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Podgrajsek R, Hodzic A, Stimpfel M, Kunej T, Peterlin B. Insight into the complexity of male infertility: a multi-omics review. Syst Biol Reprod Med 2024; 70:73-90. [PMID: 38517373 DOI: 10.1080/19396368.2024.2317804] [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: 07/20/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024]
Abstract
Male infertility is a reproductive disorder, accounting for 40-50% of infertility. Currently, in about 70% of infertile men, the cause remains unknown. With the introduction of novel omics and advancement in high-throughput technology, potential biomarkers are emerging. The main purpose of our work was to overview different aspects of omics approaches in association with idiopathic male infertility and highlight potential genes, transcripts, non-coding RNA, proteins, and metabolites worth further exploring. Using the Gene Ontology (GO) analysis, we aimed to compare enriched GO terms from each omics approach and determine their overlapping. A PubMed database screening for the literature published between February 2014 and June 2022 was performed using the keywords: male infertility in association with different omics approaches: genomics, epigenomics, transcriptomics, ncRNAomics, proteomics, and metabolomics. A GO enrichment analysis was performed using the Enrichr tool. We retrieved 281 global studies: 171 genomics (DNA level), 21 epigenomics (19 of methylation and two histone residue modifications), 15 transcriptomics, 31 non-coding RNA, 29 proteomics, two protein posttranslational modification, and 19 metabolomics studies. Gene ontology comparison showed that different omics approaches lead to the identification of different molecular factors and that the corresponding GO terms, obtained from different omics approaches, do not overlap to a larger extent. With the integration of novel omics levels into the research of idiopathic causes of male infertility, using multi-omic systems biology approaches, we will be closer to finding the potential biomarkers and consequently becoming aware of the entire spectrum of male infertility, their cause, prognosis, and potential treatment.
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Affiliation(s)
- Rebeka Podgrajsek
- Department of Human Reproduction, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Alenka Hodzic
- Clinical Institute of Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
- Faculty of Health Sciences, University of Novo mesto, Novo Mesto, Slovenia
| | - Martin Stimpfel
- Department of Human Reproduction, University Medical Center Ljubljana, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Jovanovic A, Pekmezovic T, Mesaros S, Novakovic I, Peterlin B, Veselinovic N, Tamas O, Ivanovic J, Maric G, Andabaka M, Momcilovic N, Drulovic J. Earlier age of symptom onset in younger generation of familial cases of multiple sclerosis. Neurol Sci 2024:10.1007/s10072-024-07512-w. [PMID: 38594425 DOI: 10.1007/s10072-024-07512-w] [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: 11/06/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024]
Abstract
AIM The aim of this study was to assess the prevalence of familial MS (fMS) in Belgrade MS population, discern the differences between the persons with fMS and sporadic MS, and to detect the presence of anticipation phenomenon in fMS patients. METHODS The data on the demographic and clinical characteristics of MS patients was obtained from the Belgrade MS population Registry. In cases of vertical transmission of MS, the family members were divided into the younger and older generation, in order to assess the potential presence of anticipation phenomenon. To adjust for follow-up time bias, a secondary analysis including only patients who had the onset of symptoms before 39 years (75.percentile), and those who were 39 + years, was performed. RESULTS The prevalence of fMS in Belgrade MS population is 6.4%. FMS cases had earlier age at MS symptom onset (30.4 vs. 32.3 years) compared to sporadic MS cohort. When comparing fMS cases across generations, the younger generation had significantly lower age at onset compared with the older one (25.8 vs. 35.7 years, p < 0.001). After adjustment for the different length of the follow-up, the difference in age at symptom onset between the groups was reduced, but it still existed and was statistically significant (30.0 years in younger vs. 36.4 years in older generation, p = 0.040). CONCLUSION In our study, the analysis of fMS cases across generations, showed an earlier age of symptom onset in the younger generation, even after adjustment. These results indicate the possibility of existence of anticipation phenomenon.
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Affiliation(s)
- Aleksa Jovanovic
- Institute of Epidemiology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Tatjana Pekmezovic
- Institute of Epidemiology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Sarlota Mesaros
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ivana Novakovic
- Institute of Medical Genetics, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Borut Peterlin
- Clinical Institute for Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Nikola Veselinovic
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Olivera Tamas
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jovana Ivanovic
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia
| | - Gorica Maric
- Institute of Epidemiology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Marko Andabaka
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia
| | - Nikola Momcilovic
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia
| | - Jelena Drulovic
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia.
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.
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Rački V, Bergant G, Papić E, Kovanda A, Hero M, Rožmarić G, Starčević Čizmarević N, Ristić S, Ostojić S, Kapović M, Maver A, Peterlin B, Vuletić V. GiOPARK Project: The Genetic Study of Parkinson's Disease in the Croatian Population. Genes (Basel) 2024; 15:255. [PMID: 38397244 PMCID: PMC10888376 DOI: 10.3390/genes15020255] [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: 01/29/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Parkinson's disease is a neurological disorder that affects motor function, autonomic functions, and cognitive abilities. It is likely that both genetic and environmental factors, along with age, contribute to the cause. However, there is no comprehensive guideline for genetic testing for Parkinson's disease, and more research is needed to understand genetic variations in different populations. There has been no research on the genetic background of Parkinson's disease in Croatia so far. Therefore, with the GiOPARK project, we aimed to investigate the genetic variants responsible for Parkinson's disease in 153 Croatian patients with early onset, familial onset, and sporadic late-onset using whole-exome sequencing, along with multiplex ligation-dependent probe amplification and Sanger sequencing in select patients. We found causative variants in 7.84% of the patients, with GBA being the most common gene (4.58%), followed by PRKN (1.96%), ITM2B (0.65%), and MAPT (0.65%). Moreover, variants of uncertain significance were identified in 26.14% of the patients. The causative variants were found in all three subgroups, indicating that genetic factors play a role in all the analyzed Parkinson's disease subtypes. This study emphasizes the need for more inclusive research and improved guidelines to better understand the genetic basis of Parkinson's disease and facilitate more effective clinical management.
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Affiliation(s)
- Valentino Rački
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Gaber Bergant
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Eliša Papić
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Mario Hero
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Gloria Rožmarić
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Nada Starčević Čizmarević
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Smiljana Ristić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Saša Ostojić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Miljenko Kapović
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Vladimira Vuletić
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
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Jovanovic A, Pekmezovic T, Mesaros S, Novakovic I, Peterlin B, Veselinovic N, Tamas O, Ivanovic J, Maric G, Andabaka M, Momcilovic N, Drulovic J. Exclusive breastfeeding may be a protective factor in individuals with familial multiple sclerosis. A population registry-based case-control study. Mult Scler Relat Disord 2024; 82:105392. [PMID: 38159366 DOI: 10.1016/j.msard.2023.105392] [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: 04/30/2023] [Revised: 08/22/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Multiple sclerosis (MS) is an immune-mediated disease that affects the central nervous system, which most likely results from the interplay between environmental and genetic factors. The aim of our study was to assess the effect of breastfeeding on the risk of developing familial multiple sclerosis (fMS) in persons with positive MS history, being the first such investigation performed in fMS cohort. METHODS A case-control study based on the Belgrade population MS Registry was conducted. Cases for the sporadic MS (sMS) control group were randomly selected from the Registry, and matched with individuals with fMS at a ratio of 1:1. Spouses of the persons with fMS were included as a healthy control (HC) group. A specific questionnaire that was previously validated was used to obtain the data. To evaluate risk factors associated with breastfeeding for fMS occurrence compared with sMS and HC, multinomial regression analysis was performed to compute the relative risk ratios (RRR) along with 95% confidence intervals (95% CI). The analysis was afterwards repeated, stratified by sex. Both models were adjusted for potential confounding factors. RESULTS A total of 393 participants were included in our case-control study, 131 per group. There were more individuals who were exclusively breastfed longer than six months in the sMS group compared to fMS group (RRR 2.01, 95% CI 1.22-3.32). After stratification by sex, exclusive breastfeeding was shown to be a protective factor for fMS only in male population, for individuals breastfed ≥4 months. The results of both the main and stratified analysis remained robust after adjustment. CONCLUSION Our study findings indicate that breastfeeding reduces the risk of MS in infants with family history of the disease, although this protective effect may be limited to the male population. Further investigation into the differences in risk factors between fMS and sMS is warranted to gain a more comprehensive understanding of the disease.
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Affiliation(s)
- Aleksa Jovanovic
- Institute of Epidemiology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Tatjana Pekmezovic
- Institute of Epidemiology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Sarlota Mesaros
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia; Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ivana Novakovic
- Institute of Medical Genetics, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Borut Peterlin
- Clinical Institute for Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Nikola Veselinovic
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia; Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Olivera Tamas
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia; Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jovana Ivanovic
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia
| | - Gorica Maric
- Institute of Epidemiology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Marko Andabaka
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia
| | - Nikola Momcilovic
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia
| | - Jelena Drulovic
- Clinic of Neurology, University Clinical Center of Serbia, Belgrade, Serbia; Faculty of Medicine, University of Belgrade, Belgrade, Serbia.
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Prosenc B, Cizek Sajko M, Kavsek G, Herzog M, Peterlin B. Perception of genomic newborn screening among peripartum mothers. Eur J Hum Genet 2024; 32:163-170. [PMID: 38110644 PMCID: PMC10853238 DOI: 10.1038/s41431-023-01497-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/26/2023] [Accepted: 11/08/2023] [Indexed: 12/20/2023] Open
Abstract
Advances in genomic technology have generated possibilities for expanding newborn screening from traditional procedures to genomic newborn screening (gNBS). However, before the implementation of gNBS, it is crucial to address various aspects, including parental attitudes, at the national level. With this aim, we analyzed the attitudes and expectations of Slovenian peripartum mothers regarding gNBS and the acceptability of its implementation into the Slovenian health system. A questionnaire-based study was conducted on a convenience sample of 1136 peripartum mothers (a response rate of 84.1%) in a hospital setting in Slovenia. We measured participants' level of general genetic knowledge, motivation to undergo gNBS, attitude toward its benefits and drawbacks, willingness to participate financially, and factors that would influence their decision to undergo gNBS. Most participants exhibited a positive attitude (83.2%) and were motivated to undertake gNBS (63.4%). They were willing to share genetic data and also contribute to the testing costs. Mothers with better genetic literacy and higher education level, and those with the familial genetic testing experiences were more supportive of gNBS. However, several emotional and socio-ethical concerns were raised regarding how the genetic information would influence family and social life.
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Affiliation(s)
- Bernarda Prosenc
- Clinical Institute for Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
- Faculty of Health Sciences, University of Novo mesto, Novo mesto, Slovenia
| | - Mojca Cizek Sajko
- Clinical Institute for Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Gorazd Kavsek
- Clinical Department of Perinatology, The Division of Gynaecology and Obstetrics, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Marusa Herzog
- Clinical Department of Perinatology, The Division of Gynaecology and Obstetrics, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute for Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia.
- Faculty of Health Sciences, University of Novo mesto, Novo mesto, Slovenia.
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Vodnjov N, Toplišek J, Maver A, Čuturilo G, Jaklič H, Teran N, Višnjar T, Škrjanec Pušenjak M, Hodžić A, Miljanović O, Peterlin B, Writzl K. A novel splice-site FHOD3 founder variant is a common cause of hypertrophic cardiomyopathy in the population of the Balkans-A cohort study. PLoS One 2023; 18:e0294969. [PMID: 38051749 DOI: 10.1371/journal.pone.0294969] [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: 07/13/2023] [Accepted: 11/11/2023] [Indexed: 12/07/2023] Open
Abstract
Founder variants in sarcomere protein genes account for a significant proportion of disease-causing variants in patients with hypertrophic cardiomyopathy (HCM). However, information on founder variants in non-sarcomeric protein genes, such as FHOD3, which have only recently been associated with HCM, remains scarce. In this study, we conducted a retrospective analysis of exome sequencing data of 134 probands with HCM for recurrent pathogenic variants. We discovered a novel likely pathogenic variant c.1646+2T>C in FHOD3 in heterozygous state in eight probands with HCM and confirmed its presence in seven additional relatives. Individuals with this variant had a wide range of ages at onset of the disease (4-63 years). No adverse cardiac events were observed. Haplotype analysis revealed that the individuals with this variant shared a genomic region of approximately 5 Mbp surrounding the variant, confirming the founder effect of the variant. FHOD3 c.1646+2T>C is estimated to have arisen 58 generations ago (95% CI: 45-81) in a common ancestor living on the Balkans. A founder FHOD3 c.1646+2T>C variant is the second most common genetic variant in our cohort of patients with HCM, occurring in 16% of probands with a known genetic cause of HCM, which represents a substantially higher proportion than the currently estimated 0.5-2% for causal FHOD3 variants. Our study broadens the understanding of the genetic causes of HCM and may improve the diagnosis of this condition, particularly in patients from the Balkans.
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Affiliation(s)
- Nina Vodnjov
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Janez Toplišek
- Department of Cardiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Goran Čuturilo
- Department of Medical Genetics, University Children's Hospital, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Helena Jaklič
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Nataša Teran
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Tanja Višnjar
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Maruša Škrjanec Pušenjak
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Alenka Hodžić
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | | | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- European Reference Network for Rare, Low Prevalence, or Complex Diseases of the Heart (ERN GUARD-Heart)
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Kovanda A, Lovrečić L, Rudolf G, Babic Bozovic I, Jaklič H, Leonardis L, Peterlin B. Evaluation of Optical Genome Mapping in Clinical Genetic Testing of Facioscapulohumeral Muscular Dystrophy. Genes (Basel) 2023; 14:2166. [PMID: 38136988 PMCID: PMC10743191 DOI: 10.3390/genes14122166] [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: 10/18/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is the third most common hereditary muscular dystrophy, caused by the contraction of the D4Z4 repeats on the permissive 4qA haplotype on chromosome 4, resulting in the faulty expression of the DUX4 gene. Traditional diagnostics are based on Southern blotting, a time- and effort-intensive method that can be affected by single nucleotide variants (SNV) and copy number variants (CNV), as well as by the similarity of the D4Z4 repeats located on chromosome 10. We aimed to evaluate optical genome mapping (OGM) as an alternative molecular diagnostic method for the detection of FSHD. We first performed optical genome mapping with EnFocus™ FSHD analysis using DLE-1 labeling and the Saphyr instrument in patients with inconclusive diagnostic Southern blot results, negative FSHD2 results, and clinically evident FSHD. Second, we performed OGM in parallel with the classical Southern blot analysis for our prospectively collected new FSHD cases. Finally, panel exome sequencing was performed to confirm the presence of FSHD2. In two patients with diagnostically inconclusive Southern blot results, OGM was able to identify shortened D4Z4 repeats on the permissive 4qA alleles, consistent with the clinical presentation. The results of the prospectively collected patients tested in parallel using Southern blotting and OGM showed full concordance, indicating that OGM is a useful alternative to the classical Southern blotting method for detecting FSHD1. In a patient showing clinical FSHD but no shortened D4Z4 repeats in the 4qA allele using OGM or Southern blotting, a likely pathogenic variant in SMCHD1 was detected using exome sequencing, confirming FSHD2. OGM and panel exome sequencing can be used consecutively to detect FSHD2.
