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Neary B, Qiu P. Characterization of Expression-Based Gene Clusters Gives Insights into Variation in Patient Response to Cancer Therapies. Cancer Inform 2024; 23:11769351241271560. [PMID: 39238656 PMCID: PMC11375686 DOI: 10.1177/11769351241271560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 07/01/2024] [Indexed: 09/07/2024] Open
Abstract
Background Transcriptomics can reveal much about cellular activity, and cancer transcriptomics have been useful in investigating tumor cell behaviors. Patterns in transcriptome-wide gene expression can be used to investigate biological mechanisms and pathways that can explain the variability in patient response to cancer therapies. Methods We identified gene expression patterns related to patient drug response by clustering tumor gene expression data and selecting from the resulting gene clusters those where expression of cluster genes was related to patient survival on specific drugs. We then investigated these gene clusters for biological meaning using several approaches, including identifying common genomic locations and transcription factors whose targets were enriched in these clusters and performing survival analyses to support these candidate transcription factor-drug relationships. Results We identified gene clusters related to drug-specific survival, and through these, we were able to associate observed variations in patient drug response to specific known biological phenomena. Specifically, our analysis implicated 2 stem cell-related transcription factors, HOXB4 and SALL4, in poor response to temozolomide in brain cancers. In addition, expression of SNRNP70 and its targets were implicated in cetuximab response by 3 different analyses, although the mechanism remains unclear. We also found evidence that 2 cancer-related chromosomal structural changes may impact drug efficacy. Conclusion In this study, we present the gene clusters identified and the results of our systematic analysis linking drug efficacy to specific transcription factors, which are rich sources of potential mechanistic relationships impacting patient outcomes. We also highlight the most promising of these results, which were supported by multiple analyses and by previous research. We report these findings as promising avenues for independent validation and further research into cancer treatments and patient response.
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Affiliation(s)
- Bridget Neary
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Peng Qiu
- Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA, USA
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Garcia-Etxebarria K, Etxart A, Barrero M, Nafria B, Segues Merino NM, Romero-Garmendia I, Goel A, Franke A, D’Amato M, Bujanda L. Genetic Variants as Predictors of the Success of Colorectal Cancer Treatments. Cancers (Basel) 2023; 15:4688. [PMID: 37835382 PMCID: PMC10571592 DOI: 10.3390/cancers15194688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Some genetic polymorphisms (SNPs) have been proposed as predictors for different colorectal cancer (CRC) outcomes. This work aims to assess their performance in our cohort and find new SNPs associated with them. METHODS A total of 833 CRC cases were analyzed for seven outcomes, including the use of chemotherapy, and stratified by tumor location and stage. The performance of 63 SNPs was assessed using a generalized linear model and area under the receiver operating characteristic curve, and local SNPs were detected using logistic regressions. RESULTS In total 26 of the SNPs showed an AUC > 0.6 and a significant association (p < 0.05) with one or more outcomes. However, clinical variables outperformed some of them, and the combination of genetic and clinical data showed better performance. In addition, 49 suggestive (p < 5 × 10-6) SNPs associated with one or more CRC outcomes were detected, and those SNPs were located at or near genes involved in biological mechanisms associated with CRC. CONCLUSIONS Some SNPs with clinical data can be used in our population as predictors of some CRC outcomes, and the local SNPs detected in our study could be feasible markers that need further validation as predictors.
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Affiliation(s)
- Koldo Garcia-Etxebarria
- Biodonostia, Gastrointestinal Genetics Group, 20014 San Sebastián, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08036 Barcelona, Spain;
| | - Ane Etxart
- Biodonostia, Gastrointestinal Disease Group, Universidad del País Vasco (UPV/EHU), 20014 San Sebastián, Spain; (A.E.); (M.B.); (B.N.); (N.M.S.M.)
| | - Maialen Barrero
- Biodonostia, Gastrointestinal Disease Group, Universidad del País Vasco (UPV/EHU), 20014 San Sebastián, Spain; (A.E.); (M.B.); (B.N.); (N.M.S.M.)
| | - Beatriz Nafria
- Biodonostia, Gastrointestinal Disease Group, Universidad del País Vasco (UPV/EHU), 20014 San Sebastián, Spain; (A.E.); (M.B.); (B.N.); (N.M.S.M.)
| | - Nerea Miren Segues Merino
- Biodonostia, Gastrointestinal Disease Group, Universidad del País Vasco (UPV/EHU), 20014 San Sebastián, Spain; (A.E.); (M.B.); (B.N.); (N.M.S.M.)
