1
|
McLaren S, Seidler K, Neil J. Investigating the Role of 17β-Estradiol on the Serotonergic System, Targeting Soy Isoflavones as a Strategy to Reduce Menopausal Depression: A Mechanistic Review. J Am Nutr Assoc 2024; 43:221-235. [PMID: 37695875 DOI: 10.1080/27697061.2023.2255237] [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] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 07/13/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023]
Abstract
Low serotonin is one factor implicated in the development of depression. 17β-estradiol (E2) has been shown to modulate gene expression regulating the neurotransmission of serotonin. Sex hormone levels fluctuate dramatically during the menopausal transition, coinciding with a 14-fold increased risk of depression. This review aimed to examine the effect of soy isoflavones to support decreased and variable E2 levels before and after menopause, linked to an investigation of the pathophysiological mechanisms underlying the protective influence of E2 on the serotonin pathway. The overall aim of this review is to assess the potential of soy isoflavones to reduce depression in middle-aged women. A systematic literature search was performed in three stages. 1,421 papers were screened for relevance to the research aims and objectives. 63 papers were selected based on pre-defined inclusion/exclusion criteria (13 reviews, 24 mechanistic and 26 intervention studies) and critically appraised. Available research supported the hypotheses that E2 increases serotonin synthesis and availability through stimulation of tryptophan hydroxylase-2 (TPH-2) and decreased degradation by monoamine oxidase-A (MAO-A). There was less scientific agreement on the effects of E2 on serotonin transporter (SERT) and serotonin receptors 1 A and 2 A. Studies varied widely on the effectiveness of soy isoflavones in reducing depressive symptoms in (peri)menopausal women. Animal and human studies acknowledge women's increased risk of depression linked to fluctuating E2 rather than absolute levels. However, mechanisms linking E2 variability with depression remain an underrepresented area of research. Study limitations and heterogeneity may contribute to varying results for soy isoflavones and some effects of E2 on the serotonin pathway.
Collapse
Affiliation(s)
- Scotti McLaren
- Centre for Nutrition Education and Lifestyle Management (CNELM) and Middlesex University, Wokingham, United Kingdom
| | - Karin Seidler
- Centre for Nutrition Education and Lifestyle Management (CNELM) and Middlesex University, Wokingham, United Kingdom
| | - James Neil
- Centre for Nutrition Education and Lifestyle Management (CNELM) and Middlesex University, Wokingham, United Kingdom
| |
Collapse
|
2
|
Carvalho BF, Gomez GVB, Carron J, Macedo LT, Gonçalves GM, Vazquez VDL, Serrano SV, Lourenço GJ, Lima CSP. TNFRSF1B Gene Variants in Clinicopathological Aspects and Prognosis of Patients with Cutaneous Melanoma. Int J Mol Sci 2024; 25:2868. [PMID: 38474115 DOI: 10.3390/ijms25052868] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Regulatory T lymphocytes play a critical role in immune regulation and are involved in the aberrant cell elimination by facilitating tumor necrosis factor connection to the TNFR2 receptor, encoded by the TNFRSF1B polymorphic gene. We aimed to examine the effects of single nucleotide variants TNFRSF1B c.587T>G, c.*188A>G, c.*215C>T, and c.*922C>T on the clinicopathological characteristics and survival of cutaneous melanoma (CM) patients. Patients were genotyped using RT-PCR. TNFRSF1B levels were measured using qPCR. Luciferase reporter assay evaluated the interaction of miR-96 and miR-1271 with the 3'-UTR of TNFRSF1B. The c.587TT genotype was more common in patients younger than 54 years old than in older patients. Patients with c.*922CT or TT, c.587TG or GG + c.*922CT or TT genotypes, as well as those with the haplotype TATT, presented a higher risk of tumor progression and death due to the disease effects. Individuals with the c.*922TT genotype had a higher TNFRSF1B expression than those with the CC genotype. miR-1271 had less efficient binding with the 3'-UTR of the T allele when compared with the C allele of the SNV c.*922C>T. Our findings, for the first time, demonstrate that TNFRSF1B c.587T>G and c.*922C>T variants can serve as independent prognostic factors in CM patients.
Collapse
Affiliation(s)
- Bruna Fernandes Carvalho
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas 13083-888, SP, Brazil
| | - Gabriela Vilas Bôas Gomez
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas 13083-888, SP, Brazil
| | - Juliana Carron
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas 13083-888, SP, Brazil
| | - Ligia Traldi Macedo
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas 13083-888, SP, Brazil
- Department of Anesthesiology, Oncology, and Radiology, School of Medical Sciences, University of Campinas, Campinas 13083-888, SP, Brazil
| | - Gisele Melo Gonçalves
- Melanoma and Sarcoma Surgery Department, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil
| | - Vinicius de Lima Vazquez
- Melanoma and Sarcoma Surgery Department, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil
| | - Sergio Vicente Serrano
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil
| | - Gustavo Jacob Lourenço
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas 13083-888, SP, Brazil
| | - Carmen Silvia Passos Lima
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas 13083-888, SP, Brazil
- Department of Anesthesiology, Oncology, and Radiology, School of Medical Sciences, University of Campinas, Campinas 13083-888, SP, Brazil
| |
Collapse
|
3
|
Zeng G, Jin YZ, Huang Y, Hu JS, Li MF, Tian M, Lu J, Huang R. Transcriptomic Analysis of Type 2 Diabetes Mellitus Combined with Lower Extremity Atherosclerotic Occlusive Disease. Diabetes Metab Syndr Obes 2024; 17:997-1011. [PMID: 38435631 PMCID: PMC10909374 DOI: 10.2147/dmso.s432698] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/02/2024] [Indexed: 03/05/2024] Open
Abstract
Background The pathological damage mechanism of type 2 diabetes (T2D) and macroangiopathy is extremely complex, and T2D and arteriosclerosis obliterans have different biological behaviors and clinical features. To explore the mechanism of lower extremity arteriosclerosis occlusion (LEAOD) in T2D patients, we utilized RNA-seq to identify unique gene expression signatures of T2D and LEAOD through transcriptomic analysis. Methods We obtained blood samples and performed RNA sequencing from four patients with T2D, five of whom had LEAOD. Another six age- and gender-matched blood samples from healthy volunteers were used for control. By exploring the general and specific differential expression analysis after transcriptome sequencing, specific gene expression patterns of T2D and LEAOD were verified. Results Transcriptome analysis found differentially expressed genes in T2D, and T2D + LEAOD (vs normal) separately, of which 35/486 (T2D/T2D + LEAOD) were up-regulated and 1290/2970 (T2D/T2D + LEAOD) were down-regulated. A strong overlap of 571 genes across T2D, LEAOD, and coexisting conditions was mainly involved in extracellular exosomes and the transcription process. By exploring the sex difference gene expression features between T2D, T2D + LEAOD, and healthy controls, we noticed that sex chromosome-associated genes do not participate in the sexual dimorphism gene expression profiles of T2D and LEAOD. Protein-Protein Interaction Network analysis and drug target prediction provided the drug candidates to treat T2D and LEAOD. Conclusion This study provides some evidence at the transcript level to uncover the association of T2D with LEAOD. The screened hub genes and predicted target drugs may be therapeutic targets.
Collapse
Affiliation(s)
- Guang Zeng
- Department of General Surgery, Putuo Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, People’s Republic of China
| | - Yong-Zhi Jin
- Department of General Surgery, Putuo Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, People’s Republic of China
| | - Yi Huang
- Department of General Surgery, Putuo Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, People’s Republic of China
| | - Jun-Sheng Hu
- Department of General Surgery, Putuo Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, People’s Republic of China
| | - Meng-Fan Li
- Department of General Surgery, LiQun Hospital, Shanghai, 200333, People’s Republic of China
| | - Ming Tian
- Department of Burn, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People’s Republic of China
| | - Jun Lu
- Department of Endocrinology, Putuo Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, People’s Republic of China
| | - Rong Huang
- Department of General Surgery, Putuo Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, People’s Republic of China
| |
Collapse
|
4
|
Waheed S, Ramzan K, Ahmad S, Khan MS, Wajid M, Ullah H, Umar A, Iqbal R, Ullah R, Bari A. Identification and In-Silico study of non-synonymous functional SNPs in the human SCN9A gene. PLoS One 2024; 19:e0297367. [PMID: 38394191 PMCID: PMC10889873 DOI: 10.1371/journal.pone.0297367] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/29/2023] [Indexed: 02/25/2024] Open
Abstract
Single nucleotide polymorphisms are the most common form of DNA alterations at the level of a single nucleotide in the genomic sequence. Genome-wide association studies (GWAS) were carried to identify potential risk genes or genomic regions by screening for SNPs associated with disease. Recent studies have shown that SCN9A comprises the NaV1.7 subunit, Na+ channels have a gene encoding of 1988 amino acids arranged into 4 domains, all with 6 transmembrane regions, and are mainly found in dorsal root ganglion (DRG) neurons and sympathetic ganglion neurons. Multiple forms of acute hypersensitivity conditions, such as primary erythermalgia, congenital analgesia, and paroxysmal pain syndrome have been linked to polymorphisms in the SCN9A gene. Under this study, we utilized a variety of computational tools to explore out nsSNPs that are potentially damaging to heath by modifying the structure or activity of the SCN9A protein. Over 14 potentially damaging and disease-causing nsSNPs (E1889D, L1802P, F1782V, D1778N, C1370Y, V1311M, Y1248H, F1237L, M936V, I929T, V877E, D743Y, C710W, D623H) were identified by a variety of algorithms, including SNPnexus, SNAP-2, PANTHER, PhD-SNP, SNP & GO, I-Mutant, and ConSurf. Homology modeling, structure validation, and protein-ligand interactions also were performed to confirm 5 notable substitutions (L1802P, F1782V, D1778N, V1311M, and M936V). Such nsSNPs may become the center of further studies into a variety of disorders brought by SCN9A dysfunction. Using in-silico strategies for assessing SCN9A genetic variations will aid in organizing large-scale investigations and developing targeted therapeutics for disorders linked to these variations.
Collapse
Affiliation(s)
- Sana Waheed
- Faculty of Life Science, Department of Zoology, University of Okara, Okara, Pakistan
| | - Kainat Ramzan
- Faculty of Life Science, Department of Biochemistry, University of Okara, Okara, Pakistan
| | - Sibtain Ahmad
- Faculty of Animal Husbandry, Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Saleem Khan
- Faculty of Life Science, Department of Zoology, University of Okara, Okara, Pakistan
| | - Muhammad Wajid
- Faculty of Life Science, Department of Zoology, University of Okara, Okara, Pakistan
| | - Hayat Ullah
- Department of Chemistry, University of Okara, Okara, Pakistan
| | - Ali Umar
- Faculty of Life Science, Department of Zoology, University of Okara, Okara, Pakistan
| | - Rashid Iqbal
- Faculty of Agriculture and Environment, Department of Agronomy, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Riaz Ullah
- Department of Pharmacognosy College of Pharmacy King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Bari
- Department of Pharmaceutical Chemistry, College of Pharmacy King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
5
|
Savino F, Dini M, Clemente A, Calvi C, Pau A, Galliano I, Gambarino S, Bergallo M. Nasopharyngeal and Peripheral Blood Type II Interferon Signature Evaluation in Infants during Respiratory Syncytial Virus Infection. Medicina (Kaunas) 2024; 60:259. [PMID: 38399546 PMCID: PMC10890591 DOI: 10.3390/medicina60020259] [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] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
Background and Objectives: In this study, we applied one-step real time rt-PCR technology type II INF signature to blood and nasopharyngeal (NPS) swabs of acute early recovery children < 1 years hospitalized for bronchiolitis with laboratory-confirmed RSV infection. Materials and Methods: A prospective observational case-control study was conducted in 2021-2022. The study took place in Children Hospital "Regina Margherita", Torino Italy. The study included 66 infants, of which 30 patients were hospitalized for bronchiolitis due to RSV infection and 36 age-matched controls. Inclusion criteria included a positive RSV test for infants with bronchiolitis. We collected peripheral blood and nasopharyngeal swabs for relative quantification of type II Interferon signature by One-Step Multiplex PCR real time. Results: IFN levels were downregulated in the peripheral blood of bronchiolitis patients; these data were not confirmed in the nasopharyngeal swab. There was no correlation between NPS and the type II IFN score in peripheral blood. Conclusions: our study shows for the first time that type II IFN score was significant reduced in peripheral blood of infants with bronchiolitis by RSV compared to age-matched healthy controls; in the NPS swab this resulted downregulation was not statistically significant and the type II IFN score in the NPS swab can be used as marker of resolution of infection or improvement of clinical conditions.
Collapse
Affiliation(s)
- Francesco Savino
- Early Infancy Special Care Unit, Regina Margherita Children Hospital, A.O.U. Città della Salute e della Scienza di Torino, 10126 Torino, Italy;
| | - Maddalena Dini
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- BioMole srl, Via Quarello 15/A, 10135 Turin, Italy
| | - Anna Clemente
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
| | - Cristina Calvi
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children’s Hospital, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Anna Pau
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
| | - Ilaria Galliano
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children’s Hospital, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Stefano Gambarino
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- BioMole srl, Via Quarello 15/A, 10135 Turin, Italy
| | - Massimiliano Bergallo
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- BioMole srl, Via Quarello 15/A, 10135 Turin, Italy
- Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children’s Hospital, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| |
Collapse
|
6
|
Yeo H, Ahn SS, Ou S, Yun SJ, Lim Y, Koh D, Lee YH, Shin SY. The EGR1-Artemin Axis in Keratinocytes Enhances the Innervation of Epidermal Sensory Neurons during Skin Inflammation Induced by House Dust Mite Extract from Dermatophagoidesfarinae. J Invest Dermatol 2024:S0022-202X(24)00090-3. [PMID: 38302010 DOI: 10.1016/j.jid.2024.01.017] [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: 06/27/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 02/03/2024]
Abstract
Epidermal hyperinnervation is a critical feature of pruritus during skin inflammation. However, the mechanisms underlying epidermal hyperinnervation are unclear. This study investigates the role of the transcription factor EGR1 in epidermal innervation by utilizing wild-type (Egr1+/+) and Egr1-null (Egr1‒/‒) mice topically applied Dermatophagoides farinae extract from dust mite. Our findings revealed that Egr1‒/‒ mice exhibited reduced scratching behaviors and decreased density of epidermal innervation compared with Egr1+/+ mice. Furthermore, we identified artemin, a neurotrophic factor, as an EGR1 target responsible for Dermatophagoides farinae extract-induced hyperinnervation. It has been demonstrated that Dermatophagoides farinae extract stimulates toll-like receptors in keratinocytes. To elucidate the cellular mechanism, we stimulated keratinocytes with Pam3CSK4, a toll-like receptor 1/2 ligand. Pam3CSK4 triggered a toll-like receptor 1/2-mediated signaling cascade involving IRAK4, IκB kinase, MAPKs, ELK1, EGR1, and artemin, leading to increased neurite outgrowth and neuronal migration. In addition, increased expression of EGR1 and artemin was observed in the skin tissues of patients with atopic dermatitis. These findings highlight the significance of the EGR1-artemin axis in keratinocytes, promoting the process of epidermal innervation and suggesting it as a potential therapeutic target for alleviating itch and pain associated with house dust mite-induced skin inflammation.