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Affiliation(s)
- Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Luca Lovrečić
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Gorazd Rudolf
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Ivana Babic Bozovic
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
| | - Helena Jaklič
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
| | - Lea Leonardis
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Clinical Neurophysiology, University Medical Center Ljubljana, 1000 Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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Rački V, Hero M, Papić E, Rožmarić G, Čizmarević NS, Chudy D, Peterlin B, Vuletić V. Applicability of clinical genetic testing for deep brain stimulation treatment in monogenic Parkinson's disease and monogenic dystonia: a multidisciplinary team perspective. Front Neurosci 2023; 17:1282267. [PMID: 38027472 PMCID: PMC10667448 DOI: 10.3389/fnins.2023.1282267] [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: 08/23/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
In this perspective article, we highlight the possible applicability of genetic testing in Parkinson's disease and dystonia patients treated with deep brain stimulation (DBS). DBS, a neuromodulatory technique employing electrical stimulation, has historically targeted motor symptoms in advanced PD and dystonia, yet its precise mechanisms remain elusive. Genetic insights have emerged as potential determinants of DBS efficacy. Known PD genes such as GBA, SNCA, LRRK2, and PRKN are most studied, even though further studies are required to make firm conclusions. Variable outcomes depending on genotype is present in genetic dystonia, as DYT-TOR1A, NBIA/DYTPANK2, DYT-SCGE and X-linked dystonia-parkinsonism have demonstrated promising outcomes following GPi-DBS, while varying outcomes have been documented in DYT-THAP1. We present two clinical vignettes that illustrate the applicability of genetics in clinical practice, with one PD patient with compound GBA mutations and one GNAL dystonia patient. Integrating genetic testing into clinical practice is pivotal, particularly with advancements in next-generation sequencing. However, there is a clear need for further research, especially in rarer monogenic forms. Our perspective is that applying genetics in PD and dystonia is possible today, and despite challenges, it has the potential to refine patient selection and enhance treatment outcomes.
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Affiliation(s)
- Valentino Rački
- Department of Neurology, Clinical Hospital Center Rijeka, Rijeka, Croatia
- Department of Neurology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Mario Hero
- Department of Neurology, Clinical Hospital Center Rijeka, Rijeka, Croatia
- Department of Neurology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Eliša Papić
- Department of Neurology, Clinical Hospital Center Rijeka, Rijeka, Croatia
- Department of Neurology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Gloria Rožmarić
- Department of Neurology, Clinical Hospital Center Rijeka, Rijeka, Croatia
| | - Nada Starčević Čizmarević
- Department of Medical Genomics and Biology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Darko Chudy
- Department of Neurosurgery, Clinical Hospital Dubrava, Zagreb, Croatia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Vladimira Vuletić
- Department of Neurology, Clinical Hospital Center Rijeka, Rijeka, Croatia
- Department of Neurology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
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Petrović Pajić S, Suštar Habjan M, Brecelj J, Fakin A, Volk M, Maver A, Jezernik G, Peterlin B, Glavač D, Hawlina M, Jarc-Vidmar M. Leber Hereditary Optic Neuropathy in a Family of Carriers of MT-ND5 m.13042G>T (A236S) Novel Variant. J Neuroophthalmol 2023; 43:341-347. [PMID: 36897664 DOI: 10.1097/wno.0000000000001820] [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] [Indexed: 03/11/2023]
Abstract
BACKGROUND A Slovenian three-generation family with 3 individuals with bilateral optic neuropathy and 2 unaffected relatives with a novel homoplasmic missense variant m.13042G > T (A236S) in the ND5 gene is described. A detailed phenotype at initial diagnosis and a follow-up of bilateral optic neuropathy progression is presented for 2 affected individuals. METHODS A detailed phenotype analysis with clinical examination in the early and chronic phase with electrophysiology and OCT segmentation is presented. Genotype analysis with full mitochondrial genome sequencing was performed. RESULTS Two affected male individuals (maternal cousins) had a profound visual loss at an early age (11 and 20 years) with no recovery. The maternal grandmother exhibited bilateral optic atrophy with a history of visual loss at the age 58 years. The visual loss of both affected male individuals was characterized by centrocecal scotoma, abnormal color vision, abnormal PERG N95, and VEP. Later with disease progression, retinal nerve fiber layer thinning was observed on OCT. We observed no other extraocular clinical features. Mitochondrial sequencing identified a homoplasmic novel variant m.13042G > T (A236S) in the MT-ND5 gene, belonging to a haplogroup K1a. CONCLUSIONS Novel homoplasmic variant m.13042G > T (A236S) in the ND5 gene in our family was associated with Leber hereditary optic neuropathy-like phenotype. However, predicting the pathogenicity of a novel ultra-rare missense variant in the mitochondrial ND5 gene is challenging. Genetic counseling should consider genotypic and phenotypic heterogeneity, incomplete penetrance, haplogroup type, and tissue-specific thresholds.
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Affiliation(s)
- Sanja Petrović Pajić
- Eye Hospital (SPP, MJV, BSK, MS, JB, AF, MSH), University Medical Centre Ljubljana, Ljubljana, Slovenia; Clinic for Eye Diseases (SPP), Clinical Centre of Serbia, Belgrade, Serbia; Department of Molecular Genetics (DG), Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia; Center for Human Genetics and Pharmacogenomics (GJ, DG), Faculty of Medicine, University of Maribor, Maribor, Slovenia; Clinical Institute of Genomic Medicine (MV, AM, BP), University Medical Centre Ljubljana, Ljubljana, Slovenia
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10
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Hodžić A, Maver A, Zorn B, Petrovič D, Kunej T, Peterlin B. Transcriptomic signatures for human male infertility. Front Mol Biosci 2023; 10:1226829. [PMID: 37670815 PMCID: PMC10475731 DOI: 10.3389/fmolb.2023.1226829] [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: 05/22/2023] [Accepted: 08/08/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction: Male infertility is a common, complex disorder. A better understanding of pathogenesis and etiology is needed for timely diagnosis and treatment. The aim of this study, therefore, was to identify genes involved in the pathogenesis of idiopathic male infertility based on data from transcriptomic level supported with data from genomic level. Materials and methods: First, we performed whole gene expression analysis in 20 testis biopsy samples of patients with severely impaired (10) and normal spermatogenesis (10). Further, we have performed systematic review of comparable male infertility studies and overlapped the most significantly expressed genes identified in our study with the most differentially expressed genes from selected studies. Gene Ontology analysis and KEGG functional enrichment have been performed with Enrichr analysis tool. Additionally, we have overlapped these genes with the genes where rare variants have been identified previously. Results: In 10 patients with severely impaired spermatogenesis and 10 controls, we identified more than 1,800 differentially expressed genes (p < 0.001). With the systematic review of three previously performed microarray studies that have met inclusion criteria we identified 257 overlapped differentialy expressed genes (144 downregulated and 113 upregulated). Intersection of genes from transcriptomic studies with genes with identified rare variants revealed a total of 7 genes linked with male infertility phenotype (CYP11A1, CYP17A1, RSPH3, TSGA10, AKAP4, CCIN, NDNF). Conclusion: Our comprehensive study highlighted the role of four genes in pathogenesis of male infertility and provided supporting evidence for three promising candidate genes which dysfunction may result in a male infertility disorder.
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Affiliation(s)
- Alenka Hodžić
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Branko Zorn
- Andrology Unit, Reproductive Unit, Department of Obstetrics and Gynecology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Daniel Petrovič
- Institute of Histology and Embryology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tanja Kunej
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
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11
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Vidmar Šimic M, Maver A, Zimani AN, Hočevar K, Peterlin B, Kovanda A, Premru-Sršen T. Oral microbiome and preterm birth. Front Med (Lausanne) 2023; 10:1177990. [PMID: 37608830 PMCID: PMC10441245 DOI: 10.3389/fmed.2023.1177990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/25/2023] [Indexed: 08/24/2023] Open
Abstract
Background The etiology of preterm birth (PTB) is heterogeneous and not yet well known. Maternal periodontal disease has been investigated for decades and is a known risk factor for adverse pregnancy outcomes. However, no particular bacterial species or higher taxonomic order has been found as causative of PTB, leading to studies of the whole oral microbiome. In order to determine if and how the composition of the oral microbiome is associated with PTB, we performed a large case-control study including women with term (TB) and PTB. Methods We compared oral microbiomes in PTB to TB, to examine differences in the microbial richness, diversity, and differential abundance of specific taxa. We obtained oral swab samples from 152 Caucasian pregnant women who were classified as either PTB (≤36 6/7 weeks, n = 61) or TB (≥38 0/7 weeks, n = 91) in exclusion of any other major medical or obstetric conditions. The oral microbiomes of these women were characterized by 16S ribosomal RNA (rRNA) gene sequencing of the V3-V4 region on the MiSeq platform. Results The dominant microorganisms at the phylum level in all pregnant women regardless of birth week outcomes as belonging to Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, and Actinobacteria. The phyla Firmicutes and Bacteroidetes were relatively more abundant in women with a PTB than in women with a TB, while Proteobacteria was less prevalent in women with a PTB. At the genus level, Veillonella, Prevotella, and Capnocytophaga were enriched in the PTB, and while many of the members of these genera could not be resolved to the species level, Veillonella massillensis was shown to be increased in the PTB group. Conclusion We identified the genera Veillonella, Prevotella, and Capnocytophaga in the maternal oral microbiome as being associated with PTB independently of clinically apparent infection, uterine anomalies, and other pregnancy complications, including placenta previa, and placental abruption. The clarification of the role of those taxa in the etiology of PTB merits further research.
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Affiliation(s)
- Marijana Vidmar Šimic
- Division of Obstetrics and Gynecology, Department of Perinatology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ana Nyasha Zimani
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Keli Hočevar
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tanja Premru-Sršen
- Division of Obstetrics and Gynecology, Department of Perinatology, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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12
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Dolanc Merc M, Peterlin B, Lovrecic L. The genetic approach to stillbirth: A »systematic review«. Prenat Diagn 2023; 43:1220-1228. [PMID: 37072878 DOI: 10.1002/pd.6354] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/27/2023] [Accepted: 04/09/2023] [Indexed: 04/20/2023]
Abstract
Unexplained stillbirth is defined as a stillbirth with no known cause after the exclusion of common causes, including obstetric complications, infections, placental insufficiency or abruption, umbilical cord complications, and congenital abnormalities with or without known genetic cause. More than 60% of stillbirth cases remain unexplained. The aim of this systematic review was to investigate the known genetic causes of unexplained stillbirth cases and to evaluate the current position and future directions for the use of genetic and genomic testing in expanding the knowledge in this field. A systematic search through several databases was performed using the keywords genetics and stillbirths in humans. Different methods to detect various types of causal genetic aberrations have been used in the past decades, from standard karyotyping to novel methods such as chromosomal microarray analysis and next generation sequencing technologies. Apart from common chromosomal aneuploidies, a promising hypothesis about genetic causes included genes related to cardiomyopathies and channelopathies. However, these were tested in the research settings, since molecular karyotyping is currently the standard approach in the routine evaluation of genetic causes of stillbirth. Hereby, we provide evidence that expanding knowledge using novel genetic and genomic testing might uncover new genetic causes of unexplained stillbirth.
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Affiliation(s)
- Maja Dolanc Merc
- Department of Perinatology, Division of Obstetrics and Gynecology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute for Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Luca Lovrecic
- Clinical Institute for Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
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13
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Rogac M, Kovanda A, Lovrečić L, Peterlin B. Optical genome mapping in an atypical Pelizaeus-Merzbacher prenatal challenge. Front Genet 2023; 14:1173426. [PMID: 37560384 PMCID: PMC10407396 DOI: 10.3389/fgene.2023.1173426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023] Open
Abstract
Pathogenic genetic variants represent a challenge in prenatal counseling, especially when clinical presentation in familial carriers is atypical. We describe a prenatal case involving a microarray-detected duplication of PLP1 which causes X-linked Pelizaeus-Merzbacher disease, a progressive hypomyelinating leukodystrophy. Because of atypical clinical presentation in an older male child, the duplication was examined using a novel technology, optical genome mapping, and was found to be an inverted duplication, which has not been previously described. Simultaneously, segregation analysis identified another healthy adult male carrier of this unique structural rearrangement. The novel PLP1 structural variant was reclassified, and a healthy boy was delivered. In conclusion, we suggest that examining structural variants with novel methods is warranted especially in cases with atypical clinical presentation and may in these cases lead to improved prenatal and postnatal genetic counseling.
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Affiliation(s)
- Mihael Rogac
- Clinical Institute of Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Luca Lovrečić
- Clinical Institute of Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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14
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Writzl K, Mavčič B, Maver A, Hodžić A, Peterlin B. Case Report: Non-ossifying fibromas with pathologic fractures in a patient with NONO-associated X-linked syndromic intellectual developmental disorder. Front Genet 2023; 14:1167054. [PMID: 37533431 PMCID: PMC10390693 DOI: 10.3389/fgene.2023.1167054] [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] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/24/2023] [Indexed: 08/04/2023] Open
Abstract
The NONO gene encodes a nuclear protein involved in transcriptional regulation, RNA synthesis and DNA repair. Hemizygous loss-of function, de novo or maternally inherited variants in NONO have been associated with an X-linked syndromic intellectual developmental disorder-34 (OMIM # 300967), characterized by developmental delay, intellectual disability, hypotonia, macrocephaly, elongated face, structural abnormalities of corpus callosum and/or cerebellum, congenital heart defect and left ventricular non-compaction cardiomyopathy. Few patients have been described in the literature and the phenotype data are limited. We report a 17-year-old boy with dolihocephaly, elongated face, strabismus, speech and motor delay, intellectual disability, congenital heart defect (ASD, VSD and Ebstein's anomaly), left ventricular non-compaction cardiomyopathy, bilateral inguinal hernia and cryptorchidism. Additional features included recurrent fractures due to multiple non-ossifying fibromas, thrombocytopenia, and renal anomalies. Exome sequencing revealed a de novo pathogenic variant (NM_001145408.2: c.348+2_ 348+15del) in intron 5 of the NONO gene. Renal anomalies and thrombocytopenia have been rarely reported in patients with NONO-X-linked intellectual disability syndrome, while recurrent fractures due to multiple non-ossifying fibromas have not previously been associated with this syndrome. The phenotypic spectrum of NONO-X-linked intellectual disability syndrome may be broader than currently known.
