1
|
Ghani M, Szabó B, Alkhatibe M, Amsalu H, Zohar P, Janka EA, Mótyán JA, Tar K. Serine 39 in the GTP-binding domain of Drp1 is involved in shaping mitochondrial morphology. FEBS Open Bio 2024; 14:1147-1165. [PMID: 38760979 PMCID: PMC11216946 DOI: 10.1002/2211-5463.13820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/18/2024] [Accepted: 05/08/2024] [Indexed: 05/20/2024] Open
Abstract
Continuous fusion and fission are critical for mitochondrial health. In this study, we further characterize the role played by dynamin-related protein 1 (Drp1) in mitochondrial fission. We show that a single amino acid change in Drp1 at position 39 from serine to alanine (S39A) within the GTP-binding (GTPase) domain results in a fused mitochondrial network in human SH-SY5Y neuroblastoma cells. Interestingly, the phosphorylation of Ser-616 and Ser-637 of Drp1 remains unaffected by the S39A mutation, and mitochondrial bioenergetic profile and cell viability in the S39A mutant were comparable to those observed in the control. This leads us to propose that the serine 39 residue of Drp1 plays a crucial role in mitochondrial distribution through its involvement in the GTPase activity. Furthermore, this amino acid mutation leads to structural anomalies in the mitochondrial network. Taken together, our results contribute to a better understanding of the function of the Drp1 protein.
Collapse
Affiliation(s)
- Marvi Ghani
- Department of Medical Chemistry, Faculty of MedicineUniversity of DebrecenHungary
- Doctoral School of Molecular MedicineUniversity of DebrecenHungary
| | - Bernadett Szabó
- Department of Medical Chemistry, Faculty of MedicineUniversity of DebrecenHungary
| | - Mahmoud Alkhatibe
- Department of Medical Chemistry, Faculty of MedicineUniversity of DebrecenHungary
| | - Hailemariam Amsalu
- Department of Medical Chemistry, Faculty of MedicineUniversity of DebrecenHungary
- Doctoral School of Molecular MedicineUniversity of DebrecenHungary
| | - Peleg Zohar
- Department of Medical Chemistry, Faculty of MedicineUniversity of DebrecenHungary
| | - Eszter Anna Janka
- Department of Dermatology, MTA Centre of Excellence, Faculty of MedicineUniversity of DebrecenHungary
- HUN‐REN‐UD Allergology Research GroupUniversity of DebrecenHungary
| | - János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of MedicineUniversity of DebrecenHungary
| | - Krisztina Tar
- Department of Medical Chemistry, Faculty of MedicineUniversity of DebrecenHungary
| |
Collapse
|
2
|
León P, Franco P, Hinojosa N, Torres K, Moreano A, Romero VI. TTN novel splice variant in familial dilated cardiomyopathy and splice variants review: a case report. Front Cardiovasc Med 2024; 11:1387063. [PMID: 38938651 PMCID: PMC11210389 DOI: 10.3389/fcvm.2024.1387063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/03/2024] [Indexed: 06/29/2024] Open
Abstract
This case report details the identification of a novel likely pathogenic splicing variant in the TTN gene, associated with dilated cardiomyopathy (DCM), in a 42-year-old male patient presenting with early-onset heart failure and reduced ejection fraction. DCM is a nonischemic heart condition characterized by left biventricular dilation and systolic dysfunction, with approximately one-third of cases being familial and often linked to genetic mutations. The TTN gene, encoding the largest human protein essential for muscle contraction and sarcomere structure, is implicated in about 25% of DCM cases through mutations, especially truncating variants. Our investigation revealed a previously unreported G > C mutation at the splice acceptor site in intron 356 of TTN, confirmed by Sanger sequencing and not found in population databases, suggesting a novel contribution to the understanding of DCM etiology. The case emphasizes the critical role of the TTN gene in cardiac function and the genetic complexity underlying DCM. A comprehensive literature review highlighted the prevalence and significance of splice variants in the TTN gene, particularly those affecting the titin A-band, which is known for its role in muscle contraction and stability. This variant's identification underscores the importance of genetic screening in patients with DCM, offering insights into the disease's familial transmission and potential therapeutic targets. Our findings contribute to the expanding knowledge of genetic factors in DCM, demonstrating the necessity of integrating genetic diagnostics in cardiovascular medicine. This case supports the growing evidence linking splicing mutations in specific regions of the TTN gene to DCM development and underscores the importance of genetic counseling and testing in managing heart disease.
Collapse
Affiliation(s)
- Paul León
- College of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito, Ecuador
| | - Paula Franco
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Nicole Hinojosa
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Kevin Torres
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Andrés Moreano
- Department of Cardiology, Universidad de Sao Paulo, Sao Paulo, Brazil
| | - Vanessa I. Romero
- College of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito, Ecuador
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| |
Collapse
|
3
|
Elkhateeb N, Issa MY, Elbendary HM, Elnaggar W, Ramadan A, Rafat K, Kamel M, Abdel-Ghafar SF, Amer F, Hassaan HM, Trunzo R, Pereira C, Abdel-Hamid MS, D'Arco F, Bauer P, Bertoli-Avella AM, Girgis M, Gleeson JG, Zaki MS, Selim L. The clinical and genetic landscape of developmental and epileptic encephalopathies in Egyptian children. Clin Genet 2024; 105:510-522. [PMID: 38221827 DOI: 10.1111/cge.14481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/16/2024]
Abstract
Developmental and epileptic encephalopathies (DEEs) are a heterogeneous group of epilepsies characterized by early-onset, refractory seizures associated with developmental regression or impairment, with a heterogeneous genetic landscape including genes implicated in various pathways and mechanisms. We retrospectively studied the clinical and genetic data of patients with genetic DEE who presented at two tertiary centers in Egypt over a 10-year period. Exome sequencing was used for genetic testing. We report 74 patients from 63 unrelated Egyptian families, with a high rate of consanguinity (58%). The most common seizure type was generalized tonic-clonic (58%) and multiple seizure types were common (55%). The most common epilepsy syndrome was early infantile DEE (50%). All patients showed variable degrees of developmental impairment. Microcephaly, hypotonia, ophthalmological involvement and neuroimaging abnormalities were common. Eighteen novel variants were identified and the phenotypes of five DEE genes were expanded with novel phenotype-genotype associations. Obtaining a genetic diagnosis had implications on epilepsy management in 17 patients with variants in 12 genes. In this study, we expand the phenotype and genotype spectrum of DEE in a large single ethnic cohort of patients. Reaching a genetic diagnosis guided precision management of epilepsy in a significant proportion of patients.
Collapse
Affiliation(s)
- Nour Elkhateeb
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pediatrics, Pediatric Neurology and Metabolic Medicine Unit, Kasr Al-Ainy School of Medicine, Cairo University, Cairo, Egypt
| | - Mahmoud Y Issa
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Hasnaa M Elbendary
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Walaa Elnaggar
- Department of Pediatrics, Pediatric Neurology and Metabolic Medicine Unit, Kasr Al-Ainy School of Medicine, Cairo University, Cairo, Egypt
| | - Areef Ramadan
- Department of Pediatrics, Pediatric Neurology and Metabolic Medicine Unit, Kasr Al-Ainy School of Medicine, Cairo University, Cairo, Egypt
| | - Karima Rafat
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Mona Kamel
- Department of Pediatrics, Pediatric Neurology and Metabolic Medicine Unit, Kasr Al-Ainy School of Medicine, Cairo University, Cairo, Egypt
| | - Sherif F Abdel-Ghafar
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Fawzia Amer
- Department of Pediatrics, Pediatric Neurology and Metabolic Medicine Unit, Kasr Al-Ainy School of Medicine, Cairo University, Cairo, Egypt
| | - Hebatallah M Hassaan
- Department of Pediatrics, Clinical Genetics Unit, Kasr Al-Ainy School of Medicine, Cairo University, Cairo, Egypt
| | | | | | - Mohamed S Abdel-Hamid
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Felice D'Arco
- Radiology Department, Great Ormond Street Hospital for Children, London, UK
| | | | | | - Marian Girgis
- Department of Pediatrics, Pediatric Neurology and Metabolic Medicine Unit, Kasr Al-Ainy School of Medicine, Cairo University, Cairo, Egypt
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, USA
- Rady Children's Hospital, Rady Children's Institute for Genomic Medicine, San Diego, La Jolla, USA
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Laila Selim
- Department of Pediatrics, Pediatric Neurology and Metabolic Medicine Unit, Kasr Al-Ainy School of Medicine, Cairo University, Cairo, Egypt
| |
Collapse
|
4
|
Mao D, Liu C, Wang L, Ai-Ouran R, Deisseroth C, Pasupuleti S, Kim SY, Li L, Rosenfeld JA, Meng L, Burrage LC, Wangler MF, Yamamoto S, Santana M, Perez V, Shukla P, Eng CM, Lee B, Yuan B, Xia F, Bellen HJ, Liu P, Liu Z. AI-MARRVEL - A Knowledge-Driven AI System for Diagnosing Mendelian Disorders. NEJM AI 2024; 1:10.1056/aioa2300009. [PMID: 38962029 PMCID: PMC11221788 DOI: 10.1056/aioa2300009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
BACKGROUND Diagnosing genetic disorders requires extensive manual curation and interpretation of candidate variants, a labor-intensive task even for trained geneticists. Although artificial intelligence (AI) shows promise in aiding these diagnoses, existing AI tools have only achieved moderate success for primary diagnosis. METHODS AI-MARRVEL (AIM) uses a random-forest machine-learning classifier trained on over 3.5 million variants from thousands of diagnosed cases. AIM additionally incorporates expert-engineered features into training to recapitulate the intricate decision-making processes in molecular diagnosis. The online version of AIM is available at https://ai.marrvel.org. To evaluate AIM, we benchmarked it with diagnosed patients from three independent cohorts. RESULTS AIM improved the rate of accurate genetic diagnosis, doubling the number of solved cases as compared with benchmarked methods, across three distinct real-world cohorts. To better identify diagnosable cases from the unsolved pools accumulated over time, we designed a confidence metric on which AIM achieved a precision rate of 98% and identified 57% of diagnosable cases out of a collection of 871 cases. Furthermore, AIM's performance improved after being fine-tuned for targeted settings including recessive disorders and trio analysis. Finally, AIM demonstrated potential for novel disease gene discovery by correctly predicting two newly reported disease genes from the Undiagnosed Diseases Network. CONCLUSIONS AIM achieved superior accuracy compared with existing methods for genetic diagnosis. We anticipate that this tool may aid in primary diagnosis, reanalysis of unsolved cases, and the discovery of novel disease genes. (Funded by the NIH Common Fund and others.).
Collapse
Affiliation(s)
- Dongxue Mao
- Department of Pediatrics, Baylor College of Medicine, Houston
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| | - Chaozhong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
- Graduate School of Biomedical Sciences, Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston
| | - Linhua Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
- Graduate School of Biomedical Sciences, Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston
| | - Rami Ai-Ouran
- Department of Pediatrics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
- Department of Data Science and AI, Al Hussein Technical University, Amman, Jordan
| | - Cole Deisseroth
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| | - Sasidhar Pasupuleti
- Department of Pediatrics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| | - Seon Young Kim
- Department of Pediatrics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| | - Lucian Li
- Department of Pediatrics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Baylor Genetics, Houston7
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| | | | | | | | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Baylor Genetics, Houston7
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Human Genome Sequencing Center, Baylor College of Medicine, Houston
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Baylor Genetics, Houston7
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
- Department of Neuroscience, Baylor College of Medicine, Houston
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston
- Baylor Genetics, Houston7
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, Houston
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston
| |
Collapse
|
5
|
Sloper E, Jezkova J, Thomas J, Dawson K, Halstead J, Gardner J, Burke K, Oruganti S, Calvert J, Evans J, Anderson S, Corrin S, Pottinger C, Murch O. Wales Infants' and childreN's Genome Service (WINGS): providing rapid genetic diagnoses for unwell children. Arch Dis Child 2024; 109:409-413. [PMID: 38320813 DOI: 10.1136/archdischild-2023-326579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/24/2024] [Indexed: 04/20/2024]
Abstract
INTRODUCTION This study reviews the first 3 years of delivery of the first National Health Service (NHS)-commissioned trio rapid whole genome sequencing (rWGS) service for acutely unwell infants and children in Wales. METHODS Demographic and phenotypic data were prospectively collected as patients and their families were enrolled in the Wales Infants' and childreN's Genome Service (WINGS). These data were reviewed alongside trio rWGS results. RESULTS From April 2020 to March 2023, 82 families underwent WINGS, with a diagnostic yield of 34.1%. The highest diagnostic yields were noted in skeletal dysplasias, neurological or metabolic phenotypes. Mean time to reporting was 9 days. CONCLUSION This study demonstrates that trio rWGS is having a positive impact on the care of acutely unwell infants and children in an NHS setting. In particular, the study shows that rWGS can be applied in an NHS setting, achieving a diagnostic yield comparable with the previously published diagnostic yields achieved in research settings, while also helping to improve patient care and management.
Collapse
Affiliation(s)
- Emily Sloper
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Jana Jezkova
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Joanne Thomas
- Faculty of Life Science and Education, University of South Wales, Pontypridd, UK
| | | | - Joseph Halstead
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Jennifer Gardner
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Katherine Burke
- Neonatal Intensive Care Unit, Singleton Hospital, Swansea, UK
| | - Sivakumar Oruganti
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
- College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Jennifer Calvert
- Neonatal Intensive Care Unit, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Jennifer Evans
- Child Health, Children's Hospital for Wales, Cardiff, UK
| | - Sarah Anderson
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Sian Corrin
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Caroline Pottinger
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Oliver Murch
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| |
Collapse
|
6
|
Gogus B, Elmas M, Turk Boru U. Genetic aspects of ataxias in a cohort of Turkish patients. Neurol Sci 2024:10.1007/s10072-024-07484-x. [PMID: 38587696 DOI: 10.1007/s10072-024-07484-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024]
Abstract
INTRODUCTION Ataxia is one of the clinical findings of the movement disorder disease group. Although there are many underlying etiological reasons, genetic etiology has an increasing significance thanks to the recently developing technology. The aim of this study is to present the variants detected in WES analysis excluding non-genetic causes, in patients with ataxia. METHODS Thirty-six patients who were referred to us with findings of ataxia and diagnosed through WES or other molecular genetic analysis methods were included in our study. At the same time, information such as the onset time of the complaints, consanguinity status between parents, and the presence of relatives with similar symptoms were evaluated. If available, the patient's biochemical and radiological test results were presented. RESULTS Thirty-six patients were diagnosed through WES or CES. The rate of detected autosomal recessive inheritance disease was 80.5%, while that of autosomal dominant inheritance disease was 19.5%. Abnormal cerebellum was detected on brain MRI images in 26 patients, while polyneuropathy was detected on EMG in eleven of them. While the majority of the patients were compatible with similar cases reported in the literature, five patients had different/additional features (variants in MCM3AP, AGTPBP1, GDAP2, and SH3TC2 genes). CONCLUSIONS The diagnosis of ataxia patients with unknown etiology is made possible thanks to these clues. Consideration of a genetic approach is recommended in patients with ataxia of unknown etiology.
