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Bursakov SA, Kovaleva AV, Brigida AV, Zaripov OG. Functional analysis of the GPAT4 gene mutation predicted to affect splicing. Anim Biotechnol 2024; 35:2269210. [PMID: 37906284 DOI: 10.1080/10495398.2023.2269210] [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] [Indexed: 11/02/2023]
Abstract
The GPAT4 gene is considered as a potential functional candidate for single nucleotide polymorphism (SNP) studies in dairy cattle breeding due to its association with dairy performance in cattle by encoding an enzyme responsible for the presence of diacylglycerols and triacylglycerols in milk. Using the example of the GPAT4 gene, we applied the minigene splicing assay to analyze the functional consequences of its variant that was predicted to affect normal splicing. The results of functional analysis revealed the sequence variations (rs442541537), transfection experiments in a wild type and mutant cell line model system demonstrated that the investigated mutation in the second intron of the GPAT4 gene was responsible for the presence of a second exon in mature messenger RNA (mRNA). The cases of its absence in the spliced mature mRNA transcript resulted in a truncated dysfunctional protein due to the appearance of a stop codon. Thus, the discovered SNP led to alternative splicing in pre-mRNA by the 'cassette exon' ('exon skipping') mechanism. The studied mutation can potentially be a molecular genetic marker for alternative splicing for the GPAT4 gene and, therefore contributes to economic benefits in cattle breeding programs.
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Affiliation(s)
- Sergey A Bursakov
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
- Federal State Budgetary Scientific Institution "All-Russia Research Institute of Agricultural Biotechnology", Moscow, Russia
| | - Anastasia V Kovaleva
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
| | - Artyom V Brigida
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
| | - Oleg G Zaripov
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
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2
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Clingo M, Bustamante D, Carcamo B, Ross S, Makoshi Z, Moorthy C, Chang SM. Hypertrophic pachymeningitis as an unusual presentation of a patient with SLC29A3 spectrum disorder: Considering the use of next-generation sequencing. Pediatr Blood Cancer 2024; 71:e31153. [PMID: 38932461 DOI: 10.1002/pbc.31153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024]
Affiliation(s)
- Mitchell Clingo
- Department of Pediatrics, Texas Tech University Health Sciences Center El Paso, El Paso, Texas, USA
| | - Daniel Bustamante
- Department of Pathology, Texas Tech University Health Sciences Center El Paso, El Paso, Texas, USA
| | - Benjamin Carcamo
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, Texas Tech University Health Sciences Center El Paso, El Paso, Texas, USA
| | - Steven Ross
- Department of Radiology, Texas Tech University Health Sciences Center El Pas, El Paso, Texas, USA
| | - Ziyad Makoshi
- Department of Neurosciences, El Paso Children's Hospital, El Paso, Texas, USA
| | - Chetan Moorthy
- Department of Radiology, Texas Tech University Health Sciences Center El Pas, El Paso, Texas, USA
| | - Simone M Chang
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of South Florida Morsani College of Medicine Tampa, Tampa, Florida, USA
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3
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Zhao M, Cheng X, Chen L, Zeng YH, Lin KJ, Li YL, Zheng ZH, Huang XJ, Zuo DD, Guo XX, Guo J, He D, Liu Y, Lin Y, Wang C, Lv WQ, Su HZ, Yao XP, Ye ZL, Chen XH, Lu YQ, Huang CW, Yang G, Zhang YX, Lin MT, Wang N, Xiong ZQ, Chen WJ. Antisense oligonucleotides enhance SLC20A2 expression and suppress brain calcification in a humanized mouse model. Neuron 2024:S0896-6273(24)00535-X. [PMID: 39121859 DOI: 10.1016/j.neuron.2024.07.013] [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: 07/18/2023] [Revised: 05/15/2024] [Accepted: 07/17/2024] [Indexed: 08/12/2024]
Abstract
Primary familial brain calcification (PFBC) is a genetic neurological disease, yet no effective treatment is currently available. Here, we identified five novel intronic variants in SLC20A2 gene from six PFBC families. Three of these variants increased aberrant SLC20A2 pre-mRNA splicing by altering the binding affinity of splicing machineries to newly characterized cryptic exons, ultimately causing premature termination of SLC20A2 translation. Inhibiting the cryptic-exon incorporation with splice-switching ASOs increased the expression levels of functional SLC20A2 in cells carrying SLC20A2 mutations. Moreover, by knocking in a humanized SLC20A2 intron 2 sequence carrying a PFBC-associated intronic variant, the SLC20A2-KI mice exhibited increased inorganic phosphate (Pi) levels in cerebrospinal fluid (CSF) and progressive brain calcification. Intracerebroventricular administration of ASOs to these SLC20A2-KI mice reduced CSF Pi levels and suppressed brain calcification. Together, our findings expand the genetic etiology of PFBC and demonstrate ASO-mediated splice modulation as a potential therapy for PFBC patients with SLC20A2 haploinsufficiency.
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Affiliation(s)
- Miao Zhao
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China; Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Xuewen Cheng
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience and State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; Lin Gang Laboratory, Shanghai 201602, China.
| | - Lei Chen
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience and State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Heng Zeng
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Kai-Jun Lin
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Yun-Lu Li
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Ze-Hong Zheng
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Xue-Jing Huang
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Dan-Dan Zuo
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Xin-Xin Guo
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Jun Guo
- Department of Neurology, Tangdu Hospital, Air Force Medical University, Xi'an 710038, China
| | - Dian He
- Department of Neurology, Affiliated Hospital of Guizhou Medical University, Guiyang 550001, China
| | - Ying Liu
- Department of Neurology, Affiliated Hospital of Guizhou Medical University, Guiyang 550001, China
| | - Yu Lin
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Chong Wang
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Wen-Qi Lv
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Hui-Zhen Su
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China; Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Xiang-Ping Yao
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China; Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Zi-Ling Ye
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Xiao-Hong Chen
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Ying-Qian Lu
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Chen-Wei Huang
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience and State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang Yang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yu-Xian Zhang
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience and State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Min-Ting Lin
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China; Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Ning Wang
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China; Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China
| | - Zhi-Qi Xiong
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience and State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Center for Brain Science and Brain-inspired Technology, Shanghai 201602, China.
| | - Wan-Jin Chen
- Department of Neurology, the First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China; Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, China.
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Shahin NN, Shaker OG, Mahmoud MO. GOAT rs10096097 and CREB1 rs6740584 single nucleotide polymorphisms are associated with type 2 diabetes mellitus in Egyptians. Arch Pharm (Weinheim) 2024; 357:e2400011. [PMID: 38713912 DOI: 10.1002/ardp.202400011] [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: 01/02/2024] [Revised: 04/14/2024] [Accepted: 04/17/2024] [Indexed: 05/09/2024]
Abstract
Diabetes mellitus (DM) is a chronic disorder that affects nearly half a billion people around the world and causes millions of deaths annually. Treatment of diabetes or related complications represents an economic burden not only for developing countries but also for the developed ones. Hence, new efficient therapeutic and preventive strategies and screening tools are necessary. The current work aimed to assess the potential association of single nucleotide polymorphisms (SNPs) in ghrelin O-acyltransferase (GOAT) rs10096097, cyclic adenosine monophosphate (cAMP) response element binding protein (CREB) rs6740584, and v-maf musculoaponeurotic fibrosarcoma oncogene homolog A (MafA) rs62521874 genes with type 2 DM susceptibility in Egyptians. A total of 96 patients with type 2 DM along with 72 healthy individuals participated in this study. Genotyping was executed via real-time polymerase chain reaction (PCR), and the serum protein levels of GOAT, CREB, and MafA were measured by enzyme-linked immunosorbent assay (ELISA). Genotyping revealed a significant association of GOAT rs10096097 and CREB1 rs6740584 SNPs with type 2 diabetes risk, with significantly higher GOAT rs10096097 G allele and CREB1 rs6740584 T allele frequencies in diabetic patients than in controls. However, insignificant association was identified between the MafA rs62521874 SNP and diabetes in the examined sample of the Egyptian residents. Serum GOAT, CREB1, and MafA protein levels did not vary significantly between diabetic and control individuals. Yet, significant variation in serum GOAT and CREB1 levels was detected between CREB1 rs6740584 genotypes within the diabetic group, with CT and TT genotype carriers showing higher levels than AA genotype patients. GOAT rs10096097 and CREB1 rs6740584, but not MafA rs62521874, SNPs are associated with type 2 diabetes risk in the studied Egyptians.
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Affiliation(s)
- Nancy N Shahin
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Olfat G Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed O Mahmoud
- Biochemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
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Huang F, Dai Z, Yu J, Wang K, Chen C, Chen D, Zhang J, Zhao J, Li M, Zhang W, Li X, Qi Y, Wang Y. RBM7 deficiency promotes breast cancer metastasis by coordinating MFGE8 splicing switch and NF-kB pathway. eLife 2024; 13:RP95318. [PMID: 38995840 PMCID: PMC11245308 DOI: 10.7554/elife.95318] [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] [Indexed: 07/14/2024] Open
Abstract
Aberrant alternative splicing is well-known to be closely associated with tumorigenesis of various cancers. However, the intricate mechanisms underlying breast cancer metastasis driven by deregulated splicing events remain largely unexplored. Here, we unveiled that RBM7 is decreased in lymph node and distant organ metastases of breast cancer as compared to primary lesions and low expression of RBM7 is correlated with the reduced disease-free survival of breast cancer patients. Breast cancer cells with RBM7 depletion exhibited an increased potential for lung metastasis compared to scramble control cells. The absence of RBM7 stimulated breast cancer cell migration, invasion, and angiogenesis. Mechanistically, RBM7 controlled the splicing switch of MFGE8, favoring the production of the predominant isoform of MFGE8, MFGE8-L. This resulted in the attenuation of STAT1 phosphorylation and alterations in cell adhesion molecules. MFGE8-L exerted an inhibitory effect on the migratory and invasive capability of breast cancer cells, while the truncated isoform MFGE8-S, which lack the second F5/8 type C domain had the opposite effect. In addition, RBM7 negatively regulates the NF-κB cascade and an NF-κB inhibitor could obstruct the increase in HUVEC tube formation caused by RBM7 silencing. Clinically, we noticed a positive correlation between RBM7 expression and MFGE8 exon7 inclusion in breast cancer tissues, providing new mechanistic insights for molecular-targeted therapy in combating breast cancer.
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Affiliation(s)
- Fang Huang
- Sino-US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Zhenwei Dai
- Sino-US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Jinmiao Yu
- Sino-US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Kainan Wang
- Department of Oncology & Sino-US Research Center for Cancer Translational Medicine, the Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Chaoqun Chen
- Sino-US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Dan Chen
- Department of Pathology, the First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian, China
| | - Jinrui Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Jinyao Zhao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Mei Li
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Wenjing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Xiaojie Li
- Department of Prosthodontics, College of Stomatology, Dalian Medical University, Dalian, China
| | - Yangfan Qi
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
- Soochow University Cancer Institute, Suzhou, China
| | - Yang Wang
- Sino-US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
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Hu DG, Marri S, Hulin JA, Ansaar R, Mackenzie PI, McKinnon RA, Meech R. Activation of Cryptic Donor Splice Sites within the UDP-Glucuronosyltransferase (UGT)1A First-Exon Region Generates Variant Transcripts That Encode UGT1A Proteins with Truncated Aglycone-Binding Domains. Drug Metab Dispos 2024; 52:526-538. [PMID: 38565302 DOI: 10.1124/dmd.123.001565] [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: 10/14/2023] [Revised: 02/19/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
The human UDP-glucuronosyltransferases (UGTs) have crucial roles in metabolizing and clearing numerous small lipophilic compounds. The UGT1A locus generates nine UGT1A mRNAs, 65 spliced transcripts, and 34 circular RNAs. In this study, our analysis of published UGT-RNA capture sequencing (CaptureSeq) datasets identified novel splice junctions that predict 24 variant UGT1A transcripts derived from ligation of exon 2 to unique sequences within the UGT1A first-exon region using cryptic donor splice sites. Of these variants, seven (1A1_n1, 1A3_n3, 1A4_n4, 1A5_n1, 1A8_n2, 1A9_n2, 1A10_n7) are predicted to encode UGT1A proteins with truncated aglycone-binding domains. We assessed their expression profiles and deregulation in cancer using four RNA sequencing (RNA-Seq) datasets of paired normal and cancerous drug-metabolizing tissues from large patient cohorts. Variants were generally coexpressed with their canonical counterparts with a higher relative abundance in tumor than in normal tissues. Variants showed tissue-specific expression with high interindividual variability but overall low abundance. However, 1A8_n2 showed high abundance in normal and cancerous colorectal tissues, with levels that approached or surpassed canonical 1A8 mRNA levels in many samples. We cloned 1A8_n2 and showed expression of the predicted protein (1A8_i3) in human embryonic kidney (HEK)293T cells. Glucuronidation assays with 4-methylumbelliferone (4MU) showed that 1A8_i3 had no activity and was unable to inhibit the activity of 1A8_i1 protein. In summary, the activation of cryptic donor splice sites within the UGT1A first-exon region expands the UGT1A transcriptome and proteome. The 1A8_n2 cryptic donor splice site is highly active in colorectal tissues, representing an important cis-regulatory element that negatively regulates the function of the UGT1A8 gene through pre-mRNA splicing. SIGNIFICANT STATEMENT: The UGT1A locus generates nine canonical mRNAs, 65 alternately spliced transcripts, and 34 different circular RNAs. The present study reports a series of novel UDP-glucuronosyltransferase (UGT)1A variants resulting from use of cryptic donor splice sites in both normal and cancerous tissues, several of which are predicted to encode variant UGT1A proteins with truncated aglycone-binding domains. Of these, 1A8_n2 shows exceptionally high abundance in colorectal tissues, highlighting its potential role in the first-pass metabolism in gut through the glucuronidation pathway.
