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Faizal AM, Elias MH, Jin NM, Abu MA, Syafruddin SE, Zainuddin AA, Suzuki N, Karim AKA. Unravelling the role of HAS2, GREM1, and PTGS2 gene expression in cumulus cells: implications for human oocyte development competency - a systematic review and integrated bioinformatic analysis. Front Endocrinol (Lausanne) 2024; 15:1274376. [PMID: 38524634 PMCID: PMC10957552 DOI: 10.3389/fendo.2024.1274376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
The leading indicator for successful outcomes in in-vitro fertilization (IVF) is the quality of gametes in oocytes and sperm. Thus, advanced research aims to highlight the parameter in assessing these qualities - DNA fragmentation in sperm and oocyte development capacity (ODC) via evaluation of microenvironments involving its maturation process. Regarding oocytes, most evidence reveals the role of cumulus cells as non-invasive methods in assessing their development competency, mainly via gene expression evaluation. Our review aims to consolidate the evidence of GDF-9 derivatives, the HAS2, GREM1, and PTGS2 gene expression in cumulus cells used as ODC markers in relevant publications and tailored to current IVF outcomes. In addition to that, we also added the bioinformatic analysis in our review to strengthen the evidence aiming for a better understanding of the pathways and cluster of the genes of interest - HAS2, GREM1, and PTGS2 in cumulus cell level. Otherwise, the current non-invasive method can be used in exploring various causes of infertility that may affect these gene expressions at the cumulus cell level. Nevertheless, this method can also be used in assessing the ODC in various cohorts of women or as an improvement of markers following targeted tools or procedures by evaluating the advancement of these gene expressions following the targeted intervention.
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Affiliation(s)
- Ahmad Mohd Faizal
- Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Marjanu Hikmah Elias
- Faculty of Medicine & Health Sciences, Universiti Sains Islam Malaysia, Nilai, Negeri Sembilan, Malaysia
| | - Norazilah Mat Jin
- Department of Obstetrics & Gynecology, Faculty of Medicine, Universiti Teknologi MARA, Jalan Hospital, Sungai Buloh, Selangor, Malaysia
| | - Muhammad Azrai Abu
- Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | | | - Ani Amelia Zainuddin
- Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Nao Suzuki
- Department of Obstetrics & Gynecology, St Marianna School of Medicine, Kawasaki, Japan
| | - Abdul Kadir Abdul Karim
- Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
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Munawar WASWA, Elias MH, Addnan FH, Hassandarvish P, AbuBakar S, Roslan N. Gene expression profiling of host lipid metabolism in SARS-CoV-2 infected patients: a systematic review and integrated bioinformatics analysis. BMC Infect Dis 2024; 24:124. [PMID: 38263024 PMCID: PMC10807267 DOI: 10.1186/s12879-024-08983-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND The Coronavirus disease 2019 (COVID-19) pandemic occurred due to the dispersion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Severe symptoms can be observed in COVID-19 patients with lipid-related comorbidities such as obesity and diabetes. Yet, the extensive molecular mechanisms of how SARS-CoV-2 causes dysregulation of lipid metabolism remain unknown. METHODS Here, an advanced search of articles was conducted using PubMed, Scopus, EBSCOhost, and Web of Science databases using terms from Medical Subject Heading (MeSH) like SARS-CoV-2, lipid metabolism and transcriptomic as the keywords. From 428 retrieved studies, only clinical studies using next-generation sequencing as a gene expression method in COVID-19 patients were accepted. Study design, study population, sample type, the method for gene expression and differentially expressed genes (DEGs) were extracted from the five included studies. The DEGs obtained from the studies were pooled and analyzed using the bioinformatics software package, DAVID, to determine the enriched pathways. The DEGs involved in lipid metabolic pathways were selected and further analyzed using STRING and Cytoscape through visualization by protein-protein interaction (PPI) network complex. RESULTS The analysis identified nine remarkable clusters from the PPI complex, where cluster 1 showed the highest molecular interaction score. Three potential candidate genes (PPARG, IFITM3 and APOBEC3G) were pointed out from the integrated bioinformatics analysis in this systematic review and were chosen due to their significant role in regulating lipid metabolism. These candidate genes were significantly involved in enriched lipid metabolic pathways, mainly in regulating lipid homeostasis affecting the pathogenicity of SARS-CoV-2, specifically in mechanisms of viral entry and viral replication in COVID-19 patients. CONCLUSIONS Taken together, our findings in this systematic review highlight the affected lipid-metabolic pathways along with the affected genes upon SARS-CoV-2 invasion, which could be a potential target for new therapeutic strategies study in the future.
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Grants
- FRGS/1/2021/SKK0/USIM/02/2; USIM/FRGS/FPSK/KPT/50321 Ministry of Higher Education, Malaysia
- FRGS/1/2021/SKK0/USIM/02/2; USIM/FRGS/FPSK/KPT/50321 Ministry of Higher Education, Malaysia
- FRGS/1/2021/SKK0/USIM/02/2; USIM/FRGS/FPSK/KPT/50321 Ministry of Higher Education, Malaysia
- FRGS/1/2021/SKK0/USIM/02/2; USIM/FRGS/FPSK/KPT/50321 Ministry of Higher Education, Malaysia
- FRGS/1/2021/SKK0/USIM/02/2; USIM/FRGS/FPSK/KPT/50321 Ministry of Higher Education, Malaysia
- FRGS/1/2021/SKK0/USIM/02/2; USIM/FRGS/FPSK/KPT/50321 Ministry of Higher Education, Malaysia
- PPPI/FPSK/0121/USIM/16121 USIM Internal Grant Scheme, USIM
- PPPI/FPSK/0121/USIM/16121 USIM Internal Grant Scheme, USIM
- PPPI/FPSK/0121/USIM/16121 USIM Internal Grant Scheme, USIM
- PPPI/FPSK/0121/USIM/16121 USIM Internal Grant Scheme, USIM
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Affiliation(s)
| | - Marjanu Hikmah Elias
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Malaysia
| | - Faizul Helmi Addnan
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Malaysia
| | - Pouya Hassandarvish
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Nuruliza Roslan
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Malaysia.
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Crone KK, Jomori T, Miller FS, Gralnick JA, Elias MH, Freeman MF. RiPP enzyme heterocomplex structure-guided discovery of a bacterial borosin α- N-methylated peptide natural product. RSC Chem Biol 2023; 4:804-816. [PMID: 37799586 PMCID: PMC10549244 DOI: 10.1039/d3cb00093a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/18/2023] [Indexed: 10/07/2023] Open
Abstract
Amide peptide backbone methylation is a characteristic post-translational modification found in a family of ribosomally synthesized and post-translationally modified peptide natural products (RiPPs) called borosins. Previously, we bioinformatically identified >1500 putative borosin pathways in bacteria; however, none of the pathways were associated with a known secondary metabolite. Through in-depth characterization of a borosin pathway in Shewanella oneidensis MR-1, we have now identified a bacterially derived borosin natural product named Shewanellamide A. Borosin identification was facilitated by the creation and analysis of a series of precursor variants and crystallographic interrogation of variant precursor and methyltransferase complexes. Along with assaying two proteases from S. oneidensis, probable boundaries for proteolytic maturation of the metabolite were projected and confirmed via comparison of S. oneidensis knockout and overexpression strains. All in all, the S. oneidensis natural product was found to be a 16-mer linear peptide featuring two backbone methylations, establishing Shewanellamide A as one of the few borosin metabolites yet identified, and the first from bacteria.