Collapse
Affiliation(s)
- Hyunjin Yeo
- Department of Biological Sciences, Sang-huh College of Life Science, Konkuk University, Seoul, Republic of Korea
| | - Sung Shin Ahn
- Department of Biological Sciences, Sang-huh College of Life Science, Konkuk University, Seoul, Republic of Korea
| | - Sukjin Ou
- Department of Biological Sciences, Sang-huh College of Life Science, Konkuk University, Seoul, Republic of Korea
| | - Sook Jung Yun
- Department of Dermatology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Yoongho Lim
- Division of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Dongsoo Koh
- Department of Applied Chemistry, Dongduk Women's University, Seoul, Republic of Korea
| | - Young Han Lee
- Department of Biological Sciences, Sang-huh College of Life Science, Konkuk University, Seoul, Republic of Korea; Cancer and Metabolism Institute, Konkuk University, Seoul, Republic of Korea
| | - Soon Young Shin
- Department of Biological Sciences, Sang-huh College of Life Science, Konkuk University, Seoul, Republic of Korea; Cancer and Metabolism Institute, Konkuk University, Seoul, Republic of Korea.
| |
Collapse
|
7
|
Nagaraj CB, Brightman DS, Rea H, Wakefield E, Harkavy NVG, Dyer L, Zhang W. Detection of a novel gross deletion in the UNC13D gene ends the diagnostic odyssey for a family with familial hemophagocytic lymphohistiocytosis 3. BMC Pediatr 2024; 24:34. [PMID: 38212754 PMCID: PMC10782673 DOI: 10.1186/s12887-023-04510-3] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 12/26/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Familial hemophagocytic lymphohistiocytosis (FHL) is an immunological disorder characterized by overactivation of macrophages and T lymphocytes. This autosomal recessive condition has been characterized into multiple types depending on the genetic etiology. FHL type 3 is associated with bi-allelic pathogenic variants in the UNC13D gene. CASE PRESENTATION We present a 12-year diagnostic odyssey for a family with FHL that signifies the advances of FHL genetic testing in a clinical genetic diagnostic laboratory setting. We describe the first case of a large UNC13D gross deletion in trans to a nonsense variant in a family with FHL3, which may have been mediated by Alu elements within introns 12 and 25 of the UNC13D gene. CONCLUSIONS This case highlights the importance of re-evaluating past genetic testing for a patient and family as test technology evolves in order to end a diagnostic odyssey.
Collapse
Affiliation(s)
- Chinmayee B Nagaraj
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Diana S Brightman
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH, 45229, USA
| | - Hannah Rea
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH, 45229, USA
| | - Emily Wakefield
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH, 45229, USA
| | - Nina V G Harkavy
- Department of OB/GYN, Columbia University Vagelos College of Physicians and Surgeons, New York City, NY, USA
| | - Lisa Dyer
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Wenying Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7016, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| |
Collapse
|
8
|
Hossain MU, Ahammad I, Moniruzzaman M, Akter Lubna M, Bhattacharjee A, Mahmud Chowdhury Z, Ahmed I, Hosen MB, Biswas S, Chandra Das K, Keya CA, Salimullah M. Investigation of pathogenic germline variants in gastric cancer and development of "GasCanBase" database. Cancer Rep (Hoboken) 2023; 6:e1906. [PMID: 37867380 PMCID: PMC10728505 DOI: 10.1002/cnr2.1906] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/29/2023] [Accepted: 09/14/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. AIM The aim of this study is to examine the nsSNP in GC-associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC-associated genes and their impacts. METHODS AND RESULTS A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named "GasCanBase" was developed to make data available to researchers. CONCLUSION The findings of this study and the "GasCanBase" database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/.
Collapse
Affiliation(s)
| | - Ishtiaque Ahammad
- Bioinformatics DivisionNational Institute of BiotechnologyDhakaBangladesh
| | - Md. Moniruzzaman
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| | | | | | | | - Istiak Ahmed
- Department of PharmacyNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Md. Billal Hosen
- Department of PharmacyNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Shourov Biswas
- Department of Clinical OncologyBangabandhu Sheikh Mujib Medical UniversityDhakaBangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and MicrobiologyNorth South UniversityDhakaBangladesh
| | - Md. Salimullah
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| |
Collapse
|
9
|
You Y, Wang W, Zhu W, Xu J. Identification of functional lncRNAs in atrial fibrillation based on RNA sequencing. BMC Cardiovasc Disord 2023; 23:539. [PMID: 37932671 PMCID: PMC10626701 DOI: 10.1186/s12872-023-03573-5] [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: 04/20/2023] [Accepted: 10/22/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Atrial fibrillation (AF) is one of the most common arrhythmia contributing to serious conditions such as stroke and heart failure. Recent studies demonstrated that long noncoding RNAs (lncRNAs) were related to cardiovascular disease. However, the molecular mechanisms of AF are not fully clear. This study intended to discover lncRNAs that are differentially expressed in AF compared with controls and evaluate the potential functions of these lncRNAs. METHODS Ninety-seven patients (49 patients with AF and 48 patients without AF) were included in this study. Among these patients, leucocyte suspensions of 3 AF patients and 3 controls were sent for RNA-seq analysis to select differentially expressed lncRNA and mRNA. Different lncRNA expressions were validated in another samples (46 AF patients and 45 controls). Gene ontology (GO) enrichment analysis was conducted to annotate the function of selected mRNAs. Alternative splicing (AS) analysis was performed and a lncRNA-mRNA network was also constructed. The receiver operating characteristics (ROC) curve was used to evaluate diagnostic values. Logistic regression analysis was utilized to assess the risk or protective factor of AF. RESULTS A total of 223 mRNAs and 105 lncRNAs were detected in AF patients compared with controls. Total 4 lncRNAs (LINC01781, AC009509.2, AL662844.3, AL662844.4) associated with AF were picked out for validation in another samples by quantitative real-time PCR (qRT-PCR), detecting that upregulated AC009509.2 and downregulated LINC01781 in AF patients. Multivariate logistic regression analysis illustrated that left atrial diameter (OR 1.201; 95% CI 1.093-1.320; P=0.000) and AC009509.2 (OR 1.732; 95% CI 1.092-2.747; P=0.020) were related to AF respectively. ROC curve showed that AC009509.2, LINC01781 and left atrial diameter (LAD) were predictors of AF. For LINC01781, the area under the curve (AUC) was 0.654 (95% CI 0.541-0.767, P=0.0113). For AC009509.2, the AUC was 0.710 (95% CI 0.599-0.822, P=0.0005). Bioinformatic methods (GO enrichment, AS analysis and lncRNA-mRNA network construction) were performed to reveal the role of lncRNAs. CONCLUSIONS This study discussed differentially expressed lncRNA and their potential interaction with mRNA in AF. LncRNA AC009509.2 could be a new potential biomarker for AF prediction.
Collapse
Affiliation(s)
- Yangyang You
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Wei Wang
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Wenshu Zhu
- Department of Cardiology, Bengbu First People's Hospital, Bengbu, Anhui, 233000, China
| | - Jian Xu
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
| |
Collapse
|
10
|
Al-Maini M, Maindarkar M, Kitas GD, Khanna NN, Misra DP, Johri AM, Mantella L, Agarwal V, Sharma A, Singh IM, Tsoulfas G, Laird JR, Faa G, Teji J, Turk M, Viskovic K, Ruzsa Z, Mavrogeni S, Rathore V, Miner M, Kalra MK, Isenovic ER, Saba L, Fouda MM, Suri JS. Artificial intelligence-based preventive, personalized and precision medicine for cardiovascular disease/stroke risk assessment in rheumatoid arthritis patients: a narrative review. Rheumatol Int 2023; 43:1965-1982. [PMID: 37648884 DOI: 10.1007/s00296-023-05415-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
The challenges associated with diagnosing and treating cardiovascular disease (CVD)/Stroke in Rheumatoid arthritis (RA) arise from the delayed onset of symptoms. Existing clinical risk scores are inadequate in predicting cardiac events, and conventional risk factors alone do not accurately classify many individuals at risk. Several CVD biomarkers consider the multiple pathways involved in the development of atherosclerosis, which is the primary cause of CVD/Stroke in RA. To enhance the accuracy of CVD/Stroke risk assessment in the RA framework, a proposed approach involves combining genomic-based biomarkers (GBBM) derived from plasma and/or serum samples with innovative non-invasive radiomic-based biomarkers (RBBM), such as measurements of synovial fluid, plaque area, and plaque burden. This review presents two hypotheses: (i) RBBM and GBBM biomarkers exhibit a significant correlation and can precisely detect the severity of CVD/Stroke in RA patients. (ii) Artificial Intelligence (AI)-based preventive, precision, and personalized (aiP3) CVD/Stroke risk AtheroEdge™ model (AtheroPoint™, CA, USA) that utilizes deep learning (DL) to accurately classify the risk of CVD/stroke in RA framework. The authors conducted a comprehensive search using the PRISMA technique, identifying 153 studies that assessed the features/biomarkers of RBBM and GBBM for CVD/Stroke. The study demonstrates how DL models can be integrated into the AtheroEdge™-aiP3 framework to determine the risk of CVD/Stroke in RA patients. The findings of this review suggest that the combination of RBBM with GBBM introduces a new dimension to the assessment of CVD/Stroke risk in the RA framework. Synovial fluid levels that are higher than normal lead to an increase in the plaque burden. Additionally, the review provides recommendations for novel, unbiased, and pruned DL algorithms that can predict CVD/Stroke risk within a RA framework that is preventive, precise, and personalized.
Collapse
Affiliation(s)
- Mustafa Al-Maini
- Allergy, Clinical Immunology and Rheumatology Institute, Toronto, ON, L4Z 4C4, Canada
| | - Mahesh Maindarkar
- Stroke Monitoring and Diagnostic Division, AtheroPoint™, Roseville, CA, 95661, USA
- Asia Pacific Vascular Society, New Delhi, 110001, India
| | - George D Kitas
- Academic Affairs, Dudley Group NHS Foundation Trust, Dudley, DY1 2HQ, UK
- Arthritis Research UK Epidemiology Unit, Manchester University, Manchester, M13 9PL, UK
| | - Narendra N Khanna
- Asia Pacific Vascular Society, New Delhi, 110001, India
- Department of Cardiology, Indraprastha APOLLO Hospitals, New Delhi, 110001, India
| | | | - Amer M Johri
- Division of Cardiology, Department of Medicine, Queen's University, Kingston, Canada
| | - Laura Mantella
- Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Canada
| | - Vikas Agarwal
- Department of Immunology, SGPIMS, Lucknow, 226014, India
| | - Aman Sharma
- Department of Immunology, SGPIMS, Lucknow, 226014, India
| | - Inder M Singh
- Stroke Monitoring and Diagnostic Division, AtheroPoint™, Roseville, CA, 95661, USA
| | - George Tsoulfas
- Department of Surgery, Aristoteleion University of Thessaloniki, 54124, Thessaloniki, Greece
| | - John R Laird
- Heart and Vascular Institute, Adventist Health St. Helena, St Helena, CA, 94574, USA
| | - Gavino Faa
- Department of Pathology, Azienda Ospedaliero Universitaria, 09124, Cagliari, Italy
| | - Jagjit Teji
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Monika Turk
- The Hanse-Wissenschaftskolleg Institute for Advanced Study, 27753, Delmenhorst, Germany
| | - Klaudija Viskovic
- Department of Radiology and Ultrasound, UHID, 10 000, Zagreb, Croatia
| | - Zoltan Ruzsa
- Invasive Cardiology Division, University of Szeged, Szeged, Hungary
| | - Sophie Mavrogeni
- Cardiology Clinic, Onassis Cardiac Surgery Centre, Athens, Greece
| | - Vijay Rathore
- Nephrology Department, Kaiser Permanente, Sacramento, CA, 95823, USA
| | - Martin Miner
- Men's Health Centre, Miriam Hospital Providence, Providence, RI, 02906, USA
| | - Manudeep K Kalra
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Esma R Isenovic
- Department of Radiobiology and Molecular Genetics, National Institute of the Republic of Serbia, University of Belgrade, 11000, Belgrade, Serbia
| | - Luca Saba
- Department of Radiology, Azienda Ospedaliero Universitaria, 40138, Cagliari, Italy
| | - Mostafa M Fouda
- Department of Electrical and Computer Engineering, Idaho State University, Pocatello, ID, 83209, USA
| | - Jasjit S Suri
- Stroke Monitoring and Diagnostic Division, AtheroPoint™, Roseville, CA, 95661, USA.
| |
Collapse
|
11
|
Ghazal H, Tahar A, Mason T. Are Community Pharmacists Ready to Deliver Pharmacogenomics Testing Services? Pharmacy (Basel) 2023; 11:170. [PMID: 37987380 PMCID: PMC10661254 DOI: 10.3390/pharmacy11060170] [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: 09/17/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023] Open
Abstract
This study assesses the readiness and willingness of community pharmacists in England to deliver the pharmacogenomic (PG) testing service. A survey covering demographics and four key themes including awareness and training, general views and experience, barriers, willingness, and confidence was distributed to community pharmacies in the boroughs of Croydon and Sutton in South London. A total of 51 pharmacists responded to the survey. The study revealed that most respondents had a limited familiarity or understanding of pharmacogenomics (n = 32, 63%). Moreover, on average, around 60% of participants were unable to accurately identify drugs that currently have or could have potentials for PG testing. They indicated that their pharmacogenomic education and training is inadequate, with only 2/51 pharmacists reported receiving relevant training. Time constraints, shortage of staff and lack of knowledge were identified as barriers that could hinder the implementation of PG. Over 60% of respondents expressed willingness to provide PG testing service after receiving adequate training. The study found that currently not all community pharmacists are prepared to provide PG testing services, with newly qualified pharmacists appearing to have an upper hand when it comes to understanding the subject. Therefore, consistent, and uniform training is required to allow community pharmacists with all years of experience to equally contribute to the implementation of PG testing.
