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Sharma A, Bansal C, Sharma KL, Kumar A. Circular RNA: The evolving potential in the disease world. World J Med Genet 2024; 12:93011. [DOI: 10.5496/wjmg.v12.i1.93011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/23/2024] [Accepted: 07/02/2024] [Indexed: 09/19/2024] [Imported: 09/19/2024] Open
Abstract
Circular RNAs (circRNAs), a new star of noncoding RNAs, are a group of endogenous RNAs that form a covalently closed circle and occur widely in the mammalian genome. Most circRNAs are conserved throughout species and frequently show stage-specific expression during various stages of tissue development. CircRNAs were a mystery discovery, as they were initially believed to be a product of splicing errors; however, subsequent research has shown that circRNAs can perform various functions and help in the regulation of splicing and transcription, including playing a role as microRNA (miRNA) sponges. With the application of high throughput next-generation technologies, circRNA hotspots were discovered. There are emerging indications that explain the association of circRNAs with human diseases, like cancers, developmental disorders, and inflammation, and circRNAs may be a new potential biomarker for the diagnosis and treatment outcome of various diseases, including cancer. After the discoveries of miRNAs and long noncoding RNAs, circRNAs are now acting as a novel research entity of interest in the field of RNA disease biology. In this review, we aim to focus on major updates on the biogeny and metabolism of circRNAs, along with their possible/established roles in major human diseases.
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Moxham R, Tjokrowidjaja A, Devery S, Smyth R, McLean A, Roberts DM, Wu KHC. Clinical utilities and end-user experience of pharmacogenomics: 39 mo of clinical implementation experience in an Australian hospital setting. World J Med Genet 2023; 11:39-50. [DOI: 10.5496/wjmg.v11.i4.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/06/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023] [Imported: 12/20/2023] Open
Abstract
BACKGROUND Pharmacogenomics (PG) testing is under-utilised in Australia. Our research provides Australia-specific data on the perspectives of patients who have had PG testing and those of the clinicians involved in their care, with the aim to inform wider adoption of PG into routine clinical practice.
AIM To investigate the frequency of actionable drug gene interactions and assess the perceived utility of PG among patients and clinicians.
METHODS We conducted a retrospective audit of PG undertaken by 100 patients at an Australian public hospital genetics service from 2018 to 2021. Via electronic surveys we compared and contrasted the experience, understanding and usage of results between these patients and their clinicians.
RESULTS Of 100 patients who had PG, 84% were taking prescription medications, of which 67% were taking medications with actionable drug-gene interactions. Twenty-five out of 81 invited patients and 17 out of 89 invited clinicians completed the surveys. Sixty-eight percent of patients understood their PG results and 48% had medications changed following testing. Paired patient-clinician surveys showed patient-perceived utility and experience was positive, contrasting their clinicians’ hesitancy on PG adoption who identified insufficient education/training, lack of clinical support, test turnaround time and cost as barriers to adoption.
CONCLUSION Our dichotomous findings between the perspectives of our patient and clinician cohorts suggest the uptake of PG is likely to be driven by patients and clinicians need to be prepared to provide information and guidance to their patients.
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Rafaqat S, Rafaqat S. Role of IL-2/IL-2 receptor in pathogenesis of autoimmune disorders: Genetic and therapeutic aspects. World J Med Genet 2023; 11:28-38. [DOI: 10.5496/wjmg.v11.i3.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/10/2023] [Accepted: 06/30/2023] [Indexed: 07/20/2023] [Imported: 07/20/2023] Open
Abstract
Interleukin-2 (IL-2) is an important cytokine that plays a key role in the immune response. The IL-2 receptor (IL-2R) is composed of three subunits, alpha, beta, and gamma, with the alpha subunit having the highest affinity for IL-2. Several studies reported that immune dysregulation of IL-2 may cause tissue injury as well as damage leading to the pathogenesis of various autoimmune diseases such as acute necrotizing vasculitis in systemic lupus erythematosus (SLE), inflammatory synovitis in rheumatoid arthritis (RA), salivary and lacrimal gland dys-function in Sjogren syndrome (SS), obliterative vasculopathy fibrosis in systemic sclerosis (SSc), and inflammatory demyelination in multiple sclerosis (MS). The aim of this review paper was to examine the role of IL-2/IL-2R in various autoimmune disorders, taking into account recent advancements and discoveries, gaps in the current literature, ongoing debates, and potential avenues for future research. The focus of this review is on systemic lupus erythematosus, rheumatoid arthritis, systemic sclerosis, sjogren syndrome, and multiple sclerosis, which are all linked to the malfunctioning of IL-2/IL-2R. In genetic