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Affiliation(s)
- Karin Writzl
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Blaž Mavčič
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of Orthopaedic Surgery, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Alenka Hodžić
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
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15
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Kotnik U, Maver A, Peterlin B, Lovrecic L. Assessment of pathogenic variation in gynecologic cancer genes in a national cohort. Sci Rep 2023; 13:5307. [PMID: 37002323 PMCID: PMC10066348 DOI: 10.1038/s41598-023-32397-8] [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: 12/06/2022] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Population-based estimates of pathogenic variation burden in gynecologic cancer predisposition genes are a prerequisite for the development of effective precision public health strategies. This study aims to reveal the burden of pathogenic variants in a comprehensive set of clinically relevant breast, ovarian, and endometrial cancer genes in a large population-based study. We performed a rigorous manual classification procedure to identify pathogenic variants in a panel of 17 gynecologic cancer predisposition genes in a cohort of 7091 individuals, representing 0.35% of the general population. The population burden of pathogenic variants in hereditary gynecologic cancer-related genes in our study was 2.14%. Pathogenic variants in genes ATM, BRCA1, and CDH1 are significantly enriched and the burden of pathogenic variants in CHEK2 is decreased in our population compared to the control population. We have identified a high burden of pathogenic variants in several gynecologic cancer-related genes in the Slovenian population, most importantly in the BRCA1 gene.
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Affiliation(s)
- Urška Kotnik
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia.
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Luca Lovrecic
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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16
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Pauly MG, Korenke GC, Diaw SH, Grözinger A, Cazurro-Gutiérrez A, Pérez-Dueñas B, González V, Macaya A, Serrano Antón AT, Peterlin B, Božović IB, Maver A, Münchau A, Lohmann K. The Expanding Phenotypical Spectrum of WARS2-Related Disorder: Four Novel Cases with a Common Recurrent Variant. Genes (Basel) 2023; 14:genes14040822. [PMID: 37107582 PMCID: PMC10137540 DOI: 10.3390/genes14040822] [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: 03/09/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 04/29/2023] Open
Abstract
Biallelic variants in the mitochondrial form of the tryptophanyl-tRNA synthetases (WARS2) can cause a neurodevelopmental disorder with movement disorders including early-onset tremor-parkinsonism syndrome. Here, we describe four new patients, who all presented at a young age with a tremor-parkinsonism syndrome and responded well to levodopa. All patients carry the same recurrent, hypomorphic missense variant (NM_015836.4: c.37T>G; p.Trp13Gly) either together with a previously described truncating variant (NM_015836.4: c.797Cdel; p.Pro266ArgfsTer10), a novel truncating variant (NM_015836.4: c.346C>T; p.Gln116Ter), a novel canonical splice site variant (NM_015836.4: c.349-1G>A), or a novel missense variant (NM_015836.4: c.475A>C, p.Thr159Pro). We investigated the mitochondrial function in patients and found increased levels of mitochondrially encoded cytochrome C Oxidase II as part of the mitochondrial respiratory chain as well as decreased mitochondrial integrity and branching. Finally, we conducted a literature review and here summarize the broad phenotypical spectrum of reported WARS2-related disorders. In conclusion, WARS2-related disorders are diagnostically challenging diseases due to the broad phenotypic spectrum and the disease relevance of a relatively common missense change that is often filtered out in a diagnostic setting since it occurs in ~0.5% of the general European population.
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Affiliation(s)
- Martje G Pauly
- Institute of Neurogenetics, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
- Institute of Systems Motor Science, University of Luebeck, 23562 Luebeck, Germany
- Department of Neurology, University Hospital Schleswig Holstein, 23562 Luebeck, Germany
| | - G Christoph Korenke
- Department of Neuropediatrics, University Children's Hospital, Klinikum Oldenburg, 26133 Oldenburg, Germany
| | - Sokhna Haissatou Diaw
- Institute of Neurogenetics, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
| | - Anne Grözinger
- Institute of Neurogenetics, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
| | - Ana Cazurro-Gutiérrez
- Pediatric Neurology Research Group, Autonomous University of Barcelona, Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Belén Pérez-Dueñas
- Pediatric Neurology Research Group, Autonomous University of Barcelona, Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 08035 Barcelona, Spain
| | - Victoria González
- Department of Neurology, Autonomous University of Barcelona, Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Alfons Macaya
- Pediatric Neurology Research Group, Autonomous University of Barcelona, Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Ana Teresa Serrano Antón
- Clinical Genetic Section, Pediatric Service, Hospital Clinico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Ivana Babić Božović
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Alexander Münchau
- Institute of Systems Motor Science, University of Luebeck, 23562 Luebeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
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17
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Bergant G, Abdulkhalikova D, Šuštaršič A, Peterlin B, Vrtačnik Bokal E, Maver A, Videmšek M, Burnik Papler T. Expression of Markers of Endometrial Receptivity in Obese Infertile PCOS Women before and after the Weight Loss Program-A Preliminary Study. Cells 2022; 12:cells12010164. [PMID: 36611958 PMCID: PMC9818464 DOI: 10.3390/cells12010164] [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: 12/01/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
Obesity is an increasing worldwide problem, and it is common in women with polycystic ovaries syndrome (PCOS). It is well known that women with PCOS have lower chances of spontaneous conception as well as lower success with IVF procedures. The mechanisms by which obesity causes lower fertility are not yet fully understood. The aim of the present study was to determine the effect of a lifestyle intervention weight loss program on the expression of the endometrial genes during the window of implantation (WOI). For this purpose, 15 infertile women with obesity and PCOS were included in the study. Endometrial samples were taken during the WOI before and at the end of the program, and RNASeq analysis was performed. There were no significantly differentially expressed genes before and after the weight loss program. We then compared the results of our study with previously published studies on markers of endometrial receptivity. The biomarker genes that were found to be down-regulated during the WOI in previous studies were more down-regulated after the weight loss program in the present study. Furthermore, 25% of the women who achieved the desired 5% or more weight reduction conceived spontaneously. Our study shows that weight loss might positively impact endometrial receptivity. which may lead towards the improved fertility of obese women with PCOS.
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Affiliation(s)
- Gaber Bergant
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Dzhamilyat Abdulkhalikova
- Department of Human Reproduction, Division of Obstetrics and Gynecology, University Medical Centre, 1000 Ljubljana, Slovenia
| | - Ana Šuštaršič
- Faculty of Sports, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Eda Vrtačnik Bokal
- Department of Human Reproduction, Division of Obstetrics and Gynecology, University Medical Centre, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Mateja Videmšek
- Faculty of Sports, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tanja Burnik Papler
- Department of Human Reproduction, Division of Obstetrics and Gynecology, University Medical Centre, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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18
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Tumiene B, Peters H, Melegh B, Peterlin B, Utkus A, Fatkulina N, Pfliegler G, Graessner H, Hermanns S, Scarpa M, Blay JY, Ashton S, McKay L, Baynam G. Rare disease education in Europe and beyond: time to act. Orphanet J Rare Dis 2022; 17:441. [PMID: 36536417 PMCID: PMC9761619 DOI: 10.1186/s13023-022-02527-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 10/02/2022] [Indexed: 12/23/2022] Open
Abstract
People living with rare diseases (PLWRD) still face huge unmet needs, in part due to the fact that care systems are not sufficiently aligned with their needs and healthcare workforce (HWF) along their care pathways lacks competencies to efficiently tackle rare disease-specific challenges. Level of rare disease knowledge and awareness among the current and future HWF is insufficient. In recent years, many educational resources on rare diseases have been developed, however, awareness of these resources is still limited and rare disease education is still not sufficiently taken into account by some crucial stakeholders as academia and professional organizations. Therefore, there is a need to fundamentally rethink rare disease education and HWF development across the whole spectrum from students to generalists, specialists and experts, to engage and empower PLWRD, their families and advocates, and to work towards a common coherent and complementary strategy on rare disease education and training in Europe and beyond. Special consideration should be also given to the role of nurse coordinators in care coordination, interprofessional training for integrated multidisciplinary care, patient and family-centered education, opportunities given by digital learning and fostering of social accountability to enforce the focus on socially-vulnerable groups such as PLWRD. The strategy has to be developed and implemented by multiple rare disease education and training providers: universities, medical and nursing schools and their associations, professional organizations, European Reference Networks, patient organizations, other organizations and institutions dedicated to rare diseases and rare cancers, authorities and policy bodies.
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Affiliation(s)
- Birute Tumiene
- grid.6441.70000 0001 2243 2806Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Harm Peters
- grid.6363.00000 0001 2218 4662Dieter Scheffner Center for Medical Education and Educational Research, Dean’s Office of Study Affairs, Charité - Universitätsmedizin, Berlin, Germany ,Association of Medical Schools in Europe e.V., Berlin, Germany
| | - Bela Melegh
- grid.9679.10000 0001 0663 9479Department of Medical Genetics, and Szentagothai Research Center, University of Pecs, School of Medicine, Pecs, Hungary
| | - Borut Peterlin
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Algirdas Utkus
- grid.6441.70000 0001 2243 2806Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania ,Association of Medical Schools in Europe e.V., Berlin, Germany
| | - Natalja Fatkulina
- grid.6441.70000 0001 2243 2806Institute of Health Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - György Pfliegler
- grid.7122.60000 0001 1088 8582Centre for Rare Diseases, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Holm Graessner
- grid.10392.390000 0001 2190 1447Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany ,grid.411544.10000 0001 0196 8249Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Sanja Hermanns
- grid.10392.390000 0001 2190 1447Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany ,grid.411544.10000 0001 0196 8249Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Maurizio Scarpa
- grid.411492.bRegional Center for Rare Diseases, University Hospital of Udine, Udine, Italy
| | - Jean-Yves Blay
- grid.7849.20000 0001 2150 7757Centre Léon Berard, University Claude Bernard Lyon 1& Unicancer Lyon, Lyon, France
| | - Sharon Ashton
- grid.433753.5EURORDIS - Rare Diseases Europe, Paris, France
| | - Lucy McKay
- Medics4RareDiseases, High Wycombe, England, UK
| | - Gareth Baynam
- grid.1012.20000 0004 1936 7910Telethon Kids Institute and the Faculty of Health and Medical Sciences, Division of Paediatrics, He University of Western Australia, Nedlands, WA Australia ,grid.413880.60000 0004 0453 2856Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, Perth, WA Australia ,Rare Care Centre, Child and Adolescent Health Service, Perth, WA Australia
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19
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Papić E, Rački V, Hero M, Tomić Z, Starčević-Čižmarević N, Kovanda A, Kapović M, Hauser G, Peterlin B, Vuletić V. The effects of microbiota abundance on symptom severity in Parkinson's disease: A systematic review. Front Aging Neurosci 2022; 14:1020172. [PMID: 36570528 PMCID: PMC9772822 DOI: 10.3389/fnagi.2022.1020172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction Parkinson's disease (PD) is neurodegenerative disease with a multifactorial etiopathogenesis with accumulating evidence identifying microbiota as a potential factor in the earliest, prodromal phases of the disease. Previous research has already shown a significant difference between gut microbiota composition in PD patients as opposed to healthy controls, with a growing number of studies correlating gut microbiota changes with the clinical presentation of the disease in later stages, through various motor and non-motor symptoms. Our aim in this systematic review is to compose and assess current knowledge in the field and determine if the findings could influence future clinical practice as well as therapy in PD. Methods We have conducted a systematic review according to PRISMA guidelines through MEDLINE and Embase databases, with studies being selected for inclusion via a set inclusion and exclusion criteria. Results 20 studies were included in this systematic review according to the selected inclusion and exclusion criteria. The search yielded 18 case control studies, 1 case study, and 1 prospective case study with no controls. The total number of PD patients encompassed in the studies cited in this review is 1,511. Conclusion The link between gut microbiota and neurodegeneration is a complex one and it depends on various factors. The relative abundance of various microbiota taxa in the gut has been consistently shown to have a correlation with motor and non-motor symptom severity. The answer could lie in the products of gut microbiota metabolism which have also been linked to PD. Further research is thus warranted in the field, with a focus on the metabolic function of gut microbiota in relation to motor and non-motor symptoms.