Collapse
Affiliation(s)
- Heba Ghazal
- School of Life Sciences, Pharmacy and Chemistry, Kingston University London, Kingston Upon Thames, London KT1 2EE, UK
| | | | | |
Collapse
|
12
|
Maan SS, Brar JS, Mittal A, Gill MIS, Arora NK, Sohi HS, Chhuneja P, Dhillon GS, Singh N, Thakur S. Construction of a genetic linkage map and QTL mapping of fruit quality traits in guava ( Psidium guajava L.). Front Plant Sci 2023; 14:1123274. [PMID: 37426984 PMCID: PMC10324979 DOI: 10.3389/fpls.2023.1123274] [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] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/08/2023] [Indexed: 07/11/2023]
Abstract
Guava (Psidium guajava L.) is an important fruit crop of the Indian sub-continent, with potential for improvements in quality and yield. The goal of the present study was to construct a genetic linkage map in an intraspecific cross between the elite cultivar 'Allahabad Safeda' and the Purple Guava landrace to identify the genomic regions responsible for important fruit quality traits, viz., total soluble solids, titratable acidity, vitamin C, and sugars. This population was phenotyped in field trials (as a winter crop) for three consecutive years, and showed moderate-to-high values of heterogeneity coefficients along with higher heritability (60.0%-97.0%) and genetic-advance-over-mean values (13.23%-31.17%), suggesting minimal environmental influence on the expression of fruit-quality traits and indicating that these traits can be improved by phenotypic selection methods. Significant correlations and strong associations were also detected among fruit physico-chemical traits in segregating progeny. The constructed linkage map consisted of 195 markers distributed across 11 chromosomes, spanning a length of 1,604.47 cM (average inter-loci distance of 8.80 markers) and with 88.00% coverage of the guava genome. Fifty-eight quantitative trait loci (QTLs) were detected in three environments with best linear unbiased prediction (BLUP) values using the composite interval mapping algorithm of the BIP (biparental populations) module. The QTLs were distributed on seven different chromosomes, explaining 10.95%-17.77% of phenotypic variance, with the highest LOD score being 5.96 for qTSS.AS.pau-6.2. Thirteen QTLs detected across multiple environments with BLUPs indicate stability and utility in a future breeding program for guava. Furthermore, seven QTL clusters with stable or common individual QTLs affecting two or more different traits were located on six linkage groups (LGs), explaining the correlation among fruit-quality traits. Thus, the multiple environmental evaluations conducted here have increased our understanding of the molecular basis of phenotypic variation, providing the basis for future high-resolution fine-mapping and paving the way for marker-assisted breeding of fruit-quality traits.
Collapse
Affiliation(s)
| | | | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Naresh Kumar Arora
- Department of Fruit Science, Punjab Agricultural University, Ludhiana, India
| | - Harjot Singh Sohi
- Krishi Vigyan Kendra, Guru Angad Dev Veterinary and Animal Sciences University, Barnala, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Navdeep Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Sujata Thakur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| |
Collapse
|
13
|
Ahammad I, Jamal TB, Bhattacharjee A, Chowdhury ZM, Rahman S, Hassan MR, Hossain MU, Das KC, Keya CA, Salimullah M. Impact of highly deleterious non-synonymous polymorphisms on GRIN2A protein's structure and function. PLoS One 2023; 18:e0286917. [PMID: 37319252 PMCID: PMC10270607 DOI: 10.1371/journal.pone.0286917] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/25/2023] [Indexed: 06/17/2023] Open
Abstract
GRIN2A is a gene that encodes NMDA receptors found in the central nervous system and plays a pivotal role in excitatory synaptic transmission, plasticity and excitotoxicity in the mammalian central nervous system. Changes in this gene have been associated with a spectrum of neurodevelopmental disorders such as epilepsy. Previous studies on GRIN2A suggest that non-synonymous single nucleotide polymorphisms (nsSNPs) can alter the protein's structure and function. To gain a better understanding of the impact of potentially deleterious variants of GRIN2A, a range of bioinformatics tools were employed in this study. Out of 1320 nsSNPs retrieved from the NCBI database, initially 16 were predicted as deleterious by 9 tools. Further assessment of their domain association, conservation profile, homology models, interatomic interaction, and Molecular Dynamic Simulation revealed that the variant I463S is likely to be the most deleterious for the structure and function of the protein. Despite the limitations of computational algorithms, our analyses have provided insights that can be a valuable resource for further in vitro and in vivo research on GRIN2A-associated diseases.
Collapse
Affiliation(s)
- Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Tabassum Binte Jamal
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Arittra Bhattacharjee
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Zeshan Mahmud Chowdhury
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Suparna Rahman
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka, Bangladesh
| | - Md Rakibul Hassan
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka, Bangladesh
| | - Mohammad Uzzal Hossain
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| |
Collapse
|
14
|
Shinwari K, Wu Y, Rehman HM, Xiao N, Bolkov M, Tuzankina I, Chereshnev V. In-silico assessment of high-risk non-synonymous SNPs in ADAMTS3 gene associated with Hennekam syndrome and their impact on protein stability and function. BMC Bioinformatics 2023; 24:251. [PMID: 37322437 DOI: 10.1186/s12859-023-05361-6] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/25/2023] [Indexed: 06/17/2023] Open
Abstract
Hennekam Lymphangiectasia-Lymphedema Syndrome 3 (HKLLS3) is a rare genetical disorder caused by mutations in a few genes including ADAMTS3. It is characterized by lymphatic dysplasia, intestinal lymphangiectasia, severe lymphedema and distinctive facial appearance. Up till now, no extensive studies have been conducted to elucidate the mechanism of the disease caused by various mutations. As a preliminary investigation of HKLLS3, we sorted out the most deleterious nonsynonymous single nucleotide polymorphisms (nsSNPs) that might affect the structure and function of ADAMTS3 protein by using a variety of in silico tools. A total of 919 nsSNPs in the ADAMTS3 gene were identified. 50 nsSNPs were predicted to be deleterious by multiple computational tools. 5 nsSNPs (G298R, C567Y, A370T, C567R and G374S) were found to be the most dangerous and can be associated with the disease as predicted by different bioinformatics tools. Modelling of the protein shows it can be divided into segments 1, 2 and 3, which are connected by short loops. Segment 3 mainly consists of loops without substantial secondary structures. With prediction tools and molecular dynamics simulation, some SNPs were found to significantly destabilize the protein structure and disrupt the secondary structures, especially in segment 2. The deleterious effects of mutations in segment 1 are possibly not from destabilization but from other factors such as the change in phosphorylation as suggested by post-translational modification (PTM) studies. This is the first-ever study of ADAMTS3 gene polymorphism, and the predicted nsSNPs in ADAMST3, some of which have not been reported yet in patients, will serve for diagnostic purposes and further therapeutic implications in Hennekam syndrome, contributing to better diagnosis and treatment.
Collapse
Affiliation(s)
- Khyber Shinwari
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia.
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia.
| | - Yurong Wu
- Department of Chemistry, Hong Kong University of Science and Technology, Hong Kong, China
| | | | - Ningkun Xiao
- Department of Psychology, Ural Federal University, Yekaterinburg, Russia
| | - Mikhail Bolkov
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia
| | - Irina Tuzankina
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia
| | - Valery Chereshnev
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia
| |
Collapse
|
15
|
Dehghani K, Stanek A, Bagherabadi A, Atashi F, Beygi M, Hooshmand A, Hamedi P, Farhang M, Bagheri S, Zolghadri S. CCND1 Overexpression in Idiopathic Dilated Cardiomyopathy: A Promising Biomarker? Genes (Basel) 2023; 14:1243. [PMID: 37372424 DOI: 10.3390/genes14061243] [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: 05/04/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Cardiomyopathy, a disorder of electrical or heart muscle function, represents a type of cardiac muscle failure and culminates in severe heart conditions. The prevalence of dilated cardiomyopathy (DCM) is higher than that of other types (hypertrophic cardiomyopathy and restrictive cardiomyopathy) and causes many deaths. Idiopathic dilated cardiomyopathy (IDCM) is a type of DCM with an unknown underlying cause. This study aims to analyze the gene network of IDCM patients to identify disease biomarkers. Data were first extracted from the Gene Expression Omnibus (GEO) dataset and normalized based on the RMA algorithm (Bioconductor package), and differentially expressed genes were identified. The gene network was mapped on the STRING website, and the data were transferred to Cytoscape software to determine the top 100 genes. In the following, several genes, including VEGFA, IGF1, APP, STAT1, CCND1, MYH10, and MYH11, were selected for clinical studies. Peripheral blood samples were taken from 14 identified IDCM patients and 14 controls. The RT-PCR results revealed no significant differences in the expression of the genes APP, MYH10, and MYH11 between the two groups. By contrast, the STAT1, IGF1, CCND1, and VEGFA genes were overexpressed in patients more than in controls. The highest expression was found for VEGFA, followed by CCND1 (p < 0.001). Overexpression of these genes may contribute to disease progression in patients with IDCM. However, more patients and genes need to be analyzed in order to achieve more robust results.
Collapse
Affiliation(s)
- Khatereh Dehghani
- Department of Cardiology, Jahrom University of Medical Sciences, Jahrom 7414846199, Iran
| | - Agata Stanek
- Department and Clinic of Internal Medicine, Angiology and Physical Medicine, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Batorego 15 Street, 41-902 Bytom, Poland
| | - Arash Bagherabadi
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil 5619911367, Iran
| | - Fatemeh Atashi
- Faculty of Medicine, Jahrom University of Medical Sciences, Jahrom 7414846199, Iran
| | - Mohammad Beygi
- Department of Agricultural Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan 8415683111, Iran
| | - Amirreza Hooshmand
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences & Technology, Tehran Medical Sciences, Islamic Azad University, Tehran 1916893813, Iran
| | - Pezhman Hamedi
- Research Center, Department of Medical Laboratory Sciences, Faculty of Medicine, Jahrom University of Medical Sciences, Jahrom 7414846199, Iran
| | - Mohsen Farhang
- Molecular Study and Diagnostic Center, Jahrom University of Medical Sciences, Jahrom 7414846199, Iran
| | - Soghra Bagheri
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah 6714415185, Iran
| | - Samaneh Zolghadri
- Department of Biology, Jahrom Branch, Islamic Azad University, Jahrom 7414785318, Iran
| |
Collapse
|
16
|
Xu D, Shao Q, Zhou C, Mahmood A, Zhang J. In Silico Analysis of nsSNPs of Human KRAS Gene and Protein Modeling Using Bioinformatic Tools. ACS Omega 2023; 8:13362-13370. [PMID: 37065036 PMCID: PMC10099408 DOI: 10.1021/acsomega.3c00804] [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] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
The KRAS gene belongs to the RAS family and codes for 188 amino acid residues of KRAS protein, with a molecular mass of 21.6 kD. Non-synonymous single-nucleotide polymorphisms (nsSNPs) have been identified within the coding region in which some are associated with different diseases. However, structural changes are not well defined yet. In this study, we first categorized SNPs in the KRAS coding area and then used computational methods to determine their impact on the protein structure and stability. In addition, the three-dimensional model of KRAS was taken from the Protein Data Bank for structural modeling. Furthermore, genomic data were extracted from a variety of sources, including the 1000 Genome Project, dbSNPs, and ENSEMBLE, and assessed through in silico methods. Based on various tools used in this study, 10 out of 48 missense SNPs with rsIDs were found deleterious. The substitution of alanine for proline at position 146 pushed several residues toward the center of the protein. Arginine instead of leucine has a minor effect on protein structure and stability. In addition, the substitution of proline for leucine at the 34th position disrupted the structure and led to a bigger size than the wild-type protein, hence interrupting the protein interaction. Using the well-intended computational approach and applying several bioinformatic tools, we characterized and identified most damaging nsSNPs and further explored the structural dynamics and stability of KRAS protein.
Collapse
Affiliation(s)
- Duoduo Xu
- Oncology
Department, Wenzhou Hospital of Traditional
Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, Wenzhou 325000, China
| | - Qiqi Shao
- Department
of Nursing, Central Health Center of Zeya
Town, Ouhai District, Wenzhou 325000, China
| | - Chen Zhou
- Ultrasonography
Department, Wenzhou Hospital of Traditional
Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, Wenzhou 325099, China
| | - Arif Mahmood
- Center
for Medical Genetics and Hunan Key Laboratory of Medical Genetics,
School of Life Sciences, Central South University, Changsha 410078, Hunan, China
| | - Jizhou Zhang
- Oncology
Department, Wenzhou Hospital of Traditional
Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, Wenzhou 325000, China
| |
Collapse
|
17
|
Ikemoto K, Fujimoto H, Fujimoto A. Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes. Hum Genomics 2023; 17:21. [PMID: 36895025 PMCID: PMC9996862 DOI: 10.1186/s40246-023-00467-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/01/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Long-read sequencing technologies have the potential to overcome the limitations of short reads and provide a comprehensive picture of the human genome. However, the characterization of repetitive sequences by reconstructing genomic structures at high resolution solely from long reads remains difficult. Here, we developed a localized assembly method (LoMA) that constructs highly accurate consensus sequences (CSs) from long reads. METHODS We developed LoMA by combining minimap2, MAFFT, and our algorithm, which classifies diploid haplotypes based on structural variants and CSs. Using this tool, we analyzed two human samples (NA18943 and NA19240) sequenced with the Oxford Nanopore sequencer. We defined target regions in each genome based on mapping patterns and then constructed a high-quality catalog of the human insertion solely from the long-read data. RESULTS The assessment of LoMA showed a high accuracy of CSs (error rate < 0.3%) compared with raw data (error rate > 8%) and superiority to a previous study. The genome-wide analysis of NA18943 and NA19240 identified 5516 and 6542 insertions (≥ 100 bp), respectively. Most insertions (~ 80%) were derived from tandem repeats and transposable elements. We also detected processed pseudogenes, insertions in transposable elements, and long insertions (> 10 kbp). Finally, our analysis suggested that short tandem duplications are associated with gene expression and transposons. CONCLUSIONS Our analysis showed that LoMA constructs high-quality sequences from long reads with substantial errors. This study revealed the true structures of the insertions with high accuracy and inferred the mechanisms for the insertions, thus contributing to future human genome studies. LoMA is available at our GitHub page: https://github.com/kolikem/loma .
