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Talebizadeh Z, Shah A. The AutGO Initiative: A Conceptual Framework for Developing Genetics-Outcomes Research Hypotheses. Autism Res 2020; 13:1286-1299. [PMID: 32618145 PMCID: PMC7496490 DOI: 10.1002/aur.2331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 11/20/2022]
Abstract
The increasing emphasis on translational approaches to complex neuropsychiatric and neurodevelopmental conditions research requires scientists from a broad range of disciplines to build dynamic collaborations when formulating hypotheses and framing study designs. The need to integrate the knowledge and perspectives not only from multiple scientific silos but also from the populations impacted by these conditions presents a significant challenge to researchers, particularly for a heterogeneous condition like autism. As one path toward addressing these challenges, we have previously introduced Autism Genetics Outcomes (AutGO), an initiative to support broad stakeholder partnerships and promote a new integrated concept called GO (i.e., research approaches that draw on both genetics and clinical outcomes perspectives). Herein, we developed a workflow for collecting stakeholders' feedback toward the development of a GO hypothesis. AutGO is an evolving initiative, and here we describe how its three essential components (conceptual framework, applicability, and implementation) have been developed. As a proof‐of‐concept, the AutGO team sought to demonstrate how a GO hypothesis could be developed using a semi‐structured literature review workflow. We also developed a prototype from published reports and formulated a GO hypothesis for autism. Rather than seeking community stakeholder input after a research project is conceptualized and designed, the developed conceptual framework demonstrates the feasibility of formulating scientific hypotheses by engaging stakeholders in retrospective semi‐structured literature reviews. The presented workflow, prototype, and discussed recommendations will bring awareness in the autism research community about the benefits of applying the GO approach in order to promote translational aspects in genetics research. Lay Summary We used a community‐based engagement approach to develop AutGO (Autism Genetics Outcomes), an initiative to establish stakeholder partnerships and to promote research approaches (we refer to as GO) that draw on both genetics and clinical outcomes perspectives. Specifically, we developed a conceptual framework that includes a literature review process for developing GO hypotheses and stakeholder feedback collection protocol. Our work will bring awareness in the autism research community about the benefits of integrating patient perspectives in genetics research. Autism Res 2020, 13: 1286–1299. © 2020 The Authors. Autism Research published by International Society for Autism Research published by Wiley Periodicals LLC.
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Affiliation(s)
- Zohreh Talebizadeh
- Children's Mercy Hospital, Kansas City, MO, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Ayten Shah
- Children's Mercy Hospital, Kansas City, MO, USA
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Yang Z, Liu Z. Potentially functional variants of autophagy-related genes are associated with the efficacy and toxicity of radiotherapy in patients with nasopharyngeal carcinoma. Mol Genet Genomic Med 2019; 7:e1030. [PMID: 31692259 PMCID: PMC6900379 DOI: 10.1002/mgg3.1030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 12/11/2022] Open
Abstract
Background Nasopharyngeal carcinoma (NPC) is one of the major invasive malignant neoplasms of head and neck, while radiotherapy is the primary therapy for NPC. Genetic variants could affect the efficacy and toxicities of radiotherapy in NPC patients. Methods In the current study, we aimed to investigate 10 potentially functional SNPs of autophagy‐related genes (ATG) with the efficacy and toxicity of radiotherapy in 468 NPC patients. Results We found ATG10 rs10514231, rs1864183, and rs4703533 were significantly associated with worse efficacy of radiotherapy at both at the primary tumor and lymph node, while ATG16L2 rs10898880 was significantly associated with better efficacy of radiotherapy at both primary tumor and lymph node. Besides, we also found ATG10 rs10514231 and ATG16L2 rs10898880 were significantly associated with the occurrence of grade 3–4 oral mucositis (allelic model, for rs10514231: OR = 1.95, 95% CIs = 1.31–2.9, p = .001; for rs10898880: OR = 1.56, 95% CIs = 1.19–2.04, p = .001) and grade 3–4 myelosuppression (allelic model, for rs10514231: OR = 2.08, 95% CIs = 1.39–3.09, p < .001; for rs10898880: OR = 1.51, 95% CIs = 1.1–2.06, p = .010). Conclusions This should be the first report identifying ATG10 rs10514231, rs1864183, rs4703533, and ATG16L2 rs10898880 could contribute to the efficacy and toxicity of radiotherapy in NPC patients. Further investigation of the underlying molecular mechanisms and prospective clinical trials in NPC patients are needed to validate our results.
