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Yari K, Hakimi A, Mohammadi M, Ammari-Allahyari M, Salari N, Ghasemi H. The Association of PTEN Gene Mutations with the Breast Cancer Risk: A Systematic Review and Meta-analysis. Biochem Genet 2024; 62:1617-1635. [PMID: 37658255 DOI: 10.1007/s10528-023-10464-z] [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: 12/06/2022] [Accepted: 07/18/2023] [Indexed: 09/03/2023]
Abstract
Breast cancer (BC) is the most common malignancy in women in western countries. A significant part of malignant cases is caused by genetic mutation. Mutations in the gene phosphatase and tensin homologue deleted on chromosome (PTEN) have been proven in various malignancies. The present study was conducted with the aim of investigating the prevalence of BC due to PTEN gene mutation, as well as estimating the chance of developing BC due to the occurrence of PTEN gene mutation. The present study was conducted using a systematic review method based on PRISMA 2020 statements. The search was done in PubMed, Web of Science (WOS), Scopus, and direct scientific databases. The search was performed using the keywords breast cancer, breast malignancy, PTEN, polymorphism, mutation, variant, and their equivalents. Statistical analysis was performed using the second version of Comprehensive Meta-Analysis Software. A total of 2138 articles were collected. After removing duplicate articles, checking the title and abstract, and then checking the full text of the documents, finally 64 articles were approved and entered the systematic review process. Analysis of these studies with a sample size of 231,179 showed the prevalence of breast cancer patients with PTEN mutations. The combined results of 64 studies showed that the prevalence of PTEN mutations has a 3.3 (95% CI 2.2-5) in BC patients, and an analysis of 6 studies showed that the odds ratio of developing BC due to PTEN mutation is 3.7 (95% CI 1.1-11.9). The results of this study show that mutation in the PTEN gene increases the chance of developing BC. However, it was found that a small part of patients gets BC due to the occurrence of mutation in this gene.
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Affiliation(s)
- Kheirollah Yari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Hakimi
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Masoud Mohammadi
- Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran
| | | | - Nader Salari
- Department of Biostatistics, School of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Sleep Disorders Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Hooman Ghasemi
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Ahmad H, Ali A, Khalil AT, Ali R, Khan I, Khan MM, Ahmed I, Basharat Z, Alorini M, Mehmood A. Clinico-genomic findings, molecular docking, and mutational spectrum in an understudied population with breast cancer patients from KP, Pakistan. Front Genet 2024; 15:1383284. [PMID: 38784039 PMCID: PMC11111998 DOI: 10.3389/fgene.2024.1383284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/03/2024] [Indexed: 05/25/2024] Open
Abstract
In this study, we report the mutational profiles, pathogenicity, and their association with different clinicopathologic and sociogenetic factors in patients with Pashtun ethnicity for the first time. A total of 19 FFPE blocks of invasive ductal carcinoma (IDC) from the Breast Cancer (BC) tissue and 6 normal FFPE blocks were analyzed by whole-exome sequencing (WES). Various somatic and germline mutations were identified in cancer-related genes, i.e., ATM, CHEK2, PALB2, and XRCC2. Among a total of 18 mutations, 14 mutations were somatic and 4 were germline. The ATM gene exhibited the maximum number of mutations (11/18), followed by CHEK2 (3/18), PALB2 (3/18), and XRCC2 (1/18). Except one frameshift deletion, all other 17 mutations were nonsynonymous single-nucleotide variants (SNVs). SIFT prediction revealed 7/18 (38.8%) mutations as deleterious. PolyPhen-2 and MutationTaster identified 5/18 (27.7%) mutations as probably damaging and 10/18 (55.5%) mutations as disease-causing, respectively. Mutations like PALB2 p.Q559R (6/19; 31.5%), XRCC2 p.R188H (5/19; 26.31%), and ATM p.D1853N (4/19; 21.05%) were recurrent mutations and proposed to have a biomarker potential. The protein network prediction was performed using GeneMANIA and STRING. ISPRED-SEQ indicated three interaction site mutations which were further used for molecular dynamic simulation. An average increase in the radius of gyration was observed in all three mutated proteins revealing their perturbed folding behavior. Obtained SNVs were further correlated with various parameters related to the clinicopathological status of the tumors. Three mutation positions (ATM p. D1853N, CHEK2 p.M314I, and PALB2 p.T1029S) were found to be highly conserved. Finally, the wild- and mutant-type proteins were screened for two drugs: elagolix (DrugBank ID: DB11979) and LTS0102038 (a triterpenoid, isolated from the anticancer medicinal plant Fagonia indica). Comparatively, a higher number of interactions were noted for normal ATM with both compounds, as compared to mutants.
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Affiliation(s)
- Hilal Ahmad
- Institute of Basic Medical Sciences (IBMS), Khyber Medical University, Peshawar, Pakistan
| | - Asif Ali
- Institute of Pathology and Diagnostic Medicine (IPDM), Khyber Medical University, Peshawar, Pakistan
- College of Medicine, Gulf Medical University, Ajman, United Arab Emirates
- School of Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Ali Talha Khalil
- Department of Pathology, Lady Reading Hospital Medical Teaching Institution, Peshawar, Pakistan
| | - Roshan Ali
- Institute of Basic Medical Sciences (IBMS), Khyber Medical University, Peshawar, Pakistan
| | - Ishaq Khan
- Institute of Basic Medical Sciences (IBMS), Khyber Medical University, Peshawar, Pakistan
| | - Mah Muneer Khan
- Department of Surgery, Khyber Teaching Hospital, Medical Teaching Institution, Peshawar, Pakistan
| | - Ibrar Ahmed
- Alpha Genomics (Private) Limited, Islamabad, Pakistan
- Microbiological Analysis Team, Group for Biometrology, The Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
| | | | - Mohammed Alorini
- Department of Pathology, College of Medicine, Qassim University, Unaizah, Saudi Arabia
| | - Amna Mehmood
- Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
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Ahmad H, Ali A, Ali R, Khalil AT, Khan I, Khan MM, Alorini M. Mutational Landscape and In-Silico Analysis of TP53, PIK3CA, and PTEN in Patients with Breast Cancer from Khyber Pakhtunkhwa. ACS OMEGA 2023; 8:43318-43331. [PMID: 38024667 PMCID: PMC10652387 DOI: 10.1021/acsomega.3c07472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
Herein, we report the mutational spectrum of three breast cancer candidate genes (TP53, PIK3CA, and PTEN) using WES for identifying potential biomarkers. The WES data were thoroughly analyzed using SAMtools for variant calling and identification of the mutations. Various bioinformatic tools (SIFT, PolyPhen-2, Mutation Taster, ISPRED-SEQ, SAAFEQ-SEQ, ConSurf, PROCHECK etc.) were used to determine the pathogenicity and nature of the SNVs. Selected interaction site (IS) mutations were visualized in PyMOL after building 3D structures in Swiss-Model. Ramachandran plots were generated by using the PROCHECK server. The selected IS mutations were subjected to molecular dynamic simulation (MDS) studies using Gromacs 4.5. STRING and GeneMANIA were used for the prediction of gene-gene interactions and pathways. Our results revealed that the luminal A molecular subtype of the breast cancer was most common, whereas a high percentage of was Her2 negatives. Moreover, the somatic mutations were more common as compared to the germline mutations in TP53, PIK3CA, and PTEN. 20% of the identified mutations are reported for the first time from Khyber Pakhtunkhwa. In the enrolled cohort, 23 mutations were nonsynonymous SNVs. The frequency of mutations was the highest in PIK3CA, followed by TP53 and PTEN. A total of 13 mutations were found to be highly pathogenic. Four novel mutations were identified on PIK3CA and one each on PTEN and TP53. SAAFEQ-SEQ predicted the destabilizing effect for all mutations. ISPRED-SEQ predicted 9 IS mutations (6 on TP53 and 3 on PIK3CA), whereas no IS mutation was predicted on PTEN. The TP53 IS mutations were TP53R43H, TP53Y73X, TP53K93Q, TP53K93R, TP53D149E, and TP53Q199X; whereas for PIK3CA, the IS mutations were PIK3CAL156V, PIK3CAM610K, and PIK3CAH1047R. Analysis from the ConSurf Web server revealed five SNVs with a highly conserved status (conservation score 9) across TP53 and PTEN. TP53P33R was found predominant in the grade 3 tumors, whereas PTENp.C65S was distributed on ER+, ER-, PR+, PR-, Her2+, and Her2- patients. TP53p.P33R mutation was found to be recurring in the 14/19 (73.6%) patients and, therefore, can be considered as a potential biomarker. Finally, these mutations were studied in the context of their potential association with different hormonal and social factors.