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Affiliation(s)
- Dong Gui Hu
- College of Medicine and Public Health, Flinders Health and Medical Research Institute Flinders University, Bedford Park, Australia
| | - Shashikanth Marri
- College of Medicine and Public Health, Flinders Health and Medical Research Institute Flinders University, Bedford Park, Australia
| | - Julie-Ann Hulin
- College of Medicine and Public Health, Flinders Health and Medical Research Institute Flinders University, Bedford Park, Australia
| | - Radwan Ansaar
- College of Medicine and Public Health, Flinders Health and Medical Research Institute Flinders University, Bedford Park, Australia
| | - Peter I Mackenzie
- College of Medicine and Public Health, Flinders Health and Medical Research Institute Flinders University, Bedford Park, Australia
| | - Ross A McKinnon
- College of Medicine and Public Health, Flinders Health and Medical Research Institute Flinders University, Bedford Park, Australia
| | - Robyn Meech
- College of Medicine and Public Health, Flinders Health and Medical Research Institute Flinders University, Bedford Park, Australia
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Emilius L, Bremm F, Binder AK, Schaft N, Dörrie J. Tumor Antigens beyond the Human Exome. Int J Mol Sci 2024; 25:4673. [PMID: 38731892 PMCID: PMC11083240 DOI: 10.3390/ijms25094673] [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: 03/27/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
With the advent of immunotherapeutics, a new era in the combat against cancer has begun. Particularly promising are neo-epitope-targeted therapies as the expression of neo-antigens is tumor-specific. In turn, this allows the selective targeting and killing of cancer cells whilst healthy cells remain largely unaffected. So far, many advances have been made in the development of treatment options which are tailored to the individual neo-epitope repertoire. The next big step is the achievement of efficacious "off-the-shelf" immunotherapies. For this, shared neo-epitopes propose an optimal target. Given the tremendous potential, a thorough understanding of the underlying mechanisms which lead to the formation of neo-antigens is of fundamental importance. Here, we review the various processes which result in the formation of neo-epitopes. Broadly, the origin of neo-epitopes can be categorized into three groups: canonical, noncanonical, and viral neo-epitopes. For the canonical neo-antigens that arise in direct consequence of somatic mutations, we summarize past and recent findings. Beyond that, our main focus is put on the discussion of noncanonical and viral neo-epitopes as we believe that targeting those provides an encouraging perspective to shape the future of cancer immunotherapeutics.
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Affiliation(s)
- Lisabeth Emilius
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Franziska Bremm
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Amanda Katharina Binder
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Niels Schaft
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Jan Dörrie
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
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8
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Gao S, Zhang Q, Ding Y, Wang L, Li Z, Hu F, Yao RE, Yu T, Chang G, Wang X. Molecular and phenotypic characteristics of Bardet-Biedl syndrome in Chinese patients. Orphanet J Rare Dis 2024; 19:149. [PMID: 38584252 PMCID: PMC11000329 DOI: 10.1186/s13023-024-03150-9] [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: 09/08/2023] [Accepted: 03/27/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND Bardet-Biedl syndrome (BBS) is a type of non-motile ciliopathy. To date, 26 genes have been reported to be associated with BBS. However, BBS is genetically heterogeneous, with significant clinical overlap with other ciliopathies, which complicates diagnosis. Disability and mortality rates are high in BBS patients; therefore, it is urgent to improve our understanding of BBS. Thus, our study aimed to describe the genotypic and phenotypic spectra of BBS in China and to elucidate genotype-phenotype correlations. METHODS Twenty Chinese patients diagnosed with BBS were enrolled in this study. We compared the phenotypes of Chinese BBS patients in this study with those from other countries to analyze the phenotypic differences across patients worldwide. In addition, genotype-phenotype correlations were described for our cohort. We also summarized all previously reported cases of BBS in Chinese patients (71 patients) and identified common and specific genetic variants in the Chinese population. RESULTS Twenty-eight variants, of which 10 are novel, in 5 different BBS-associated genes were identified in 20 Chinese BBS patients. By comparing the phenotypes of BBSome-coding genes (BBS2,7,9) with those of chaperonin-coding genes (BBS10,12), we found that patients with mutations in BBS10 and 12 had an earlier age of onset (1.10 Vs. 2.20, p < 0.01) and diagnosis (4.64 Vs. 13.17, p < 0.01), whereas patients with mutations in BBS2, 7, and 9 had a higher body mass index (28.35 Vs. 24.21, p < 0.05) and more vision problems (p < 0.05). Furthermore, in 91 Chinese BBS patients, mutations were predominant in BBS2 (28.89%) and BBS7 (15.56%), and the most frequent variants were in BBS2: c.534 + 1G > T (10/182 alleles) and BBS7: c.1002delT (7/182 alleles), marking a difference from the genotypic spectra of BBS reported abroad. CONCLUSIONS We recruited 20 Chinese patients with BBS for genetic and phenotypic analyses, and identified common clinical manifestations, pathogenic genes, and variants. We also described the phenotypic differences across patients worldwide and among different BBS-associated genes. This study involved the largest cohort of Chinese patients with BBS, and provides new insights into the distinctive clinical features of specific pathogenic variants.
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Affiliation(s)
- Shiyang Gao
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Qianwen Zhang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yu Ding
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Libo Wang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Zhiying Li
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Feihan Hu
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Ru-En Yao
- Department of Genetic Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Tingting Yu
- Department of Genetic Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Guoying Chang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| | - Xiumin Wang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
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9
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Yue X, Liu B, Han T, Guo D, Ding R, Wang G. The first pineoblastoma case report of a patient with Sotos syndrome harboring NSD1 germline mutation. BMC Pediatr 2024; 24:166. [PMID: 38459438 PMCID: PMC10921566 DOI: 10.1186/s12887-024-04636-y] [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: 07/27/2023] [Accepted: 02/09/2024] [Indexed: 03/10/2024] Open
Abstract
Germline mutations of NSD1 are associated with Sotos syndrome, characterized by distinctive facial features, overgrowth, and developmental delay. Approximately 3% of individuals with Sotos syndrome develop tumors. In this study, we describe an infant in pineoblastoma with facial anomalies, learning disability and mild autism at 1 years diagnosed as Sotos syndrome owing to carrying a novel mutation de novo germline NSD1 likely pathogenic variant. This patient expands both the mutation and phenotype spectrum of the Sotos Syndrome and provides new clinical insights into the potential mechanism of underlying pinealoblastoma pathology.
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Affiliation(s)
- Xizan Yue
- Department of Neurosurgery, 1 Children's Hospital Affiliated to Shandong University, 2 Jinan Children's Hospital, Jinan, China
| | - Bo Liu
- Department of Neurosurgery, 1 Children's Hospital Affiliated to Shandong University, 2 Jinan Children's Hospital, Jinan, China
| | - Tiantian Han
- The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co, Ltd, Nanjing, China
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, China
| | - Didi Guo
- The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co, Ltd, Nanjing, China
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, China
| | - Ran Ding
- The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co, Ltd, Nanjing, China
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, China
| | - Guangyu Wang
- Department of Neurosurgery, 1 Children's Hospital Affiliated to Shandong University, 2 Jinan Children's Hospital, Jinan, China.
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10
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Yang Y, Qin M, Zhao Y, Wang X. Digenic inheritance accounts for phenotypic variability in amelogenesis imperfecta. Clin Genet 2024; 105:243-253. [PMID: 37937686 DOI: 10.1111/cge.14449] [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: 07/27/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/09/2023]
Abstract
Amelogenesis imperfecta (AI) represents a group of clinically and genetically heterogeneous disorders that affect enamel formation and mineralization. Although AI is commonly considered a monogenic disorder, digenic inheritance is rarely reported. In this study, we recruited two nonconsanguineous Chinese families exhibiting diverse phenotypes of enamel defects among affected family members. Digenic variants were discovered in both probands. In family 1, the proband inherited a paternal frameshift variant in LAMA3 (NM_198129.4:c.3712dup) and a maternal deletion encompassing the entire AMELX gene. This resulted in a combined hypoplastic and hypomineralized AI phenotype, which was distinct from the parents' manifestations. In family 2, whole-exome sequencing analysis revealed the proband carried a maternal heterozygous splicing variant in COL17A1 (NC_000010.11 (NM_000494.3): c.4156 + 2dup) and compound heterozygous variants in RELT (paternal: NM_032871.4:c.260A > T; maternal: NM_032871.4:c.521 T > G). These genetic changes caused the abundant irregular enamel defects observed in the proband, whereas other affected family members carrying heterozygous variants in both COL17A1 and RELT displayed only horizontal grooves as their phenotype. The pathogenicity of the novel COL17A1 splice site variant was confirmed through RT-PCR and minigene assay. This study enhances our understanding by highlighting the potential association between the co-occurrence of variants in two genes and variable phenotypes observed in AI patients.
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Affiliation(s)
- Yi Yang
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
| | - Man Qin
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
| | - Yuming Zhao
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
| | - Xin Wang
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
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11
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Machida R, Ogawa T, Min Soe K, Moriyama K. Nonsense-mediated mRNA decay affects hyperactive root formation in oculo-facio-cardio-dental syndrome via up-frameshift protein 1. J Oral Biosci 2024; 66:225-231. [PMID: 38244688 DOI: 10.1016/j.job.2024.01.008] [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: 09/11/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/22/2024]
Abstract
OBJECTIVES Oculo-facio-cardio-dental (OFCD) syndrome is a rare X-linked genetic disorder caused by mutations in the BCL6 co-repressor (BCOR) and is mainly characterized by radiculomegaly (elongated dental roots). All BCOR mutations reported to date have been associated with premature termination codons, indicating that nonsense-mediated mRNA decay (NMD) might play a vital role in the pathogenesis of OFCD syndrome. However, the molecular mechanisms underlying NMD remain unclear. In this study, we investigated the involvement of up-frameshift protein 1 (UPF1), which plays a central role in NMD, in the hyperactive root formation caused by BCOR mutations. METHODS Periodontal ligament cells, isolated from a Japanese woman with a c.3668delC frameshift mutation in BCOR, and primary human periodontal ligament fibroblasts (HPdLFs) were used for an RNA immunoprecipitation assay to confirm the binding of UPF1 to mutated BCOR. Additionally, the effects of UPF1 on the BCOR transcription levels and corresponding gene expression were determined by performing relative quantitative real-time polymerase chain reactions. RESULTS RNA immunoprecipitation revealed that UPF1 binds to exon 9 of mutated BCOR. Additionally, UPF1 knockdown via siRNA upregulated the transcription of BCOR, whereas overexpression of wild-type and mutated BCOR with the same frameshift mutation in HPdLFs altered bone morphogenetic protein 2 (BMP2) expression. CONCLUSIONS Our findings indicate that BCOR mutations regulate the transcription of BCOR via UPF1, which may in turn regulate the expression of BMP2. NMD, caused by a c.3668delC mutation, potentially leads to an OFCD syndrome phenotype, including elongated dental roots.