Collapse
Affiliation(s)
- Ko Ikemoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo, Japan
| | - Hinano Fujimoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo, Japan
| | - Akihiro Fujimoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo, Japan.
| |
Collapse
|
18
|
Abdallah HY, Fareed A, Abdelmaogood AKK, Allam S, Abdelgawad M, Deen LATE. Introducing Circulating Vasculature-Related Transcripts as Biomarkers in Coronary Artery Disease. Mol Diagn Ther 2023; 27:243-259. [PMID: 36538237 PMCID: PMC10008268 DOI: 10.1007/s40291-022-00622-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Atherosclerotic plaque is considered the hallmark of atherosclerotic lesions in coronary atherosclerosis (CAS), the primary pathogenesis in coronary artery disease (CAD), which develops and progresses through a complex interplay between immune cells, vascular cells, and endothelial shear stresses. Early diagnosis of CAS is critical for avoiding plaque rupture and sudden death. Therefore, identifying new CAD biomarkers linked to vessel wall functions, such as RNA molecules with their distinct signature, is a promising development for these patients. With this rationale, the present study investigated the expression level of the vascular-related RNA transcripts (lncRNA ANRIL, miRNA-126-5p, CDK4, CDK6, TGF-β, E-cadherin, and TNF-α) implicated in the cellular vascular function, proliferation, and inflammatory processes. METHODS A case-control study design with a total of 180 subjects classified participants into two groups; CAD and control groups. The relative expression levels of the seven transcripts under study-selected using online bioinformatics tools and current literature-were assessed in the plasma of all study participants using RT-qPCR. Their predictive significance testing, scoring of disease prioritization, enrichment analysis, and the miRNA-mRNA regulatory network was investigated. RESULTS The relative expression levels of all seven of the circulating vascular-related transcripts under study were statistically significant between CAD patients and controls. Receiver operating characteristic (ROC) analysis results indicated the statistical significance of all the transcripts under study with CDK4 showing the highest area under the curve (AUC) equivalent to 0.91, followed by E-cadherin (0.90), miRNA-126-5p (0.83), ANRIL (0.82), TNF-α (0.63), TGF-β (0.62), and CDK6 (0.59), in descending order. A strong association was detected between most of the transcripts studied in CAD patients with a significant Spearman's correlation coefficient with a two-tailed significance of p < 0.001. Network analysis revealed a strong relationship between the five circulating vasculature transcripts studied and their target miRNAs and miR-126-5p, but not for ANRIL. CONCLUSION The seven circulating vascular-related RNA transcripts under study could serve as potential CAD biomarkers, reflecting the cellular vascular function, proliferation, and inflammatory processes in CAD patients. Therefore, blood transcriptome analysis opens new frontiers for the non-invasive diagnosis of CAD.
Collapse
Affiliation(s)
- Hoda Y Abdallah
- Medical Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt. .,Center of Excellence in Molecular and Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.
| | - Ahmed Fareed
- Department of Cardiology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Asmaa K K Abdelmaogood
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Sahar Allam
- Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Mai Abdelgawad
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences (PSAS), Beni-Suef University, Beni-Suef, Egypt
| | - Loaa A Tag El Deen
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| |
Collapse
|
19
|
Arshad MW, Shabbir MI, Asif S, Shahzad M, Leydier L, Rai SK. FRMD7 Gene Alterations in a Pakistani Family Associated with Congenital Idiopathic Nystagmus. Genes (Basel) 2023; 14:genes14020346. [PMID: 36833273 PMCID: PMC9957179 DOI: 10.3390/genes14020346] [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] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Congenital idiopathic nystagmus (CIN) is an oculomotor disorder characterized by repetitive and rapid involuntary movement of the eye that usually develops in the first six months after birth. Unlike other forms of nystagmus, CIN is widely associated with mutations in the FRMD7 gene. This study involves the molecular genetic analysis of a consanguineous Pakistani family with individuals suffering from CIN to undermine any potential pathogenic mutations. Blood samples were taken from affected and normal individuals of the family. Genomic DNA was extracted using an in-organic method. Whole Exome Sequencing (WES) and analysis were performed to find any mutations in the causative gene. To validate the existence and co-segregation of the FRMD7 gene variant found using WES, sanger sequencing was also carried out using primers that targeted all of the FRMD7 coding exons. Additionally, the pathogenicity of the identified variant was assessed using different bioinformatic tools. The WES results identified a novel nonsense mutation in the FRMD7 (c.443T>A; p. Leu148 *) gene in affected individuals from the Pakistani family, with CIN resulting in a premature termination codon, further resulting in the formation of a destabilized protein structure that was incomplete. Co-segregation analysis revealed that affected males are hemizygous for the mutated allele c.443T>A; p. Leu148 * and the affected mother is heterozygous. Overall, such molecular genetic studies expand our current knowledge of the mutations associated with the FRMD7 gene in Pakistani families with CIN and significantly enhance our understanding of the molecular mechanisms involved in genetic disorders.
Collapse
Affiliation(s)
- Muhammad Waqar Arshad
- Department of Psychiatry, Yale School of Medicine, VA CT Healthcare Center S116A2, West Haven, CT 06516, USA
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44080, Pakistan
| | - Muhammad Imran Shabbir
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Sector H-10, Islamabad 44000, Pakistan
- Correspondence: (M.I.S.); (S.K.R.)
| | - Saaim Asif
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Sector H-10, Islamabad 44000, Pakistan
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Islamabad 45550, Pakistan
| | - Mohsin Shahzad
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44080, Pakistan
| | - Larissa Leydier
- Department of Molecular Biology, Medical University of the Americas, Charlestown KN 1102, Saint Kitts and Nevis, West Indies
| | - Sunil Kumar Rai
- Department of Molecular Biology, Medical University of the Americas, Charlestown KN 1102, Saint Kitts and Nevis, West Indies
- Correspondence: (M.I.S.); (S.K.R.)
| |
Collapse
|
20
|
de Castro GAP, Petean IBF, de Paula-Silva FWG, Kuchler EC, Antunes LDS, Segato RAB, da Silva LAB, Silva-Sousa AC, Sousa-Neto MD. Genetic polymorphism in the tumour necrosis factor alpha gene (G-308A) is associated with persistent apical periodontitis in Brazilians. Int Endod J 2023; 56:17-26. [PMID: 36183324 DOI: 10.1111/iej.13841] [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: 05/03/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 12/13/2022]
Abstract
AIM To investigate if there was an association between genetic polymorphisms in tumour necrosis factor (TNF)-⍺ and its receptors TNFRSF1A and TNFRSF1B with persistent apical periodontitis (PAP) in Brazilian subjects. METHODOLOGY Patients who had pulpal necrosis and apical periodontitis at the time of treatment, with at least 1-year of follow-up after non-surgical root canal treatment were recalled. Three hundred and seventy eight subjects were included, 150 subjects with signs/symptoms of PAP and 228 subjects with root canal-treated teeth exhibiting healthy perirradicular tissues (healed). Genomic DNA was extracted from saliva and used for TNF-⍺ (rs1800629), TNFRSF1A (rs1800693) and TNFRSF1B (rs1061622) genotyping by real-time PCR. Genotypes and alleles frequencies were evaluated by c2 or Fisher's exact tests and odds ratios were implemented (α = 5%). RESULTS The genetic polymorphism in TNF-α (rs1800629) was associated as a protective factor for the development of PAP (p < .05), once subjects who presented at least one allele A (AA+AG X GG), had a higher chance to lesion repair (p < .05). The polymorphisms rs1800693 and rs1061622 in TNF receptors (TNFRSF1A and TNFRSF1B, respectively) were not associated with the development of PAP (p > .05). CONCLUSIONS The observed results demonstrate that polymorphism in TNF-α but not in its receptors is associated with PAP.
Collapse
Affiliation(s)
| | - Igor Bassi Ferreira Petean
- Department of Restorative Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | | | - Erika Calvano Kuchler
- Department of Pediatric Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, São Paulo, Brazil.,Department of Orthodontics, University of Regensburg, Regensburg, Germany
| | - Leonardo Dos Santos Antunes
- Research Unit, Fluminense Federal University, Rio de Janeiro, Brazil.,Specific Formation Department, School of Dentistry of Nova Friburgo, Fluminense Federal University, Rio de Janeiro, Brazil
| | - Raquel Assed Bezerra Segato
- Department of Pediatric Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Lea Assed Bezerra da Silva
- Department of Pediatric Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Alice Corrêa Silva-Sousa
- Department of Restorative Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Manoel Damião Sousa-Neto
- Department of Restorative Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
21
|
Ong CSB, Fok RW, Tan RCA, Fung SM, Sun S, Ngeow JYY. General practitioners' (GPs) experience, attitudes and needs on clinical genetic services: a systematic review. Fam Med Community Health 2022; 10:fmch-2021-001515. [PMID: 36450397 PMCID: PMC9717000 DOI: 10.1136/fmch-2021-001515] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
OBJECTIVE The proliferation and growing demands of genetic testing are anticipated to revolutionise medical practice. As gatekeepers of healthcare systems, general practitioners (GPs) are expected to play a critical role in the provision of clinical genetic services. This paper aims to review existing literature on GPs' experience, attitudes and needs towards clinical genetic services. DESIGN A systematic mixed studies review of papers published between 2010 and 2022. ELIGIBILITY CRITERIA The inclusion criterion was peer-reviewed articles in English and related to GPs' experience, views and needs on any genetic testing. INFORMATION SOURCES The PubMed, PsycINFO, Cochrane, EMBASE databases were searched using Mesh terms, Boolean and wildcards combinations to identify peer-reviewed articles published from 2010 to 2022. Study quality was assessed using Mixed Methods Appraisal Tool. Only articles that fulfilled the inclusion criteria were selected. A thematic meta-synthesis was conducted on the final sample of selected articles to identify key themes. RESULTS A total of 62 articles were included in the review. Uncertainty over GPs' role in providing genetic services were attributed by the lack of confidence and time constraints and rarity of cases may further exacerbate their reluctance to shoulder an expanded role in clinical genetics. Although educational interventions were found to increasing GPs' knowledge and confidence to carry out genetic tasks, varied interest on genetic testing and preference for a shared care model with other genetic health professionals have resulted in minimal translation to clinical adoption. CONCLUSION This review highlights the need for deeper exploration of GPs' varied experience and attitudes towards clinical genetic services to better facilitate targeted intervention in the adoption of clinical genetics.
Collapse
Affiliation(s)
- Cheryl Siow Bin Ong
- Sociology, School of Social Sciences, Nanyang Technological University, Singapore
| | - Rose Wai‑Yee Fok
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Ryo Chee Ann Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Si Ming Fung
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Shirley Sun
- Sociology, School of Social Sciences, Nanyang Technological University, Singapore
| | - Joanne Yuen Yie Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| |
Collapse
|
22
|
Sychev D, Fedina L, Poptsova M, Zateyshchikov D, Mirzaev K, Tsimbal E, Sychev I, Rastvorova T. A survey of physician opinions in Russia in the field of pharmacogenetics of cardiovascular disease. Pharmacogenomics 2022; 23:847-856. [PMID: 36093937 DOI: 10.2217/pgs-2022-0048] [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] [Indexed: 11/21/2022] Open
Abstract
Aims: To study the readiness of Russian physicians with experience and younger physicians undergoing clinical residency and postgraduate education to apply pharmacogenetic testing in their clinical practice. Materials & methods: The sociological study involved physicians (n = 378) living in different regions of the Russian Federation, as well as residents and graduate students (n = 185) of the Russian Medical Academy of Continuing Professional Medical Education. The survey consisted of 35 questions, and 23 were created on the online platform of professional surveys, Testograf.ru. Results: Every second respondent was willing to use pharmacogenetic testing in clinical practice to predict the efficacy and safety of medications in patients with cardiovascular disease (p = 0.06). Factors impeding the clinical implementation of pharmacogenetic testing in Russia were identified: physicians' ignorance of pharmacogenetics (p = 0.015), a lack of pharmacogenetic testing in clinical guidelines and treatment standards (p = 0.175) and a lack of economic justification for using pharmacogenetic testing (p = 0.320). Conclusion: Russian physicians have a positive attitude toward pharmacogenetic testing. However, the level of test implementation remains low.
Collapse
Affiliation(s)
- Dmitry Sychev
- Russian Medical Academy of Continuous Professional Education of The Ministry of Health of The Russian Federation, 2/1 Barrikadnaya Street, Moscow, 123995, Russian Federation
| | - Ludmila Fedina
- Russian Medical Academy of Continuous Professional Education of The Ministry of Health of The Russian Federation, 2/1 Barrikadnaya Street, Moscow, 123995, Russian Federation
| | - Maria Poptsova
- Laboratory of Bioinformatics, Big Data & Information Retrieval School, Faculty of Computer Science, National Research University Higher School of Economics, 3 Kochnovsky Proezd, Moscow, 109028, Russian Federation
| | - Dmitry Zateyshchikov
- National Medical Research Center for Cardiology, Laboratory of Functional Genomics of Cardiovascular Diseases, Moscow, 121552, Russian Federation
| | - Karin Mirzaev
- Russian Medical Academy of Continuous Professional Education of The Ministry of Health of The Russian Federation, 2/1 Barrikadnaya Street, Moscow, 123995, Russian Federation
| | - Evgeny Tsimbal
- Russian Medical Academy of Continuous Professional Education of The Ministry of Health of The Russian Federation, 2/1 Barrikadnaya Street, Moscow, 123995, Russian Federation
| | - Igor Sychev
- Russian Medical Academy of Continuous Professional Education of The Ministry of Health of The Russian Federation, 2/1 Barrikadnaya Street, Moscow, 123995, Russian Federation
| | - Tatiana Rastvorova
- Russian Medical Academy of Continuous Professional Education of The Ministry of Health of The Russian Federation, 2/1 Barrikadnaya Street, Moscow, 123995, Russian Federation
| |
Collapse
|
23
|
Meng H, Ruan J, Yan Z, Chen Y, Liu J, Li X, Meng F. New Progress in Early Diagnosis of Atherosclerosis. Int J Mol Sci 2022; 23:ijms23168939. [PMID: 36012202 PMCID: PMC9409135 DOI: 10.3390/ijms23168939] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/30/2022] [Accepted: 08/06/2022] [Indexed: 11/18/2022] Open
Abstract
Coronary atherosclerosis is a potentially chronic circulatory condition that endangers human health. The biological cause underpinning cardiovascular disease is coronary atherosclerosis, and acute cardiovascular events can develop due to thrombosis, platelet aggregation, and unstable atherosclerotic plaque rupture. Coronary atherosclerosis is progressive, and three specific changes appear, with fat spots and stripes, atherosclerosis and thin-walled fiber atherosclerosis, and then complex changes in arteries. The progression and severity of cardiovascular disease are correlated with various levels of calcium accumulation in the coronary artery. The therapy and diagnosis of coronary atherosclerosis benefit from the initial assessment of the size and degree of calcification. This article will discuss the new progress in the early diagnosis of coronary atherosclerosis in terms of three aspects: imaging, gene and protein markers, and trace elements. This study intends to present the latest methods for diagnosing patients with early atherosclerosis through a literature review.