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Affiliation(s)
- K K Crone
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota - Twin Cities St. Paul 55108 USA
| | - T Jomori
- The BioTechnology Institute, University of Minnesota - Twin Cities St. Paul 55108 USA
| | - F S Miller
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota - Twin Cities St. Paul 55108 USA
| | - J A Gralnick
- The BioTechnology Institute, University of Minnesota - Twin Cities St. Paul 55108 USA
- Department of Plant and Microbial Biology, University of Minnesota - Twin Cities St. Paul 55108 USA
| | - M H Elias
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota - Twin Cities St. Paul 55108 USA
- The BioTechnology Institute, University of Minnesota - Twin Cities St. Paul 55108 USA
| | - M F Freeman
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota - Twin Cities St. Paul 55108 USA
- The BioTechnology Institute, University of Minnesota - Twin Cities St. Paul 55108 USA
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Lazim N, Elias MH, Sutaji Z, Abdul Karim AK, Abu MA, Ugusman A, Syafruddin SE, Mokhtar MH, Ahmad MF. Expression of HOXA10 Gene in Women with Endometriosis: A Systematic Review. Int J Mol Sci 2023; 24:12869. [PMID: 37629050 PMCID: PMC10454210 DOI: 10.3390/ijms241612869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
The homeobox A10 (HOXA10) gene is known to be related to endometriosis; however, due to a lack of knowledge/evidence in the pathogenesis of endometriosis, the mechanisms that link HOXA10 to endometriosis still need to be clarified. This review addresses the difference in the expression of the HOXA10 gene in endometriotic women versus non-endometriotic women across populations by country and discusses its influences on women's fertility. An organized search of electronic databases was conducted in Scopus, ScienceDirect, PubMed, and Web of Science. The keywords used were (HOXA10 OR "homeobox A10" OR PL OR HOX1 OR HOX1H OR HOX1.8) AND ("gene expression") AND (endometriosis). The initial search resulted in 623 articles, 10 of which were included in this review. All ten papers included in this study were rated fair in terms of the quality of the studies conducted. The expression of the HOXA10 gene was found to be downregulated in most studies. However, one study provided evidence of the downregulation and upregulation of HOXA10 gene expression due to the localization of endometriotic lesions. Measuring the expression of the HOXA10 gene in women is clinically essential to predicting endometriosis, endometrial receptivity, and the development of pinopodes in the endometrium during the luteal phase.
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Affiliation(s)
- Nurunnajah Lazim
- Advanced Reproductive Centre (ARC) HCTM UKM, Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia; (N.L.); (M.H.E.); (Z.S.); (M.A.A.); (A.K.A.K.)
| | - Marjanu Hikmah Elias
- Advanced Reproductive Centre (ARC) HCTM UKM, Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia; (N.L.); (M.H.E.); (Z.S.); (M.A.A.); (A.K.A.K.)
- Faculty of Medicine & Health Sciences, Universiti Sains Islam Malaysia, Nilai 71800, Negeri Sembilan, Malaysia
| | - Zulazmi Sutaji
- Advanced Reproductive Centre (ARC) HCTM UKM, Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia; (N.L.); (M.H.E.); (Z.S.); (M.A.A.); (A.K.A.K.)
- Faculty of Medicine & Health Sciences, Universiti Sains Islam Malaysia, Nilai 71800, Negeri Sembilan, Malaysia
| | - Abdul Kadir Abdul Karim
- Advanced Reproductive Centre (ARC) HCTM UKM, Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia; (N.L.); (M.H.E.); (Z.S.); (M.A.A.); (A.K.A.K.)
| | - Mohammad Azrai Abu
- Advanced Reproductive Centre (ARC) HCTM UKM, Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia; (N.L.); (M.H.E.); (Z.S.); (M.A.A.); (A.K.A.K.)
| | - Azizah Ugusman
- Department of Physiology, Faculty of Medicine, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia; (A.U.); (M.H.M.)
| | - Saiful Effendi Syafruddin
- Medical Molecular Biology Institute, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia;
| | - Mohd Helmy Mokhtar
- Department of Physiology, Faculty of Medicine, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia; (A.U.); (M.H.M.)
| | - Mohd Faizal Ahmad
- Advanced Reproductive Centre (ARC) HCTM UKM, Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia; (N.L.); (M.H.E.); (Z.S.); (M.A.A.); (A.K.A.K.)
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Ahmad MF, Elias MH, Mat Jin N, Abu MA, Syafruddin SE, Zainuddin AA, Suzuki N, Abdul Karim AK. The spectrum of in vitro maturation in clinical practice: the current insight. Front Endocrinol (Lausanne) 2023; 14:1192180. [PMID: 37455921 PMCID: PMC10338224 DOI: 10.3389/fendo.2023.1192180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
In vitro oocyte maturation (IVM) has been used worldwide. Despite the long-term implementation, the uptake of this procedure to complement current in vitro fertilization (IVF) remains low. The main reason is likely due to the non-synchronization of protocol and definition criteria, leading to difficulty in collective proper outcome data worldwide and, thus, lack of understanding of the exact IVM procedure. The review aims to consolidate the current clinical practice of IVM by dissecting relevant publications to be tailored for a current spectrum of clinical practice. Nevertheless, the background theories of oocyte maturation were also explored to provide a comprehensive understanding of the basis of IVM theories. Additional discussion of other potential uses of IVM in the future, such as in ovarian tissue cryopreservation known as OTO-IVM for fertility preservation and among women with diminished ovarian reserve, was also explored. Otherwise, future collaboration among all IVM centers is paramount for better collection of clinical data to provide valid recommendations for IVM in clinical practice, especially in molecular integrity and possible DNA alteration if present for IVM offspring outcome safety purposes.