studies, gene polymorphisms of IL-2 such as IL-2 330/T, IL-2 330/G, and rs2069763 are involved in increasing the risk of SLE. Furthermore, genetic associations of IL-2/IL-2R such as rs791588, rs2281089, rs2104286, rs11594656, and rs35285258 are significantly associated with RA susceptibility. The IL-2 polymorphism including rs2069762A, rs6822844T, rs6835457G, and rs907715T are significant connections with systemic sclerosis. In addition, rs2104286 (IL-2), rs11594656 (IL-2RA), rs35285258 (IL-2RB) gene polymorphism significant increases the risk of multiple sclerosis. In therapeutic approaches, low-dose IL-2 therapy could regulate Tfr and Tfh cells, resulting in a reduction in disease activity in the SLE patients. In addition, elevated sIL-2R levels in the peripheral blood of SLE patients could be linked to an immunoregulatory imbalance, which may contribute to the onset and progression of SLE. Consequently, sIL-2R could potentially be a target for future SLE therapy. Moreover, Low dose-IL2 was well-tolerated, and low levels of Treg and high levels of IL-21 were associated with positive responses to Ld-IL2 suggested to be a safe and effective treatment for RA. Additionally, low-dose IL-2 treatment improves the exocrine glands' ability to secrete saliva in SS-affected mice. Whereas, Basiliximab targets the alpha chain of the IL-2 receptor suggested as a potential treatment for SSc. Also, pre-and post-treatment with Tregs, MDSCs, and IL-2 may have the potential to prevent EAE induction in patients with MS. It is suggested that further studies should be conducted on IL-2 polymorphism in Sjogren syndrome.
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Chapleau RR. Genome-wide associations, polygenic risk, and Mendelian randomization reveal limited interactions between John Henryism and cynicism. World J Med Genet 2023; 11:8-20. [DOI: 10.5496/wjmg.v11.i2.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/28/2023] [Accepted: 05/22/2023] [Indexed: 06/02/2023] [Imported: 07/06/2023] Open
Abstract
BACKGROUND John Henryism (JH) is a strategy for dealing with chronic psychological stress characterized by high levels of physical effort and work. Cynicism is a belief that people are motivated primarily by self-interest. High scores on the JH scale and cynicism measures correlate with an increased risk of cardiovascular disease. High cynicism is also a hallmark of burnout syndrome, another known risk factor for heart disease.
AIM To evaluate possible interactions between JH and cynicism hoping to clarify risk factors of burnout.
METHODS We analyzed genetic and psychological data available from the Database of Genotypes and Phenotypes for genome-wide associations with these traits. We split the total available samples and used plink to perform the association studies on the discovery set (n = 1852, 80%) and tested for replication using the validation set (n = 465). We used scikit-learn to perform supervised machine learning for developing genetic risk algorithms.
RESULTS We identified 2, 727, and 204 genetic associations for scores on the JH, cynicism and cynical distrust (CD) scales, respectively. We also found 173 associations with high cynicism, 109 with high CD, but no associations with high JH. We also produced polygenic classifiers for high cynicism using machine learning with areas under the receiver operator characteristics curve greater than 0.7.
CONCLUSION We found significant genetic components to these traits but no evidence of an interaction. Therefore, while there may be a genetic risk, JH is not likely a burnout risk factor.
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Franceschi R, Rivieri F, Novelli A, Ferretti D, Anesi A, Soffiati M, Porretti G, Maines E, Mucciolo M, Radetti G. Mosaicism of a novel variant in the ANKRD11 gene in a child with a mild KBG phenotype: A case report. World J Med Genet 2023; 11:21-27. [DOI: 10.5496/wjmg.v11.i2.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/03/2023] [Accepted: 05/19/2023] [Indexed: 06/02/2023] [Imported: 07/06/2023] Open
Abstract
BACKGROUND KBG syndrome is likely underdiagnosed because of mild and non-specific features in some affected patients especially before the upper permanent central incisors eruption at about the age of 7-8 years. Somatic mosaicisms are usually recognized in the parents only after a typically affected son is diagnosed with KBG syndrome. We describe for the first time the mosaicism of a novel variant in a child with a mild KBG phenotype.
CASE SUMMARY Our patient presented at 24 mo of age with short stature, hand abnormalities, facial dysmorphism and mild developmental delay. Pituitary hypoplasia and central hypothyroidism were also detected. By next generation sequencing (NGS) analysis we found a novel deletion in the ANKRD11 gene (c.4880_4893del.), that can be classified as likely pathogenic for the syndrome, with the percentage of mutated allele of 36%. We considered this finding as causative of the mild and non-specific phenotype for KBG syndrome in our patient, as previously reported in adults. A heterozygous variant in HESX1 gene, classified as variant of uncertain significance, but suspected of causing pituitary hypoplasia and hormonal deficiency, was also found. The patient started levothyroxine and growth hormone treatment.