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Affiliation(s)
- Hilal Ahmad
- Institute
of Basic Medical Sciences Khyber Medical University, Khyber Medical University, Phase V, Peshawar 25000, Pakistan
| | - Asif Ali
- Institute
of Basic Medical Sciences Khyber Medical University, Khyber Medical University, Phase V, Peshawar, Peshawar 25000, Pakistan
- College
of Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates
- School
of Medicine, University of Glasgow, Glasgow G12 8QQ, U.K.
| | - Roshan Ali
- Institute
of Basic Medical Sciences Khyber Medical University, Khyber Medical University, Phase V, Peshawar 25000, Pakistan
| | - Ali Talha Khalil
- Department
of Pathology, Lady Reading Hospital Medical
Teaching Institution (LRH-MTI), Peshawar, Khyber Pakhtunkhwa 25000, Pakistan
| | - Ishaq Khan
- Institute
of Basic Medical Sciences Khyber Medical University, Khyber Medical University, Phase V, Peshawar 25000, Pakistan
| | - Mah Muneer Khan
- General Surgery, Khyber Teaching Hospital Medical Teaching Institute, Peshawar 25000, Pakistan
| | - Mohammed Alorini
- Department
of Basic Medical Sciences, Unaizah College of Medicine and Medical
Sciences, Qassim University, Unaizah, 56219, Saudi Arabia
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Bhai P, Turowec J, Santos S, Kerkhof J, Pickard L, Foroutan A, Breadner D, Cecchini M, Levy MA, Stuart A, Welch S, Howlett C, Lin H, Sadikovic B. Molecular profiling of solid tumors by next-generation sequencing: an experience from a clinical laboratory. Front Oncol 2023; 13:1208244. [PMID: 37483495 PMCID: PMC10359709 DOI: 10.3389/fonc.2023.1208244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/05/2023] [Indexed: 07/25/2023] Open
Abstract
Background Personalized targeted therapies have transformed management of several solid tumors. Timely and accurate detection of clinically relevant genetic variants in tumor is central to the implementation of molecular targeted therapies. To facilitate precise molecular testing in solid tumors, targeted next-generation sequencing (NGS) assays have emerged as a valuable tool. In this study, we provide an overview of the technical validation, diagnostic yields, and spectrum of variants observed in 3,164 solid tumor samples that were tested as part of the standard clinical diagnostic assessment in an academic healthcare institution over a period of 2 years. Methods The Ion Ampliseq™ Cancer Hotspot Panel v2 assay (ThermoFisher) that targets ~2,800 COSMIC mutations from 50 oncogenes and tumor suppressor genes was validated, and a total of 3,164 tumor DNA samples were tested in 2 years. A total of 500 tumor samples were tested by the comprehensive panel containing all the 50 genes. Other samples, including 1,375 lung cancer, 692 colon cancer, 462 melanoma, and 135 brain cancer, were tested by tumor-specific targeted subpanels including a few clinically actionable genes. Results Of 3,164 patient samples, 2,016 (63.7%) tested positive for at least one clinically relevant variant. Of 500 samples tested by a comprehensive panel, 290 had a clinically relevant variant with TP53, KRAS, and PIK3CA being the most frequently mutated genes. The diagnostic yields in major tumor types were as follows: breast (58.4%), colorectal (77.6%), lung (60.4%), pancreatic (84.6%), endometrial (72.4%), ovary (57.1%), and thyroid (73.9%). Tumor-specific targeted subpanels also demonstrated high diagnostic yields: lung (69%), colon (61.2%), melanoma (69.7%), and brain (20.7%). Co-occurrence of mutations in more than one gene was frequently observed. Conclusions The findings of our study demonstrate the feasibility of integrating an NGS-based gene panel screen as part of a standard diagnostic protocol for solid tumor assessment. High diagnostic rates enable significant clinical impact including improved diagnosis, prognosis, and clinical management in patients with solid tumors.
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Affiliation(s)
- Pratibha Bhai
- Molecular Genetics Laboratory, London Health Sciences Centre, London, ON, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Jacob Turowec
- Molecular Genetics Laboratory, London Health Sciences Centre, London, ON, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Stephanie Santos
- Molecular Genetics Laboratory, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, London Health Sciences Centre, London, ON, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - LeeAnne Pickard
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Aidin Foroutan
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Daniel Breadner
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Matthew Cecchini
- Molecular Genetics Laboratory, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael A. Levy
- Molecular Genetics Laboratory, London Health Sciences Centre, London, ON, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, London Health Sciences Centre, London, ON, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Stephen Welch
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Christopher Howlett
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Hanxin Lin
- Molecular Genetics Laboratory, Alberta Precision Laboratories, Edmonton, AB, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, London Health Sciences Centre, London, ON, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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Chen JW, Murugesan K, Newberg JY, Sokol ES, Savage HM, Stout TJ, Maund SL, Hutchinson KE. Comparison of PIK3CA Mutation Prevalence in Breast Cancer Across Predicted Ancestry Populations. JCO Precis Oncol 2022; 6:e2200341. [PMID: 36446041 PMCID: PMC9812634 DOI: 10.1200/po.22.00341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/31/2022] [Accepted: 10/11/2022] [Indexed: 11/30/2022] Open
Abstract
PURPOSE Understanding the differences in biomarker prevalence that may exist among diverse populations is invaluable to accurately forecast biomarker-driven clinical trial enrollment metrics and to advance inclusive research and health equity. This study evaluated the frequency and types of PIK3CA mutations (PIK3CAmut) detected in predicted genetic ancestry subgroups across breast cancer (BC) subtypes. METHODS Analyses were conducted using real-world genomic data from adult patients with BC treated in an academic or community setting in the United States and whose tumor tissue was submitted for comprehensive genomic profiling. RESULTS Of 36,151 patients with BC (median age, 58 years; 99% female), the breakdown by predicted genetic ancestry was 75% European, 14% African, 6% Central/South American, 3% East Asian, and 1% South Asian. We demonstrated that patients of African ancestry are less likely to have tumors that harbor PIK3CAmut compared with patients of European ancestry with estrogen receptor-positive/human epidermal growth factor receptor 2-negative (ER+/HER2-) BC (37% [949/2,593] v 44% [7,706/17,637]; q = 4.39E-11) and triple-negative breast cancer (8% [179/2,199] v 14% [991/7,072]; q = 6.07E-13). Moreover, we found that PIK3CAmut were predominantly composed of hotspot mutations, of which mutations at H1047 were the most prevalent across BC subtypes (35%-41% ER+/HER2- BC; 43%-61% HER2+ BC; 40%-59% triple-negative breast cancer). CONCLUSION This analysis established that tumor PIK3CAmut prevalence can differ among predicted genetic ancestries across BC subtypes on the basis of the largest comprehensive genomic profiling data set of patients with cancer treated in the United States. This study highlights the need for equitable representation in research studies, which is imperative to ensuring better health outcomes for all.
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Affiliation(s)
- Jessica W. Chen
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA
| | | | | | - Ethan S. Sokol
- Cancer Genomics Research, Foundation Medicine, Inc, Cambridge, MA
| | - Heidi M. Savage
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA
| | - Thomas J. Stout
- Product Development Oncology, Genentech, Inc, South San Francisco, CA
| | - Sophia L. Maund
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA
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Wang T, Heng YJ, Baker GM, Bret-Mounet VC, Quintana LM, Frueh L, Hankinson SE, Holmes MD, Chen WY, Willett WC, Rosner B, Tamimi RM, Eliassen AH. Loss of PTEN Expression, PIK3CA Mutations, and Breast Cancer Survival in the Nurses' Health Studies. Cancer Epidemiol Biomarkers Prev 2022; 31:1926-1934. [PMID: 35914729 PMCID: PMC9532372 DOI: 10.1158/1055-9965.epi-22-0672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/28/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The relationships between PTEN loss and/or PIK3CA mutation and breast cancer prognosis remain controversial. We aim to examine the associations in large epidemiologic cohorts. METHODS We followed women with invasive breast cancer from the Nurses' Health Studies with available data on tumor PTEN expression (n = 4,111) and PIK3CA mutation (n = 2,930). PTEN expression was evaluated by IHC and digitally scored (0%-100%). Pyrosequencing of six hotspot mutations of PIK3CA was performed. RESULTS We found loss of PTEN expression (≤10%) occurred in 17% of cases, and PIK3CA mutations were detected in 11% of cases. After adjusting for clinical and lifestyle factors, PTEN loss was not associated with worse breast cancer-specific mortality among all samples [HR, 0.85; 95% confidence intervals (CI), 0.71-1.03] or among estrogen receptor (ER)-positive tumors (HR, 0.99; 95% CI, 0.79-1.24). However, among ER-negative tumors, PTEN loss was associated with lower breast cancer-specific mortality (HR, 0.68; 95% CI, 0.48-0.95). PIK3CA mutation was not strongly associated with breast cancer-specific mortality (HR, 0.89; 95% CI, 0.67-1.17). Compared with tumors without PTEN loss and without PIK3CA mutation, those with alterations (n = 540) were not at higher risk (HR, 1.07; 95% CI, 0.86-1.34). However, women with both PTEN loss and PIK3CA mutation (n = 38) were at an increased risk of breast cancer-specific mortality (HR, 1.65; 95% CI, 0.83-3.26). CONCLUSIONS In this large epidemiologic study, the PTEN-mortality association was more pronounced for ER-negative tumors, and the joint PTEN loss and PIK3CA mutation may be associated with worse prognosis. IMPACT Further studies with a larger sample of ER-negative tumors are needed to replicate our findings and elucidate underlying mechanisms.