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Affiliation(s)
- Mohd Faizal Ahmad
- Department of Obstetrics and Gynecology, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Marjanu Hikmah Elias
- Faculty of Medicine Health Sciences, Universiti Sains Islam Malaysia, Nilai, Malaysia
| | - Norazilah Mat Jin
- Department of Obstetrics and Gynecology, Faculty of Medicine, Universiti Teknologi MARA, Jalan Hospital, Sungai Buloh Selangor, Malaysia
| | - Muhammad Azrai Abu
- Department of Obstetrics and Gynecology, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | | | - Ani Amelia Zainuddin
- Department of Obstetrics and Gynecology, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Nao Suzuki
- Department of Obstetrics Gynecology, St Marianna School of Medicine, Kawasaki, Japan
| | - Abdul Kadir Abdul Karim
- Department of Obstetrics and Gynecology, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
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Yuan WS, Abu MA, Ahmad MF, Elias MH, Abdul Karim AK. Effects of Dehydroepiandrosterone (DHEA) Supplementation on Ovarian Cumulus Cells following In Vitro Fertilization (IVF)/Intra-Cytoplasmic Sperm Injection (ICSI) Treatment-A Systematic Review. Life (Basel) 2023; 13:1237. [PMID: 37374020 DOI: 10.3390/life13061237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 06/29/2023] Open
Abstract
Despite many studies exploring the effects of DHEA supplementation, its application in IVF procedure continues to be a subject of debate owing to the inconsistent findings and the lack of rigorously designed, large-scale, randomized trials. Our review aims to explore the effectiveness of DHEA supplementation in ovarian cumulus cells following IVF/ICSI treatment. We conducted a literature search of Pub-Med, Ovid MEDLINE, and SCOPUS (inception to June 2022) for all relevant articles, including the keywords of "dehydroepiandrosterone/DHEA", "oocyte", and "cumulus cells". From the preliminary search, 69 publications were identified, and following a thorough screening process, seven studies were ultimately incorporated into the final review. Four hundred twenty-four women were enrolled in these studies, with DHEA supplementation being administered exclusively to women exhibiting poor ovarian response/diminished ovarian reserve or belonging to an older age demographic. The intervention in the studies was DHEA 75-90 mg daily for at least 8-12 weeks. The only randomized controlled trial showed no difference in clinical or cumulus cell-related outcomes between the control and treatment groups. However, the remaining six studies (two cohorts, four case-controls) showed significant beneficial effects of DHEA in cumulus cell-related outcomes compared to the group (older age or POR/DOR) without DHEA supplementation. All studies revealed no significant difference in stimulation and pregnancy outcomes. Our review concludes that DHEA supplementation did show beneficial effect on ovarian cumulus cells in improving oocyte quality for women of advanced age or with poor ovarian responders.
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Affiliation(s)
- Woon Shu Yuan
- Advanced Reproductive Center, Department of Obstetrics and Gynaecology, UKM Medical Centre, Kuala Lumpur 56000, Malaysia
| | - Muhammad Azrai Abu
- Advanced Reproductive Center, Department of Obstetrics and Gynaecology, UKM Medical Centre, Kuala Lumpur 56000, Malaysia
| | - Mohd Faizal Ahmad
- Advanced Reproductive Center, Department of Obstetrics and Gynaecology, UKM Medical Centre, Kuala Lumpur 56000, Malaysia
| | - Marjanu Hikmah Elias
- Faculty of Medicine & Health Sciences, Universiti Sains Islam Malaysia, Bandar Baru Nilai 71800, Malaysia
| | - Abdul Kadir Abdul Karim
- Advanced Reproductive Center, Department of Obstetrics and Gynaecology, UKM Medical Centre, Kuala Lumpur 56000, Malaysia
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Elias MH, Lazim N, Sutaji Z, Abu MA, Abdul Karim AK, Ugusman A, Syafruddin SE, Mokhtar MH, Ahmad MF. HOXA10 DNA Methylation Level in the Endometrium Women with Endometriosis: A Systematic Review. Biology (Basel) 2023; 12:biology12030474. [PMID: 36979165 PMCID: PMC10045497 DOI: 10.3390/biology12030474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Endometriosis is an inflammatory chronic systemic disease resulting in pelvic pain and infertility. However, despite a high prevalence of endometriosis, disease identification is still insufficient, and a high percentage of misdiagnosing was observed. Hence, a comprehensive study needs to be done to improve our understanding of the pathogenesis of endometriosis. Aberrant hypermethylation of HOXA10 has been reported to play a role in endometriosis. Thus, a comprehensive literature search was conducted to identify the DNA methylation level of HOXA10 among endometriosis patients across populations. The literature search was done using PubMed, Scopus, EBSCOhost, and Science Direct applying (HOXA10 OR "homeobox A10" OR "HOXA-10" OR HOX1) AND ("DNA methylation" OR methylation) AND (endometriosis OR endometrioma) as keywords. From 491 retrieved studies, five original articles investigating the DNA methylation level of HOXA10 from endometrium tissues among endometriosis women were included. All five included studies were classified as high-quality studies. High HOXA10 DNA methylation level was observed in the endometrium tissue of women with endometriosis in all the included studies. The secretory phase was identified as the best sampling time for HOXA10 DNA methylation study in endometriosis, and the most studied DNA methylation site is the promoter region of the HOXA10. However, more studies are needed to expose the HOXA10 mechanism in the pathogenesis of endometriosis.
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Affiliation(s)
- Marjanu Hikmah Elias
- Advanced Reproductive Centre (ARC) HCTM UKM, Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia
- Faculty of Medicine & Health Sciences, Universiti Sains Islam Malaysia, Nilai 71800, Negeri Sembilan, Malaysia
| | - Nurunnajah Lazim
- Advanced Reproductive Centre (ARC) HCTM UKM, Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia
| | - Zulazmi Sutaji
- Advanced Reproductive Centre (ARC) HCTM UKM, Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia
- Faculty of Medicine & Health Sciences, Universiti Sains Islam Malaysia, Nilai 71800, Negeri Sembilan, Malaysia
| | - Mohammad Azrai Abu
- Advanced Reproductive Centre (ARC) HCTM UKM, Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia
| | - Abdul Kadir Abdul Karim
- Advanced Reproductive Centre (ARC) HCTM UKM, Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia
| | - Azizah Ugusman
- Department of Physiology, Faculty of Medicine, National Univeristy of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia
| | - Saiful Effendi Syafruddin
- Medical Molecular Biology Institute, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia
| | - Mohd Helmy Mokhtar
- Department of Physiology, Faculty of Medicine, National Univeristy of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia
| | - Mohd Faizal Ahmad
- Advanced Reproductive Centre (ARC) HCTM UKM, Department of Obstetrics & Gynecology, Faculty of Medicine, National University of Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur 56000, Malaysia
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Elias MH, Das S, Abdul Hamid N. Candidate Genes and Pathways in Cervical Cancer: A Systematic Review and Integrated Bioinformatic Analysis. Cancers (Basel) 2023; 15:cancers15030853. [PMID: 36765810 PMCID: PMC9913780 DOI: 10.3390/cancers15030853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Cervical cancer is the leading cause of cancer-related death among women in developing countries. However, no comprehensive molecular mechanism for cervical cancer has been established, as many studies were small-cohort studies conducted with small sample sizes. A thorough literature search was performed using the PubMed, Scopus, EBSCOhost, and Science Direct databases. Medical Subject Heading (MeSH) terms such as "Uterine Cervical Neoplasms" and "gene expression" were used as the keywords in all fields. A total of 4027 studies were retrieved, and only clinical studies, which used the microarray method to identify differentially expressed genes (DEGs) in the cervical tissue of cervical cancer patients, were selected. Following the screening, 6 studies were selected and 1128 DEGs were extracted from the data. Sixty-two differentially expressed genes from at least two studies were selected for further analysis by DAVID, STRING, and Cytoscape software. In cervical cancer pathogenesis, three significant clusters with high intermolecular interactions from the Protein-Protein Interaction (PPI) network complex revealed three major molecular mechanisms, including cell signaling, cell cycle, and cell differentiation. Subsequently, eight genes were chosen as the candidate genes based on their involvement in the relevant gene ontology (GO) and their interaction with other genes in the PPI network through undirected first neighbor nodes. The present systematic review improves our understanding of the molecular mechanism of cervical cancer and the proposed genes that can be used to expand the biomarker panel in the screening for cervical cancer. The targeted genes may be beneficial for the development of better treatment strategies.
