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McKay L, Petrelli B, Pind M, Reynolds JN, Wintle RF, Chudley AE, Drögemöller B, Fainsod A, Scherer SW, Hanlon-Dearman A, Hicks GG. Risk and Resilience Variants in the Retinoic Acid Metabolic and Developmental Pathways Associated with Risk of FASD Outcomes. Biomolecules 2024; 14:569. [PMID: 38785976 PMCID: PMC11117505 DOI: 10.3390/biom14050569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Fetal Alcohol Spectrum Disorder (FASD) is a common neurodevelopmental disorder that affects an estimated 2-5% of North Americans. FASD is induced by prenatal alcohol exposure (PAE) during pregnancy and while there is a clear genetic contribution, few genetic factors are currently identified or understood. In this study, using a candidate gene approach, we performed a genetic variant analysis of retinoic acid (RA) metabolic and developmental signaling pathway genes on whole exome sequencing data of 23 FASD-diagnosed individuals. We found risk and resilience alleles in ADH and ALDH genes known to normally be involved in alcohol detoxification at the expense of RA production, causing RA deficiency, following PAE. Risk and resilience variants were also identified in RA-regulated developmental pathway genes, especially in SHH and WNT pathways. Notably, we also identified significant variants in the causative genes of rare neurodevelopmental disorders sharing comorbidities with FASD, including STRA6 (Matthew-Wood), SOX9 (Campomelic Dysplasia), FDG1 (Aarskog), and 22q11.2 deletion syndrome (TBX1). Although this is a small exploratory study, the findings support PAE-induced RA deficiency as a major etiology underlying FASD and suggest risk and resilience variants may be suitable biomarkers to determine the risk of FASD outcomes following PAE.
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Affiliation(s)
- Leo McKay
- Department of Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Berardino Petrelli
- Department of Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Molly Pind
- Department of Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - James N. Reynolds
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 2V7, Canada
| | - Richard F. Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Albert E. Chudley
- Department of Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Pediatrics and Child Health, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
| | - Britt Drögemöller
- Department of Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Paul Albrechtsen Research Institute CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
- Children’s Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Centre on Aging, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Abraham Fainsod
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, P.O. Box 12271, Jerusalem 9112102, Israel
| | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, ON M5G 1L7, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ana Hanlon-Dearman
- Department of Pediatrics and Child Health, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
| | - Geoffrey G. Hicks
- Department of Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Paul Albrechtsen Research Institute CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
- Children’s Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada
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Furrer D, Dragic D, Chang SL, Fournier F, Droit A, Jacob S, Diorio C. Association between genome-wide epigenetic and genetic alterations in breast cancer tissue and response to HER2-targeted therapies in HER2-positive breast cancer patients: new findings and a systematic review. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:995-1015. [PMID: 36627894 PMCID: PMC9771759 DOI: 10.20517/cdr.2022.63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/25/2022] [Accepted: 10/08/2022] [Indexed: 01/12/2023]
Abstract
Recent evidence suggests that genetic and epigenetic mechanisms might be associated with acquired resistance to cancer therapies. The aim of this study was to assess the association of genome-wide genetic and epigenetic alterations with the response to anti-HER2 agents in HER2-positive breast cancer patients. PubMed was screened for articles published until March 2021 on observational studies investigating the association of genome-wide genetic and epigenetic alterations, measured in breast cancer tissues or blood, with the response to targeted treatment in HER2-positive breast cancer patients. Sixteen studies were included in the review along with ours, in which we compared the genome-wide DNA methylation pattern in breast tumor tissues of patients who acquired resistance to treatment (case group, n = 6) to that of patients who did not develop resistance (control group, n = 6). Among genes identified as differentially methylated between the breast cancer tissue of cases and controls, one of them, PRKACA, was also reported as differentially expressed in two studies included in the review. Although included studies were heterogeneous in terms of methodology and study population, our review suggests that genes of the PI3K pathway may play an important role in developing resistance to anti-HER2 agents in breast cancer patients. Genome-wide genetic and epigenetic alterations measured in breast cancer tissue or blood might be promising markers of resistance to anti-HER2 agents in HER2-positive breast cancer patients. Further studies are needed to confirm these data.