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), 48940 Leioa, Spain
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany;
| | - Mauro D’Amato
- Gastrointestinal Genetics Lab, CIC bioGUNE, Basque Research and Technology Alliance, 48160 Derio, Spain;
- IKERBASQUE, Basque Foundation for Sciences, 48009 Bilbao, Spain
- Department of Medicine and Surgery, LUM University, 70010 Casamassima, Italy
| | - Luis Bujanda
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08036 Barcelona, Spain;
- Biodonostia, Gastrointestinal Disease Group, Universidad del País Vasco (UPV/EHU), 20014 San Sebastián, Spain; (A.E.); (M.B.); (B.N.); (N.M.S.M.)
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Romero-Garmendia I, Garcia-Etxebarria K. From Omic Layers to Personalized Medicine in Colorectal Cancer: The Road Ahead. Genes (Basel) 2023; 14:1430. [PMID: 37510334 PMCID: PMC10379575 DOI: 10.3390/genes14071430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/05/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Colorectal cancer is a major health concern since it is a highly diagnosed cancer and the second cause of death among cancers. Thus, the most suitable biomarkers for its diagnosis, prognosis, and treatment have been studied to improve and personalize the prevention and clinical management of colorectal cancer. The emergence of omic techniques has provided a great opportunity to better study CRC and make personalized medicine feasible. In this review, we will try to summarize how the analysis of the omic layers can be useful for personalized medicine and the existing difficulties. We will discuss how single and multiple omic layer analyses have been used to improve the prediction of the risk of CRC and its outcomes and how to overcome the challenges in the use of omic layers in personalized medicine.
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Affiliation(s)
- Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), 48940 Leioa, Spain
| | - Koldo Garcia-Etxebarria
- Biodonostia, Gastrointestinal Genetics Group, 20014 San Sebastián, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08036 Barcelona, Spain
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Curtis A, Yu Y, Carey M, Parfrey P, Yilmaz YE, Savas S. Examining SNP-SNP interactions and risk of clinical outcomes in colorectal cancer using multifactor dimensionality reduction based methods. Front Genet 2022; 13:902217. [PMID: 35991579 PMCID: PMC9385108 DOI: 10.3389/fgene.2022.902217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
Background: SNP interactions may explain the variable outcome risk among colorectal cancer patients. Examining SNP interactions is challenging, especially with large datasets. Multifactor Dimensionality Reduction (MDR)-based programs may address this problem.Objectives: 1) To compare two MDR-based programs for their utility; and 2) to apply these programs to sets of MMP and VEGF-family gene SNPs in order to examine their interactions in relation to colorectal cancer survival outcomes.Methods: This study applied two data reduction methods, Cox-MDR and GMDR 0.9, to study one to three way SNP interactions. Both programs were run using a 5-fold cross validation step and the top models were verified by permutation testing. Prognostic associations of the SNP interactions were verified using multivariable regression methods. Eight datasets, including SNPs from MMP family genes (n = 201) and seven sets of VEGF-family interaction networks (n = 1,517 SNPs) were examined.Results: ∼90 million potential interactions were examined. Analyses in the MMP and VEGF gene family datasets found several novel 1- to 3-way SNP interactions. These interactions were able to distinguish between the patients with different outcome risks (regression p-values 0.03–2.2E-09). The strongest association was detected for a 3-way interaction including CHRM3.rs665159_EPN1.rs6509955_PTGER3.rs1327460 variants.Conclusion: Our work demonstrates the utility of data reduction methods while identifying potential prognostic markers in colorectal cancer.