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Affiliation(s)
- Tengteng Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham & Women’s Hospital, and Harvard Medical School, Boston, MA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Yujing J. Heng
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA
| | - Gabrielle M. Baker
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA
| | | | - Liza M. Quintana
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA
| | - Lisa Frueh
- Channing Division of Network Medicine, Department of Medicine, Brigham & Women’s Hospital, and Harvard Medical School, Boston, MA
| | - Susan E. Hankinson
- Department of Biostatistics and Epidemiology, University of Massachusetts School of Public Health and Health Sciences, Amherst, MA
| | - Michelle D. Holmes
- Channing Division of Network Medicine, Department of Medicine, Brigham & Women’s Hospital, and Harvard Medical School, Boston, MA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Wendy Y. Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham & Women’s Hospital, and Harvard Medical School, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Walter C. Willett
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Bernard Rosner
- Channing Division of Network Medicine, Department of Medicine, Brigham & Women’s Hospital, and Harvard Medical School, Boston, MA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Rulla M. Tamimi
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY
| | - A. Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham & Women’s Hospital, and Harvard Medical School, Boston, MA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA
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Scandolara TB, Valle SF, Esteves C, Scherer NDM, de Armas EM, Furtado C, Gomes R, Boroni M, Jaques HDS, Alves FM, Rech D, Panis C, Bonvicino CR. Somatic DNA Damage Response and Homologous Repair Gene Alterations and Its Association With Tumor Variant Burden in Breast Cancer Patients With Occupational Exposure to Pesticides. Front Oncol 2022; 12:904813. [PMID: 35875117 PMCID: PMC9305859 DOI: 10.3389/fonc.2022.904813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Homologous recombination is a crucial pathway that is specialized in repairing double-strand breaks; thus, alterations in genes of this pathway may lead to loss of genomic stability and cell growth suppression. Pesticide exposure potentially increases cancer risk through several mechanisms, such as the genotoxicity caused by chronic exposure, leading to gene alteration. To analyze this hypothesis, we investigated if breast cancer patients exposed to pesticides present a different mutational pattern in genes related to homologous recombination (BRCA1, BRCA2, PALB2, and RAD51D) and damage-response (TP53) concerning unexposed patients. We performed multiplex PCR-based assays and next-generation sequencing (NGS) of all coding regions and flanking splicing sites of BRCA1, BRCA2, PALB2, TP53, and RAD51D in 158 unpaired tumor samples from breast cancer patients on MiSeq (Illumina) platform. We found that exposed patients had tumors with more pathogenic and likely pathogenic variants than unexposed patients (p = 0.017). In general, tumors that harbored a pathogenic or likely pathogenic variant had a higher mutational burden (p < 0.001). We also observed that breast cancer patients exposed to pesticides had a higher mutational burden when diagnosed before 50 years old (p = 0.00978) and/or when carrying BRCA1 (p = 0.0138), BRCA2 (p = 0.0366), and/or PALB2 (p = 0.00058) variants, a result not found in the unexposed group. Our results show that pesticide exposure impacts the tumor mutational landscape and could be associated with the carcinogenesis process, therapy response, and disease progression. Further studies should increase the observation period in exposed patients to better evaluate the impact of these findings.
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Affiliation(s)
- Thalita Basso Scandolara
- Department of Genetics, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sara Ferreira Valle
- Department of Genetics, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cristiane Esteves
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Nicole de Miranda Scherer
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Elvismary Molina de Armas
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
- Department of Informatics, Pontificia Universidade Católica (PUC)-Rio, Rio de Janeiro, Brazil
| | - Carolina Furtado
- Division of Genetics, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Renan Gomes
- Division of Genetics, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Mariana Boroni
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | | | - Fernanda Mara Alves
- Laboratory of Tumor Biology, State University of West Paraná, Francisco Beltrão, Brazil
| | - Daniel Rech
- Laboratory of Tumor Biology, State University of West Paraná, Francisco Beltrão, Brazil
- Francisco Beltrão Cancer Hospital, Francisco Beltrão, Brazil
| | - Carolina Panis
- Laboratory of Tumor Biology, State University of West Paraná, Francisco Beltrão, Brazil
| | - Cibele Rodrigues Bonvicino
- Department of Genetics, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Division of Genetics, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
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Cho YA, Ko SY, Suh YJ, Kim S, Park JH, Park HR, Seo J, Choi HG, Kang HS, Lim H, Park HY, Kwon MJ. PIK3CA Mutation as Potential Poor Prognostic Marker in Asian Female Breast Cancer Patients Who Received Adjuvant Chemotherapy. Curr Oncol 2022; 29:2895-2908. [PMID: 35621626 PMCID: PMC9140087 DOI: 10.3390/curroncol29050236] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 12/02/2022] Open
Abstract
Background: The prognostic relevance of the PIK3CA mutation together with PD-L1, c-Met, and mismatch repair deficiency (dMMR) have not been fully investigated in Asian women with breast cancer (BC) who have undergone postoperative adjuvant chemotherapy. Methods: We analyzed PIK3CA mutations via peptide nucleic acid (PNA)-mediated real-time PCR assay, PD-L1/c-Met expression via immunohistochemistry (IHC), and microsatellite instability (MSI) status using PCR and IHC, in 191 resected BCs from 2008 to 2011. The Cancer Genome Atlas (TCGA) dataset for the involvement of the PIK3CA mutation with PD-L1/c-Met/MMR was explored. Results: The PNA clamp-mediated assay was able to detect the PIK3CA mutation in 1% of the mutant population in the cell line validation. Using this method, the PIK3CA mutation was found in 78 (49.4%) of 158 samples. c-Met and PD-L1 positivity were identified in 31.4 and 21.8% of samples, respectively, which commonly correlated with high histologic grade and triple-negative subtype. MSI/dMMR was observed in 8.4% of patients, with inconsistency between MMR IHC and the MSI PCR. The PIK3CA mutation exhibited a poor prognostic association regarding recurrence-free survival (RFS) in both overall and triple-negative BCs. In subgroup analyses, the PIK3CA-mutated tumors showed poorer RFS than the PIK3CA-wildtype within the c-Met-positive, MSS, triple-negative, or age onset <50 years subgroups, which showed a similar trend of association in TCGA data. Conclusions: PIK3CA mutation together with c-Met or dMMR/MSI status might be relevant to poor prognosis in BC subsets, especially in Asian women.
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Affiliation(s)
- Yoon Ah Cho
- Department of Pathology, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Korea; (Y.A.C.); (H.-R.P.); (J.S.)
| | - Seung Yeon Ko
- Division of Breast and Endocrine Surgery, Catholic Kwandong University International St. Mary’s Hospital, Catholic Kwandong University College of Medicine, Incheon 22711, Korea;
| | - Yong Joon Suh
- Division of Breast and Endocrine Surgery, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Korea; (Y.J.S.); (S.K.); (J.H.P.)
| | - Sanghwa Kim
- Division of Breast and Endocrine Surgery, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Korea; (Y.J.S.); (S.K.); (J.H.P.)
| | - Jung Ho Park
- Division of Breast and Endocrine Surgery, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Korea; (Y.J.S.); (S.K.); (J.H.P.)
| | - Hye-Rim Park
- Department of Pathology, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Korea; (Y.A.C.); (H.-R.P.); (J.S.)
| | - Jinwon Seo
- Department of Pathology, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Korea; (Y.A.C.); (H.-R.P.); (J.S.)
| | - Hyo Geun Choi
- Department of Otorhinolaryngology-Head & Neck Surgery, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Korea;
| | - Ho Suk Kang
- Division of Gastroenterology, Department of Internal Medicine, Hallym University Sacred Heart Hospital, Anyang 14068, Korea; (H.S.K.); (H.L.)
| | - Hyun Lim
- Division of Gastroenterology, Department of Internal Medicine, Hallym University Sacred Heart Hospital, Anyang 14068, Korea; (H.S.K.); (H.L.)
| | - Ha Young Park
- Department of Pathology, Busan Paik Hospital, Inje University College of Medicine, Busan 48108, Korea;
| | - Mi Jung Kwon
- Department of Pathology, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Korea; (Y.A.C.); (H.-R.P.); (J.S.)
