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Yılmaz M, Kamaşak T, Teralı K, Çebi AH, Türkyılmaz A. The first Turkish family with a novel biallelic missense variant of the ALKBH8 gene: A study on the clinical and variant spectrum of ALKBH8-related intellectual developmental disorders. Am J Med Genet A 2024; 194:e63535. [PMID: 38189198 DOI: 10.1002/ajmg.a.63535] [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: 09/24/2023] [Revised: 12/12/2023] [Accepted: 12/26/2023] [Indexed: 01/09/2024]
Abstract
ABH8, the protein encoded by the ALKBH8 gene, modifies tRNAs by methylating their anticodon wobble uridine residues. The variations in the ALKBH8 gene are associated with the "intellectual developmental disorder, autosomal recessive type 71" (MIM: 618504) phenotype in the OMIM database. This phenotype is characterized by global developmental delay, facial dysmorphic features, and psychiatric problems. To date, 12 patients from five distinct families carrying variants of the ALKBH8 gene have been reported in the literature. In the present study, we report the first Turkish family harboring a novel homozygous missense variant, NM_138775.3:c.1874G > C (p.Arg625Pro), in the last exon of the ALKBH8 gene. Two affected siblings in this family showed signs of global developmental delay and intellectual disability. Based on the dysmorphological assessment of the cases, fifth finger clinodactyly and fetal fingertip pads were prominent, in addition to the dysmorphic findings similar to those reported in previous studies. Minor dysmorphic limb anomalies in relation to this phenotype have not yet been previously reported in the literature. Our computational studies revealed the potential deleterious effects of the Arg-to-Pro substitution on the structure and stability of the ABH8 methyltransferase domain. In the present report, the first Turkish family with an ultrarare disease associated with the ALKBH8 gene was reported, and a novel deleterious variant in the ALKBH8 gene and additional clinical features that were not reported with this condition have been reported.
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Affiliation(s)
- Mustafa Yılmaz
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Tülay Kamaşak
- Department of Pediatric Neurology, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Kerem Teralı
- Department of Medical Biochemistry, Faculty of Medicine, Cyprus International University, Nicosia, Cyprus
| | - Alper Han Çebi
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Ayberk Türkyılmaz
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
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Madhwani KR, Sayied S, Ogata CH, Hogan CA, Lentini JM, Mallik M, Dumouchel JL, Storkebaum E, Fu D, O’Connor-Giles KM. tRNA modification enzyme-dependent redox homeostasis regulates synapse formation and memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.566895. [PMID: 38014328 PMCID: PMC10680711 DOI: 10.1101/2023.11.14.566895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Post-transcriptional modification of RNA regulates gene expression at multiple levels. ALKBH8 is a tRNA modifying enzyme that methylates wobble uridines in specific tRNAs to modulate translation. Through methylation of tRNA-selenocysteine, ALKBH8 promotes selenoprotein synthesis and regulates redox homeostasis. Pathogenic variants in ALKBH8 have been linked to intellectual disability disorders in the human population, but the role of ALKBH8 in the nervous system is unknown. Through in vivo studies in Drosophila, we show that ALKBH8 controls oxidative stress in the brain to restrain synaptic growth and support learning and memory. ALKBH8 null animals lack wobble uridine methylation and exhibit a global reduction in protein synthesis, including a specific decrease in selenoprotein levels. Loss of ALKBH8 or independent disruption of selenoprotein synthesis results in ectopic synapse formation. Genetic expression of antioxidant enzymes fully suppresses synaptic overgrowth in ALKBH8 null animals, confirming oxidative stress as the underlying cause of dysregulation. ALKBH8 animals also exhibit associative learning and memory impairments that are reversed by pharmacological antioxidant treatment. Together, these findings demonstrate the critical role of tRNA modification in redox homeostasis in the nervous system and reveal antioxidants as a potential therapy for ALKBH8-associated intellectual disability.