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Affiliation(s)
- Ryoto Machida
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
| | - Takuya Ogawa
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
| | - Kyaw Min Soe
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
| | - Keiji Moriyama
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
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12
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Villafuerte-de la Cruz RA, Garza-Garza LA, Garza-Leon M, Rodriguez-De la Torre C, Parra-Bernal C, Vazquez-Camas I, Ramos-Gonzalez D, Rangel-Padilla A, Espino Barros-Palau A, Nava-García J, Castillo-Velazquez J, Castillo-De Leon E, Del Valle-Penella A, Valdez-Garcia JE, Rojas-Martinez A. Spectrum of variants associated with inherited retinal dystrophies in Northeast Mexico. BMC Ophthalmol 2024; 24:60. [PMID: 38347443 PMCID: PMC10860328 DOI: 10.1186/s12886-023-03276-7] [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: 08/30/2023] [Accepted: 12/26/2023] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Inherited retinal dystrophies are hereditary diseases which have in common the progressive degeneration of photoreceptors. They are a group of diseases with clinical, genetic, and allelic heterogeneity. There is limited information regarding the genetic landscape of inherited retinal diseases in Mexico, therefore, the present study was conducted in the northeast region of the country. METHODS Patients with inherited retinal dystrophies were included. A complete history, full ophthalmological and medical genetics evaluations, and genetic analysis through a targeted NGS panel for inherited retinal dystrophies comprising at least 293 genes were undertaken. RESULTS A total of 126 patients were included. Cases were solved in 74.6% of the study's population. Retinitis pigmentosa accounted for the most found inherited retinal disease. Ninety-nine causal variants were found, being USH2A and ABCA4 the most affected genes (26 and 15 cases, respectively). CONCLUSIONS The present study documents the most prevalent causative genes in IRDs, as USH2A, in northeastern Mexico. This contrasts with previous reports of IRDs in other zones of the country. Further studies, targeting previously unstudied populations in Mexico are important to document the genetic background of inherited retinal dystrophies in the country.
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Affiliation(s)
- Rocio A Villafuerte-de la Cruz
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
- Destellos de Luz, San Pedro Garza García, México
| | | | - Manuel Garza-Leon
- Destellos de Luz, San Pedro Garza García, México
- Clinical Science Department, Health Sciences Division, University of Monterrey, Monterrey, México
| | - Cesar Rodriguez-De la Torre
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
| | - Cinthya Parra-Bernal
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
| | - Ilse Vazquez-Camas
- Tecnologico de Monterrey, The Institute for Obesity Research, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
- Tecnologico Nacional de Mexico Campus Tuxtla Gutierrez, Tuxtla Gutierrez, Mexico
| | - David Ramos-Gonzalez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
| | - Andrea Rangel-Padilla
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
| | - Angelina Espino Barros-Palau
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
| | - Jose Nava-García
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
| | | | | | | | - Jorge E Valdez-Garcia
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico.
- Tecnologico de Monterrey, The Institute for Obesity Research, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico.
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13
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Ouedraogo ZG, Janel C, Janin A, Millat G, Langlais S, Pontier B, Biard M, Lepage M, Francannet C, Laffargue F, Creveaux I. Relevance of Extending FGFR3 Gene Analysis in Osteochondrodysplasia to Non-Coding Sequences: A Case Report. Genes (Basel) 2024; 15:225. [PMID: 38397214 PMCID: PMC10888313 DOI: 10.3390/genes15020225] [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: 12/20/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Skeletal dysplasia, also called osteochondrodysplasia, is a category of disorders affecting bone development and children's growth. Up to 552 genes, including fibroblast growth factor receptor 3 (FGFR3), have been implicated by pathogenic variations in its genesis. Frequently identified causal mutations in osteochondrodysplasia arise in the coding sequences of the FGFR3 gene: c.1138G>A and c.1138G>C in achondroplasia and c.1620C>A and c.1620C>G in hypochondroplasia. However, in some cases, the diagnostic investigations undertaken thus far have failed to identify the causal anomaly, which strengthens the relevance of the diagnostic strategies being further refined. We observed a Caucasian adult with clinical and radiographic features of achondroplasia, with no common pathogenic variant. Exome sequencing detected an FGFR3(NM_000142.4):c.1075+95C>G heterozygous intronic variation. In vitro studies showed that this variant results in the aberrant exonization of a 90-nucleotide 5' segment of intron 8, resulting in the substitution of the alanine (Ala359) for a glycine (Gly) and the in-frame insertion of 30 amino acids. This change may alter FGFR3's function. Our report provides the first clinical description of an adult carrying this variant, which completes the phenotype description previously provided in children and confirms the recurrence, the autosomal-dominant pathogenicity, and the diagnostic relevance of this FGFR3 intronic variant. We support its inclusion in routinely used diagnostic tests for osteochondrodysplasia. This may increase the detection rate of causal variants and therefore could have a positive impact on patient management. Finally, FGFR3 alteration via non-coding sequence exonization should be considered a recurrent disease mechanism to be taken into account for new drug design and clinical trial strategies.
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Affiliation(s)
- Zangbéwendé Guy Ouedraogo
- Service de Biochimie et Génétique Moléculaire, CHU Gabriel Montpied, CHU Clermont-Ferrand, 63000 Clermont-Ferrand, France; (C.J.); (S.L.); (M.L.)
- Université Clermont Auvergne, CNRS, Inserm, iGReD, 63001 Clermont-Ferrand, France
| | - Caroline Janel
- Service de Biochimie et Génétique Moléculaire, CHU Gabriel Montpied, CHU Clermont-Ferrand, 63000 Clermont-Ferrand, France; (C.J.); (S.L.); (M.L.)
| | - Alexandre Janin
- Unité Fonctionnelle Cardiogénétique, Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, 69677 Bron, France; (A.J.); (G.M.)
- CNRS UMR5261, INSERM U1315, Pathophysiology and Genetics of Neuron and Muscle, Institut Neuromyogène, Université Claude Bernard Lyon 1, 69008 Lyon, France
| | - Gilles Millat
- Unité Fonctionnelle Cardiogénétique, Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, 69677 Bron, France; (A.J.); (G.M.)
- CNRS UMR5261, INSERM U1315, Pathophysiology and Genetics of Neuron and Muscle, Institut Neuromyogène, Université Claude Bernard Lyon 1, 69008 Lyon, France
| | - Sarah Langlais
- Service de Biochimie et Génétique Moléculaire, CHU Gabriel Montpied, CHU Clermont-Ferrand, 63000 Clermont-Ferrand, France; (C.J.); (S.L.); (M.L.)
| | - Bénédicte Pontier
- Service de Génétique Médicale, CHU Estaing, CHU Clermont-Ferrand, 63100 Clermont-Ferrand, France; (B.P.); (C.F.); (F.L.)
| | - Marie Biard
- Service de Radiologie Pédiatrique, CHU Estaing, CHU Clermont-Ferrand, 63100 Clermont-Ferrand, France;
| | - Mathis Lepage
- Service de Biochimie et Génétique Moléculaire, CHU Gabriel Montpied, CHU Clermont-Ferrand, 63000 Clermont-Ferrand, France; (C.J.); (S.L.); (M.L.)
| | - Christine Francannet
- Service de Génétique Médicale, CHU Estaing, CHU Clermont-Ferrand, 63100 Clermont-Ferrand, France; (B.P.); (C.F.); (F.L.)
| | - Fanny Laffargue
- Service de Génétique Médicale, CHU Estaing, CHU Clermont-Ferrand, 63100 Clermont-Ferrand, France; (B.P.); (C.F.); (F.L.)
| | - Isabelle Creveaux
- Service de Biochimie et Génétique Moléculaire, CHU Gabriel Montpied, CHU Clermont-Ferrand, 63000 Clermont-Ferrand, France; (C.J.); (S.L.); (M.L.)
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14
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Yang J, Ni L, Li A, Li M, Ruan S, Xiang D, Zhu Z, Ye L. A novel homozygous splice-site mutation of JK gene leads to Jk(a-b-) phenotype. Transfus Med 2024; 34:39-45. [PMID: 37950522 DOI: 10.1111/tme.13016] [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: 04/28/2023] [Revised: 09/28/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
OBJECTIVES This study aimed to investigate the molecular mechanism of the Jk(a-b-) phenotype in a Chinese transfusion patient. BACKGROUND Many different mutation types relating to Jk(a-b-) phenotype have been reported. However, the splice-site mutation is relatively rare and the related functional verification is lacking. MATERIALS AND METHODS In this study, the blood sample was collected from a transfusion patient with the Jk(a-b-) phenotype. Serotyping was performed using routine serological methods. The exons sequences and coding regions of the JK gene were amplified using polymerase chain reaction and directly sequenced. To perform a minigene splicing assay, the intronic mutation sequences were cloned into a pSPL3 splice reporting vector. The splicing reporter minigene assay was performed in HEK 293T cells. RESULTS The Jk(a-b-) phenotype of the blood sample was identified through serological testing. Sequencing results revealed that the sample had a novel homozygous splice-site mutation JK*02N (NM_015865.7: c.663+3A>C). Further analysis, including cDNA sequencing and minigene splicing assay, confirmed that the novel splice-site mutation resulted in exon skipping. Interestingly, different numbers of exons being skipped were obtained by the two methods. CONCLUSION This study revealed a novel homozygous splicing-site mutation associated with the Jk(a-b-) phenotype in Chinese population. Our results emphasise the importance of the in vitro functional method minigene splicing assay, while also acknowledging its potential limitations when compared to cDNA sequencing.
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Affiliation(s)
- Jiaxuan Yang
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Lina Ni
- Department of Blood Transfusion, Weihai Central Hospital, Weihai, China
| | - Aijing Li
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Minghao Li
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Shulin Ruan
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Dong Xiang
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Ziyan Zhu
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Luyi Ye
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
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15
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Tuncer SB, Celik B, Erciyas SK, Erdogan OS, Gültaslar BK, Odemis DA, Avsar M, Sen F, Saip PM, Yazici H. Germline mutational variants of Turkish ovarian cancer patients suspected of Hereditary Breast and Ovarian Cancer (HBOC) by next-generation sequencing. Pathol Res Pract 2024; 254:155075. [PMID: 38219492 DOI: 10.1016/j.prp.2023.155075] [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: 08/25/2023] [Revised: 12/11/2023] [Accepted: 12/29/2023] [Indexed: 01/16/2024]
Abstract
Hereditary Breast and Ovarian Cancer (HBOC) syndrome is characterized by an increased risk of developing breast cancer (BC) and ovarian cancer (OC) due to inherited genetic mutations. Understanding the genetic variants associated with HBOC is crucial for identifying individuals at high risk and implementing appropriate preventive measures. The study included 630 Turkish OC patients with confirmed diagnostic criteria of The National Comprehensive Cancer Network (NCCN) concerning HBOC. Genomic DNA was extracted from peripheral blood samples, and targeted Next-generation sequencing (NGS) was performed. Bioinformatics analysis and variant interpretation were conducted to identify pathogenic variants (PVs). Our analysis revealed a spectrum of germline pathogenic variants associated with HBOC in Turkish OC patients. Notably, several pathogenic variants in BRCA1, BRCA2, and other DNA repair genes were identified. Specifically, we observed germline PVs in 130 individuals, accounting for 20.63% of the total cohort. 76 distinct PVs in genes, BRCA1 (40 PVs), BRCA2 (29 PVs), ATM (1 PV), CHEK2 (2 PVs), ERCC2 (1 PV), MUTYH (1 PV), RAD51C (1 PV), and TP53 (1PV) and also, two different PVs (i.e., c.135-2 A>G p.? in BRCA1 and c.6466_6469delTCTC in BRCA2) were detected in a 34-year-old OC patient. In conclusion, our study contributes to a better understanding of the genetic variants underlying HBOC in Turkish OC patients. These findings provide valuable insights into the genetic architecture of HBOC in the Turkish population and shed light on the potential contribution of specific germline PVs to the increased risk of OC.
