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Zeng W, Xie F, Pan Y, Chen Z, Chen H, Liu X, Tian K, Xu D. A comprehensive prognostic score for head and neck squamous cancer driver genes and phenotype traits. Discov Oncol 2023; 14:193. [PMID: 37897503 PMCID: PMC10613197 DOI: 10.1007/s12672-023-00796-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/19/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Head and neck squamous cancer (HNSCC) presents variable phenotype and progression features. Clinically applicable, high-accuracy multifactorial prognostic models for HNSCC survival outcomes are warranted and an active area of research. This study aimed to construct a comprehensive prognostic tool for HNSCC overall survival by integrating cancer driver genes with tumor clinical and phenotype information. METHODS Key overall survival-related cancer driver genes were screened from among main effector and reciprocal gene pairs using TCGA data using univariate Cox proportional hazard regression analysis. Independent validation was performed using the GSE41613 dataset. The main effector genes among these were selected using LASSO regression and transcriptome score modeling was performed using multivariate Cox regression followed by validation analysis of the prognostic score. Next, multivariate Cox regression analysis was performed using the transcriptome score combined with age, grade, gender, and stage. An 'Accurate Prediction Model of HNSCC Overall Survival Score' (APMHO) was computed and validated. Enriched functional pathways, gene mutational landscape, immune cell infiltration, and immunotherapy sensitivity markers associated with high and low APMHO scores were analyzed. RESULTS Screening 107 overall survival-related cancer genes and 402 interacting gene pairs, 6 genes: CRLF2, HSP90AA1, MAP2K1, PAFAH1B2, MYCL and SET genes, were identified and a transcriptional score was obtained. Age, stage and transcriptional score were found to be significant predictors in Cox regression analysis and used to construct a final APMHO model showing an AUC > 0.65 and validated. Transcriptional score, age, pathologic_N, pathologic_T, stage, and TCGA_subtype were significantly different in distribution between high and low APMHO groups. High APMHO samples showed significantly higher mutation rate, enriched tumor-related pathways including Hypoxia, unfold_protein_response, Glycolysis, and mTORC1 signaling, along with differences in immune cell infiltration and immune checkpoint, interferon-γ pathway and m6A regulator expression patterns. CONCLUSION The APMHO score combining transcriptional and clinical variables showed good prognostic ability for HNSCC overall survival outcomes and was associated with different patterns of phenotypical features, immune and mutational landscape, and immunotherapy sensitivity marker expression. Future studies should validate this score in independent clinical cohorts.
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Affiliation(s)
- Wen Zeng
- Ganzhou Cancer Hospital, Gannan Medical College Affiliated Cancer Hospital, No.19, Huayuan Road, Zhanggong Avenue, Ganzhou, Jiangxi, People's Republic of China
| | - Fangfang Xie
- Ganzhou People's Hospital, Ganzhou, 341000, Jiangxi, People's Republic of China
| | - Yiyun Pan
- Ganzhou Cancer Hospital, Gannan Medical College Affiliated Cancer Hospital, No.19, Huayuan Road, Zhanggong Avenue, Ganzhou, Jiangxi, People's Republic of China
| | - Zhengcong Chen
- Ganzhou Cancer Hospital, Gannan Medical College Affiliated Cancer Hospital, No.19, Huayuan Road, Zhanggong Avenue, Ganzhou, Jiangxi, People's Republic of China
| | - Hailong Chen
- Ganzhou Cancer Hospital, Gannan Medical College Affiliated Cancer Hospital, No.19, Huayuan Road, Zhanggong Avenue, Ganzhou, Jiangxi, People's Republic of China
| | - Xiaomei Liu
- Ganzhou Cancer Hospital, Gannan Medical College Affiliated Cancer Hospital, No.19, Huayuan Road, Zhanggong Avenue, Ganzhou, Jiangxi, People's Republic of China
| | - Keqiang Tian
- Ganzhou Cancer Hospital, Gannan Medical College Affiliated Cancer Hospital, No.19, Huayuan Road, Zhanggong Avenue, Ganzhou, Jiangxi, People's Republic of China.
| | - Dechang Xu
- Ganzhou Cancer Hospital, Gannan Medical College Affiliated Cancer Hospital, No.19, Huayuan Road, Zhanggong Avenue, Ganzhou, Jiangxi, People's Republic of China.