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Affiliation(s)
- Aaron Curtis
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Megan Carey
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Patrick Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Yildiz E. Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John’s, NL, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- *Correspondence: Sevtap Savas,
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Bignucolo A, Scarabel L, Toffoli G, Cecchin E, De Mattia E. Predicting drug response and toxicity in metastatic colorectal cancer: the role of germline markers. Expert Rev Clin Pharmacol 2022; 15:689-713. [PMID: 35829762 DOI: 10.1080/17512433.2022.2101447] [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: 11/04/2022]
Abstract
INTRODUCTION Despite the introduction of targeted agents leading to therapeutic advances, clinical management of patients with metastatic colorectal cancer (mCRC) is still challenged by significant interindividual variability in treatment outcomes, both in terms of toxicity and therapy efficacy. The study of germline genetic variants could help to personalize and optimize therapeutic approaches in mCRC. AREAS COVERED A systematic review of pharmacogenetic studies in mCRC patients published on PubMed between 2011 and 2021, evaluating the role of germline variants as predictive markers of toxicity and efficacy of drugs currently approved for treatment of mCRC, was perfomed. EXPERT OPINION Despite the large amount of pharmacogenetic data published to date, only a few genetic markers (i.e., DPYD and UGT1A1 variants) reached the clinical practice, mainly to prevent the toxic effects of chemotherapy. The large heterogeneity of available studies represents the major limitation in comparing results and identifying potential markers for clinical use, the role of which remains exploratory in most cases. However, the available published findings are an important starting point for future investigations. They highlighted new promising pharmacogenetic markers within the network of inflammatory and immune response signaling. In addition, the emerging role of previously overlooked rare variants has been pointed out.
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Affiliation(s)
- Alessia Bignucolo
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via Franco Gallini 2, 33081 Aviano (PN), Italy
| | - Lucia Scarabel
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via Franco Gallini 2, 33081 Aviano (PN), Italy
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via Franco Gallini 2, 33081 Aviano (PN), Italy
| | - Erika Cecchin
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via Franco Gallini 2, 33081 Aviano (PN), Italy
| | - Elena De Mattia
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via Franco Gallini 2, 33081 Aviano (PN), Italy
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Yu Y, Werdyani S, Carey M, Parfrey P, Yilmaz YE, Savas S. A comprehensive analysis of SNPs and CNVs identifies novel markers associated with disease outcomes in colorectal cancer. Mol Oncol 2021; 15:3329-3347. [PMID: 34309201 PMCID: PMC8637572 DOI: 10.1002/1878-0261.13067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/29/2021] [Accepted: 07/24/2021] [Indexed: 12/15/2022] Open
Abstract
We aimed to examine the associations of a genome-wide set of single nucleotide polymorphisms (SNPs) and 254 copy number variations (CNVs) and/or insertion/deletions (INDELs) with clinical outcomes in colorectal cancer patients (n = 505). We also aimed to investigate whether their associations changed (e.g., appeared, diminished) over time. Multivariable Cox proportional hazards and piece-wise Cox regression models were used to examine the associations. The Cancer Genome Atlas (TCGA) datasets were used for replication purposes and to examine the gene expression differences between tumor and nontumor tissue samples. A common SNP (WBP11-rs7314075) was associated with disease-specific survival with P-value of 3.2 × 10-8 . Association of this region with disease-specific survival was also detected in the TCGA patient cohort. Two expression quantitative trait loci (eQTLs) were identified in this locus that were implicated in the regulation of ERP27 expression. Interestingly, expression levels of ERP27 and WBP11 were significantly different between colorectal tumors and nontumor tissues. Three SNPs predicted the risk of recurrent disease only after 5 years postdiagnosis. Overall, our study identified novel variants, one of which also showed an association in the TCGA dataset, but no CNVs/INDELs, that associated with outcomes in colorectal cancer. Three SNPs were candidate predictors of long-term recurrence/metastasis risk.