CONCLUSION The increased use of NGS analysis may expand the phenotypic spectrum of KBG syndrome because it allows genetic diagnosis of somatic mosaicisms also in children.
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Esmaeili S, Xian CJ. Phenotypic and cytogenetic features of an Iranian child with tetrasomy 18p syndrome: A case report. World J Med Genet 2023; 11:1-7. [DOI: 10.5496/wjmg.v11.i1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/16/2023] [Accepted: 03/01/2023] [Indexed: 03/10/2023] [Imported: 07/06/2023] Open
Abstract
BACKGROUND Tetrasomy 18p is a rare chromosome abnormality disorder known to have considerable variability in clinical features and gathering data from different cases will help clinicians and researchers learn about its genotype-phenotype relationship and diagnosis.
CASE SUMMARY Herein, we have reviewed the literature on phenotypic features of this disorder and described the phenotypic and cytogenetic features of a girl of early childhood with tetrasomy 18p for the first time from Iran. This patient showed a strong sense of smell (a unique feature not reported previously for this syndrome), had clenched hand, pes planus, forward head posture in walking and hirsutism (dysmorphic features less reported), and showed 10 clinical features that are generally observed in previously reported cases, including developmental delay/intellectual disability, triangular face, smooth philtrum, feeding difficulties, hypotonia, epicanthus, strabismus, history of constipation, growth retardation and foot anomalies. G-banding chromosome analysis from peripheral blood revealed an abnormal female karyotype with a small marker chromosome (47,XX, +mar), and oligo-array comparative genomic hybridization displayed a gain of 14Mb of the 18p arm containing 56 Online Mendelian Inheritance in Man (OMIM) genes in this patient. Overall, this patient seems to have mild phenotypes.
CONCLUSION This Iranian tetrasomy 18p child displays a uniquely strong sense of smell, some less reported dysmorphic features and ten features generally reported.
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Yahaya TO, Bashar DM, Oladele EO, Umar J, Anyebe D, Izuafa A. Epigenetics in the etiology and management of infertility. World J Med Genet 2022; 10:7-21. [DOI: 10.5496/wjmg.v10.i2.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/28/2022] [Accepted: 10/12/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Epigenetic disruptions have been implicated in some cases of infertility and can serve as therapeutic targets. However, the involvement of epigenetics in infertility has not received adequate attention.
AIM This study aimed to determine the epigenetic basis of infertility in order to enhance public knowledge.
METHODS Relevant articles on the subject were collected from PubMed, RCA, Google Scholar, SpringerLink, and Scopus. The articles were pooled together and duplicates were removed using Endnote software.
RESULTS Available information shows that epigenetic mechanisms, mainly DNA methylation, histone modification, and microRNA interference are necessary for normal gametogenesis and embryogenesis. As a result, epigenetic disruptions in genes that control gametogenesis and embryogenesis, such as DDX3X, ADH4, AZF, PLAG1, D1RAS3, CYGB, MEST, JMJD1A, KCNQ1, IGF2, H19, and MTHFR may result in infertility. Aberrant DNA methylation during genomic imprinting and parental epigenetic mark erasures, in particular, may affect the DNA epigenomes of sperm and oocytes, resulting in reproductive abnormalities. Histone epigenetic dysregulation during oocyte development and histone-protamine replacement in the sperm may also cause reproductive abnormalities. Furthermore, overexpression or repression of certain microRNAs embedded in the ovary, testis, embryo, as well as granulosa cells and oocytes may impair reproduction. Male infertility is characterized by spermatogenesis failure, which includes oligozoospermia, asthenozoospermia, and teratozoospermia, while female infertility is characterized by polycystic ovary syndrome. Some epigenetic modifications can be reversed by deactivating the regulatory enzymes, implying that epigenetic reprogramming could help treat infertility in some cases. For some disorders, epigenetic drugs are available, but none have been formulated for infertility.
CONCLUSION Some cases of infertility have an epigenetic etiology and can be treated by reversing the same epigenetic mechanism that caused it. As a result, medical practitioners are urged to come up with epigenetic treatments for infertility that have an epigenetic cause.
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Maness LR. Celiac sprue - a cryptic disease: A case report. World J Med Genet 2022; 10:1-6. [DOI: 10.5496/wjmg.v10.i1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/29/2022] [Accepted: 06/20/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Celiac sprue, or celiac disease, is a relatively common disease whereby many are unaware that they have it. It often manifests with symptoms outside of the digestive system. Many health care providers are unaware of the wide variety of symptoms of celiac disease as well as diseases that are associated with it, often delaying diagnosis and treatment.