Collapse
Affiliation(s)
- Basak Gogus
- Ministry of Health General Directorate of Public Health, Ankara, Turkey.
- Department of Medical Genetics, Afyonkarahisar Health Sciences University, Afyonkarahisar, Turkey.
| | - Muhsin Elmas
- Department of Medical Genetics, İstanbul Medipol University, Istanbul, Turkey
| | - Ulku Turk Boru
- Department of Neurology, Afyonkarahisar Health Sciences University, Afyonkarahisar, Turkey
| |
Collapse
|
7
|
Cheng J, Wang Z, Tang M, Zhang W, Li G, Tan S, Mu C, Hu M, Zhang D, Jia X, Wen Y, Guo H, Xu D, Liu L, Li J, Xia K, Li F, Duan R, Xu Z, Yuan L. KCTD10 regulates brain development by destabilizing brain disorder-associated protein KCTD13. Proc Natl Acad Sci U S A 2024; 121:e2315707121. [PMID: 38489388 PMCID: PMC10963008 DOI: 10.1073/pnas.2315707121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/02/2024] [Indexed: 03/17/2024] Open
Abstract
KCTD10 belongs to the KCTD (potassiumchannel tetramerization domain) family, many members of which are associated with neuropsychiatric disorders. However, the biological function underlying the association with brain disorders remains to be explored. Here, we reveal that Kctd10 is highly expressed in neuronal progenitors and layer V neurons throughout brain development. Kctd10 deficiency triggers abnormal proliferation and differentiation of neuronal progenitors, reduced deep-layer (especially layer V) neurons, increased upper-layer neurons, and lowered brain size. Mechanistically, we screened and identified a unique KCTD10-interacting protein, KCTD13, associated with neurodevelopmental disorders. KCTD10 mediated the ubiquitination-dependent degradation of KCTD13 and KCTD10 ablation resulted in a considerable increase of KCTD13 expression in the developing cortex. KCTD13 overexpression in neuronal progenitors led to reduced proliferation and abnormal cell distribution, mirroring KCTD10 deficiency. Notably, mice with brain-specific Kctd10 knockout exhibited obvious motor deficits. This study uncovers the physiological function of KCTD10 and provides unique insights into the pathogenesis of neurodevelopmental disorders.
Collapse
Affiliation(s)
- Jianbo Cheng
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Zhen Wang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Manpei Tang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Wen Zhang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Guozhong Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Senwei Tan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Chenjun Mu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Mengyuan Hu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Dan Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing100101, China
| | - Xiangbin Jia
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Yangxuan Wen
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
| | - Hui Guo
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Dan Xu
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical University, Fuzhou350005, China
| | - Liang Liu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing100053, China
| | - Jiada Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Kun Xia
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Faxiang Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Ranhui Duan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing100101, China
| | - Ling Yuan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Key Lab of Rare Pediatric Diseases of Ministry of Education, School of Life Sciences, Central South University, Changsha, Hunan410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan410078, China
| |
Collapse
|
8
|
Li RK, Li H, Tian MQ, Li Y, Luo S, Liang XY, Liu WH, Li BM, Shi XQ, Li J, Li B, Shu XM. Investigation of FRMPD4 variants associated with X-linked epilepsy. Seizure 2024; 116:45-50. [PMID: 37330374 DOI: 10.1016/j.seizure.2023.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND The etiology of unexplained epilepsy in most patients remains unclear. Variants of FRMPD4 are suggested to be associated with neurodevelopmental disorders. Therefore, we screened for disease-causing FRMPD4 variants in patients with epilepsy. METHODS Trios-based whole-exome sequencing was conducted on a cohort of 85 patients with unexplained epilepsy, their parents, and extended family members. Additional cases with FRMPD4 variants were identified from the China Epilepsy Gene Matching Platform V.1.0. The frequency of variants was analyzed, and their subregional effects were predicted using in silico tools. The genotype-phenotype correlation of the newly defined causative genes and protein stability were analyzed using I-Mutant V.3.0 and Grantham scores. RESULTS Two novel missense variants of FRMPD4 were identified in two families. Using the gene matching platform, we identified three additional novel missense variants. These variants presented at low or no allele frequencies in the gnomAD database. All the variants were located outside the three FRMPD4 main domains (WW, PDZ, and FERM). In silico analyses revealed that the variants were damaging and were predicted to be the least stable. All patients eventually became seizure-free. Eight of the 21 patients with FRMPD4 variants had epilepsy, of which five (63%) had missense variants located outside the domains, two had deletions involving exon 2, and one had a frameshift variant located outside the domains. Patients with epilepsy caused by missense variants were often free of intellectual disabilities (4/5), whereas patients with epilepsy caused by truncated variants had intellectual disabilities and structural brain abnormalities (3/3). CONCLUSIONS The FRMPD4 gene is potentially associated with epilepsy. The genotype-phenotype correlation of FRMPD4 variants indicated that differences in variant types and locations of FRMPD4 may explain their phenotypic variation.
Collapse
Affiliation(s)
- Ren-Ke Li
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Children's Hospital of Guizhou Province, Zunyi 563003, China
| | - Huan Li
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Mao-Qiang Tian
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Children's Hospital of Guizhou Province, Zunyi 563003, China
| | - Yun Li
- Department of Brain Function and Neuroelectrophysiology, the Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421002, China
| | - Sheng Luo
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Xiao-Yu Liang
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Wen-Hui Liu
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Bin-Mei Li
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Xiao-Qi Shi
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Children's Hospital of Guizhou Province, Zunyi 563003, China
| | - Juan Li
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Children's Hospital of Guizhou Province, Zunyi 563003, China
| | - Bin Li
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China.
| | - Xiao-Mei Shu
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Children's Hospital of Guizhou Province, Zunyi 563003, China.
| |
Collapse
|
9
|
Chopra M, Savatt JM, Bingaman TI, Good ME, Morgan A, Cooney C, Rossel AM, VanHoute B, Cordova I, Mahida S, Lanzotti V, Baldridge D, Gurnett CA, Piven J, Hazlett H, Pomeroy SL, Sahin M, Payne PRO, Riggs ER, Constantino JN. Clinical variants paired with phenotype: A rich resource for brain gene curation. Genet Med 2024; 26:101035. [PMID: 38059438 PMCID: PMC10939875 DOI: 10.1016/j.gim.2023.101035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023] Open
Abstract
PURPOSE Clinically ascertained variants are under-utilized in neurodevelopmental disorder research. We established the Brain Gene Registry (BGR) to coregister clinically identified variants in putative brain genes with participant phenotypes. Here, we report 179 genetic variants in the first 179 BGR registrants and analyze the proportion that were novel to ClinVar at the time of entry and those that were absent in other disease databases. METHODS From 10 academically affiliated institutions, 179 individuals with 179 variants were enrolled into the BGR. Variants were cross-referenced for previous presence in ClinVar and for presence in 6 other genetic databases. RESULTS Of 179 variants in 76 genes, 76 (42.5%) were novel to ClinVar, and 62 (34.6%) were absent from all databases analyzed. Of the 103 variants present in ClinVar, 37 (35.9%) were uncertain (ClinVar aggregate classification of variant of uncertain significance or conflicting classifications). For 5 variants, the aggregate ClinVar classification was inconsistent with the interpretation from the BGR site-provided classification. CONCLUSION A significant proportion of clinical variants that are novel or uncertain are not shared, limiting the evidence base for new gene-disease relationships. Registration of paired clinical genetic test results with phenotype has the potential to advance knowledge of the relationships between genes and neurodevelopmental disorders.
Collapse
Affiliation(s)
- Maya Chopra
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital; Boston, MA; Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA.
| | - Juliann M Savatt
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Taylor I Bingaman
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Molly E Good
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Alexis Morgan
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Caitlin Cooney
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Allison M Rossel
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Bryanna VanHoute
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Ineke Cordova
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Sonal Mahida
- Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA
| | - Virginia Lanzotti
- Washington University School of Medicine Intellectual and Developmental Disability Research Center, St. Louis, MO
| | - Dustin Baldridge
- Washington University School of Medicine Intellectual and Developmental Disability Research Center, St. Louis, MO
| | - Christina A Gurnett
- Washington University School of Medicine Intellectual and Developmental Disability Research Center, St. Louis, MO
| | - Joseph Piven
- Department of Psychiatry, University of North Carolina Intellectual and Developmental Disability Research Center, Chapel Hill, NC
| | - Heather Hazlett
- Department of Psychiatry, University of North Carolina Intellectual and Developmental Disability Research Center, Chapel Hill, NC
| | - Scott L Pomeroy
- Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA
| | - Mustafa Sahin
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital; Boston, MA; Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA
| | - Philip R O Payne
- Institute for Informatics Washington University in St. Louis, St. Louis, MO
| | - Erin Rooney Riggs
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - John N Constantino
- Division of Behavioural and Mental Health, Children's Healthcare of Atlanta, Departments of Psychiatry and Paediatrics, Emory University, Atlanta, GA
| |
Collapse
|
10
|
Nashabat M, Nabavizadeh N, Saraçoğlu HP, Sarıbaş B, Avcı Ş, Börklü E, Beillard E, Yılmaz E, Uygur SE, Kayhan CK, Bosco L, Eren ZB, Steindl K, Richter MF, Bademci G, Rauch A, Fattahi Z, Valentino ML, Connolly AM, Bahr A, Viola L, Bergmann AK, Rocha ME, Peart L, Castro-Rojas DL, Bültmann E, Khan S, Giarrana ML, Teleanu RI, Gonzalez JM, Pini A, Schädlich IS, Vill K, Brugger M, Zuchner S, Pinto A, Donkervoort S, Bivona SA, Riza A, Streata I, Gläser D, Baquero-Montoya C, Garcia-Restrepo N, Kotzaeridou U, Brunet T, Epure DA, Bertoli-Avella A, Kariminejad A, Tekin M, von Hardenberg S, Bönnemann CG, Stettner GM, Zanni G, Kayserili H, Oflazer ZP, Escande-Beillard N. SNUPN deficiency causes a recessive muscular dystrophy due to RNA mis-splicing and ECM dysregulation. Nat Commun 2024; 15:1758. [PMID: 38413582 PMCID: PMC10899626 DOI: 10.1038/s41467-024-45933-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
SNURPORTIN-1, encoded by SNUPN, plays a central role in the nuclear import of spliceosomal small nuclear ribonucleoproteins. However, its physiological function remains unexplored. In this study, we investigate 18 children from 15 unrelated families who present with atypical muscular dystrophy and neurological defects. Nine hypomorphic SNUPN biallelic variants, predominantly clustered in the last coding exon, are ascertained to segregate with the disease. We demonstrate that mutant SPN1 failed to oligomerize leading to cytoplasmic aggregation in patients' primary fibroblasts and CRISPR/Cas9-mediated mutant cell lines. Additionally, mutant nuclei exhibit defective spliceosomal maturation and breakdown of Cajal bodies. Transcriptome analyses reveal splicing and mRNA expression dysregulation, particularly in sarcolemmal components, causing disruption of cytoskeletal organization in mutant cells and patient muscle tissues. Our findings establish SNUPN deficiency as the genetic etiology of a previously unrecognized subtype of muscular dystrophy and provide robust evidence of the role of SPN1 for muscle homeostasis.
Collapse
Affiliation(s)
- Marwan Nashabat
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Nasrinsadat Nabavizadeh
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Hilal Pırıl Saraçoğlu
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Burak Sarıbaş
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Şahin Avcı
- Diagnostic Center for Genetic Diseases, Department of Medical Genetics, Koç University Hospital, Istanbul, Turkey
| | - Esra Börklü
- Diagnostic Center for Genetic Diseases, Department of Medical Genetics, Koç University Hospital, Istanbul, Turkey
| | | | - Elanur Yılmaz
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Seyide Ecesu Uygur
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Cavit Kerem Kayhan
- Pathology Laboratory, Acıbadem Maslak Hospital, Istanbul, Turkey
- Department of Biotechnology, Nişantaşı University, Istanbul, Turkey
| | - Luca Bosco
- Unit of Muscular and Neurodegenerative Disorders and Developmental Neurology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Science, University "Roma Tre", Rome, Italy
| | - Zeynep Bengi Eren
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | | | - Guney Bademci
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
- Research Priority Program (URPP) ITINERARE: Innovative Therapies in Rare Diseases, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology & Genetics Centre, Tehran, Iran
| | - Maria Lucia Valentino
- IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Anne M Connolly
- Division of Neurology, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Angela Bahr
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Laura Viola
- Unit of Clinical Pediatrics, State Hospital, San Marino Republic, Italy
| | | | | | - LeShon Peart
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derly Liseth Castro-Rojas
- Genomics Laboratory, Center of Immunology and Genetics (CIGE), SURA Ayudas Diagnosticas, Medellín, Colombia
| | - Eva Bültmann
- Institute of Diagnostic and Interventional Neuroradiology, Hannover Medical School, Hannover, Germany
| | | | | | - Raluca Ioana Teleanu
- Dr Victor Gomoiu Children's Hospital, Bucharest, Romania
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Joanna Michelle Gonzalez
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Antonella Pini
- Neuromuscular Pediatric Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Ines Sophie Schädlich
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Katharina Vill
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children's Hospital, LMU Hospital, Ludwig-Maximilians-University, Munich, Germany
- Department of Human Genetics, Technical University of Munich, School of Medicine, Munich, Germany
| | - Melanie Brugger
- Department of Human Genetics, Technical University of Munich, School of Medicine, Munich, Germany
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- John P. Hussmann Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie Ann Bivona
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anca Riza
- Human Genomics Laboratory, University of Medicine and Pharmacy, Craiova, Romania
- Regional Centre of Medical Genetics Dolj, County Clinical Emergency Hospital, Craiova, Romania
| | - Ioana Streata
- Human Genomics Laboratory, University of Medicine and Pharmacy, Craiova, Romania
- Regional Centre of Medical Genetics Dolj, County Clinical Emergency Hospital, Craiova, Romania
| | | | | | | | - Urania Kotzaeridou
- Division of Child Neurology and Inherited Metabolic Diseases, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Theresa Brunet
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children's Hospital, LMU Hospital, Ludwig-Maximilians-University, Munich, Germany
- Department of Human Genetics, Technical University of Munich, School of Medicine, Munich, Germany
| | | | | | | | - Mustafa Tekin
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- John P. Hussmann Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Georg M Stettner
- Neuromuscular Center Zurich and Department of Pediatric Neurology, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ginevra Zanni
- Unit of Muscular and Neurodegenerative Disorders and Developmental Neurology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Hülya Kayserili
- Diagnostic Center for Genetic Diseases, Department of Medical Genetics, Koç University Hospital, Istanbul, Turkey
- Department of Medical Genetics, Koç University School of Medicine (KUSoM), Istanbul, Turkey
| | - Zehra Piraye Oflazer
- Department of Neurology, Koç University Hospital Muscle Center, Istanbul, Turkey
| | - Nathalie Escande-Beillard
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey.