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2
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De Silva DL, Stafford L, Skandarajah AR, Sinclair M, Devereux L, Hogg K, Kentwell M, Park A, Lal L, Zethoven M, Jayawardana MW, Chan F, Butow PN, James PA, Mann GB, Campbell IG, Lindeman GJ. Universal genetic testing for women with newly diagnosed breast cancer in the context of multidisciplinary team care. Med J Aust 2023; 218:368-373. [PMID: 37005005 PMCID: PMC10952347 DOI: 10.5694/mja2.51906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 04/04/2023]
Abstract
OBJECTIVE To determine the feasibility of universal genetic testing of women with newly diagnosed breast cancer, to estimate the incidence of pathogenic gene variants and their impact on patient management, and to evaluate patient and clinician acceptance of universal testing. DESIGN, SETTING, PARTICIPANTS Prospective study of women with invasive or high grade in situ breast cancer and unknown germline status discussed at the Parkville Breast Service (Melbourne) multidisciplinary team meeting. Women were recruited to the pilot (12 June 2020 - 22 March 2021) and expansion phases (17 October 2021 - 8 November 2022) of the Mutational Assessment of newly diagnosed breast cancer using Germline and tumour genomICs (MAGIC) study. MAIN OUTCOME MEASURES Germline testing by DNA sequencing, filtered for nineteen hereditary breast and ovarian cancer genes that could be classified as actionable; only pathogenic variants were reported. Surveys before and after genetic testing assessed pilot phase participants' perceptions of genetic testing, and psychological distress and cancer-specific worry. A separate survey assessed clinicians' views on universal testing. RESULTS Pathogenic germline variants were identified in 31 of 474 expanded study phase participants (6.5%), including 28 of 429 women with invasive breast cancer (6.5%). Eighteen of the 31 did not meet current genetic testing eligibility guidelines (probability of a germline pathogenic variant ≥ 10%, based on CanRisk, or Manchester score ≥ 15). Clinical management was changed for 24 of 31 women after identification of a pathogenic variant. Including 68 further women who underwent genetic testing outside the study, 44 of 542 women carried pathogenic variants (8.1%). Acceptance of universal testing was high among both patients (90 of 103, 87%) and clinicians; no decision regret or adverse impact on psychological distress or cancer-specific worry were reported. CONCLUSION Universal genetic testing following the diagnosis of breast cancer detects clinically significant germline pathogenic variants that might otherwise be missed because of testing guidelines. Routine testing and reporting of pathogenic variants is feasible and acceptable for both patients and clinicians.
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Affiliation(s)
- Dilanka L De Silva
- The University of MelbourneMelbourneVIC
- Parkville Familial Cancer CentrePeter MacCallum Cancer Centre and Royal Melbourne HospitalMelbourneVIC
- Memorial Sloan Kettering Cancer CenterNew YorkNYUnited States of America
| | - Lesley Stafford
- The University of MelbourneMelbourneVIC
- The Royal Melbourne HospitalMelbourneVIC
| | - Anita R Skandarajah
- The University of MelbourneMelbourneVIC
- The Royal Melbourne HospitalMelbourneVIC
| | | | - Lisa Devereux
- The University of MelbourneMelbourneVIC
- Peter MacCallum Cancer CentreMelbourneVIC
| | - Kirsten Hogg
- The University of MelbourneMelbourneVIC
- Walter and Eliza Hall Institute of Medical ResearchMelbourneVIC
| | - Maira Kentwell
- The University of MelbourneMelbourneVIC
- Parkville Familial Cancer CentrePeter MacCallum Cancer Centre and Royal Melbourne HospitalMelbourneVIC
| | - Allan Park
- The Royal Melbourne HospitalMelbourneVIC
| | - Luxi Lal
- The Royal Melbourne HospitalMelbourneVIC
- Peter MacCallum Cancer CentreMelbourneVIC
- Walter and Eliza Hall Institute of Medical ResearchMelbourneVIC
| | | | - Madawa W Jayawardana
- The University of MelbourneMelbourneVIC
- Peter MacCallum Cancer CentreMelbourneVIC
| | - Fiona Chan
- The Royal Children's Hospital MelbourneMelbourneVIC
| | - Phyllis N Butow
- Centre for Medical Psychology and Evidence‐based Decision Making, the University of SydneySydneyNSW
| | - Paul A James
- The University of MelbourneMelbourneVIC
- Parkville Familial Cancer CentrePeter MacCallum Cancer Centre and Royal Melbourne HospitalMelbourneVIC
- The Royal Melbourne HospitalMelbourneVIC
- Peter MacCallum Cancer CentreMelbourneVIC
| | - G Bruce Mann
- The University of MelbourneMelbourneVIC
- The Royal Melbourne HospitalMelbourneVIC
- Royal Women's HospitalMelbourneVIC
| | - Ian G Campbell
- The University of MelbourneMelbourneVIC
- Peter MacCallum Cancer CentreMelbourneVIC
| | - Geoffrey J Lindeman
- The University of MelbourneMelbourneVIC
- Parkville Familial Cancer CentrePeter MacCallum Cancer Centre and Royal Melbourne HospitalMelbourneVIC
- Peter MacCallum Cancer CentreMelbourneVIC
- Walter and Eliza Hall Institute of Medical ResearchMelbourneVIC
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McCart Reed AE, Hollway G, Lakhani S. The Queensland IMplementation of PRecision Oncology in brEast cancer (Q-IMPROvE) pilot study. Med J Aust 2023; 218:374-375. [PMID: 36958289 DOI: 10.5694/mja2.51900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/24/2023] [Accepted: 03/07/2023] [Indexed: 03/25/2023]
Affiliation(s)
- Amy E McCart Reed
- UQ Centre for Clinical Research, the University of Queensland, Brisbane, QLD
| | - Georgina Hollway
- genomiQa, Brisbane, QLD
- QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | | | - Sunil Lakhani
- UQ Centre for Clinical Research, the University of Queensland, Brisbane, QLD
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD
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4
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De Silva DL, James PA, Mann GB, Lindeman GJ. Universal genetic testing of patients with newly diagnosed breast cancer - ready for prime time? Med J Aust 2021; 215:449-453. [PMID: 34676562 DOI: 10.5694/mja2.51317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/20/2021] [Accepted: 08/04/2021] [Indexed: 11/17/2022]
Affiliation(s)
- Dilanka L De Silva
- Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC.,Memorial Sloan Kettering Cancer Center, New York, USA
| | - Paul A James
- Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC.,University of Melbourne, Melbourne, VIC
| | - G Bruce Mann
- University of Melbourne, Melbourne, VIC.,Royal Melbourne and Royal Women's Hospitals, Melbourne, VIC.,Peter MacCallum Cancer Centre, Melbourne, VIC
| | - Geoffrey J Lindeman
- Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC.,University of Melbourne, Melbourne, VIC.,Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC
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Kumar RD, Burns BA, Vandeventer PJ, Luna PN, Shaw CA. Selection for or against escape from nonsense mediated decay is a novel signature for the detection of cancer genes. Cancer Genet 2021; 258-259:80-84. [PMID: 34592632 DOI: 10.1016/j.cancergen.2021.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/18/2021] [Accepted: 09/20/2021] [Indexed: 01/02/2023]
Abstract
Escape from nonsense mediated mRNA decay (NMD-) can produce activated or inactivated gene products, and bias in rates of escape can identify functionally important genes in germline disease. We hypothesized that the same would be true of cancer genes, and tested for NMD- bias within The Cancer Genome Atlas pan-cancer somatic mutation dataset. We identify 29 genes that show significantly elevated or suppressed rates of NMD-. This novel approach to cancer gene discovery reveals genes not previously cataloged as potentially tumorigenic, and identifies many potential driver mutations in known cancer genes for functional characterization.