Collapse
Affiliation(s)
- Heyu Meng
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
| | - Jianjun Ruan
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
| | - Zhaohan Yan
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
| | - Yanqiu Chen
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
| | - Jinsha Liu
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
| | - Xiangdong Li
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
| | - Fanbo Meng
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Correspondence: ; Tel.: +86-15948346855
| |
Collapse
|
24
|
Chakraborty M, Rao A, Mohanty K. Role of Mitochondrial Mutations in Ocular Aggregopathy. Cureus 2022; 14:e27129. [PMID: 36004037 PMCID: PMC9392836 DOI: 10.7759/cureus.27129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2022] [Indexed: 12/01/2022] Open
Abstract
Background Mitochondria are essential cellular organelles that are responsible for oxidative stress-induced damage in age-dependent neurodegenerations such as glaucoma. Previous studies have linked mitochondrial DNA (mtDNA) mutations to cellular energy shortages that result in eye degeneration. Methodology To look for nucleotide variations in mtDNA in exfoliation syndrome/glaucoma (XFS/XFG), we performed a polymerase chain reaction (PCR) to amplify the entire coding region of the mitochondrial genome from peripheral blood of XFS/XFG (n = 25) patients and controls (n = 25). Results This study identified a total of 65 variations in XFS/XFG patients, of which 25 (38%) variations were non-synonymous single-nucleotide polymorphism (nsSNPs). Out of 25 nsSNPs, seven (five nsSNP in MT-ND4 and two in MT-ATP6 gene) were predicted as pathogenic using four different software, namely, SIFT, Polyphene2, mutation taster, and MutPred2. The pathogenic nsSNPs were then subjected to structural change analysis using online tools. Conclusions The pathogenic nsSNPs were found in both proteins’ transmembrane domains and were expected to be conserved, but with lower protein stability (ΔΔG <− 0.5), indicating a possibly harmful effect in exfoliation. However, three-dimensional protein analysis indicated that the predicted mutations in MT-ND4 and MT-ATP6 were unlikely to alter the protein function.
Collapse
|
25
|
Zhang Y, Duan X. A Novel 90-kbp Deletion of RUNX2 Associated with Cleidocranial Dysplasia. Genes (Basel) 2022; 13:genes13071128. [PMID: 35885911 PMCID: PMC9322484 DOI: 10.3390/genes13071128] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 12/02/2022] Open
Abstract
Cleidocranial dysplasia (CCD) is a rare autosomal dominant skeletal dysplasia caused by runt-related transcription factor 2 (RUNX2) mutations. In addition to the regular missense, small or large fragment deletions are the common mutation types of RUNX2. This study aimed to find the rules of deletions in RUNX2. The clinical information of one Chinese CCD family was collected. Genomic DNA was extracted for whole-exome sequencing (WES). Bioinformatics analyzed the pathogenicity of the variants. Polymerase chain reaction (PCR) and Sanger sequencing were carried out using specific primers. RT-PCR and Q-PCR were also used to detect the mRNA level of RUNX2. The CCD studies related with deletions in RUNX2 from 1999 to 2021 from HGMD and PubMed were collected and analyzed for the relationship between the phenotypes and the length of deleted fragments. The proband presented typical CCD features, including delayed closure of cranial sutures, clavicle dysplasia, abnormal teeth. WES, PCR with specific primers and Sanger sequencing revealed a novel heterozygous 90-kbp deletion in RUNX2 (NG_008020.2 g.103671~193943), which caused a substitution (p.Asn183Ile) and premature termination (p.Asp184*). In addition, the mRNA expression of RUNX2 was decreased by 75.5% in the proband. Herein, 31 types of deletions varying from 2 bp to 800 kbp or covering the whole gene of RUNX2 were compared and the significant phenotypic difference was not found among these deletions. The CCD phenotypes were related with the final effects of RUNX2 mutation instead of the length of deletion. WES has the defects in identifying large indels, and direct PCR with specific primers and Sanger sequencing could make up for the shortcoming.
Collapse
|
26
|
Andreini D, Melotti E, Vavassori C, Chiesa M, Piacentini L, Conte E, Mushtaq S, Manzoni M, Cipriani E, Ravagnani PM, Bartorelli AL, Colombo GI. Whole-Blood Transcriptional Profiles Enable Early Prediction of the Presence of Coronary Atherosclerosis and High-Risk Plaque Features at Coronary CT Angiography. Biomedicines 2022; 10:biomedicines10061309. [PMID: 35740331 PMCID: PMC9219643 DOI: 10.3390/biomedicines10061309] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/17/2022] [Accepted: 05/31/2022] [Indexed: 12/10/2022] Open
Abstract
Existing tools to estimate cardiovascular (CV) risk have sub-optimal predictive capacities. In this setting, non-invasive imaging techniques and omics biomarkers could improve risk-prediction models for CV events. This study aimed to identify gene expression patterns in whole blood that could differentiate patients with severe coronary atherosclerosis from subjects with a complete absence of detectable coronary artery disease and to assess associations of gene expression patterns with plaque features in coronary CT angiography (CCTA). Patients undergoing CCTA for suspected coronary artery disease (CAD) were enrolled. Coronary stenosis was quantified and CCTA plaque features were assessed. The whole-blood transcriptome was analyzed with RNA sequencing. We detected highly significant differences in the circulating transcriptome between patients with high-degree coronary stenosis (≥70%) in the CCTA and subjects with an absence of coronary plaque. Notably, regression analysis revealed expression signatures associated with the Leaman score, the segment involved score, the segment stenosis score, and plaque volume with density <150 HU at CCTA. This pilot study shows that patients with significant coronary stenosis are characterized by whole-blood transcriptome profiles that may discriminate them from patients without CAD. Furthermore, our results suggest that whole-blood transcriptional profiles may predict plaque characteristics.
Collapse
Affiliation(s)
- Daniele Andreini
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
- Department of Biomedical and Clinical Science “Luigi Sacco”, University of Milan, 20121 Milan, Italy
- Correspondence: (D.A.); (G.I.C.); Tel.: +39-0258002577 (D.A.); +39-0258002464 (G.I.C.)
| | - Eleonora Melotti
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
| | - Chiara Vavassori
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
- Department of Clinical Sciences and Community Health, University of Milan, 20121 Milan, Italy
| | - Mattia Chiesa
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
- Department of Electronics, Information and Biomedical Engineering, Politecnico di Milano, 20133 Milan, Italy
| | - Luca Piacentini
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
| | - Edoardo Conte
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
- Department of Biomedical Sciences for Health, University of Milan, 20121 Milan, Italy
| | - Saima Mushtaq
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
| | - Martina Manzoni
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
| | - Eleonora Cipriani
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
| | - Paolo M. Ravagnani
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
| | - Antonio L. Bartorelli
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
- Department of Biomedical and Clinical Science “Luigi Sacco”, University of Milan, 20121 Milan, Italy
| | - Gualtiero I. Colombo
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
- Correspondence: (D.A.); (G.I.C.); Tel.: +39-0258002577 (D.A.); +39-0258002464 (G.I.C.)
| |
Collapse
|
27
|
Nissen CG, Mosley DD, Kharbanda KK, Katafiasz DM, Bailey KL, Wyatt TA. Malondialdehyde Acetaldehyde-Adduction Changes Surfactant Protein D Structure and Function. Front Immunol 2022; 13:866795. [PMID: 35669781 PMCID: PMC9164268 DOI: 10.3389/fimmu.2022.866795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/13/2022] [Indexed: 11/23/2022] Open
Abstract
Alcohol consumption with concurrent cigarette smoking produces malondialdehyde acetaldehyde (MAA)-adducted lung proteins. Lung surfactant protein D (SPD) supports innate immunity via bacterial aggregation and lysis, as well as by enhancing macrophage-binding and phagocytosis. MAA-adducted SPD (SPD-MAA) has negative effects on lung cilia beating, macrophage function, and epithelial cell injury repair. Because changes in SPD multimer structure are known to impact SPD function, we hypothesized that MAA-adduction changes both SPD structure and function. Purified human SPD and SPD-MAA (1 mg/mL) were resolved by gel filtration using Sephadex G-200 and protein concentration of each fraction determined by Bradford assay. Fractions were immobilized onto nitrocellulose by slot blot and assayed by Western blot using antibodies to SPD and to MAA. Binding of SPD and SPD-MAA was determined fluorometrically using GFP-labeled Streptococcus pneumoniae (GFP-SP). Anti-bacterial aggregation of GFP-SP and macrophage bacterial phagocytosis were assayed by microscopy and permeability determined by bacterial phosphatase release. Viral injury was measured as LDH release in RSV-treated airway epithelial cells. Three sizes of SPD were resolved by gel chromatography as monomeric, trimeric, and multimeric forms. SPD multimer was the most prevalent, while the majority of SPD-MAA eluted as trimer and monomer. SPD dose-dependently bound to GFP-SP, but SPD-MAA binding to bacteria was significantly reduced. SPD enhanced, but MAA adduction of SPD prevented, both aggregation and macrophage phagocytosis of GFP-SP. Likewise, SPD increased bacterial permeability while SPD-MAA did not. In the presence of RSV, BEAS-2B cell viability was enhanced by SPD, but not protected by SPD-MAA. Our results demonstrate that MAA adduction changes the quaternary structure of SPD from multimer to trimer and monomer leading to a decrease in the native anti-microbial function of SPD. These findings suggest one mechanism for increased pneumonia observed in alcohol use disorders.
Collapse
Affiliation(s)
- Claire G. Nissen
- Department of Environmental, Agricultural and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE, United States
| | - Deanna D. Mosley
- Department of Internal Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Kusum K. Kharbanda
- Department of Internal Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
- Research Service Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, NE, United States
| | - Dawn M. Katafiasz
- Department of Internal Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Kristina L. Bailey
- Department of Internal Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
- Research Service Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, NE, United States
| | - Todd A. Wyatt
- Department of Environmental, Agricultural and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE, United States
- Department of Internal Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
- Research Service Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, NE, United States
| |
Collapse
|
28
|
Lee M, Chang Y, Ahmadinejad N, Johnson-Agbakwu C, Bailey C, Liu L. COVID-19 mortality is associated with pre-existing impaired innate immunity in health conditions. PeerJ 2022; 10:e13227. [PMID: 35547187 PMCID: PMC9083528 DOI: 10.7717/peerj.13227] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/15/2022] [Indexed: 01/12/2023] Open
Abstract
COVID-19 can be life-threatening to individuals with chronic diseases. To prevent severe outcomes, it is critical that we comprehend pre-existing molecular abnormalities found in common health conditions that predispose patients to poor prognoses. In this study, we focused on 14 pre-existing health conditions for which increased hazard ratios of COVID-19 mortality have been documented. We hypothesized that dysregulated gene expression in these pre-existing health conditions were risk factors of COVID-19 related death, and the magnitude of dysregulation (measured by fold change) were correlated with the severity of COVID-19 outcome (measured by hazard ratio). To test this hypothesis, we analyzed transcriptomics data sets archived before the pandemic in which no sample had COVID-19. For a given pre-existing health condition, we identified differentially expressed genes by comparing individuals affected by this health condition with those unaffected. Among genes differentially expressed in multiple health conditions, the fold changes of 70 upregulated genes and 181 downregulated genes were correlated with hazard ratios of COVID-19 mortality. These pre-existing dysregulations were molecular risk factors of severe COVID-19 outcomes. These genes were enriched with endoplasmic reticulum and mitochondria function, proinflammatory reaction, interferon production, and programmed cell death that participate in viral replication and innate immune responses to viral infections. Our results suggest that impaired innate immunity in pre-existing health conditions is associated with increased hazard of COVID-19 mortality. The discovered molecular risk factors are potential prognostic biomarkers and targets for therapeutic intervention.