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Affiliation(s)
- Zhiguang Yang
- Department of Nuclear medicine, Shengjing Hospital Affiliated to China Medical University, Shenyang, China
| | - Zhaoyu Liu
- Department of Radiology, Shengjing Hospital Affiliated to China Medical University, Shenyang, China
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Domínguez ER, Orona J, Lin K, Pérez CJ, Benavides F, Kusewitt DF, Johnson DG. The p53 R72P polymorphism does not affect the physiological response to ionizing radiation in a mouse model. Cell Cycle 2017; 16:1153-1163. [PMID: 28594296 DOI: 10.1080/15384101.2017.1312234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Tissue culture and mouse model studies show that the presence of the arginine (R) or proline (P) coding single nucleotide polymorphism (SNP) of the tumor suppressor gene p53 at codon 72 (p53 R72P) differentially affects the responses to genotoxic insult. Compared to the P variant, the R variant shows increased apoptosis in most cell cultures and mouse model tissues in response to genotoxins, and epidemiological studies suggest that the R variant may enhance cancer survival and reduce the risks of adverse reactions to genotoxic cancer treatment. As ionizing radiation (IR) treatment is often used in cancer therapy, we sought to test the physiological effects of IR in mouse models of the p53 R72P polymorphism. By performing blood counts, immunohistochemical (IHC) staining and survival studies in mouse populations rigorously controlled for strain background, sex and age, we discovered that p53 R72P polymorphism did not differentially affect the physiological response to IR. Our findings suggest that genotyping for this polymorphism to personalize IR therapy may have little clinical utility.
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Affiliation(s)
- Emily R Domínguez
- a Department of Epigenetics and Molecular Carcinogenesis , The University of Texas MD Anderson Cancer Center , Smithville , TX , USA
| | - Jennifer Orona
- a Department of Epigenetics and Molecular Carcinogenesis , The University of Texas MD Anderson Cancer Center , Smithville , TX , USA
| | - Kevin Lin
- a Department of Epigenetics and Molecular Carcinogenesis , The University of Texas MD Anderson Cancer Center , Smithville , TX , USA
| | - Carlos J Pérez
- a Department of Epigenetics and Molecular Carcinogenesis , The University of Texas MD Anderson Cancer Center , Smithville , TX , USA
| | - Fernando Benavides
- a Department of Epigenetics and Molecular Carcinogenesis , The University of Texas MD Anderson Cancer Center , Smithville , TX , USA
| | - Donna F Kusewitt
- b Department of Pathology , The University of Mexico School of Medicine , Albuquerque , NM , USA
| | - David G Johnson
- a Department of Epigenetics and Molecular Carcinogenesis , The University of Texas MD Anderson Cancer Center , Smithville , TX , USA
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Ma WL, Liu R, Huang LH, Zou C, Huang J, Wang J, Chen SJ, Meng XG, Yang JK, Li H, Yang GP, Guo CX. Impact of polymorphisms in angiogenesis-related genes on clinical outcomes of radiotherapy in patients with nasopharyngeal carcinoma. Clin Exp Pharmacol Physiol 2017; 44:539-548. [PMID: 28199751 DOI: 10.1111/1440-1681.12738] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/20/2017] [Accepted: 01/26/2017] [Indexed: 12/01/2022]
Affiliation(s)
- Wan-Le Ma
- Centre of Clinical Pharmacology; the Third Xiangya Hospital; Central South University; Changsha Hunan China
| | - Rong Liu
- Department of Clinical Pharmacology; Xiangya Hospital; Central South University; Changsha Hunan China
| | - Li-Hua Huang
- Centre of Clinical Pharmacology; the Third Xiangya Hospital; Central South University; Changsha Hunan China
| | - Chan Zou
- Centre of Clinical Pharmacology; the Third Xiangya Hospital; Central South University; Changsha Hunan China
| | - Jie Huang
- Centre of Clinical Pharmacology; the Third Xiangya Hospital; Central South University; Changsha Hunan China
| | - Jing Wang
- Jiangxi Province Tumour Hospital; Nanchang Jiangxi China
| | - Shao-Jun Chen
- Department of Oncology; Fourth Affiliated Hospital; Guangxi Medical University; Liuzhou Guangxi China
| | - Xiang-Guang Meng
- Laboratory of Cardiovascular Disease and Drug Research; Zhengzhou No. 7 People's Hospital; Zhengzhou Henan China
| | - Jing-Ke Yang
- Department of Haematology; Affiliated Cancer Hospital; Zhengzhou University; Zhengzhou Henan China
| | - Han Li