CASE SUMMARY The following case indicates an otherwise healthy 20-year-old female who presents with a variety of symptoms and is ultimately diagnosed with shingles, infectious mononucleosis, and celiac disease
CONCLUSION Although it is known that risk-factors are genetic as well as environmental, much more research is needed to better understand the relationship of potential causes. In addition, continuing education is needed in health care so that more practitioners better understand celiac disease.
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Fontana P, Passaretti FF, Maioli M, Cantalupo G, Scarano F, Lonardo F. Clinical and molecular spectrum of Wiedemann-Steiner syndrome, an emerging member of the chromatinopathy family. World J Med Genet 2020; 9:1-11. [DOI: 10.5496/wjmg.v9.i1.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/19/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
Wiedemann-Steiner syndrome (OMIM #605130) is a rare congenital malformation syndrome characterized by hypertrichosis cubiti associated with short stature; consistent facial features, including long eyelashes, thick or arched eyebrows with a lateral flare, wide nasal bridge, and downslanting and vertically narrow palpebral fissures; mild to moderate intellectual disability; behavioral difficulties; and hypertrichosis on the back. It is caused by heterozygous pathogenic variants in KMT2A. This gene has an established role in histone methylation, which explains the overlap of Wiedemann-Steiner syndrome with other chromatinopathies, a heterogeneous group of syndromic conditions that share a common trigger: The disruption of one of the genes involved in chromatin modification, leading to dysfunction of the epigenetic machinery.
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Lamba A, Parekh P, Dvorak CT, Karlitz JJ. Pedigree analysis supports a correlation between an AXIN2 variant and polyposis/colorectal cancer. World J Med Genet 2018; 8:1-4. [DOI: 10.5496/wjmg.v8.i1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/18/2017] [Accepted: 12/29/2017] [Indexed: 02/06/2023] Open
Abstract
We present a patient with a history of colonic polyposis and family history significant for colon polyps and colorectal cancer (CRC). The patient and the family also had a history of bone loss of the jaw and early tooth loss, consistent with oligodontia. Genetic testing revealed the patient to have a previously unpublished variant of unknown significance (VUS) in the AXIN2 gene. These clinical findings have been demonstrated previously in only two other families, both of which exhibited oligodontia, colorectal neoplasia (polyps and cancer) and a heterozygous mutation in AXIN2. The AXIN2 protein is component of the Wnt pathway, which is known to be vital for organism development and cellular homeostasis. Alterations of the Wnt pathway lead to cell proliferation and neoplasm, in addition to agenesis of physical structures (such as teeth). The analysis of our pedigree further supports an association between colonic neoplasm (polyposis and CRC), the AXIN2 gene in general, and this particular VUS. It also highlights the importance of analyzing and disseminating information on pedigrees with less commonly encountered genomic abnormalities so that genotypic-phenotypic correlations can be solidified.
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Lucarelli M. New era of cystic fibrosis: Full mutational analysis and personalized therapy. World J Med Genet 2017; 7:1-9. [DOI: 10.5496/wjmg.v7.i1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/19/2016] [Accepted: 02/21/2017] [Indexed: 02/07/2023] Open
Abstract
Despite its apparently simple genetics, cystic fibrosis (CF) is a rather complex genetic disease. A lot of variability in the steps of the path from the cystic fibrosis transmembrane conductance regulator (CFTR) gene to the clinical manifestations originates an uncertain genotype - phenotype relationship. A major determinant of this uncertainty is the incomplete knowledge of the CFTR mutated genotypes, due to the high number of CFTR mutations and to the higher number of their combinations in trans and in cis. Also the very limited knowledge of functional effects of CFTR mutated alleles severely impairs our diagnostic and prognostic ability. The final phenotypic modulation exerted by CFTR modifier genes and interactome further complicates the framework. The next generation sequencing approach is a rapid, low-cost and high-throughput tool that allows a near complete structural characterization of CFTR mutated genotypes, as well as of genotypes of several other genes cooperating to the final CF clinical manifestations. This powerful method perfectly complements the new personalized therapeutic approach for CF. Drugs active on specific CFTR mutational classes are already available for CF patients or are in phase 3 trials. A complete genetic characterization has been becoming crucial for a correct personalized therapy. However, the need of a functional classification of each CFTR mutation potently arises. Future big efforts towards an ever more detailed knowledge of both structural and functional CFTR defects, coupled to parallel personalized therapeutic interventions decisive for CF cure can be foreseen.