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Affiliation(s)
- Runjun D Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Briana A Burns
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Paul J Vandeventer
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States; Baylor Genetics, Houston, TX, United States; Department of Statistics, Rice University, Houston, TX, United States.
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6
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Hettipathirana T, Macdonald C, Xie J, Moodie K, Michael C, Phillips KA. The value of clinical breast examination in a breast cancer surveillance program for women with germline BRCA1 or BRCA2 mutations. Med J Aust 2021; 215:460-464. [PMID: 34420218 DOI: 10.5694/mja2.51226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To assess the sensitivity and specificity of clinical breast examination for detecting breast cancer in asymptomatic women with predisposing germline mutations enrolled in a cancer risk management program that includes radiologic screening. DESIGN, SETTING Retrospective, longitudinal cohort study of women with BRCA1/2 mutations who attended the Breast and Ovarian Cancer Risk Management Clinic at the Peter MacCallum Cancer Centre, a tertiary referral centre in Melbourne, during 1 September 2001 - 31 December 2019. PARTICIPANTS Consecutive women with BRCA1/2 mutations who did not have personal histories of cancer and had not undergone bilateral risk-reducing mastectomy, and who had visited the clinic at least twice during the study period. Participants had generally undergone breast examination at 6- or 12-month intervals, and annual breast imaging (mammography; and magnetic resonance imaging [MRI] for women aged 50 years or younger). MAIN OUTCOME MEASURES Sensitivity (proportion of all biopsy-confirmed breast cancers detected by breast examination alone) and specificity of breast examination for detecting breast cancer. RESULTS Of 414 eligible women (mean age, 35.5 years; SD, 11.2 years), 35 were diagnosed with breast cancer during 1761 woman-years of follow-up. Only two were diagnosed based on breast examination alone (ie, without radiologic evidence), neither of whom was undergoing MRI screening. The sensitivity of breast examination was 6% (95% CI, 1-19%), the specificity 97% (95% CI, 95-98%); the positive predictive value was 14% (95% CI, 2-43%), the negative predictive value 92% (95% CI, 89-94%). CONCLUSION Clinical breast examination did not increase the number of breast cancers detected in MRI-screened women with BRCA1/2 mutations. Removing breast examination from surveillance programs that include MRI may be reasonable for these women.
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Affiliation(s)
- Tamara Hettipathirana
- University of Melbourne, Melbourne, VIC.,Peter MacCallum Cancer Centre, Melbourne, VIC
| | | | - Jing Xie
- Peter MacCallum Cancer Centre, Melbourne, VIC
| | - Kate Moodie
- Peter MacCallum Cancer Centre, Melbourne, VIC
| | | | - Kelly-Anne Phillips
- University of Melbourne, Melbourne, VIC.,Peter MacCallum Cancer Centre, Melbourne, VIC
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7
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Lerebours A, Murzina S, Song Y, Tollefsen KE, Benedetti M, Regoli F, Rotchell JM, Nahrgang J. Susceptibility of polar cod (Boreogadus saida) to a model carcinogen. Mar Environ Res 2021; 170:105434. [PMID: 34333338 DOI: 10.1016/j.marenvres.2021.105434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Studies that aim to characterise the susceptibility of the ecologically relevant and non-model fish polar cod (Boreogadus saida) to model carcinogens are required. Polar cod were exposed under laboratory conditions for six months to control, 0.03 μg BaP/g fish/week and 0.3 μg BaP/g fish/week dietary benzo(a)pyrene (BaP), a reference carcinogen. The concentrations of the 3-OH-BaP bile metabolite and transcriptional responses of genes involved in DNA adduct recognition (xpc), helicase activity (xpd), DNA repair (xpf, rad51) and tumour suppression (tp53) were assessed after 0, 1, 3 and 6 months of exposure, alongside body condition indexes (gonadosomatic index, hepatosomatic index and condition factor). Micronuclei and nuclear abnormalities in blood and spleen, and liver histopathological endpoints were assessed at the end of the experiment. Fish grew steadily over the whole experiment and no mortality was recorded. The concentrations of 3-OH-BaP increased significantly after 1 month of exposure to the highest BaP concentration and after 6 months of exposure to all BaP concentrations showing the biotransformation of the mother compound. Nevertheless, no significant induction of gene transcripts involved in DNA damage repair or tumour suppression were observed at the selected sampling times. These results together with the absence of chromosomal damage in blood and spleen cells, the subtle increase in nuclear abnormalities observed in spleen cells and the low occurrence of foci of cellular alteration suggested that the exposure was below the threshold of observable effects. Taken together, the results showed that polar cod was not susceptible to carcinogenesis using the BaP exposure regime employed herein.