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Affiliation(s)
- Daniela Furrer
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine sociale et préventive, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Dzevka Dragic
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine sociale et préventive, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada.,Université Paris-Saclay, UVSQ, Inserm, CESP U1018, Exposome and Heredity Team, Gustave Roussy, Villejuif 94807, France
| | - Sue-Ling Chang
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada
| | - Frédéric Fournier
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine moléculaire, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Arnaud Droit
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine moléculaire, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Simon Jacob
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de biologie moléculaire, de biochimie médicale et de pathologie, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada.,Centre des Maladies du Sein, Hôpital du Saint-Sacrement, Québec, QC G1S 4L8, Canada
| | - Caroline Diorio
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine sociale et préventive, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada.,Centre des Maladies du Sein, Hôpital du Saint-Sacrement, Québec, QC G1S 4L8, Canada.,Correspondence to: Prof. Caroline Diorio, Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, 1050 chemin Ste-Foy, Québec, QC G1S 4L8, Canada. E-mail:
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Botticelli A, Pomati G, Marchetti P. Target therapy in cancer treatment. Nucl Med Mol Imaging 2022. [DOI: 10.1016/b978-0-12-822960-6.00152-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Alimardani M, Moghbeli M, Rastgar-Moghadam A, Shandiz FH, Abbaszadegan MR. Single nucleotide polymorphisms as the efficient prognostic markers in breast cancer. Curr Cancer Drug Targets 2021; 21:768-793. [PMID: 34036920 DOI: 10.2174/1568009621666210525151846] [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: 10/24/2020] [Revised: 03/15/2021] [Accepted: 04/19/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Breast cancer (BC) is known as the most common malignancy in women. Environmental and genetic factors are associated with BC progression. Genetic polymorphisms have been reported as important risk factors of BC prognosis and drug response. Main body: Therefore, in the present review, we have summarized all single nucleotide polymorphisms (SNPs) which have been significantly associated with drug response in BC patients around the world. We have also categorized the reported SNPs based on their related genes functions to clarify the molecular biology of drug responses in BC. CONCLUSION The majority of SNPs were reported in detoxifying enzymes, which introduced such genes as the main genetic risk factors during BC drug responses. This review paves the way for introducing a prognostic panel of SNPs for the BC patients in the world.
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Affiliation(s)
- Maliheh Alimardani
- Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Azam Rastgar-Moghadam
- Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Homaei Shandiz
- Department of Radiotherapy/Oncology, Omid Hospital, Mashhad University of Medical Science, Mashhad, Iran
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Abstract
Since the discovery that DNA alterations initiate tumorigenesis, scientists and clinicians have been exploring ways to counter these changes with targeted therapeutics. The sequencing of tumor DNA was initially limited to highly actionable hot spots-areas of the genome that are frequently altered and have an approved matched therapy in a specific tumor type. Large-scale genome sequencing programs quickly developed technological improvements that enabled the deployment of whole-exome and whole-genome sequencing technologies at scale for pristine sample materials in research environments. However, the turning point for precision medicine in oncology was the innovations in clinical laboratories that improved turnaround time, depth of coverage, and the ability to reliably sequence archived, clinically available samples. Today, tumor genome sequencing no longer suffers from significant technical or financial hurdles, and the next opportunity for improvement lies in the optimal utilization of the technologies and data for many different tumor types.