Collapse
Affiliation(s)
- Matthew Lee
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States
| | - Yung Chang
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Navid Ahmadinejad
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States
| | | | - Celeste Bailey
- Valleywise Health Medical Center, Phoenix, AZ, United States
| | - Li Liu
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States,Biodesign Institute, Arizona State University, Tempe, AZ, United States
| |
Collapse
|
29
|
Soares-Schanoski A, Sauerwald N, Goforth CW, Periasamy S, Weir DL, Lizewski S, Lizewski R, Ge Y, Kuzmina NA, Nair VD, Vangeti S, Marjanovic N, Cappuccio A, Cheng WS, Mofsowitz S, Miller CM, Yu XB, George MC, Zaslavsky E, Bukreyev A, Troyanskaya OG, Sealfon SC, Letizia AG, Ramos I. Asymptomatic SARS-CoV-2 Infection Is Associated With Higher Levels of Serum IL-17C, Matrix Metalloproteinase 10 and Fibroblast Growth Factors Than Mild Symptomatic COVID-19. Front Immunol 2022; 13:821730. [PMID: 35479098 PMCID: PMC9037090 DOI: 10.3389/fimmu.2022.821730] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 11/24/2021] [Accepted: 03/11/2022] [Indexed: 12/12/2022] Open
Abstract
Young adults infected with SARS-CoV-2 are frequently asymptomatic or develop only mild disease. Because capturing representative mild and asymptomatic cases require active surveillance, they are less characterized than moderate or severe cases of COVID-19. However, a better understanding of SARS-CoV-2 asymptomatic infections might shed light into the immune mechanisms associated with the control of symptoms and protection. To this aim, we have determined the temporal dynamics of the humoral immune response, as well as the serum inflammatory profile, of mild and asymptomatic SARS-CoV-2 infections in a cohort of 172 initially seronegative prospectively studied United States Marine recruits, 149 of whom were subsequently found to be SARS-CoV-2 infected. The participants had blood samples taken, symptoms surveyed and PCR tests for SARS-CoV-2 performed periodically for up to 105 days. We found similar dynamics in the profiles of viral load and in the generation of specific antibody responses in asymptomatic and mild symptomatic participants. A proteomic analysis using an inflammatory panel including 92 analytes revealed a pattern of three temporal waves of inflammatory and immunoregulatory mediators, and a return to baseline for most of the inflammatory markers by 35 days post-infection. We found that 23 analytes were significantly higher in those participants that reported symptoms at the time of the first positive SARS-CoV-2 PCR compared with asymptomatic participants, including mostly chemokines and cytokines associated with inflammatory response or immune activation (i.e., TNF-α, TNF-β, CXCL10, IL-8). Notably, we detected 7 analytes (IL-17C, MMP-10, FGF-19, FGF-21, FGF-23, CXCL5 and CCL23) that were higher in asymptomatic participants than in participants with symptoms; these are known to be involved in tissue repair and may be related to the control of symptoms. Overall, we found a serum proteomic signature that differentiates asymptomatic and mild symptomatic infections in young adults, including potential targets for developing new therapies and prognostic tests.
Collapse
Affiliation(s)
| | - Natalie Sauerwald
- Center for Computational Biology, Flatiron Institute, New York, NY, United States
| | - Carl W Goforth
- Naval Medical Research Center, Silver Spring, MD, United States
| | - Sivakumar Periasamy
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States.,Galveston National Laboratory, Galveston, TX, United States
| | - Dawn L Weir
- Naval Medical Research Center, Silver Spring, MD, United States
| | | | | | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Natalia A Kuzmina
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States.,Galveston National Laboratory, Galveston, TX, United States
| | - Venugopalan D Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sindhu Vangeti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Nada Marjanovic
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Antonio Cappuccio
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Wan Sze Cheng
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sagie Mofsowitz
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Clare M Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Xuechen B Yu
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Mary-Catherine George
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States.,Galveston National Laboratory, Galveston, TX, United States.,Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Olga G Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, NY, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, United States.,Department of Computer Science, Princeton University, Princeton, NJ, United States
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| |
Collapse
|
30
|
Shinwari K, Rehman HM, Liu G, Bolkov MA, Tuzankina IA, Chereshnev VA. Novel Disease-Associated Missense Single-Nucleotide Polymorphisms Variants Predication by Algorithms Tools and Molecular Dynamics Simulation of Human TCIRG1 Gene Causing Congenital Neutropenia and Osteopetrosis. Front Mol Biosci 2022; 9:879875. [PMID: 35573728 PMCID: PMC9095858 DOI: 10.3389/fmolb.2022.879875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022] Open
Abstract
T Cell Immune Regulator 1, ATPase H + Transporting V0 Subunit A3 (TCIRG1 gene provides instructions for making one part, the a3 subunit, of a large protein complex known as a vacuolar H + -ATPase (V-ATPase). V-ATPases are a group of similar complexes that act as pumps to move positively charged hydrogen atoms (protons) across membranes. Single amino acid changes in highly conserved areas of the TCIRG1 protein have been linked to autosomal recessive osteopetrosis and severe congenital neutropenia. We used multiple computational approaches to classify disease-prone single nucleotide polymorphisms (SNPs) in TCIRG1. We used molecular dynamics analysis to identify the deleterious nsSNPs, build mutant protein structures, and assess the impact of mutation. Our results show that fifteen nsSNPs (rs199902030, rs200149541, rs372499913, rs267605221, rs374941368, rs375717418, rs80008675, rs149792489, rs116675104, rs121908250, rs121908251, rs121908251, rs149792489 and rs116675104) variants are likely to be highly deleterious mutations as by incorporating them into wild protein they destabilize the wild protein structure and function. They are also located in the V-ATPase I domain, which may destabilize the structure and impair TCIRG1 protein activation, as well as reduce its ATPase effectiveness. These mutants have not yet been identified in patients suffering from CN and osteopetrosis while (G405R, R444L, and D517N) reported in our study are already associated with osteopetrosis. Mutation V52L reported in our study was identified in a patient suspected for CN. Finally, these mutants can help to further understand the broad pool of illness susceptibilities associated with TCIRG1 catalytic kinase domain activation and aid in the development of an effective treatment for associated diseases.
Collapse
Affiliation(s)
- Khyber Shinwari
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- *Correspondence: Khyber Shinwari,
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- Alnoorians Group of Institutes, Shad Bagh, Lahore, Pakistan
| | - Guojun Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Mikhail A. Bolkov
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Irina A. Tuzankina
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Valery. A. Chereshnev
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| |
Collapse
|
31
|
Ruan J, Meng H, Chen Y, Yan Z, Li X, Meng F. Expression of ATP-binding cassette subfamily B member 1 gene in peripheral blood of patients with acute myocardial infarction. Bioengineered 2022; 13:11095-105. [PMID: 35473443 DOI: 10.1080/21655979.2022.2068881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
This study aimed to determine the amount of expression of the ATP-binding cassette subfamily B member 1 (ABCB1) gene chip as a prospective diagnostic marker for acute myocardial infarction (AMI) in a wide population . In the AMI and control groups, 113 patients with AMI and 83 persons with non-coronary artery disease were selected for peripheral venous leukocyte collection. Western blot and real-time polymerase chain reaction (RT-PCR) were employed to detect relative ABCB1 expression in both groups. The results showed that the ABCB1 transcription and protein levels in the AMI group were higher than in the control. The relative mRNA expression of ABCB1 was 0.26 (0.03-0.79) in the AMI group and 0.13 (0.01-0.52) in the control group (P < 0.05). The expression of the ABCB1 gene at the protein level in the AMI group was 1.65 times that in the control (P < 0.05). Further, the subjects in the AMI group were older (P < 0.001), had lower levels of high-density lipoprotein cholesterol (P = 0.038), and had higher incidence of type II diabetes mellitus (P = 0.003) compared with the control. Logistic regression analysis showed that the expression of ABCB1 in peripheral blood was correlated with the occurrence of AMI (P = 0.003). High ABCB1 expression, type II diabetes, and advanced age were found to serve as potential independent risk factors for AMI, with a 4.88-fold, 2.99-fold, and 2.63-fold increased risk of AMI. Overall, the high expression of ABCB1 in peripheral blood might be related to the occurrence of AMI.
Collapse
|
32
|
Meng H, Li L, Ruan J, Chen Y, Yan Z, Liu J, Li X, Mao C, Yang P, Jiang W. Association of Low Expression of NUMB in Peripheral Blood with Acute Myocardial Infarction. Cardiol Res Pract 2022; 2022:1-7. [PMID: 35529060 PMCID: PMC9072008 DOI: 10.1155/2022/7981637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/12/2022] [Indexed: 12/29/2022] Open
Abstract
Objective Our study's goal was to find out acute myocardial infarction (AMI) patients' NUMB gene expression patterns and to evaluate its role as a diagnostic marker for AMI detection. Methods Peripheral blood was drawn from 124 individuals who had an AMI and 115 patients who had stable coronary artery disease (SCAD). The real-time quantitative polymerase chain reaction was used to measure the mRNA expression level of the NUMB gene in peripheral blood. Results The AMI group's NUMB gene expression was 0.906 (0.181–0.954), whereas the SCAD group's expression was 1.024 (0.207–1.127). However, the AMI group had 0.885 times lower NUMB mRNA expression than the SCAD group (P < 0.05). Conclusion Multivariate logistic regression evaluation found that lower NUMB expression was correlated with an increased risk of coronary artery disease. However, age and fasting plasma glucose levels were not associated with decreased NUMB expression.
Collapse
|
33
|
Guemri J, Pierre-Jean M, Brohard S, Oussada N, Horgues C, Bonnet E, Mauger F, Deleuze JF. Methylated ccfDNA from plasma biomarkers of Alzheimer's disease using targeted bisulfite sequencing. Epigenomics 2022; 14:451-468. [PMID: 35416052 DOI: 10.2217/epi-2021-0491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Noninvasive biomarkers such as methylated ccfDNA from plasma could help to support the diagnosis of Alzheimer's disease (AD). Methods: A targeted sequencing protocol was developed to identify candidate biomarkers of AD in methylated ccfDNA extracted from plasma. Results: The authors identified differentially methylated CpGs, regions of which were the same as those identified in previous AD studies. Specifically, a differentially methylated CpG of the LHX2 gene previously identified in a plasma study of AD was replicated in the study. The MBP and DUSP22 regions have been identified in other brain studies of AD and in the authors' study. Conclusion: Although these biomarkers must be validated in other cohorts, methylated ccfDNA could be a relevant noninvasive biomarker in AD.
Collapse
Affiliation(s)
- Julien Guemri
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Morgane Pierre-Jean
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Solène Brohard
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Nouara Oussada
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Caroline Horgues
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Eric Bonnet
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Florence Mauger
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Jean-François Deleuze
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| |
Collapse
|
34
|
Yeo H, Ahn SS, Jung E, Lim Y, Lee YH, Shin SY. Transcription factor EGR1 regulates the expression of the clock gene PER2 under IL-4 stimulation in human keratinocytes. J Invest Dermatol 2022; 142:2677-2686.e9. [DOI: 10.1016/j.jid.2022.03.021] [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] [Received: 11/30/2021] [Revised: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 11/24/2022]
|
35
|
Ogawa C, Hirasawa A, Ida N, Nakamura K, Masuyama H. Hereditary gynecologic tumors and precision cancer medicine. J Obstet Gynaecol Res 2022; 48:1076-1090. [PMID: 35229413 DOI: 10.1111/jog.15197] [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: 11/30/2021] [Accepted: 02/09/2022] [Indexed: 11/29/2022]
Abstract
Gynecologic cancers are more often caused by genetic factors than other cancers. Genetic testing has become a promising avenue for the prevention, prognosis, and treatment of cancers. This review describes molecular features of gynecologic tumors linked to hereditary syndromes, gives an overview of the current state of clinical management, and clarifies the role of gynecology in the treatment of hereditary tumors. Typical hereditary gynecologic tumors include hereditary breast and ovarian cancer, Lynch syndrome, Peutz-Jeghers syndrome, and Cowden syndrome. Multigene panel testing, which analyzes a preselected subset of genes for genetic variants, has recently become the first-choice test because it can provide more accurate risk assessment than a single test. Furthermore, comprehensive genomic cancer profiling enables personalized cancer treatment and aids in germline findings.
Collapse
Affiliation(s)
- Chikako Ogawa
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Akira Hirasawa
- Department of Clinical Genomic Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Naoyuki Ida
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Keiichiro Nakamura
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Hisashi Masuyama
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| |
Collapse
|
36
|
Li L, Meng H, Wang X, Ruan J, Tian X, Meng F. Low ZCCHC9 Gene Expression in Peripheral Blood May Be an Acute Myocardial Infarction Genetic Molecular Marker in Patients with Stable Coronary Atherosclerotic Disease. Int J Gen Med 2022; 15:1795-1804. [PMID: 35210844 PMCID: PMC8863191 DOI: 10.2147/ijgm.s346335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 10/26/2021] [Accepted: 01/25/2022] [Indexed: 12/11/2022] Open
Abstract
Purpose Patients and Methods Results Conclusion
Collapse
Affiliation(s)
- Lihong Li
- Department of Cardiology, The Third Hospital of Jilin University, Changchun, People’s Republic of China
| | - Heyu Meng
- Department of Cardiology, The Third Hospital of Jilin University, Changchun, People’s Republic of China
| | - Xue Wang
- Department of Cardiology, The Third Hospital of Jilin University, Changchun, People’s Republic of China
| | - Jianjun Ruan
- Department of Cardiology, The Third Hospital of Jilin University, Changchun, People’s Republic of China
| | - Xiaomin Tian
- Department of Cardiology, The Third Hospital of Jilin University, Changchun, People’s Republic of China
| | - Fanbo Meng
- Department of Cardiology, The Third Hospital of Jilin University, Changchun, People’s Republic of China
- Correspondence: Fanbo Meng, Department of Cardiology, The Third Hospital of Jilin University, Changchun, People’s Republic of China, Tel +86-15948346855, Fax + 86-431-84995228, Email
| |
Collapse
|
37
|
Arafah A, Rehman MU, Syed W, Babelghaith SD, Alwhaibi A, Al Arifi MN. Knowledge, Attitude and Perception of Pharmacy Students towards Pharmacogenomics and Genetics: An Observational Study from King Saud University. Genes (Basel) 2022; 13:genes13020269. [PMID: 35205314 PMCID: PMC8872085 DOI: 10.3390/genes13020269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 12/30/2022] Open
Abstract
Pharmacists are considered among the most accessible healthcare workers in fundamental positions to implement new clinical initiatives, such as pharmacogenomics services. The scope of pharmacogenomics in improving health outcomes and the quality of health care is well-known. Implementation of such initiatives requires adequate knowledge, perception, and positive attitudes among pharmacists. A study was conducted on pharmacy students at King Saud University in Riyadh to analyze their attitudes, knowledge, and perceptions concerning pharmacogenomics to explore the feasibility of establishing full-time pharmacogenomics instruction and services. A cross-sectional study was carried out in one of the significant pharmacy schools of Saudi Arabia, using a simple questionnaire-based survey in pharmacy students pursuing Bpharm and PharmD courses to obtain preliminary information about pharmacogenomics among the surveyed population. The study’s secondary objective was to determine the perceived belief about pharmacogenomics implementation in clinical practice. Out of the total of 552 participants, 41.8% correctly defined pharmacogenomics and 81.3% understood that genetic change could lead to adverse reactions. More than half of the participants agreed that the FDA recommends pharmacogenomics testing for certain drugs. The knowledge about a year of use of pharmacogenomics in clinical practice was found to be very low; only 15.2% could correctly answer. Only 60% of students agreed on pharmacogenomics testing for selecting the therapy with the most negligible adverse effects. Due to the limited knowledge about and understanding of pharmacogenomics, there is a lack of interest among pharmacy students in implementing pharmacogenomics testing in clinical practice. Our study highlights the need for improving pharmacy students’ knowledge about pharmacogenomics and pharmacogenetics so that the implementation of pharmacogenomics testing in clinical practice will become easier. There is a need to introduce an up-to-date curriculum for pharmacy courses other pharmacogenomics-based health education programs in Saudi Arabia.