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Patel BJ, Vignesh NK, Hortelano G. Chitosan DNA nanoparticles for oral gene delivery. World J Med Genet 2016; 6:22-33. [DOI: 10.5496/wjmg.v6.i3.22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 08/08/2016] [Indexed: 02/06/2023] Open
Abstract
Gene therapy is a promising technology with potential applications in the treatment of medical conditions, both congenital and acquired. Despite its label as breakthrough technology for the 21st century, the simple concept of gene therapy - the introduction of a functional copy of desired genes in affected individuals - is proving to be more challenging than expected. Oral gene delivery has shown intriguing results and warrants further exploration. In particular, oral administration of chitosan DNA nanoparticles, one the most commonly used formulations of therapeutic DNA, has repeatedly demonstrated successful in vitro and in vivo gene transfection. While oral gene therapy has shown immense promise as treatment options in a variety of diseases, there are still significant barriers to overcome before it can be considered for clinical applications. In this review we provide an overview of the physiologic challenges facing the use of chitosan DNA nanoparticles for oral gene delivery at both the extracellular and intracellular level. From administration at the oral cavity, chitosan nanoparticles must traverse the gastrointestinal tract and protect its DNA contents from significant jumps in pH levels, various intestinal digestive enzymes, thick mucus layers with high turnover, and a proteinaceous glycocalyx meshwork. Once these extracellular barriers are overcome, chitosan DNA nanoparticles must enter intestinal cells, escape endolysosomes, and disassociate from genetic material at the appropriate time allowing transport of genetic material into the nucleus to deliver a therapeutic effect. The properties of chitosan nanoparticles and modified nanoparticles are discussed in this review. An understanding of the barriers to oral gene delivery and how to overcome them would be invaluable for future gene therapy development.
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Kaufman CS, Butler MG. Mutation in TNXB gene causes moderate to severe Ehlers-Danlos syndrome. World J Med Genet 2016; 6:17-21. [PMID: 28344932 PMCID: PMC5363719 DOI: 10.5496/wjmg.v6.i2.17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 05/27/2016] [Accepted: 06/16/2016] [Indexed: 02/07/2023] Open
Abstract
We report a 28-year-old female who presented with severe joint pain, chronic muscle weakness, Raynaud’s phenomenon, and hypermobility. She was found to have a 6074A > T nucleotide transition in the TNXB gene causing an amino acid protein change at Asp2025Val classified as likely pathogenic. We add this clinical report to the literature and classical human disease gene catalogs to identify this specific mutation as disease-causing. This gene variant was reported previously in a different 36-year-old patient who shared our patient’s symptoms of joint hypermobility, skeletal and joint pain, skin elasticity and musculoskeletal problems, thereby causing a more severe presentation than seen in the hypermobility type of Ehlers-Danlos syndrome (EDS). At the time of writing, a few mutations in the TNXB gene have been recognized as pathogenic causing EDS due to tenascin-X deficiency, but the variant identified in our patient has not been recognized as pathogenic in online genetic databases. Our case study in combination with peer-reviewed literature suggests that the 6074A > T nucleotide transition in the TNXB gene may be classified as disease-causing for EDS due to tenascin-X deficiency.
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Franco D, Lozano-Velasco E, Aranega A. Gene regulatory networks in atrial fibrillation. World J Med Genet 2016; 6:1-16. [DOI: 10.5496/wjmg.v6.i1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/15/2015] [Accepted: 02/17/2016] [Indexed: 02/06/2023] Open
Abstract
Atrial fibrillation (AF) is the most frequent arrhythmogenic syndrome in humans. With an estimate incidence of 1%-2% in the general population, AF raises up to almost 10%-12% in 80+ years. Thus, AF represents nowadays a highly prevalent medical problem generating a large economic burden. At the electrophysiological level, distinct mechanisms have been elucidated. Yet, despite its prevalence, the genetic and molecular culprits of this pandemic cardiac electrophysiological abnormality have remained largely obscure. Molecular genetics of AF familiar cases have demonstrated that single nucleotide mutations in distinct genes encoding for ion channels underlie the onset of AF, albeit such alterations only explain a minor subset of patients with AF. In recent years, analyses by means of genome-wide association studies have unraveled a more complex picture of the etiology of AF, pointing out to distinct cardiac-enriched transcription factors, as well as to other regulatory genes. Furthermore a new layer of regulatory mechanisms have emerged, i.e., post-transcriptional regulation mediated by non-coding RNA, which have been demonstrated to exert pivotal roles in cardiac electrophysiology. In this manuscript, we aim to provide a comprehensive review of the genetic regulatory networks that if impaired exert electrophysiological abnormalities that contribute to the onset, and subsequently, on self-perpetuation of AF.