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Affiliation(s)
| | - Shanzeh Sayied
- Department of Neuroscience, Brown University, Providence, RI, USA
| | | | - Caley A. Hogan
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Jenna M. Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Moushami Mallik
- Molecular Neurobiology Laboratory, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, NL
| | | | - Erik Storkebaum
- Molecular Neurobiology Laboratory, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, NL
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Kate M. O’Connor-Giles
- Department of Neuroscience, Brown University, Providence, RI, USA
- Carney Institute for Brain Sciences, Brown University, Providence, RI, USA
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Khan S, Umair M, Abbas S, Ali U, Zaman G, Ansar M, Wang R, Zhang X, Houlden H, Harlalka GV, Gul A. Overlapping neurological phenotypes in two extended consanguineous families with novel variants in the CNTNAP1 and ADGRG1 genes. J Gene Med 2023; 25:e3513. [PMID: 37178061 DOI: 10.1002/jgm.3513] [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: 01/05/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Population diversity is important and rare disease isolates can frequently reveal novel homozygous or biallelic mutations that lead to expanded clinical heterogeneity, with diverse clinical presentations. METHODS The present study describes two consanguineous families with a total of seven affected individuals suffering from a clinically similar severe syndromic neurological disorder, with abnormal development and central nervous system (CNS) and peripheral nervous system (PNS) abnormalities. Whole exome sequencing (WES) and Sanger sequencing followed by 3D protein modeling was performed to identify the disease-causing gene. RNA was extracted from the fresh blood of both families affected and healthy individuals. RESULTS The families were clinically assessed in the field in different regions of Khyber Pakhtunkhwa. Magnetic resonance imagining was obtained in the probands and blood was collected for DNA extraction and WES was performed. Sanger sequencing confirmed a homozygous, likely pathogenic mutation (GRCh38: chr17:42684199G>C; (NM_003632.3): c.333G>C);(NP_003623.1): p.(Trp111Cys) in the CNTNAP1 gene in family A, previously associated with Congenital Hypo myelinating Neuropathy 3 (CHN3; OMIM # 618186) and a novel nonsense variant in family B, (GRCh38: chr16: 57654086C>T; NC_000016.10 (NM_001370440.1): c.721C>T); (NP_001357369.1): p.(Gln241Ter) in the ADGRG1 gene previously associated with bilateral frontoparietal polymicrogyria (OMIM # 606854); both families have extended CNS and PNS clinical manifestations. In addition, 3D protein modeling was performed for the missense variant, p.(Trp111Cys), identified in the CNTNAP1, suggesting extensive secondary structure changes that might lead to improper function or downstream signaling. No RNA expression was observed in both families affected and healthy individuals hence showing that these genes are not expressed in blood. CONCLUSIONS In the present study, two novel biallelic variants in the CNTNAP1 and ADGRG1 genes in two different consanguineous families with a clinical overlap in the phenotype were identified. Thus, the clinical and mutation spectrum is expanded to provide further evidence that CNTNAP1 and ADGRG1 are very important for widespread neurological development.
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Affiliation(s)
- Shazia Khan
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, UK
- Hafeez Institute of Medical Sciences, Islamabad, Pakistan
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Safdar Abbas
- Department of Biological Science, Dartmouth College, Hanover, NH, USA
| | - Uroba Ali
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Gohar Zaman
- Department of Computer Science, Abbottabad University of Science and Technology, Havelian, Abbottabad, Pakistan
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rongrong Wang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- The Research Center for Medical Genomics, China Medical University, Shenyang, China
| | - Henry Houlden
- Department of Neuromuscular Disorder, UCL Institute of Neurology, London, UK
| | - Gaurav V Harlalka
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, UK
- Department of Pharmacology, Samarth College of Pharmacy, Deulgaon Raja, Dist. Buldana, Maharashtra, India
| | - Asma Gul
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
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Nawaz H, Khan SA, Bibi F, Waqas A, Bari A, Khan N, Muhammad N, Khan A, Paracha SA, Alam Q, Kamal MA, Rafeeq MM, Muhammad N, Haq FU, Khan S, Mahmood A, Khan S, Umair M. Biallelic Variants in Seven Different Genes Associated with Clinically Suspected Bardet-Biedl Syndrome. Genes (Basel) 2023; 14:genes14051113. [PMID: 37239474 DOI: 10.3390/genes14051113] [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: 04/08/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is a rare clinically and genetically heterogeneous autosomal recessive multi-systemic disorder with 22 known genes. The primary clinical and diagnostic features include six different hallmarks, such as rod-cone dystrophy, learning difficulties, renal abnormalities, male hypogonadism, post-axial polydactyly, and obesity. Here, we report nine consanguineous families and a non-consanguineous family with several affected individuals presenting typical clinical features of BBS. In the present study, 10 BBS Pakistani families were subjected to whole exome sequencing (WES), which revealed novel/recurrent gene variants, including a homozygous nonsense mutation (c.94C>T; p.Gln32Ter) in the IFT27 (NM_006860.5) gene in family A, a homozygous nonsense mutation (c.160A>T; p.Lys54Ter) in the BBIP1 (NM_001195306.1) gene in family B, a homozygous nonsense variant (c.720C>A; p.Cys240Ter) in the WDPCP (NM_015910.7) in family C, a homozygous nonsense variant (c.505A>T; p.Lys169Ter) in the LZTFL1 (NM_020347.4) in family D, pathogenic homozygous 1 bp deletion (c.775delA; p.Thr259Leufs*21) in the MKKS/BBS5 (NM_170784.3) gene in family E, a pathogenic homozygous missense variant (c.1339G>A; p.Ala447Thr) in BBS1 (NM_024649.4) in families F and G, a pathogenic homozygous donor splice site variant (c.951+1G>A; p?) in BBS1 (NM_024649.4) in family H, a pathogenic bi-allelic nonsense variant in MKKS (NM_170784.3) (c.119C>G; p.Ser40*) in family I, and homozygous pathogenic frameshift variants (c.196delA; p.Arg66Glufs*12) in BBS5 (NM_152384.3) in family J. Our findings extend the mutation and phenotypic spectrum of four different types of ciliopathies causing BBS and also support the importance of these genes in the development of multi-systemic human genetic disorders.