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Affiliation(s)
- Kenna R Mills Shaw
- Khalifa Bin Zayed Institute for Personalized Cancer Therapy and Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;
| | - Anirban Maitra
- Khalifa Bin Zayed Institute for Personalized Cancer Therapy and Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;
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Anoushirvani AA, Aghabozorgi R, Ahmadi A, Arjomandzadegan M, Sahraei M, Khalili S, Fereydouni T, Khademi Z. Association of rs1042522 SNP with Clinicopathologic Factors of Breast Cancer Patients in the Markazi Province of Iran. Open Access Maced J Med Sci 2018; 6:2277-2282. [PMID: 30607176 PMCID: PMC6311483 DOI: 10.3889/oamjms.2018.486] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/13/2018] [Accepted: 10/14/2018] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND: The nucleotide changes in different genetic loci increased the incidence risk of breast cancer. AIM: The aim of present study was to investigate genotype distribution at codon 72 of the TP53 gene (rs1042522) in breast cancer patients to achieve a potential diagnostic marker related to some demographic feathers. METHODS: In our case-control study, blood samples were collected from a total of 34 patients harboured breast cancer. DNA was extracted, and nested-PCR was performed. Products were digested with AccII and subsequently were sequenced. Results were compared with samples characteristics. RESULTS: The PCR results indicated the correct implementation of extraction and amplification protocol. The genotypic distribution at codon 72 of TP53 in control group was 20%, 62.4% and 16.6% for Arg (wildtype), Arg/Pro (heterozygous) and Pro (homozygous variant) respectively. Also, this distribution in the patient group was 23.52% homozygous, 50% heterozygous, and 26.47% another homozygous variant (Adjusted odds ratio: 1.12 and 95%CI = 0.57 to 2.2, P = 0.03). The absence of Arg at codon 72 of TP53 is relevant with age higher than 40 years and metastasis to other organs. CONCLUSION: Polymorphism at codon 72 of TP53 was associated with high-grades of breast cancer risk and different responses to chemotherapy treatment. It is recommended genotype distribution of codon 72 of TP53 before chemotherapy.
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Affiliation(s)
- Ali Arash Anoushirvani
- Khansari Hospital and Department of Internal Medicine, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Reza Aghabozorgi
- Khansari Hospital and Department of Internal Medicine, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Azam Ahmadi
- Infectious Diseases Research Center (IDRC), Arak University of Medical Sciences, Arak, Iran
| | | | - Maryam Sahraei
- Infectious Diseases Research Center (IDRC), Arak University of Medical Sciences, Arak, Iran
| | - Sara Khalili
- Infectious Diseases Research Center (IDRC), Arak University of Medical Sciences, Arak, Iran
| | - Taha Fereydouni
- Infectious Diseases Research Center (IDRC), Arak University of Medical Sciences, Arak, Iran
| | - Zoha Khademi
- Infectious Diseases Research Center (IDRC), Arak University of Medical Sciences, Arak, Iran
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Germline single nucleotide polymorphisms in ERBB3 and BARD1 genes result in a worse relapse free survival response for HER2-positive breast cancer patients treated with adjuvant based docetaxel, carboplatin and trastuzumab (TCH). PLoS One 2018; 13:e0200996. [PMID: 30071039 PMCID: PMC6071997 DOI: 10.1371/journal.pone.0200996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/06/2018] [Indexed: 12/30/2022] Open
Abstract
Breast cancer is the leading cause of cancer related deaths in women worldwide and is classified into subtypes based on the cancer’s receptor status. Of these subtypes, those expressing the human epidermal growth factor receptor 2 (HER2) receptor were traditionally associated with poor prognosis. Several advances have been made in the treatment of HER2-positive breast cancer, yet issues of resistance and poor response to therapy remains prevalent. In this study we explored the impact of HER-family and homologous recombination deficiency SNPs on response to patients who received TCH-based (docetaxel (T), carboplatin (C), and trastuzumab (H)) treatment versus those who received other treatment regimens. Using Cox regression analysis, we identified 6 SNPs that correlate with recurrence free survival in our patients and supported our findings using support vector machines. We also used reverse phase protein array analysis to examine the impact ERBB3 SNPs may have on both the PI3K/AKT and MAPK/ERK signaling pathways. Finally, using cell line models, we correlated SNP status with sensitivity to platinum based drugs and docetaxel. We found that patients on a TCH based regimen with the minor allele of the ERBB3 (rs2229046 and rs773123) and BARD1 (rs2070096) SNPs, were significantly more likely to relapse than those women who were not. Additionally, we observed that patients with these ERBB3 SNPs had shown elevated protein expression/phosphorylation of Src kinase, c-MET (Y1234/1235), GSK-3β (S9) and p27, indicating that these SNPs are associated with non-PI3K/AKT signaling. Finally, using cell line models, we demonstrate that the BARD1 SNP (rs2229571) is associated with greater sensitivity to both carboplatin and cisplatin. The BARD1 and ERBB3 SNPs can potentially be used to determine those patients that will have a worse response to TCH based treatment, an effect that may arise from the SNPs impact on altered cellular signaling.