- Research Center for Translational Medicine (KUTTAM), Koç University School of Medicine (KUSoM), Istanbul, Turkey.
| |
Collapse
|
11
|
Abolhassani A, Fattahi Z, Beheshtian M, Fadaee M, Vazehan R, Ahangari F, Dehdahsi S, Faraji Zonooz M, Parsimehr E, Kalhor Z, Peymani F, Mozaffarpour Nouri M, Babanejad M, Noudehi K, Fatehi F, Zamanian Najafabadi S, Afroozan F, Yazdan H, Bozorgmehr B, Azarkeivan A, Sadat Mahdavi S, Nikuei P, Fatehi F, Jamali P, Ashrafi MR, Karimzadeh P, Habibi H, Kahrizi K, Nafissi S, Kariminejad A, Najmabadi H. Clinical application of next generation sequencing for Mendelian disease diagnosis in the Iranian population. NPJ Genom Med 2024; 9:12. [PMID: 38374194 PMCID: PMC10876633 DOI: 10.1038/s41525-024-00393-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 01/29/2024] [Indexed: 02/21/2024] Open
Abstract
Next-generation sequencing (NGS) has been proven to be one of the most powerful diagnostic tools for rare Mendelian disorders. Several studies on the clinical application of NGS in unselected cohorts of Middle Eastern patients have reported a high diagnostic yield of up to 48%, correlated with a high level of consanguinity in these populations. We evaluated the diagnostic utility of NGS-based testing across different clinical indications in 1436 patients from Iran, representing the first study of its kind in this highly consanguineous population. A total of 1075 exome sequencing and 361 targeted gene panel sequencing were performed over 8 years at a single clinical genetics laboratory, with the majority of cases tested as proband-only (91.6%). The overall diagnostic rate was 46.7%, ranging from 24% in patients with an abnormality of prenatal development to over 67% in patients with an abnormality of the skin. We identified 660 pathogenic or likely pathogenic variants, including 241 novel variants, associated with over 342 known genetic conditions. The highly consanguineous nature of this cohort led to the diagnosis of autosomal recessive disorders in the majority of patients (79.1%) and allowed us to determine the shared carrier status of couples for suspected recessive phenotypes in their deceased child(ren) when direct testing was not possible. We also highlight the observations of recessive inheritance of genes previously associated only with dominant disorders and provide an expanded genotype-phenotype spectrum for multiple less-characterized genes. We present the largest mutational spectrum of known Mendelian disease, including possible founder variants, throughout the Iranian population, which can serve as a unique resource for clinical genomic studies locally and beyond.
Collapse
Affiliation(s)
- Ayda Abolhassani
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zohreh Fattahi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Mahsa Fadaee
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Raheleh Vazehan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Ahangari
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Shima Dehdahsi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Elham Parsimehr
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zahra Kalhor
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Peymani
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Noudehi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Fatehi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Fariba Afroozan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Hilda Yazdan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Bita Bozorgmehr
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Azita Azarkeivan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Nasle Salem Genetic Counseling Center, Bandar Abbas, Iran
| | - Farzad Fatehi
- Department of Neurology, Neuromuscular Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Payman Jamali
- Genetic Counseling Center, Shahroud Welfare Organization, Semnan, Iran
| | | | - Parvaneh Karimzadeh
- Pediatric Neurology Department, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Haleh Habibi
- Hamedan University of Medical Science, Hamedan, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahriar Nafissi
- Department of Neurology, Neuromuscular Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Hossein Najmabadi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran.
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
| |
Collapse
|
12
|
Pardo LM, Aanicai R, Zonic E, Hakonen AH, Zielske S, Bauer P, Bertoli-Avella AM. Adding to the evidence of gene-disease association of RAP1B and syndromic thrombocytopenia. Clin Genet 2024; 105:196-201. [PMID: 37850357 DOI: 10.1111/cge.14438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023]
Abstract
Syndromic constitutive thrombocytopenia encompasses a heterogeneous group of disorders characterised by quantitative and qualitative defects of platelets while featuring other malformations. Recently, heterozygous, de novo variants in RAP1B were reported in three cases of syndromic thrombocytopenia. Here, we report two additional, unrelated individuals identified retrospectively in our data repository with heterozygous variants in RAP1B: NM_001010942.2(RAP1B):c.35G>A, p.(Gly12Glu) (de novo) and NM_001010942.2(RAP1B):c.178G>A, p.(Gly60Arg). Both individuals had thrombocytopenia, as well as congenital malformations, and neurological, behavioural, and dysmorphic features, in line with previous reports. Our data supports the causal role of monoallelic RAP1B variants that disrupt RAP1B GTPase activity in syndromic congenital thrombocytopenia.
Collapse
Affiliation(s)
- Luba M Pardo
- Medical Genetics, Reporting & Research, CENTOGENE GmbH, Rostock, Germany
| | - Ruxandra Aanicai
- Medical Genetics, Reporting & Research, CENTOGENE GmbH, Rostock, Germany
| | - Emir Zonic
- Medical Genetics, Reporting & Research, CENTOGENE GmbH, Rostock, Germany
| | - Anna H Hakonen
- Department of Clinical Genetics, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Susan Zielske
- Medical Genetics, Reporting & Research, CENTOGENE GmbH, Rostock, Germany
| | - Peter Bauer
- Medical Genetics, Reporting & Research, CENTOGENE GmbH, Rostock, Germany
- Department of Internal Medicine III - Hematology, Oncology, and Palliative Medicine, University of Rostock, Rostock, Germany
| | | |
Collapse
|
13
|
Sedlackova L, Sterbova K, Vlckova M, Seeman P, Zarubova J, Marusic P, Krsek P, Krijtova H, Musilova A, Lassuthova P. Yield of exome sequencing in patients with developmental and epileptic encephalopathies and inconclusive targeted gene panel. Eur J Paediatr Neurol 2024; 48:17-29. [PMID: 38008000 DOI: 10.1016/j.ejpn.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 10/25/2023] [Accepted: 10/28/2023] [Indexed: 11/28/2023]
Abstract
OBJECTIVE Developmental and epileptic encephalopathies (DEEs) are a group of severe, early-onset epilepsies characterised by refractory seizures, developmental delay, or regression and generally poor prognosis. DEE are now known to have an identifiable molecular genetic basis and are usually examined using a gene panel. However, for many patients, the genetic cause has still not been identified. The aims of this study were to identify causal variants for DEE in patients for whom the previous examination with a gene panel did not determine their genetic diagnosis. It also aims for a detailed description and broadening of the phenotypic spectrum of several rare DEEs. METHODS In the last five years (2015-2020), 141 patients from all over the Czech Republic were referred to our department for genetic testing in association with their diagnosis of epilepsy. All patients underwent custom-designed gene panel testing prior to enrolment into the study, and their results were inconclusive. We opted for whole exome sequencing (WES) to identify the cause of their disorder. If a causal or potentially causal variant was identified, we performed a detailed clinical evaluation and phenotype-genotype correlation study to better describe the specific rare subtypes. RESULTS Explanatory causative variants were detected in 20 patients (14%), likely pathogenic variants that explain the epilepsy in 5 patients (3.5%) and likely pathogenic variants that do not fully explain the epilepsy in 11 patients (7.5%), and variants in candidate genes in 4 patients (3%). Variants were mostly de novo 29/40 (72.5%). SIGNIFICANCE WES enables us to identify the cause of the disease in additional patients, even after gene panel testing. It is very important to perform a WES in DEE patients as soon as possible, since it will spare the patients and their families many years of a diagnostic odyssey. In particular, patients with rare epilepsies might significantly benefit from this approach, and we propose using WES as a new standard in the diagnosis of DEE instead of targeted gene panel testing.
Collapse
Affiliation(s)
- Lucie Sedlackova
- Neurogenetic Laboratory, Department of Paediatric Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Katalin Sterbova
- Department of Paediatric Neurology, Second Faculty of Medicine, Motol Epilepsy Center, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Marketa Vlckova
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Pavel Seeman
- Neurogenetic Laboratory, Department of Paediatric Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic; Department of Medical Genetics, Masaryk Hospital, Ústí nad Labem, Czech Republic.
| | - Jana Zarubova
- Department of Neurology, Motol Epilepsy Center, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Petr Marusic
- Department of Neurology, Motol Epilepsy Center, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Pavel Krsek
- Department of Paediatric Neurology, Second Faculty of Medicine, Motol Epilepsy Center, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Hana Krijtova
- Department of Neurology, Motol Epilepsy Center, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Alena Musilova
- Neurogenetic Laboratory, Department of Paediatric Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Petra Lassuthova
- Neurogenetic Laboratory, Department of Paediatric Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| |
Collapse
|
14
|
Hattori Y, Sawada T, Kido J, Sugawara K, Yoshida S, Matsumoto S, Inoue T, Hirose S, Nakamura K. Frequency of iduronate-2-sulfatase gene variants detected in newborn screening for mucopolysaccharidosis type II in Japan. Mol Genet Metab Rep 2023; 37:101003. [PMID: 38053932 PMCID: PMC10694771 DOI: 10.1016/j.ymgmr.2023.101003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/19/2023] [Accepted: 08/20/2023] [Indexed: 12/07/2023] Open
Abstract
Mucopolysaccharidosis II (MPS II) is an X-linked, recessive, inborn metabolic disorder caused by defects in iduronate-2-sulfatase (IDS). The age at onset, disease severity, and rate of progression vary significantly among patients. This disease is classified into severe or mild forms depending on neurological symptom involvement. The severe form is associated with progressive cognitive decline while the mild form is predominantly associated with somatic features. Newborn screening (NBS) for MPS II has been performed since December 2016, mainly in Kyushu, Japan, where 197,700 newborns were screened using a fluorescence enzyme activity assay of dried blood spots. We diagnosed one newborn with MPS II with lower IDS activity, elevated urinary glycosaminoglycans, and a novel variant of the IDS gene. In the future, NBS for MPS II is expected to be performed in many regions of Japan and will contribute to the detection of more patients with MPS II, which is crucial to the early treatment of the disorder.
Collapse
Affiliation(s)
- Yusuke Hattori
- Department of Pediatrics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
- Department of Pediatrics, Kumamoto University Hospital, Kumamoto, Japan
| | - Takaaki Sawada
- Department of Pediatrics, Kumamoto University Hospital, Kumamoto, Japan
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Jun Kido
- Department of Pediatrics, Kumamoto University Hospital, Kumamoto, Japan
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Keishin Sugawara
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | | | - Shirou Matsumoto
- Department of Pediatrics, Kumamoto University Hospital, Kumamoto, Japan
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takahito Inoue
- Department of Pediatrics, School of Medicine, Fukuoka University, Fukuoka, Japan
- Department of Pediatrics, Fukuoka University Chikushi Hospital, Fukuoka, Japan
| | - Shinichi Hirose
- General Medical Research Center, School of Medicine, Fukuoka University, Fukuoka, Japan
| | - Kimitoshi Nakamura
- Department of Pediatrics, Kumamoto University Hospital, Kumamoto, Japan
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| |
Collapse
|
15
|
Assaleh YA, Tabarki B. Further Characterization of the Neuroendocrine Phenotype Associated With the PPOX-Related Variegate Porphyria. Pediatr Neurol 2023; 149:141-144. [PMID: 37879139 DOI: 10.1016/j.pediatrneurol.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/27/2023] [Accepted: 09/14/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND Variegate porphyria is caused by mutations in the PPOX gene; it usually presents in adolescents and adults as an autosomal dominant condition, with cutaneous features or acute peripheral and/or central nervous system crises. A rarer variant, homozygous variegate porphyria, presents in childhood with cutaneous manifestations as well as neurophenotypes. This study sought to further characterize the homozygous PPOX-related neuroendocrine phenotype. METHODS This study is a retrospective review of the patients' charts, including their clinical evaluation and molecular genetics, neurodiagnostic, and neuroradiological investigations. RESULTS We describe here three children from a consanguineous family who presented with nystagmus, developmental delay and ataxia, photosensitive skin manifestations, and adrenal insufficiency. Analysis of porphyrins in plasma, urine, and stool together with a genetic study of the PPOX gene confirmed the diagnosis. Interestingly, brain MRI showed severe hypomyelination, a finding rarely reported in variegate porphyria, together with adrenal insufficiency. CONCLUSION We recommend analysis of porphyrins in unexplained hypomyelination disorders. Patients with variegate porphyria should be tested for adrenal insufficiency.
Collapse
Affiliation(s)
- Yousef A Assaleh
- Faculty of Medicine, Department of Pediatrics, Zawia University, Libya
| | - Brahim Tabarki
- Division of Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.
| |
Collapse
|
16
|
Campbell L, Fredericks J, Mathivha K, Moshesh P, Coovadia A, Chirwa P, Dillon B, Ghoor A, Lawrence D, Nair L, Mabaso N, Mokwele D, Novellie M, Krause A, Carstens N. The implementation and utility of clinical exome sequencing in a South African infant cohort. Front Genet 2023; 14:1277948. [PMID: 38028619 PMCID: PMC10665497 DOI: 10.3389/fgene.2023.1277948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Genetic disorders are significant contributors to infant hospitalization and mortality globally. The early diagnosis of these conditions in infants remains a considerable challenge. Clinical exome sequencing (CES) has shown to be a successful tool for the early diagnosis of genetic conditions, however, its utility in African infant populations has not been investigated. The impact of the under-representation of African genomic data, the cost of testing, and genomic workforce shortages, need to be investigated and evidence-based implementation strategies accounting for locally available genetics expertise and diagnostic infrastructure need to be developed. We evaluated the diagnostic utility of singleton CES in a cohort of 32 ill, South African infants from two State hospitals in Johannesburg, South Africa. We analysed the data using a series of filtering approaches, including a curated virtual gene panel consisting of genes implicated in neonatal-and early childhood-onset conditions and genes with known founder and common variants in African populations. We reported a diagnostic yield of 22% and identified seven pathogenic variants in the NPHS1, COL2A1, OCRL, SHOC2, TPRV4, MTM1 and STAC3 genes. This study demonstrates the utility value of CES in the South African State healthcare setting, providing a diagnosis to patients who would otherwise not receive one and allowing for directed management. We anticipate an increase in the diagnostic yield of our workflow with further refinement of the study inclusion criteria. This study highlights important considerations for the implementation of genomic medicine in under-resourced settings and in under-represented African populations where variant interpretation remains a challenge.