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Affiliation(s)
- Hamed Nawaz
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Farhana Bibi
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Ahmed Waqas
- Department Zoology, Division of Science and Technology, University of Education, Lahore 54782, Pakistan
| | - Abdul Bari
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Niamatullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Nazif Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Amjad Khan
- Faculty of Science, Department of Biological Sciences (Zoology), University of Lakki Marwat, Lakki Marwat 28420, Pakistan
| | - Sohail Aziz Paracha
- Department of Anatomy, KMU Institute of Medical Sciences (KIMS), Kohat 26000, Pakistan
| | - Qamre Alam
- Molecular Genomics and Precision Medicine, ExpressMed Laboratories, Block Zinj, Manama 359, Bahrain
| | - Mohammad Azhar Kamal
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj 11942, Saudi Arabia
| | - Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Fayaz Ul Haq
- Department of Radiological Sciences, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 12271, Saudi Arabia
| | - Shazia Khan
- Hafeez Institute of Medical Sciences, Islamabad 44000, Pakistan
- Department of Biological Sciences, International Islamic University Islamabad, H-10, Islamabad 44000, Pakistan
| | - Arif Mahmood
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat 26000, Pakistan
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh 12271, Saudi Arabia
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore 14611, Pakistan
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Umair M, Bilal M, Shah K, Said G, Ahmad F. Homozygous Missense Variant in the Solute Carrier Organic Anion Transporter 2A1 ( SLCO2A1) Gene Underlies Isolated Nail Clubbing. Genes (Basel) 2023; 14:430. [PMID: 36833358 PMCID: PMC9957043 DOI: 10.3390/genes14020430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/19/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Inherited isolated nail clubbing is a very rare Mendelian condition in humans, characterized by enlargement of the terminal segments of fingers and toes with thickened nails. Mutations in two genes have been reported to cause isolated nail clubbing in humans, which are the SLCO2A1 gene and the HPGD gene. OBJECTIVES An extended Pakistani family having two affected siblings born of unaffected consanguineous union was included in the study. Predominant isolated congenital nail clubbing (ICNC) without any other systemic abnormalities was observed, which we aimed to characterize at clinico-genetic level. METHODS Whole exome coupled with Sanger sequencing were employed to uncover the sequence variant as a cause of the disease. Furthermore, protein modeling was carried out to reveal the predicted possible effect of the mutation at the protein level. RESULTS Whole exome sequencing data analysis revealed a novel biallelic sequence variant (c.155T>A; p.Phe52Tyr) in the SLCO2A1 gene. Further, Sanger sequencing analysis validated and confirmed the segregation of the novel variant in the entire family. Subsequently, protein modeling of the wild-type and mutated SLCO2A1 revealed broad-scale change, which might compromise the proteins' secondary structure and function. CONCLUSION The present study adds another mutation to the SLCO2A1-related pathophysiology. The involvement of SLCO2A1 in the pathogenesis of ICNC may open exciting perceptions of this gene in nail development/morphogenesis.