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Quinn GP, Peshkin BN, Sehovic I, Bowman M, Tamargo C, Vadaparampil ST. Oncofertility in adolescent and young adult hereditary cancer: Considerations for genetics professionals. World J Med Genet 2015; 5:52-59. [DOI: 10.5496/wjmg.v5.i4.52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/07/2015] [Accepted: 09/28/2015] [Indexed: 02/06/2023] Open
Abstract
Adolescents and young adults (AYA) with a cancer diagnosis or those at risk for cancer due to hereditary cancer syndromes may benefit from genetic counseling and testing not only to manage personal risk but also to address reproductive concerns, especially fertility. The opportunity for genetic counselors to provide important risk information is relevant to both the newly diagnosed as well as to unaffected carriers and survivors. However, genetic counselors may need additional training in reproductive options related to AYA cancer to provide this valuable counsel. This commentary uses hereditary breast and ovarian cancer syndrome as a model to highlight important considerations when discussing preimplanatation genetic diagnosis and prenatal diagnosis, particularly in the context of expanded testing for hereditary cancer risk including multigene panels or whole exome or whole genome sequencing. Other hereditary cancers are also addressed; however, less is known about the psychosocial and fertility concerns in these AYA populations. Additionally, we provide an overview of the concept of “oncofertility” - the linkage between cancer care and reproductive medicine that aims to expand the reproductive opportunities of cancer patients - and offer support for the expansion of guidelines to include genetic counselors in AYA cancer patients’ treatment planning related to reproductive health and fertility.
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Timson DJ. Value of predictive bioinformatics in inherited metabolic diseases. World J Med Genet 2015; 5:46-51. [DOI: 10.5496/wjmg.v5.i3.46] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/28/2015] [Accepted: 05/18/2015] [Indexed: 02/06/2023] Open
Abstract
Typically, inherited metabolic diseases arise from point mutations in genes encoding metabolic enzymes. Although some of these mutations directly affect amino acid residues in the active sites of these enzymes, the majority do not. It is now well accepted that the majority of these disease-associated mutations exert their effects through alteration of protein stability, which causes a reduction in enzymatic activity. This finding suggests a way to predict the severity of newly discovered mutations. In silico prediction of the effects of amino acid sequence alterations on protein stability often correlates with disease severity. However, no stability prediction tool is perfect and, in general, better results are obtained if the predictions from a variety of tools are combined and then interpreted. In addition to predicted alterations to stability, the degree of conservation of a particular residue can also be a factor which needs to be taken into account: alterations to highly conserved residues are more likely to be associated with severe forms of the disease. The approach has been successfully applied in a variety of inherited metabolic diseases, but further improvements are necessary to enable robust translation into clinically useful tools.
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Chen H. Adeno-associated virus vectors for human gene therapy. World J Med Genet 2015; 5:28-45. [DOI: 10.5496/wjmg.v5.i3.28] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/08/2015] [Accepted: 05/18/2015] [Indexed: 02/06/2023] Open
Abstract
Adeno-associated virus (AAV) is a small, non-enveloped virus that contains a single-stranded DNA genome. It was the first gene therapy drug approved in the Western world in November 2012 to treat patients with lipoprotein lipase deficiency. AAV made history and put human gene therapy in the forefront again. More than four decades of research on AAV vector biology and human gene therapy has generated a huge amount of valuable information. Over 100 AAV serotypes and variants have been isolated and at least partially characterized. A number of them have been used for preclinical studies in a variety of animal models. Several AAV vector production platforms, especially the baculovirus-based system have been established for commercial-scale AAV vector production. AAV purification technologies such as density gradient centrifugation, column chromatography, or a combination, have been well developed. More than 117 clinical trials have been conducted with AAV vectors. Although there are still challenges down the road, such as cross-species variation in vector tissue tropism and gene transfer efficiency, pre-existing humoral immunity to AAV capsids and vector dose-dependent toxicity in patients, the gene therapy community is forging ahead with cautious optimism. In this review I will focus on the properties and applications of commonly used AAV serotypes and variants, and the technologies for AAV vector production and purification. I will also discuss the advancement of several promising gene therapy clinical trials.
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Marfany G, Gonzàlez-Duarte R. Clinical applications of high-throughput genetic diagnosis in inherited retinal dystrophies: Present challenges and future directions. World J Med Genet 2015; 5:14-22. [DOI: 10.5496/wjmg.v5.i2.14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/30/2014] [Accepted: 02/09/2015] [Indexed: 02/06/2023] Open
Abstract
The advent of next generation sequencing (NGS) techniques has greatly simplified the molecular diagnosis and gene identification in very rare and highly heterogeneous Mendelian disorders. Over the last two years, these approaches, especially whole exome sequencing (WES), alone or combined with homozygosity mapping and linkage analysis, have proved to be successful in the identification of more than 25 new causative retinal dystrophy genes. NGS-approaches have also identified a wealth of new mutations in previously reported genes and have provided more comprehensive information concerning the landscape of genotype-phenotype correlations and the genetic complexity/diversity of human control populations. Although whole genome sequencing is far more informative than WES, the functional meaning of the genetic variants identified by the latter can be more easily interpreted, and final diagnosis of inherited retinal dystrophies is extremely successful, reaching 80%, particularly for recessive cases. Even considering the present limitations of WES, the reductions in costs and time, the continual technical improvements, the implementation of refined bioinformatic tools and the unbiased comprehensive genetic information it provides, make WES a very promising diagnostic tool for routine clinical and genetic diagnosis in the future.
