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia.
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9
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Yun H, Shi R, Yang Q, Zhang X, Wang Y, Zhou X, Mu K. Over expression of hRad9 protein correlates with reduced chemosensitivity in breast cancer with administration of neoadjuvant chemotherapy. Sci Rep 2014; 4:7548. [PMID: 25520248 PMCID: PMC5378947 DOI: 10.1038/srep07548] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 12/01/2014] [Indexed: 02/04/2023] Open
Abstract
Human Rad 9 (hRad9), part of the Rad9-Hus1-Rad1 complex plays an important role in DNA damage repair as an up-stream regulator of checkpoint signaling, however little is known about its role in response to chemotherapy of breast cancer and whether hRad9 inhibition can potentiate the cytotoxic effects of chemotherapy on breast cancer cells remains to be elucidated. Fifty cases of breast cancer receiving neoadjuvant therapy were collected. All these cases were revised and classified into chemotherapy sensitive (CS) or chemotherapy resistant (CR) group according to the Miller and Payne (MP) grading system. Immunohistochemically, hRad9 positive tumours showed nuclear and/or cytoplasmic staining. hRad9 over-expression was associated with an impaired neoadjuvant chemotherapy response. A significant correlation was found between expression of hRad9 and Cyclin D1. In vitro, hRad9 was knocked down using siRNA in breast cancer cell line MCF-7 and MDA-MB-231. Deregulated expression of Rad9 accompanied by down expression of chk1 enhanced the sensitivity of human breast cancer cells to doxorubicin. Our work suggests that hRad9 might be a potential predictor for the response to chemotherapy in patients with breast cancer and its clinical value as a target for improving chemosensitivity needs further exploration.
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Affiliation(s)
- Haiqin Yun
- Department of Pathology, Shandong University School of Medicine, Jinan 250012, China
| | - Ranran Shi
- Department of Pathology, Shandong University School of Medicine, Jinan 250012, China
| | - Qingrui Yang
- Department of Rheumatology and Immunology, Provincial Hospital Affiliated to Shandong University, Jinan 250021, China
| | - Xiaofang Zhang
- Department of Pathology, Shandong University School of Medicine, Jinan 250012, China
| | - Yan Wang
- Department of Pathology, Shandong University School of Medicine, Jinan 250012, China
| | - Xingchen Zhou
- Department of Pathology, Shandong University School of Medicine, Jinan 250012, China
| | - Kun Mu
- Department of Pathology, Shandong University School of Medicine, Jinan 250012, China
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10
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Inference of tumor phylogenies from genomic assays on heterogeneous samples. J Biomed Biotechnol 2012; 2012:797812. [PMID: 22654484 PMCID: PMC3359715 DOI: 10.1155/2012/797812] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 02/21/2012] [Indexed: 12/11/2022] Open
Abstract
Tumorigenesis can in principle result from many combinations of mutations, but only a few roughly equivalent sequences of mutations, or "progression pathways," seem to account for most human tumors. Phylogenetics provides a promising way to identify common progression pathways and markers of those pathways. This approach, however, can be confounded by the high heterogeneity within and between tumors, which makes it difficult to identify conserved progression stages or organize them into robust progression pathways. To tackle this problem, we previously developed methods for inferring progression stages from heterogeneous tumor profiles through computational unmixing. In this paper, we develop a novel pipeline for building trees of tumor evolution from the unmixed tumor data. The pipeline implements a statistical approach for identifying robust progression markers from unmixed tumor data and calling those markers in inferred cell states. The result is a set of phylogenetic characters and their assignments in progression states to which we apply maximum parsimony phylogenetic inference to infer tumor progression pathways. We demonstrate the full pipeline on simulated and real comparative genomic hybridization (CGH) data, validating its effectiveness and making novel predictions of major progression pathways and ancestral cell states in breast cancers.
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