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Song L, Bhuvaneshwar K, Wang Y, Feng Y, Shih IM, Madhavan S, Gusev Y. CINdex: A Bioconductor Package for Analysis of Chromosome Instability in DNA Copy Number Data. Cancer Inform 2017; 16:1176935117746637. [PMID: 29343938 PMCID: PMC5761903 DOI: 10.1177/1176935117746637] [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: 07/10/2017] [Accepted: 10/26/2017] [Indexed: 01/10/2023] Open
Abstract
The CINdex Bioconductor package addresses an important area of high-throughput genomic analysis. It calculates the chromosome instability (CIN) index, a novel measurement that quantitatively characterizes genome-wide copy number alterations (CNAs) as a measure of CIN. The advantage of this package is an ability to compare CIN index values between several groups for patients (case and control groups), which is a typical use case in translational research. The differentially changed cytobands or chromosomes can then be linked to genes located in the affected genomic regions, as well as pathways. This enables in-depth systems biology-based network analysis and assessment of the impact of CNA on various biological processes or clinical outcomes. This package was successfully applied to analysis of DNA copy number data in colorectal cancer as a part of multi-omics integrative study as well as for analysis of several other cancer types. The source code, along with an end-to-end tutorial, and example data are freely available in Bioconductor at http://bioconductor.org/packages/CINdex/.
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Affiliation(s)
- Lei Song
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
| | - Krithika Bhuvaneshwar
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
| | - Yue Wang
- The Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA
| | - Yuanjian Feng
- The Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA
| | - Ie-Ming Shih
- Department of Gynecology and Obstetrics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
| | - Yuriy Gusev
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
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Cervantes-Madrid D, Wettergren Y, Falk P, Lundholm K, Asting AG. DNA alterations in Cd133+ and Cd133- tumour cells enriched from intra-operative human colon tumour biopsies. BMC Cancer 2017; 17:219. [PMID: 28347289 PMCID: PMC5369016 DOI: 10.1186/s12885-017-3206-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 03/18/2017] [Indexed: 11/10/2022] Open
Abstract
Background Tumour stem cells are considered important to promote disease progression, recurrence and treatment resistance following chemotherapy in colon cancer. However, genomic analyses of colorectal cancer have mainly been performed on integrated tumour tissue consisting of several different cell types in addition to differentiated tumour cells. The purpose of the present study was to compare genomic alterations in two cell fractions enriched of CD133+ and CD133−/EpCAM+ cells, respectively, obtained from fresh intraoperative human tumour biopsies. Methods The tumour biopsies were fractionated into CD133+ and CD133−/EpCAM+ cells by immunomagnetic separation, confirmed by immunocytochemistry and Q-PCR. DNA were extracted and used for array comparative genome hybridization (aCGH) after whole genome amplification. Frozen tumour tissue biopsies were used for DNA/RNA extraction and Q-PCR analyses to check for DNA alterations detected in the cell fractions. Results The number and size of DNA alterations were equally distributed across the cell fractions; however, large deletions were detected on chromosome 1, 7 and 19 in CD133−/EpCAM+ cells. Deletions were frequent in both cell fractions and a deletion on chromosome 19p was confirmed in 90% of the patients. Conclusion Isolation of enriched cells derived from tumour tissue revealed mainly genomic deletions, which were not observed in tumour tissue DNA analyses. CD133+ cells were genetically heterogeneous among patients without any defined profile compared to CD133−/EpCAM+ cells. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3206-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diana Cervantes-Madrid
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Yvonne Wettergren
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Peter Falk
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kent Lundholm
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Annika G Asting
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. .,Department of Surgery, Sahlgrenska University Hospital, S-413 45, Gothenburg, Sweden.
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Kawai M, Komiyama H, Hosoya M, Okubo H, Fujii T, Yokoyama N, Sato C, Ueyama T, Okuzawa A, Goto M, Kojima Y, Takahashi M, Sugimoto K, Ishiyama S, Munakata S, Ogura D, Niwa SI, Tomiki Y, Ochiai T, Sakamoto K. Impact of chromosome 17q deletion in the primary lesion of colorectal cancer on liver metastasis. Oncol Lett 2016; 12:4773-4778. [PMID: 28101224 DOI: 10.3892/ol.2016.5271] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 03/01/2016] [Indexed: 01/15/2023] Open
Abstract
Colorectal cancer is a prevalent malignancy worldwide, and investigations are required to elucidate the underlying carcinogenic mechanisms. Amongst these mechanisms, de novo carcinogenesis and the adenoma to carcinoma sequence, are the most understood. Metastasis of colorectal cancer to the liver often results in fatality, therefore, it is important for any associated risk factors to be identified. Regarding the treatment of the disease, it is important to manage not only the primary colorectal tumor, but also the liver metastases. Previously, through gene variation analysis, chromosomal loss has been indicated to serve an important role in liver metastasis. Such analysis may aid in the prediction of liver metastasis risk, alongside individual responses to treatment, thus improving the management of colorectal cancer. In the present study, we aimed to clarify a cause of the liver metastasis of colorectal cancer using comparative genomic hybridization analysis. A total of 116 frozen samples were analyzed from patients with advanced colorectal cancer that underwent surgery from 2004 to 2011. The present study analyzed mutations within tumor suppressor genes non-metastatic gene 23 (NM23), deleted in colorectal carcinoma (DCC) and deleted in pancreatic carcinoma, locus 4 (DPC4), which are located on chromosomes 17 and 18 and have all been reported to affect liver metastasis of colorectal cancer. The association between chromosomal abnormalities (duplication and deletion) and liver metastasis of colorectal cancer was evaluated using comparative genomic hybridization. Cluster analysis indicated that the group of patients lacking the long arm of chromosome 17 demonstrated the highest rate of liver metastasis. No significant association was observed between the frequency of liver metastases for synchronous and heterochronous colorectal cancer cases and gene variation (P=0.206). However, when these liver metastasis cases were divided into the synchronous and heterochronous types, the ratio of each was significantly different between gene variation groups, classified by the existence of the 17q deletion (P=0.023). These results indicate that the deletion of 17q may act as a predictive marker of liver metastasis in postoperative states.