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Affiliation(s)
- Seref Bugra Tuncer
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye.
| | - Betul Celik
- Erzincan Binali Yıldırım University, Department of Molecular Biology, Erzincan, Türkiye
| | - Seda Kilic Erciyas
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Ozge Sukruoglu Erdogan
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Busra Kurt Gültaslar
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Demet Akdeniz Odemis
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Mukaddes Avsar
- Health Services Vocational of Higher Education, T.C. Istanbul Aydın University, Istanbul, Türkiye
| | - Fatma Sen
- Clinic of Medical Oncology, Avrasya Hospital, Istanbul, Türkiye
| | - Pınar Mualla Saip
- Department of Medical Oncology, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Hulya Yazici
- Istanbul Arel University, Arel Medical Faculty, Department of Medical Biology and Genetics, Istanbul, Türkiye
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16
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Spurná Z, Čapková P, Punová L, DuchoslavovÁ J, Aleksijevic D, Venháčová P, Srovnal J, Štellmachová J, Curtisová V, Bitnerová V, Petřková J, Kolaříková K, Janíková M, Kratochvílová R, Vrtěl P, Vodička R, Vrtěl R, Zapletalová J. Clinical-genetic analysis of selected genes involved in the development of the human skeleton in 128 Czech patients with suspected congenital skeletal abnormalities. Gene 2024; 892:147881. [PMID: 37806643 DOI: 10.1016/j.gene.2023.147881] [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: 06/01/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Congenital skeletal abnormalities are a heterogeneous group of diseases most commonly associated with small or disproportionate growth, cranial and facial dysmorphisms, delayed bone maturation, etc. Nonetheless, no detailed genotype-phenotype correlation in patients with specific genetic variants is readily available. Ergo, this study focuses on the analysis of patient phenotypes with candidate variants in genes involved in bone growth as detected by molecular genetic analysis. METHODS In this study we used molecular genetic methods to analyse the ACAN, COL2A1, FGFR3, IGFALS, IGF1, IGF1R, GHR, NPR2, STAT5B and SHOX genes in 128 Czech children with suspected congenital skeletal abnormalities. Pathogenic variants and variants of unclear clinical significance were identified and we compared their frequency in this study cohort to the European non-Finnish population. Furthermore, a prediction tool was utilised to determine their possible impact on the final protein. All clinical patient data was obtained during pre-test genetic counselling. RESULTS Pathogenic variants were identified in the FGFR3, GHR, COL2A1 and SHOX genes in a total of six patients. Furthermore, we identified 23 variants with unclear clinical significance and high allelic frequency in this cohort of patients with skeletal abnormalities. Five of them have not yet been reported in the scientific literature. CONCLUSION Congenital skeletal abnormalities may lead to a number of musculoskeletal, neurological, cardiovascular problems. Knowledge of specific pathogenic variants may help us in therapeutic procedures.
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Affiliation(s)
- Z Spurná
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - P Čapková
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic.
| | - L Punová
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - J DuchoslavovÁ
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - D Aleksijevic
- Paediatrics Department, Palacký University and University Hospital, Olomouc, Czech Republic
| | - P Venháčová
- Paediatrics Department, Palacký University and University Hospital, Olomouc, Czech Republic
| | - J Srovnal
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic; Institute of Molecular and Translational Medicine, Czech Advanced Technology and Research Institute, Palacky University in Olomouc, Czech Republic; Cancer Research Czech Republic, Olomouc, Czech Republic
| | - J Štellmachová
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - V Curtisová
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - V Bitnerová
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - J Petřková
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; First Department of Internal Medicine - Cardiology, University Hospital Olomouc, Olomouc, Czech Republic; First Department of Internal Medicine - Cardiology, Palacký University in Olomouc, Olomouc, Czech Republic; Institute of Pathological Physiology, Palacký University in Olomouc, Olomouc, Czech Republic
| | - K Kolaříková
- Department of Neurology, University Hospital Olomouc, Czech Republic; Department of Neurology, Palacky University Olomouc, Czech Republic
| | - M Janíková
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic; Institute of Clinical and Molecular Pathology, Palacký University in Olomouc, Olomouc, Czech Republic
| | - R Kratochvílová
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic
| | - P Vrtěl
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - R Vodička
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - R Vrtěl
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - J Zapletalová
- Paediatrics Department, Palacký University and University Hospital, Olomouc, Czech Republic
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17
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Fernández-Castillejo S, Roig B, Melé M, Serrano S, Salvat M, Querol M, Brunet J, Pineda M, Cisneros A, Parada D, Badia J, Borràs J, Rodríguez-Balada M, Gumà J. Opportunistic genetic screening increases the diagnostic yield and is medically valuable for care of patients and their relatives with hereditary cancer. J Med Genet 2023; 61:69-77. [PMID: 37591735 PMCID: PMC10803988 DOI: 10.1136/jmg-2023-109389] [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: 05/10/2023] [Accepted: 07/23/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Multigene panel testing by next-generation sequencing (MGP-NGS) enables the detection of germline pathogenic or likely pathogenic variants (PVs/LPVs) in genes beyond those associated with a certain cancer phenotype. Opportunistic genetic screening based on MGP-NGS in patients with suspicion of hereditary cancer reveals these incidental findings (IFs). METHODS MGP-NGS was performed in patients who fulfilled the clinical criteria to undergo genetic testing according to the Catalan Health Service guidelines. Variants were classified following the American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines and the Cancer Variant Interpretation Group UK guidelines. RESULTS IFs were identified in 10 (1.22%) of the 817 patients who underwent MGP-NGS. The mean age at cancer diagnosis was 49.4±9.5 years. Three IFs (30.0%) were detected in PMS2, two (20.0%) in ATM and TP53 and one (10.0%) in MSH6, NTHL1 and VHL. Seven (70.0%) IFs were single-nucleotide substitutions, two (20.0%) were deletions and one (10.0%) was a duplication. Three (30.0) IFs were located in intronic regions, three (30.3%) were nonsense, two (20.0%) were frameshift and two (20.0%) were missense variations. Six (60.0%) IFs were classified as PVs and four (40.0%) as LPVs. CONCLUSIONS Opportunistic genetic screening increased the diagnostic yield by 1.22% in our cohort. Most of the identified IFs were present in clinically actionable genes (n=7; 70.0%), providing these families with an opportunity to join cancer early detection programmes, as well as secondary cancer prevention. IFs might facilitate the diagnosis of asymptomatic individuals and the early management of cancer once it develops.
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Affiliation(s)
- Sara Fernández-Castillejo
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Bàrbara Roig
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Mireia Melé
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Sara Serrano
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Mònica Salvat
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Montserrat Querol
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and Biomedical Research Centre Network for Oncology (CIBERONC), L'Hospitalet de Llobregat, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBGI, Girona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and Biomedical Research Centre Network for Oncology (CIBERONC), L'Hospitalet de Llobregat, Spain
| | - Adela Cisneros
- Hematology Department, ICO and Hospital Germans Trias i Pujol, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - David Parada
- Pathology Molecular Unit, Department of Pathology, Hospital Universitari Sant Joan de Reus (HUSJR), Spain. Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Joan Badia
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Joan Borràs
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Marta Rodríguez-Balada
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Josep Gumà
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
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18
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Hiramoto T, Inaba H, Baatartsogt N, Kashiwakura Y, Hayakawa M, Kamoshita N, Nishimasu H, Nureki O, Kinai E, Ohmori T. Genome editing of patient-derived iPSCs identifies a deep intronic variant causing aberrant splicing in hemophilia A. Blood Adv 2023; 7:7017-7027. [PMID: 37792826 PMCID: PMC10690555 DOI: 10.1182/bloodadvances.2023010838] [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: 05/30/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023] Open
Abstract
The importance of genetic diagnosis for patients with hemophilia has been recently demonstrated. However, the pathological variant cannot be identified in some patients. Here, we aimed to identify the pathogenic intronic variant causing hemophilia A using induced pluripotent stem cells (iPSCs) from patients and genome editing. We analyzed siblings with moderate hemophilia A and without abnormalities in the F8 exon. Next-generation sequencing of the entire F8 revealed 23 common intron variants. Variant effect predictor software indicated that the deep intronic variant at c.5220-8563A>G (intron 14) might act as a splicing acceptor. We developed iPSCs from patients and used genome editing to insert the elongation factor 1α promoter to express F8 messenger RNA (mRNA). Then, we confirmed the existence of abnormal F8 mRNA derived from aberrant splicing, resulting in a premature terminal codon as well as a significant reduction in F8 mRNA in iPSCs due to nonsense-mediated RNA decay. Gene repair by genome editing recovered whole F8 mRNA expression. Introduction of the intron variant into human B-domain-deleted F8 complementary DNA suppressed factor VIII (FVIII) activity and produced abnormal FVIII lacking the light chain in HEK293 cells. Furthermore, genome editing of the intron variant restored FVIII production. In summary, we have directly proven that the deep intronic variant in F8 results in aberrant splicing, leading to abnormal mRNA and nonsense-mediated RNA decay. Additionally, genome editing targeting the variant restored F8 mRNA and FVIII production. Our approach could be useful not only for identifying causal variants but also for verifying the therapeutic effect of personalized genome editing.
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Affiliation(s)
- Takafumi Hiramoto
- Department of Biochemistry, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | - Hiroshi Inaba
- Department of Laboratory Medicine, Tokyo Medical University, Tokyo, Japan
| | - Nemekhbayar Baatartsogt
- Department of Biochemistry, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | - Yuji Kashiwakura
- Department of Biochemistry, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | - Morisada Hayakawa
- Department of Biochemistry, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
- Center for Gene Therapy Research, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Nobuhiko Kamoshita
- Department of Biochemistry, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
- Center for Gene Therapy Research, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Hiroshi Nishimasu
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ei Kinai
- Department of Laboratory Medicine, Tokyo Medical University, Tokyo, Japan
| | - Tsukasa Ohmori
- Department of Biochemistry, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
- Center for Gene Therapy Research, Jichi Medical University, Shimotsuke, Tochigi, Japan
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19
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Henry Z, Janin A, Nony S, Marmontel O, Cariou B, Marrec M, Caussy C, Charrière S, Moulin P, Rieusset J, Perros F, Di Filippo M. Interest of minigene splicing reporter assay in familial hypobetalipoproteinemia genetic diagnosis: the example of the missense mutation APOB c.1468C>T. Clin Chem Lab Med 2023; 61:e259-e262. [PMID: 37309596 DOI: 10.1515/cclm-2023-0330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/02/2023] [Indexed: 06/14/2023]
Affiliation(s)
- Zoé Henry
- Service de Biochimie et Biologie Moléculaire, Laboratoire de Biologie Médicale MultiSites, Hospices Civils de Lyon, Bron, France
- Fédération d'endocrinologie, maladies métaboliques, diabète et nutrition, Hôpital Louis Pradel, Hospices Civils de Lyon, Bron, France
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Claude Bernard Lyon 1, Pierre-Bénite, France
| | - Alexandre Janin
- Service de Biochimie et Biologie Moléculaire, Laboratoire de Biologie Médicale MultiSites, Hospices Civils de Lyon, Bron, France
- CNRS UMR5261, INSERM U1315, Institut NeuroMyoGène, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Séverine Nony
- Service de Biochimie et Biologie Moléculaire, Laboratoire de Biologie Médicale MultiSites, Hospices Civils de Lyon, Bron, France
| | - Oriane Marmontel
- Service de Biochimie et Biologie Moléculaire, Laboratoire de Biologie Médicale MultiSites, Hospices Civils de Lyon, Bron, France
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Claude Bernard Lyon 1, Pierre-Bénite, France
| | - Bertrand Cariou
- Nantes Université, CHU Nantes, CNRS, INSERM, L'institut du Thorax, Nantes, France
| | - Marie Marrec
- Nantes Université, CHU Nantes, CNRS, INSERM, L'institut du Thorax, Nantes, France
| | - Cyrielle Caussy
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Claude Bernard Lyon 1, Pierre-Bénite, France
- Hôpital Lyon Sud, Département Endocrinologie, Diabète et Nutrition, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Sybil Charrière
- Fédération d'endocrinologie, maladies métaboliques, diabète et nutrition, Hôpital Louis Pradel, Hospices Civils de Lyon, Bron, France
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Claude Bernard Lyon 1, Pierre-Bénite, France
| | - Philippe Moulin
- Fédération d'endocrinologie, maladies métaboliques, diabète et nutrition, Hôpital Louis Pradel, Hospices Civils de Lyon, Bron, France
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Claude Bernard Lyon 1, Pierre-Bénite, France
| | - Jennifer Rieusset
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Claude Bernard Lyon 1, Pierre-Bénite, France
| | - Frédéric Perros
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Claude Bernard Lyon 1, Pierre-Bénite, France
| | - Mathilde Di Filippo
- Service de Biochimie et Biologie Moléculaire, Laboratoire de Biologie Médicale MultiSites, Hospices Civils de Lyon, Bron, France
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Claude Bernard Lyon 1, Pierre-Bénite, France
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20
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Zhang Z, Tong F, Chen C, Zhang T, Qian G, Yang X, Huang X, Yang R, Zhao Z. Long-term follow-up of children with carbamoyl phosphate synthase 1 deficiency detected in newborn screening. Zhejiang Da Xue Xue Bao Yi Xue Ban 2023; 52:721-726. [PMID: 37986659 PMCID: PMC10764181 DOI: 10.3724/zdxbyxb-2023-0359] [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: 08/01/2023] [Accepted: 10/05/2023] [Indexed: 11/22/2023]
Abstract
OBJECTIVES To investigate genotype-phenotype characteristics and long-term prognosis of neonatal carbamoyl phosphate synthetase 1 (CPS1) deficiency among children through newborn screening in Zhejiang province. METHODS The clinical and follow-up data of children with CPS1 deficiency detected through neonatal screening and confirmed by tandem mass spectrometry and genetic testing in Zhejiang Province Newborn Disease Screening Center from September 2013 to August 2023 were retrospectively analyzed. RESULTS A total of 4 056 755 newborns were screened and 6 cases of CPS1 deficiency were diagnosed through phenotypic and genetic testing. Ten different variations of CPS1 genewere identified in genetic testing, including 2 known pathogenic variations (c.2359C>T and c.1549+1G>T) and 8 unreported variations (c.3405-1G>T, c.2372C>T, c.1436C>T, c.2228T>C, c.2441G>A, c.3031G>A, c.3075T>C and c.390-403del). All patients had decreased citrulline levels (2.72-6.21 μmol/L), and varying degrees of elevated blood ammonia. The patients received restricted natural protein intake (special formula), arginine and supportive therapy after diagnosis, and were followed-up for a period ranging from 9 months to 10 years. Three patients experienced hyperammonemia, and one patient each had attention deficit hyperactivity disorder, transient facial twitching and increased muscle tone. One patient died, while the other five surviving patients had normal scores of the Ages & Stages Questionnaires (ASQ) and Griffiths Development Scales up to the present time; 4 cases had combined height or weight lag and one case was normal in height and weight. CONCLUSIONS Low citrulline levels and hyperammonemia are common in CPS1 deficiency patients in Zhejiang. Most gene variants identified were specific to individual families, and no hotspot mutations were found. Early diagnosis through newborn screening and following standardized treatment can significantly improve the prognosis of the patients.