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9
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Noor F, Noor A, Ishaq AR, Farzeen I, Saleem MH, Ghaffar K, Aslam MF, Aslam S, Chen JT. Recent Advances in Diagnostic and Therapeutic Approaches for Breast Cancer: A Comprehensive Review. Curr Pharm Des 2021; 27:2344-2365. [PMID: 33655849 DOI: 10.2174/1381612827666210303141416] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/22/2021] [Indexed: 11/22/2022]
Abstract
A silent monster, breast cancer, is a challenging medical task for researchers. Breast cancer is a leading cause of death in women with respect to other cancers. A case of breast cancer is diagnosed among women every 19 seconds, and every 74 seconds, a woman dies of breast cancer somewhere in the world. Several risk factors, such as genetic and environmental factors, favor breast cancer development. This review tends to provide deep insights regarding the genetics of breast cancer along with multiple diagnostic and therapeutic approaches as problem-solving negotiators to prevent the progression of breast cancer. This assembled data mainly aims to discuss omics-based approaches to provide enthralling diagnostic biomarkers and emerging novel therapies to combat breast cancer. This review article intends to pave a new path for the discovery of effective treatment options.
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Affiliation(s)
- Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University Allama Iqbal Road, 38000 Faisalabad, Pakistan
| | - Ayesha Noor
- Department of Zoology, Government College University Allama Iqbal Road, 38000 Faisalabad, Pakistan
| | - Ali Raza Ishaq
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan 430062, China
| | - Iqra Farzeen
- Department of Zoology, Government College University Allama Iqbal Road, 38000 Faisalabad, Pakistan
| | - Muhammad Hamzah Saleem
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan 430062, China
| | - Kanwal Ghaffar
- Department of Zoology, Government College University Allama Iqbal Road, 38000 Faisalabad, Pakistan
| | - Muhammad Farhan Aslam
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Sidra Aslam
- Department of Bioinformatics and Biotechnology, Government College University Allama Iqbal Road, 38000 Faisalabad, Pakistan
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, China
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10
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Russell LE, Zhou Y, Almousa AA, Sodhi JK, Nwabufo CK, Lauschke VM. Pharmacogenomics in the era of next generation sequencing - from byte to bedside. Drug Metab Rev 2021; 53:253-278. [PMID: 33820459 DOI: 10.1080/03602532.2021.1909613] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Pharmacogenetic research has resulted in the identification of a multitude of genetic variants that impact drug response or toxicity. These polymorphisms are mostly common and have been included as actionable information in the labels of numerous drugs. In addition to common variants, recent advances in Next Generation Sequencing (NGS) technologies have resulted in the identification of a plethora of rare and population-specific pharmacogenetic variations with unclear functional consequences that are not accessible by conventional forward genetics strategies. In this review, we discuss how comprehensive sequencing information can be translated into personalized pharmacogenomic advice in the age of NGS. Specifically, we provide an update of the functional impacts of rare pharmacogenetic variability and how this information can be leveraged to improve pharmacogenetic guidance. Furthermore, we critically discuss the current status of implementation of pharmacogenetic testing across drug development and layers of care. We identify major gaps and provide perspectives on how these can be minimized to optimize the utilization of NGS data for personalized clinical decision-support.
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Affiliation(s)
| | - Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Ahmed A Almousa
- Department of Pharmacy, London Health Sciences Center, Victoria Hospital, London, ON, Canada
| | - Jasleen K Sodhi
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Drug Metabolism and Pharmacokinetics, Plexxikon, Inc., Berkeley, CA, USA
| | | | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
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11
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Comprehensive omic characterization of breast cancer in Mexican-Hispanic women. Nat Commun 2021; 12:2245. [PMID: 33854067 PMCID: PMC8046804 DOI: 10.1038/s41467-021-22478-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/16/2021] [Indexed: 12/26/2022] Open
Abstract
Breast cancer is a heterogeneous pathology, but the genomic basis of its variability remains poorly understood in populations other than Caucasians. Here, through DNA and RNA portraits we explored the molecular features of breast cancers in a set of Hispanic-Mexican (HM) women and compared them to public multi-ancestry datasets. HM patients present an earlier onset of the disease, particularly in aggressive clinical subtypes, compared to non-Hispanic women. The age-related COSMIC signature 1 was more frequent in HM women than in those from other ancestries. We found the AKT1E17K hotspot mutation in 8% of the HM women and identify the AKT1/PIK3CA axis as a potentially druggable target. Also, HM luminal breast tumors present an enhanced immunogenic phenotype compared to Asiatic and Caucasian tumors. This study is an initial effort to include patients from Hispanic populations in the research of breast cancer etiology and biology to further understand breast cancer disparities. Cancers in different populations have been shown to be genetically distinct. Here, the authors sequence breast cancers from Mexican-Hispanic patients and find that these patients have a higher percentage of Akt1 mutations compared to Caucasian and Asian populations, suggesting these are clinically actionable.
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12
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Jiang B, Zhu H, Tang L, Gao T, Zhou Y, Gong F, Tan Y, Xie L, Wu X, Li Y. Apatinib Inhibits Stem Properties and Malignant Biological Behaviors of Breast Cancer Stem Cells by Blocking Wnt/β-catenin Signal Pathway Through Down-regulating LncRNA ROR. Anticancer Agents Med Chem 2021; 22:1723-1734. [PMID: 33845750 DOI: 10.2174/1871520621666210412103849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 02/01/2021] [Accepted: 02/21/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cancer stem cells could influence tumor recurrence and metastasis. OBJECTIVE To develop a new effective treatment modality targeting breast cancer stem cells (BCSCs), and to explore the role of Apatinib in BCSCs. METHODS BCSCs were isolated from MDA-MB-231 cells by immune magnetic beads method. BCSCs were treated with Apatinib, lentiviral plasmids (lncRNA ROR) and iCRT-3 (Wnt pathway inhibitors). Viability, colony numbers, sphere numbers, apoptosis, migration, invasion of BCSCs were detected by MTT, colony formation, tumor sphere, flow cytometry, wound-healing, transwell assays, respectively. The expressions of markers (ABCG2, CD44, CD90, and CD24), epithelial-mesenchymal transition (EMT)-related molecules (E-cadherin, N-cadherin, Vimentin, MMP-2, MMP-9), and Wnt/β-catenin pathway-related proteins (Wnt3a, Wnt5a, β-catenin) in breast cancer stem cells were determined by performing Western blot and qRT-PCR analysis. RESULTS Apatinib decreased the viability and colony numbers of BCSCs in a concentration-dependent manner, and it also reduced sphere numbers, suppressed migration, invasion and lncRNA ROR expression, and induced apoptosis of BCSCs. However, these results were partially reversed by lncRNA ROR overexpression. Apatinib suppressed stem property, EMT process and Wnt/β-catenin pathway in BCSCs, which was partially reversed by lncRNA ROR overexpression. Moreover, lncRNA ROR overexpression increased the colony and sphere numbers, and promoted the cell viability, apoptosis inhibition, migration and invasion of BCSCs, but these effects were partially reversed by iCRT-3. LncRNA ROR overexpression increased the stem property, EMT process and Wnt/β-catenin pathway, which were partially counteracted by iCRT-3. CONCLUSION Apatinib inhibited stem property and malignant biological behaviors of BCSCs by blocking Wnt/β-catenin signal pathway through down-regulating lncRNA ROR.