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Affiliation(s)
- Yajun Yu
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Present address:
Division of Biomedical SciencesFaculty of MedicineMemorial UniversitySt. John’sNLCanada
| | - Salem Werdyani
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Present address:
Division of Biomedical SciencesFaculty of MedicineMemorial UniversitySt. John’sNLCanada
| | - Megan Carey
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
| | - Patrick Parfrey
- Discipline of MedicineFaculty of MedicineMemorial UniversitySt. John’sNLCanada
| | - Yildiz E. Yilmaz
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Discipline of MedicineFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Department of Mathematics and StatisticsFaculty of ScienceMemorial UniversitySt. John’sNLCanada
| | - Sevtap Savas
- Discipline of GeneticsFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Discipline of OncologyFaculty of MedicineMemorial UniversitySt. John’sNLCanada
- Present address:
Division of Biomedical SciencesFaculty of MedicineMemorial UniversitySt. John’sNLCanada
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7
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Leow YC, Roslani AC, Xavier RG, Lee FY. Pathological Complete Response After Neoadjuvant Therapy in Rectal Adenocarcinoma: a 5-Year Follow-up. Indian J Surg 2021; 83:768-775. [PMID: 34075282 PMCID: PMC8154108 DOI: 10.1007/s12262-021-02945-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/13/2021] [Indexed: 11/26/2022] Open
Abstract
Neoadjuvant therapy is the gold standard treatment of locally advanced rectal cancer. It may induce complete sterilization of tumor cell and decreases its local recurrence rate. While 15–20% of patients were found to have pathological complete response (pCR) with combined multimodal therapy, Asian data were generally scarce. pCR rate can indicate the suitability of applying the “watch-and-wait” strategy, which advocates deferment of surgery that can alleviate surgery-associated morbidity.To determine the percentage of pCR of rectal cancer after neoadjuvant therapy. Patients diagnosed with rectal cancer underwent treatment from 2013 to 2017 were retrieved retrospectively. Demographic data, tumor localization, pre- and post-operative pathological reports, neoadjuvant therapy, and pCR status were collected from patients’ records. A total of 242 out of 259 patients were treated with definitive rectal surgery. Mean age was 67.1 years old. Chinese ethnicity and male gender were predominant (n = 131, 54.1% and n = 146, 64.3% respectively). More than half (n = 124, 51.2%) had tumor located at mid or low rectum. Histologically, moderate differentiated adenocarcinoma was predominant (n = 227, 93.8%). Merely half (n = 123, 50.8%) of the patients received neoadjuvant chemoradiation therapy, but only 12 (9.8%) had a pCR. From follow-up on these 12 pCR patients, most had 2-year disease-free survival but 1 (8.3%) of the pCR had distant metastasis within 1-year post-surgery. The pathological complete response rate in our center was lower than reported. Stringent patient selection with close follow-up for patients should be carried out if the “watch-and-wait” strategy is implemented in our population.
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Affiliation(s)
- Yeen Chin Leow
- Department of Surgery, Colorectal Unit, University Malaya Medical Centre (UMMC), Kuala Lumpur, Malaysia
- Department of Surgery, Hospital Taiping, Ministry of Health Malaysia, Perak, Malaysia
| | - April Camilla Roslani
- Department of Surgery, Colorectal Unit, University Malaya Medical Centre (UMMC), Kuala Lumpur, Malaysia
| | - Ruben Gregory Xavier
- Department of Surgery, Colorectal Unit, University Malaya Medical Centre (UMMC), Kuala Lumpur, Malaysia
| | - Fei Yee Lee
- Clinical Research Centre, Selayang Hospital, Ministry of Health Malaysia, Selangor, Malaysia
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Ubels J, Schaefers T, Punt C, Guchelaar HJ, de Ridder J. RAINFOREST: a random forest approach to predict treatment benefit in data from (failed) clinical drug trials. Bioinformatics 2020; 36:i601-i609. [PMID: 33381829 DOI: 10.1093/bioinformatics/btaa799] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION When phase III clinical drug trials fail their endpoint, enormous resources are wasted. Moreover, even if a clinical trial demonstrates a significant benefit, the observed effects are often small and may not outweigh the side effects of the drug. Therefore, there is a great clinical need for methods to identify genetic markers that can identify subgroups of patients which are likely to benefit from treatment as this may (i) rescue failed clinical trials and/or (ii) identify subgroups of patients which benefit more than the population as a whole. When single genetic biomarkers