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Affiliation(s)
- Eliša Papić
- Department of Neurology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia,Clinic of Neurology, Clinical Hospital Center Rijeka, Rijeka, Croatia
| | - Valentino Rački
- Department of Neurology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia,Clinic of Neurology, Clinical Hospital Center Rijeka, Rijeka, Croatia
| | - Mario Hero
- Department of Neurology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia,Clinic of Neurology, Clinical Hospital Center Rijeka, Rijeka, Croatia
| | - Zoran Tomić
- Clinic of Neurology, Clinical Hospital Center Rijeka, Rijeka, Croatia
| | - Nada Starčević-Čižmarević
- Department of Medical Genetics and Biology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Anja Kovanda
- Clinical Institute of Genomic Medicine, Ljubljana University Medical Center, Ljubljana, Slovenia
| | - Miljenko Kapović
- Department of Medical Genetics and Biology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Goran Hauser
- Department of Internal Medicine, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, Ljubljana University Medical Center, Ljubljana, Slovenia
| | - Vladimira Vuletić
- Department of Neurology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia,Clinic of Neurology, Clinical Hospital Center Rijeka, Rijeka, Croatia,*Correspondence: Vladimira Vuletić,
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20
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Rijavec M, Maver A, Turner PJ, Hočevar K, Košnik M, Yamani A, Hogan S, Custovic A, Peterlin B, Korošec P. Integrative transcriptomic analysis in human and mouse model of anaphylaxis identifies gene signatures associated with cell movement, migration and neuroinflammatory signalling. Front Immunol 2022; 13:1016165. [PMID: 36569939 PMCID: PMC9772259 DOI: 10.3389/fimmu.2022.1016165] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/10/2022] [Indexed: 12/12/2022] Open
Abstract
Background Anaphylaxis is an acute life-threatening allergic reaction and a concern at a global level; therefore, further progress in understanding the underlying mechanisms and more effective strategies for diagnosis, prevention and management are needed. Objective We sought to identify the global architecture of blood transcriptomic features of anaphylaxis by integrating expression data from human patients and mouse model of anaphylaxis. Methods Bulk RNA-sequencings of peripheral whole blood were performed in: i) 14 emergency department (ED) patients with acute anaphylaxis, predominantly to Hymenoptera venom, ii) 11 patients with peanut allergy undergoing double-blind, placebo-controlled food challenge (DBPCFC) to peanut, iii) murine model of IgE-mediated anaphylaxis. Integrative characterisation of differential gene expression, immune cell-type-specific gene expression profiles, and functional and pathway analysis was undertaken. Results 1023 genes were commonly and significantly dysregulated during anaphylaxis in ED and DBPCFC patients; of those genes, 29 were also dysregulated in the mouse model. Cell-type-specific gene expression profiles showed a rapid downregulation of blood basophil and upregulation of neutrophil signature in ED and DBPCFC patients and the mouse model, but no consistent and/or significant differences were found for other blood cells. Functional and pathway analysis demonstrated that human and mouse blood transcriptomic signatures of anaphylaxis follow trajectories of upregulation of cell movement, migration and neuroinflammatory signalling, and downregulation of lipid activating nuclear receptors signalling. Conclusion Our study highlights the matched and extensive blood transcriptomic changes and suggests the involvement of discrete cellular components and upregulation of migration and neuroinflammatory pathways during anaphylaxis.
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Affiliation(s)
- Matija Rijavec
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Medical Genetics, University Medical Centre, Ljubljana, Slovenia
| | - Paul J. Turner
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Keli Hočevar
- Clinical Institute of Medical Genetics, University Medical Centre, Ljubljana, Slovenia
| | - Mitja Košnik
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
- Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Amnah Yamani
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
- Mary H. Weiser Food Allergy Center (MHWFAC), Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Simon P. Hogan
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
- Mary H. Weiser Food Allergy Center (MHWFAC), Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre, Ljubljana, Slovenia
| | - Peter Korošec
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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21
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Kovanda A, Rački V, Bergant G, Georgiev D, Flisar D, Papić E, Brankovic M, Jankovic M, Svetel M, Teran N, Maver A, Kostic VS, Novakovic I, Pirtošek Z, Rakuša M, Vuletić V, Peterlin B. A multicenter study of genetic testing for Parkinson’s disease in the clinical setting. NPJ Parkinsons Dis 2022; 8:149. [PMCID: PMC9636217 DOI: 10.1038/s41531-022-00408-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
Parkinson’s disease (PD) guidelines lack clear criteria for genetic evaluation. We assessed the yield and rationale of genetic testing for PD in a routine clinical setting on a multicenter cohort of 149 early-onset and familial patients by exome sequencing and semi-quantitative multiplex ligation-dependent probe amplification of evidence-based PD-associated gene panel. We show that genetic testing for PD should be considered for both early-onset and familial patients alike, and a clinical yield of about 10% in the Caucasian population can be expected.
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Affiliation(s)
- Anja Kovanda
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Valentino Rački
- grid.22939.330000 0001 2236 1630Department of Neurology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Gaber Bergant
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Dejan Georgiev
- grid.29524.380000 0004 0571 7705Department of Neurology, University Medical Centre Ljubljana, Ljubljana, Slovenia ,grid.8954.00000 0001 0721 6013Artificial Intelligence Lab, Faculty of Computer and Information Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Dušan Flisar
- grid.29524.380000 0004 0571 7705Department of Neurology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Eliša Papić
- grid.22939.330000 0001 2236 1630Department of Neurology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Marija Brankovic
- grid.7149.b0000 0001 2166 9385Neurology Clinic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Marina Svetel
- grid.7149.b0000 0001 2166 9385Neurology Clinic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Nataša Teran
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Vladimir S. Kostic
- grid.7149.b0000 0001 2166 9385Neurology Clinic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ivana Novakovic
- grid.7149.b0000 0001 2166 9385Institute of Human Genetics and Neurology Clinic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Zvezdan Pirtošek
- grid.29524.380000 0004 0571 7705Department of Neurology, University Medical Centre Ljubljana, Ljubljana, Slovenia ,grid.8954.00000 0001 0721 6013Department of Neurology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Martin Rakuša
- grid.412415.70000 0001 0685 1285Department of Neurology, University Medical Centre Maribor, Maribor, Slovenia
| | - Vladimira Vuletić
- grid.22939.330000 0001 2236 1630Department of Neurology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Borut Peterlin
- grid.29524.380000 0004 0571 7705Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
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22
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Petrovic Pajic S, Jarc-Vidmar M, Fakin A, Sustar Habjan M, Brecelj J, Volk M, Maver A, Peterlin B, Hawlina M. Case report: Long-term follow-up of two patients with LHON caused by DNAJC30:c.152G>A pathogenic variant-case series. Front Neurol 2022; 13:1003046. [PMID: 36388184 PMCID: PMC9649972 DOI: 10.3389/fneur.2022.1003046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 07/25/2022] [Accepted: 09/22/2022] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND We present the disease course and long-term follow-up of two patients who were phenotypically diagnosed with atypical Leber Hereditary Optic Neuropathy (LHON) 14 and 12 years ago, respectively, whereby whole exome sequencing revealed recently described recessive DNAJC30:c.152G>A 152 A>G (p.Tyr51Cys) homozygous pathogenic variant with significant spontaneous visual acuity recovery in one. CASE PRESENTATION Two presented unrelated males with atypical LHON with sequential visual acuity (VA) loss were followed for many years. Both patients had negative family history. At the presentation at ages 17 (Case 1) and 18 years (Case 2), both had reduced visual acuity (Snellen): (Case 1) right eye (RE):CF 3m, left eye (LE):0.6, (Case 2) RE:0.2, LE:0.15; and color vision (Ishihara): (Case 1) 1/15 and 13/15; (Case 2) 2/15 and 3/15. Both had hyperemic optic disks (PNO) and central scotoma in their visual fields. Electrophysiology in the acute phase showed reduced and delayed visually evoked potentials (VEP) P100 in both patients, with reduced N95 amplitude in Case 2, and initially normal N95 amplitude in Case 1. Fluorescein angiography showed no early leakage with some late pooling at optic disks. Extensive clinical workout, including brain magnetic resonance imaging (MRI), aquaporin 4 (Aq4), and anti-myelin oligodendrocyte protein (anti-MOG) antibodies, was negative. Intravenous corticosteroids did not improve vision. Both experienced further deterioration several months after the onset accompanied by thinning of the peripapillary retinal nerve fiber layer (RNFL). Genetic testing for typical LHON pathogenic variants and whole mitochondrial DNA (mtDNA) sequencing was negative. 1 year after the onset, modest VA improvement began in Case 2 and continued over the next 3 years. VA improved bilaterally to 0.7, color vision 15/15, and islands of vision appeared within the visual field scotoma. VEP P100 peak time shortened, and amplitude increased, despite further RNFL thinning on optical coherent tomography (OCT). The patient's visual function remained stable during the entire 12-year follow-up period. Case 1 experienced modest VA improvement to 0.1 with some improvement in the visual field seven years after the disease onset, remaining stable during the entire 14-year follow-up period. VEP P100 wave remained undetectable. CONCLUSIONS Presented are two autosomal recessive LHON (arLHON, OMIM:619382) cases with the same DNAJC30:c.152G>A pathogenic variant and different degrees of spontaneous visual recovery despite progressive RNFL thinning during a long-term follow-up. This mutation should be screened in every atypical LHON patient.
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Affiliation(s)
- Sanja Petrovic Pajic
- Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Clinic for Eye Diseases, University Clinical Centre of Serbia, Belgrade, Serbia
| | | | - Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | | | - Jelka Brecelj
- Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Marija Volk
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Ales Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Marko Hawlina
- Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
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23
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Beyltjens T, Boudin E, Revencu N, Boeckx N, Bertrand M, Schütz L, Haack TB, Weber A, Biliouri E, Vinkšel M, Zagožen A, Peterlin B, Pai S, Telegrafi A, Henderson LB, Ells C, Turner L, Wuyts W, Van Hul W, Hendrickx G, Mortier GR. Heterozygous pathogenic variants involving CBFB cause a new skeletal disorder resembling cleidocranial dysplasia. J Med Genet 2022; 60:498-504. [PMID: 36241386 PMCID: PMC10176335 DOI: 10.1136/jmg-2022-108739] [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: 06/29/2022] [Accepted: 09/03/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Cleidocranial dysplasia (CCD) is a rare skeletal dysplasia with significant clinical variability. Patients with CCD typically present with delayed closure of fontanels and cranial sutures, dental anomalies, clavicular hypoplasia or aplasia and short stature. Runt-related transcription factor 2 (RUNX2) is currently the only known disease-causing gene for CCD, but several studies have suggested locus heterogeneity. METHODS The cohort consists of eight subjects from five unrelated families partially identified through GeneMatcher. Exome or genome sequencing was applied and in two subjects the effect of the variant was investigated at RNA level. RESULTS In each subject a heterozygous pathogenic variant in CBFB was detected, whereas no genomic alteration involving RUNX2 was found. Three CBFB variants (one splice site alteration, one nonsense variant, one 2 bp duplication) were shown to result in a premature stop codon. A large intragenic deletion was found to delete exon 4, without affecting CBFB expression. The effect of a second splice site variant could not be determined but most likely results in a shortened or absent protein. Affected individuals showed similarities with RUNX2-related CCD, including dental and clavicular abnormalities. Normal stature and neurocognitive problems were however distinguishing features. CBFB encodes the core-binding factor β subunit, which can interact with all RUNX proteins (RUNX1, RUNX2, RUNX3) to form heterodimeric transcription factors. This may explain the phenotypic differences between CBFB-related and RUNX2-related CCD. CONCLUSION We confirm the previously suggested locus heterogeneity for CCD by identifying five pathogenic variants in CBFB in a cohort of eight individuals with clinical and radiographic features reminiscent of CCD.
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Affiliation(s)
- Tessi Beyltjens
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Eveline Boudin
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Nicole Revencu
- Center for Human Genetics, Cliniques universitaires Saint-Luc and University of Louvain, Brussels, Belgium
| | - Nele Boeckx
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Leon Schütz
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Axel Weber
- Institute of Human Genetics, Justus Liebig University, Giessen, Germany
| | - Eleni Biliouri
- Institute of Human Genetics, Justus Liebig University, Giessen, Germany
| | - Mateja Vinkšel
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana Division of Internal Medicine, Ljubljana, Slovenia
| | - Anja Zagožen
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana Division of Internal Medicine, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana Division of Internal Medicine, Ljubljana, Slovenia
| | - Shashidhar Pai
- Children's Health, Division of Genetics, Medical University of South Carolina, Charleston, South Carolina, USA
| | | | | | - Courtney Ells
- Provincial Medical Genetics Program, Eastern Health, St. John's, Newfoundland, Canada
| | - Lesley Turner
- Provincial Medical Genetics Program, Eastern Health, St. John's, Newfoundland, Canada.,Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Wim Wuyts
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Gretl Hendrickx
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium .,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Geert R Mortier
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium.,Center for Human Genetics, University Hospital Leuven, Leuven, Belgium
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24
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Petrovic Pajic S, Lapajne L, Vratanar B, Fakin A, Jarc-Vidmar M, Sustar Habjan M, Volk M, Maver A, Peterlin B, Hawlina M. The Relative Preservation of the Central Retinal Layers in Leber Hereditary Optic Neuropathy. J Clin Med 2022; 11:jcm11206045. [PMID: 36294366 PMCID: PMC9604528 DOI: 10.3390/jcm11206045] [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: 09/01/2022] [Revised: 09/30/2022] [Accepted: 10/08/2022] [Indexed: 11/22/2022] Open
Abstract
(1) Background: The purpose of this study was to evaluate the thickness of retinal layers in Leber hereditary optic neuropathy (LHON) in the atrophic stage compared with presumably inherited bilateral optic neuropathy of unknown cause with the aim of seeing if any LHON-specific patterns exist. (2) Methods: 14 patients (24 eyes) with genetically confirmed LHON (LHON group) were compared with 13 patients (23 eyes) with negative genetic testing results (mtDNA + WES) and without identified etiology of bilateral optic atrophy (nonLHON group). Segmentation analysis of retinal layers in the macula and peripapillary RNFL (pRNFL) measurements was performed using Heidelberg Engineering Spectralis SD-OCT. (3) Results: In the LHON group, the thickness of ganglion cell complex (GCC) (retinal nerve fiber layer (RNFL)—ganglion cell layer (GCL)—inner plexiform layer (IPL)) in the central ETDRS (Early Treatment Diabetic Retinopathy Study) circle was significantly higher than in the nonLHON group (p < 0.001). In all other ETDRS fields, GCC was thinner in the LHON group. The peripapillary RNFL (pRNFL) was significantly thinner in the LHON group in the temporal superior region (p = 0.001). Longitudinal analysis of our cohort during the follow-up time showed a tendency of thickening of the RNFL, GCL, and IPL in the LHON group in the central circle, as well as a small recovery of the pRNFL in the temporal region, which corresponds to the observed central macular thickening. (4) Conclusions: In LHON, the retinal ganglion cell complex thickness (RNFL-GCL-IPL) appears to be relatively preserved in the central ETDRS circle compared to nonLHON optic neuropathies in the chronic phase. Our findings may represent novel biomarkers as well as a structural basis for possible recovery in some patients with LHON.