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Christopoulou G, Papageorgiou EA, Patsalis PC, Velissariou V. Comparison of next generation sequencing-based and methylated DNA immunoprecipitation-based approaches for fetal aneuploidy non-invasive prenatal testing. World J Med Genet 2015; 5:23-27. [DOI: 10.5496/wjmg.v5.i2.23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 04/07/2015] [Accepted: 04/20/2015] [Indexed: 02/06/2023] Open
Abstract
Over the past few years, many researchers have attempted to develop non-invasive prenatal testing methods in order to investigate the genetic status of the fetus. The aim is to avoid invasive procedures such as chorionic villus and amniotic fluid sampling, which result in a significant risk for pregnancy loss. The discovery of cell free fetal DNA circulating in the maternal blood has great potential for the development of non-invasive prenatal testing (NIPT) methodologies. Such strategies have been successfully applied for the determination of the fetal rhesus status and inherited monogenic disease but the field of fetal aneuploidy investigation seems to be more challenging. The main reason for this is that the maternal cell free DNA in the mother’s plasma is far more abundant, and because it is identical to half of the corresponding fetal DNA. Approaches developed are mainly based on next generation sequencing (NGS) technologies and epigenetic genetic modifications, such as fetal-maternal DNA differential methylation. At present, genetic services for non-invasive fetal aneuploidy detection are offered using NGS-based approaches but, for reasons that are presented herein, they still serve as screening tests which are not readily accessed by the majority of couples. Here we discuss the limitations of both strategies for NIPT and the future potential of the methods developed.
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Noh MJ, Copeland O, O’Mara M, Lee KH. Cell mediated gene therapy: A guide for doctors in the clinic. World J Med Genet 2015; 5:1-13. [DOI: 10.5496/wjmg.v5.i1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/16/2014] [Accepted: 01/19/2015] [Indexed: 02/06/2023] Open
Abstract
The recent approval of gene therapy products in Europe and Asia and the upsurge of gene therapy products in clinical trials signal the rebound of this technology not only for many orphan diseases but also for non-life threatening diseases. Following the success of induced pluripotent stem (iPS) cells in research, other modified ex vivo gene therapies are also knocking on the door of the clinic. Historically, gene therapy has experienced many ups and downs and still faces many challenges. During the past 10 years, many new ideas have been tried, and the goal of making this technology a more effective treatment modality through greater safety and control is coming within reach. The first clinical trial of iPS cells has begun, and cell mediated gene therapy products have reached phase III in some countries. The potential for tumorigenicity and immunogenicity are still concerns with these products, so physicians should understand the biological aspects of engineered cells in the clinic. In this review article, we attempted to provide a summary update of the current state of knowledge regarding this technology: that is, we reviewed products that have finished clinical trials, are still in clinical trials and/or are at the research stage. We also focused on the challenges, future directions, and strategies for making this technology available in the clinic. In addition, the available measures for making gene therapy products safer are within the scope of this article. It is also important to understand the manufacturing process for gene therapy products, because cell characteristics can change during the cell expansion process. When physicians use gene therapy products in the clinic, they should be aware of the viability, temperature sensitivity and stability of these cells because biologic products are different from chemical products. Although we may not be able to answer all possible questions and concerns, we believe that this is the right time for physicians to increase their interest in and understanding of this evolving technology.
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Schilders K, Ochieng JK, van de Ven CP, Gontan C, Tibboel D, Rottier RJ. Role of SOX2 in foregut development in relation to congenital abnormalities. World J Med Genet 2014; 4:94-104. [DOI: 10.5496/wjmg.v4.i4.94] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/14/2014] [Accepted: 09/10/2014] [Indexed: 02/06/2023] Open
Abstract
The uptake of the two essential ingredients for life, oxygen and nutrients, occurs primarily through the oral cavity, but these two lifelines need to be separated with high accuracy once inside the body. The two systems, the gas exchange pulmonary system and the gastro-intestinal feeding system, are derived from the same primitive embryonic structure during development, the foregut, which need to be separated before birth. In certain newborns, this separation occurs not or insufficiently, leading to life threatening conditions, sometimes incompatible with life. The development of the foregut, trachea and lungs is influenced and coordinated by a multitude of signaling cascades and transcription factors. In this review, we will highlight the development of the foregut and pulmonary system and focus on associated congenital abnormalities in light of known genetic alterations with specific attention to the transcription factor SOX2.