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Affiliation(s)
- Adélaïde Lerebours
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom; UMR CNRS LIENSs, Littoral Environnement et Sociétés, Université de La Rochelle, La Rochelle, 17 000, France.
| | - Svetlana Murzina
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences (IB KarRC RAS), 185910, Petrozavodsk, Russia
| | - You Song
- Norwegian Institute for Water Research (NIVA), Section of Ecotoxicology and Risk Assessment, Gaustadalléen 21, N-0349, Oslo, Norway
| | - Knut Erik Tollefsen
- Norwegian Institute for Water Research (NIVA), Section of Ecotoxicology and Risk Assessment, Gaustadalléen 21, N-0349, Oslo, Norway
| | - Maura Benedetti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy
| | - Francesco Regoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy
| | - Jeanette M Rotchell
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull, HU6 7RX, United Kingdom
| | - Jasmine Nahrgang
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics UiT the Arctic University of Norway, 9037, Tromsø, Norway
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Yu T, Choi KP, Chen ES, Zhang L. Stage-specific protein-domain mutational profile of invasive ductal breast cancer. BMC Med Genomics 2020; 13:150. [PMID: 33087126 PMCID: PMC7580001 DOI: 10.1186/s12920-020-00777-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the mechanisms underlying the malignant progression of cancer cells is crucial for early diagnosis and therapeutic treatment for cancer. Mutational heterogeneity of breast cancer suggests that about a dozen of cancer genes consistently mutate, together with many other genes mutating occasionally, in patients. METHODS Using the whole-exome sequences and clinical information of 468 patients in the TCGA project data portal, we analyzed mutated protein domains and signaling pathway alterations in order to understand how infrequent mutations contribute aggregately to tumor progression in different stages. RESULTS Our findings suggest that while the spectrum of mutated domains was diverse, mutations were aggregated in Pkinase, Pkinase Tyr, Y-Phosphatase and Src-homology 2 domains, highlighting the genetic heterogeneity in activating the protein tyrosine kinase signaling pathways in invasive ductal breast cancer. CONCLUSIONS The study provides new clues to the functional role of infrequent mutations in protein domain regions in different stages for invasive ductal breast cancer, yielding biological insights into metastasis for invasive ductal breast cancer.
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Affiliation(s)
- Ting Yu
- Department of Mathematics, National University of Singapore, 10 Lower Kent Ridge Road, Singapore, 119076 Singapore
- Computational Biology Programme, National University of Singapore, 8 Medical Drive, Singapore, 117596 Singapore
| | - Kwok Pui Choi
- Department of Mathematics, National University of Singapore, 10 Lower Kent Ridge Road, Singapore, 119076 Singapore
- Department of Statistics and Applied Probability, National University of Singapore, 6 Science Drive 2, Singapore, 117546 Singapore
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore, 117596 Singapore
| | - Louxin Zhang
- Department of Mathematics, National University of Singapore, 10 Lower Kent Ridge Road, Singapore, 119076 Singapore
- Computational Biology Programme, National University of Singapore, 8 Medical Drive, Singapore, 117596 Singapore
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Abstract
We increasingly recognize the importance of alterations in DNA in the development of cancer. Beginning with the first somatic mutation identified in a urinary bladder carcinoma cell line, recombinant-DNA technology has led to an explosion of this field, bringing a wealth of data, yet to be fully analyzed. As the number of putative cancer genes has grown several groups have compiled lists of cancer genes with the Catalogue Of Somatic Mutations In Cancer, list as one of several highly regarded. With an interest in the distribution of cancer genes in human chromosomes and discerning whether some chromosomes predominated in cancer gene content, we undertook this review of their distribution in the modern-day human genome. We conclude that cancer genes are uniformly distributed across all human chromosomes having been accreted to the evolving human genome likely in a random fashion over the millennia.