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Affiliation(s)
- Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh 14611, Saudi Arabia
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore 54770, Punjab, Pakistan
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Khadim Shah
- Department of Dermatology, Yale School of Medicine, Yale University, New Heaven, CT 06511, USA
| | - Gulab Said
- Department of Chemistry, Women University Swabi, Swabi 23430, Khyber Pakhtunkhwa (KPK), Pakistan
| | - Farooq Ahmad
- Department of Biochemistry, Women University Swabi, Swabi 23430, Khyber Pakhtunkhwa (KPK), Pakistan
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Younus M, Rasheed M, Lin Z, Asiri SA, Almazni IA, Alshehri MA, Shafiq S, Iqbal I, Khan A, Ullah H, Umair M, Waqas A. Homozygous Missense Variant in the N-Terminal Region of ANK3 Gene Is Associated with Developmental Delay, Seizures, Speech Abnormality, and Aggressive Behavior. Mol Syndromol 2023; 14:11-20. [PMID: 36777705 PMCID: PMC9912002 DOI: 10.1159/000526381] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
Introduction Intellectual disability (ID) is a lifelong disability that affects an individual‧s learning capacity and adaptive behavior. Such individuals depend on their families for day-to-day survival and pose a significant challenge to the healthcare system, especially in developing countries. ID is a heterogeneous condition, and genetic studies are essential to unravel the underlying cellular pathway for brain development and functioning. Methods Here we studied a female index patient, born to a consanguineous Pakistani couple, showing clinical symptoms of ID, ataxia, hypotonia, developmental delay, seizures, speech abnormality, and aggressive behavior. Whole exome sequencing (WES) coupled with Sanger sequencing was performed for molecular diagnosis. Further, 3D protein modeling was performed to see the effect of variant on protein structure. Results WES identified a novel homozygous missense variant (c.178T>C; p.Tyr60His) in the ANK3 gene. In silico analysis and 3-dimensional (3D) protein modeling supports the deleterious impact of this variant on the encoding protein, which compromises the protein‧s overall structure and function. Conclusion Our finding supports the clinical and genetic diversity of the ANK3 gene as a plausible candidate gene for ID syndrome. Intelligence is a complex polygenic human trait, and understanding molecular and biological pathways involved in learning and memory can solve the complex puzzle of how cognition develops. Intellectual disability (ID) is defined as a deficit in an individual‧s learning and adaptive behavior at an early age of onset [American Psychiatric Association, 2013]. It is one of the major medical, and cognitive disorders with a prevalence of 1-3% in the population worldwide [Leonard and Wen, 2002]. ID often exists with other disabling mental conditions such as autism, attention deficit hyperactivity disorder, epilepsy, schizophrenia, bipolar disorder, or depression. Almost half of the cases appear to have a genetic explanation that ranges from cytogenetically visible abnormalities to monogenic defects [Flint, 2001; Ropers, 2010; Tucker-Drob et al., 2013]. Intellectual disability is a genetically heterogeneous condition, and more than 700 genes have been identified to cause ID alone or as a part of the syndrome. Research in X-linked ID has identified more than 100 disease-causing genes on the X chromosome that play a role in cognition; however, research into autosomal causes of ID is still ongoing [Vissers et al., 2016].
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Affiliation(s)
- Muhammad Younus
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology and Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Memoona Rasheed
- Department of Pathology, Islamabad Medical and Dental College, Islamabad, Pakistan
| | - Zhaohan Lin
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology and Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Saeed A. Asiri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Ibrahim A. Almazni
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Mohammed Ali Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Sarfraz Shafiq
- Department of Anatomy and Cell Biology, University of Western Ontario, London, Ontario, Canada
| | - Imran Iqbal
- Department of PLR, Institute of Active Polymers, Helmholtz-Zentrum Hereon, Teltow, Germany
| | - Amjad Khan
- Faculty of Science, Department of Biological Sciences (Zoology), University of Lakki Marwat, Lakki Marwat, Pakistan
| | - Hanif Ullah
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia,Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan,*Muhammad Umair,
| | - Ahmed Waqas
- Department of Zoology, Division of Science and Technology, University of Education Lahore, Lahore, Pakistan,**Ahmed Waqas,
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Cui W, Zhao D, Jiang J, Tang F, Zhang C, Duan C. tRNA Modifications and Modifying Enzymes in Disease, the Potential Therapeutic Targets. Int J Biol Sci 2023; 19:1146-1162. [PMID: 36923941 PMCID: PMC10008702 DOI: 10.7150/ijbs.80233] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/26/2023] [Indexed: 03/14/2023] Open
Abstract
tRNA is one of the most conserved and abundant RNA species, which plays a key role during protein translation. tRNA molecules are post-transcriptionally modified by tRNA modifying enzymes. Since high-throughput sequencing technology has developed rapidly, tRNA modification types have been discovered in many research fields. In tRNA, numerous types of tRNA modifications and modifying enzymes have been implicated in biological functions and human diseases. In our review, we talk about the relevant biological functions of tRNA modifications, including tRNA stability, protein translation, cell cycle, oxidative stress, and immunity. We also explore how tRNA modifications contribute to the progression of human diseases. Based on previous studies, we discuss some emerging techniques for assessing tRNA modifications to aid in discovering different types of tRNA modifications.