Collapse
Affiliation(s)
- L. Campbell
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J. Fredericks
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - K. Mathivha
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson Mandela Children’s Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - P. Moshesh
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson Mandela Children’s Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Coovadia
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - P. Chirwa
- Nelson Mandela Children’s Hospital, Johannesburg, South Africa
| | - B. Dillon
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Ghoor
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - D. Lawrence
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - L. Nair
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N. Mabaso
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - D. Mokwele
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - M. Novellie
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Krause
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N. Carstens
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
| |
Collapse
|
17
|
Ferri-Rufete D, López-González A, Casas-Alba D, Cuadras D, Palau F, Martínez-Monseny A. Clinical Genetics Assessment Triangle (CGAT): A simple tool to identify patients with genetic conditions. Eur J Med Genet 2023; 66:104858. [PMID: 37758166 DOI: 10.1016/j.ejmg.2023.104858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/04/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
OBJECTIVE The objective of this study was to develop a simple tool for general physicians to promptly identify and refer pediatric patients with a higher probability of having a genetic condition. STUDY DESIGN This retrospective, descriptive study was conducted at a tertiary pediatric hospital's Clinical Genetics Unit from June 2019 to January 2020. We included patients under 18 years of age who visited the unit, excluding those without genetic testing. Epidemiological, clinical, and genetic variables were collected from electronic medical records. The primary outcome was the diagnosis of a genetic condition based on genetic testing. RESULTS Among 445 patients, 304 were included; 163 (53.6%) were male, and mean age was 7.4 years (SD 5.1 years). A genetic condition was diagnosed in 139 patients (45.7%). Using a multiple logistic regression model, five variables significantly contributed to reaching a diagnosis: suspected diagnosis at referral (OR 3.45, P < 0.001), short stature (OR 3.11, P < 0.001), global developmental delay/intellectual disability (OR 2.65, P < 0.001), dysmorphic craniofacial features (OR 1.99, P = 0.035), and multiple congenital anomalies (OR 2.54, P = 0.033). The association strength (OR) increased when these variables were paired with each other. The study's findings are presented in the form of a triangle, known as the Clinical Genetics Assessment Triangle (CGAT), which summarizes the results. A decision tree model is applied to guide clinical department referrals based on the affected sides of the triangle. CONCLUSIONS The CGAT has the potential to enable general physicians to promptly identify pediatric patients with an increased probability of having a genetic condition.
Collapse
Affiliation(s)
- David Ferri-Rufete
- Pediatrics Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950, Spain.
| | - Aitor López-González
- Pediatrics Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950, Spain.
| | - Dídac Casas-Alba
- Department of Genetic Medicine, Pediatric Institute of Rare Diseases (IPER), Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950, Spain.
| | - Daniel Cuadras
- Statistics Department, Fundació Sant Joan de Déu, Esplugues de Llobregat, 08950, Spain.
| | - Francesc Palau
- Department of Genetic Medicine, Pediatric Institute of Rare Diseases (IPER), Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, 28029, Spain.
| | - Antonio Martínez-Monseny
- Department of Genetic Medicine, Pediatric Institute of Rare Diseases (IPER), Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950, Spain.
| |
Collapse
|
18
|
Meyer AP, Ma J, Brock G, Hashimoto S, Cottrell CE, Mathew M, Hunter JM, Leung ML, Corsmeier D, Jayaraman V, Waldrop MA, Flanigan KM. Exome sequencing in the pediatric neuromuscular clinic leads to more frequent diagnosis of both neuromuscular and neurodevelopmental conditions. Muscle Nerve 2023; 68:833-840. [PMID: 37789688 DOI: 10.1002/mus.27976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 09/06/2023] [Accepted: 09/10/2023] [Indexed: 10/05/2023]
Abstract
INTRODUCTION/AIMS Exome sequencing (ES) has proven to be a valuable diagnostic tool for neuromuscular disorders, which often pose a diagnostic challenge. The aims of this study were to investigate the clinical outcomes associated with utilization of ES in the pediatric neuromuscular clinic and to determine if specific phenotypic features or abnormal neurodiagnostic tests were predictive of a diagnostic result. METHODS This was a retrospective medical record review of 76 pediatric neuromuscular clinic patients who underwent ES. Based upon clinical assessment prior to ES, patients were divided into two groups: affected by neuromuscular (n = 53) or non-neuromuscular (n = 23) syndromes. RESULTS A diagnosis was made in 28/76 (36.8%), with 29 unique disorders identified. In the neuromuscular group, a neuromuscular condition was confirmed in 78% of those receiving a genetic diagnosis. Early age of symptom onset was associated with a significantly higher diagnostic yield. The most common reason neuromuscular diagnoses were not detected on prior testing was due to causative genes not being present on disease-specific panels. Changes to medical care were made in 57% of individuals receiving a diagnosis on ES. DISCUSSION These data further support ES as a powerful diagnostic tool in the pediatric neuromuscular clinic and highlight the advantages of ES over gene panels, including the ability to identify diagnoses regardless of etiology, identify genes newly associated with disease, and identify multiple confounding diagnoses. Rapid and accurate diagnosis by ES can not only end the patient's diagnostic odyssey, but often impacts patients' medical management and genetic counseling of families.
Collapse
Affiliation(s)
- Alayne P Meyer
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Jianing Ma
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
| | - Guy Brock
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
| | - Sayaka Hashimoto
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Catherine E Cottrell
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Mariam Mathew
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Jesse M Hunter
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Marco L Leung
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Don Corsmeier
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Megan A Waldrop
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Department of Neurology, Nationwide Children's Hospital & The Ohio State University, Columbus, Ohio, USA
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kevin M Flanigan
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Department of Neurology, Nationwide Children's Hospital & The Ohio State University, Columbus, Ohio, USA
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, Ohio, USA
| |
Collapse
|
19
|
Shamseldin HE, Sadagopan M, Martini J, Al-Ali R, Radefeldt M, Ataei M, Lemke S, Rahbeeni Z, Al Mutairi F, Ababneh F, AlRukban HA, Abdulwahab F, Alhajj SM, Bauer P, Bertoli-Avella A, Alkuraya FS. A founder DBR1 variant causes a lethal form of congenital ichthyosis. Hum Genet 2023; 142:1491-1498. [PMID: 37656279 DOI: 10.1007/s00439-023-02597-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/18/2023] [Indexed: 09/02/2023]
Abstract
DBR1 encodes the only known human lariat debranching enzyme and its deficiency has been found to cause an autosomal recessive inborn error of immunity characterized by pediatric brainstem viral-induced encephalitis (MIM 619441). We describe a distinct allelic disorder caused by a founder recessive DBR1 variant in four families (DBR1(NM_016216.4):c.200A > G (p.Tyr67Cys)). Consistent features include prematurity, severe intrauterine growth deficiency, congenital ichthyosis-like presentation (collodion membrane, severe skin peeling and xerosis), and death before the first year of life. Patient-derived fibroblasts displayed the characteristic accumulation of intron lariats in their RNA as revealed by targeted and untargeted analysis, in addition to a marked reduction of DBR1 on immunoblot analysis. We propose a novel DBR1-related developmental disorder that is distinct from DBR1-related encephalitis susceptibility and highlight the apparent lack of correlation with the degree of DBR1 deficiency.
Collapse
Affiliation(s)
- Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | | | | | | | | | | | - Zuhair Rahbeeni
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fuad Al Mutairi
- Genetic and Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, 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, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Faroug Ababneh
- Genetic and Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, 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, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Hadeel A AlRukban
- Department of Pediatrics, King Abdullah Bin Abdulaziz University Hospital, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Saleh Mohammed Alhajj
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Peter Bauer
- CENTOGENE GmbH, Rostock, Germany
- University Medicine Rostock, Center for internal Medicine, Rostock, Germany
| | | | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
| |
Collapse
|
20
|
Popescu C. Combined genotype of HCRTR2 and CLOCK variants in a large family of cluster headache with familial periodicity phenotype. J Neurol 2023; 270:5064-5070. [PMID: 37418013 DOI: 10.1007/s00415-023-11851-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/08/2023]
Abstract
PURPOSE Cluster headache (CH) is a debilitating condition with severe and recurrent headaches characterized by circannual and circadian rhythms. A genetic contingent was suggested, and several loci were described in large cohorts. However, no variant associated with CH for multiplex families has been described. The purpose of our study was to examine candidate genes and new genetic variants in a multigenerational family of cluster headaches in which two members have original chronobiological characteristics that we have called the phenomenon of "family periodicity". METHODS AND RESULTS We performed a whole genome sequencing in four patients in a large multigenerational family of cluster headache to identify additional loci associated with CH. This allowed us to replicate the genomic association of HCRTR2 and CLOCK as candidate genes. In two family members with the same phenotypic circadian pattern (familial periodicity) the association of polymorphism NM_001526.4:c.922G > A was shown in the HCRTR2 gene, and NM_004898.4:c.213T > C in the CLOCK gene. INTERPRETATION This whole genome sequencing reproduced two genetic risk loci for CH already involved in its pathogenicity. This is the first time that the combination of HCRTR2 and CLOCK gene variants is identified in a multigenerational family of CH with striking periodicity characteristics. Our study supports the hypothesis that the combination of HCRTR2 and CLOCK gene variants can contribute to the risk of cluster headache and offer the prospect of a new area of research on the molecular circadian clock.
Collapse
|
21
|
Guatibonza Moreno P, Pardo LM, Pereira C, Schroeder S, Vagiri D, Almeida LS, Juaristi C, Hosny H, Loh CCY, Leubauer A, Torres Morales G, Oppermann S, Iurașcu MI, Fischer S, Steinicke TM, Viceconte N, Cozma C, Kandaswamy KK, Pinto Basto J, Böttcher T, Bauer P, Bertoli-Avella A. At a glance: the largest Niemann-Pick type C1 cohort with 602 patients diagnosed over 15 years. Eur J Hum Genet 2023; 31:1108-1116. [PMID: 37433892 PMCID: PMC10545733 DOI: 10.1038/s41431-023-01408-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/04/2023] [Accepted: 06/07/2023] [Indexed: 07/13/2023] Open
Abstract
Niemann-Pick type C1 disease (NPC1 [OMIM 257220]) is a rare and severe autosomal recessive disorder, characterized by a multitude of neurovisceral clinical manifestations and a fatal outcome with no effective treatment to date. Aiming to gain insights into the genetic aspects of the disease, clinical, genetic, and biomarker PPCS data from 602 patients referred from 47 countries and diagnosed with NPC1 in our laboratory were analyzed. Patients' clinical data were dissected using Human Phenotype Ontology (HPO) terms, and genotype-phenotype analysis was performed. The median age at diagnosis was 10.6 years (range 0-64.5 years), with 287 unique pathogenic/likely pathogenic (P/LP) variants identified, expanding NPC1 allelic heterogeneity. Importantly, 73 P/LP variants were previously unpublished. The most frequent variants detected were: c.3019C > G, p.(P1007A), c.3104C > T, p.(A1035V), and c.2861C > T, p.(S954L). Loss of function (LoF) variants were significantly associated with earlier age at diagnosis, highly increased biomarker levels, and a visceral phenotype (abnormal abdomen and liver morphology). On the other hand, the variants p.(P1007A) and p.(S954L) were significantly associated with later age at diagnosis (p < 0.001) and mildly elevated biomarker levels (p ≤ 0.002), consistent with the juvenile/adult form of NPC1. In addition, p.(I1061T), p.(S954L), and p.(A1035V) were associated with abnormality of eye movements (vertical supranuclear gaze palsy, p ≤ 0.05). We describe the largest and most heterogenous cohort of NPC1 patients published to date. Our results suggest that besides its utility in variant classification, the biomarker PPCS might serve to indicate disease severity/progression. In addition, we establish new genotype-phenotype relationships for "frequent" NPC1 variants.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Peter Bauer
- CENTOGENE GmbH, Rostock, Germany.
- Univesrity of Rostock, Rostock, Germany.
| | | |
Collapse
|
22
|
Alqahtani AS, Alotibi RS, Aloraini T, Almsned F, Alassali Y, Alfares A, Alhaddad B, Al Eissa MM. Prospect of genetic disorders in Saudi Arabia. Front Genet 2023; 14:1243518. [PMID: 37799141 PMCID: PMC10548463 DOI: 10.3389/fgene.2023.1243518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023] Open
Abstract
Introduction: Rare diseases (RDs) create a massive burden for governments and families because sufferers of these diseases are required to undergo long-term treatment or rehabilitation to maintain a normal life. In Saudi Arabia (SA), the prevalence of RDs is high as a result of cultural and socio-economic factors. This study, however, aims to shed light on the genetic component of the prevalence of RDs in SA. Methodology: A retrospective study was conducted between September 2020 and December 2021 at King Saud Medical City, a tertiary hospital of the Ministry of Health (MOH), SA. A total of 1080 individuals with 544 potentially relevant variants were included. The index was 738, and the samples were tested in a commercialized laboratory using different molecular techniques, including next-generation sequencing. Result: A total of 867 molecular genetics tests were conducted on 738 probands. These tests included 610 exome sequencing (ES) tests, four genome sequencing (GS) tests, 82 molecular panels, 106 single nucleotide polymorphism (SNP) array, four methylation studies, 58 single-gene studies and three mitochondrial genome sequencing tests. The diagnostic yield among molecular genetics studies was 41.8% in ES, 24% in panels, 12% in SNP array and 24% in single gene studies. The majority of the identified potential variants (68%) were single nucleotide variants (SNV). Other ascertained variants included frameshift (11%), deletion (10%), duplication (5%), splicing (9%), in-frame deletion (3%) and indels (1%). The rate of positive consanguinity was 56%, and the autosomal recessive accounted for 54%. We found a significant correlation between the ES detection rate and positive consanguinity. We illustrated the presence of rare treatable conditions in DNAJC12, SLC19A3, and ALDH7A1, and the presence of the founder effect variant in SKIC2. Neurodevelopmental disorders were the main phenotype for which genetics studies were required (35.7%). Conclusion: This is the sixth-largest local study reporting next-generation sequencing. The results indicate the influence of consanguineous marriages on genetic disease and the burden it causes for the Kingdom of SA. This study highlights the need to enrich our society's knowledge of genetic disorders. We recommend utilising ES as a first-tier test to establish genetic diagnosis in a highly consanguineous population.
Collapse
Affiliation(s)
- Amerh S. Alqahtani
- Medical Genetics Department, King Saud Medical City, Riyadh, Saudi Arabia
| | - Raniah S. Alotibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Centre (KAIMRC), Riyadh, Saudi Arabia
- Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City, Department of Genetics, King Abdullah Specialized Children Hospital, MNGHA, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
- Department of Genetics, King Abdullah Specialized Children Hospital, MNGHA, Riyadh, Saudi Arabia
| | - Fahad Almsned
- Research Centre, King Fahad Specialist Hospital in Dammam (KFSH-D), Dammam, Saudi Arabia
- Population Health Management, Eastern Health Cluster, Dammam, Saudi Arabia
- Research and Development Department, NovoGenomics, Riyadh, Saudi Arabia
| | - Yara Alassali
- Medical School, AlFaisal University, Riyadh, Saudi Arabia
| | - Ahmed Alfares
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Bader Alhaddad
- Molecular Genetics Department, King Saud Medical City, Riyadh, Saudi Arabia
- Laboratory Medicine Department, King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Al Khobar, Saudi Arabia
| | - Mariam M. Al Eissa
- Medical School, AlFaisal University, Riyadh, Saudi Arabia
- Public Health Authority, Public Health Lab, Molecular Genetics Laboratory, Riyadh, Saudi Arabia
| |
Collapse
|
23
|
Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
Collapse
Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
| |
Collapse
|
24
|
Song J, Zhu K, Wang X, Yang Q, Yu S, Zhang Y, Fu Z, Wang H, Zhao Y, Lin K, Yuan G, Guo J, Shi Y, Liu C, Ai J, Zhang H, Zhang W. Utility of clinical metagenomics in diagnosing malignancies in a cohort of patients with Epstein-Barr virus positivity. Front Cell Infect Microbiol 2023; 13:1211732. [PMID: 37674580 PMCID: PMC10477599 DOI: 10.3389/fcimb.2023.1211732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/25/2023] [Indexed: 09/08/2023] Open
Abstract
Backgrounds Differentiation between benign and malignant diseases in EBV-positive patients poses a significant challenge due to the lack of efficient diagnostic tools. Metagenomic Next-Generation Sequencing (mNGS) is commonly used to identify pathogens of patients with fevers of unknown-origin (FUO). Recent studies have extended the application of Next-Generation Sequencing (NGS) in identifying tumors in body fluids and cerebrospinal fluids. In light of these, we conducted this study to develop and apply metagenomic methods to validate their role in identifying EBV-associated malignant disease. Methods We enrolled 29 patients with positive EBV results in the cohort of FUO in the Department of Infectious Diseases of Huashan Hospital affiliated with Fudan University from 2018 to 2019. Upon enrollment, these patients were grouped for benign diseases, CAEBV, and malignant diseases according to their final diagnosis, and CNV analysis was retrospectively performed in 2022 using samples from 2018 to 2019. Results Among the 29 patients. 16 of them were diagnosed with benign diseases, 3 patients were diagnosed with CAEBV and 10 patients were with malignant diseases. 29 blood samples from 29 patients were tested for mNGS. Among all 10 patients with malignant diagnosis, CNV analysis suggested neoplasms in 9 patients. Of all 19 patients with benign or CAEBV diagnosis, 2 patients showed abnormal CNV results. The sensitivity and specificity of CNV analysis for the identification for tumors were 90% and 89.5%, separately. Conclusions The application of mNGS could assist in the identification of microbial infection and malignancies in EBV-related diseases. Our results demonstrate that CNV detection through mNGS is faster compared to conventional oncology tests. Moreover, the convenient collection of peripheral blood samples adds to the advantages of this approach.