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Affiliation(s)
- Zhanming Zhang
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China.
| | - Fan Tong
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Chi Chen
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Ting Zhang
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Guling Qian
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Xin Yang
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Xinwen Huang
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Rulai Yang
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Zhengyan Zhao
- Department of Genetic and Metabolism,Children's Hospital,Zhejiang University School of Medicine,National Clinical Research Center for Child Health, Hangzhou 310052, China.
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21
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Drehmann P, Milanos S, Schaefer N, Kasaragod VB, Herterich S, Holzbach-Eberle U, Harvey RJ, Villmann C. Dual Role of Dysfunctional Asc-1 Transporter in Distinct Human Pathologies, Human Startle Disease, and Developmental Delay. eNeuro 2023; 10:ENEURO.0263-23.2023. [PMID: 37903619 PMCID: PMC10668224 DOI: 10.1523/eneuro.0263-23.2023] [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: 07/27/2023] [Accepted: 09/11/2023] [Indexed: 11/01/2023] Open
Abstract
Human startle disease is associated with mutations in distinct genes encoding glycine receptors, transporters or interacting proteins at glycinergic synapses in spinal cord and brainstem. However, a significant number of diagnosed patients does not carry a mutation in the common genes GLRA1, GLRB, and SLC6A5 Recently, studies on solute carrier 7 subfamily 10 (SLC7A10; Asc-1, alanine-serine-cysteine transporter) knock-out (KO) mice displaying a startle disease-like phenotype hypothesized that this transporter might represent a novel candidate for human startle disease. Here, we screened 51 patients from our patient cohort negative for the common genes and found three exonic (one missense, two synonymous), seven intronic, and single nucleotide changes in the 5' and 3' untranslated regions (UTRs) in Asc-1. The identified missense mutation Asc-1G307R from a patient with startle disease and developmental delay was investigated in functional studies. At the molecular level, the mutation Asc-1G307R did not interfere with cell-surface expression, but disrupted glycine uptake. Substitution of glycine at position 307 to other amino acids, e.g., to alanine or tryptophan did not affect trafficking or glycine transport. By contrast, G307K disrupted glycine transport similar to the G307R mutation found in the patient. Structurally, the disrupted function in variants carrying positively charged residues can be explained by local structural rearrangements because of the large positively charged side chain. Thus, our data suggest that SLC7A10 may represent a rare but novel gene associated with human startle disease and developmental delay.
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Affiliation(s)
- Paul Drehmann
- Institute for Clinical Neurobiology, Julius Maximilians University of Würzburg, 97078 Würzburg, Germany
| | - Sinem Milanos
- Institute for Clinical Neurobiology, Julius Maximilians University of Würzburg, 97078 Würzburg, Germany
| | - Natascha Schaefer
- Institute for Clinical Neurobiology, Julius Maximilians University of Würzburg, 97078 Würzburg, Germany
| | - Vikram Babu Kasaragod
- Neurobiology Division, Medical Reserach Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Sarah Herterich
- Institute for Clinical Neurobiology, Julius Maximilians University of Würzburg, 97078 Würzburg, Germany
| | - Ulrike Holzbach-Eberle
- Center for Pediatrics and Adolescent Medicine, Pediatric Neurology, Social Pediatrics and Epileptology, University Hospital Gießen, 35392 Giessen, Germany
| | - Robert J Harvey
- School of Health, University of the Sunshine Coast, Sippy Downs, QLD 4558, Australia
- Sunshine Coast Health Institute, Birtinya, QLD 4575, Australia
| | - Carmen Villmann
- Institute for Clinical Neurobiology, Julius Maximilians University of Würzburg, 97078 Würzburg, Germany
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22
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He T, Yao Q, Xu B, Yang M, Jiang J, Xiang Q, Xiao L, Liu S, Wang H, Zhang X. A novel splicing variation in L1CAM is responsible for recurrent fetal hydrocephalus. Mol Genet Genomic Med 2023; 11:e2253. [PMID: 37489051 PMCID: PMC10655515 DOI: 10.1002/mgg3.2253] [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: 11/24/2021] [Revised: 02/20/2023] [Accepted: 07/13/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND The L1 cell adhesion molecule (L1CAM, OMIM 308840) gene is primarily expressed in the nervous system and encodes the L1 adhesion molecule protein. Variations in L1CAM cause a wide spectrum of X-linked neurological disorders summarized as the L1 syndrome. METHODS We report a 29-year-old pregnant woman who experienced multiple adverse pregnancy outcomes due to recurrent fetal hydrocephalus with an X-linked recessive inheritance. Genomic DNA was extracted from the third aborted male fetus and analyzed via trio whole-exome sequencing (WES). Total RNA was isolated from the pregnant woman to assess splicing variation at the mRNA level, and amniotic fluid was extracted from the woman for prenatal diagnosis on her fourth fetus. RESULTS All four male fetuses were affected by severe hydrocephalus. We identified a maternally derived hemizygous splicing variation NM_000425.5:[c.3046 + 1G > A]; NP_000416.1 p.(Gly1016AspfsTer6) (chrX:153130275) in Intron 22 of the L1CAM. This variation disrupts the donor splice site and causes the retention of Intron 22, which results in frame shift and a premature termination codon at position 1021 with the ability to produce a truncated protein without the fifth fibronectin-repeat III, transmembrane, and cytoplasmic domains or to induce the degradation of mRNAs by nonsense-mediated mRNA decay. The same hemizygous variant was also detected in the amniocytes. CONCLUSION This report enhances our knowledge of genetic and phenotypic characteristics of X-linked fetal hydrocephalus, providing a new genetic basis for prenatal diagnosis and pre-implantation prenatal diagnosis.
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Affiliation(s)
- Tiantian He
- Department of Medical Genetics & Prenatal Diagnosis CenterWest China Second University Hospital, Sichuan UniversityChengduChina
- Department of Obstetrics and GynecologyWest China Second University Hospital, Sichuan UniversityChengduChina
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of EducationChengduChina
| | - Qiang Yao
- Department of Obstetrics and GynecologyWest China Second University Hospital, Sichuan UniversityChengduChina
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of EducationChengduChina
| | - Bocheng Xu
- Department of Medical Genetics & Prenatal Diagnosis CenterWest China Second University Hospital, Sichuan UniversityChengduChina
- Department of Obstetrics and GynecologyWest China Second University Hospital, Sichuan UniversityChengduChina
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of EducationChengduChina
| | - Mei Yang
- Department of Medical Genetics & Prenatal Diagnosis CenterWest China Second University Hospital, Sichuan UniversityChengduChina
- Department of Obstetrics and GynecologyWest China Second University Hospital, Sichuan UniversityChengduChina
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of EducationChengduChina
| | - Jieni Jiang
- Department of Medical Genetics & Prenatal Diagnosis CenterWest China Second University Hospital, Sichuan UniversityChengduChina
- Department of Obstetrics and GynecologyWest China Second University Hospital, Sichuan UniversityChengduChina
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of EducationChengduChina
| | - Qingqing Xiang
- Department of Medical Genetics & Prenatal Diagnosis CenterWest China Second University Hospital, Sichuan UniversityChengduChina
- Department of Obstetrics and GynecologyWest China Second University Hospital, Sichuan UniversityChengduChina
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of EducationChengduChina
| | - Like Xiao
- Department of Medical Genetics & Prenatal Diagnosis CenterWest China Second University Hospital, Sichuan UniversityChengduChina
- Department of Obstetrics and GynecologyWest China Second University Hospital, Sichuan UniversityChengduChina
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of EducationChengduChina
| | - Shanling Liu
- Department of Medical Genetics & Prenatal Diagnosis CenterWest China Second University Hospital, Sichuan UniversityChengduChina
- Department of Obstetrics and GynecologyWest China Second University Hospital, Sichuan UniversityChengduChina
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of EducationChengduChina
| | - He Wang
- Department of Medical Genetics & Prenatal Diagnosis CenterWest China Second University Hospital, Sichuan UniversityChengduChina
- Department of Obstetrics and GynecologyWest China Second University Hospital, Sichuan UniversityChengduChina
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of EducationChengduChina
| | - Xuemei Zhang
- Department of Medical Genetics & Prenatal Diagnosis CenterWest China Second University Hospital, Sichuan UniversityChengduChina
- Department of Obstetrics and GynecologyWest China Second University Hospital, Sichuan UniversityChengduChina
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of EducationChengduChina
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23
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Yang W, Chen X, Zhou Y, Tang X, Sun Y, Dong Y, Yang H, Chen Y, Zhang M. Investigation of a Fused in Sarcoma Splicing Mutation in a Chinese Amyotrophic Lateral Sclerosis Patient. Can J Neurol Sci 2023; 50:891-896. [PMID: 36511129 DOI: 10.1017/cjn.2022.336] [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] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Genetic mutations of fused in sarcoma (FUS) causing amyotrophic lateral sclerosis (ALS) may disrupt mRNA splicing events. For example, the FUS c.1394-2delA variant was reported in two western ALS patients, but its molecular mechanism is unclear. In this study, we aim to investigate FUS splice site mutations in Chinese ALS patients. METHODS Sanger sequencing was used to identify FUS splicing mutations in Chinese ALS patients. We combined a deep learning tool (SpliceAI), RNA sequencing, and RT-PCR/RT-qPCR to analyze the effect of FUS c.1394-2delA mutation on RNA splicing and expression. AlphaFold was used to predict the protein structure of mutant FUS. In transfected cell lines, we used immunofluorescence to assess cytoplasmic mislocalization of mutant FUS protein. RESULTS We identified a de novo FUS splice acceptor site mutation (c.1394-2delA, p. Gly466Valfs*14) in one Chinese sporadic ALS patient, which is linked to exon 14 skipping, and upregulated total FUS mRNA expression. The FUS splice site mutation was predicted to be translated into a truncated protein product at C-terminal. In vitro studies revealed that the FUS mutation increased cytoplasmic mislocalization in both HEK293T and SH-SY5Y cells. CONCLUSIONS We identified a de novo FUS splicing mutation (c.1394-2delA, p. Gly466Valfs*14) in 1 out of 233 Chinese ALS patients. It caused abnormal RNA splicing, upregulated gene expression, truncated FUS translation, and cytosolic mislocalization. Our findings suggested that FUS splice site mutation is rare in Chinese ALS patients and extended our knowledge of molecular mechanisms of the FUS c.1394-2delA mutation.