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Affiliation(s)
- Sanja Petrovic Pajic
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia
- Clinic for Eye Diseases, University Clinical Centre of Serbia, Pasterova 2, 11000 Belgrade, Serbia
| | - Luka Lapajne
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia
| | - Bor Vratanar
- Institute for Biostatistics and Medical Informatics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia
| | - Martina Jarc-Vidmar
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia
| | - Maja Sustar Habjan
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia
| | - Marija Volk
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Šlajmajerjeva ulica 4, 1000 Ljubljana, Slovenia
| | - Ales Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Šlajmajerjeva ulica 4, 1000 Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Šlajmajerjeva ulica 4, 1000 Ljubljana, Slovenia
| | - Marko Hawlina
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia
- Correspondence: ; Tel.: +386-1-522-1900; Fax: +386-1-522-1960
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25
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Maver A, Zigman T, Rangrez AY, Coric M, Homolak J, Saric D, Skific I, Udovicic M, Zekusic M, Saleem U, Laufer SD, Hansen A, Frey N, Baric I, Peterlin B. A biallelic loss-of-function variant in MYZAP is associated with a recessive form of severe dilated cardiomyopathy. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006221. [PMID: 35840178 PMCID: PMC9528970 DOI: 10.1101/mcs.a006221] [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] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/05/2022] [Indexed: 11/25/2022] Open
Abstract
PURPOSE Dilated cardiomyopathy (DCM) is a primary disorder of the cardiac muscle, characterised by dilatation of the left ventricle and contractile dysfunction. About 50% of DCM cases can be attributed to monogenic causes, whereas the aetiology in the remaining patients remains unexplained. METHODS We report a family with two brothers affected by severe DCM with onset in the adolescent period. Using exome sequencing, we identified a homozygous premature termination variant in the MYZAP gene in both affected sibs. MYZAP encodes for myocardial zonula adherens protein - a conserved cardiac protein in the intercalated disc structure of cardiomyocytes. RESULTS The effect of the variant was demonstrated by light and electron microscopy of the heart muscle and immunohistochemical and Western blot analysis of MYZAP protein in the heart tissue of the proband. Functional characterization using patient-derived induced pluripotent stem cell cardiomyocytes revealed significantly lower force and longer time to peak contraction and relaxation consistent with severe contractile dysfunction. CONCLUSION We provide independent support for the role of biallelic loss-of-function MYZAP variants in dilated cardiomyopathy. This report extends the spectrum of cardiac disease associated with dysfunction of cardiac intercalated disc junction and sheds light on the mechanisms leading to DCM.
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Affiliation(s)
- Ales Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Tamara Zigman
- Department of Pediatrics, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Ashraf Yusuf Rangrez
- Department of Internal Medicine III, Cardiology and Angiology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Marijana Coric
- Clinical Department of Pathology and Cytology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Jan Homolak
- Department of Pharmacology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Dalibor Saric
- Department of Pediatrics, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Iva Skific
- Department of Pathology, University Hospital Dubrava, Zagreb, Croatia
| | - Mario Udovicic
- Division of Cardiology, Department of Internal Medicine, University Hospital Dubrava, Zagreb
| | - Marija Zekusic
- Department of Transfusion and Regenerative Medicine, University Hospital Center Sestre milosrdnice, Zagreb, Croatia
| | - Umber Saleem
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sandra D Laufer
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Arne Hansen
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Norbert Frey
- Department of Internal Medicine III (Cardiology, Angiology & Pulmology), University of Heidelberg, Germany
| | - Ivo Baric
- Department of Pediatrics, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia;
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Salamun V, Rizzo M, Lovrecic L, Hocevar K, Papler Burnik T, Janez A, Jensterle M, Vrtacnik Bokal E, Peterlin B, Maver A. The Endometrial Transcriptome of Metabolic and Inflammatory Pathways During the Window of Implantation Is Deranged in Infertile Obese Polycystic Ovarian Syndrome Women. Metab Syndr Relat Disord 2022; 20:384-394. [PMID: 35834645 DOI: 10.1089/met.2021.0149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 11/13/2022] Open
Abstract
Introduction and Aim: Obese women with polycystic ovarian syndrome (PCOS) have a reduced rate of spontaneous conception even when their cycles are ovulatory. Endometrial receptivity is an important factor for poor implantation and increased miscarriage rates. Mechanisms in which both pathologies modify the endometrium are not fully clarified. The aim of our study was to compare the endometrial transcriptomic profiles between infertile obese PCOS (O-PCOS) women and infertile normal weight subjects during the window of implantation in ovulatory menstrual cycles. Methods: We conducted a prospective transcriptomic analysis of the endometrium using RNA sequencing. In this way, potential endometrial mechanisms leading to the poor reproductive outcome in O-PCOS patients could be characterized. Endometrial samples during days 21-23 of the menstrual cycle were collected from infertile O-PCOS women (n = 11) and normal weight controls (n = 10). Subgroups were defined according to the ovulatory/anovulatory status in the natural cycles, and O-PCOS women were grouped into the O-PCOS ovulatory (O-PCOS-ovul) subgroup. RNA isolation, sequencing with library reparation, and subsequent RNAseq data analysis were performed. Results: Infertile O-PCOS patients had 610 differentially expressed genes (DEGs), after adjustment for multiple comparisons with normal weight infertile controls, related to obesity (MXRA5 and ECM1), PCOS (ADAMTS19 and SLC18A2), and metabolism (VNN1 and PC). In the ovulatory subgroup, no DEGs were found, but significant differences in canonical pathways and the upstream regulator were revealed. According to functional and upstream analyses of ovulatory subgroup comparisons, the most important biological processes were related to inflammation (TNFR1 signaling), insulin signaling (insulin receptor signaling and PI3/AKT), fatty acid metabolism (stearate biosynthesis I and palmitate biosynthesis I), and lipotoxicity (unfolded protein response pathway). Conclusions: We demonstrated that endometrial transcription in ovulatory O-PCOS patients is deranged in comparison with the control ovulatory endometrium. The most important pathways of differentiation include metabolism and inflammation. These processes could also represent potential mechanisms for poor embryo implantation, which prevent the development of a successful pregnancy. ClinicalTrials.gov ID: NCT03353948.
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Affiliation(s)
- Vesna Salamun
- Division of Obstetrics and Gynecology, Department of Human Reproduction, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Manfredi Rizzo
- Division of Endocrinology, Diabetes, and Metabolism, University of South Carolina School of Medicine, Columbia, South Carolina, USA.,Department of Laboratory Medicine, DIBIMIS, University of Palermo, Italy
| | - Luca Lovrecic
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.,Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Keli Hocevar
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Tanja Papler Burnik
- Division of Obstetrics and Gynecology, Department of Human Reproduction, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Andrej Janez
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.,Department of Endocrinology, Diabetes and Metabolic Diseases, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Mojca Jensterle
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.,Department of Endocrinology, Diabetes and Metabolic Diseases, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Eda Vrtacnik Bokal
- Division of Obstetrics and Gynecology, Department of Human Reproduction, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.,Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Ales Maver
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.,Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Višnjar T, Maver A, Writzl K, Maloku O, Bergant G, Jaklič H, Neubauer D, Fogolari F, Pečarič Meglič N, Peterlin B. Biallelic ATOH1 Gene Variant in Siblings With Pontocerebellar Hypoplasia, Developmental Delay, and Hearing Loss. Neurol Genet 2022; 8:e677. [PMID: 35518571 PMCID: PMC9067583 DOI: 10.1212/nxg.0000000000000677] [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: 11/09/2021] [Accepted: 03/04/2022] [Indexed: 11/15/2022]
Abstract
Background and Objectives To report on the novel association of biallelic variant in atonal basic helix-loop-helix transcription factor 1 (ATOH1) gene and pontocerebellar hypoplasia (PCH), severe global developmental delay, intellectual disability, and hearing loss in a family with 2 affected siblings. Methods A detailed clinical assessment and exome sequencing of peripheral blood sample were performed. Segregation analysis with Sanger sequencing and structural modeling of the variant was performed to support the pathogenicity of the variant. Results A homozygous missense variant (NM_005172.1:c.481C>G) in the ATOH1 gene was identified in the proband and his affected sister. The segregation analysis subsequently confirmed its segregation with an apparently recessive PCH in this family. ATOH1 encodes for the atonal basic helix-loop-helix (bHLH) transcription factor 1, a core transcription factor in the developing cerebellum, brainstem, and dorsal spinal cord, and in the ear. The identified variant results in the p.(Arg161Gly) amino acid substitution in the evolutionarily conserved DNA-binding bHLH domain of the ATOH1 protein. Biallelic missense variants in this domain were previously reported to result in disordered cerebellar development and hearing loss in animal models. In silico homology modeling revealed that p.Arg161Gly in ATOH1 protein probably disrupts a salt bridge with DNA backbone phosphate and increases the flexibility of the bHLH helix-both of which together affect the binding capability of the bHLH domain to the DNA. Discussion Based on the sequencing results and evidence from structural modeling of the identified variant, as well as with previous reports of ATOH1 gene disruption, we conclude that ATOH1 may represent a novel candidate gene associated with the phenotype of PCH, global developmental delay, and hearing loss in humans.
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Affiliation(s)
- Tanja Višnjar
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Aleš Maver
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Karin Writzl
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Ornela Maloku
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Gaber Bergant
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Helena Jaklič
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - David Neubauer
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Federico Fogolari
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Nuška Pečarič Meglič
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
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Miroševič Š, Klemenc-Ketiš Z, Peterlin B. Family history tools for primary care: A systematic review. Eur J Gen Pract 2022; 28:75-86. [PMID: 35510897 PMCID: PMC9090347 DOI: 10.1080/13814788.2022.2061457] [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] [Indexed: 11/09/2022] Open
Abstract
Background Many medical family history (FH) tools are available for various settings. Although FH tools can be a powerful health screening tool in primary care (PC), they are currently underused. Objectives This review explores the FH tools currently available for PC and evaluates their clinical performance. Methods Five databases were systematically searched until May 2021. Identified tools were evaluated on the following criteria: time-to-complete, integration with electronic health record (EMR) systems, patient administration, risk-assessment ability, evidence-based management recommendations, analytical and clinical validity and clinical utility. Results We identified 26 PC FH tools. Analytical and clinical validity was poorly reported and agreement between FH and gold standard was commonly inadequately reported and assessed. Sensitivity was acceptable; specificity was found in half of the reviewed tools to be poor. Most reviewed tools showed a capacity to successfully identify individuals with increased risk of disease (6.2–84.6% of high and/or moderate or increased risk individuals). Conclusion Despite the potential of FH tools to improve risk stratification of patients in PC, clinical performance of current tools remains limited as well as their integration in EMR systems. Twenty-one FH tools are designed to be self-administered by patients.
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Affiliation(s)
- Špela Miroševič
- Department of Family Medicine, Medical Faculty Ljubljana, Ljubljana, Slovenia
| | - Zalika Klemenc-Ketiš
- Department of Family Medicine, Medical Faculty Ljubljana, Ljubljana, Slovenia.,Department of Family Medicine, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Community Health Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute for Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Pereza N, Peterlin B, Ostojić S, Poslon Ž. Editorial: The Importance of Genetic Literacy and Education in Medicine. Front Genet 2022; 13:910530. [PMID: 35571030 PMCID: PMC9095920 DOI: 10.3389/fgene.2022.910530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Nina Pereza
- Centre for Genetic Education, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- *Correspondence: Nina Pereza,
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Saša Ostojić
- Centre for Genetic Education, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Željka Poslon
- Centre for Genetic Education, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
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Leonardis L, Skrjanec Pusenjak M, Maver A, Jaklic H, Ozura Brecko A, Koritnik B, Peterlin B, Writzl K. Axonal Polyneuropathy in 2 Brothers With a Homozygous Missense Variant in the First Catalytic Domain of PCYT2. Neurol Genet 2022; 8:e658. [PMID: 35243002 PMCID: PMC8889895 DOI: 10.1212/nxg.0000000000000658] [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: 07/11/2021] [Accepted: 12/27/2021] [Indexed: 11/15/2022]
Abstract
Background and Objectives To expand the phenotype and genotype associated with PCYT2-related disorder. Methods Exome sequencing data from a patient with molecularly undiagnosed complex spastic paraplegia and axonal motor and sensory polyneuropathy were analyzed. Clinical data and nerve conduction studies of the patient and his affected brother were collected, and their phenotype and genotype were compared with previously reported patients with PCYT2-related disorder. Results A novel homozygous missense variant in PCYT2 (NM_001184917.2) c.88T>G; p.(Cys30Gly) was identified. This variant is located in a highly conserved tyrosine kinase site and is predicted damaging by several variant annotation tools. Both patients reported here and the previously published patients share several phenotypic features, including short stature, spastic tetraparesis, cerebellar ataxia, epilepsy, and cognitive decline. Axonal polyneuropathy, diagnosed in both brothers, was not previously reported. Discussion This family with a novel PCYT2 variant expands the clinical spectrum of PCYT2-related disorder to include axonal motor and sensory polyneuropathy and the genetic spectrum to include the variant located in the first catalytic domain, whereas all previously reported variants are located in the second catalytic domain. Further research is required to disentangle the underlying pathophysiologic mechanisms, leading to the complex phenotype of PCYT2-related disorder.