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Affiliation(s)
- Baohong Jiang
- Department of Pharmacy, The First Affiliated Hospital, University of South China. China
| | - Hongbo Zhu
- Department of Medical Oncology, The First Affiliated Hospital, University of South China. China
| | - Liting Tang
- Department of Medical Oncology, The First Affiliated Hospital, University of South China. China
| | - Ting Gao
- Department of Medical Oncology, The First Affiliated Hospital, University of South China. China
| | - Yu Zhou
- Department of Medical Oncology, The First Affiliated Hospital, University of South China. China
| | - Fuqiang Gong
- Department of Medical Oncology, The First Affiliated Hospital, University of South China. China
| | - Yeru Tan
- Department of Medical Oncology, The First Affiliated Hospital, University of South China. China
| | - Liming Xie
- Department of Medical Oncology, The First Affiliated Hospital, University of South China. China
| | - Xiaoping Wu
- Department of Medical Oncology, The First Affiliated Hospital, University of South China. China
| | - Yuehua Li
- Department of Medical Oncology, The First Affiliated Hospital, University of South China, No.69, Chuanshan Road, Hengyang, Hunan Province, 421001. China
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13
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Kołodziej P, Nicoś M, Krawczyk PA, Bogucki J, Karczmarczyk A, Zalewski D, Kubrak T, Kołodziej E, Makuch-Kocka A, Madej-Czerwonka B, Płachno BJ, Kocki J, Bogucka-Kocka A. The Correlation of Mutations and Expressions of Genes within the PI3K/Akt/mTOR Pathway in Breast Cancer-A Preliminary Study. Int J Mol Sci 2021; 22:2061. [PMID: 33669698 PMCID: PMC7922286 DOI: 10.3390/ijms22042061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/08/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
There is an urgent need to seek new molecular biomarkers helpful in diagnosing and treating breast cancer. In this elaboration, we performed a molecular analysis of mutations and expression of genes within the PI3K/Akt/mTOR pathway in patients with ductal breast cancer of various malignancy levels. We recognized significant correlations between the expression levels of the studied genes. We also performed a bioinformatics analysis of the data available on the international database TCGA and compared them with our own research. Studies on mutations and expression of genes were conducted using High-Resolution Melt PCR (HRM-PCR), Allele-Specific-quantitative PCR (ASP-qPCR), Real-Time PCR molecular methods in a group of women with ductal breast cancer. Bioinformatics analysis was carried out using web source Ualcan and bc-GenExMiner. In the studied group of women, it was observed that the prevalence of mutations in the studied PIK3CA and AKT1 genes was 29.63%. It was stated that the average expression level of the PIK3CA, PIK3R1, PTEN genes in the group of breast cancer patients is lower in comparison to the control group, while the average expression level of the AKT1 and mTOR genes in the studied group was higher in comparison to the control group. It was also indicated that in the group of patients with mutations in the area of the PIK3CA and AKT1 genes, the PIK3CA gene expression level is statistically significantly lower than in the group without mutations. According to our knowledge, we demonstrate, for the first time, that there is a very strong positive correlation between the levels of AKT1 and mTOR gene expression in the case of patients with mutations and without mutations.
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Affiliation(s)
- Przemysław Kołodziej
- Chair and Department of Biology and Genetics, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Marcin Nicoś
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-954 Lublin, Poland; (M.N.); (P.A.K.)
| | - Paweł A. Krawczyk
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-954 Lublin, Poland; (M.N.); (P.A.K.)
| | - Jacek Bogucki
- Department of Organic Chemistry, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Agnieszka Karczmarczyk
- Department of Experimental Haematooncology, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Daniel Zalewski
- Chair and Department of Biology and Genetics, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Tomasz Kubrak
- Department of Biochemistry and General Chemistry, Faculty of Medicine, University of Rzeszow, 35-310 Rzeszów, Poland;
| | - Elżbieta Kołodziej
- Department of Clinical Genetics, Medical University of Lublin, 20-080 Lublin, Poland; (E.K.); (J.K.)
| | - Anna Makuch-Kocka
- Department of Pharmacology, Medical University of Lublin, 20-059 Lublin, Poland;
| | - Barbara Madej-Czerwonka
- Department of Breast Surgery, District Specialist Hospital of Stefan Cardinal Wyszynski in Lublin, 20-718 Lublin, Poland;
- Department of Human Anatomy, Medical University of Lublin, 20-090 Lublin, Poland
| | - Bartosz J. Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, 30-387 Kraków, Poland;
| | - Janusz Kocki
- Department of Clinical Genetics, Medical University of Lublin, 20-080 Lublin, Poland; (E.K.); (J.K.)
| | - Anna Bogucka-Kocka
- Chair and Department of Biology and Genetics, Medical University of Lublin, 20-093 Lublin, Poland;
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14
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Nassir R, Esheba G, Elmoneim HMA, Altowairqi AS, Nouman G. Expression and Clinical Significance of <i>PIK3CA</i>, <i>c-MET</i> and <i>c-KIT</i> Mutations in Saudi Breast Cancer Patients. ADVANCES IN BREAST CANCER RESEARCH 2021; 10:60-74. [DOI: 10.4236/abcr.2021.103005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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15
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Jia M, Liao N, Chen B, Zhang G, Wang Y, Li X, Cao L, Mok H, Ren C, Li K, Li C, Wen L, Lin J, Wei G, Balch CM. PIK3CA somatic alterations in invasive breast cancers: different spectrum from Caucasians to Chinese detected by next generation sequencing. Breast Cancer 2021; 28:644-652. [PMID: 33386585 PMCID: PMC8065000 DOI: 10.1007/s12282-020-01199-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/27/2020] [Indexed: 12/31/2022]
Abstract
Purpose Somatic alteration of phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) is a crucial therapeutic target in breast cancer (BC) and PI3Kα-specific inhibitor Alpelisib has been used in clinics. This study investigates the PIK3CA alterations in Chinese and Caucasians BC patients for the purpose of selecting anti-PI3K therapy. Methods The molecular profile of the PIK3CA gene was analyzed in 412 Chinese patients with untreated invasive BC using a 540 gene next-generation sequencing panel. The results were compared with data of the Caucasian BC patients in The Cancer Genome Atlas (TCGA-white). Results PIK3CA alterations were frequently found in BC of estrogen receptor (ER) positive (49.3%, p = 0.024), low ki67 proliferation index (58.3%, p = 0.007) and low pathological grade (grade I/II/III 80%, 53.4%, 35.9%, p < 0.001). Compared to TCGA-white, Chinese BC patients had a higher alteration frequency (45.6% vs. 34.7%, p < 0.001) with larger proportion of p.H1047R mutation among three common mutation sites (p.E545K, p.E542K and p.H1047R) (66.1% vs. 43.7%, p = 0.01). Across four molecular subtypes, ER + /human epidermal growth factor receptor 2 positive (HER2 +) tumors harbored the most PIK3CA alterations (51.6%), while ER-/HER2- harbored the least alteration (30.0%) but the most copy number amplification (19.05%). Conclusion PIK3CA alterations prevail in Chinese BC patients and have different molecular features compared to that of Caucasians. The results provide precise annotations of PIK3CA genomic alterations of Chinese in the context of application of PIK3CA inhibitor.
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Affiliation(s)
- Minghan Jia
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, Guangdong, China
| | - Ning Liao
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, Guangdong, China. .,School of Medicine, South China University of Technology, Guangzhou, China. .,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.
| | - Bo Chen
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, Guangdong, China
| | - Guochun Zhang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, Guangdong, China
| | - Yulei Wang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, Guangdong, China
| | - Xuerui Li
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, Guangdong, China
| | - Li Cao
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, Guangdong, China
| | - Hsiaopei Mok
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, Guangdong, China
| | - Chongyang Ren
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, Guangdong, China
| | - Kai Li
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, Guangdong, China
| | - Cheukfai Li
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, Guangdong, China
| | - Lingzhu Wen
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, Guangdong, China
| | - Jiali Lin
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, Guangdong, China.,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Guangnan Wei
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, Guangdong, China.,School of Medicine, South China University of Technology, Guangzhou, China
| | - Charles M Balch
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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16
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Dirican E, Kankaya B, Büyükaşık S, Alış H, Velidedeoğlu M, İlvan S, İlvan A. Investigation of alterations in PIK3CA and OCT-4 gene expression in breast cancer. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Ciocan-Cartita CA, Jurj A, Zanoaga O, Cojocneanu R, Pop LA, Moldovan A, Moldovan C, Zimta AA, Raduly L, Pop-Bica C, Buse M, Budisan L, Virag P, Irimie A, Diaz SMG, Berindan-Neagoe I, Braicu C. New insights in gene expression alteration as effect of doxorubicin drug resistance in triple negative breast cancer cells. J Exp Clin Cancer Res 2020; 39:241. [PMID: 33187552 PMCID: PMC7664031 DOI: 10.1186/s13046-020-01736-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Triple negative breast cancer (TNBC) is a heterogeneous disease with aggressive behavior and an unfavorable prognosis rate. Due to the lack of surface receptors, TNBC must be intensely investigated in order to establish a suitable treatment for patients with this pathology. Chemoresistance is an important reason for therapeutic failure in TNBC. METHOD The aim of this study was to investigate the effect of doxorubicin in TNBC cell lines and to highlight cellular and molecular alterations after a long exposure to doxorubicin. RESULTS The results revealed that doxorubicin significantly increased the half maximal inhibitory concentration (IC50) values at P12 and P24 compared to parenteral cells P0. Modifications in gene expression were investigated through microarray technique, and for detection of mutational pattern was used Next Generation Sequencing (NGS). 196 upregulated and 115 downregulated genes were observed as effect of multiple dose exposure, and 15 overexpressed genes were found to be involved in drug resistance. Also, the presence of some additional mutations in both cell lines was observed. CONCLUSION The outcomes of this research may provide novel biomarkers for drug resistance in TNBC. Also, this activity can highlight the potential mechanisms associated with drug resistance, as well as the potential therapies to counteract these mechanisms.