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Affiliation(s)
- Wanli Yang
- The First Rehabilitation Hospital of Shanghai, Department of Medical Genetics, School of Medicine, Tongji University, Shanghai, China
| | - Xi Chen
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, China
| | - Yu Zhou
- The First Rehabilitation Hospital of Shanghai, Department of Medical Genetics, School of Medicine, Tongji University, Shanghai, China
| | - Xuelin Tang
- The First Rehabilitation Hospital of Shanghai, Department of Medical Genetics, School of Medicine, Tongji University, Shanghai, China
| | - Yimin Sun
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, China
| | - Yi Dong
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, China
| | - Hong Yang
- The First Rehabilitation Hospital of Shanghai, Department of Medical Genetics, School of Medicine, Tongji University, Shanghai, China
| | - Yan Chen
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, China
| | - Ming Zhang
- The First Rehabilitation Hospital of Shanghai, Department of Medical Genetics, School of Medicine, Tongji University, Shanghai, China
- Clinical Center for Brain and Spinal Cord Research, Tongji University, Shanghai, China
- Institute for Advanced Study, Tongji University, Shanghai, China
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24
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Chen X, Qu H, Yao Q, Cai X, He T, Zhang X. Case report: Analysis of a gene variant and prenatal diagnosis in a family with megalencephalic leukoencephalopathy with subcortical cysts. Front Neurol 2023; 14:1253398. [PMID: 37928140 PMCID: PMC10622957 DOI: 10.3389/fneur.2023.1253398] [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: 07/05/2023] [Accepted: 09/18/2023] [Indexed: 11/07/2023] Open
Abstract
Megalencephalic leukoencephalopathy with subcortical cysts (MLC) is a rare inherited cerebral white matter disorder in children. Pathogenic variations in the causative gene MLC1 are found in approximately 76% of patients and are inherited in an autosomal recessive manner. In this study, we identified an IVS2 + 1delG variant in MLC1 in the firstborn girl of a pregnant woman who has the clinical features of MLC, including macrocephaly, motor development delay, progressive functional deterioration, and myelinopathy, whereas no obvious subcortical cysts were observed by magnetic resonance imaging of the brain. The proband is homozygous for the IVS2 + 1delG mutation, which was inherited from the parents. This variant disrupts the donor splice site, causing an abnormal transcript that results in a premature termination codon and produces a truncated protein, which was confirmed to affect splicing by MLC1 cDNA analysis. This variant was also detected in family members, and a prenatal diagnosis for the fetus was undertaken. Eventually, the couple gave birth to an unaffected baby. Furthermore, we conducted a long-term follow-up of the proband's clinical course. This report improves our understanding of the genetic and phenotypic characteristics of MLC and provides a new genetic basis for prenatal diagnosis and genetic counseling.
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Affiliation(s)
- Xi Chen
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Haibo Qu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Radiology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Qiang Yao
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xiaotang Cai
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Rehabilitation, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Tiantian He
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xuemei Zhang
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
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25
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Akbar F, Saleem SM, Khalid E, Ibrahim S, Afroze B, Kirmani S, Khan S. The spectrum of hereditary neuromuscular disorders in the Pakistani population. Am J Med Genet A 2023; 191:2536-2550. [PMID: 37366078 DOI: 10.1002/ajmg.a.63332] [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: 03/02/2023] [Revised: 05/21/2023] [Accepted: 06/07/2023] [Indexed: 06/28/2023]
Abstract
Hereditary neuromuscular disorders (NMDs) are a broad group of clinically heterogeneous disorders with varying inheritance patterns, that are associated with over 500 implicated genes. In the context of a highly consanguineous Pakistani population, we expect that autosomal recessive NMDs may have a higher prevalence compared with patients of European descent. This is the first study to offer a detailed description of the spectrum of genes causing hereditary NMDs in the Pakistani population using NGS testing. To study the clinical and genetic profiles of patients presenting for evaluation of a hereditary neuromuscular disorder. This is a retrospective chart review of patients seen in the Neuromuscular Disorders Clinic and referred to the Genetics Clinic with a suspected hereditary neuromuscular disorder, between 2016 and 2020 at the Aga Khan University Hospital, Karachi and Mukhtiar A. Sheikh Hospital, Multan, Pakistan. The genetic testing for these patients included NGS-based single gene sequencing, NGS-based multi-gene panel and whole exome sequencing. In a total of 112 patients studied, 35 (31.3%) were female. The mean age of onset in all patients was 14.6 years (SD ±12.1 years), with the average age at presentation to the clinic of 22.4 years (SD ±14.10 years). Forty-seven (41.9%) patients had a positive genetic test result, 53 (47.3%) had one or more variants of uncertain significance (VUS), and 12 (10.7%) had a negative result. Upon further genotype-phenotype correlation and family segregation analysis, the diagnostic yield improved, with 59 (52.7%) patients reaching a diagnosis of a hereditary NMD. We also report probable founder variants in COL6A2, FKTN, GNE, and SGCB, previously reported in populations that have possible shared ancestry with the Pakistani population. Our findings reemphasizes that the rate of VUSs can be reduced by clinical correlation and family segregation studies.
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Affiliation(s)
- Fizza Akbar
- Division of Women and Child Health, The Aga Khan University, Karachi, Pakistan
| | | | | | - Shahnaz Ibrahim
- Department of Paediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Bushra Afroze
- Department of Paediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Salman Kirmani
- Division of Women and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Sara Khan
- Department of Neurology, The Aga Khan University, Karachi, Pakistan
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26
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Liu Y, Qu HQ, Chang X, Mentch FD, Qiu H, Wang X, Saeidian AH, Watson D, Glessner J, Hakonarson H. Genomic variants exclusively identified in children with birth defects and concurrent malignant tumors predispose to cancer development. Mol Cancer 2023; 22:126. [PMID: 37543594 PMCID: PMC10403830 DOI: 10.1186/s12943-023-01828-5] [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: 05/16/2023] [Accepted: 07/18/2023] [Indexed: 08/07/2023] Open
Abstract
Children with birth defects (BD) express distinct clinical features that often have various medical consequences, one of which is predisposition to the development of cancers. Identification of the underlying genetic mechanisms related to the development of cancer in BD patients would allow for preventive measures. We performed a whole genome sequencing (WGS) study on blood-derived DNA samples from 1566 individuals without chromosomal anomalies, including 454 BD probands with at least one type of malignant tumors, 767 cancer-free BD probands, and 345 healthy individuals. Exclusive recurrent variants were identified in BD-cancer and BD-only patients and mapped to their corresponding genomic regions. We observed statistically significant overlaps for protein-coding/ncRNA with exclusive variants in exons, introns, ncRNAs, and 3'UTR regions. Exclusive exonic variants, especially synonymous variants, tend to occur in prior exons locus in BD-cancer children. Intronic variants close to splicing site (< 500 bp from exon) have little overlaps in BD-cancer and BD-only patients. Exonic variants in non-coding RNA (ncRNA) tend to occur in different ncRNAs exons regardless of the overlaps. Notably, genes with 5' UTR variants are almost mutually exclusive between the two phenotypes. In conclusion, we conducted the first genomic study to explore the impact of recurrent variants exclusive to the two distinguished clinical phenotypes under study, BD with or without cancer, demonstrating enrichment of selective protein-coding/ncRNAs differentially expressed between these two phenotypes, suggesting that selective genetic factors may underlie the molecular processes of pediatric cancer development in BD children.
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Affiliation(s)
- Yichuan Liu
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA.
| | - Hui-Qi Qu
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
| | - Xiao Chang
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
| | - Frank D Mentch
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
| | - Haijun Qiu
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
| | - Xiang Wang
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
| | - Amir Hossein Saeidian
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
| | - Deborah Watson
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Joseph Glessner
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA.
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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27
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Houssaini H, Bouallegui E, Abida O, Tahri S, Elloumi N, Hachicha H, Marzouk S, Bahloul Z, Masmoudi H, Fakhfakh R. ICOS gene polymorphisms in systemic lupus erythematosus: A case-control study. Int J Immunogenet 2023; 50:194-205. [PMID: 37338463 DOI: 10.1111/iji.12625] [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: 02/06/2023] [Revised: 05/23/2023] [Accepted: 06/11/2023] [Indexed: 06/21/2023]
Abstract
The inducible T-cell costimulator (ICOS) may play an important role in adaptive immunity by regulating the interaction between T cells and antigen-presenting cells. Disruption of this molecule can lead to autoimmune diseases, in particular systemic lupus erythematosus (SLE). In this study, we aimed to explore the possible association between ICOS gene polymorphisms and SLE as well as their influence on disease susceptibility and clinical outcomes. A further objective was to assess the potential impact of these polymorphisms on RNA expression. A case-control study, including 151 patients with SLE, and 291 unrelated healthy controls (HC) matched in gender, and geographical origin, was performed to genotype two polymorphisms located in the ICOS gene: rs11889031 (-693 G/A) and rs10932029 (IVS1 + 173 T/C); using the polymerase chain reaction (PCR)-restriction fragment length polymorphism method. The different genotypes were validated by direct sequencing. The expression level of ICOS mRNA was assessed by quantitative PCR in peripheral blood mononuclear cells of SLE patients and HC. The results were analysed using Shesis and spss.20. Our results revealed a significant association between ICOS gene rs11889031 > CC genotype and SLE disease (codominant genetic model 1, (C/C vs. C/T), p = .001, odds ratio [OR] = 2.18 IC [1.36-3.49]); codominant genetic model 2, (C/C vs. T/T) p = .007, OR = 15.29 IC [1.97-118.5]); dominant genetic model, (C/C vs. C/T + T/T) p = .0001, OR = 2.44 IC [1.53-3.9]). Besides, there was a marginal association between rs11889031 > TT genotype and T allele with a protective role from SLE (recessive genetic model, p = .016, OR = 0.08 IC [0.01-0.63] and p = 7.6904E - 05, OR = 0.43 IC = [0.28-0.66], respectively). Moreover, statistical analysis indicated that the rs11889031 > CC genotype was linked with clinical and serological manifestations of SLE, including blood pressure, and anti-SSA antibodies production in SLE patients. However, the ICOS gene rs10932029 polymorphism was not associated with susceptibility to SLE. On the other side, we did not note any effect of the two selected polymorphisms on the level of ICOS mRNA gene expression. The study showed a significant predisposing association of the ICOS rs11889031 > CC genotype with SLE, in contrast to a protective effect of rs11889031 > TT genotype in Tunisian patients. Our results suggest that ICOS rs11889031 may act as a risk factor for SLE and could be used as a genetic susceptibility biomarker.
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Affiliation(s)
- Hana Houssaini
- Autoimmunity, Cancer, and Immunogenetics Research Laboratory, LR18SP12, Habib Bourguiba University Hospital of Sfax, University of Sfax, Sfax, Tunisia
| | - Emna Bouallegui
- Autoimmunity, Cancer, and Immunogenetics Research Laboratory, LR18SP12, Habib Bourguiba University Hospital of Sfax, University of Sfax, Sfax, Tunisia
| | - Olfa Abida
- Autoimmunity, Cancer, and Immunogenetics Research Laboratory, LR18SP12, Habib Bourguiba University Hospital of Sfax, University of Sfax, Sfax, Tunisia
| | - Safa Tahri
- Autoimmunity, Cancer, and Immunogenetics Research Laboratory, LR18SP12, Habib Bourguiba University Hospital of Sfax, University of Sfax, Sfax, Tunisia
| | - Nesrine Elloumi
- Autoimmunity, Cancer, and Immunogenetics Research Laboratory, LR18SP12, Habib Bourguiba University Hospital of Sfax, University of Sfax, Sfax, Tunisia
| | - Hend Hachicha
- Autoimmunity, Cancer, and Immunogenetics Research Laboratory, LR18SP12, Habib Bourguiba University Hospital of Sfax, University of Sfax, Sfax, Tunisia
- Department of Immunology, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia
| | - Sameh Marzouk
- Internal Medicine Department, HediChaker University Hospital, University of Sfax, Sfax, Tunisia
| | - Zouhir Bahloul
- Internal Medicine Department, HediChaker University Hospital, University of Sfax, Sfax, Tunisia
| | - Hatem Masmoudi
- Autoimmunity, Cancer, and Immunogenetics Research Laboratory, LR18SP12, Habib Bourguiba University Hospital of Sfax, University of Sfax, Sfax, Tunisia
- Department of Immunology, Habib Bourguiba University Hospital, University of Sfax, Sfax, Tunisia
| | - Raouia Fakhfakh
- Autoimmunity, Cancer, and Immunogenetics Research Laboratory, LR18SP12, Habib Bourguiba University Hospital of Sfax, University of Sfax, Sfax, Tunisia
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28
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Gotthardt M, Badillo-Lisakowski V, Parikh VN, Ashley E, Furtado M, Carmo-Fonseca M, Schudy S, Meder B, Grosch M, Steinmetz L, Crocini C, Leinwand L. Cardiac splicing as a diagnostic and therapeutic target. Nat Rev Cardiol 2023; 20:517-530. [PMID: 36653465 DOI: 10.1038/s41569-022-00828-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/09/2022] [Indexed: 01/19/2023]
Abstract
Despite advances in therapeutics for heart failure and arrhythmias, a substantial proportion of patients with cardiomyopathy do not respond to interventions, indicating a need to identify novel modifiable myocardial pathobiology. Human genetic variation associated with severe forms of cardiomyopathy and arrhythmias has highlighted the crucial role of alternative splicing in myocardial health and disease, given that it determines which mature RNA transcripts drive the mechanical, structural, signalling and metabolic properties of the heart. In this Review, we discuss how the analysis of cardiac isoform expression has been facilitated by technical advances in multiomics and long-read and single-cell sequencing technologies. The resulting insights into the regulation of alternative splicing - including the identification of cardiac splice regulators as therapeutic targets and the development of a translational pipeline to evaluate splice modulators in human engineered heart tissue, animal models and clinical trials - provide a basis for improved diagnosis and therapy. Finally, we consider how the medical and scientific communities can benefit from facilitated acquisition and interpretation of splicing data towards improved clinical decision-making and patient care.