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Affiliation(s)
- Lea Leonardis
- Institute of Clinical Neurophysiology (L.L., B.K.), University Medical Center Ljubljana; Department of Neurology (L.L., B.K.), Faculty of Medicine, University of Ljubljana; Clinical Institute of Genomic Medicine (M.S.P., A.M., H.J., B.P., K.W.), University Medical Centre Ljubljana; Medical Faculty (A.M., K.W.), University of Ljubljana; and Division of Neurology (A.O.B.), University Medical Centre Ljubljana, Slovenia
| | - Marusa Skrjanec Pusenjak
- Institute of Clinical Neurophysiology (L.L., B.K.), University Medical Center Ljubljana; Department of Neurology (L.L., B.K.), Faculty of Medicine, University of Ljubljana; Clinical Institute of Genomic Medicine (M.S.P., A.M., H.J., B.P., K.W.), University Medical Centre Ljubljana; Medical Faculty (A.M., K.W.), University of Ljubljana; and Division of Neurology (A.O.B.), University Medical Centre Ljubljana, Slovenia
| | - Ales Maver
- Institute of Clinical Neurophysiology (L.L., B.K.), University Medical Center Ljubljana; Department of Neurology (L.L., B.K.), Faculty of Medicine, University of Ljubljana; Clinical Institute of Genomic Medicine (M.S.P., A.M., H.J., B.P., K.W.), University Medical Centre Ljubljana; Medical Faculty (A.M., K.W.), University of Ljubljana; and Division of Neurology (A.O.B.), University Medical Centre Ljubljana, Slovenia
| | - Helena Jaklic
- Institute of Clinical Neurophysiology (L.L., B.K.), University Medical Center Ljubljana; Department of Neurology (L.L., B.K.), Faculty of Medicine, University of Ljubljana; Clinical Institute of Genomic Medicine (M.S.P., A.M., H.J., B.P., K.W.), University Medical Centre Ljubljana; Medical Faculty (A.M., K.W.), University of Ljubljana; and Division of Neurology (A.O.B.), University Medical Centre Ljubljana, Slovenia
| | - Ana Ozura Brecko
- Institute of Clinical Neurophysiology (L.L., B.K.), University Medical Center Ljubljana; Department of Neurology (L.L., B.K.), Faculty of Medicine, University of Ljubljana; Clinical Institute of Genomic Medicine (M.S.P., A.M., H.J., B.P., K.W.), University Medical Centre Ljubljana; Medical Faculty (A.M., K.W.), University of Ljubljana; and Division of Neurology (A.O.B.), University Medical Centre Ljubljana, Slovenia
| | - Blaz Koritnik
- Institute of Clinical Neurophysiology (L.L., B.K.), University Medical Center Ljubljana; Department of Neurology (L.L., B.K.), Faculty of Medicine, University of Ljubljana; Clinical Institute of Genomic Medicine (M.S.P., A.M., H.J., B.P., K.W.), University Medical Centre Ljubljana; Medical Faculty (A.M., K.W.), University of Ljubljana; and Division of Neurology (A.O.B.), University Medical Centre Ljubljana, Slovenia
| | - Borut Peterlin
- Institute of Clinical Neurophysiology (L.L., B.K.), University Medical Center Ljubljana; Department of Neurology (L.L., B.K.), Faculty of Medicine, University of Ljubljana; Clinical Institute of Genomic Medicine (M.S.P., A.M., H.J., B.P., K.W.), University Medical Centre Ljubljana; Medical Faculty (A.M., K.W.), University of Ljubljana; and Division of Neurology (A.O.B.), University Medical Centre Ljubljana, Slovenia
| | - Karin Writzl
- Institute of Clinical Neurophysiology (L.L., B.K.), University Medical Center Ljubljana; Department of Neurology (L.L., B.K.), Faculty of Medicine, University of Ljubljana; Clinical Institute of Genomic Medicine (M.S.P., A.M., H.J., B.P., K.W.), University Medical Centre Ljubljana; Medical Faculty (A.M., K.W.), University of Ljubljana; and Division of Neurology (A.O.B.), University Medical Centre Ljubljana, Slovenia
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Mikec Š, Kolenc Ž, Peterlin B, Horvat S, Pogorevc N, Kunej T. Syndromic male subfertility: a network view of genome-phenome associations. Andrology 2022; 10:720-732. [PMID: 35218153 PMCID: PMC9314622 DOI: 10.1111/andr.13167] [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: 08/14/2020] [Revised: 01/18/2022] [Accepted: 02/11/2022] [Indexed: 11/26/2022]
Abstract
Background Male infertility is a disorder of the reproductive system with a highly complex genetic landscape. In most cases, the reason for male infertility remains unknown; however, the importance of genetic abnormalities in the diagnosis of subfertility/infertility is becoming increasingly recognized. Several syndromes include impaired male fertility in the clinical picture, although a comprehensive analysis of genetic causes of the syndromology perspective of male reproduction is not yet available. Objectives (1) To develop a catalog of syndromes and corresponding genes associated with impaired male fertility and (2) to visualize an up‐to‐date genome–phenome network of syndromic male subfertility. Materials and methods Published literature was retrieved from the Online Mendelian Inheritance in Man, Orphanet, Human Phenotype Ontology and PubMed databases using keywords “male infertility,” “syndrome,” “gene,” and “case report”; time period from 1980 to September, 2021. Retrieved data were organized as a catalog and complemented with identification numbers of syndromes (MIM ID) and genes (Gene ID). The genome–phenome network and the phenome network were visualized using Cytoscape and Gephi software platforms. Protein–protein interaction analysis was performed using STRING tool. Results Retrieved syndromes were presented as (1) a catalog containing 63 syndromes and 93 associated genes, (2) a genome–phenome network including CHD7 and WT1 genes and Noonan and Kartagener syndromes, and (3) a phenome network including 63 syndromes, and 25 categories of clinical features. Discussion The developed catalog will contribute to the advances and translational impact toward understanding the factors of syndromic male infertility. Visualized networks provide simple, flexible tools for clinicians and researchers to quickly generate hypotheses and gain a deeper understanding of underlying mechanisms affecting male reproduction. Conclusion Recognition of the significance of genome–phenome visualization as part of network medicine can help expedite efforts toward unravelling molecular mechanisms and enable advances personal/precision medicine of male reproduction and other complex traits.
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Affiliation(s)
- Špela Mikec
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Domžale, Slovenia
| | - Živa Kolenc
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Domžale, Slovenia
| | - Borut Peterlin
- University Medical Center Ljubljana, Clinical Institute of Medical Genetics, Ljubljana, Slovenia
| | - Simon Horvat
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Domžale, Slovenia
| | - Neža Pogorevc
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Domžale, Slovenia
| | - Tanja Kunej
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Domžale, Slovenia
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Rožmarić G, Hero M, Rački V, Vuletić V, Chudy D, Peterlin B. A case report of a novel GNB1 pathogenic variant and the response to deep brain stimulation. Acta Neurol Belg 2022; 123:603-605. [PMID: 35122616 DOI: 10.1007/s13760-022-01883-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/27/2022] [Indexed: 04/28/2023]
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Pereza N, Terzić R, Plaseska-Karanfilska D, Miljanović O, Novaković I, Poslon Ž, Ostojić S, Peterlin B. Current State of Compulsory Basic and Clinical Courses in Genetics for Medical Students at Medical Faculties in Balkan Countries With Slavic Languages. Front Genet 2022; 12:793834. [PMID: 35082836 PMCID: PMC8785856 DOI: 10.3389/fgene.2021.793834] [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] [Received: 10/12/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction: In this study we aimed to perform the first research on the current state of compulsory basic and clinical courses in genetics for medical students offered at medical faculties in six Balkan countries with Slavic languages (Bosnia and Herzegovina, Croatia, Montenegro, North Macedonia, Serbia, and Slovenia). Materials and Methods: The study was conducted from June to September 2021. One representative from each country was invited to collect and interpret the data for all medical faculties in their respective country. All representatives filled a questionnaire, which consisted of two sets of questions. The first set of questions was factual and contained specific questions about medical faculties and design of compulsory courses, whereas the second set of questions was more subjective and inquired the opinion of the representatives about mandatory education in clinical medical genetics in their countries and internationally. In addition, full course syllabi were analysed for course aims, learning outcomes, course content, methods for student evaluation and literature. Results: Detailed analysis was performed for a total of 22 medical faculties in Bosnia and Herzegovina (6), Croatia (4), Montenegro (1), North Macedonia (3), Serbia (6), and Slovenia (2). All but the two medical faculties in Slovenia offer either compulsory courses in basic education in human genetics (16 faculties/courses) or clinical education in medical genetics (3 faculties/courses). On the other hand, only the medical faculty in Montenegro offers both types of education, including one course in basic education in human genetics and one in clinical education in medical genetics. Most of the basic courses in human genetics have similar aims, learning outcomes and content. Conversely, clinical courses in medical genetics are similar concerning study year position, number of contact hours, ECTS (European Credit Transfer and Accumulation System) and contents, but vary considerably regarding aims, learning outcomes, ratio of types of classes, teaching methods and student evaluation. Conclusion: Our results emphasise the need for future collaboration in reaching a consensus on medical genetics education in Balkan countries with Slavic languages. Further research warrants the analysis of performance of basic courses, as well as introducing clinical courses in medical genetics to higher years of study across Balkan countries.
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Affiliation(s)
- Nina Pereza
- Centre for Genetic Education, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.,Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Rifet Terzić
- Department of Biology, Faculty of Science, University of Tuzla, Tuzla, Bosnia and Herzegovina
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Sciences and Arts, Skopje, North Macedonia
| | - Olivera Miljanović
- Center for Medical Genetic and Immunology, Clinical Center of Montenegro, Podgorica, Montenegro.,Clinical Center of Montenegro, Medical Faculty, University of Montenegro, Podgorica, Montenegro
| | - Ivana Novaković
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Željka Poslon
- Centre for Genetic Education, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.,Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Saša Ostojić
- Centre for Genetic Education, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.,Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Starčević Čizmarević N, Ćurko-Cofek B, Barac-Latas V, Peterlin B, Ristić S. Lack of association between C282Y and H63D polymorphisms in the hemochromatosis gene and risk of multiple sclerosis: A meta-analysis. Biomed Rep 2022; 16:12. [PMID: 34987796 DOI: 10.3892/br.2021.1495] [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] [Received: 09/28/2021] [Accepted: 11/09/2021] [Indexed: 12/27/2022] Open
Abstract
Increasing evidence supports the potential role of iron metabolism in multiple sclerosis (MS). Previous studies examining the association between polymorphisms of the hemochromatosis gene (HFE) and susceptibility to MS have yielded inconsistent results. In the present study, a meta-analysis of 7 studies was performed conducted in populations of Caucasian origin using the Comprehensive Meta-analysis 3.0 software. The strength of association between the C282Y and H63D polymorphisms in HFE and MS risk was estimated by odds ratios with 95% confidence intervals. Cochran's Q statistic and I2 tests were applied to quantify heterogeneity between studies. An Egger's test was used to estimate publication bias. The C282Y and H63D polymorphisms had no significant association with increased MS risk (all P≥0.05) in the following genetic comparison models: Dominant model (YY + CY vs. CC or DD + HD vs. HH) and allele contrast (Y vs. C or D vs. H). No apparent publication bias or significant heterogeneity was found between studies. These results suggest that the HFE polymorphisms C282Y and H63D are not associated with susceptibility to MS in populations of Caucasian origin. Further studies should be performed in a larger series of MS patients to evaluate the contribution of HFE and other genetic variants associated with iron regulation in the development and progression of MS.
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Affiliation(s)
- Nada Starčević Čizmarević
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Božena Ćurko-Cofek
- Department of Physiology and Immunology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Vesna Barac-Latas
- Department of Physiology and Immunology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Smiljana Ristić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
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Barišić A, Stanković A, Stojković L, Pereza N, Ostojić S, Peterlin A, Peterlin B, Vraneković J. Maternal LINE-1 DNA Methylation in Early Spontaneous Preterm Birth. Biol Res Nurs 2021; 24:85-93. [PMID: 34727781 DOI: 10.1177/10998004211043571] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Despite considerable effort aimed at decreasing the incidence of spontaneous preterm birth (SPTB), it remains the leading cause of infant mortality and morbidity. The aim of this study was to evaluate maternal LINE-1 DNA methylation (DNAm), along with DNMT polymorphisms and factors proposed to modulate DNAm, in patients who delivered early preterm. This case-control study included women who delivered spontaneously early preterm (23-336/7 weeks of gestation), and control women. DNAm was analyzed in peripheral blood lymphocytes by quantification of LINE-1 DNAm using the MethyLight method. There was no significant difference in LINE-1 DNAm between patients with early PTB and controls. Among the investigated predictors, only the history of previous PTB was significantly associated with LINE-1 DNAm in PTB patients (β = -0.407; R2 = 0.131; p = 0.011). The regression analysis showed the effect of DNMT3B rs1569686 TT+TG genotypes on LINE-1 DNAm in patients with familial PTB (β = -0.524; R2 = 0.275; p = 0.037). Our findings suggest novel associations of maternal LINE-1 DNA hypomethylation with DNMT3B rs1569686 T allele. These results also contribute to the understanding of a complex (epi)genetic and environmental relationship underlying the early PTB.
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Affiliation(s)
- Anita Barišić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Aleksandra Stanković
- Department for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Serbia
| | - Ljiljana Stojković
- Department for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Serbia
| | - Nina Pereza
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Saša Ostojić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Ana Peterlin
- Institute of Histology and Embryology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Center Ljubljana, Slovenia
| | - Jadranka Vraneković
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
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Arkar U, Vipotnik Vesnaver T, Maver A, Perković Benedik M, Peterlin B, Osredkar D. Children with cavernous malformations of the central nervous system. Eur J Paediatr Neurol 2021; 35:61-66. [PMID: 34634677 DOI: 10.1016/j.ejpn.2021.10.001] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/22/2021] [Accepted: 10/03/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Cavernous malformations (CM) of the central nervous system (CNS) are a rare pathology in the pediatric population that may present with an acute onset of severe neurological symptoms. OBJECTIVE The aim of our study was to evaluate the clinical presentation, family history, genetic background, radiological features, treatment and outcome of children with CM. METHODS This observational cohort study included all children with CM of the CNS diagnosed in the period 2000-2020 at University Children's Hospital in Ljubljana, Slovenia. Whole exome sequencing was utilized. RESULTS We identified a cohort of 20 children with CM (mean age 9.3 years, range: 10 days-18.4 years). In our cohort, 16 patients were symptomatic and 4 were asymptomatic; 7 patients had a solitary lesion, and 13 had multiple lesions. Children with multiple lesions become symptomatic at an earlier age compared with children with solitary lesions. We identified five families with familiar cavernous malformation (FCM) syndrome affecting two or more generations; FCM represented 65% of all pediatric cases identified in our study. We confirmed a mutation in FCM associated genes in all but one patient with multiple lesions, with the KRIT1 mutation being the most common. CONCLUSION Multiple CM lesions and symptomatic brainstem lesions are associated with worse neurological deficits in pediatric patients. Not all cases of multiple lesions can be linked to mutations in KRIT1, CCM2, or PDCD10, which may indicate that there are other as yet unidentified genes associated with FCM.
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Affiliation(s)
- Ula Arkar
- Department of Pediatric Neurology, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia.
| | | | - Aleš Maver
- Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.
| | - Mirjana Perković Benedik
- Department of Pediatric Neurology, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia.
| | - Borut Peterlin
- Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.
| | - Damjan Osredkar
- Department of Pediatric Neurology, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia; University of Ljubljana, Faculty of Medicine, Center for Developmental Neuroscience, Ljubljana, Slovenia.