Collapse
Affiliation(s)
- Jieyu Song
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kun Zhu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaojia Wang
- Medical Department, Matridx Biotechnology Co., Ltd., Hangzhou, Zhejiang, China
| | - Qingluan Yang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shenglei Yu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhangfan Fu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongyu Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuanhan Zhao
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ke Lin
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guanmin Yuan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingxin Guo
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yingqi Shi
- Medical Department, Matridx Biotechnology Co., Ltd., Hangzhou, Zhejiang, China
| | - Chao Liu
- Medical Department, Matridx Biotechnology Co., Ltd., Hangzhou, Zhejiang, China
| | - Jingwen Ai
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haocheng Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Huashan Institute of Microbes and Infections, Shanghai, China
- Shanghai Huashen Institute of Microbes and Infections, Shanghai, China
| |
Collapse
|
25
|
Gomes GRF, Mariano TC, Braga VLL, Ribeiro EM, Guimarães IP, Pereira KSAF, Nóbrega PR, Pessoa ALS. Bailey-Bloch Congenital Myopathy in Brazilian Patients: A Very Rare Myopathy with Malignant Hyperthermia Susceptibility. Brain Sci 2023; 13:1184. [PMID: 37626540 PMCID: PMC10452826 DOI: 10.3390/brainsci13081184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Congenital myopathy-13 (CMYP13), also known as Bailey-Bloch congenital myopathy and Native American myopathy (NAM), is a condition caused by biallelic missense pathogenic variants in STAC3, which encodes an important protein necessary for the excitation-relaxation coupling machinery in the muscle. Patients with biallelic pathogenic variants in STAC3 often present with congenital weakness and arthrogryposis, cleft palate, ptosis, myopathic facies, short stature, kyphoscoliosis, and susceptibility to malignant hyperthermia provoked by anesthesia. We present two unrelated cases of Bailey-Bloch congenital myopathy descendants of non-consanguineous parents, which were investigated for delayed psychomotor development and generalized weakness. To the best of our knowledge, these are the first descriptions of CMYP13 in Brazil. In both patients, we found the previously described pathogenic missense variant p.Trp284Ser in homozygosity. CONCLUSION We seek to highlight the need for screening for CMYP13 in patients expressing the typical phenotype of the disease even in the absence of Lumbee Native American ancestry, and to raise awareness to possible complications like malignant hyperthermia in Bailey-Bloch congenital myopathy.
Collapse
Affiliation(s)
| | - Tamiris Carneiro Mariano
- Albert Sabin Pediatric Hospital (HIAS), Fortaleza 60410-794, Brazil; (T.C.M.); (V.L.L.B.); (E.M.R.)
| | - Vitor Lucas Lopes Braga
- Albert Sabin Pediatric Hospital (HIAS), Fortaleza 60410-794, Brazil; (T.C.M.); (V.L.L.B.); (E.M.R.)
| | - Erlane Marques Ribeiro
- Albert Sabin Pediatric Hospital (HIAS), Fortaleza 60410-794, Brazil; (T.C.M.); (V.L.L.B.); (E.M.R.)
- Faculty of Medicine, Unichristus University, Fortaleza 60160-196, Brazil;
| | - Ingred Pimentel Guimarães
- Faculty of Medicine, Ceará State University, Fortaleza 60714-903, Brazil; (G.R.F.G.); (I.P.G.); (K.S.A.F.P.)
| | | | - Paulo Ribeiro Nóbrega
- Faculty of Medicine, Unichristus University, Fortaleza 60160-196, Brazil;
- Division of Neurology, Department of Clinical Medicine, Federal University of Ceará, Fortaleza 60430-372, Brazil
| | - André Luiz Santos Pessoa
- Faculty of Medicine, Ceará State University, Fortaleza 60714-903, Brazil; (G.R.F.G.); (I.P.G.); (K.S.A.F.P.)
- Albert Sabin Pediatric Hospital (HIAS), Fortaleza 60410-794, Brazil; (T.C.M.); (V.L.L.B.); (E.M.R.)
| |
Collapse
|
26
|
Glotov OS, Chernov AN, Glotov AS. Human Exome Sequencing and Prospects for Predictive Medicine: Analysis of International Data and Own Experience. J Pers Med 2023; 13:1236. [PMID: 37623486 PMCID: PMC10455459 DOI: 10.3390/jpm13081236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023] Open
Abstract
Today, whole-exome sequencing (WES) is used to conduct the massive screening of structural and regulatory genes in order to identify the allele frequencies of disease-associated polymorphisms in various populations and thus detect pathogenic genetic changes (mutations or polymorphisms) conducive to malfunctional protein sequences. With its extensive capabilities, exome sequencing today allows both the diagnosis of monogenic diseases (MDs) and the examination of seemingly healthy populations to reveal a wide range of potential risks prior to disease manifestation (in the future, exome sequencing may outpace costly and less informative genome sequencing to become the first-line examination technique). This review establishes the human genetic passport as a new WES-based clinical concept for the identification of new candidate genes, gene variants, and molecular mechanisms in the diagnosis, prediction, and treatment of monogenic, oligogenic, and multifactorial diseases. Various diseases are addressed to demonstrate the extensive potential of WES and consider its advantages as well as disadvantages. Thus, WES can become a general test with a broad spectrum pf applications, including opportunistic screening.
Collapse
Affiliation(s)
- Oleg S. Glotov
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 St. Petersburg, Russia;
- Department of Experimental Medical Virology, Molecular Genetics and Biobanking of Pediatric Research and Clinical Center for Infectious Diseases, 197022 St. Petersburg, Russia
| | - Alexander N. Chernov
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 St. Petersburg, Russia;
- Department of General Pathology and Pathological Physiology, Institute of Experimental Medicine, 197376 St. Petersburg, Russia
| | - Andrey S. Glotov
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 St. Petersburg, Russia;
| |
Collapse
|
27
|
Shimojima Yamamoto K, Yoshimura A, Yamamoto T. Biallelic KCTD3 nonsense variant derived from paternal uniparental isodisomy of chromosome 1 in a patient with developmental epileptic encephalopathy and distinctive features. Hum Genome Var 2023; 10:22. [PMID: 37550298 PMCID: PMC10406933 DOI: 10.1038/s41439-023-00250-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/06/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
A biallelic nonsense variant of the potassium channel tetramerization domain-containing protein 3 gene (KCTD3) [c.1192C>T; p.R398*] was identified in a patient with developmental epileptic encephalopathy with distinctive features and brain structural abnormalities. The patient showed isodisomy of chromosome 1, where KCTD3 is located, and the father was heterozygous for the same variant. Based on these findings, paternal uniparental disomy was considered to cause the biallelic involvement of KCTD3.
Collapse
Affiliation(s)
- Keiko Shimojima Yamamoto
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Ayumi Yoshimura
- Department of Pediatrics, Seirei Mikatahara General Hospital, Hamamatsu, 433-8558, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
| |
Collapse
|
28
|
Boeykens F, Bhatti SFM, Peelman L, Broeckx BJG. VariantscanR: an R-package as a clinical tool for variant filtering of known phenotype-associated variants in domestic animals. BMC Bioinformatics 2023; 24:305. [PMID: 37528412 PMCID: PMC10394849 DOI: 10.1186/s12859-023-05426-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/20/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND Since the introduction of next-generation sequencing (NGS) techniques, whole-exome sequencing (WES) and whole-genome sequencing (WGS) have not only revolutionized research, but also diagnostics. The gradual switch from single gene testing to WES and WGS required a different set of skills, given the amount and type of data generated, while the demand for standardization remained. However, most of the tools currently available are solely applicable for human analysis because they require access to specific databases and/or simply do not support other species. Additionally, a complicating factor in clinical genetics in animals is that genetic diversity is often dangerously low due to the breeding history. Combined, there is a clear need for an easy-to-use, flexible tool that allows standardized data processing and preferably, monitoring of genetic diversity as well. To fill these gaps, we developed the R-package variantscanR that allows an easy and straightforward identification and prioritization of known phenotype-associated variants identified in dogs and other domestic animals. RESULTS The R-package variantscanR enables the filtering of variant call format (VCF) files for the presence of known phenotype-associated variants and allows for the estimation of genetic diversity using multi-sample VCF files. Next to this, additional functions are available for the quality control and processing of user-defined input files to make the workflow as easy and straightforward as possible. This user-friendly approach enables the standardisation of complex data analysis in clinical settings. CONCLUSION We developed an R-package for the identification of known phenotype-associated variants and calculation of genetic diversity.
Collapse
Affiliation(s)
- Fréderique Boeykens
- Laboratory of Animal Genetics, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820, Merelbeke, Belgium.
| | - Sofie F M Bhatti
- Small Animal Department, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Luc Peelman
- Laboratory of Animal Genetics, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820, Merelbeke, Belgium
| | - Bart J G Broeckx
- Laboratory of Animal Genetics, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820, Merelbeke, Belgium.
| |
Collapse
|
29
|
Ballesta-Martínez MJ, Pérez-Fernández V, López-González V, Sánchez-Soler MJ, Serrano-Antón AT, Rodríguez-Peña LI, Barreda-Sánchez M, Armengol-Dulcet L, Guillén-Navarro E. Validation of clinical exome sequencing in the diagnostic procedure of patients with intellectual disability in clinical practice. Orphanet J Rare Dis 2023; 18:201. [PMID: 37480025 PMCID: PMC10362575 DOI: 10.1186/s13023-023-02809-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/05/2023] [Indexed: 07/23/2023] Open
Abstract
Intellectual disability (ID) has a prevalence of 1-3% and aproximately 30-50% of ID cases have a genetic cause. Development of next-generation sequencing has shown a high diagnostic potential. The aim of this work was to evaluate the diagnostic yield of clinical exome sequencing in 188 ID patients and the economic impact of its introduction in clinical practice. An analysis of diagnostic yield according to the different clinical variables was performed in order to establish an efficient diagnostic protocol for ID patients. Diagnostic yield of clinical exome sequencing was significant (34%) supporting its utility in diagnosis of ID patients. Wide genetic heterogeneity and predominance of autosomal dominant de novo variants in ID patients were observed. Time to diagnosis was shortened and diagnostic study costs decreased by 62% after implementation of clinical exome sequencing. No association was found between any of the variables analyzed and a higher diagnostic yield; added to the fact that many of the diagnoses weren't clinically detectable, the reduction of time to diagnosis and the economic savings with respect to classical diagnostic studies, strengthen the clinical and economical convenience of early implementation of clinical exome sequencing in the diagnostic workup of ID patients in clinical practice.
Collapse
Affiliation(s)
- María Juliana Ballesta-Martínez
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain.
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain.
- Centro de Investigación Biomédica en Red-Enfermedades Raras (CIBERER-Instituto de Salud Carlos III), Madrid, Spain.
| | - Virginia Pérez-Fernández
- Departamento de Ciencias Sociosanitarias-Área de Bioestadística, Facultad de Medicina, Universidad de Murcia, Murcia, Spain
| | - Vanesa López-González
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain
- Centro de Investigación Biomédica en Red-Enfermedades Raras (CIBERER-Instituto de Salud Carlos III), Madrid, Spain
| | - María José Sánchez-Soler
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain
| | - Ana Teresa Serrano-Antón
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain
| | - Lidia Isolina Rodríguez-Peña
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | | | - Lluís Armengol-Dulcet
- Quantitative Genomic Medicine Laboratories (qGenomics), Esplugues del Llobregat, Catalonia, Spain
| | - Encarna Guillén-Navarro
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain.
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain.
- Centro de Investigación Biomédica en Red-Enfermedades Raras (CIBERER-Instituto de Salud Carlos III), Madrid, Spain.
| |
Collapse
|
30
|
Chu Y, Li S, Tang J, Wu H. The potential of the Medical Digital Twin in diabetes management: a review. Front Med (Lausanne) 2023; 10:1178912. [PMID: 37547605 PMCID: PMC10397506 DOI: 10.3389/fmed.2023.1178912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Diabetes is a chronic prevalent disease that must be managed to improve the patient's quality of life. However, the limited healthcare management resources compared to the large diabetes mellitus (DM) population are an obstacle that needs modern information technology to improve. Digital twin (DT) is a relatively new approach that has emerged as a viable tool in several sectors of healthcare, and there have been some publications on DT in disease management. The systematic summary of the use of DTs and its potential applications in DM is less reported. In this review, we summarized the key techniques of DTs, proposed the potentials of DTs in DM management from different aspects, and discussed the concerns of this novel technique in DM management.
Collapse
|
31
|
Masri AT, Oweis L, Ali M, Hamamy H. Global developmental delay and intellectual disability in the era of genomics: Diagnosis and challenges in resource limited areas. Clin Neurol Neurosurg 2023; 230:107799. [PMID: 37236004 DOI: 10.1016/j.clineuro.2023.107799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 05/28/2023]
Abstract
AIMS To report the diagnostic yield of clinical singleton whole exome sequencing (WES) performed among a group of Jordanian children presenting with global developmental delay /intellectual disability (GDD/ID), discuss the underlying identified genetic disorders and the challenges encountered. PATIENTS AND METHODS This retrospective medical record review study included 154 children who were diagnosed with GDD/ID at our clinic at Jordan University Hospital between 2016 and 2021, and whose diagnostic work up included WES. RESULTS Consanguinity among parents was reported in 94/154 (61.0%) patients and history of other affected siblings in 35/154 (22.7%) patients. Pathogenic and likely pathogenic variants (solved cases) were reported in 69/154 (44.8%) patients, a variant of uncertain significance was reported in 54/154 (35.0%) and a negative result was reported in 31/154 (20.1%) cases. In the solved cases, autosomal recessive diseases were the most common (33/69; 47.8%). Metabolic disorders were identified in 20/69 (28.9%) patients, followed by developmental and epileptic encephalopathies (9/69; 13.0%) and MECP2 related disorders (7/69; 10.1%). Other single gene disorders were identified in 33/69; 47.8%) patients. CONCLUSION This study had several limitations, as it was hospital-based and only including patients who were able to afford the test. Nevertheless, it yielded several important findings. In resource-limited countries, WES may be a reasonable approach. We discussed the challenges that clinicians meet in the context of shortage of resources.