- Zhang Zhongjing College of Chinese Medicine; Nanyang Institute of Technology; Nanyang Henan China
| | - Guo-Ping Yang
- Centre of Clinical Pharmacology; the Third Xiangya Hospital; Central South University; Changsha Hunan China
| | - Cheng-Xian Guo
- Centre of Clinical Pharmacology; the Third Xiangya Hospital; Central South University; Changsha Hunan China
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Association of p53 codon72 Arg>Pro polymorphism with susceptibility to nasopharyngeal carcinoma: evidence from a case-control study and meta-analysis. Oncogenesis 2016; 5:e225. [PMID: 27159678 PMCID: PMC4945748 DOI: 10.1038/oncsis.2016.31] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 12/24/2016] [Accepted: 01/26/2016] [Indexed: 12/28/2022] Open
Abstract
Tumor suppressor p53 is a critical player in the fight against cancer as it controls the cell cycle check point, apoptotic pathways and genomic stability. It is known to be the most frequently mutated gene in a wide variety of human cancers. Single-nucleotide polymorphism of p53 at codon72 leading to substitution of proline (Pro) in place of arginine (Arg) has been identified as a risk factor for development of many cancers, including nasopharyngeal carcinoma (NPC). However, the association of this polymorphism with NPC across the published literature has shown conflicting results. We aimed to conduct a case–control study for a possible relation of p53 codon72 Arg>Pro polymorphism with NPC risk in underdeveloped states of India, combine the result with previously available records from different databases and perform a meta-analysis to draw a more definitive conclusion. A total of 70 NPC patients and 70 healthy controls were enrolled from different hospitals of north-eastern India. The p53 codon72 Arg>Pro polymorphism was typed by polymerase chain reaction, which showed an association with NPC risk. In the meta-analysis consisting of 1842 cases and 2330 controls, it was found that individuals carrying the Pro allele and the ProPro genotype were at a significantly higher risk for NPC as compared with those with the Arg allele and the ArgArg genotype, respectively. Individuals with a ProPro genotype and a combined Pro genotype (ProPro+ArgPro) also showed a significantly higher risk for NPC over a wild homozygote ArgArg genotype. Additionally, the strength of each study was tested by power analysis and genotype distribution by Hardy–Weinberg equilibrium. The outcome of the study indicated that both allele frequency and genotype distribution of p53 codon72 Arg>Pro polymorphism were significantly associated with NPC risk. Stratified analyses based on ethnicity and source of samples supported the above result.
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Zhuo X, Ye H, Li Q, Xiang Z, Zhang X. Is MDM2 SNP309 Variation a Risk Factor for Head and Neck Carcinoma?: An Updated Meta-Analysis Based on 11,552 Individuals. Medicine (Baltimore) 2016; 95:e2948. [PMID: 26945408 PMCID: PMC4782892 DOI: 10.1097/md.0000000000002948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Murine double minute-2 (MDM2) is a negative regulator of P53, and its T309G polymorphism has been suggested as a risk factor for a variety of cancers. Increasing evidence has shown the association of MDM2 T309G polymorphism with head and neck carcinoma (HNC) risk. However, the results are inconsistent. Thus, we performed a meta-analysis to elucidate the association. The meta-analysis retrieved studies published up to August 2015, and essential information was extracted for analysis. Separate analyses on ethnicity, source of controls, sample size, detection method, and cancer types were also conducted. Odds ratios (ORs) and their 95% confidence intervals (CIs) were used to estimate the association. Pooled data from 16 case-control studies including 4625 cases and 6927 controls failed to indicate a significant association. However, in the subgroup analysis of sample sizes, an increased risk was observed in the largest sample size group (>1000) under a recessive model (OR = 1.52; 95% CI = 1.08-2.13). Increased risks were also found in the nasopharyngeal cancer in the subgroup analysis of cancer types (GG vs TT: OR = 2.07; 95% CI = 1.38-3.12; dominant model: OR = 1.48; 95% CI = 1.13-1.93; recessive model: OR = 1.76; 95% CI = 1.17-2.65). The results suggest that homozygote GG alleles of MDM2 SNP309 may be a low-penetrant risk factor for HNC, and G allele may confer nasopharyngeal cancer susceptibility.