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Affiliation(s)
- Cristina Alexandra Ciocan-Cartita
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ancuta Jurj
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Oana Zanoaga
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Roxana Cojocneanu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Laura-Ancuta Pop
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alin Moldovan
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristian Moldovan
- MedFuture Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alina Andreea Zimta
- MedFuture Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Lajos Raduly
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cecilia Pop-Bica
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihail Buse
- MedFuture Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Liviuta Budisan
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Piroska Virag
- Laboratory of Radiotherapy, Radiobiology and Tumor Biology, “Prof. Dr. Ion Chiricuta” Oncology Institute, Cluj-Napoca, Romania
| | - Alexandru Irimie
- Department of Surgical Oncology and Gynecological Oncology, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Surgery, “Prof. Dr. Ion Chiricuta” Oncology Institute, Cluj-Napoca, Romania
| | - Sandra Martha Gomez Diaz
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Functional Genomics and Experimental Pathology, “Prof. Dr. Ion Chiricuta” Oncology Institute, Cluj-Napoca, Romania
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
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18
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Ramirez-Valles EG, Rodríguez-Pulido A, Barraza-Salas M, Martínez-Velis I, Meneses-Morales I, Ayala-García VM, Alba-Fierro CA. A Quest for New Cancer Diagnosis, Prognosis and Prediction Biomarkers and Their Use in Biosensors Development. Technol Cancer Res Treat 2020; 19:1533033820957033. [PMID: 33107395 PMCID: PMC7607814 DOI: 10.1177/1533033820957033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Traditional techniques for cancer diagnosis, such as nuclear magnetic resonance, ultrasound and tissue analysis, require sophisticated devices and highly trained personnel, which are characterized by elevated operation costs. The use of biomarkers has emerged as an alternative for cancer diagnosis, prognosis and prediction because their measurement in tissues or fluids, such as blood, urine or saliva, is characterized by shorter processing times. However, the biomarkers used currently, and the techniques used for their measurement, including ELISA, western-blot, polymerase chain reaction (PCR) or immunohistochemistry, possess low sensitivity and specificity. Therefore, the search for new proteomic, genomic or immunological biomarkers and the development of new noninvasive, easier and cheaper techniques that meet the sensitivity and specificity criteria for the diagnosis, prognosis and prediction of this disease has become a relevant topic. The purpose of this review is to provide an overview about the search for new cancer biomarkers, including the strategies that must be followed to identify them, as well as presenting the latest advances in the development of biosensors that possess a high potential for cancer diagnosis, prognosis and prediction, mainly focusing on their relevance in lung, prostate and breast cancers.
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Affiliation(s)
- Eda G Ramirez-Valles
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Dgo, Mexico
| | | | - Marcelo Barraza-Salas
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Dgo, Mexico
| | - Isaac Martínez-Velis
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Dgo, Mexico
| | - Iván Meneses-Morales
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Dgo, Mexico
| | - Víctor M Ayala-García
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Dgo, Mexico
| | - Carlos A Alba-Fierro
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Dgo, Mexico
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19
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Potential Molecular Mechanisms of Chaihu-Shugan-San in Treatment of Breast Cancer Based on Network Pharmacology. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:3670309. [PMID: 33062007 PMCID: PMC7533014 DOI: 10.1155/2020/3670309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 08/05/2020] [Indexed: 12/16/2022]
Abstract
Breast cancer is one of the most common cancers endangering women's health all over the world. Traditional Chinese medicine is increasingly recognized as a possible complementary and alternative therapy for breast cancer. Chaihu-Shugan-San is a traditional Chinese medicine prescription, which is extensively used in clinical practice. Its therapeutic effect on breast cancer has attracted extensive attention, but its mechanism of action is still unclear. In this study, we explored the molecular mechanism of Chaihu-Shugan-San in the treatment of breast cancer by network pharmacology. The results showed that 157 active ingredients and 8074 potential drug targets were obtained in the TCMSP database according to the screening conditions. 2384 disease targets were collected in the TTD, OMIM, DrugBank, GeneCards disease database. We applied the Bisogenet plug-in in Cytoscape 3.7.1 to obtain 451 core targets. The biological process of gene ontology (GO) involves the mRNA catabolic process, RNA catabolic process, telomere organization, nucleobase-containing compound catabolic process, heterocycle catabolic process, and so on. In cellular component, cytosolic part, focal adhesion, cell-substrate adherens junction, and cell-substrate junction are highly correlated with breast cancer. In the molecular function category, most proteins were addressed to ubiquitin-like protein ligase binding, protein domain specific binding, and Nop56p-associated pre-rRNA complex. Besides, the results of the KEGG pathway analysis showed that the pathways mainly involved in apoptosis, cell cycle, transcriptional dysregulation, endocrine resistance, and viral infection. In conclusion, the treatment of breast cancer by Chaihu-Shugan-San is the result of multicomponent, multitarget, and multipathway interaction. This study provides a certain theoretical basis for the treatment of breast cancer by Chaihu-Shugan-San and has certain reference value for the development and application of new drugs.
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20
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Kwong A, Cheuk IWY, Shin VY, Ho CYS, Au CH, Ho DNY, Wong EYL, Yu SWY, Chen J, Chan KKL, Ngan HYS, Chan TL, Ma ESK. Somatic mutation profiling in BRCA-negative breast and ovarian cancer patients by multigene panel sequencing. Am J Cancer Res 2020; 10:2919-2932. [PMID: 33042626 PMCID: PMC7539773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 07/11/2020] [Indexed: 06/11/2023] Open
Abstract
Targeted therapeutic agents such as poly (ADP-ribose) polymerases (PARP) inhibitors have emerged in treating cancers associated with germline BRCA mutations. Recently studies demonstrated the effectiveness of PARP inhibitors in treating patients with somatic BRCA mutations. Somatic mutations in 122 Chinese breast or ovarian cancer patients without BRCA, PTEN and TP53 mutations were screened using multigene sequencing panel. The five most frequent pathogenic or likely pathogenic mutated genes identified in breast cancer patients were PIK3CA (28.6%), TP53 (16.9%), MAP3K1 (14.3%), GATA3 (14.3%) and PTEN (5.2%). The five most frequently mutated genes identified in ovarian patients were TP53 (52.9%), KRAS (23.5%) and PIK3CA (11.8%), BRCA1 (5.9%) and RB1 (5.9%). Somatic PIK3CA and TP53 mutations were common events in both germline BRCA-negative breast and ovarian cancer patients. In contrast, somatic screening of BRCA mutations in BRCA-negative breast cancer patients has limited value. The results highlight the benefit of somatic testing to guide future research directions on other targeted therapies for breast and ovarian malignancies.
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Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong SAR
- Department of Surgery, Hong Kong Sanatorium & HospitalHong Kong SAR
- Hong Kong Hereditary Breast Cancer Family RegistryHong Kong SAR
| | - Isabella WY Cheuk
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong SAR
| | - Vivian Yvonne Shin
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong SAR
| | - Cecilia YS Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & HospitalHong Kong SAR
| | - Chun-Hang Au
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & HospitalHong Kong SAR
| | - Dona NY Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & HospitalHong Kong SAR
| | - Elaine YL Wong
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & HospitalHong Kong SAR
| | - Stephanie WY Yu
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong SAR
| | - Jiawei Chen
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong SAR
| | - Karen KL Chan
- Department of Obstetrics and Gynaecology, The University of Hong KongHong Kong SAR
| | - Hextan YS Ngan
- Department of Obstetrics and Gynaecology, The University of Hong KongHong Kong SAR
| | - Tsun-Leung Chan
- Hong Kong Hereditary Breast Cancer Family RegistryHong Kong SAR
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & HospitalHong Kong SAR
| | - Edmond SK Ma
- Hong Kong Hereditary Breast Cancer Family RegistryHong Kong SAR
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & HospitalHong Kong SAR
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21
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Ashrafizadeh M, Najafi M, Ang HL, Moghadam ER, Mahabady MK, Zabolian A, Jafaripour L, Bejandi AK, Hushmandi K, Saleki H, Zarrabi A, Kumar AP. PTEN, a Barrier for Proliferation and Metastasis of Gastric Cancer Cells: From Molecular Pathways to Targeting and Regulation. Biomedicines 2020; 8:E264. [PMID: 32756305 PMCID: PMC7460532 DOI: 10.3390/biomedicines8080264] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/23/2020] [Accepted: 07/23/2020] [Indexed: 02/06/2023] Open
Abstract
Cancer is one of the life-threatening disorders that, in spite of excellent advances in medicine and technology, there is no effective cure for. Surgery, chemotherapy, and radiotherapy are extensively applied in cancer therapy, but their efficacy in eradication of cancer cells, suppressing metastasis, and improving overall survival of patients is low. This is due to uncontrolled proliferation of cancer cells and their high migratory ability. Finding molecular pathways involved in malignant behavior of cancer cells can pave the road to effective cancer therapy. In the present review, we focus on phosphatase and tensin homolog (PTEN) signaling as a tumor-suppressor molecular pathway in gastric cancer (GC). PTEN inhibits the PI3K/Akt pathway from interfering with the migration and growth of GC cells. Its activation leads to better survival of patients with GC. Different upstream mediators of PTEN in GC have been identified that can regulate PTEN in suppressing growth and invasion of GC cells, such as microRNAs, long non-coding RNAs, and circular RNAs. It seems that antitumor agents enhance the expression of PTEN in overcoming GC. This review focuses on aforementioned topics to provide a new insight into involvement of PTEN and its downstream and upstream mediators in GC. This will direct further studies for evaluation of novel signaling networks and their targeting for suppressing GC progression.