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Zečkanović A, Maver A, Ristić S, Čizmarević NS, Peterlin B, Lovrečić L. Potential protective role of a NOD2 polymorphism in the susceptibility to multiple sclerosis is not associated with interferon therapy. Biomed Rep 2021; 15:100. [PMID: 34667597 DOI: 10.3892/br.2021.1476] [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: 02/11/2021] [Accepted: 05/28/2021] [Indexed: 11/06/2022] Open
Abstract
Pattern recognition receptors, such as specific nucleotide-binding oligomerization domain protein 2, and their polymorphisms may be involved in the pathogenesis of multiple sclerosis (MS). They may also play a role in the formation of neutralizing antibodies against interferon-β (INF-β), and may exhibit lowered efficacy. Identification of these polymorphisms may be useful for early identification of potential non-responders and to allow for modification of treatment regimens earlier. The differences in genotype distribution and allele frequency of the rs3135499 and rs2066842 NOD2 polymorphisms between patients with MS and healthy controls were analysed in the present study. The group of patients were divided into responders and non-responders to INF-β therapy to evaluate the association of both polymorphisms with response to therapy. No differences in the genotype frequencies between the responder and non-responder groups were observed. However, a statistically significant difference in genotype frequencies of TT homozygotes for rs2066842 between patients with MS and healthy controls was observed (χ2=11.8; P=0.003). A recessive genotype model and allele distribution in rs2066842 suggest that the genotype TT and allele T itself are protective against MS. The odds ratio of 0.12 represents an 8.33x lower risk for MS if an individual has a TT genotype. The significantly lower incidence of the TT genotype of rs2066842 in patients with MS suggests that the TT genotype and T allele may be a protective genetic factor against MS.
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Affiliation(s)
- Aida Zečkanović
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Smiljana Ristić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Nada Starčević Čizmarević
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Luca Lovrečić
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
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Berezin AE, Peterlin B, Lichtenauer M, Mozos I. Editorial: Prognostication of Heart Failure Evolution: From Circulating Biomarkers to Genetic Risk Predictive Score. Front Cardiovasc Med 2021; 8:687232. [PMID: 34646870 PMCID: PMC8502918 DOI: 10.3389/fcvm.2021.687232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022] Open
Affiliation(s)
- Alexander E Berezin
- Internal Medicine Department, State Medical University, Ministry of Health of Ukraine, Zaporizhzhia, Ukraine
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Michael Lichtenauer
- Division of Cardiology, Department of Internal Medicine II, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Ioana Mozos
- Department of Functional Sciences-Pathophysiology, Center for Translational Research and Systems Medicine, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania
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Abstract
Genomics is an advancing field of medicine, science, ethics, and legislation. Keeping up to date with this challenging discipline requires continuous education and exchange of knowledge between many target groups. Specific challenges in genomic education include tailoring complex topics to diverse audiences ranging from the general public and patients to highly educated professionals. National genomic projects face many of the same challenges and thus offer many opportunities to highlight common educational strategies for improving genomic literacy. We have reviewed 41 current national genomic projects and have identified 16 projects specifically describing their approach to genomic education. The following target groups were included in the educational efforts: the general public (nine projects), patients (six projects), and genomic professionals (16 projects), reflecting the general overall aims of the projects such as determining normal and pathological genomic variation, improving infrastructure, and facilitating personalized medicine. The national genomic projects aim to increase genomic literacy through supplementing existing national education in genomics as well as independent measures specifically tailored to each target group, such as training events, research collaboration, and online resources for healthcare professionals, patients, and patient organizations. This review provides the current state of educational activities within national genomic projects for different target groups and identifies good practices that could contribute to patient empowerment, public engagement, proficient healthcare professionals, and lend support to personalized medicine.
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Affiliation(s)
- Ana Nyasha Zimani
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Tekavčič Pompe M, Vrabič N, Volk M, Meglič A, Jarc-Vidmar M, Peterlin B, Hawlina M, Fakin A. Disease Progression in CNGA3 and CNGB3 Retinopathy; Characteristics of Slovenian Cohort and Proposed OCT Staging Based on Pooled Data from 126 Patients from 7 Studies. Curr Issues Mol Biol 2021; 43:941-957. [PMID: 34449556 PMCID: PMC8929018 DOI: 10.3390/cimb43020067] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 11/20/2022] Open
Abstract
Achromatopsia has been proposed to be a morphologically predominately stable retinopathy with rare reports of progression of structural changes in the macula. A five-grade system of optical coherence tomography (OCT) features has been used for the classification of structural macular changes. However, their association with age remains questionable. We characterized the Slovenian cohort of 12 patients with pathogenic variants in CNGA3 or CNGB3 who had been followed up with OCT for up to 9 years. Based on observed structural changes in association with age, the following four-stage classification of retinal morphological changes was proposed: (I) preserved inner segment ellipsoid band (Ise), (II) disrupted ISe, (III) ISe loss and (IV) ISe and RPE loss. Data from six previously published studies reporting OCT morphology in CNGA3 and CNGB3 patients were additionally collected, forming the largest CNGA3/CNGB3 cohort to date, comprising 126 patients aged 1–71 years. Multiple regression analysis showed a significant correlation of OCT stage with age (p < 0.001) and no correlation with gene (p > 0.05). The median ages of patients with stages I–IV were 12 years, 23 years, 27 years and 48 years, respectively, and no patient older than 50 years had continuous ISe. Our findings suggest that achromatopsia presents with slowly but steadily progressive structural changes of the macular outer retinal layers. However, whether morphological changes in time follow the proposed four-stage linear pattern needs to be confirmed in a long-term study.
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Affiliation(s)
- Manca Tekavčič Pompe
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.T.P.); (N.V.); (A.M.); (M.J.-V.); (M.H.)
| | - Nika Vrabič
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.T.P.); (N.V.); (A.M.); (M.J.-V.); (M.H.)
| | - Marija Volk
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.V.); (B.P.)
| | - Andrej Meglič
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.T.P.); (N.V.); (A.M.); (M.J.-V.); (M.H.)
| | - Martina Jarc-Vidmar
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.T.P.); (N.V.); (A.M.); (M.J.-V.); (M.H.)
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.V.); (B.P.)
| | - Marko Hawlina
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.T.P.); (N.V.); (A.M.); (M.J.-V.); (M.H.)
| | - Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.T.P.); (N.V.); (A.M.); (M.J.-V.); (M.H.)
- Correspondence:
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Vuletić V, Rački V, Papić E, Peterlin B. A Systematic Review of Parkinson's Disease Pharmacogenomics: Is There Time for Translation into the Clinics? Int J Mol Sci 2021; 22:ijms22137213. [PMID: 34281267 PMCID: PMC8268929 DOI: 10.3390/ijms22137213] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is the second most frequent neurodegenerative disease, which creates a significant public health burden. There is a challenge for the optimization of therapies since patients not only respond differently to current treatment options but also develop different side effects to the treatment. Genetic variability in the human genome can serve as a biomarker for the metabolism, availability of drugs and stratification of patients for suitable therapies. The goal of this systematic review is to assess the current evidence for the clinical translation of pharmacogenomics in the personalization of treatment for Parkinson's disease. METHODS We performed a systematic search of Medline database for publications covering the topic of pharmacogenomics and genotype specific mutations in Parkinson's disease treatment, along with a manual search, and finally included a total of 116 publications in the review. RESULTS We analyzed 75 studies and 41 reviews published up to December of 2020. Most research is focused on levodopa pharmacogenomic properties and catechol-O-methyltransferase (COMT) enzymatic pathway polymorphisms, which have potential for clinical implementation due to changes in treatment response and side-effects. Likewise, there is some consistent evidence in the heritability of impulse control disorder via Opioid Receptor Kappa 1 (OPRK1), 5-Hydroxytryptamine Receptor 2A (HTR2a) and Dopa decarboxylase (DDC) genotypes, and hyperhomocysteinemia via the Methylenetetrahydrofolate reductase (MTHFR) gene. On the other hand, many available studies vary in design and methodology and lack in sample size, leading to inconsistent findings. CONCLUSIONS This systematic review demonstrated that the evidence for implementation of pharmacogenomics in clinical practice is still lacking and that further research needs to be done to enable a more personalized approach to therapy for each patient.
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Affiliation(s)
- Vladimira Vuletić
- Clinic of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.)
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
- Correspondence:
| | - Valentino Rački
- Clinic of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.)
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Eliša Papić
- Clinic of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.)
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Center Ljubljana, 1000 Ljubljana, Slovenia;
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Babić Božović I, Maver A, Leonardis L, Meznaric M, Osredkar D, Peterlin B. Diagnostic yield of exome sequencing in myopathies: Experience of a Slovenian tertiary centre. PLoS One 2021; 16:e0252953. [PMID: 34106991 PMCID: PMC8189452 DOI: 10.1371/journal.pone.0252953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/25/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Our aim was to present the experience of systematic, routine use of next generation sequencing (NGS) in clinical diagnostics of myopathies. METHODS Exome sequencing was performed on patients with high risk for inherited myopathy, which were selected based on the history of the disease, family history, clinical presentation, and diagnostic workup. Exome target capture was performed, followed by sequencing on HiSeq 2500 or MiSeq platforms. Data analysis was performed using internally developed bioinformatic pipeline. RESULTS The study comprised 86 patients, including 22 paediatric cases (26%). The largest group were patients referred with an unspecified myopathy (47%), due to non-specific or incomplete clinical and laboratory findings, followed by congenital myopathies (22%) and muscular dystrophies (22%), congenital myotonias (6%), and mitochondrial myopathies (3%). Altogether, a diagnostic yield was 52%; a high diagnostic rate was present in paediatric patients (64%), while in patients with unspecified myopathies the rate was 35%. We found 51 pathogenic/likely pathogenic variants in 23 genes and two pathogenic copy number variations. CONCLUSION Our results provide evidence that phenotype driven exome analysis diagnostic approach facilitates the diagnostic rate of complex, heterogeneous disorders, such as myopathies, particularly in paediatric patients and patients with unspecified myopathies.
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Affiliation(s)
- Ivana Babić Božović
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Lea Leonardis
- Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Department of Neurology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Marija Meznaric
- Institute of Anatomy, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Damjan Osredkar
- Department of Paediatric Neurology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Atemin S, Todorov T, Maver A, Chamova T, Georgieva B, Tincheva S, Pacheva I, Ivanov I, Taneva A, Zlatareva D, Tournev I, Guergueltcheva V, Gospodinova M, Chochkova L, Peterlin B, Mitev V, Todorova A. MYH7-related disorders in two Bulgarian families: Novel variants in the same region associated with different clinical manifestation and disease penetrance. Neuromuscul Disord 2021; 31:633-641. [PMID: 34053846 DOI: 10.1016/j.nmd.2021.04.004] [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: 12/29/2020] [Revised: 04/04/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022]
Abstract
Pathogenic variants in MYH7 cause a wide range of cardiac and skeletal muscle diseases with childhood or adult onset. These include dilated and/or hypertrophic cardiomyopathy, left ventricular non-compaction cardiomyopathy, congenital myopathies with multi-minicores and myofiber type disproportion, myosin storage myopathy, Laing distal myopathy and others (scapulo-peroneal or limb-girdle muscle forms). Here we report the results from molecular genetic analyses (NGS and Sanger sequencing) of 4 patients in two families with variable neuromuscular phenotypes with or without cardiac involvement. Interestingly, variants in MYH7 gene appeared to be the cause in all the cases. A novel nonsense variant c.5746C>T, p.(Gln1916Ter) was found in the patient in Family 1 who deceased at the age of 2 years 4 months with the clinical diagnosis of dilated cardiomyopathy, whose father died before the age of 40 years, due to cardiac failure with clinical diagnosis of suspected limb-girdle muscular dystrophy. A splice acceptor variant c.5560-2A>C in MYH7 was detected in the second proband and her sister, with late onset distal myopathy without cardiac involvement. These different phenotypes (muscular involvement with severe cardiomyopathy and pure late onset neuromuscular phenotype without heart involvement) may result from novel MYH7 variants, which most probably impact the LMM (light meromyosin) domain's function of the mature protein.
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Affiliation(s)
- Slavena Atemin
- Department of Medical Chemistry and Biochemistry, Medical University Sofia, Sofia, Bulgaria; Genetic Medico-Diagnostic Laboratory "Genica", Sofia, Bulgaria.
| | - Tihomir Todorov
- Genetic Medico-Diagnostic Laboratory "Genica", Sofia, Bulgaria
| | - Ales Maver
- Clinical Institute of Medical Genetics, UMC Ljubljana, Šlajmerjeva 4, SI-1000 Ljubljana, Slovenia
| | - Teodora Chamova
- Department of Neurology, University hospital "Alexandrovska", Medical University Sofia, Sofia, Bulgaria
| | - Bilyana Georgieva
- Department of Medical Chemistry and Biochemistry, Medical University Sofia, Sofia, Bulgaria
| | - Savina Tincheva
- Genetic Medico-Diagnostic Laboratory "Genica", Sofia, Bulgaria
| | - Iliyana Pacheva
- Department of Pediatrics and Medical Genetics, Medical University - Plovdiv, Bulgaria; Department of Pediatrics, University Hospital "St. George", Plovdiv, Bulgaria
| | - Ivan Ivanov
- Department of Pediatrics and Medical Genetics, Medical University - Plovdiv, Bulgaria; Department of Pediatrics, University Hospital "St. George", Plovdiv, Bulgaria
| | - Ani Taneva
- Department of Neurology, University hospital "Alexandrovska", Medical University Sofia, Sofia, Bulgaria
| | - Dora Zlatareva
- Department of Diagnostic Imaging, University Hospital "Alexandrovska", Medical University, Sofia, Bulgaria
| | - Ivailo Tournev
- Department of Neurology, University hospital "Alexandrovska", Medical University Sofia, Sofia, Bulgaria; Department of Cognitive Science and Psychology, New Bulgarian University, Sofia, Bulgaria
| | | | | | - Lyubov Chochkova
- Department of Pediatrics and Medical Genetics, Medical University - Plovdiv, Bulgaria; Department of Pediatrics, University Hospital "St. George", Plovdiv, Bulgaria
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, UMC Ljubljana, Šlajmerjeva 4, SI-1000 Ljubljana, Slovenia
| | - Vanyo Mitev
- Department of Medical Chemistry and Biochemistry, Medical University Sofia, Sofia, Bulgaria
| | - Albena Todorova
- Department of Medical Chemistry and Biochemistry, Medical University Sofia, Sofia, Bulgaria; Genetic Medico-Diagnostic Laboratory "Genica", Sofia, Bulgaria
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Nair D, Li D, Erdogan H, Yoon A, Harr MH, Bergant G, Peterlin B, Škrjanec Pušenjak M, Jayakar P, Pfundt R, Jansen S, McWalter K, Sidhu A, Saliganan S, Agolini E, Jacob A, Pasquier J, Arash R, Kahrizi K, Najmabadi H, Ropers HH, Bhoj EJ. Discovery of a neuromuscular syndrome caused by biallelic variants in ASCC3. Human Genetics and Genomics Advances 2021; 2:100024. [PMID: 35047834 PMCID: PMC8756546 DOI: 10.1016/j.xhgg.2021.100024] [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] [Received: 09/14/2020] [Accepted: 01/13/2021] [Indexed: 11/11/2022] Open
Abstract
Activating Signal Cointegrator 1 Complex, Subunit 3 (ASCC3) is part of the four-part ASC-1 transcriptional cointegrator complex. This complex includes ASCC1 (associated with spinal muscular atrophy with congenital bone fractures 2), TRIP4 (associated with spinal muscular atrophy with congenital bone fractures 1), and ASCC2 (not yet associated with human disease.) ASCC3 encodes a DNA helicase responsible for generating single-stranded DNA as part of the DNA damage response. Interestingly, ASCC3 expresses coding and non-coding isoforms, which act in opposition to balance the recovery of gene transcription after UV-induced DNA damage. Here we report the discovery of ASCC3 as the cause of a neuromuscular syndrome in seven unreported individuals from six unrelated families and updates on the one previously reported family. All the individuals share a neurologic phenotype that ranges from severe developmental delay to muscle fatigue. There appears to be genotype-phenotype correlation, as the most mildly affected individual is homozygous for a rare missense variant, while the more severely affected individuals are compound heterozygotes for a missense and a presumed loss-of-function (LOF) variant. There are no individuals with biallelic presumed LOF variants in our cohort or in gnomAD, as this genotype may not be compatible with life. In summary we report a syndrome in these eleven individuals from seven families with biallelic variants in ASCC3.