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Affiliation(s)
- Weifang Cui
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China
| | - Deze Zhao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China
| | - Junjie Jiang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China
| | - Faqing Tang
- Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410008, Hunan, PR China
| | - Chunfang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China
| | - Chaojun Duan
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, PR China.,National Clinical Research Center for Geriatric Disorders, Changsha, 410008, Hunan, PR China.,Institute of Medical Sciences, Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, PR China
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Waqas A, Liaqat R, Shaheen S, Khan AZ, Habib AH, Binothman N, Aljadani M, Zehri Z, Shaheen S, Alkathiri A, Naz R, Umair M, Abbas S. A novel homozygous truncating variant in PPFIBP1 further delineates PPFIBP1-associated neurodevelopmental disorder. Int J Dev Neurosci 2022; 83:191-200. [PMID: 36527195 DOI: 10.1002/jdn.10247] [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: 08/24/2022] [Revised: 11/21/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are classified as a group of disorders affecting function and development of the brain and having wide clinical variability. Herein, we describe two affected individuals segregating a recessive NDD. The affected individuals exhibited phenotypes such as global developmental delay (GDD), intellectual disability (ID), microcephaly and speech delay. Whole-exome sequencing (WES) followed by bidirectional Sanger sequencing techniques identified a homozygous nonsense variant (c.466C > T; p.Gln156*) in the PPFIBP1 gene (NM_003622.4) that segregated with the disease phenotype. Further, to elucidate the effect of the variant on protein structure, 3D protein modelling was performed for the mutant and normal protein that suggested substantial reduction of the mutant protein. Our data support the evidence that PPFIBP1 has a pivotal role in neurodevelopment in humans, and loss-of-function variants cause clinically variable neurodevelopmental phenotypes.
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Affiliation(s)
- Ahmed Waqas
- Department Zoology, Division of Science and Technology, University of Education, Lahore, Punjab, Pakistan
| | - Romana Liaqat
- Institute of Chemical Science, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Sidrah Shaheen
- Department of Higher Education, Government Girls degree College No. 1, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Ali Zaman Khan
- Department of Surgery, Surgical Ward 'A', Khyber Teaching Hospital, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najat Binothman
- Department of Chemistry, College of Sciences and Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Majidah Aljadani
- Department of Chemistry, College of Sciences and Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Zamrud Zehri
- Shaheed Nawab Ghous Bakhsh Raisani Memorial Hospital, Mastung, Balochistan, Pakistan
| | - Shabnam Shaheen
- Department of Higher Education, Government Girls Degree College, Lakki Marwat, Khyber Pakhtunkhwa, Pakistan
| | - Afnan Alkathiri
- Medical Genetics, Laboratory Medicine Department, Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Rubina Naz
- Institute of Chemical Science, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Umair
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Punjab, Pakistan
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Safdar Abbas
- Department of Biological Science, Dartmouth College, Hanover, NH, USA
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Cavallin I, Bartosovic M, Skalicky T, Rengaraj P, Demko M, Schmidt-Dengler MC, Drino A, Helm M, Vanacova S. HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs. RNA (NEW YORK, N.Y.) 2022; 28:1568-1581. [PMID: 36192131 PMCID: PMC9670814 DOI: 10.1261/rna.079421.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Transfer RNAs acquire a large plethora of chemical modifications. Among those, modifications of the anticodon loop play important roles in translational fidelity and tRNA stability. Four human wobble U-containing tRNAs obtain 5-methoxycarbonylmethyluridine (mcm5U34) or 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U34), which play a role in decoding. This mark involves a cascade of enzymatic activities. The last step is mediated by alkylation repair homolog 8 (ALKBH8). In this study, we performed a transcriptome-wide analysis of the repertoire of ALKBH8 RNA targets. Using a combination of HITS-CLIP and RIP-seq analyses, we uncover ALKBH8-bound RNAs. We show that ALKBH8 targets fully processed and CCA modified tRNAs. Our analyses uncovered the previously known set of wobble U-containing tRNAs. In addition, both our approaches revealed ALKBH8 binding to several other types of noncoding RNAs, in particular C/D box snoRNAs.
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Affiliation(s)
- Ivana Cavallin
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Marek Bartosovic
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Tomas Skalicky
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Praveenkumar Rengaraj
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Martin Demko
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | | | - Aleksej Drino
- Medical University of Vienna, Center for Anatomy and Cell Biology, 1090 Vienna, Austria
| | - Mark Helm
- Johannes Gutenberg-Universität Mainz, Institute of Pharmaceutical and Biomedical Science (IPBS), D-55128 Mainz, Germany
| | - Stepanka Vanacova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
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