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Affiliation(s)
- Xianlu Zhuo
- From the Department of Otolaryngology, Southwest Hospital, Third Military Medical University, Chongqing (XZ, QL, ZX, XZ); and Affiliated Hospital of Guiyang Medical University, Guiyang, China (XZ, HY)
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Kerns SL, West CML, Andreassen CN, Barnett GC, Bentzen SM, Burnet NG, Dekker A, De Ruysscher D, Dunning A, Parliament M, Talbot C, Vega A, Rosenstein BS. Radiogenomics: the search for genetic predictors of radiotherapy response. Future Oncol 2014; 10:2391-406. [PMID: 25525847 DOI: 10.2217/fon.14.173] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
'Radiogenomics' is the study of genetic variation associated with response to radiotherapy. Radiogenomics aims to uncover the genes and biologic pathways responsible for radiotherapy toxicity that could be targeted with radioprotective agents and; identify genetic markers that can be used in risk prediction models in the clinic. The long-term goal of the field is to develop single nucleotide polymorphism-based risk models that can be used to stratify patients to more precisely tailored radiotherapy protocols. The field has evolved over the last two decades in parallel with advances in genomics, moving from narrowly focused candidate gene studies to large, collaborative genome-wide association studies. Several confirmed genetic variants have been identified and the field is making progress toward clinical translation.
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Affiliation(s)
- Sarah L Kerns
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Long Z, Wang B, Tao D, Huang Y, Tao Z. Hypofractionated radiotherapy induces miR-34a expression and enhances apoptosis in human nasopharyngeal carcinoma cells. Int J Mol Med 2014; 34:1388-94. [PMID: 25231528 DOI: 10.3892/ijmm.2014.1937] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 09/10/2014] [Indexed: 11/05/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a relatively radiosensitive disease. However, the therapeutic effects of radiotherapy are not always satisfactory due to radioresistance. The hypofractionated schema is currently widely used in clinical practice. In the present study, we investigated the effects of hypofractionated radiotherapy on NPC cells and explored the mechanisms involved. In addition, we aimed to determine the role of miR-34a in the effects of hypofractionated radiotherapy and whether these effects occur in a p53-dependent manner. For this purpose, we used CNE1 and CNE2 NPC cells which were subjected to hyperfractionated and hypofractionated radiotherapy. The viability of the cells was measured by MTT assay and acridine orange (AO) and ethidium bromide (EB) staining was used to observe morphological changes. In addition, Annexin V-propidium iodide (PI) staining and flow cytometry were used to determine the number of apoptotic cells and mRNA and protein expression was measured by qPCR and western blot analysis, respectively. The results revealed that hypofractionated radiotherapy enhanced apoptosis and increased the expression of miR-34a and p53 in the NPC cells. In addition, it stimulated p53 promoter activity and downregulated the protein expression of c-Myc in the human NPC cells. Furthermore, the knockdown of miR-34a suppressed the growth inhibitory effects induced by hypofractionated radiotherapy. Thus, our results suggest that the enhanced apoptosis of NPC cells may be associated with the miR-34a-mediated suppression of c-Myc in a p53-dependent manner.
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Affiliation(s)
- Zhixiong Long
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Bin Wang
- Department of Otolaryngology (ENT), The Fifth Hospital of Wuhan, Wuhan, Hubei 430051, P.R. China
| | - Dan Tao
- Department of Oncology, The Fifth Hospital of Wuhan, Wuhan, Hubei 430051, P.R. China
| | - Ying Huang
- Department of Oncology, The Fifth Hospital of Wuhan, Wuhan, Hubei 430051, P.R. China
| | - Zezhang Tao
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
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