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Affiliation(s)
- Bahar Laderian
- Columbia University Irving Medical Center, New York City, NY.
| | - Mengxi Zhou
- Columbia University Irving Medical Center, New York City, NY
| | - Tito Fojo
- Columbia University Irving Medical Center, New York City, NY; James J. Peters VA Medical Center, New York City, NY
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10
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Nonino A, Campregher PV, de Souza Santos FP, Mazzeu JF, Pereira RW. Genomic characterization and prognostication applied to a Brazilian cohort of patients with myelofibrosis. Int J Hematol 2020; 112:361-8. [PMID: 32535855 DOI: 10.1007/s12185-020-02906-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/20/2020] [Accepted: 05/29/2020] [Indexed: 12/20/2022]
Abstract
Genomic characterization of patients with myeloproliferative neoplasms (MPN) may lead to better diagnostic classification, prognostic assessment, and treatment decisions. These goals are particularly important in myelofibrosis (MF). We performed target Next Generation Sequencing for a panel of 255 genes and Chromosome Microarray Analysis (CMA) in 27 patients with MF. Patients were classified according to genomic findings and we compared the performance of a personalized prognostication system with IPSS, MIPSS70 and MIPSS70 + v2. Twenty-six patients presented mutations: 11.1% had single driver mutations in either JAK2, CALR or MPL; 85.2% had mutations in non-restricted genes (median: 2 per patient). CMA was abnormal in 91.7% of the 24 cases with available data. Copy-Number-Neutral Loss-of-Heterozygosity was the most common finding (66.7%). Del13q was the most frequent copy number variation, and we could define a 2.4 Mb minimally affected region encompassing RB1, SUCLA2 and CLLS2 loci. The largest genomic subgroup consisted of patients with mutations in genes involved with chromatin organization and splicing control (40.7%) and the personalized system showed better concordance and accuracy than the other prognostic systems. Comprehensive genomic characterization reveals the striking genetic complexity of MF and, when combined with clinical data, led, in our cohort, to better prognostication performance.
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Repana D, Nulsen J, Dressler L, Bortolomeazzi M, Venkata SK, Tourna A, Yakovleva A, Palmieri T, Ciccarelli FD. The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens. Genome Biol 2019; 20:1. [PMID: 30606230 PMCID: PMC6317252 DOI: 10.1186/s13059-018-1612-0] [Citation(s) in RCA: 336] [Impact Index Per Article: 67.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 12/12/2018] [Indexed: 02/06/2023] Open
Abstract
The Network of Cancer Genes (NCG) is a manually curated repository of 2372 genes whose somatic modifications have known or predicted cancer driver roles. These genes were collected from 275 publications, including two sources of known cancer genes and 273 cancer sequencing screens of more than 100 cancer types from 34,905 cancer donors and multiple primary sites. This represents a more than 1.5-fold content increase compared to the previous version. NCG also annotates properties of cancer genes, such as duplicability, evolutionary origin, RNA and protein expression, miRNA and protein interactions, and protein function and essentiality. NCG is accessible at http://ncg.kcl.ac.uk/ .
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Affiliation(s)
- Dimitra Repana
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Joel Nulsen
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Lisa Dressler
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Michele Bortolomeazzi
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Santhilata Kuppili Venkata
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Aikaterini Tourna
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Anna Yakovleva
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Tommaso Palmieri
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Francesca D. Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
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12
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Gorlov IP, Pikielny CW, Frost HR, Her SC, Cole MD, Strohbehn SD, Wallace-Bradley D, Kimmel M, Gorlova OY, Amos CI. Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples. BMC Bioinformatics 2018; 19:430. [PMID: 30453881 PMCID: PMC6245819 DOI: 10.1186/s12859-018-2455-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/31/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Because driver mutations provide selective advantage to the mutant clone, they tend to occur at a higher frequency in tumor samples compared to selectively neutral (passenger) mutations. However, mutation frequency alone is insufficient to identify cancer genes because mutability is influenced by many gene characteristics, such as size, nucleotide composition, etc. The goal of this study was to identify gene characteristics associated with the frequency of somatic mutations in the gene in tumor samples. RESULTS We used data on somatic mutations detected by genome wide screens from the Catalog of Somatic Mutations in Cancer (COSMIC). Gene size, nucleotide composition, expression level of the gene, relative replication time in the cell cycle, level of evolutionary conservation and other gene characteristics (totaling 11) were used as predictors of the number of somatic mutations. We applied stepwise multiple linear regression to predict the number of mutations per gene. Because missense, nonsense, and frameshift mutations are associated with different sets of gene characteristics, they were modeled separately. Gene characteristics explain 88% of the variation in the number of missense, 40% of nonsense, and 23% of frameshift mutations. Comparisons of the observed and expected numbers of mutations identified genes with a higher than expected number of mutations- positive outliers. Many of these are known driver genes. A number of novel candidate driver genes was also identified. CONCLUSIONS By comparing the observed and predicted number of mutations in a gene, we have identified known cancer-associated genes as well as 111 novel cancer associated genes. We also showed that adding the number of silent mutations per gene reported by genome/exome wide screens across all cancer type (COSMIC data) as a predictor substantially exceeds predicting accuracy of the most popular cancer gene predicting tool - MutsigCV.