cannot be found, machine learning approaches that find multivariate signatures are required. For single nucleotide polymorphism (SNP) profiles, this is extremely challenging owing to the high dimensionality of the data. Here, we introduce RAINFOREST (tReAtment benefIt prediction using raNdom FOREST), which can predict treatment benefit from patient SNP profiles obtained in a clinical trial setting. RESULTS We demonstrate the performance of RAINFOREST on the CAIRO2 dataset, a phase III clinical trial which tested the addition of cetuximab treatment for metastatic colorectal cancer and concluded there was no benefit. However, we find that RAINFOREST is able to identify a subgroup comprising 27.7% of the patients that do benefit, with a hazard ratio of 0.69 (P = 0.04) in favor of cetuximab. The method is not specific to colorectal cancer and could aid in reanalysis of clinical trial data and provide a more personalized approach to cancer treatment, also when there is no clear link between a single variant and treatment benefit. AVAILABILITY AND IMPLEMENTATION The R code used to produce the results in this paper can be found at github.com/jubels/RAINFOREST. A more configurable, user-friendly Python implementation of RAINFOREST is also provided. Due to restrictions based on privacy regulations and informed consent of participants, phenotype and genotype data of the CAIRO2 trial cannot be made freely available in a public repository. Data from this study can be obtained upon request. Requests should be directed toward Prof. Dr. H.J. Guchelaar (h.j.guchelaar@lumc.nl). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joske Ubels
- Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands.,Erasmus MC Cancer Institute, ErasmusMC, Rotterdam, The Netherlands.,SkylineDx, Rotterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Tilman Schaefers
- Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Cornelis Punt
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht,The Netherlands
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen de Ridder
- Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
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Penney KL, Banbury BL, Bien S, Harrison TA, Hua X, Phipps AI, Sun W, Song M, Joshi AD, Alberts SR, Allegra CJ, Atkins J, Colangelo LH, George TJ, Goldberg RM, Lucas PC, Nair SG, Shi Q, Sinicrope FA, Wolmark N, Yothers G, Peters U, Newcomb PA, Chan AT. Genetic Variant Associated With Survival of Patients With Stage II-III Colon Cancer. Clin Gastroenterol Hepatol 2020; 18:2717-2723.e3. [PMID: 31811950 PMCID: PMC7269796 DOI: 10.1016/j.cgh.2019.11.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/29/2019] [Accepted: 11/17/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Many genetic variants have been associated with colorectal cancer risk, although few have been associated with survival times of patients. Identification of genetic variants associated with survival times might improve our understanding of disease progression and aid in outcome prediction. We performed a genome-wide association study to identify variants associated with colon cancer survival time. METHODS We performed a post hoc analysis of data from NCCTG N0147 (Alliance), a randomized phase 3 trial of patients with resected stage III colon cancer, and from NSABP C-08 (NRG), a phase 3 trial that compared therapy regimens for patients with resected stage II or III colon cancer. Genotype analyses were performed on DNA from blood samples from 4974 patients. We used Cox proportional hazards regression to evaluate the association of each single nucleotide polymorphism with times of overall survival and disease-free survival, adjusting for age at diagnosis, sex, treatment group, and principal components of genetic ancestry. We performed the analysis for studies N0147 and C-08 separately, and results were combined in a fixed-effects meta-analysis. RESULTS A locus on chromosome 7p15.2 was significantly associated with overall survival time (P ≤ 5x10-08). The most significant variant at this locus, rs76766811 (P = 1.6x10-08), is common among African Americans (minor allele frequency, approximately 18%) but rare in European Americans (minor allele frequency <0.1%). Within strata of self-reported ancestry, this variant was associated with times of overall survival and disease-free survival in only African Americans (hazard ratio for overall survival, 2.82; 95% CI, 1.88-4.23; P = 5.0x10-07 and hazard ratio for disease-free survival, 2.27; 95% CI, 1.62-3.18; P = 1.8x10-06). CONCLUSIONS In an analysis of data from 2 trials of patients with stage II or III colon cancer, we identified rs76766811 as a potential prognostic variant in African American patients. This finding should be confirmed in additional study populations. ClinicalTrials.gov Identifiers: NCT00096278 (NSABP C-08) and NCT00079274 (NCCTG N0147).