Collapse
|
38
|
Abstract
Defects in the replication, maintenance, and repair of mitochondrial DNA (mtDNA) constitute a growing and genetically heterogeneous group of mitochondrial disorders. Multiple genes participate in these processes, including thymidine kinase 2 (TK2) encoding the mitochondrial matrix protein TK2, a critical component of the mitochondrial nucleotide salvage pathway. TK2 deficiency (TK2d) causes mtDNA depletion, multiple deletions, or both, which manifest predominantly as mitochondrial myopathy. A wide clinical spectrum phenotype includes a severe, rapidly progressive, early onset form (median survival: < 2 years); a less severe childhood-onset form; and a late-onset form with a variably slower rate of progression. Clinical presentation typically includes progressive weakness of limb, neck, facial, oropharyngeal, and respiratory muscle, whereas limb myopathy with ptosis, ophthalmoparesis, and respiratory involvement is more common in the late-onset form. Deoxynucleoside monophosphates and deoxynucleosides that can bypass the TK2 enzyme defect have been assessed in a mouse model, as well as under open-label compassionate use (expanded access) in TK2d patients, indicating clinical efficacy with a favorable side-effect profile. This treatment is currently undergoing testing in clinical trials intended to support approval in the US and European Union (EU). In the early expanded access program, growth differentiation factor 15 (GDF-15) appears to be a useful biomarker that correlates with therapeutic response. With the advent of a specific treatment and given the high morbidity and mortality associated with TK2d, clinicians need to know how to recognize and diagnose this disorder. Here, we summarize translational research about this rare condition emphasizing clinical aspects.
Collapse
Affiliation(s)
- Andres Berardo
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Kristin Engelstad
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Michio Hirano
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| |
Collapse
|
39
|
Abstract
Rho guanosine triphosphatase (GTPases), as molecular switches, have been identified to be dysregulated and involved in the pathogenesis of various rheumatic diseases, mainly including rheumatoid arthritis, osteoarthritis, systemic sclerosis, and systemic lupus erythematosus. Downstream pathways involving multiple types of cells, such as fibroblasts, chondrocytes, synoviocytes, and immunocytes are mediated by activated Rho GTPases to promote pathogenesis. Targeted therapy via inhibitors of Rho GTPases has been implicated in the treatment of rheumatic diseases, demonstrating promising effects. In this review, the effects of Rho GTPases in the pathogenesis of rheumatic diseases are summarized, and the Rho GTPase-mediated pathways are elucidated. Therapeutic strategies using Rho GTPase inhibitors in rheumatic diseases are also discussed to provide insights for further exploration of targeted therapy in preclinical studies and clinical practice. Future directions on studies of Rho GTPases in rheumatic diseases based on current understandings are provided.
Collapse
Affiliation(s)
- Ruijie Zeng
- Department of Gastroenterology, Guangdong Academy of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou 510080, China
- Shantou University Medical College, Shantou 515041, China
| | - Zewei Zhuo
- Department of Gastroenterology, Guangdong Academy of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou 510080, China
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Yujun Luo
- Department of Gastroenterology, Guangdong Academy of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou 510080, China
| | - Weihong Sha
- Department of Gastroenterology, Guangdong Academy of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou 510080, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
- School of Medicine, South China University of Technology, Guangzhou 510006, China
- Corresponding author
| | - Hao Chen
- Department of Gastroenterology, Guangdong Academy of Medical Sciences, Guangdong Provincial People's Hospital, Guangzhou 510080, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
- School of Medicine, South China University of Technology, Guangzhou 510006, China
- Corresponding author
| |
Collapse
|
40
|
Wang Y, Han B, Fan Y, Yi Y, Lv J, Wang J, Yang X, Jiang D, Zhao L, Zhang J, Yuan H. Next-Generation Sequencing Reveals Novel Genetic Variants for Dilated Cardiomyopathy in Pediatric Chinese Patients. Pediatr Cardiol 2022; 43:110-120. [PMID: 34350506 DOI: 10.1007/s00246-021-02698-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/26/2021] [Indexed: 12/30/2022]
Abstract
Dilated cardiomyopathy (DCM) is a myocardial disease characterized by bilateral or left ventricular cardiac dilation and systolic dysfunction that can lead to heart failure and sudden cardiac death in children. Many studies have focused on genetic variation in DCM-related genes in adult populations; however, the mutational landscape in pediatric DCM patients remains undetermined, especially in the Chinese population. We applied next-generation sequencing (NGS) technology to genetically analyze 46 pediatric DCM patients to reveal genotype-phenotype correlations. Our results indicated DCM-associated pathogenic mutations in 10 genes related to the structure or function of the sarcomere, desmosome, and cytoskeleton. We also identified 6 pathogenic mutations (5 novel) in the Titin (TTN) gene that resulted in truncated TTN variants in 6 (13%) out of 46 patients. Correlations between TTN mutations and clinical outcomes were assessed. Our data indicate that one-third of pediatric DCM cases are caused by genetic mutations. The role of TTN variants should not be underestimated in pediatric DCM and age-dependent pathogenic penetrance of these mutations should be considered for familial DCM cases. We argue that genetic testing of DCM cases is valuable for predicting disease severity, prognosis, and recurrence risk, and for screening first-degree relatives.
Collapse
Affiliation(s)
- Yan Wang
- Department of Pediatrics, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, People's Republic of China
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Bo Han
- Department of Pediatrics, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, People's Republic of China.
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China.
| | - Youfei Fan
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Yingchun Yi
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Jianli Lv
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Jing Wang
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Xiaofei Yang
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Diandong Jiang
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Lijian Zhao
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Jianjun Zhang
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Hui Yuan
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| |
Collapse
|
41
|
Lee JH, Kim DY, Pantha R, Lee EH, Bae JH, Han E, Song DK, Kwon TK, Im SS. Identification of Pre-Diabetic Biomarkers in the Progression of Diabetes Mellitus. Biomedicines 2021; 10:biomedicines10010072. [PMID: 35052752 PMCID: PMC8773205 DOI: 10.3390/biomedicines10010072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/25/2021] [Accepted: 12/29/2021] [Indexed: 01/11/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a major global health issue. The development of T2DM is gradual and preceded by the pre-diabetes mellitus (pre-DM) stage, which often remains undiagnosed. This study aimed to identify novel pre-DM biomarkers in a high-fat diet (HFD)-induced pre-DM mouse model. Male C57BL/6J mice were fed either a chow diet or HFD for 12 weeks. Serum and liver samples were isolated in a time-dependent manner. Semi-quantitative assessment of secretory cytokines was performed by cytokine array analysis, and 13 cytokines were selected for further analysis based on the changes in expression levels in the pre-DM and T2DM stages. HFD-fed mice gained body weight and exhibited high serum lipid, liver enzyme, glucose, and insulin levels during the progression of pre-DM to T2DM. The mRNA expression of inflammatory and lipogenic genes was elevated in HFD-fed mice The mRNA expression of Fc receptor, IgG, low affinity Iib, lectin, galactose binding, soluble 1, vascular cell adhesion molecule 1, insulin-like growth factor binding protein 5, and growth arrest specific 6 was elevated in the pre-DM, which was confirmed by measuring protein levels. Our study identified novel pre-DM biomarkers that may help to delay or prevent the progression of T2DM.
Collapse
Affiliation(s)
- Jae-Ho Lee
- Department of Physiology, Keimyung University School of Medicine, Daegu 42601, Korea; (J.-H.L.); (D.-Y.K.); (R.P.); (E.-H.L.); (J.-H.B.); (D.-K.S.)
| | - Do-Young Kim
- Department of Physiology, Keimyung University School of Medicine, Daegu 42601, Korea; (J.-H.L.); (D.-Y.K.); (R.P.); (E.-H.L.); (J.-H.B.); (D.-K.S.)
| | - Rubee Pantha
- Department of Physiology, Keimyung University School of Medicine, Daegu 42601, Korea; (J.-H.L.); (D.-Y.K.); (R.P.); (E.-H.L.); (J.-H.B.); (D.-K.S.)
| | - Eun-Ho Lee
- Department of Physiology, Keimyung University School of Medicine, Daegu 42601, Korea; (J.-H.L.); (D.-Y.K.); (R.P.); (E.-H.L.); (J.-H.B.); (D.-K.S.)
| | - Jae-Hoon Bae
- Department of Physiology, Keimyung University School of Medicine, Daegu 42601, Korea; (J.-H.L.); (D.-Y.K.); (R.P.); (E.-H.L.); (J.-H.B.); (D.-K.S.)
| | - Eugene Han
- Department of Internal Medicine, Division of Endocrinology, Keimyung University School of Medicine, Daegu 42601, Korea;
| | - Dae-Kyu Song
- Department of Physiology, Keimyung University School of Medicine, Daegu 42601, Korea; (J.-H.L.); (D.-Y.K.); (R.P.); (E.-H.L.); (J.-H.B.); (D.-K.S.)
| | - Taeg Kyu Kwon
- Department of Immunology, Keimyung University School of Medicine, Daegu 42601, Korea;
| | - Seung-Soon Im
- Department of Physiology, Keimyung University School of Medicine, Daegu 42601, Korea; (J.-H.L.); (D.-Y.K.); (R.P.); (E.-H.L.); (J.-H.B.); (D.-K.S.)
- Correspondence: ; Tel.: +82-53-258-7423; Fax: +82-53-258-7412
| |
Collapse
|
42
|
Manoj F, Tai LW, Wang KSM, Kuhlman TE. Targeted insertion of large genetic payloads using cas directed LINE-1 reverse transcriptase. Sci Rep 2021; 11:23625. [PMID: 34880381 PMCID: PMC8654924 DOI: 10.1038/s41598-021-03130-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/29/2021] [Indexed: 11/25/2022] Open
Abstract
A difficult genome editing goal is the site-specific insertion of large genetic constructs. Here we describe the GENEWRITE system, where site-specific targetable activity of Cas endonucleases is coupled with the reverse transcriptase activity of the ORF2p protein of the human retrotransposon LINE-1. This is accomplished by providing two RNAs: a guide RNA targeting Cas endonuclease activity and an appropriately designed payload RNA encoding the desired insertion. Using E. coli as a simple platform for development and deployment, we show that with proper payload design and co-expression of helper proteins, GENEWRITE can enable insertion of large genetic payloads to precise locations, although with off-target effects, using the described approach. Based upon these results, we describe a potential strategy for implementation of GENEWRITE in more complex systems.
Collapse
Affiliation(s)
- Femila Manoj
- Microbiology Program, University of California Riverside, Riverside, CA, 92521, USA
| | - Laura W Tai
- Department of Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Katelyn Sun Mi Wang
- Department of Physics and Astronomy, University of California Riverside, Riverside, CA, 92521, USA
| | - Thomas E Kuhlman
- Department of Physics and Astronomy, University of California Riverside, Riverside, CA, 92521, USA.
| |
Collapse
|
43
|
Lira SS, Ahammad I. A comprehensive in silico investigation into the nsSNPs of Drd2 gene predicts significant functional consequences in dopamine signaling and pharmacotherapy. Sci Rep 2021; 11:23212. [PMID: 34853389 DOI: 10.1038/s41598-021-02715-z] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 11/18/2021] [Indexed: 01/01/2023] Open
Abstract
DRD2 is a neuronal cell surface protein involved in brain development and function. Variations in the Drd2 gene have clinical significance since DRD2 is a pharmacotherapeutic target for treating psychiatric disorders like ADHD and schizophrenia. Despite numerous studies on the disease association of single nucleotide polymorphisms (SNPs) in the intronic regions, investigation into the coding regions is surprisingly limited. In this study, we aimed at identifying potential functionally and pharmaco-therapeutically deleterious non-synonymous SNPs of Drd2. A wide array of bioinformatics tools was used to evaluate the impact of nsSNPs on protein structure and functionality. Out of 260 nsSNPs retrieved from the dbSNP database, initially 9 were predicted as deleterious by 15 tools. Upon further assessment of their domain association, conservation profile, homology models and inter-atomic interaction, the mutant F389V was considered as the most impactful. In-depth analysis of F389V through Molecular Docking and Dynamics Simulation revealed a decline in affinity for its native agonist dopamine and an increase in affinity for the antipsychotic drug risperidone. Remarkable alterations in binding interactions and stability of the protein-ligand complex in simulated physiological conditions were also noted. These findings will improve our understanding of the consequence of nsSNPs in disease-susceptibility and therapeutic efficacy.
Collapse
|
44
|
Manikam R, Mui WS, Kong YY, Raju CS, Sekaran SD. Differential Analysis and Putative Roles of Genes, Cytokines and Apoptotic Proteins in Blood Samples of Patients with Respiratory Viral Infections: A Single Center Study. J Pure Appl Microbiol 2021; 15:2448-61. [DOI: 10.22207/jpam.15.4.72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Insights into the molecular pathogenesis of respiratory viral infections were investigated using serum and peripheral blood from patients with clinical syndromes. Signatures of expression of cytokines, genes and apoptotic proteins that discriminate symptomatic individuals from healthy individuals were determined among 21 patients. In symptomatic patients, significant upregulation of IL-1β, IL-2, IL-4, IL-6, IL-8, IL-12, IL-15, TNF-a and IFN-g (P<0.05) was noted, while IL-10 was significantly downregulated (P<0.05). This is accompanied by either up or down-regulation of various pro-apoptotic and anti-apoptotic markers, suggesting a protective role of immune responses against viral infection and the capacity of viruses to subvert host cell apoptosis. Gene expression analysis for both T and B cells were categorized according to their functional status of activation, proliferation, and differentiation. Of note, genes SH2D1A and TCL1A were upregulated only in rhinovirus samples, while PSMB7, CD4, CD8A, HLA-DMA, HLA-DRA and CD69 were upregulated in samples of Flu A and RSV but were not significant in samples of rhinovirus as compared to healthy individuals. These results demonstrated Flu A and RSV elicit different alterations in human peripheral blood gene expression as compared to rhinovirus. Overall, despite the small number of study subjects, the current study for the first time has recognized signature genes, cytokines and proteins that are used by some respiratory viruses that may serve as candidates for rapid diagnosis as well as targets for therapeutic interventions.