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Affiliation(s)
- Masaya Kawai
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Hiromitsu Komiyama
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Masaki Hosoya
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Haruna Okubo
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Tomoaki Fujii
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Norihiko Yokoyama
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Chiyo Sato
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Takae Ueyama
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Atsushi Okuzawa
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Michitoshi Goto
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Yutaka Kojima
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Makoto Takahashi
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Kiichi Sugimoto
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Shun Ishiyama
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Shinya Munakata
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Dai Ogura
- Link Genomics Inc., Tokyo 103-0012, Japan
| | | | - Yuichi Tomiki
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Takumi Ochiai
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Kazuhiro Sakamoto
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
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Copy number alterations and allelic ratio in relation to recurrence of rectal cancer. BMC Genomics 2015; 16:438. [PMID: 26048403 PMCID: PMC4458034 DOI: 10.1186/s12864-015-1550-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/17/2015] [Indexed: 12/16/2022] Open
Abstract
Background In rectal cancer, total mesorectal excision surgery combined with preoperative (chemo)radiotherapy reduces local recurrence rates but does not improve overall patient survival, a result that may be due to the harmful side effects and/or co-morbidity of preoperative treatment. New biomarkers are needed to facilitate identification of rectal cancer patients at high risk for local recurrent disease. This would allow for preoperative (chemo)radiotherapy to be restricted to high-risk patients, thereby reducing overtreatment and allowing personalized treatment protocols. We analyzed genome-wide DNA copy number (CN) and allelic alterations in 112 tumors from preoperatively untreated rectal cancer patients. Sixty-six patients with local and/or distant recurrent disease were compared to matched controls without recurrence. Results were validated in a second cohort of tumors from 95 matched rectal cancer patients. Additionally, we performed a meta-analysis that included 42 studies reporting on CN alterations in colorectal cancer and compared results to our own data. Results The genomic profiles in our study were comparable to other rectal cancer studies. Results of the meta-analysis supported the hypothesis that colon cancer and rectal cancer may be distinct disease entities. In our discovery patient study cohort, allelic retention of chromosome 7 was significantly associated with local recurrent disease. Data from the validation cohort were supportive, albeit not statistically significant, of this finding. Conclusions We showed that retention of heterozygosity on chromosome 7 may be associated with local recurrence in rectal cancer. Further research is warranted to elucidate the mechanisms and effect of retention of chromosome 7 on the development of local recurrent disease in rectal cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1550-0) contains supplementary material, which is available to authorized users.
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Abstract
PURPOSE "Cure" is an important word in oncology but its use in the published literature has not been examined. I investigated all oncology articles using cure in the title field and published in 2012. The definition of cure was examined, specifically whether or not authors use the word to connote some surviving subset of patients who go on to experience outcomes similar to age-matched, normal controls-a definition favored by researchers and employed in survival function analyses. METHODS All articles published between January 1, 2012, and December 31, 2012, with the word cure in the title field were retrieved from Thompson Reuters' Web of Science. After exclusions, articles were read in full to examine what definitions of cure was used. Additionally, for each situation (type of cancer, stage/grade) where the word cure was used, a literature search was performed to ascertain whether there existed documented cases of cure. RESULTS Twenty-nine oncology articles used the word cure in their title in 2012. Nearly half, 14 (48%) of 29, used the term in situations (cancer type, stage/grade) currently considered incurable. Approximately one-third (34.5%) of the articles used the word consistent with the definition that, after a set period of time, some surviving subset of patients experience survival similar to normal controls. CONCLUSION There is heterogeneity in the use of the word cure in the literature.
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Affiliation(s)
- Vinay Prasad
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Madhavan S, Gusev Y, Natarajan TG, Song L, Bhuvaneshwar K, Gauba R, Pandey A, Haddad BR, Goerlitz D, Cheema AK, Juhl H, Kallakury B, Marshall JL, Byers SW, Weiner LM. Genome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse. Front Genet 2013; 4:236. [PMID: 24312117 PMCID: PMC3834519 DOI: 10.3389/fgene.2013.00236] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 10/23/2013] [Indexed: 12/12/2022] Open
Abstract
The use and benefit of adjuvant chemotherapy to treat stage II colorectal cancer (CRC) patients is not well understood since the majority of these patients are cured by surgery alone. Identification of biological markers of relapse is a critical challenge to effectively target treatments to the ~20% of patients destined to relapse. We have integrated molecular profiling results of several “omics” data types to determine the most reliable prognostic biomarkers for relapse in CRC using data from 40 stage I and II CRC patients. We identified 31 multi-omics features that highly correlate with relapse. The data types were integrated using multi-step analytical approach with consecutive elimination of redundant molecular features. For each data type a systems biology analysis was performed to identify pathways biological processes and disease categories most affected in relapse. The biomarkers detected in tumors urine and blood of patients indicated a strong association with immune processes including aberrant regulation of T-cell and B-cell activation that could lead to overall differences in lymphocyte recruitment for tumor infiltration and markers indicating likelihood of future relapse. The immune response was the biologically most coherent signature that emerged from our analyses among several other biological processes and corroborates other studies showing a strong immune response in patients less likely to relapse.
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Affiliation(s)
- Subha Madhavan
- Department of Oncology, Innovation Center for Biomedical Informatics, Georgetown University Medical Center Washington, DC, USA ; Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center Washington DC, USA
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