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Affiliation(s)
- Kathryn L Penney
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | | | - Stephanie Bien
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Xinwei Hua
- Fred Hutchinson Cancer Research Center, Seattle, Washington; University of Washington, Seattle, Washington
| | - Amanda I Phipps
- Fred Hutchinson Cancer Research Center, Seattle, Washington; University of Washington, Seattle, Washington
| | - Wei Sun
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mingyang Song
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Clinical and Translational Epidemiology Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Steven R Alberts
- Department of Health Science Research, Mayo Clinic, Rochester, Minnesota
| | - Carmen J Allegra
- University of Florida, Gainesville, Florida; NRG Oncology, Pittsburgh, Pennsylvania
| | - James Atkins
- NRG Oncology, Pittsburgh, Pennsylvania; Southeast Clinical Oncology Research (SCOR) Consortium NCORP, Winston-Salem, North Carolina
| | - Linda H Colangelo
- NRG Oncology, Pittsburgh, Pennsylvania; University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Thomas J George
- University of Florida, Gainesville, Florida; NRG Oncology, Pittsburgh, Pennsylvania
| | - Richard M Goldberg
- NRG Oncology, Pittsburgh, Pennsylvania; West Virginia University Cancer Institute, Morgantown, West Virginia
| | - Peter C Lucas
- NRG Oncology, Pittsburgh, Pennsylvania; University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Suresh G Nair
- Lehigh Valley Hospital-Cedar Crest, Allentown, Pennsylvania
| | - Qian Shi
- Department of Health Science Research, Mayo Clinic, Rochester, Minnesota; Alliance Statistics and Data Center, Mayo Clinic, Rochester, Minnesota
| | - Frank A Sinicrope
- Department of Health Science Research, Mayo Clinic, Rochester, Minnesota
| | - Norman Wolmark
- NRG Oncology, Pittsburgh, Pennsylvania; Allegheny Health Network Cancer Institute, Pittsburgh, Pennsylvania
| | - Greg Yothers
- NRG Oncology, Pittsburgh, Pennsylvania; University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ulrike Peters
- Fred Hutchinson Cancer Research Center, Seattle, Washington; University of Washington, Seattle, Washington
| | - Polly A Newcomb
- Fred Hutchinson Cancer Research Center, Seattle, Washington; University of Washington, Seattle, Washington
| | - Andrew T Chan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Clinical and Translational Epidemiology Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts; Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.
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10
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Sun J, Xu H, Qi M, Zhang C, Shi J. Identification of key genes in osteosarcoma by meta‑analysis of gene expression microarray. Mol Med Rep 2019; 20:3075-3084. [PMID: 31432118 PMCID: PMC6755242 DOI: 10.3892/mmr.2019.10543] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 06/17/2019] [Indexed: 12/17/2022] Open
Abstract
Osteosarcoma (OS) is one of the most malignant tumors in children and young adults. To better understand the underlying mechanism, five related datasets deposited in the Gene Expression Omnibus were included in the present study. The Bioconductor ‘limma’ package was used to identify differentially expressed genes (DEGs) and the ‘Weighted Gene Co-expression Network Analysis’ package was used to construct a weighted gene co-expression network to identify key modules and hub genes, associated with OS. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes overrepresentation analyses were used for functional annotation. The results indicated that 1,405 genes were dysregulated in OS, including 927 upregulated and 478 downregulated genes, when the cut off value was set at a ≥2 fold-change and an adjusted P-value of P<0.01 was used. Functional annotation of DEGs indicated that these genes were involved in the extracellular matrix (ECM) and that they function in several processes, including biological adhesion, ECM organization, cell migration and leukocyte migration. These findings suggested that dysregulation of the ECM shaped the tumor microenvironment and modulated the OS hallmark. Genes assigned to the yellow module were positively associated with OS and could contribute to the development of OS. In conclusion, the present study has identified several key genes that are potentially druggable genes or therapeutics targets in OS. Functional annotations revealed that the dysregulation of the ECM may contribute to OS development and, therefore, provided new insights to improve our understanding of the mechanisms underlying OS.