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Affiliation(s)
- Marjanu Hikmah Elias
- Department of Basic Medical Sciences I, Faculty of Medicine & Health Sciences, Universiti Sains Islam Malaysia, Nilai 71800, Malaysia
| | - Srijit Das
- Department of Human & Clinical Anatomy, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat 123, Oman
| | - Nazefah Abdul Hamid
- Department of Basic Medical Sciences I, Faculty of Medicine & Health Sciences, Universiti Sains Islam Malaysia, Nilai 71800, Malaysia
- Correspondence:
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Qatrun Nada D, Masniza ML, Abdullah N, Marlini M, Elias MH, Pathmanathan SG, Hayati AR, Fadlul Azim F, Hamid AA, Nur Fariha MM. Distinct microRNA expression pattern in breast cancer cells following anti-neoplastic treatment: A systematic review and functional analysis of microRNA target genes. Malays J Pathol 2022; 44:367-385. [PMID: 36591707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Breast cancer remains a significant cause of mortality in females worldwide, despite advances in technology and treatment. MicroRNA expression in breast cancer is studied both as potential biomarkers and for therapeutic purposes. Accumulated evidence revealed microRNA profile of various types of cancer cells following antineoplastic treatment. The progression of research in this area provides better understanding on the anti-cancer mechanism of various natural compounds and drugs specifically on the microRNA regulation. Hence, we aim to systematically review differentially expressed microRNA in MCF-7, a commonly studied breast cancer cell line, after treatment with anti-neoplastic agents. Relevant keywords were used to screen for research articles that reported on the differentially expressed microRNAs in experimental models of MCF-7 before and after anti-neoplastic treatment. Target genes of microRNAs were identified from MiRTarbase and further in silico functional analysis of the target genes were performed using DAVID bioinformatic resources. Two upregulated microRNAs (mir-200c and let-7d) and 3 downregulated microRNAs (mir-27a, mir-27b and mir-203) were identified by highest number of studies. Three microRNAs (let-7a, mir-23a and mir-7) showed inconsistent direction of expression. Genes functional analysis revealed the regulatory effect of microRNA on genes related to angiogenesis, hypoxia, P53, FoxO and PI3K-AKT signalling. Clusters of genes associated to the pathway of angiogenesis, cancers, cell proliferation and apoptosis were noted through protein-protein interaction analysis. MicroRNAs, especially the mir-200c, let-7d, mir-27a, mir-27b and mir-203 from this review could be further validated experimentally to serve as molecular target or biomarkers for anti-neoplastic therapy.
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Affiliation(s)
- D Qatrun Nada
- Universiti Sains Islam Malaysia, Faculty of Medicine and Health Sciences, Department of Medical Sciences I, 71800 Nilai, Negeri Sembilan, Malaysia
| | - M L Masniza
- Universiti Sains Islam Malaysia, Faculty of Medicine and Health Sciences, Department of Medical Sciences I, 71800 Nilai, Negeri Sembilan, Malaysia
| | - N Abdullah
- Universiti Sains Islam Malaysia, Faculty of Medicine and Health Sciences, Department of Medical Sciences II, 71800 Nilai, Negeri Sembilan, Malaysia
| | - M Marlini
- Universiti Sains Islam Malaysia, Faculty of Medicine and Health Sciences, Department of Medical Sciences I, 71800 Nilai, Negeri Sembilan, Malaysia
| | - M H Elias
- Universiti Sains Islam Malaysia, Faculty of Medicine and Health Sciences, Department of Medical Sciences I, 71800 Nilai, Negeri Sembilan, Malaysia
| | - S G Pathmanathan
- Universiti Sains Islam Malaysia, Faculty of Medicine and Health Sciences, Department of Medical Sciences II, 71800 Nilai, Negeri Sembilan, Malaysia
| | - A R Hayati
- Universiti Sains Islam Malaysia, Faculty of Medicine and Health Sciences, Department of Medical Sciences II, 71800 Nilai, Negeri Sembilan, Malaysia
| | - F Fadlul Azim
- Universiti Sains Islam Malaysia, Faculty of Medicine and Health Sciences, Department of Medical Sciences II, 71800 Nilai, Negeri Sembilan, Malaysia
| | - A A Hamid
- Universiti Kebangsaan Malaysia, Faculty of Medicine, Department of Physiology, 56000 Kuala Lumpur, Malaysia
| | - M M Nur Fariha
- Universiti Sains Islam Malaysia, Faculty of Medicine and Health Sciences, Department of Medical Sciences I, 71800 Nilai, Negeri Sembilan, Malaysia.
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Elias MH, Syed Mohamad SF, Abdul Hamid N. A Systematic Review of Candidate miRNAs, Its Targeted Genes and Pathways in Chronic Myeloid Leukemia-An Integrated Bioinformatical Analysis. Front Oncol 2022; 12:848199. [PMID: 35330714 PMCID: PMC8940286 DOI: 10.3389/fonc.2022.848199] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/15/2022] [Indexed: 12/04/2022] Open
Abstract
Chronic myeloid leukaemia is blood cancer due to a reciprocal translocation, resulting in a BCR-ABL1 oncogene. Although tyrosine kinase inhibitors have been successfully used to treat CML, there are still cases of resistance. The resistance occurred mainly due to the mutation in the tyrosine kinase domain of the BCR-ABL1 gene. However, there are still many cases with unknown causes of resistance as the etiopathology of CML are not fully understood. Thus, it is crucial to figure out the complete pathogenesis of CML, and miRNA can be one of the essential pathogeneses. The objective of this study was to systematically review the literature on miRNAs that were differentially expressed in CML cases. Their target genes and downstream genes were also explored. An electronic search was performed via PubMed, Scopus, EBSCOhost MEDLINE, and Science Direct. The following MeSH (Medical Subject Heading) terms were used: chronic myeloid leukaemia, genes and microRNAs in the title or abstract. From 806 studies retrieved from the search, only clinical studies with in-vitro experimental evidence on the target genes of the studied miRNAs in CML cells were included. Two independent reviewers independently scrutinised the titles and abstracts before examining the eligibility of studies that met the inclusion criteria. Study design, sample size, sampling type, and the molecular method used were identified for each study. The pooled miRNAs were analysed using DIANA tools, and target genes were analysed with DAVID, STRING and Cytoscape MCODE. Fourteen original research articles on miRNAs in CML were included, 26 validated downstream genes and 187 predicted target genes were analysed and clustered into 7 clusters. Through GO analysis, miRNAs’ target genes were localised throughout the cells, including the extracellular region, cytosol, and nucleus. Those genes are involved in various pathways that regulate genomic instability, proliferation, apoptosis, cell cycle, differentiation, and migration of CML cells.