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Affiliation(s)
- Ivan P Gorlov
- The Geisel School of Medicine, Department of Biomedical Data Science, Dartmouth College, HB7936, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Beirut, NH, 03756, Lebanon.
| | - Claudio W Pikielny
- The Geisel School of Medicine, Department of Biomedical Data Science, Dartmouth College, HB7936, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Beirut, NH, 03756, Lebanon
| | - Hildreth R Frost
- The Geisel School of Medicine, Department of Biomedical Data Science, Dartmouth College, HB7936, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Beirut, NH, 03756, Lebanon
| | - Stephanie C Her
- The Geisel School of Medicine, Department of Biomedical Data Science, Dartmouth College, HB7936, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Beirut, NH, 03756, Lebanon
| | - Michael D Cole
- The Geisel School of Medicine, Department of Biomedical Data Science, Dartmouth College, HB7936, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Beirut, NH, 03756, Lebanon
| | - Samuel D Strohbehn
- The Geisel School of Medicine, Department of Biomedical Data Science, Dartmouth College, HB7936, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Beirut, NH, 03756, Lebanon
| | - David Wallace-Bradley
- Department of Statistics, Rice University, M.S. 138, 6100 Main Street, Houston, TX, 77005, USA
| | - Marek Kimmel
- Department of Statistics, Rice University, M.S. 138, 6100 Main Street, Houston, TX, 77005, USA
| | - Olga Y Gorlova
- The Geisel School of Medicine, Department of Biomedical Data Science, Dartmouth College, HB7936, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Beirut, NH, 03756, Lebanon
| | - Christopher I Amos
- The Geisel School of Medicine, Department of Biomedical Data Science, Dartmouth College, HB7936, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Beirut, NH, 03756, Lebanon
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13
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Barber A, Farmer K, Martin KR, Smith PD. Retinal regeneration mechanisms linked to multiple cancer molecules: A therapeutic conundrum. Prog Retin Eye Res 2016; 56:19-31. [PMID: 27586058 DOI: 10.1016/j.preteyeres.2016.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 03/06/2016] [Accepted: 03/07/2016] [Indexed: 11/26/2022]
Abstract
Over the last decade, a large number of research articles have been published demonstrating regeneration and/or neuroprotection of retinal ganglion cells following manipulation of specific genetic and molecular targets. Interestingly, of the targets that have been identified to promote repair following visual system damage, many are genes known to be mutated in different types of cancer. This review explores recent literature on the potential for modulating cancer genes as a therapeutic strategy for visual system repair and looks at the potential clinical challenges associated with implementing this type of therapy. We also discuss signalling mechanisms that have been implicated in cancer and consider how similar mechanisms may improve axonal regeneration in the optic nerve.
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Affiliation(s)
- Amanda Barber
- John van Geest Centre for Brain Repair, University of Cambridge, UK
| | - Kyle Farmer
- Department of Neuroscience, Carleton University, Ottawa, Ontario, Canada
| | - Keith R Martin
- John van Geest Centre for Brain Repair, University of Cambridge, UK; Medical Research Council - Wellcome Trust Cambridge Stem Cell Institute, Cambridge, UK; Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Patrice D Smith
- John van Geest Centre for Brain Repair, University of Cambridge, UK; Department of Neuroscience, Carleton University, Ottawa, Ontario, Canada.
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14
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Daakour S, Hajingabo LJ, Kerselidou D, Devresse A, Kettmann R, Simonis N, Dequiedt F, Twizere JC. Systematic interactome mapping of acute lymphoblastic leukemia cancer gene products reveals EXT-1 tumor suppressor as a Notch1 and FBWX7 common interactor. BMC Cancer 2016; 16:335. [PMID: 27229929 PMCID: PMC4882867 DOI: 10.1186/s12885-016-2374-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/19/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Perturbed genotypes in cancer can now be identified by whole genome sequencing of large number of diverse tumor samples, and observed gene mutations can be used for prognosis and classification of cancer subtypes. Although mutations in a few causative genes are directly linked to key signaling pathways perturbation, a global understanding of how known cancer genes drive oncogenesis in human is difficult to assess. METHODS We collected available information about mutated genes in Acute Lymphoblastic Leukemia (ALL). Validated human protein interactions (PPI) were collected from IntAct, HPRD and BioGRID interactomics databases, or obtained using yeast two-hybrid screening assay. RESULTS We have mapped interconnections between 116 cancer census gene products associated with ALL. Combining protein-protein interactions data and cancer-specific gene mutations information, we observed that 63 ALL-gene products are interconnected and identified 37 human proteins interacting with at least 2 ALL-gene products. We highlighted exclusive and coexistence genetic alterations in key signaling pathways including the PI3K/AKT and the NOTCH pathways. We then used different cell lines and reporter assay systems to validate the involvement of EXT1 in the Notch pathway. CONCLUSION We propose that novel ALL-gene candidates can be identified based on their functional association with well-known cancer genes. We identified EXT1, a gene not previously linked to ALL via mutations, as a common interactor of NOTCH1 and FBXW7 regulating the NOTCH pathway in an FBXW7-dependend manner.
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Affiliation(s)
- Sarah Daakour
- Laboratory of Protein Signaling and Interactions, Molecular Biology in Diseases Unit, GIGA-Research, University of Liège, Liège, B-4000, Belgium
| | - Leon Juvenal Hajingabo
- Laboratory of Protein Signaling and Interactions, Molecular Biology in Diseases Unit, GIGA-Research, University of Liège, Liège, B-4000, Belgium.,Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles (ULB), Bruxelles, B-1050, Belgium
| | - Despoina Kerselidou
- Laboratory of Protein Signaling and Interactions, Molecular Biology in Diseases Unit, GIGA-Research, University of Liège, Liège, B-4000, Belgium
| | - Aurelie Devresse
- Laboratory of Protein Signaling and Interactions, Molecular Biology in Diseases Unit, GIGA-Research, University of Liège, Liège, B-4000, Belgium
| | - Richard Kettmann
- Laboratory of Protein Signaling and Interactions, Molecular Biology in Diseases Unit, GIGA-Research, University of Liège, Liège, B-4000, Belgium
| | - Nicolas Simonis
- Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles (ULB), Bruxelles, B-1050, Belgium
| | - Franck Dequiedt
- Laboratory of Protein Signaling and Interactions, Molecular Biology in Diseases Unit, GIGA-Research, University of Liège, Liège, B-4000, Belgium
| | - Jean-Claude Twizere
- Laboratory of Protein Signaling and Interactions, Molecular Biology in Diseases Unit, GIGA-Research, University of Liège, Liège, B-4000, Belgium.