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Affiliation(s)
- Milad Ashrafizadeh
- Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz 5166616471, Iran;
| | - Masoud Najafi
- Radiology and Nuclear Medicine Department, School of Paramedical Sciences, Kermanshah University of Medical Sciences, Kermanshah 6715847141, Iran;
| | - Hui Li Ang
- Cancer Science Institute of Singapore and Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
| | - Ebrahim Rahmani Moghadam
- Department of Anatomical Sciences, School of Medicine, Student Research Committee, Shiraz University of Medical Sciences, Shiraz 7134814336, Iran;
- Kazerun Health Technology Incubator, Shiraz University of Medical Sciences, Shiraz 6461665145, Iran
| | - Mahmood Khaksary Mahabady
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan 8715988141, Iran;
| | - Amirhossein Zabolian
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran 1916893813, Iran; (A.Z.); (A.K.B.); (H.S.)
| | - Leila Jafaripour
- Department of Anatomy, School of Medicine, Dezful University of Medical Sciences, Dezful 3419759811, Iran;
| | - Atefe Kazemzade Bejandi
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran 1916893813, Iran; (A.Z.); (A.K.B.); (H.S.)
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran 1417414418, Iran;
| | - Hossein Saleki
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran 1916893813, Iran; (A.Z.); (A.K.B.); (H.S.)
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla 34956, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla 34956, Istanbul, Turkey
| | - Alan Prem Kumar
- Cancer Science Institute of Singapore and Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
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22
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Nassar A, Abouelhoda M, Mansour O, Loutfy SA, Hafez MM, Gomaa M, Bahnassy A, El-Din Youssef AS, Lotfy MM, Ismail H, Ahmed OS, Abou-Bakr AAE, Zekri ARN. Targeted next generation sequencing identifies somatic mutations in a cohort of Egyptian breast cancer patients. J Adv Res 2020; 24:149-157. [PMID: 32322420 PMCID: PMC7167517 DOI: 10.1016/j.jare.2020.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/17/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023] Open
Abstract
Breast cancer (BC) incidence is progressively increasing in Egypt. However, there is insufficient knowledge of the acquired somatic mutations in Egyptian BC patients which limit our understanding of its progression. To the best of our knowledge, this is the first Egyptian cohort to sequence a multiple-gene panel of cancer related genes on BC patients. Four hundred and nine cancer related genes were sequenced in 46 fresh breast tumors of Egyptian BC patients to identify somatic mutations and their frequencies. TP53 and PIK3CA were the most top two frequently mutated genes. We detected 15 different somatic mutations in TP53 and 8 different ones in PIK3CA, each in 27 samples (58.7%). According to Clinvar database; we found 19 pathogenic somatic mutations: 7 in Tp53, 5 in PIK3CA, and single variants of VHL, STK11, AKT1, KRAS, IDH2, PTEN and ERBB2. We also identified 5 variants with uncertain significance (4 in TP53 and 1 in CEBPA) and 4 variants with conflicting interpretations of pathogenicity (2 in TP53 and 1 in each of APC and JAK3). Moreover, one drug response variant (p.P72R) in TP53 was detected in 8 samples. Furthermore, four novel variants were identified in JAK2, MTOR, KIT and EPHB. Further analysis, by Ingenuity Variant Analysis software (IVA), showed that PI3K/AKT signaling is altered in greater than 50% of Egyptian BC patients which implicates PI3K/AKT signaling as a therapeutic target. In this cohort, we shed the light on the most frequently detected somatic mutations and the most altered pathway in Egyptian BC patients.
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Affiliation(s)
- Auhood Nassar
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | | | - Osman Mansour
- Medical Oncology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Samah A. Loutfy
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mohamed M. Hafez
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - M. Gomaa
- Radiology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Abeer Bahnassy
- Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | | | - Mai M. Lotfy
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Hoda Ismail
- Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Ola S. Ahmed
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | | | - Abdel-Rahman N. Zekri
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
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23
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Tao Z, Li T, Feng Z, Liu C, Shao Y, Zhu M, Gong C, Wang B, Cao J, Wang L, Du Y, Lizaso A, Li B, Zhang J, Hu X. Characterizations of Cancer Gene Mutations in Chinese Metastatic Breast Cancer Patients. Front Oncol 2020; 10:1023. [PMID: 32695676 PMCID: PMC7338574 DOI: 10.3389/fonc.2020.01023] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 05/22/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Breast cancer (BC) is a type of disease with high heterogeneity. Molecular profiling, by revealing the intrinsic nature of its various subtypes, has extensively improved the therapeutic management of BC patients. However, the genomic mutation landscape of Chinese metastatic BC has not been fully explored. Methods: Matched plasma and mononuclear cells from 290 Chinese women with metastatic BC were sequenced using either of the two commercially-available panels consisting of 520 cancer-related and 108 BC-related genes. Both panels cover the same critical regions of 91 genes. The circulating tumor DNA mutation profile from our cohort was then compared with publicly-available metastatic BC datasets from Memorial Sloan Kettering Cancer Center (MSKCC) and Pan-cancer analysis of whole genomes (PCAWG). Results: A total of 1,201 mutations spanning 91 genes were detected from 234 patients, resulting in a mutation detection rate of 80.7%. TP53 (64.1%) was the gene with highest mutation frequency, followed by PIK3CA (31%), PTEN (11%), and RB1 (10%). Copy number amplifications (CNAs) in MYC (14.1%), FGFR1 (13.3%), CCND1 (6.6%), FGF3 (6.6%), FGF4 (6.2%) and FGF19 (6.2%) were also detected from our cohort. TP53 mutations were significantly more frequent among triple negative BC (TNBC), HR-/HER2+, and HR+/HER2+ BC, while less common in HR+/HER2- (P < 0.01). Meanwhile, PIK3CA mutations were significantly more frequent among HR+/HER2+, HR+/HER2-, and HR-/HER2+ BC, while less common in TNBC (P < 0.01). Pathogenic or likely pathogenic BRCA1/2 germline mutations were detected in 5.9% of the cohort and 4.4% in TNBC subgroup. Maximum allelic fraction (maxAF) of TP53, RB1, and PIK3CA mutations were associated with multiple organ metastasis. Patients with PIK3CA, PTEN, and RB1 mutation were more likely to have liver metastasis (P < 0.02). Compared with MSKCC and PCAWG dataset, Chinese patients had observably difference in genetic variation rates in different molecular subtypes (TNBC: TP53 73.0 vs. 91.5%, P < 0.001; PIK3CA 21.2 vs. 13.2%, P = 0.061; HR+/HER2-: FGFR1 3.3 vs. 0.7%, P = 0.035; TP 53 46.2 vs. 27.7%, P < 0.001; RB1 6.6 vs. 2.7%, P = 0.046; CDKN2A 7.7 vs. 1.0%, P < 0.001; PIK3CA 30.8 vs. 44.2%, P = 0.012; CDH1 1.1 vs. 18.2%, P < 0.001; GATA3 7.7 vs. 17.2%, P = 0.02). Conclusions: A distinct gene mutation profile was elucidated in Chinese women with metastatic BC, justifying further research. Liquid biopsy provides a quick, real-time, and minimally invasive tool for future clinical trial and routine practice.