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Affiliation(s)
- Marjanu Hikmah Elias
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Malaysia
| | - Syarifah Faezah Syed Mohamad
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Malaysia.,Faculty of Applied Sciences, Universiti Teknologi MARA Cawangan Pahang, Jengka, Malaysia
| | - Nazefah Abdul Hamid
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Malaysia
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11
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Sutaji Z, Elias MH, Ahmad MF, Karim AKA, Abu MA. A Systematic Review and Integrated Bioinformatic Analysis of Candidate Genes and Pathways in the Endometrium of Patients With Polycystic Ovary Syndrome During the Implantation Window. Front Endocrinol (Lausanne) 2022; 13:900767. [PMID: 35860699 PMCID: PMC9289743 DOI: 10.3389/fendo.2022.900767] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is a common disorder with wide-ranging clinical heterogeneity that causes infertility. However, the comprehensive molecular mechanisms of PCOS in causing infertility is remaining unclear. Hence, a comprehensive literature search was conducted using PubMed, Scopus, EBSCOhost, and Science Direct. Medical Subject Heading (MeSH) terms like PCOS, gene expression, implantation window and endometrium were used as the keywords. From 138 studies retrieved, original articles with RNA profiling on human endometrial tissues in PCOS women during the implantation window were included. Study design, sample size, sample type, method, and differentially expressed genes (DEGs) were identified from all publications. The DEGs were analyzed using the software packages DAVID, STRING, and Cytoscape. Three studies that met inclusion criteria were included, and 368 DEGs were identified. Twelve significant clusters from the protein-protein interaction network (PPI) complex were found, and cluster 1 showed very high intermolecular interactions. Five candidate genes (AURKA, CDC25C, KIF23, KIF2C, and NDC80) were identified from the systematic review and integrated bioinformatics analysis. It is concluded that cell cycle is the fundamental biological processes that were dysregulated in the endometrium of PCOS women, affecting decidualization progression in the endometrium during the implantation window.
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Affiliation(s)
- Zulazmi Sutaji
- Department of Obstetrics & Gynecology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
- Faculty of Medicine & Health Sciences, Universiti Sains Islam Malaysia, Bandar Baru Nilai, Malaysia
| | - Marjanu Hikmah Elias
- Faculty of Medicine & Health Sciences, Universiti Sains Islam Malaysia, Bandar Baru Nilai, Malaysia
| | - Mohd Faizal Ahmad
- Department of Obstetrics & Gynecology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Abdul Kadir Abdul Karim
- Department of Obstetrics & Gynecology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Muhammad Azrai Abu
- Department of Obstetrics & Gynecology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
- *Correspondence: Muhammad Azrai Abu,
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Mohamad SFS, Elias MH. Potential treatment for chronic myeloid leukemia using microRNA: in silico comparison between plants and human microRNAs in targeting BCR-ABL1 gene. Egypt J Med Hum Genet 2021. [DOI: 10.1186/s43042-021-00156-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Chronic myeloid leukemia (CML) is a myeloproliferative disorder characterized by the expression of the BCR-ABL1 fusion gene. Tyrosine kinase inhibitors (TKI) are used to treat CML, but mutations in the tyrosine kinase domain contribute to CML chemo-resistance. Therefore, finding alternative molecular-targeted therapy is important for the comprehensive treatment of CML. MicroRNAs (miRNA) are small non-coding regulatory RNAs which suppress the expression of their target genes by binding to the 3′ untranslated region (3′UTR) of the target mRNA. Hypothetically, the miRNA-mRNA interaction would suppress BCR-ABL1 expression and consequently reduce and inhibit CML cell proliferation. Thus, our objective was to determine the target interaction of human and plant miRNAs targeting the 3′UTR region of BCR-ABL1 in terms of miRNA binding conformity, protein interaction network, and pathways using in silico analysis. The 3′UTR sequence of BCR-ABL1 is obtained from Ensembl Genome Browser while the binding conformity was determined using the PsRNATarget Analysis Server, RNA22, Target Rank Server, and DIANA TOOLS. Protein-protein interaction network and pathway analysis are determined using STRING, Cytoscape, and KEGG pathway analysis.
Results
Five plants and five human miRNAs show strong binding conformity with 3′UTR of BCR-ABL1. The strongest binding conformity was shown by Oryza sativa’s Osa-miR1858a and osa-miR1858b with −24.4 kcal/mol folding energy and a p value of 0.0077. Meanwhile, in human miRNA, the hsa-miR-891a-3p shows the highest miTG score of 0.99 with −12 kcal/mol folding energy and a p value of 0.037. Apart from ABL1, osa-miR1858a/osa-miR1858b and hsa-miR891a-3p also target other 720 and 645 genes, respectively. The interaction network of Osa-miR1858a/osa-miR1858b and hsa-miR891a-3p identifies nineteen and twelve ABL1’s immediate neighboring proteins, respectively. The pathways analysis focuses on the RAS, MAPK, CML, and hematopoietic cell lineage pathway.
Conclusion
Both plant and human miRNAs tested in this study could be a potential therapeutic prospect in CML treatment, but thermodynamically, osa-miR1858a/osa-miR1858b binding to ABL1 is more favorable. However, it is important to carry out more research in vitro and in vivo and clinical studies to assess its efficacy as a targeted therapy for CML.