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15
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Valdespino-Gómez VM, Valdespino-Castillo VE. [Usefulness of the oncogenetic molecular counselling in adults whith familial cancer]. Rev Med Inst Mex Seguro Soc 2016; 54:364-374. [PMID: 27100983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
More than 200 cancer susceptibility syndromes (CSS) have been recognized through performing classic epidemiologic studies and genetic linkage analysis. In most CSSs clinical conditions of the patients have been identified as well as their hereditary patterns and the predisponent genes to cancer development. Cancer hereditary identification is a useful condition, since cancer family integrants may benefit of efficient strategies in early screening and in tumor prevention strategies; this consultation is performed by oncogenetic molecular medical consultants who must be scientifically competent for Human Genetics and Cancer molecular biology domains. The oncogenetic molecular consult of patients and family relatives of cancer predisposition families is a medical service in health programs of developed and developing countries; in our country this type of medical service needs to be organized and settled to be part of the integral oncology medical service. The oncogenetic molecular consultation is a structural process of assessment and communication of the associated integral problems of the cancer inherited susceptibility in familial cancer.
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Affiliation(s)
- Víctor M Valdespino-Gómez
- Departamento de Atención a la Salud, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana Xochimilco, Ciudad de México, México.
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16
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Abstract
Colorectal cancer (CRC) constitutes a major public health problem as the third most commonly diagnosed and third most lethal malignancy worldwide. The prevalence and the physical accessibility to colorectal tumors have made CRC an ideal model for the study of tumor genetics. Early research efforts using patient derived CRC samples led to the discovery of several highly penetrant mutations (e.g., APC, KRAS, MMR genes) in both hereditary and sporadic CRC tumors. This knowledge has enabled researchers to develop genetically engineered and chemically induced tumor models of CRC, both of which have had a substantial impact on our understanding of the molecular basis of CRC. Despite these advances, the morbidity and mortality of CRC remains a cause for concern and highlight the need to uncover novel genetic drivers of CRC. This review focuses on mouse models of CRC with particular emphasis on a newly developed cancer gene discovery tool, the Sleeping Beauty transposon-based mutagenesis model of CRC.
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MESH Headings
- Adenomatous Polyposis Coli/genetics
- Adenomatous Polyposis Coli/metabolism
- Adenomatous Polyposis Coli/pathology
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Colorectal Neoplasms, Hereditary Nonpolyposis/genetics
- Colorectal Neoplasms, Hereditary Nonpolyposis/metabolism
- Colorectal Neoplasms, Hereditary Nonpolyposis/pathology
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Humans
- Mice
- Mutation
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/metabolism
- Neoplasms, Experimental/pathology
- Phenotype
- Transposases/genetics
- Transposases/metabolism
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17
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Abstract
The occurrence of chimeric transcripts has been reported in many cancer cells and seen as potential biomarkers and therapeutic targets. Modern high-throughput sequencing technologies offer a way to investigate individual chimeric transcripts and the systematic information of associated gene expressions about underlying genome structural variations and genomic interactions. The detection methods of finding chimeric transcripts from massive amount of short read sequence data are discussed here. Both assembly-based and alignment-based methods are used for the investigation of chimeric transcripts.
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18
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Buchanan AH, Datta SK, Skinner CS, Hollowell GP, Beresford HF, Freeland T, Rogers B, Boling J, Marcom PK, Adams MB. Randomized Trial of Telegenetics vs. In-Person Cancer Genetic Counseling: Cost, Patient Satisfaction and Attendance. J Genet Couns 2015; 24:961-70. [PMID: 25833335 DOI: 10.1007/s10897-015-9836-6] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/19/2015] [Indexed: 10/23/2022]
Abstract
Telegenetics-genetic counseling via live videoconferencing-can improve access to cancer genetic counseling (CGC) in underserved areas, but studies on cancer telegenetics have not applied randomized methodology or assessed cost. We report cost, patient satisfaction and CGC attendance from a randomized trial comparing telegenetics with in-person CGC among individuals referred to CGC in four rural oncology clinics. Participants (n = 162) were randomized to receive CGC at their local oncology clinic in-person or via telegenetics. Cost analyses included telegenetics system; mileage; and personnel costs for genetic counselor, IT specialist, and clinic personnel. CGC attendance was tracked via study database. Patient satisfaction was assessed 1 week post-CGC via telephone survey using validated scales. Total costs were $106 per telegenetics patient and $244 per in-person patient. Patient satisfaction did not differ by group on either satisfaction scale. In-person patients were significantly more likely to attend CGC than telegenetics patients (89 vs. 79 %, p = 0.03), with bivariate analyses showing an association between lesser computer comfort and lower attendance rate (Chi-square = 5.49, p = 0.02). Our randomized trial of telegenetics vs. in-person counseling found that telegenetics cost less than in-person counseling, with high satisfaction among those who attended. This study provides support for future randomized trials comparing multiple service delivery models on longer-term psychosocial and behavioral outcomes.