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Affiliation(s)
- Zhonghua Tao
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ting Li
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhe Feng
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chang Liu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yilin Shao
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Mingyu Zhu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chengcheng Gong
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Biyun Wang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jun Cao
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Leipin Wang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yiqun Du
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | | | - Bing Li
- Burning Rock Biotech, Guangzhou, China
| | - Jian Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xichun Hu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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24
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The frequency of PTEN germline mutations in Chinese breast cancer patients: The PTEN gene may not be closely associated with breast cancer in the Chinese population. Gene 2020; 744:144630. [PMID: 32234455 DOI: 10.1016/j.gene.2020.144630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/17/2020] [Accepted: 03/26/2020] [Indexed: 11/24/2022]
Abstract
BACKGROUND PTEN is a tumour suppressor gene that has been proven to be related to breast cancer incidence and tumour progression. The aim of this study was to investigate the frequency of PTEN mutations in breast carcinomas in China and the relationships of PTEN mutations with clinicopathological parameters and clinical outcomes. MATERIAL AND METHODS Trimmomatic, Burrows-Wheeler Aligner (BWA), ANNOVAR, SAMtools, and Sanger sequencing were used to analyse PTEN mutations and identify variants in Chinese breast cancer. The frequency of PTEN mutations and the relationships of PTEN mutations with clinicopathological parameters and clinical outcomes were evaluated in breast carcinomas in China. RESULTS The rate of PTEN germline mutation was 0.23% (n = 9) among 3955 unselected primary breast cancer patients. Of these 9 patients, 2 carried pathogenic mutations, and both were identified as having infiltrative carcinoma. One patient had a family history. The other 7 patients carried only PTEN germline variants that were not identified as pathogenic mutations. CONCLUSIONS We studied the frequency of PTEN germline mutations in a sequential cohort of Chinese breast carcinoma patients. Based on these data, we hypothesize that the germline mutation of the PTEN gene is not closely related to the occurrence of breast cancer in the Chinese population. In the clinic, the PTEN germline mutation cannot be used as the basis for the detection of breast cancer.
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25
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Isik E, Simsir OS, Solmaz AE, Onay H, Atik T, Aykut A, Durmaz A, Cogulu O, Ozkinay F. Clinical and molecular aspects of
PTEN
mutations in 10 pediatric patients. Ann Hum Genet 2020; 84:324-330. [DOI: 10.1111/ahg.12380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/09/2019] [Accepted: 01/10/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Esra Isik
- Subdivision of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine Ege University Izmir Turkey
| | - Ozguc Semih Simsir
- Subdivision of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine Ege University Izmir Turkey
| | - Asli Ece Solmaz
- Department of Medical Genetics Faculty of Medicine, Ege University Izmir Turkey
| | - Huseyin Onay
- Department of Medical Genetics Faculty of Medicine, Ege University Izmir Turkey
| | - Tahir Atik
- Subdivision of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine Ege University Izmir Turkey
| | - Ayca Aykut
- Department of Medical Genetics Faculty of Medicine, Ege University Izmir Turkey
| | - Asude Durmaz
- Department of Medical Genetics Faculty of Medicine, Ege University Izmir Turkey
| | - Ozgur Cogulu
- Subdivision of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine Ege University Izmir Turkey
- Department of Medical Genetics Faculty of Medicine, Ege University Izmir Turkey
| | - Ferda Ozkinay
- Subdivision of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine Ege University Izmir Turkey
- Department of Medical Genetics Faculty of Medicine, Ege University Izmir Turkey
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26
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Hinz N, Jücker M. Distinct functions of AKT isoforms in breast cancer: a comprehensive review. Cell Commun Signal 2019; 17:154. [PMID: 31752925 PMCID: PMC6873690 DOI: 10.1186/s12964-019-0450-3] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/04/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND AKT, also known as protein kinase B, is a key element of the PI3K/AKT signaling pathway. Moreover, AKT regulates the hallmarks of cancer, e.g. tumor growth, survival and invasiveness of tumor cells. After AKT was discovered in the early 1990s, further studies revealed that there are three different AKT isoforms, namely AKT1, AKT2 and AKT3. Despite their high similarity of 80%, the distinct AKT isoforms exert non-redundant, partly even opposing effects under physiological and pathological conditions. Breast cancer as the most common cancer entity in women, frequently shows alterations of the PI3K/AKT signaling. MAIN CONTENT A plethora of studies addressed the impact of AKT isoforms on tumor growth, metastasis and angiogenesis of breast cancer as well as on therapy response and overall survival in patients. Therefore, this review aimed to give a comprehensive overview about the isoform-specific effects of AKT in breast cancer and to summarize known downstream and upstream mechanisms. Taking account of conflicting findings among the studies, the majority of the studies reported a tumor initiating role of AKT1, whereas AKT2 is mainly responsible for tumor progression and metastasis. In detail, AKT1 increases cell proliferation through cell cycle proteins like p21, p27 and cyclin D1 and impairs apoptosis e.g. via p53. On the downside AKT1 decreases migration of breast cancer cells, for instance by regulating TSC2, palladin and EMT-proteins. However, AKT2 promotes migration and invasion most notably through regulation of β-integrins, EMT-proteins and F-actin. Whilst AKT3 is associated with a negative ER-status, findings about the role of AKT3 in regulation of the key properties of breast cancer are sparse. Accordingly, AKT1 is mutated and AKT2 is amplified in some cases of breast cancer and AKT isoforms are associated with overall survival and therapy response in an isoform-specific manner. CONCLUSIONS Although there are several discussed hypotheses how isoform specificity is achieved, the mechanisms behind the isoform-specific effects remain mostly unrevealed. As a consequence, further effort is necessary to achieve deeper insights into an isoform-specific AKT signaling in breast cancer and the mechanism behind it.
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Affiliation(s)
- Nico Hinz
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Manfred Jücker
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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27
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McKay MJ, Southey M. Improving our understanding of breast cancer tumorigenesis across ethnicities. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:364. [PMID: 31555678 DOI: 10.21037/atm.2019.07.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Michael J McKay
- School of Cancer Medicine, La Trobe University, Olivia Newton-John Cancer Research Institute at Austin Campus, Heidelberg, Australia
| | - Melissa Southey
- School of Clinical Sciences at Monash Health Medicine, Nursing and Health Sciences, Monash University Clayton, Clayton, Australia
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Murugan AK, Qasem E, Al-Hindi H, Alzahrani AS. GPCR-mediated PI3K pathway mutations in pediatric and adult thyroid cancer. Oncotarget 2019; 10:4107-4124. [PMID: 31289610 PMCID: PMC6609254 DOI: 10.18632/oncotarget.26993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022] Open
Abstract
Whole exome sequencing (WES) recently identified frequent mutations in the genes of GPCR-mediated PI3K pathway (LPAR4, PIK3CA, and PTEN) in a Chinese population with papillary thyroid cancers (PTCs). The study found LPAR4 mutations as novel gene mutations in adult population with differentiated thyroid cancer (DTC). Here, we determine the prevalence of somatic mutations in this pathway (LPAR4 (exon 1), PIK3CA (exons 9 and 20) and PTEN (exons 5, 6, 7 and 8) in 323 thyroid samples consisting of 17 multinodular goiters (MNG), 89 pediatric DTCs, 204 adult DTCs, and 13 aggressive thyroid cancers including 10 poorly differentiated (PDTC) and 3 anaplastic thyroid cancer (ATC) from another ethnic population. We found 3.37% and 2.45% (includes Q214H, a novel PTEN mutation) in GPCR-mediated PI3K pathway of pediatric and adult DTCs, respectively. Analyses of 507 DTCs from thyroid Cancer Genome Atlas data (TCGA) revealed a low prevalence of mutations in this pathway (1.18%). In 13 cases with PDTC and ATC, we found no mutation in genes of this pathway. By contrast, analyses of 117 aggressive thyroid cancers (PDTC and ATC) from TCGA showed 13% of mutations in this pathway. Moreover, analyses of 1080 pan-cancer cell lines and 9020 solid tumors of TCGA data revealed high rates of mutations in this pathway (cell lines, 24.8%; tumors, 24.8%). In addition, PIK3CA + PTEN (p = <0.001) and LPAR4 + PIK3CA (p = 0.003) significantly co-occurred. Our study reveals a low prevalence of GPCR-mediated PI3K pathway mutations both in pediatric and adult DTCs corroborating the TCGA data and suggests a significant role of this pathway only in a small portion of DTCs. The high prevalence of mutations in this pathway in other solid malignancies suggests an important role in their pathogenesis making it an attractive target for therapeutic intervention both in a small subset of DTCs and other solid cancers.
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Affiliation(s)
| | - Ebtesam Qasem
- Division of Molecular Endocrinology, Department of Molecular Oncology, Riyadh 11211, Saudi Arabia
| | - Hindi Al-Hindi
- Department of Pathology and Laboratory Medicine, Riyadh 11211, Saudi Arabia
| | - Ali S. Alzahrani
- Division of Molecular Endocrinology, Department of Molecular Oncology, Riyadh 11211, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
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