Graphical abstract
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Abdul Wahab N, Elias MH, Raja Ali RA, Mohd Mokhtar N. Chronic Consumption of Fructose Dysregulates Genes Related to Glucose and Lipid Metabolism in Prostate Tissue. SAINS MALAYS 2018. [DOI: 10.17576/jsm-2018-4710-27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Elias MH, Azlan H, Sulong S, Baba AA, Ankathil R. Aberrant DNA methylation at HOXA4 and HOXA5 genes are associated with resistance to imatinib mesylate among chronic myeloid leukemia patients. Cancer Rep (Hoboken) 2018; 1:e1111. [PMID: 32721103 DOI: 10.1002/cnr2.1111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 05/03/2018] [Accepted: 05/04/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Imatinib mesylate is a molecularly targeted tyrosine kinase inhibitor drug. It is effectively used in the treatment of chronic myeloid leukemia (CML) patients. However, development of resistance to imatinib mesylate as a result of BCR-ABL dependent and BCR-ABL independent mechanisms has emerged as a daunting problem in the management of CML patients. Between these mechanisms, BCR-ABL independent mechanisms are still not robustly understood. AIM To investigate the correlation of HOXA4 and HOXA5 promoter DNA hypermethylation with imatinib resistance among CML patients. METHODS AND RESULTS Samples from 175 Philadelphia positive CML patients (83 good response and 92 BCR-ABL non-mutated imatinib resistant patients) were subjected to Methylation Specific High Resolution Melt Analysis for methylation levels quantification of the HOXA4 and HOXA5 promoter regions. Receiver operating characteristic curve analysis was done to elucidate the optimal methylation cut-off point followed by multiple logistic regression analysis. Log-Rank analysis was done to measure the overall survival difference between CML groups. The optimal methylation cut-off point was found to be at 62.5% for both HOXA4 and HOXA5. Chronic myeloid leukemia patients with ≥63% HOXA4 and HOXA5 methylation level were shown to have 3.78 and 3.95 times the odds, respectively, to acquire resistance to imatinib. However, overall survival of CML patients that have ≤62% and ≥ 63% methylation levels of HOXA4 and HOXA5 genes were found to be not significant (P-value = 0.126 for HOXA4; P-value = 0.217 for HOXA5). CONCLUSION Hypermethylation of the HOXA4 and HOXA5 promoter is correlated with imatinib resistance and with further investigation, it could be a potential epigenetic biomarker in supplement to the BCR-ABL gene mutation in predicting imatinib treatment response among CML patients but could not be considered as a prognostic marker.
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Affiliation(s)
- Marjanu Hikmah Elias
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Malaysia
| | - Husin Azlan
- Haemato-Oncology Unit, Department of Internal Medicine, Universiti Sains Malaysia Hospital, Kota Bharu, Malaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | | | - Ravindran Ankathil
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
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Elias MH, Azlan H, Baba AA, Ankathil R. Aberrant DNA Methylation of SOCS1 Gene is Not Associated with Resistance to Imatinib Mesylate among Chronic Myeloid Leukemia Patients. Cardiovasc Hematol Disord Drug Targets 2018; 18:234-238. [PMID: 29669505 DOI: 10.2174/1871529x18666180419101416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/12/2018] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND In exploring the cause of Imatinib Mesylate (IM) resistance among Chronic Myeloid Leukemia (CML) patients who do not harbor BCR-ABL dependent mechanism, BCR-ABL independent pathways are the most probable pathways that should be explored. In BCR-ABL independent pathway, SOCS1 plays an important role as it helps in regulating optimal JAK/STAT activity. OBJECTIVE To identify the association of SOCS1 gene hypermethylation in mediating IM Resistance. METHOD The SOCS1 promoter methylation level of 92 BCR-ABL non mutated IM resistant CML patients, 83 IM good response CML patients and 5 normal samples from healthy individuals were measured using Methylation Specific-High Resolution Melt (MS-HRM) analysis. RESULTS Both primers used to amplify promoter region from -333 to -223 and from -332 to -188 showed less than 10% methylation in all CML and normal samples. Consequently, there was no significant difference in SOCS1 promoter methylation level between IM resistant and IM good response patients. CONCLUSION SOCS1 promoter methylation level is not suitable to be used as one of the biomarkers for predicting the possibility of acquiring resistance among CML patients treated with IM.
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Affiliation(s)
| | - Husin Azlan
- Haemato-Oncology Unit, Department of Internal Medicine, Universiti Sains Malaysia Hospital, Malaysia
| | - Abdul Aziz Baba
- International Medical University, Universiti Sains Malaysia, USM Pinang, Malaysia
| | - Ravindran Ankathil
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, USM Pinang, Malaysia
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16
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Loong TH, Soon NC, Nik Mahmud NRK, Naidu J, Rani RA, Abdul Hamid N, Elias MH, Mohamed Rose I, Tamil A, Mokhtar NM, Raja Ali RA. Serum pepsinogen and gastrin-17 as potential biomarkers for pre-malignant lesions in the gastric corpus. Biomed Rep 2017; 7:460-468. [PMID: 29181158 DOI: 10.3892/br.2017.985] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/21/2017] [Indexed: 02/07/2023] Open
Abstract
There is a lack of non-invasive screening modalities to diagnose chronic atrophic gastritis (CAG) and intestinal metaplasia (IM). Thus, the aim of the present study was to determine the sensitivity and specificity of serum pepsinogen I (PGI), PGI:II, the PGI:II ratio and gastrin-17 (G-17) in diagnosing CAG and IM, and the correlations between these serum biomarkers and pre-malignant gastric lesions. A cross-sectional study of 72 patients (82% of the calculated sample size) who underwent oesophageal-gastro-duodenoscopy for dyspepsia was performed in the present study. The mean age of the participants was 56.2±16.2 years. Serum PGI:I, PGI:II, G-17 and Helicobacter pylori antibody levels were measured by enzyme-linked immunosorbent assay. Median levels of PGI:I, PGI:II, the PGI:II ratio and G-17 for were 129.9 µg/l, 10.3 µg/l, 14.7 and 4.4 pmol/l, respectively. Subjects with corpus CAG/IM exhibited a significantly lower PGI:II ratio (7.2) compared with the control group (15.7; P<0.001). Histological CAG and IM correlated well with the serum PGI:II ratio (r=-0.417; P<0.001). The cut-off value of the PGI:II ratio of ≤10.0 demonstrated high sensitivity (83.3%), specificity (77.9%) and area under the receiver operating characteristic curve of 0.902 in detecting the two conditions. However, the sensitivity was particularly low at a ratio of ≤3.0. The serum PGI:II ratio is a sensitive and specific marker to diagnose corpus CAG/IM, but at a high cut-off value. This ratio may potentially be used as an outpatient, non-invasive biomarker for detecting corpus CAG/IM.