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19
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Melaiu O, Melissari E, Mutti L, Bracci E, De Santi C, Iofrida C, Di Russo M, Cristaudo A, Bonotti A, Cipollini M, Garritano SI, Foddis R, Lucchi M, Pellegrini S, Gemignani F, Landi S. Expression status of candidate genes in mesothelioma tissues and cell lines. Mutat Res 2015; 771:6-12. [PMID: 25771974 DOI: 10.1016/j.mrfmmm.2014.11.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 10/14/2014] [Accepted: 11/04/2014] [Indexed: 01/08/2023]
Abstract
In order to broaden knowledge on the pathogenesis of malignant pleural mesothelioma (MPM), we reviewed studies on the MPM-transcriptome and identified 119 deregulated genes. However, there was poor consistency among the studies. Thus, the expression of these genes was further investigated in the present work using reverse transcriptase-quantitative PCR (RT-qPCR) in 15 MPM and 20 non-MPM tissue samples. Fifty-nine genes showed a statistically significant deregulation and were further evaluated in two epithelioid MPM cell lines (compared to MET-5A, a non-MPM cell line). Nine genes (ACSL1, CCNO, CFB, PDGFRB, SULF1, TACC1, THBS2, TIMP3, XPOT) were deregulated with statistical significance in both cell lines, 12 (ASS1, CCNB1, CDH11, COL1A1, CXADR, EIF4G1, GALNT7, ITGA4, KRT5, PTGIS, RAN, SOD1) in at least one cell line, whereas 7 (DSP, HEG1, MCM4, MSLN, NME2, NMU, TNPO2) were close but did not reach the statistical significance in any of the cell line. Patients whose MPM tissues expressed elevated mRNA levels of BIRC5, DSP, NME2, and THBS2 showed a statistically significant shorter overall survival. Although MPM is a poorly studied cancer, some features are starting to emerge. Novel cancer genes are suggested here, in particular those involved in cell-cell and cell-matrix interactions.
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20
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Abstract
Protein-protein interaction (PPI) network analysis has been widely applied in the investigation of the mechanisms of diseases, especially cancer. Recent studies revealed that cancer proteins tend to interact more strongly than other categories of proteins, even essential proteins, in the human interactome. However, it remains unclear whether this observation was introduced by the bias towards more cancer studies in humans. Here, we examined this important issue by uniquely comparing network characteristics of cancer proteins with three other sets of proteins in four organisms, three of which (fly, worm, and yeast) whose interactomes are essentially not biased towards cancer or other diseases. We confirmed that cancer proteins had stronger connectivity, shorter distance, and larger betweenness centrality than non-cancer disease proteins, essential proteins, and control proteins. Our statistical evaluation indicated that such observations were overall unlikely attributed to random events. Considering the large size and high quality of the PPI data in the four organisms, the conclusion that cancer proteins interact strongly in the PPI networks is reliable and robust. This conclusion suggests that perturbation of cancer proteins might cause major changes of cellular systems and result in abnormal cell function leading to cancer.
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Affiliation(s)
- Junfeng Xia
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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21
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Datta MW, Suckow MA, Twigger S, Pollard M, Jacob H, Tonellato PJ. Using Comparative Genomics to Leverage Animal Models in the Identification of Cancer Genes. Examples in Prostate Cancer. Cancer Genomics Proteomics 2005; 2:137-144. [PMID: 31394645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2005] [Accepted: 04/19/2005] [Indexed: 06/10/2023] Open
Abstract
The identification of cancer biomarkers that will predict susceptibility to disease and subsequent clinical outcome are key components of future genomics-based tailored medical care. Animal models of disease provide a rich resource for the identification of potential cancer biomarkers. Animal models of prostate cancer in particular offer the potential to identify cancer genes associated with dietary and environmental factors. The key issue is the timely and efficient identification of candidate genes that are likely to impact on human prostate cancer. Here, we demonstrate comparative genomics-based methods for the identification of candidate genes in animal models that are associated with human chromosomal regions implicated in prostate cancer. Using publicly available bioinformatics tools, comparisons can be made between cancer-specific datasets, genomic sequencing data and cross-species comparative maps to identify potential cancer biomarkers. This process is demonstrated by using rat models of prostate cancer to identify candidate human prostate cancer genes. Genes identified through these techniques can be screened as biomarkers for response to chemopreventive agents, as well as being used in transgenic or knockout mice to engineer better animal models of human prostate cancer. The bioinformatics techniques outlined here can be used to leverage genomic data from any animal cancer model for use in the study and treatment of human cancer.
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Affiliation(s)
- Milton W Datta
- Department of Pathology and Urology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Mark A Suckow
- Walther Cancer Center, University of Notre Dame, Notre Dame, Indiana
| | - Simon Twigger
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Morris Pollard
- Walther Cancer Center, University of Notre Dame, Notre Dame, Indiana
| | - Howard Jacob
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Peter J Tonellato
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
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