Collapse
|
45
|
Liu D, Liu Y, Zhang X, Wang Y, Zhang C, Zheng S. An Exploration of Mutagenesis in a Family with Cleidocranial Dysplasia without RUNX2 Mutation. Front Genet 2021; 12:748111. [PMID: 34737766 PMCID: PMC8560734 DOI: 10.3389/fgene.2021.748111] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/29/2021] [Indexed: 11/22/2022] Open
Abstract
Cleidocranial dysplasia (CCD) is an autosomal dominant inheritable skeletal disorder characterized by cranial dysplasia, clavicle hypoplasia, and dental abnormalities. Mutations involving Runt-related transcription factor 2 (RUNX2) are currently the only known molecular etiology for CCD but are not identified in all CCD patients. No RUNX2 abnormality can be detected in about 20–30% of patients, and the molecular cause remains unknown. The present study includes a family case with typical features of CCD. RUNX2 mutation was first screened by sequencing analysis, and no mutation was detected. Copy number alterations of the RUNX2 gene were then measured by quantitative PCR and multiplex ligation-dependent probe amplification (MLPA). No copy number variation in RUNX2 could be detected. We performed whole-exome sequencing (WES) to identify the underlying genetic mutations. Unexpectedly, no abnormalities could be detected in genes related to the RUNX2 signaling pathway. Therefore, it was supposed that other new unknown gene variations might contribute to the CCD phenotype. We focused on Immunoglobulin superfamily member 10 (IGSF10), a gene related to bone development. An IGSF10 frameshift mutation (c.6001_6002delCT, p.Leu2001Valfs*24) was detected by WES. Sanger sequencing verified that this mutation was only detected in the patient and her affected mother but not in her unaffected father. Bioinformatics studies demonstrated that this mutation could change the 3D structure of the IGSF10 protein and severely damage its function. In addition, alkaline phosphatase (ALP) activity and the ability to form mineralized nodules were inhibited by IGSF10 knockdown compared with normal controls. The expression of bone sialoprotein (BSP) was significantly reduced by IGSF10 knockdown, but not that of other osteogenic markers. Our results provide new genetic evidence that IGSF10 mutation might contribute to CCD.
Collapse
Affiliation(s)
- Dandan Liu
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
| | - Yang Liu
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
| | - XianLi Zhang
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China.,Department of Stomatology, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Yixiang Wang
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Central Laboratory, Department of Oral and Maxillofacial Surgery, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
| | - Chenying Zhang
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
| | - Shuguo Zheng
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
| |
Collapse
|
46
|
Skóra JP, Antkiewicz M, Kupczyńska D, Kulikowska K, Strzelec B, Janczak D, Barć P. Local intramuscular administration of ANG1 and VEGF genes using plasmid vectors mobilizes CD34+ cells to peripheral tissues and promotes angiogenesis in an animal model. Biomed Pharmacother 2021; 143:112186. [PMID: 34649339 DOI: 10.1016/j.biopha.2021.112186] [Citation(s) in RCA: 1] [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: 06/05/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION Patients with peripheral artery disease have poor prognosis despite advances in vascular surgery. Therefore, attempts have been made at using gene and cell therapy to stimulate angiogenesis in the lower limbs in patients with critical lower limb ischemia (CLI). METHODS The study included 30 rats divided into 3 groups. An intramuscular injection of a therapeutic gene or cells in the right hind limb was administered in each group: angiopoietin-1 (ANG1) plasmid in group 1, ANG1/vascular endothelial growth factor (ANG1/VEGF) bicistronic construct in group 2, and naked plasmid in group 3 (control). After 3 months of follow-up, tissue samples were harvested, and vessels that stained positively for CD34 cells were quantified. RESULTS The highest CD34+ cell count was noted in the ANG1/VEGF group (98.26 cells), followed by the ANG1 group (80.31) and control group (47.93). The CD34+ cell count was significantly higher in the ANG1/VEGF and ANG1 groups than in the control group. There was no significant difference in the CD34+ cell count between the ANG1/VEGF and ANG1 groups. CONCLUSION Our study confirmed that therapy with ANG1 plasmid alone or ANG1/VEGF bicistronic construct is safe and effective in a rat model. The therapy resulted in the recruitment of more CD34+ vascular endothelial cells than in the control group receiving naked plasmid.
Collapse
Affiliation(s)
- Jan Paweł Skóra
- Department and Clinic of Vascular, General and Transplantation Surgery, Jan Mikulicz-Radecki University Hospital, Wroclaw Medical University, Wroclaw, Poland
| | - Maciej Antkiewicz
- Department and Clinic of Vascular, General and Transplantation Surgery, Jan Mikulicz-Radecki University Hospital, Wroclaw Medical University, Wroclaw, Poland.
| | - Diana Kupczyńska
- Department and Clinic of Vascular, General and Transplantation Surgery, Jan Mikulicz-Radecki University Hospital, Wroclaw Medical University, Wroclaw, Poland
| | - Katarzyna Kulikowska
- Department and Clinic of Vascular, General and Transplantation Surgery, Jan Mikulicz-Radecki University Hospital, Wroclaw Medical University, Wroclaw, Poland
| | - Bartłomiej Strzelec
- Department and Clinic of Vascular, General and Transplantation Surgery, Jan Mikulicz-Radecki University Hospital, Wroclaw Medical University, Wroclaw, Poland
| | - Dariusz Janczak
- Department and Clinic of Vascular, General and Transplantation Surgery, Jan Mikulicz-Radecki University Hospital, Wroclaw Medical University, Wroclaw, Poland
| | - Piotr Barć
- Department and Clinic of Vascular, General and Transplantation Surgery, Jan Mikulicz-Radecki University Hospital, Wroclaw Medical University, Wroclaw, Poland
| |
Collapse
|
47
|
P R, Ramireddy S, Chakraborty S, Mukherjee S, J S, C S. Structural localization of pathogenic mutations in the central nucleotide-binding domain (NBD) of nucleotide-binding oligomerization domain-2 (NOD2) protein and their inference in inflammatory disorders. Nucleosides Nucleotides Nucleic Acids 2021; 40:1198-1219. [PMID: 34622739 DOI: 10.1080/15257770.2021.1986719] [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] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The human NBD domain which is centrally located in the NOD2 protein displays an essential role in oligomerization and initiates the immune response via CARD-RIPK2 interaction. The mutations associated with the NBD domain have been largely implicated in inflammatory disorders such as Blau syndrome and sarcoidosis. This study aims to determine the structural and phenotypic effect of a lethal mutation that occurs in the NBD domain which has an axiomatic impact on protein dysfunction. Initially, the most deleterious missense mutations were screened through various in silico analysis. Out of 33 variants, I-Mutant 3.0, SIFT, PolyPhen 2, Align GVGD, PHD SNP and SNP&GO have statistically identified 5 variants (R42W, D90E, E91K, G189D & W198L) as less stable, deleterious and damaging. Our predicted models have paved the way to understand the various structural properties such as physiochemical, secondary structural arrangements and stabilizing residues in folding associated with the native and mutant NBD domain especially of the functionally important regions. From the aforementioned results, R42W and G189D were found to be the more predominant among the mutants. Precisely, through molecular simulation, we have strongly justified the significant conformational disruption of R42W and G189D through the stabilization factors, folding and essential dynamics. Conclusively, these regions (α341-44, α13185-191 and β6133-143β7) seem to adopt such structures that are not conducive to wild-type-like functionality. Our prediction and validation of lethal mutations based on structural stability may be useful for conducting experimental studies in detail to uncover the protein deregulation leading to inflammatory disorders.
Collapse
Affiliation(s)
- Raghuraman P
- Department of Biotechnology, School of Bioscience and Technology, Vellore Institute of Technology, Vellore, India
| | - Sriroopreddy Ramireddy
- Department of Biotechnology, School of Bioscience and Technology, Vellore Institute of Technology, Vellore, India
| | - Sulagno Chakraborty
- Department of Biotechnology, School of Bioscience and Technology, Vellore Institute of Technology, Vellore, India
| | - Sayani Mukherjee
- Department of Biotechnology, School of Bioscience and Technology, Vellore Institute of Technology, Vellore, India
| | - Sreeshma J
- Department of Biotechnology, School of Bioscience and Technology, Vellore Institute of Technology, Vellore, India
| | - Sudandiradoss C
- Department of Biotechnology, School of Bioscience and Technology, Vellore Institute of Technology, Vellore, India
| |
Collapse
|
48
|
Abstract
Network modeling, from the ecological to the molecular scale has become an essential tool for studying the structure, dynamics and complex behavior of living systems. Graph representations of the relationships between biological components open up a wide variety of methods for discovering the mechanistic and functional properties of biological systems. Many biological networks are organized into a modular structure, so methods to discover such modules are essential if we are to understand the biological system as a whole. However, most of the methods used in biology to this end, have a limited applicability, as they are very specific to the system they were developed for. Conversely, from the statistical physics and network science perspective, graph modularity has been theoretically studied and several methods of a very general nature have been developed. It is our perspective that in particular for the modularity detection problem, biology and theoretical physics/network science are less connected than they should. The central goal of this review is to provide the necessary background and present the most applicable and pertinent methods for community detection in a way that motivates their further usage in biological research.
Collapse
Affiliation(s)
- Sergio Antonio Alcalá-Corona
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Santiago Sandoval-Motta
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico.,National Council on Science and Technology, Mexico City, Mexico
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
49
|
Albitar L, Alchamat GA. Pharmacogenetics: Knowledge assessment amongst Syrian pharmacists and physicians. BMC Health Serv Res 2021; 21:1031. [PMID: 34592972 PMCID: PMC8485485 DOI: 10.1186/s12913-021-07040-9] [Citation(s) in RCA: 2] [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: 05/12/2021] [Accepted: 09/10/2021] [Indexed: 12/15/2022] Open
Abstract
Background Pharmacogenetics targets genetic variations that influence drug response. It is relatively a new science that has not been vastly employed in most developing countries including Syria. Therefore we aimed at evaluating the depth of knowledge in pharmacogenetics and the attitude towards it amongst Syrian pharmacists and physicians. Methods We carried out an internet-based questionnaire consisted of 26 questions, sent through specialized websites and private groups with a large number of pharmacists and physicians members. The survey was available online for a period of 1 month. Results The total number of respondents was 154, mostly female pharmacists. Our statistical analysis showed a strong positive association between profession (in favour of pharmacists) and pharmacogenetics knowledge p = 0.049; however, no correlation with experience p = 0.811 was found. A significant difference was reported between the knowledge of pharmacists and physicians p = 0.001 concerning drugs that need pharmacogenetics testing before being prescribed. The majority of respondents had no information about applying genetic tests in Syria before prescribing medications nor did they possess the knowledge regarding drugs that show differential responses in patients according to their unique genotypes. In our study, the percentage knowledge assessment score was low in general (mean ± Standard deviation, SD) (46% ± 13.9%). The majority of the respondents agreed that pharmacists should provide counselling to patients on the subject of pharmacogenetics. Respondents’ opinions varied concerning making pharmacogenetics learning a priority. Conclusion Lack of pharmacogenetics knowledge was found amongst respondents in general. Our findings raise concerns about the lack of awareness amongst physicians, which may hinder the implementation of this crucial field in Syria. We suggest an emphasis on the role of education, training, and conducting genotyping research on the Syrian population. Supplementary Information The online version contains supplementary material available at 10.1186/s12913-021-07040-9.
Collapse
Affiliation(s)
- Lina Albitar
- Department of Pharmaceutics, Faculty of Pharmacy, Arab International University, Damascus, Syria
| | - Ghalia Abou Alchamat
- Department of Biology, Faculty of Science, Damascus University, Damascus, Syria.
| |
Collapse
|
50
|
Su M, Page S, Haag M, Swisshelm K, Hennerich D, Graw S, LeRoux J, Brzeskiewicz P, Svihovec S, Bao L. Clinical utility and cost-effectiveness analysis of chromosome testing concomitant with chromosomal microarray of patients with constitutional disorders in a U.S. academic medical center. J Genet Couns 2021; 31:364-374. [PMID: 34397147 DOI: 10.1002/jgc4.1496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 01/28/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 12/11/2022]
Abstract
Chromosomal microarray (CMA) is now widely used as first-tier testing for the detection of copy number variants (CNVs) and absence of heterozygosity (AOH) in patients with multiple congenital anomalies (MCA), autism spectrum disorder (ASD), developmental delay (DD), and/or intellectual disability (ID). Chromosome analysis is commonly used to complement CMA in the detection of balanced genomic aberrations. However, the cost-effectiveness and the impact on clinical management of chromosome analysis concomitant with CMA were not well studied, and there is no consensus on how to best utilize these two tests. To assess the clinical utility and cost-effectiveness of chromosome analysis concomitant with CMA in patients with MCA, ASD, DD, and/or ID, we retrospectively analyzed 3,360 postnatal cases for which CMA and concomitant chromosome analysis were performed in the Colorado Genetic Laboratory (CGL) at the University Of Colorado School Of Medicine. Chromosome analysis alone yielded a genetic diagnosis in two patients (0.06%) and contributed additional information to CMA results in 199 (5.92%) cases. The impact of abnormal chromosome results on patient management was primarily related to counseling for reproductive and recurrence risks assessment (101 cases, 3.01%) while a few (5 cases, 0.15%) led to changes in laboratory testing and specialist referral (25 cases, 0.74%). The incremental cost-effectiveness ratio (ICER) of combined testing demonstrated the cost of each informative chromosome finding was significantly higher for patients with clinically insignificant (CI) CMA findings versus clinically significant (CS) CMA results. Our results suggest that a stepwise approach with CMA testing with reflex to chromosome analysis on cases with CS CMA findings is a more cost-effective testing algorithm for patients with MCA, ASD, and/or DD/ID.
Collapse
Affiliation(s)
- Meng Su
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Stephanie Page
- Genetics Counseling Program, Department of Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Mary Haag
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Karen Swisshelm
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Deborrah Hennerich
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sharon Graw
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jamie LeRoux
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Peter Brzeskiewicz
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Shayna Svihovec
- Clinical Genetics and Metabolism, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Liming Bao
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| |
Collapse
|