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Affiliation(s)
- Tan Han Loong
- Unit of Gastroenterology and Hepatology, Department of Medicine, Pusat Perubatan Universiti Kebangsaan Malaysia, Bandar Tun Razak, 56000 Kuala Lumpur, Malaysia
| | - Ngiu Chai Soon
- Unit of Gastroenterology and Hepatology, Department of Medicine, Pusat Perubatan Universiti Kebangsaan Malaysia, Bandar Tun Razak, 56000 Kuala Lumpur, Malaysia
| | - Nik Ritza Kosai Nik Mahmud
- Unit of Upper Gastrointestinal and Bariatric Surgery, Department of Surgery, Pusat Perubatan Universiti Kebangsaan Malaysia, Bandar Tun Razak, 56000 Kuala Lumpur, Malaysia
| | - Jeevinesh Naidu
- Unit of Gastroenterology and Hepatology, Department of Medicine, Pusat Perubatan Universiti Kebangsaan Malaysia, Bandar Tun Razak, 56000 Kuala Lumpur, Malaysia
| | - Rafiz Abdul Rani
- Unit of Gastroenterology and Hepatology, Department of Medicine, Pusat Perubatan Universiti Kebangsaan Malaysia, Bandar Tun Razak, 56000 Kuala Lumpur, Malaysia.,Faculty of Medicine, Universiti Teknologi MARA, 40450 Shah Alam, Selangor, Malaysia
| | - Nazefah Abdul Hamid
- Department of Physiology, Pusat Perubatan Universiti Kebangsaan Malaysia, Bandar Tun Razak, 56000 Kuala Lumpur, Malaysia.,Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, 71800 Negeri Sembilan, Malaysia
| | - Marjanu Hikmah Elias
- Department of Physiology, Pusat Perubatan Universiti Kebangsaan Malaysia, Bandar Tun Razak, 56000 Kuala Lumpur, Malaysia
| | - Isa Mohamed Rose
- Department of Pathology, Pusat Perubatan Universiti Kebangsaan Malaysia, Bandar Tun Razak, 56000 Kuala Lumpur, Malaysia
| | - Azmi Tamil
- Department of Community Health, Pusat Perubatan Universiti Kebangsaan Malaysia, Bandar Tun Razak, 56000 Kuala Lumpur, Malaysia
| | - Norfilza M Mokhtar
- Department of Physiology, Pusat Perubatan Universiti Kebangsaan Malaysia, Bandar Tun Razak, 56000 Kuala Lumpur, Malaysia
| | - Raja Affendi Raja Ali
- Unit of Gastroenterology and Hepatology, Department of Medicine, Pusat Perubatan Universiti Kebangsaan Malaysia, Bandar Tun Razak, 56000 Kuala Lumpur, Malaysia
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Yap E, Tumian NR, Azma RZ, Sharifah NA, Salwati S, Hamidah NH, Elias MH, Wong CL. Primary imatinib resistance in chronic myeloid leukemia patients in a developing country: BCR-ABL kinase domain mutations or BCR-ABL independent mechanisms? Malays J Pathol 2017; 39:107-113. [PMID: 28866691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Clinical resistance to imatinib (IM) in chronic myeloid leukemia (CML) carries adverse consequences. We investigated 22 CML patients who developed IM-resistance for BCR-ABL kinase domain (KD) mutations. The median follow-up for this study was 101.9 months (range: 22.2 to 176.5 months) and the estimated mean overall survival was 150.87 months (95% CI: 130.0 to 171.0). Five out of 22 patients tested positive for BCR-ABL KD mutations: 2 had T315I, 2 had E255K and 1 had V289F mutations. Of the remaining 17 patients who did not harbor BCR-ABL KD mutations, 11 patients received nilotinib while the rest continued on IM. All 17 achieved haematological remission but only 5 patients achieved complete cytogenetic remission, 4 of whom did so after switching to nilotinib. Our study shows that most of our IM-resistant patients do not test positive for BCR-ABL KD mutations by available testing methods and the role of second generation tyrosine kinase inhibitors remains undetermined. A critical analysis of the BCR-ABL KD mutations and the underlying mechanisms/ pathways of BCR-ABL independent IM-resistance along with potential treatments in the horizon will be discussed.
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Affiliation(s)
- E Yap
- Universiti Kebangsaan Malaysia Medical Centre, Department of Medicine, Haematology Unit, Malaysia.
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Naidu J, Wong Z, Palaniappan S, Ngiu CS, Yaacob NY, Abdul Hamid H, Hikmah Elias M, Mokhtar NM, Raja Ali RA. Radiation Exposure in Patients with Inflammatory Bowel Disease: a Fourteen-Year Review at a Tertiary Care Centre in Malaysia. Asian Pac J Cancer Prev 2017; 18:933-939. [PMID: 28545190 PMCID: PMC5494242 DOI: 10.22034/apjcp.2017.18.4.933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background and Aims: Patients with inflammatory bowel disease (IBD) are subjected to a large amount of ionizing radiation during the course of their illness. This may increase their risk of malignancy to a greater level than that due to the disease itself. In Caucasian patients with Crohn’s disease, this has been well documented and recommendations are in place to avoid high radiation imaging protocols. However, there are limited data available on radiation exposure in Asian IBD patients. We therefore sought to identify total radiation exposure and any differences between ethnically diverse ulcerative colitis (UC) and Crohn’s disease (CD) patients at our centre along with determining factors that may contribute to any variation. Methods: The cumulative effective dose (CED) was calculated retrospectively from 2000 to 2014 using data from our online radiology database and patients’ medical records. Total CED in the IBD population was measured. High exposure was defined as a radiation dose of greater than 0.2mSv (equivalent to slightly less than ½ a year of background radiation). Results: A total of 112 cases of IBD (36 CD and 76 UC) were reviewed. Our CD patients were diagnosed at an earlier age than our UC cases (mean age 26.1 vs 45.7). The total CED in our IBD population was 8.53 (95% CI: 4.53-12.52). Patients with CD were exposed to significantly higher radiation compared to those with UC. The mean CED was 18.6 (7.30-29.87) and 3.65 (1.74-5.56, p=0.01) for CD and UC patients respectively. 2 patients were diagnosed as having a malignancy during follow up with respective CED values of 1.76mSv and 10mSv. Conclusions: CD patients, particularly those with complicated disease, received a higher frequency of diagnostic imaging over a shorter period when compared to UC patients. Usage of low radiation imaging protocols should be encouraged in IBD patients to reduce their risk of consequent malignancy.
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Affiliation(s)
- Jeevinesh Naidu
- Gastroenterology Unit, Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia.
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Elias MH, Azlan H, Sulong S, Hassan R, Baba AA, Ankathil R. Molecular genetic and epigenetic markers of Imatinib resistance in chronic myeloid leukemia patients. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw522.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Rahman FA, Naidu J, Ngiu CS, Yaakob Y, Mohamed Z, Othman H, Jarmin R, Elias MH, Hamid NA, Mokhtar NM, Ali RR. Conventional versus Doxorubicin-Eluting Beads Transarterial Chemoembolization for Unresectable Hepatocellular Carcinoma: a Tertiary Medical Centre Experience in Malaysia. Asian Pac J Cancer Prev 2016; 17:4037-4041. [PMID: 27644658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a common cancer that is frequently diagnosed at an advanced stage. Transarterial chemoembolisation (TACE) is an effective palliative treatment for patients who are not eligible for curative treatment. The two main methods for performing TACE are conventional (c-TACE) or with drug eluting beads (DEB-TACE). We sought to compare survival rates and tumour response between patients undergoing c-TACE and DEB-TACE at our centre. MATERIALS AND METHODS A retrospective cohort study of patients undergoing either treatment was carried out from January 2009 to December 2014. Tumour response to the procedures was evaluated according to the modified Response Evaluation Criteria in Solid Tumors (mRECIST). Kaplan-Meier analysis was used to assess and compare the overall survival in the two groups. RESULTS A total of 79 patients were analysed (34 had c-TACE, 45 had DEB-TACE) with a median follow-up of 11.8 months. A total of 20 patients in the c-TACE group (80%) and 12 patients in the DEB-TACE group (44%) died during the follow up period. The median survival durations in the c-TACE and DEB-TACE groups were 4.9 ± 3.2 months and 8.3 ± 2.0 months respectively (p=0.008). There was no statistically significant difference noted among the two groups with respect to mRECIST criteria. CONCLUSIONS DEB-TACE demonstrated a significant improvement in overall survival rates for patients with unresectable HCC when compared to c-TACE. It is a safe and promising approach and should potentially be considered as a standard of care in the management of unresectable HCC.