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Affiliation(s)
- Junkui Sun
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Hongen Xu
- Precision Medicine Center, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Muge Qi
- Henan Center for Disease Control and Prevention, Zhengzhou, Henan 450016, P.R. China
| | - Chi Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Jianxiang Shi
- Precision Medicine Center, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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11
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Baas J, Krens L, Bohringer S, Mol L, Punt C, Guchelaar HJ, Gelderblom H. Genome wide association study to identify predictors for severe skin toxicity in colorectal cancer patients treated with cetuximab. PLoS One 2018; 13:e0208080. [PMID: 30557370 PMCID: PMC6296548 DOI: 10.1371/journal.pone.0208080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 11/06/2018] [Indexed: 11/18/2022] Open
Abstract
EGFR-antibodies are associated with significant skin toxicity, including acneiform rash and folliculitis. It remains impossible to predict the occurrence of severe skin toxicity due to the lack of predictive markers. Here, we present the first genome-wide association study (GWAS) to find single nucleotide polymorphisms (SNPs) associated with EGFR inhibitor-induced skin toxicity using data of the multicentre randomized phase III CAIRO2 trial (clinicaltrials.gov NCT00208546). In this study, advanced or metastatic colorectal cancer patients were treated with capecitabine, oxaliplatin and bevacizumab with or without cetuximab. Germline DNA was available in 282 of the 368 patients in the cetuximab arm. Mild skin toxicity occurred in 195 patients (i.e. CTC grade 1 or 2, respectively 91 and 104 patients) and severe skin toxicity (i.e. grade 3) in 36 patients. Grade 4 skin toxicity did not occur. None of the SNPs reached the formal genome wide threshold for significance of 5x10(-8), though SNPs of at least 8 loci did show moderate association (p-value between 5x10(-7) and 5x10(-5)) with the occurrence of grade 3 (severe) skin toxicity. These SNPs did not overlap with SNPs associated with cetuximab efficacy as found in a previous GWAS in the same CAIRO2 cohort. If formally proven by replication, the SNPs associated with severe EGFR induced skin toxicity may be helpful to predict the occurrence and severity of skin toxicity in patients that will receive cetuximab and allow for adequate information on the risk of skin toxicity and prophylactic measurements.
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Affiliation(s)
- Jara Baas
- Department of Clinical Oncology, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
| | - Lisanne Krens
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Stefan Bohringer
- Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Linda Mol
- Clinical Trial Department, Comprehensive cancer center The Netherlands, Nijmegen, The Netherlands
| | - Cornelis Punt
- Department of Medical Oncology, Academic Medical Center Amsterdam, Amsterdam, The Netherlands
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Gelderblom
- Department of Clinical Oncology, Leiden University Medical Center, Leiden, The Netherlands
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12
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Theodoratou E, Farrington SM, Timofeeva M, Din FV, Svinti V, Tenesa A, Liu T, Lindblom A, Gallinger S, Campbell H, Dunlop MG. Genome-wide scan of the effect of common nsSNPs on colorectal cancer survival outcome. Br J Cancer 2018; 119:988-993. [PMID: 30135471 PMCID: PMC6203849 DOI: 10.1038/s41416-018-0117-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/16/2018] [Accepted: 04/20/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND We conducted a genome-wide scan to identify non-synonymous SNPs (nsSNPs) that might influence survival after a diagnosis of colorectal cancer (CRC). METHODS We genotyped 7679 nsSNPs in 1939 Scottish patients from the Scottish Colorectal Cancer Study recruited soon after a CRC diagnosis and prospectively followed for survival outcomes. All-cause and CRC-specific survival analyses were conducted using Cox proportional hazard models adjusted for stage, age and sex for all cancer cases, after cancer type stratification and assuming additive and recessive models of inheritance. For all the SNPs that had a p-value < 0.10 a meta-analysis was performed combining the results of the discovery set and a replication set of 899 Scottish CRC patients. The p-value threshold of significance was set as at p < 10-8. RESULTS 897 and 894 nsSNPs were associated with all-cause and CRC-specific mortality, respectively, at a p-value level < 0.10 in the discovery set. Meta-analysis of the results from the discovery and replication sets was performed overall and for cancers of colon and rectum separately and none of the variants reached a p-value < 10-8. CONCLUSIONS This large scale well-powered analysis demonstrates that common nsSNPs are not associated with CRC prognosis overall.
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Affiliation(s)
- Evropi Theodoratou
- Centre of Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Susan M Farrington
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Maria Timofeeva
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Farhat Vn Din
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Albert Tenesa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Tao Liu
- Department of Molecular Medicine and Surgery, Karolinska Institute and Department of Clinical Genetics, Karolinska University Hospital, Solna, SE-17176, Stockholm, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institute and Department of Clinical Genetics, Karolinska University Hospital, Solna, SE-17176, Stockholm, Sweden
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Harry Campbell
- Centre of Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, EH4 2XU, UK.
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