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Zeng F, Fu J, Hu F, Tang Y, Fang X, Zeng F, Chu Y. Identification of key pathways and genes in response to trastuzumab treatment in breast cancer using bioinformatics analysis. Oncotarget 2018; 9:32149-32160. [PMID: 30181805 PMCID: PMC6114942 DOI: 10.18632/oncotarget.24605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/25/2018] [Indexed: 01/06/2023] Open
Abstract
Breast cancer (BC) is one of the leading causes of death among women worldwide. The gene expression profile GSE22358 was downloaded from the Gene Expression Omnibus (GEO) database, which included 154 operable early-stage breast cancer samples treated with neoadjuvant capecitabine plus docetaxel, with (34) or without trastuzumab (120), to identify gene signatures during trastuzumab treatment and uncover their potential mechanisms. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed, and a protein–protein interaction (PPI) network of the differentially expressed genes (DEGs) was constructed by Cytoscape software. There were 2284 DEGs, including 1231 up-regulated genes enriched in DNA replication, protein N-linked glycosylation via asparagine, and response to toxic substances, while 1053 down-regulated genes were enriched in axon guidance, protein localization to plasma membrane, protein stabilization, and protein glycosylation. Eight hub genes were identified from the PPI network, including GSK3B, RAC1, PXN, ERBB2, HSP90AA1, FGF2, PIK3R1 and RAC2. Our experimental results showed that GSK3B was also highly expressed in breast cancer tissues and was associated with poor survival, as was β-catenin. In conclusion, the present study indicated that the identified DEGs and hub genes further our understanding of the molecular mechanisms underlying trastuzumab treatment in BC and highlighted GSK3B, which might be used as a molecular target for the treatment of BC.
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Affiliation(s)
- Fanxin Zeng
- Institute of Molecular Medicine, Peking University, Beijing, China.,Dazhou Central Hospital Clinic Medical Center, Dazhou, Sichuan, China.,Department of Oncology, Dazhou Central Hospital, Dazhou, Sichuan, China
| | - Jiangping Fu
- Dazhou Central Hospital Clinic Medical Center, Dazhou, Sichuan, China.,Department of Oncology, Dazhou Central Hospital, Dazhou, Sichuan, China
| | - Fang Hu
- Dazhou Central Hospital Clinic Medical Center, Dazhou, Sichuan, China.,Department of Oncology, Dazhou Central Hospital, Dazhou, Sichuan, China
| | - Yani Tang
- Dazhou Central Hospital Clinic Medical Center, Dazhou, Sichuan, China
| | - Xiangdong Fang
- Dazhou Central Hospital Clinic Medical Center, Dazhou, Sichuan, China.,Department of Oncology, Dazhou Central Hospital, Dazhou, Sichuan, China
| | - Fanwei Zeng
- Dazhou Central Hospital Clinic Medical Center, Dazhou, Sichuan, China
| | - Yanpeng Chu
- Dazhou Central Hospital Clinic Medical Center, Dazhou, Sichuan, China
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