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Affiliation(s)
- F Abdul Rahman
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia (UKM), Jalan Raja Muda Aziz, Kuala Lumpur, Malaysia E-mail :
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Elias MH, Baba AA, Azlan H, Rosline H, Sim GA, Padmini M, Fadilah SAW, Ankathil R. BCR-ABL kinase domain mutations, including 2 novel mutations in imatinib resistant Malaysian chronic myeloid leukemia patients-Frequency and clinical outcome. Leuk Res 2014; 38:454-9. [PMID: 24456693 DOI: 10.1016/j.leukres.2013.12.025] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 12/26/2013] [Accepted: 12/29/2013] [Indexed: 10/25/2022]
Abstract
Discovery of imatinib mesylate (IM) as the targeted BCR-ABL protein tyrosine kinase inhibitor (TKI) has resulted in its use as the frontline therapy for chronic myeloid leukemia (CML) across the world. Although high response rates are observed in CML patients who receive IM treatment, a significant number of patients develop resistance to IM. Resistance to IM in patients has been associated with a heterogeneous array of mechanisms of which point mutations within the ABL tyrosine kinase domain (TKD) are the frequently documented. The types and frequencies of mutations reported in different population studies have shown wide variability. We screened 125 Malaysian CML patients on IM therapy who showed either TKI refractory or resistance to IM to investigate the frequency and pattern of BCR-ABL kinase domain mutations among Malaysian CML patients undergoing IM therapy and to determine the clinical significance. Mutational screening using denaturing high performance liquid chromatography (dHPLC) followed by DNA sequencing was performed on 125 IM resistant Malaysian CML patients. Mutations were detected in 28 patients (22.4%). Fifteen different types of mutations (T315I, E255K, G250E, M351T, F359C, G251E, Y253H, V289F, E355G, N368S, L387M, H369R, A397P, E355A, D276G), including 2 novel mutations were identified, with T315I as the predominant type of mutation. The data generated from clinical and molecular parameters studied were correlated with the survival of CML patients. Patients with Y253H, M351T and E355G TKD mutations showed poorer prognosis compared to those without mutation. Interestingly, when the prognostic impact of the observed mutations was compared inter-individually, E355G and Y253H mutations were associated with more adverse prognosis and shorter survival (P=0.025 and 0.005 respectively) than T315I mutation. Results suggest that apart from those mutations occurring in the three crucial regions (catalytic domain, P-loop and activation-loop), other rare mutations also may have high impact in the development of resistance and adverse prognosis. Presence of mutations in different regions of BCR-ABL TKD leads to different levels of resistance and early detection of emerging mutant clones may help in decision making for alternative treatment. Serial monitoring of BCR-ABL1 transcripts in CML patients allows appropriate selection of CML patients for BCR-ABL1 KD mutation analysis associated with acquired TKI resistance. Identification of these KD mutations is essential in order to direct alternative treatments in such CML patients.
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Affiliation(s)
- Marjanu Hikmah Elias
- Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Malaysia
| | - Abdul Aziz Baba
- Haemato-Oncology Unit, Department of Internal Medicine, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Malaysia
| | - Husin Azlan
- Haemato-Oncology Unit, Department of Internal Medicine, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Malaysia
| | - Hassan Rosline
- Hematology Department, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Malaysia
| | | | | | | | - Ravindran Ankathil
- Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Malaysia.
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Elias MH, Baba AA, Husin A, Abdullah AD, Hassan R, Sim GA, Wahid SFA, Ankathil R. Contribution of BCR-ABL kinase domain mutations to imatinib mesylate resistance in Philadelphia chromosome positive Malaysian chronic myeloid leukemia patients. Hematol Rep 2012; 4:e23. [PMID: 23355941 PMCID: PMC3555211 DOI: 10.4081/hr.2012.e23] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 10/23/2012] [Accepted: 10/31/2012] [Indexed: 01/26/2023] Open
Abstract
Development of resistance to imatinib mesylate (IM) in chronic myeloid leukemia (CML) patients is mediated by different mechanisms that can be classified as BCR-ABL dependent or BCR-ABL independent pathways. BCR-ABL dependent mechanisms are most frequently associated with point mutations in tyrosine kinase domain (TKD) of BCR-ABL1 and also with BCR-ABL gene amplification. Many different types and frequencies of mutations have been reported in different studies, probably due to the different composition of study cohorts. Since no reports are available from Malaysia, this study was undertaken to investigate the frequency and pattern of BCR-ABL kinase domain mutations using dHPLC followed by sequencing, and also status of BCR-ABL gene amplification using fluorescence in situ hybridization (FISH) on 40 IM resistant Malaysian CML patients. Mutations were detected in 13 patients (32.5%). Five different types of mutations (T315I, E255K, Y253H, M351T, V289F) were identified in these patients. In the remaining 27 IM resistant CML patients, we investigated the contribution made by BCR-ABL gene amplification, but none of these patients showed amplification. It is presumed that the mechanisms of resistance in these 27 patients might be due to BCR-ABL independent pathways. Different mutations confer different levels of resistance and, therefore, detection and characterization of TKD mutations is highly important in order to guide therapy in CML patients.
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Elias MH, Ankathil R, Salmi AR, Sudhikaran W, Limprasert P, Zilfalil BA. A New Method for FMR1 Gene Methylation Screening by Multiplex Methylation-Specific Real-Time Polymerase Chain Reaction. Genet Test Mol Biomarkers 2011; 15:387-93. [DOI: 10.1089/gtmb.2010.0191] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Marjanu Hikmah Elias
- Human Genome Center, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Ravindran Ankathil
- Human Genome Center, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Abdul Razak Salmi
- Pediatric Department, Universiti Sains Malaysia Hospital, Kubang Kerian, Malaysia
| | - Wanna Sudhikaran
- Human Genetics Unit, Department of Pathology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
| | - Pornprot Limprasert
- Human Genetics Unit, Department of Pathology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
| | - Bin Alwi Zilfalil
- Pediatric Department, Universiti Sains Malaysia Hospital, Kubang Kerian, Malaysia
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