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Affiliation(s)
- Michael Gotthardt
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- DZHK (German Center for Cardiovascular Research Partner Site Berlin), Berlin, Germany.
- Department of Cardiology, Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Victor Badillo-Lisakowski
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Center for Cardiovascular Research Partner Site Berlin), Berlin, Germany
| | - Victoria Nicole Parikh
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Euan Ashley
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Palo Alto, CA, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Marta Furtado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Sarah Schudy
- Institute for Cardiomyopathies, Department of Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Benjamin Meder
- Institute for Cardiomyopathies, Department of Medicine III, University of Heidelberg, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research Partner Site Heidelberg-Mannheim), Heidelberg, Germany
| | - Markus Grosch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Lars Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Claudia Crocini
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Leslie Leinwand
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado, Boulder, CO, USA
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29
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Kavousi S, Pourahmadiyan A, Soleymani F, Noruzinia M. Identification of a Novel de novo Splicing Mutation in Duchenne Muscular Dystrophy Gene in an Iranian Family. Mol Syndromol 2023; 14:331-340. [PMID: 37766830 PMCID: PMC10521217 DOI: 10.1159/000528035] [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: 11/23/2021] [Accepted: 11/05/2022] [Indexed: 09/29/2023] Open
Abstract
Introduction Duchenne muscular dystrophy (DMD) (NM_004006.3) is one of the most notable neuromuscular disorders of early years. The majority of DMD cases are caused by deletions or duplications in dystrophin, while point mutations are less prevalent in dystrophin abnormalities. It is a common knowledge that the severity of the disease depends on the effect of the mutation on the translational reading frame of the dystrophin mRNA. Case Report We studied an 8-year-old boy with relevant clinical presentations for DMD. Deletion/duplication screening was performed by using multiplex ligation-dependent probe amplification, and whole-exome sequencing was conducted in order to identify potential variants. A novel de novo splice site variant was identified in the DMD gene (DMD: c.8548-2A>G). To explore the effect of a novel variant in DMD, various in silico analyses were carried out to investigate the pathogenicity of the causative variant. To study the structure of a DMD protein and information on how the genetic variant impacts splicing site in models of wild-type and mutated DMD, we carried out different computational studies. Sanger sequencing was performed for the purpose of variant confirmation and familial segregation analysis. Discussion This novel de novo variant was predicted to have an effect on splicing, which leads to DMD due to its significant impacts on dystrophin functionality. The novel mutation would be expected to disrupt the protein structure.
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Affiliation(s)
- Saeideh Kavousi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | | | | | - Mehrdad Noruzinia
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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30
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Peixoto J, Príncipe C, Pestana A, Osório H, Pinto MT, Prazeres H, Soares P, Lima RT. Using a Dual CRISPR/Cas9 Approach to Gain Insight into the Role of LRP1B in Glioblastoma. Int J Mol Sci 2023; 24:11285. [PMID: 37511044 PMCID: PMC10379115 DOI: 10.3390/ijms241411285] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
LRP1B remains one of the most altered genes in cancer, although its relevance in cancer biology is still unclear. Recent advances in gene editing techniques, particularly CRISPR/Cas9 systems, offer new opportunities to evaluate the function of large genes, such as LRP1B. Using a dual sgRNA CRISPR/Cas9 gene editing approach, this study aimed to assess the impact of disrupting LRP1B in glioblastoma cell biology. Four sgRNAs were designed for the dual targeting of two LRP1B exons (1 and 85). The U87 glioblastoma (GB) cell line was transfected with CRISPR/Cas9 PX459 vectors. To assess LRP1B-gene-induced alterations and expression, PCR, Sanger DNA sequencing, and qRT-PCR were carried out. Three clones (clones B9, E6, and H7) were further evaluated. All clones presented altered cellular morphology, increased cellular and nuclear size, and changes in ploidy. Two clones (E6 and H7) showed a significant decrease in cell growth, both in vitro and in the in vivo CAM assay. Proteomic analysis of the clones' secretome identified differentially expressed proteins that had not been previously associated with LRP1B alterations. This study demonstrates that the dual sgRNA CRISPR/Cas9 strategy can effectively edit LRP1B in GB cells, providing new insights into the impact of LRP1B deletions in GBM biology.
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Grants
- PTDC/MEC-ONC/31520/2017 FEEI, FEDER through COMPETE 2020 -POCI, Portugal 2020, and by Portuguese funds through FCT/Ministério da Ciência, Tecnologia e Ensino Superior
- POCI-01-0145-FEDER-028779 (PTDC/BIA-MIC/28779/2017) FEEI, FEDER through COMPETE 2020 -POCI, Portugal 2020, and by Portuguese funds through FCT/Ministério da Ciência, Tecnologia e Ensino Superior
- project "Institute for Research and Innovation in Health Sciences" (UID/BIM/04293/2019) FEEI, FEDER through COMPETE 2020 -POCI, Portugal 2020, and by Portuguese funds through FCT/Ministério da Ciência, Tecnologia e Ensino Superior
- "Cancer Research on Therapy Resistance: From Basic Mechanisms to Novel Targets"-NORTE-01-0145-FEDER-000051 Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF
- The Porto Comprehensive Cancer Center" with the reference NORTE-01-0145-FEDER-072678 - Consórcio PORTO.CCC - Porto.Comprehensive Cancer Center Raquel Seruca European Regional Development Fund
- ROTEIRO/0028/2013; LISBOA-01-0145-FEDER-022125 Portuguese Mass Spectrometry Network, integrated in the National Roadmap of Research Infra-structures of Strategic Relevance
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Affiliation(s)
- Joana Peixoto
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
| | - Catarina Príncipe
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
- Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Ana Pestana
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
| | - Hugo Osório
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- FMUP-Department of Pathology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Marta Teixeira Pinto
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
| | - Hugo Prazeres
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
| | - Paula Soares
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- FMUP-Department of Pathology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Raquel T Lima
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- FMUP-Department of Pathology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
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Barington M, Dunø M, Birkedal U, Vissing J, Born AP, Krag T, Hansen TVO, Østergaard E. Homozygous splice variant (c.1741-6G>A) of the COL6A1 gene in three patients with Ullrich congenital muscular dystrophy. Neuromuscul Disord 2023; 33:539-545. [PMID: 37315421 DOI: 10.1016/j.nmd.2023.05.007] [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: 01/27/2023] [Revised: 05/09/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023]
Abstract
The three major collagen VI genes: COL6A1, COL6A2, and COL6A3 encode microfibrillar components of extracellular matrices in multiple tissues including muscles and tendons. Pathogenic variants in the collagen VI genes cause collagen VI-related dystrophies representing a continuum of conditions from Bethlem myopathy at the milder end to Ullrich congenital muscular dystrophy at the more severe end. Here we describe a pathogenic variant in the COL6A1 gene (NM_001848.3; c.1741-6G>A) found in homozygosity in three patients with Ullrich congenital muscular dystrophy. The patients suffered from severe muscle impairment characterised by proximal weakness, distal hyperlaxity, joint contractures, wheelchair-dependency, and use of nocturnal non-invasive ventilation. The pathogenicity was verified by RNA analyses showing that the variant induced aberrant splicing leading to a frameshift and loss of function. The analyses were in line with immunocytochemistry studies of patient-derived skin fibroblasts and muscle tissue demonstrating impaired secretion of collagen VI into the extracellular matrix. Thereby, we add the variant c.1741-6G>A to the list of pathogenic, recessive, splice variants in COL6A1 causing Ullrich congenital muscular dystrophy. The variant is listed in ClinVar as of "uncertain significance" and "likely benign" and may presumably have been overlooked in other patients.
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Affiliation(s)
- Maria Barington
- Department of Genetics, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark.
| | - Morten Dunø
- Department of Genetics, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Ulf Birkedal
- Department of Genetics, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - John Vissing
- Copenhagen Neuromuscular Center, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Alfred Peter Born
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Thomas Krag
- Copenhagen Neuromuscular Center, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Thomas van Overeem Hansen
- Department of Genetics, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Elsebet Østergaard
- Department of Genetics, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
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Zhang L, Shen M, Shu X, Zhou J, Ding J, Zhong C, Pan B, Wang B, Zhang C, Guo W. Intronic position +9 and -9 are potentially splicing sites boundary from intronic variants analysis of whole exome sequencing data. BMC Med Genomics 2023; 16:146. [PMID: 37365551 DOI: 10.1186/s12920-023-01542-7] [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: 10/25/2022] [Accepted: 05/12/2023] [Indexed: 06/28/2023] Open
Abstract
Whole exome sequencing (WES) can also detect some intronic variants, which may affect splicing and gene expression, but how to use these intronic variants, and the characteristics about them has not been reported. This study aims to reveal the characteristics of intronic variant in WES data, to further improve the clinical diagnostic value of WES. A total of 269 WES data was analyzed, 688,778 raw variants were called, among these 367,469 intronic variants were in intronic regions flanking exons which was upstream/downstream region of the exon (default is 200 bps). Contrary to expectation, the number of intronic variants with quality control (QC) passed was the lowest at the +2 and -2 positions but not at the +1 and -1 positions. The plausible explanation was that the former had the worst effect on trans-splicing, whereas the latter did not completely abolish splicing. And surprisingly, the number of intronic variants that passed QC was the highest at the +9 and -9 positions, indicating a potential splicing site boundary. The proportion of variants which could not pass QC filtering (false variants) in the intronic regions flanking exons generally accord with "S"-shaped curve. At +5 and -5 positions, the number of variants predicted damaging by software was most. This was also the position at which many pathogenic variants had been reported in recent years. Our study revealed the characteristics of intronic variant in WES data for the first time, we found the +9 and -9 positions might be a potentially splicing sites boundary and +5 and -5 positions were potentially important sites affecting splicing or gene expression, the +2 and -2 positions seem more important splicing site than +1 and -1 positions, and we found variants in intronic regions flanking exons over ± 50 bps may be unreliable. This result can help researchers find more useful variants and demonstrate that WES data is valuable for intronic variants analysis.
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Affiliation(s)
- Li Zhang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Minna Shen
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xianhong Shu
- Department of Echocardiography, Zhongshan Hospital, Shanghai Institute of Cardiovascular Diseases, Shanghai Institute of Medical Imaging, Fudan University, Shanghai, China
| | - Jingmin Zhou
- Department of Cardiology Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jing Ding
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunjiu Zhong
- Department of Neurology, Zhongshan Hospital, State Key Laboratory, Fudan University, Shanghai, China
| | - Baishen Pan
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Beili Wang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunyan Zhang
- Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China.
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China.