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Vinkšel M, Writzl K, Maver A, Peterlin B. Improving diagnostics of rare genetic diseases with NGS approaches. J Community Genet 2021; 12:247-256. [PMID: 33452619 PMCID: PMC8141085 DOI: 10.1007/s12687-020-00500-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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] [Received: 07/22/2020] [Accepted: 12/08/2020] [Indexed: 01/08/2023] Open
Abstract
According to a rough estimate, one in fifteen people worldwide is affected by a rare disease. Rare diseases are therefore common in clinical practice; however, timely diagnosis of rare diseases is still challenging. Introduction of novel methods based on next-generation sequencing (NGS) technology offers a successful diagnosis of genetically heterogeneous disorders, even in case of unclear clinical diagnostic hypothesis. However, the application of novel technology differs among the centres and health systems significantly. Our goal is to discuss the impact of the implementation of NGS in the diagnosis of rare diseases and present advantages along with challenges of diagnostic approach. Systematic implementation of NGS in health systems can significantly improve the access of patients with rare diseases to diagnosis and reduce the dependence of national health systems for cross-border collaboration.
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Affiliation(s)
- Mateja Vinkšel
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia.
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Ahmed A, Wang M, Bergant G, Maroofian R, Zhao R, Alfadhel M, Nashabat M, AlRifai MT, Eyaid W, Alswaid A, Beetz C, Qin Y, Zhu T, Tian Q, Xia L, Wu H, Shen L, Dong S, Yang X, Liu C, Ma L, Zhang Q, Khan R, Shah AA, Guo J, Tang B, Leonardis L, Writzl K, Peterlin B, Guo H, Malik S, Xia K, Hu Z. Biallelic loss-of-function variants in NEMF cause central nervous system impairment and axonal polyneuropathy. Hum Genet 2021; 140:579-592. [PMID: 33048237 DOI: 10.1007/s00439-020-02226-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
We aimed to detect the causative gene in five unrelated families with recessive inheritance pattern neurological disorders involving the central nervous system, and the potential function of the NEMF gene in the central nervous system. Exome sequencing (ES) was applied to all families and linkage analysis was performed on family 1. A minigene assay was used to validate the splicing effect of the relevant discovered variants. Immunofluorescence (IF) experiment was performed to investigate the role of the causative gene in neuron development. The large consanguineous family confirms the phenotype-causative relationship with homozygous frameshift variant (NM_004713.6:c.2618del) as revealed by ES. Linkage analysis of the family showed a significant single-point LOD of 4.5 locus. Through collaboration in GeneMatcher, four additional unrelated families' likely pathogenic NEMF variants for a spectrum of central neurological disorders, two homozygous splice-site variants (NM_004713.6:c.574+1G>T and NM_004713.6:c.807-2A>C) and a homozygous frameshift variant (NM_004713.6: c.1234_1235insC) were subsequently identified and segregated with all affected individuals. We further revealed that knockdown (KD) of Nemf leads to impairment of axonal outgrowth and synapse development in cultured mouse primary cortical neurons. Our study demonstrates that disease-causing biallelic NEMF variants result in central nervous system impairment and other variable features. NEMF is an important player in mammalian neuron development.
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Affiliation(s)
- Ashfaque Ahmed
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Meng Wang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Gaber Bergant
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Rongjuan Zhao
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Marwan Nashabat
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Muhammad Talal AlRifai
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Wafaa Eyaid
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research Centre (KAIMRC), King Saud Bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | | | | | - Yan Qin
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Tengfei Zhu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qi Tian
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Huidan Wu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Shen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Shanshan Dong
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xinyi Yang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Cenying Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Linya Ma
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qiumeng Zhang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Rizwan Khan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Abid Ali Shah
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, 410008, Hunan, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, 410008, Hunan, China
| | - Lea Leonardis
- Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Department of Neurology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Karin Writzl
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Borut Peterlin
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Hui Guo
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Changsha, Hunan, China
| | - Sajid Malik
- Human Genetics Program, Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Kun Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.
- CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Chinese Academy of Sciences, Shanghai, China.
- Hunan Key Laboratory of Molecular Precisional Medicine, Central South University, Changsha, China.
| | - Zhengmao Hu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, Changsha, Hunan, China.
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Hadalin V, Šuštar M, Volk M, Maver A, Sajovic J, Jarc-Vidmar M, Peterlin B, Hawlina M, Fakin A. Cone Dystrophy Associated with a Novel Variant in the Terminal Codon of the RPGR- ORF15. Genes (Basel) 2021; 12:genes12040499. [PMID: 33805381 PMCID: PMC8066792 DOI: 10.3390/genes12040499] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/30/2022] Open
Abstract
Mutations in RPGRORF15 are associated with rod-cone or cone/cone-rod dystrophy, the latter associated with mutations at the distal end. We describe the phenotype associated with a novel variant in the terminal codon of the RPGRORF15 c.3457T>A (Ter1153Lysext*38), which results in a C-terminal extension. Three male patients from two families were recruited, aged 31, 35, and 38 years. Genetic testing was performed by whole exome sequencing. Filtered variants were analysed according to the population frequency, ClinVar database, the variant’s putative impact, and predicted pathogenicity; and were classified according to the ACMG guidelines. Examination included visual acuity (Snellen), colour vision (Ishihara), visual field, fundus autofluorescence (FAF), optical coherence tomography (OCT), and electrophysiology. All patients were myopic, and had central scotoma and reduced colour vision. Visual acuities on better eyes were counting fingers, 0.3 and 0.05. Electrophysiology showed severely reduced cone-specific responses and macular dysfunction, while the rod-specific response was normal. FAF showed hyperautofluorescent ring centred at the fovea encompassing an area of photoreceptor loss approximately two optic discs in diameter (3462–6342 μm). Follow up after 2–11 years showed enlargement of the diameter (avg. 100 μm/year). The novel c.3457T>A (Ter1153Lysext*38) mutation in the terminal RPGRORF15 codon is associated with cone dystrophy, which corresponds to the previously described phenotypes associated with mutations in the distal end of the RPGRORF15. Minimal progression during follow-up years suggests a relatively stable disease after the initial loss of the central cones.
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Affiliation(s)
- Vlasta Hadalin
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia; (V.H.); (M.Š.); (J.S.); (M.J.-V.); (M.H.)
| | - Maja Šuštar
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia; (V.H.); (M.Š.); (J.S.); (M.J.-V.); (M.H.)
| | - Marija Volk
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Šlajmerjeva ulica 4, 1000 Ljubljana, Slovenia; (M.V.); (A.M.); (B.P.)
| | - Aleš Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Šlajmerjeva ulica 4, 1000 Ljubljana, Slovenia; (M.V.); (A.M.); (B.P.)
| | - Jana Sajovic
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia; (V.H.); (M.Š.); (J.S.); (M.J.-V.); (M.H.)
| | - Martina Jarc-Vidmar
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia; (V.H.); (M.Š.); (J.S.); (M.J.-V.); (M.H.)
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Šlajmerjeva ulica 4, 1000 Ljubljana, Slovenia; (M.V.); (A.M.); (B.P.)
| | - Marko Hawlina
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia; (V.H.); (M.Š.); (J.S.); (M.J.-V.); (M.H.)
| | - Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia; (V.H.); (M.Š.); (J.S.); (M.J.-V.); (M.H.)
- Correspondence:
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Abstract
An increasing number of countries are investing efforts to exploit the human genome, in order to improve genetic diagnostics and to pave the way for the integration of precision medicine into health systems. The expected benefits include improved understanding of normal and pathological genomic variation, shorter time-to-diagnosis, cost-effective diagnostics, targeted prevention and treatment, and research advances.We review the 41 currently active individual national projects concerning their aims and scope, the number and age structure of included subjects, funding, data sharing goals and methods, and linkage with biobanks, medical data, and non-medical data (exposome). The main aims of ongoing projects were to determine normal genomic variation (90%), determine pathological genomic variation (rare disease, complex diseases, cancer, etc.) (71%), improve infrastructure (59%), and enable personalized medicine (37%). Numbers of subjects to be sequenced ranges substantially, from a hundred to over a million, representing in some cases a significant portion of the population. Approximately half of the projects report public funding, with the rest having various mixed or private funding arrangements. 90% of projects report data sharing (public, academic, and/or commercial with various levels of access) and plan on linking genomic data and medical data (78%), existing biobanks (44%), and/or non-medical data (24%) as the basis for enabling personal/precision medicine in the future.Our results show substantial diversity in the analysed categories of 41 ongoing national projects. The overview of current designs will hopefully inform national initiatives in designing new genomic projects and contribute to standardisation and international collaboration.
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Affiliation(s)
- Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Slajmerjeva 4, Ljubljana, Slovenia
| | - Ana Nyasha Zimani
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Slajmerjeva 4, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Slajmerjeva 4, Ljubljana, Slovenia.
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Bergant G, Maver A, Peterlin B. Whole-Genome Sequencing in Diagnostics of Selected Slovenian Undiagnosed Patients with Rare Disorders. Life (Basel) 2021; 11:life11030205. [PMID: 33807868 PMCID: PMC8001615 DOI: 10.3390/life11030205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Received: 01/31/2021] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 11/16/2022] Open
Abstract
Several patients with rare genetic disorders remain undiagnosed following comprehensive diagnostic testing using whole-exome sequencing (WES). In these patients, pathogenic genetic variants may reside in intronic or regulatory regions or they may emerge through mutational mechanisms not detected by WES. For this reason, we implemented whole-genome sequencing (WGS) in routine clinical diagnostics of patients with undiagnosed genetic disorders and report on the outcome in 30 patients. Criteria for consideration included (1) negative WES, (2) a high likelihood of a genetic cause for the disorders, (3) positive family history, (4) detection of large blocks of homozygosity or (5) detection of a single pathogenic variant in a gene associated with recessive conditions. We successfully discovered a causative genetic variant in 6 cases, a retrotranspositional event in the APC gene, non-coding variants in the intronic region of the OTC gene and the promotor region of the UFM1 gene, repeat expansion in the RFC1 gene and a single exon duplication in the CNGB3 gene. We also discovered one coding variant, an indel, which was missed by variant caller during WES data analysis. Our study demonstrates the impact of WGS in the group of patients with undiagnosed genetic diseases after WES in the clinical setting and the diversity of mutational mechanisms discovered, which would remain undetected using other methods.
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50
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Kobal N, Krašovec T, Šuštar M, Volk M, Peterlin B, Hawlina M, Fakin A. Stationary and Progressive Phenotypes Caused by the p.G90D Mutation in Rhodopsin Gene. Int J Mol Sci 2021; 22:ijms22042133. [PMID: 33669941 PMCID: PMC7924842 DOI: 10.3390/ijms22042133] [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] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 12/30/2022] Open
Abstract
Mutations in rhodopsin gene (RHO) are a frequent cause of retinitis pigmentosa (RP) and less often, congenital stationary night blindness (CSNB). Mutation p.G90D has previously been associated with CSNB based on the examination of one family. This study screened 60 patients. Out of these 60 patients, 32 were affected and a full characterization was conducted in 15 patients. We described the clinical characteristics of these 15 patients (12 male, median age 42 years, range 8-71) from three families including visual field (Campus Goldmann), fundus autofluorescence (FAF), optical coherence tomography (OCT) and electrophysiology. Phenotypes were classified into four categories: CSNB (N = 3, 20%) sector RP (N = 3, 20%), pericentral RP (N = 1, 6.7%) and classic RP (N = 8, 53.3% (8/15)). The phenotypes were not associated with family, sex or age (Kruskal-Wallis, p > 0.05), however, cystoid macular edema (CME) was observed only in one family. Among the subjects reporting nyctalopia, 69% (22/32) were male. The clinical characteristics of the largest p.G90D cohort so far showed a large frequency of progressive retinal degeneration with 53.3% developing RP, contrary to the previous report.
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Affiliation(s)
- Nina Kobal
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia; (N.K.); (T.K.); (M.Š.); (M.H.)
| | - Tjaša Krašovec
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia; (N.K.); (T.K.); (M.Š.); (M.H.)
| | - Maja Šuštar
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia; (N.K.); (T.K.); (M.Š.); (M.H.)
| | - Marija Volk
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Šlajmerjeva ulica 4, 1000 Ljubljana, Slovenia; (M.V.); (B.P.)
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Šlajmerjeva ulica 4, 1000 Ljubljana, Slovenia; (M.V.); (B.P.)
| | - Marko Hawlina
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia; (N.K.); (T.K.); (M.Š.); (M.H.)
| | - Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia; (N.K.); (T.K.); (M.Š.); (M.H.)
- Correspondence:
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