Collapse
Affiliation(s)
- Amira T Masri
- Faculty of Medicine, Paediatric Department, Division of Child Neurology, The University of Jordan, Jordan.
| | - Liyana Oweis
- Faculty of Medicine, The University of Jordan, Jordan
| | - Majd Ali
- Faculty of Medicine, The University of Jordan, Jordan
| | - Hanan Hamamy
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| |
Collapse
|
32
|
Zhang K, Lin G, Han Y, Peng R, Li J. Analysis of Clinical Laboratory Detecting Challenging Variants from Exome Sequencing Using Simulated Patient-Parent Trio Sample: Pilot Study for Neurodevelopmental Disorder de Novo Variants. J Mol Diagn 2023; 25:378-387. [PMID: 37208049 DOI: 10.1016/j.jmoldx.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/19/2023] [Accepted: 02/24/2023] [Indexed: 05/21/2023] Open
Abstract
To date, there has been no systematic analysis for the clinical laboratory in detecting technically challenging variants using the trio-based exome sequencing (ES) approach. Here, we present an interlaboratory pilot proficiency testing study that used synthetic patient-parent specimens to assess the detection of challenging variants with de novo dominant inheritance modes for neurodevelopmental disorders using various trio-based ES. In total, 27 clinical laboratories that performed diagnostic exome analyses participated in the survey. One of the 26 challenging variants was identified by all laboratories, whereas all 26 variants were identified by only nine laboratories. The lack of identification of mosaic variants was often due to the bioinformatics analysis that excluded the variant. For missing intended heterozygous variants, probable root causes were related to the technical bioinformatics pipeline and variant interpretation and reporting. For each missing variant, there may be more than one probable reason from the different laboratories. There was considerable variation in interlaboratory performance for detecting challenging variants using trio-based ES. This finding may have important implications for the design and validation of tests for different variant types in clinical laboratories, especially for technically challenging variants, and necessary workflow modification can potentially improve trio-based ES performance.
Collapse
Affiliation(s)
- Kuo Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Rongxue Peng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.
| |
Collapse
|
33
|
Smits DJ, Schot R, Popescu CA, Dias KR, Ades L, Briere LC, Sweetser DA, Kushima I, Aleksic B, Khan S, Karageorgou V, Ordonez N, Sleutels FJGT, van der Kaay DCM, Van Mol C, Van Esch H, Bertoli-Avella AM, Roscioli T, Mancini GMS. De novo MCM6 variants in neurodevelopmental disorders: a recognizable phenotype related to zinc binding residues. Hum Genet 2023:10.1007/s00439-023-02569-7. [PMID: 37198333 DOI: 10.1007/s00439-023-02569-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/03/2023] [Indexed: 05/19/2023]
Abstract
The minichromosome maintenance (MCM) complex acts as a DNA helicase during DNA replication, and thereby regulates cell cycle progression and proliferation. In addition, MCM-complex components localize to centrosomes and play an independent role in ciliogenesis. Pathogenic variants in genes coding for MCM components and other DNA replication factors have been linked to growth and developmental disorders as Meier-Gorlin syndrome and Seckel syndrome. Trio exome/genome sequencing identified the same de novo MCM6 missense variant p.(Cys158Tyr) in two unrelated individuals that presented with overlapping phenotypes consisting of intra-uterine growth retardation, short stature, congenital microcephaly, endocrine features, developmental delay and urogenital anomalies. The identified variant affects a zinc binding cysteine in the MCM6 zinc finger signature. This domain, and specifically cysteine residues, are essential for MCM-complex dimerization and the induction of helicase activity, suggesting a deleterious effect of this variant on DNA replication. Fibroblasts derived from the two affected individuals showed defects both in ciliogenesis and cell proliferation. We additionally traced three unrelated individuals with de novo MCM6 variants in the oligonucleotide binding (OB)-fold domain, presenting with variable (neuro)developmental features including autism spectrum disorder, developmental delay, and epilepsy. Taken together, our findings implicate de novo MCM6 variants in neurodevelopmental disorders. The clinical features and functional defects related to the zinc binding residue resemble those observed in syndromes related to other MCM components and DNA replication factors, while de novo OB-fold domain missense variants may be associated with more variable neurodevelopmental phenotypes. These data encourage consideration of MCM6 variants in the diagnostic arsenal of NDD.
Collapse
Affiliation(s)
- Daphne J Smits
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands.
| | - Rachel Schot
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
- Discovery Unit, Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Cristiana A Popescu
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Kerith-Rae Dias
- Neuroscience Research Australia (NeuRA), University of New South Wales, Sydney, Australia
| | - Lesley Ades
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David A Sweetser
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Itaru Kushima
- Medical Genomics Center, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Psychiatry, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Branko Aleksic
- Department of Psychiatry, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | | | | | | | - Frank J G T Sleutels
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Daniëlle C M van der Kaay
- Department of Pediatrics, Subdivision of Endocrinology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, 3000, Leuven, Belgium
| | | | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), University of New South Wales, Sydney, Australia
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| |
Collapse
|
34
|
Paulhus K, Glasscock E. Novel Genetic Variants Expand the Functional, Molecular, and Pathological Diversity of KCNA1 Channelopathy. Int J Mol Sci 2023; 24:8826. [PMID: 37240170 PMCID: PMC10219020 DOI: 10.3390/ijms24108826] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
The KCNA1 gene encodes Kv1.1 voltage-gated potassium channel α subunits, which are crucial for maintaining healthy neuronal firing and preventing hyperexcitability. Mutations in the KCNA1 gene can cause several neurological diseases and symptoms, such as episodic ataxia type 1 (EA1) and epilepsy, which may occur alone or in combination, making it challenging to establish simple genotype-phenotype correlations. Previous analyses of human KCNA1 variants have shown that epilepsy-linked mutations tend to cluster in regions critical for the channel's pore, whereas EA1-associated mutations are evenly distributed across the length of the protein. In this review, we examine 17 recently discovered pathogenic or likely pathogenic KCNA1 variants to gain new insights into the molecular genetic basis of KCNA1 channelopathy. We provide the first systematic breakdown of disease rates for KCNA1 variants in different protein domains, uncovering potential location biases that influence genotype-phenotype correlations. Our examination of the new mutations strengthens the proposed link between the pore region and epilepsy and reveals new connections between epilepsy-related variants, genetic modifiers, and respiratory dysfunction. Additionally, the new variants include the first two gain-of-function mutations ever discovered for KCNA1, the first frameshift mutation, and the first mutations located in the cytoplasmic N-terminal domain, broadening the functional and molecular scope of KCNA1 channelopathy. Moreover, the recently identified variants highlight emerging links between KCNA1 and musculoskeletal abnormalities and nystagmus, conditions not typically associated with KCNA1. These findings improve our understanding of KCNA1 channelopathy and promise to enhance personalized diagnosis and treatment for individuals with KCNA1-linked disorders.
Collapse
Affiliation(s)
| | - Edward Glasscock
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275, USA;
| |
Collapse
|
35
|
Gorukmez O, Gorukmez O, Topak A. Clinical exome sequencing findings in 1589 patients. Am J Med Genet A 2023; 191:1557-1564. [PMID: 36964972 DOI: 10.1002/ajmg.a.63190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/31/2023] [Accepted: 03/15/2023] [Indexed: 03/27/2023]
Abstract
Clinical exome sequencing (CES) is important for the diagnosis of Mendelian diseases, which are clinically and etiologically heterogeneous. Sharing of large amounts of CES data associated with clinical findings will increase the accuracy of variant interpretation. We performed a retrospective study to state the diagnostic yield of CES in 1589 patients with a wide phenotypic spectrum. CES was performed using the Sophia Clinical Exome Sequencing Kit with 4493 genes, followed by sequencing on a NextSeq 500 system. The diagnosis rate was 36.8% when only pathogenic and likely pathogenic variants were included. Consanguineous unions and positive family history were associated with a high diagnostic yield. The neurological disease group had the highest number of patients. The groups with high diagnosis rates were ear, eye, and muscle disease groups. Seven candidate genes (EFHC2, HSPB3, FAAH2, ITGB1, GYG2, CD177, and CSTF2T) that are not yet associated with human diseases were identified. Owing to the high diagnostic yield of CES compared with that of other genetic tests, it can be used as a standard diagnostic test in patients with rare genetic disorders that require a wide differential diagnosis, especially in laboratories with limited resources.
Collapse
Affiliation(s)
- Ozlem Gorukmez
- Department of Medical Genetics, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Turkey
| | - Orhan Gorukmez
- Department of Medical Genetics, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Turkey
| | - Ali Topak
- Department of Medical Genetics, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Turkey
| |
Collapse
|
36
|
Hühns M, Ameziane N, Holzmann C, Al-Ali R, Prall F. Clonal and "Intrinsic" Heterogeneity of Somatic Variants in Microsatellite-Stable Colorectal Carcinomas and Their Metastases. J Transl Med 2023; 103:100132. [PMID: 36966951 DOI: 10.1016/j.labinv.2023.100132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/07/2023] [Accepted: 03/19/2023] [Indexed: 04/21/2023] Open
Abstract
To test the traditional model of tumor progression, Darwinian-type evolution, against the more recent Big Bang model, we selected 6 microsatellite-stable colorectal standard-type adenocarcinomas and their synchronous lymph node and liver metastases. Somatic genomic variants were identified by whole-exome sequencing (WES) of large tumor fragments from the primaries and 1 liver metastasis each, and used to design targeted resequencing next-generation sequencing (NGS) panels, 1 per case. Targeted deep resequencing (mean coverage, 2725; median, 2222) was performed with DNA from punch samples (1-mm tissue microarrayer needles) obtained from different regions of the primaries and their metastases. In total, 255 genomic variants were interrogated in 108 punch samples. Clonal heterogeneity was infrequent: a pattern of clonal heterogeneity consistent with a role in metastasis formation was observed only in 1 case in a single gene (p. Asp604Tyr of the PTPRT gene). However, when comparing variant allele frequencies (VAFs) of genomic variants in adjacent positions on chromosomes ("matched genomic variant loci") across punch samples, differences that exceeded 2 SD of the NGS assay variations (ad hoc dubbed VAF dysbalance) were observed in 7.1% of the punch samples (2.6%-12.0% per case), which indicates an intricate intermixing of mutated and nonmutated tumor cells ("intrinsic heterogeneity"). Additional OncoScan array analyses on a subset of the punch samples (31 in total) showed gross genomic aberrations as a possible explanation in only some (39.2%) of the matched genomic variant loci with VAF dysbalance. Our study provides a fairly direct (statistical model-free) view of the genomic states of microsatellite-stable colorectal carcinomas and their metastases, and suggests that Darwinian-type tumor evolution is not the key pathway of the metastasizing disease; instead, we recorded an "intrinsic" genomic heterogeneity, which may echo an initial Big Bang-like event.
Collapse
Affiliation(s)
- Maja Hühns
- Institute of Pathology, University Medicine of Rostock, Strempelstraße, Rostock, Germany
| | - Najim Ameziane
- Centogene AG, Am Strande, Rostock, Germany; Arcensus GmbH, Goethestraße, Rostock, Germany
| | - Carsten Holzmann
- Institute of Medical Genetics, Rostock University Medical Center, Ernst-Heydemann-Straße, Rostock, Germany
| | | | - Friedrich Prall
- Institute of Pathology, University Medicine of Rostock, Strempelstraße, Rostock, Germany.
| |
Collapse
|
37
|
Chang YT, Hong SY, Lin WD, Lin CH, Lin SS, Tsai FJ, Chou IC. Genetic Testing in Children with Developmental and Epileptic Encephalopathies: A Review of Advances in Epilepsy Genomics. CHILDREN 2023; 10:children10030556. [PMID: 36980114 PMCID: PMC10047509 DOI: 10.3390/children10030556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
Advances in disease-related gene discovery have led to tremendous innovations in the field of epilepsy genetics. Identification of genetic mutations that cause epileptic encephalopathies has opened new avenues for the development of targeted therapies. Clinical testing using extensive gene panels, exomes, and genomes is currently accessible and has resulted in higher rates of diagnosis and better comprehension of the disease mechanisms underlying the condition. Children with developmental disabilities have a higher risk of developing epilepsy. As our understanding of the mechanisms underlying encephalopathies and epilepsies improves, there may be greater potential to develop innovative therapies tailored to an individual’s genotype. This article provides an overview of the significant progress in epilepsy genomics in recent years, with a focus on developmental and epileptic encephalopathies in children. The aim of this review is to enhance comprehension of the clinical utilization of genetic testing in this particular patient population. The development of effective and precise therapeutic strategies for epileptic encephalopathies may be facilitated by a comprehensive understanding of their molecular pathogenesis.
Collapse
Affiliation(s)
- Yu-Tzu Chang
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung 40447, Taiwan; (Y.-T.C.)
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
| | - Syuan-Yu Hong
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Department of Medicine, School of Medicine, China Medical University, Taichung 40447, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40447, Taiwan
| | - Wei-De Lin
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung 40447, Taiwan; (Y.-T.C.)
- Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
| | - Chien-Heng Lin
- Division of Pediatric Pulmonology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Department of Biomedical Imaging and Radiological Science, College of Medicine, China Medial University, Taichung 40447, Taiwan
| | - Sheng-Shing Lin
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung 40447, Taiwan; (Y.-T.C.)