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Zybina TG, Zybina EV. Genome variation in the trophoblast cell lifespan: Diploidy, polyteny, depolytenization, genome segregation. World J Med Genet 2014; 4:77-93. [DOI: 10.5496/wjmg.v4.i4.77] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 04/11/2014] [Accepted: 08/31/2014] [Indexed: 02/06/2023] Open
Abstract
The lifespan of mammalian trophoblast cells includes polyploidization, its degree and peculiarities are, probably, accounted for the characteristics of placenta development. The main ways of genome multiplication-endoreduplication and reduced mitosis-that basically differ by the extent of repression of mitotic events, play, most probably, different roles in the functionally different trophoblast cells in a variety of mammalian species. In the rodent placenta, highly polyploid (512-2048c) trophoblast giant cells (TGC) undergoing endoreduplication serve a barrier with semiallogenic maternal tissues whereas series of reduced mitoses allow to accumulate a great number of low-ploid junctional zone and labyrinth trophoblast cells. Endoreduplication of TGC comes to the end with formation of numerous low-ploid subcellular compartments that show some signs of viable cells though mitotically inactive; it makes impossible their ectopic proliferation inside maternal tissues. In distinct from rodent trophoblast, deviation from (2n)c in human and silver fox trophoblast suggests a possibility of aneuploidy and other chromosome changes (aberrations, etc.). It suggests that in mammalian species with lengthy period of pregnancy, polyploidy is accompanied by more diverse genome changes that may be useful to select a more specific response to stressful factors that may appear occasionally during months of intrauterine development.
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Kuliev A, Rechitsky S. Preimplantation HLA typing: Practical tool for stem cell transplantation treatment of congenital disorders. World J Med Genet 2014; 4:105-109. [DOI: 10.5496/wjmg.v4.i4.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 08/31/2014] [Indexed: 02/06/2023] Open
Abstract
It is well known that to achieve an acceptable engraftment and survival in stem cell therapy, an human leukocyte antigens (HLA) identical stem cell transplant is strongly required. However, the availability of the HLA matched donors even among family members is extremely limited, so preimplantation HLA typing provides an attractive practical tool of stem cell therapy for children requiring HLA matched stem cell transplantation. The present experience of preimplantation genetic diagnosis (PGD) for HLA typing of over one thousand cases shows that PGD provides the at-risk couples with the option to establish an unaffected pregnancy, which may benefit the affected member of the family with hemoglobinopathies, immunodeficiencies and other congenital or acquired bone marrow failures. Despite ethical issues involved in preimplantation HLA typing, the data presented below show an extremely high attractiveness of this option for the couples with affected children requiring HLA compatible stem cell transplantation.
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Horii T, Hatada I. Genome engineering using the CRISPR/Cas system. World J Med Genet 2014; 4:69-76. [DOI: 10.5496/wjmg.v4.i3.69] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/12/2014] [Accepted: 05/19/2014] [Indexed: 02/06/2023] Open
Abstract
Recently, an epoch-making genome engineering technology using clustered regularly at interspaced short palindromic repeats (CRISPR) and CRISPR associated (Cas) nucleases, was developed. Previous technologies for genome manipulation require the time-consuming design and construction of genome-engineered nucleases for each target and have, therefore, not been widely used in mouse research where standard techniques based on homologous recombination are commonly used. The CRISPR/Cas system only requires the design of sequences complementary to a target locus, making this technology fast and straightforward. In addition, CRISPR/Cas can be used to generate mice carrying mutations in multiple genes in a single step, an achievement not possible using other methods. Here, we review the uses of this technology in genetic analysis and manipulation, including achievements made possible to date and the prospects for future therapeutic applications.
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Rigterink A, Houpt K. Genetics of canine behavior: A review. World J Med Genet 2014; 4:46-57. [DOI: 10.5496/wjmg.v4.i3.46] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 05/20/2014] [Accepted: 06/11/2014] [Indexed: 02/06/2023] Open
Abstract
The past decade has seen rapid progress in the field of canid behavioral genetics. The recent advances are summarized in this review. The identification of the genes responsible for tameness in silver foxes is the culmination of a half century of behavioral testing and, more recently, genomic investigation. There is agreement that domestic dogs evolved from wolves, but when and from which population remains controversial. The genetic differences between wolves and dogs identified include those for neurotransmitters and digestion. Breed differences in behavior are well known, but only recently have the genetics underlying these differences been investigated. The genes responsible for flank sucking in Doberman Pinschers and for several other obsessive compulsive problems in other breeds have been identified. Aggression is the least desirable canine trait, and several laboratories have detected differences in neurotransmitters and their receptors between aggressive and non-aggressive dogs. In English Cocker Spaniels, the genes linked to aggressive behavior code for dopamine, serotonin, and glutamate receptors. A dopamine transporter gene has been associated with impulsive behavior in Malinois.
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