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
- Division of Genetics and Metabolism, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Department of Medical Genetics, China Medical University Hospital, Taichung 40447, Taiwan
- School of Chinese Medicine, China Medical University, Taichung 40447, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 40447, Taiwan
| | - I-Ching Chou
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Graduate Institute of Integrated Medicine, China Medical University, Taichung 40447, Taiwan
- Correspondence: ; Tel.: +886-4-22052121
| |
Collapse
|
38
|
den Hollander B, Veenvliet ARJ, Rothuizen-Lindenschot M, van Essen P, Peters G, Santos-Gómez A, Olivella M, Altafaj X, Brands MM, Jacobs BAW, van Karnebeek CD. Evidence for effect of l-serine, a novel therapy for GRIN2B-related neurodevelopmental disorder. Mol Genet Metab 2023; 138:107523. [PMID: 36758276 DOI: 10.1016/j.ymgme.2023.107523] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
RATIONALE To date, causal therapy is potentially available for GRIN2B-related neurodevelopmental disorder (NDD) due to loss-of-function (LoF) variants in GRIN2B, resulting in dysfunction of the GluN2B subunit-containing N-methyl-d-aspartate receptor (NMDAR). Recently, in vitro experiments showed that high doses of NMDAR co-agonist d-serine has the potential to boost the activity in GluN2B LoF variant-containing NMDARs. Initial reports of GRIN2B-NDD patients LoF variants, treated with l-serine using different regimens, showed varying effects on motor and cognitive performance, communication, behavior and EEG. Here, this novel treatment using a standardized protocol with an innovative developmental outcome measure is explored further in an open-label observational GRIN2B-NDD study. METHODS Initially, in vitro studies were conducted in order to functionally stratify two de novo GRIN2B variants present in two female patients (18 months and 4 years old). Functional studies showed that both variants are LoF, and thus the patients were treated experimentally according to an approved protocol with oral l-serine (500 mg/kg/day in 4 doses) for a period of 12 months. Both patients showed a heterogeneous clinical phenotype, however overlapping symptoms were present: intellectual developmental disability (IDD), behavioral abnormalities and hypotonia. Outcome measures included laboratory tests, quality of life, sleep, irritability, stool, and performance skills, measured by, among others, the Perceive-Recall-Plan-Perform System of Task Analysis (PRPP-Assessment). RESULTS Both patients tolerated l-serine without adverse effects. In one patient, improvement in psychomotor development and cognitive functioning was observed after 12 months (PRPP mastery score 10% at baseline, 78% at twelve months). In the most severe clinically affected patient no significant objective improvement in validated outcomes was observed. Caregivers of both patients reported subjective increase of alertness and improved communication skills. CONCLUSION Our observational study confirms that l-serine supplementation is safe in patients with GRIN2B-NDD associated with LoF variants, and may accelerate psychomotor development and ameliorate cognitive performance in some but not all patients. The PRPP-Assessment, a promising instrument to evaluate everyday activities and enhance personalized and value-based care, was not performed in the severely affected patient, meaning that possible positive results may have been missed. To generate stronger evidence for effect of l-serine in GRIN2B-NDD, we will perform placebo-controlled n-of-1 trials.
Collapse
Affiliation(s)
- B den Hollander
- Amsterdam University Medical Centers, University of Amsterdam, Department of Pediatrics, Emma Children's Hospital, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands; Amsterdam UMC, Emma Center for Personalized Medicine, Amsterdam, The Netherlands; United for Metabolic Diseases, The Netherlands
| | - A R J Veenvliet
- Amsterdam University Medical Centers, University of Amsterdam, Department of Pediatrics, Emma Children's Hospital, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands; Amsterdam UMC, Emma Center for Personalized Medicine, Amsterdam, The Netherlands; United for Metabolic Diseases, The Netherlands; Radboud University Medical Center, Department of Pediatrics, Amalia Children's Hospital, Geert Grooteplein Zuid 10, Nijmegen, The Netherlands
| | - M Rothuizen-Lindenschot
- Radboud University Medical Center, Department of Rehabilitation Medicine, Geert Grooteplein Zuid 10, Nijmegen, The Netherlands; HAN University of Applied Sciences, Department of Occupational Therapy, Kapittelweg 33, Nijmegen, The Netherlands
| | - P van Essen
- Radboud University Medical Center, Department of Pediatrics, Amalia Children's Hospital, Geert Grooteplein Zuid 10, Nijmegen, The Netherlands
| | - G Peters
- Radboud University Medical Center, Department of Rehabilitation Medicine, Geert Grooteplein Zuid 10, Nijmegen, The Netherlands
| | - A Santos-Gómez
- Neurophysiology Laboratory, Department of Biomedicine, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain; August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - M Olivella
- Biosciences Department, Faculty of Sciences and Technology, University of Vic-Central University of Catalonia, Barcelona, Spain
| | - X Altafaj
- Neurophysiology Laboratory, Department of Biomedicine, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain; August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - M M Brands
- Amsterdam University Medical Centers, University of Amsterdam, Department of Pediatrics, Emma Children's Hospital, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands; Amsterdam UMC, Emma Center for Personalized Medicine, Amsterdam, The Netherlands; United for Metabolic Diseases, The Netherlands
| | - B A W Jacobs
- Amsterdam University Medical Centers, Department of Pharmacy and Clinical Pharmacology, Meibergdreef 9, Amsterdam, The Netherlands; Medicine for Society, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - C D van Karnebeek
- Amsterdam University Medical Centers, University of Amsterdam, Department of Pediatrics, Emma Children's Hospital, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands; Amsterdam UMC, Emma Center for Personalized Medicine, Amsterdam, The Netherlands; United for Metabolic Diseases, The Netherlands; Amsterdam University Medical Centers, Department of Human Genetics, Amsterdam Reproduction and Development, Meibergdreef 9, Amsterdam, The Netherlands.
| |
Collapse
|
39
|
Pfrieger FW. The Niemann-Pick type diseases – A synopsis of inborn errors in sphingolipid and cholesterol metabolism. Prog Lipid Res 2023; 90:101225. [PMID: 37003582 DOI: 10.1016/j.plipres.2023.101225] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Disturbances of lipid homeostasis in cells provoke human diseases. The elucidation of the underlying mechanisms and the development of efficient therapies represent formidable challenges for biomedical research. Exemplary cases are two rare, autosomal recessive, and ultimately fatal lysosomal diseases historically named "Niemann-Pick" honoring the physicians, whose pioneering observations led to their discovery. Acid sphingomyelinase deficiency (ASMD) and Niemann-Pick type C disease (NPCD) are caused by specific variants of the sphingomyelin phosphodiesterase 1 (SMPD1) and NPC intracellular cholesterol transporter 1 (NPC1) or NPC intracellular cholesterol transporter 2 (NPC2) genes that perturb homeostasis of two key membrane components, sphingomyelin and cholesterol, respectively. Patients with severe forms of these diseases present visceral and neurologic symptoms and succumb to premature death. This synopsis traces the tortuous discovery of the Niemann-Pick diseases, highlights important advances with respect to genetic culprits and cellular mechanisms, and exposes efforts to improve diagnosis and to explore new therapeutic approaches.
Collapse
|
40
|
Ritchie FD, Lizarraga SB. The role of histone methyltransferases in neurocognitive disorders associated with brain size abnormalities. Front Neurosci 2023; 17:989109. [PMID: 36845425 PMCID: PMC9950662 DOI: 10.3389/fnins.2023.989109] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 01/17/2023] [Indexed: 02/12/2023] Open
Abstract
Brain size is controlled by several factors during neuronal development, including neural progenitor proliferation, neuronal arborization, gliogenesis, cell death, and synaptogenesis. Multiple neurodevelopmental disorders have co-morbid brain size abnormalities, such as microcephaly and macrocephaly. Mutations in histone methyltransferases that modify histone H3 on Lysine 36 and Lysine 4 (H3K36 and H3K4) have been identified in neurodevelopmental disorders involving both microcephaly and macrocephaly. H3K36 and H3K4 methylation are both associated with transcriptional activation and are proposed to sterically hinder the repressive activity of the Polycomb Repressor Complex 2 (PRC2). During neuronal development, tri-methylation of H3K27 (H3K27me3) by PRC2 leads to genome wide transcriptional repression of genes that regulate cell fate transitions and neuronal arborization. Here we provide a review of neurodevelopmental processes and disorders associated with H3K36 and H3K4 histone methyltransferases, with emphasis on processes that contribute to brain size abnormalities. Additionally, we discuss how the counteracting activities of H3K36 and H3K4 modifying enzymes vs. PRC2 could contribute to brain size abnormalities which is an underexplored mechanism in relation to brain size control.
Collapse
|
41
|
Robertson GL, Riffle S, Patel M, Bodnya C, Marshall A, Beasley HK, Garza-Lopez E, Shao J, Vue Z, Hinton A, Stoll MS, de Wet S, Theart RP, Chakrabarty RP, Loos B, Chandel NS, Mears JA, Gama V. DRP1 mutations associated with EMPF1 encephalopathy alter mitochondrial membrane potential and metabolic programs. J Cell Sci 2023; 136:jcs260370. [PMID: 36763487 PMCID: PMC10657212 DOI: 10.1242/jcs.260370] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 12/22/2022] [Indexed: 02/11/2023] Open
Abstract
Mitochondria and peroxisomes are dynamic signaling organelles that constantly undergo fission, driven by the large GTPase dynamin-related protein 1 (DRP1; encoded by DNM1L). Patients with de novo heterozygous missense mutations in DNM1L present with encephalopathy due to defective mitochondrial and peroxisomal fission (EMPF1) - a devastating neurodevelopmental disease with no effective treatment. To interrogate the mechanisms by which DRP1 mutations cause cellular dysfunction, we used human-derived fibroblasts from patients who present with EMPF1. In addition to elongated mitochondrial morphology and lack of fission, patient cells display lower coupling efficiency, increased proton leak and upregulation of glycolysis. Mitochondrial hyperfusion also results in aberrant cristae structure and hyperpolarized mitochondrial membrane potential. Peroxisomes show a severely elongated morphology in patient cells, which is associated with reduced respiration when cells are reliant on fatty acid oxidation. Metabolomic analyses revealed impaired methionine cycle and synthesis of pyrimidine nucleotides. Our study provides insight into the role of mitochondrial dynamics in cristae maintenance and the metabolic capacity of the cell, as well as the disease mechanism underlying EMPF1.
Collapse
Affiliation(s)
| | - Stellan Riffle
- Vanderbilt University, Cell and Developmental Biology, Nashville, TN 37232, USA
| | - Mira Patel
- Vanderbilt University, Cell and Developmental Biology, Nashville, TN 37232, USA
| | - Caroline Bodnya
- Vanderbilt University, Cell and Developmental Biology, Nashville, TN 37232, USA
| | - Andrea Marshall
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Heather K. Beasley
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Edgar Garza-Lopez
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Jianqiang Shao
- Central Microscopy Research Facility, University of Iowa, Iowa City, IA 52246, USA
| | - Zer Vue
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Antentor Hinton
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Maria S. Stoll
- Case Western Reserve University, Department of Pharmacology and Center for Mitochondrial Diseases, Cleveland, OH 44106, USA
| | - Sholto de Wet
- Stellenbosch University, Department of Physiological Sciences, Matieland, 7602, Stellenbosch, South Africa
| | - Rensu P. Theart
- Stellenbosch University, Department of Electrical and Electronic Engineering, Matieland, 7602, Stellenbosch, South Africa
| | - Ram Prosad Chakrabarty
- Northwestern University, Feinberg School of Medicine Department of Medicine Division of Pulmonary and Critical Care Medicine, Chicago, IL 60611, USA
| | - Ben Loos
- Stellenbosch University, Department of Electrical and Electronic Engineering, Matieland, 7602, Stellenbosch, South Africa
| | - Navdeep S. Chandel
- Northwestern University, Feinberg School of Medicine Department of Medicine Division of Pulmonary and Critical Care Medicine, Chicago, IL 60611, USA
- Northwestern University, Feinberg School of Medicine Department of Biochemistry and Molecular Genetics, Chicago, IL 60611, USA
| | - Jason A. Mears
- Case Western Reserve University, Department of Pharmacology and Center for Mitochondrial Diseases, Cleveland, OH 44106, USA
| | - Vivian Gama
- Vanderbilt University, Cell and Developmental Biology, Nashville, TN 37232, USA
- Vanderbilt University, Vanderbilt Center for Stem Cell Biology, Nashville, TN 37232, USA
- Vanderbilt University, Vanderbilt Brain Institute, Nashville, TN 37232, USA
| |
Collapse
|
42
|
Gupta N. Deciphering Intellectual Disability. Indian J Pediatr 2023; 90:160-167. [PMID: 36441387 DOI: 10.1007/s12098-022-04345-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022]
Abstract
Intellectual disability (ID) is a common cause of referral to the pediatricians, geneticists, and pediatric neurologists. A thorough clinical evaluation and a stepwise investigative approach using a combination of traditional genetic techniques and appropriate latest genomic technologies can help in arriving at a diagnosis. In the current "omics" era, adopting a multiomics approach would further assist in solving the undiagnosed cases with intellectual disability.
Collapse
Affiliation(s)
- Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, Ansari Nagar, Old OT Block, New Delhi, 110029, India.
| |
Collapse
|
43
|
Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
Collapse
Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| |
Collapse
|
44
|
von den Driesch J, Flöttmann J, Prall F, Mullins CS, Linnebacher M, Bürtin F. HROP68: A rare case of medullary pancreatic cancer-characterization and chemosensitivity of the first patient-derived cell line. Front Oncol 2023; 12:1082927. [PMID: 36761421 PMCID: PMC9904236 DOI: 10.3389/fonc.2022.1082927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/23/2022] [Indexed: 01/25/2023] Open
Abstract
Introduction Medullary pancreatic carcinoma (MPC) is a rare subtype of pancreatic ductal adenocarcinoma. MPCs represent less than 1% of all pancreatic cancers, and, with only 26 cases in the literature, knowledge regarding drug response and treatment outcome is very limited. Material and methods We present the case of a 64-year-old male patient with MPC who was treated by left pancreatic resection and adjuvant chemotherapy. Due to local recurrence, the patient underwent intended curative reoperation. From both surgical specimens, patient-derived xenografts (PDXs) and, from the recurrence, a patient-derived cell line (PDCL) were established. We subsequently performed an in-depth characterization of this cell line including phenotypic characterization, surface protein expression, growth, and migratory performance as well as mutational analysis using whole-exome sequencing (WES). Additionally, in vitro drug sensitivity toward the standard-of-care chemotherapeutic regimen and selected targeted therapies was evaluated. Results The pathological and molecular properties of this rare MPC case observed in the patient's tumors are preserved in the corresponding PDX and the PDCL of HROP68Tu2. Despite displaying an "immunogenic phenotype" with marked T-cell infiltration and a high-level expression of HLA II and Programmed death-ligand 1 (PD-L1), molecular analysis revealed microsatellite stability but a multitude of mutations affecting KRAS, TP53, KAT6B, FOXG1, RUNX1, and GRIK2 among others. Furthermore, HROP68Tu2 cells were susceptible toward 5-FU, irinotecan, oxaliplatin, gemcitabine, paclitaxel, and erlotinib as single agents, but only a moderate synergistic response was seen to the drugs of the FOLFIRINOX regimen. Even worse, the drugs of the two combinations gemcitabine plus paclitaxel and gemcitabine plus erlotinib showed antagonistic effects. Moreover, lapatinib, PRIMA-Met1, and olaparib selected as targeted therapeutics according to the mutational profiles and protein expression inhibited HROP68Tu2 cells' growth. Conclusion This study illustrates the establishment of the first preclinical MPC models as well as the first in-depth characterization of an MPC PDCL. Since the scientific and clinical knowledge of this rare pancreatic cancer type is very limited, the presented models contribute to a better understanding of MPC and might be a valuable tool for the development of future treatment options.
Collapse
Affiliation(s)
- Jens von den Driesch
- Clinic of General, Visceral, Vascular and Transplantation Surgery, University Medical Center Rostock, University of Rostock, Rostock, Germany
| | - Jana Flöttmann
- Clinic of General, Visceral, Vascular and Transplantation Surgery, University Medical Center Rostock, University of Rostock, Rostock, Germany
| | - Friedrich Prall
- Institute of Pathology, University Medical Center Rostock, University of Rostock, Rostock, Germany
| | - Christina S. Mullins
- Clinic of General, Visceral, Vascular and Transplantation Surgery, University Medical Center Rostock, University of Rostock, Rostock, Germany
| | - Michael Linnebacher
- Clinic of General, Visceral, Vascular and Transplantation Surgery, University Medical Center Rostock, University of Rostock, Rostock, Germany,*Correspondence: Michael Linnebacher,
| | - Florian Bürtin
- Clinic of General, Visceral, Vascular and Transplantation Surgery, University Medical Center Rostock, University of Rostock, Rostock, Germany
| |
Collapse
|
45
|
Smits DJ, Dekker J, Schot R, Tabarki B, Alhashem A, Demmers JAA, Dekkers DHW, Romito A, van der Spek PJ, van Ham TJ, Bertoli-Avella AM, Mancini GMS. CLEC16A interacts with retromer and TRIM27, and its loss impairs endosomal trafficking and neurodevelopment. Hum Genet 2023; 142:379-397. [PMID: 36538041 PMCID: PMC9950183 DOI: 10.1007/s00439-022-02511-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
CLEC16A is a membrane-associated C-type lectin protein that functions as a E3-ubiquitin ligase. CLEC16A regulates autophagy and mitophagy, and reportedly localizes to late endosomes. GWAS studies have associated CLEC16A SNPs to various auto-immune and neurological disorders, including multiple sclerosis and Parkinson disease. Studies in mouse models imply a role for CLEC16A in neurodegeneration. We identified bi-allelic CLEC16A truncating variants in siblings from unrelated families presenting with a severe neurodevelopmental disorder including microcephaly, brain atrophy, corpus callosum dysgenesis, and growth retardation. To understand the function of CLEC16A in neurodevelopment we used in vitro models and zebrafish embryos. We observed CLEC16A localization to early endosomes in HEK293T cells. Mass spectrometry of human CLEC16A showed interaction with endosomal retromer complex subunits and the endosomal ubiquitin ligase TRIM27. Expression of the human variant leading to C-terminal truncated CLEC16A, abolishes both its endosomal localization and interaction with TRIM27, suggesting a loss-of-function effect. CLEC16A knockdown increased TRIM27 adhesion to early endosomes and abnormal accumulation of endosomal F-actin, a sign of disrupted vesicle sorting. Mutagenesis of clec16a by CRISPR-Cas9 in zebrafish embryos resulted in accumulated acidic/phagolysosome compartments, in neurons and microglia, and dysregulated mitophagy. The autophagocytic phenotype was rescued by wild-type human CLEC16A but not the C-terminal truncated CLEC16A. Our results demonstrate that CLEC16A closely interacts with retromer components and regulates endosomal fate by fine-tuning levels of TRIM27 and polymerized F-actin on the endosome surface. Dysregulation of CLEC16A-mediated endosomal sorting is associated with neurodegeneration, but it also causes accumulation of autophagosomes and unhealthy mitochondria during brain development.
Collapse
Affiliation(s)
- Daphne J Smits
- Department of Clinical Genetics, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands.
| | - Jordy Dekker
- Department of Clinical Genetics, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands.
| | - Rachel Schot
- Department of Clinical Genetics, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands
| | - Brahim Tabarki
- Division of Pediatric Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, 12233, Saudi Arabia
| | - Amal Alhashem
- Division of Pediatric Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, 12233, Saudi Arabia
| | - Jeroen A A Demmers
- Department of Molecular Genetics, Proteomics Center, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands
| | - Dick H W Dekkers
- Department of Molecular Genetics, Proteomics Center, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands
| | | | - Peter J van der Spek
- Department of Pathology, Clinical Bioinformatics, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands
| | - Tjakko J van Ham
- Department of Clinical Genetics, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands
| | | | - Grazia M S Mancini
- Department of Clinical Genetics, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands
| |
Collapse
|
46
|
Lieberwirth JK, Büttner B, Klöckner C, Platzer K, Popp B, Abou Jamra R. AutoCaSc: Prioritizing candidate genes for neurodevelopmental disorders. Hum Mutat 2022; 43:1795-1807. [PMID: 35998261 DOI: 10.1002/humu.24451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/24/2022] [Accepted: 08/18/2022] [Indexed: 01/24/2023]
Abstract
Routine exome sequencing (ES) in individuals with neurodevelopmental disorders (NDD) remains inconclusive in >50% of the cases. Research analysis of unsolved cases can identify novel candidate genes but is time-consuming, subjective, and hard to compare between labs. The field, therefore, requires automated and standardized assessment methods to prioritize candidates for matchmaking. We developed AutoCaSc (https://autocasc.uni-leipzig.de) based on our candidate scoring scheme. We validated our approach using synthetic trios and real in-house trio ES data. AutoCaSc consistently (94.5% of all cases) scored the relevant variants in valid novel NDD genes in the top three ranks. In 93 real trio exomes, AutoCaSc identified most (97.5%) previously manually scored variants while evaluating additional high-scoring variants missed in manual evaluation. It identified candidate variants in previously undescribed NDD candidate genes (CNTN2, DLGAP1, SMURF1, NRXN3, and PRICKLE1). AutoCaSc enables anybody to quickly screen a variant for its plausibility in NDD. After contributing >40 descriptions of NDD-associated genes, we provide usage recommendations based on our extensive experience. Our implementation is capable of pipeline integration and therefore allows the screening of large cohorts for candidate genes. AutoCaSc empowers even small labs to a standardized matchmaking collaboration and to contribute to the ongoing identification of novel NDD entities.
Collapse
Affiliation(s)
| | - Benjamin Büttner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Chiara Klöckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.,Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Center of Functional Genomics, Berlin, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| |
Collapse
|
47
|
Schwarz S, Schmitz J, Löffler MW, Ghosh M, Rammensee HG, Olshvang E, Markel M, Mockel-Tenbrinck N, Dzionek A, Krake S, Arslan B, Kampe KD, Wendt A, Bauer P, Mullins CS, Schlosser A, Linnebacher M. T cells of colorectal cancer patients' stimulated by neoantigenic and cryptic peptides better recognize autologous tumor cells. J Immunother Cancer 2022; 10:jitc-2022-005651. [PMID: 36460334 PMCID: PMC9723954 DOI: 10.1136/jitc-2022-005651] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Patients with cancers that exhibit extraordinarily high somatic mutation numbers are ideal candidates for immunotherapy and enable identifying tumor-specific peptides through stimulation of tumor-reactive T cells (Tc). METHODS Colorectal cancers (CRC) HROC113 and HROC285 were selected based on high TMB, microsatellite instability and HLA class I expression. Their HLA ligandome was characterized using mass spectrometry, compared with the HLA ligand atlas and HLA class I-binding affinity was predicted. Cryptic peptides were identified using Peptide-PRISM. Patients' Tc were isolated from either peripheral blood (pTc) or tumor material (tumor-infiltrating Tc, TiTc) and expanded. In addition, B-lymphoblastoid cells (B-LCL) were generated and used as antigen-presenting cells. pTc and TiTc were stimulated twice for 7 days using peptide pool-loaded B-LCL. Subsequently, interferon gamma (IFNγ) release was quantified by ELISpot. Finally, cytotoxicity against autologous tumor cells was assessed in a degranulation assay. RESULTS 100 tumor-specific candidate peptides-97 cryptic peptides and 3 classically mutated neoantigens-were selected. The neoantigens originated from single nucleotide substitutions in the genes IQGAP1, CTNNB1, and TRIT1. Cryptic and neoantigenic peptides inducing IFNγ secretion of Tc were further investigated. Stimulation of pTc and TiTc with neoantigens and selected cryptic peptides resulted in increased release of cytotoxic granules in the presence of autologous tumor cells, substantiating their improved tumor cell recognition. Tetramer staining showed an enhanced number of pTc and TiTc specific for the IQGAP1 neoantigen. Subpopulation analysis prior to peptide stimulation revealed that pTc mainly consisted of memory Tc, whereas TiTc constituted primarily of effector and effector memory Tc. This allows to infer that TiTc reacting to neoantigens and cryptic peptides must be present within the tumor microenvironment. CONCLUSION These results prove that the analyzed CRC present both mutated neoantigenic and cryptic peptides on their HLA class I molecules. Moreover, stimulation with these peptides significantly strengthened tumor cell recognition by Tc. Since the overall number of neoantigenic peptides identifiable by HLA ligandome analysis hitherto is small, our data emphasize the relevance of increasing the target scope for cancer vaccines by the cryptic peptide category.
Collapse
Affiliation(s)
- Sandra Schwarz
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
| | - Johanna Schmitz
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
| | - Markus W Löffler
- Department of General, Visceral and Transplant Surgery, Universitätsklinikum Tübingen, Tubingen, Germany,Department of Immunology, University of Tübingen, Tubingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, University of Tübingen, Tübingen, Germany,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany,Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany
| | - Michael Ghosh
- Department of Immunology, University of Tübingen, Tubingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, University of Tübingen, Tubingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, University of Tübingen, Tübingen, Germany
| | | | - Marvin Markel
- Miltenyi Biotec BV & Co KG, Bergisch Gladbach, Germany
| | | | | | | | | | | | | | | | - Christina S Mullins
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
| | - Andreas Schlosser
- Center for Integrative and Translational Bioimaging, Rudolf-Virchow Center, University of Würzburg, Würzburg, Germany
| | - Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
| |
Collapse
|
48
|
Spangenberg MN, Grille S, Simoes C, Dell'Oca N, Boada M, Guillermo C, Raggio V, Spangenberg L. Two mutations in the SBDS gene reveal a diagnosis of Shwachman-Diamond syndrome in a patient with atypical symptoms. Cold Spring Harb Mol Case Stud 2022; 8:a006237. [PMID: 36577524 PMCID: PMC9808556 DOI: 10.1101/mcs.a006237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/10/2022] [Indexed: 12/30/2022] Open
Abstract
We present the case of a 53-yr-old woman with an inherited bone marrow failure coexisting with uncommon extrahematological symptoms, such as cirrhosis and skin abnormalities. Whole-exome sequencing revealed a diagnosis of Shwachman-Diamond syndrome (SDS) with an atypical presentation. Unexpected was the age of disease expression, normally around the pediatric age, with a predominantly median survival age of 36 yr. To our knowledge, she was the first adult patient with a molecular diagnosis of Shwachman-Diamond in Uruguay. The patient was referred to our service when she was 43-yr-old with a history of bone marrow failure with anemia and thrombocytopenia. All secondary causes of pancytopenia were excluded. Bone marrow aspirate and biopsy specimens were hypocellular for the patient's age. Numerous dysplastic features were observed in the three lineages. She had a normal karyotype and normal chromosomal fragility. A diagnosis of low-risk hypoplastic MDS was made. Dermatological examination revealed reticulate skin pigmentation with hypopigmented macules involving the face, neck, and extremities; nail dystrophy; premature graying; and thin hair. Extrahematological manifestations were present (e.g., learning difficulties, short stature). Last, she was diagnosed with cryptogenic liver cirrhosis CHILD C. This rules out all other possible causes of chronic liver disease. This clinical presentation initially oriented the diagnosis toward telomeropathy, so we did a telomeropathy NGS panel that came up negative. Finally, we did an exome sequencing that confirmed the diagnosis of SDS. Using whole-exome sequencing, we were able to find two compound heterozygous mutations in the SBDS gene that were responsible for the phenotype of a patient that was undiagnosed for 10 years. An earlier genetic diagnosis could have influenced our patient's outcome.
Collapse
Affiliation(s)
- María Noel Spangenberg
- Departamento de Hematología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
| | - Sofia Grille
- Departamento de Hematología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
- Departamento Básico de Medicina, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
| | - Camila Simoes
- Departamento Básico de Medicina, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
- Bioinformatics Unit, Institut Pasteur de Montevideo, 11400 Montevideo, Uruguay
| | - Nicolás Dell'Oca
- Departamento de Genética, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay
| | - Matilde Boada
- Departamento de Hematología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
| | - Cecilia Guillermo
- Departamento de Hematología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
| | - Victor Raggio
- Departamento de Genética, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay
| | - Lucía Spangenberg
- Departamento Básico de Medicina, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
- Bioinformatics Unit, Institut Pasteur de Montevideo, 11400 Montevideo, Uruguay
| |
Collapse
|
49
|
Zhang K, Yu L, Lin G, Li J. A multi-laboratory assessment of clinical exome sequencing for detection of hereditary disease variants: 4441 ClinVar variants for clinical genomic test development and validation. Clin Chim Acta 2022; 535:99-107. [PMID: 35985503 DOI: 10.1016/j.cca.2022.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/01/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND AIMS Whole-exome sequencing (WES) technology has become an essential tool in the clinical diagnostic for rare genetic disorders, however, the issues that reduce testing precision, sensitivity, and concordance are not clear under routine testing conditions. The study is to systematically evaluate the comparability of clinical WES testing results in laboratories under routine conditions. METHODS We designed a multi-laboratory study across 24 participating laboratories in China. We assessed sequencing quality across capture methods and sequencing platforms, benchmarked the impact of coverage and callable regions on detecting single nucleotide variants (SNVs), small insertions and deletions (Indels) under the same computational approaches, and compared the sensitivity, precision and reproducibility on detecting mutations across laboratories. RESULTS High inter-laboratory variability on variants detection were found across participating laboratories. Sample DNA concentration and sequencing evenness are two major variables that lead to the coverage variation. The difference in bioinformatics tools and computational settings affect the sensitivity and precision of the final output. Besides, copy-number variants (CNVs) identification is less reproducible than SNVs and Indels in the WES testing. We also compiled a list of 4441 low coverage ClinVar variants of 1176 genes from this study, which can be used as a source for creating in silico and synthetic DNA reference materials for clinical genetic disorder detection. CONCLUSIONS The considerable inter-laboratory variability seen in both sequencing coverage evenness and variants detection highlights the urgent need to improve the precision, sensitivity and comparability of the results generated across different laboratories. The list of low coverage variants can have important implications for the development and validation of clinical genetic disorder tests by laboratories. This study also serves to best practice inform guidelines for detecting clinical genetic disorders by exome sequencing.
Collapse
Affiliation(s)
- Kuo Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
| | - Lijia Yu
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
| |
Collapse
|
50
|
Developing CIRdb as a catalog of natural genetic variation in the Canary Islanders. Sci Rep 2022; 12:16132. [PMID: 36168029 PMCID: PMC9514705 DOI: 10.1038/s41598-022-20442-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
The current inhabitants of the Canary Islands have a unique genetic makeup in the European diversity landscape due to the existence of African footprints from recent admixture events, especially of North African components (> 20%). The underrepresentation of non-Europeans in genetic studies and the sizable North African ancestry, which is nearly absent from all existing catalogs of worldwide genetic diversity, justify the need to develop CIRdb, a population-specific reference catalog of natural genetic variation in the Canary Islanders. Based on array genotyping of the selected unrelated donors and comparisons against available datasets from European, sub-Saharan, and North African populations, we illustrate the intermediate genetic differentiation of Canary Islanders between Europeans and North Africans and the existence of within-population differences that are likely driven by genetic isolation. Here we describe the overall design and the methods that are being implemented to further develop CIRdb. This resource will help to strengthen the implementation of Precision Medicine in this population by contributing to increase the diversity in genetic studies. Among others, this will translate into improved ability to fine map disease genes and simplify the identification of causal variants and estimate the prevalence of unattended Mendelian diseases.
Collapse
|