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Heshmatzad K, Naderi N, Maleki M, Abbasi S, Ghasemi S, Ashrafi N, Fazelifar AF, Mahdavi M, Kalayinia S. Role of non-coding variants in cardiovascular disease. J Cell Mol Med 2023; 27:1621-1636. [PMID: 37183561 PMCID: PMC10273088 DOI: 10.1111/jcmm.17762] [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: 10/31/2022] [Revised: 03/29/2023] [Accepted: 04/25/2023] [Indexed: 05/16/2023] Open
Abstract
Cardiovascular diseases (CVDs) constitute one of the significant causes of death worldwide. Different pathological states are linked to CVDs, which despite interventions and treatments, still have poor prognoses. The genetic component, as a beneficial tool in the risk stratification of CVD development, plays a role in the pathogenesis of this group of diseases. The emergence of genome-wide association studies (GWAS) have led to the identification of non-coding parts associated with cardiovascular traits and disorders. Variants located in functional non-coding regions, including promoters/enhancers, introns, miRNAs and 5'/3' UTRs, account for 90% of all identified single-nucleotide polymorphisms associated with CVDs. Here, for the first time, we conducted a comprehensive review on the reported non-coding variants for different CVDs, including hypercholesterolemia, cardiomyopathies, congenital heart diseases, thoracic aortic aneurysms/dissections and coronary artery diseases. Additionally, we present the most commonly reported genes involved in each CVD. In total, 1469 non-coding variants constitute most reports on familial hypercholesterolemia, hypertrophic cardiomyopathy and dilated cardiomyopathy. The application and identification of non-coding variants are beneficial for the genetic diagnosis and better therapeutic management of CVDs.
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Affiliation(s)
- Katayoun Heshmatzad
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Niloofar Naderi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Majid Maleki
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Shiva Abbasi
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Serwa Ghasemi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Nooshin Ashrafi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Amir Farjam Fazelifar
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Mohammad Mahdavi
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
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Forsyth R, Peretz RH, Dempsey A, Britton J, Kratz L, Hamosh A, Vernon H, Batshaw ML, Valle D. The remarkable journey of one female individual with ornithine transcarbamylase deficiency diagnosed post-mortem. JIMD Rep 2023; 64:233-237. [PMID: 37151362 PMCID: PMC10159862 DOI: 10.1002/jmd2.12361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Abstract
Urea cycle disorders (UCDs) comprise a group of inborn errors of metabolism with impaired ammonia clearance and an incidence of ~1:35 000 individuals. First described in the 1970s, the diagnosis and management of these disorders has evolved dramatically. We report on a 59-year-old woman with a UCD who contributed to advances in the understanding and treatment of this group of disorders. This individual was diagnosed with carbamoyl phosphate synthetase 1 deficiency based on a biochemical assay under a research context predating genetic sequencing, treated longitudinally as having this metabolic disorder, and was among the first participants to trial UCD pharmaceutical therapies. She ultimately succumbed to a SARS-CoV-2 infection while maintaining unexpectedly normal ammonium levels. Postmortem genetic testing revealed ornithine transcarbamylase deficiency. This individual's contributions to the field of UCDs is discussed herein.
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Affiliation(s)
- RaeLynn Forsyth
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Ryan H. Peretz
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Angela Dempsey
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jacquelyn Britton
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Lisa Kratz
- Biochemical Genetics LaboratoryKennedy Krieger InstituteBaltimoreMarylandUSA
| | - Ada Hamosh
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Hilary Vernon
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Mark L. Batshaw
- Center for Genetic Medicine ResearchChildren's National HospitalWashingtonDCUSA
| | - David Valle
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
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Jasiak A, Koczkowska M, Stukan M, Wydra D, Biernat W, Izycka-Swieszewska E, Buczkowski K, Eccles MR, Walker L, Wasag B, Ratajska M. Analysis of BRCA1 and BRCA2 alternative splicing in predisposition to ovarian cancer. Exp Mol Pathol 2023; 130:104856. [PMID: 36791903 DOI: 10.1016/j.yexmp.2023.104856] [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: 08/08/2022] [Revised: 01/25/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND The mRNA splicing is regulated on multiple levels, resulting in the proper distribution of genes' transcripts in each cell and maintaining cell homeostasis. At the same time, the expression of alternative transcripts can change in response to underlying genetic variants, often missed during routine diagnostics. AIM The main aim of this study was to define the frequency of aberrant splicing in BRCA1 and BRCA2 genes in blood RNA extracted from ovarian cancer patients who were previously found negative for the presence of pathogenic alterations in the 25 most commonly analysed ovarian cancer genes, including BRCA1 and BRCA2. MATERIAL AND METHODS Frequency and spectrum of splicing alterations in BRCA1 and BRCA2 genes were analysed in blood RNA from 101 ovarian cancer patients and healthy controls (80 healthy women) using PCR followed by gel electrophoresis and Sanger sequencing. The expression of splicing events was examined using RT-qPCR. RESULTS We did not identify any novel, potentially pathogenic splicing alterations. Nevertheless, we detected six naturally occurring transcripts, named BRCA1ΔE9-10, BRCA1ΔE11, BRCA1ΔE11q, and BRCA2ΔE3, BRCA2ΔE12 and BRCA2ΔE17-18 of which three (BRCA1ΔE11q, BRCA1ΔE11 and BRCA2ΔE3) were significantly higher expressed in the ovarian cancer cohort than in healthy controls (p ≤ 0.0001). CONCLUSIONS This observation indicates that the upregulation of selected naturally occurring transcripts can be stimulated by non-genetic mechanisms and be a potential systemic response to disease progression and/or treatment. However, this hypothesis requires further examination.
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Affiliation(s)
- Anna Jasiak
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland.
| | - Magdalena Koczkowska
- 3P Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland; Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Maciej Stukan
- Department of Gynecologic Oncology, Gdynia Oncology Center, Pomeranian Hospitals, Gdynia, Poland; Department Oncological Propedeutics, Medical University of Gdansk, Gdansk, Poland
| | - Dariusz Wydra
- Department of Gynaecology, Gynaecological Oncology and Gynaecological Endocrinology, Medical University of Gdansk, Gdansk, Poland
| | - Wojciech Biernat
- Department of Pathology, Medical University of Gdansk, Gdansk, Poland
| | | | - Kamil Buczkowski
- Department of Pathology & Neuropathology, Medical University of Gdansk, Gdansk, Poland
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Logan Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Bartosz Wasag
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland; Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Magdalena Ratajska
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland; Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand.
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Orosz G, Szabó L, Bereti S, Zámbó V, Csala M, Kereszturi É. Molecular Basis of Unequal Alternative Splicing of Human SCD5 and Its Alteration by Natural Genetic Variations. Int J Mol Sci 2023; 24:ijms24076517. [PMID: 37047490 PMCID: PMC10095032 DOI: 10.3390/ijms24076517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/22/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Alternative splicing (AS) is a major means of post-transcriptional control of gene expression, and provides a dynamic versatility of protein isoforms. Cancer-related AS disorders have diagnostic, prognostic and therapeutic values. Changes in the expression and AS of human stearoyl-CoA desaturase-5 (SCD5) are promising specific tumor markers, although the transcript variants (TVs) of the gene have not yet been confirmed. Our in silico, in vitro and in vivo study focuses on the distribution of SCD5 TVs (A and B) in human tissues, the functionality of the relevant splice sites, and their modulation by certain single-nucleotide variations (SNVs). An order of magnitude higher SCD5A expression was found compared with SCD5B. This unequal splicing is attributed to a weaker recognition of the SCD5B-specific splicing acceptor site, based on predictions confirmed by an optimized minigene assay. The pronounced dominance of SCD5A was largely modified (rs1430176385_A, rs1011850309_A) or even inverted (rs1011850309_C) by natural SNVs at the TV-specific splice sites. Our results provide long missing data on the proportion of SCD5 TVs in human tissues and reveal mutation-driven changes in SCD5 AS, potentially affecting tumor-associated reprogramming of lipid metabolism, thus having prognostic significance, which may be utilized for novel and personalized therapeutic approaches.
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Affiliation(s)
- Gabriella Orosz
- Department of Molecular Biology, Semmelweis University, H-1085 Budapest, Hungary
| | - Luca Szabó
- Department of Molecular Biology, Semmelweis University, H-1085 Budapest, Hungary
| | - Szanna Bereti
- Department of Molecular Biology, Semmelweis University, H-1085 Budapest, Hungary
| | - Veronika Zámbó
- Department of Molecular Biology, Semmelweis University, H-1085 Budapest, Hungary
| | - Miklós Csala
- Department of Molecular Biology, Semmelweis University, H-1085 Budapest, Hungary
| | - Éva Kereszturi
- Department of Molecular Biology, Semmelweis University, H-1085 Budapest, Hungary
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Aguilera C, Padró-Miquel A, Esteve-Garcia A, Cerdà P, Torres-Iglesias R, Llecha N, Riera-Mestre A. Improving Hereditary Hemorrhagic Telangiectasia Molecular Diagnosis: A Referral Center Experience. Genes (Basel) 2023; 14:genes14030772. [PMID: 36981042 PMCID: PMC10048779 DOI: 10.3390/genes14030772] [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: 02/28/2023] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Hereditary hemorrhagic telangiectasia (HHT) is a rare vascular disease inherited in an autosomal dominant manner. Disease-causing variants in endoglin (ENG) and activin A receptor type II-like 1 (ACVRL1) genes are detected in more than 90% of the patients undergoing molecular testing. The identification of variants of unknown significance is often seen as a challenge in clinical practice that makes family screening and genetic counseling difficult. Here, we show that the implementation of cDNA analysis to assess the effect of splice site variants on mRNA splicing is a powerful tool. METHODS Gene panel sequencing of genes associated with HHT and other arteriovenous malformation-related syndromes was performed. To evaluate the effect of the splice site variants, cDNA analysis of ENG and ACVRL1 genes was carried out. RESULTS three novel splice site variants were identified in ENG (c.68-2A > T and c.1311+4_1311+8del) and ACVLR1 (c.526-6C > G) genes correspondingly in three individuals with HHT that met ≥ 3 Curaçao criteria. All three variants led to an aberrant splicing inducing exon skipping (ENG:c.68-2A > T and ACVRL1:c.526-6C > G) or intron retention (ENG:c.1311+4_1311+8del) allowing the confirmation of the predicted effect on splicing and the reclassification from unknown significance to pathogenic/likely pathogenic of two of them. CONCLUSIONS RNA analysis should be performed to assess and/or confirm the impact of variants on splicing. The molecular diagnosis of HHT patients is crucial to allow family screening and accurate genetic counseling. A multidisciplinary approach including clinicians and geneticists is crucial when dealing with patients with rare diseases.
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Affiliation(s)
- Cinthia Aguilera
- Hereditary Hemorrhagic Telangiectasia Unit, Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Spain
- Genetics Laboratory, Laboratori Clínic Territorial Metropolitana Sud, Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Spain
| | - Ariadna Padró-Miquel
- Hereditary Hemorrhagic Telangiectasia Unit, Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Spain
- Genetics Laboratory, Laboratori Clínic Territorial Metropolitana Sud, Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Spain
| | - Anna Esteve-Garcia
- Hereditary Hemorrhagic Telangiectasia Unit, Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Spain
- Clinical Genetics Unit, Laboratori Clínic Territorial Metropolitana Sud, Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Spain
| | - Pau Cerdà
- Hereditary Hemorrhagic Telangiectasia Unit, Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Spain
- Internal Medicine Department, Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Spain
| | - Raquel Torres-Iglesias
- Hereditary Hemorrhagic Telangiectasia Unit, Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Spain
- Internal Medicine Department, Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Spain
| | - Núria Llecha
- Genetics Laboratory, Laboratori Clínic Territorial Metropolitana Sud, Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Spain
- Clinical Genetics Unit, Laboratori Clínic Territorial Metropolitana Sud, Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Spain
| | - Antoni Riera-Mestre
- Hereditary Hemorrhagic Telangiectasia Unit, Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Spain
- Internal Medicine Department, Hospital Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Spain
- Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08907 L'Hospitalet de Llobregat, Spain
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Harries LW. Dysregulated RNA processing and metabolism: a new hallmark of ageing and provocation for cellular senescence. FEBS J 2023; 290:1221-1234. [PMID: 35460337 DOI: 10.1111/febs.16462] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/28/2022] [Accepted: 04/21/2022] [Indexed: 12/23/2022]
Abstract
The human genome is capable of producing hundreds of thousands of different proteins and non-coding RNAs from <20 000 genes, in a co-ordinated and regulated fashion. This is achieved by a collection of phenomena known as mRNA processing and metabolism, and encompasses events in the life cycle of an RNA from synthesis to degradation. These factors are critical determinants of cellular adaptability and plasticity, which allows the cell to adjust its transcriptomic output in response to its internal and external environment. Evidence is building that dysfunctional RNA processing and metabolism may be a key contributor to the development of cellular senescence. Senescent cells by definition have exited cell cycle, but have gained functional features such as the secretion of the senescence-associated secretory phenotype (SASP), a known driver of chronic disease and perhaps even ageing itself. In this review, I will outline the impact of dysregulated mRNA processing and metabolism on senescence and ageing at the level of genes, cells and systems, and describe the mechanisms by which progressive deterioration in these processes may impact senescence and organismal ageing. Finally, I will present the evidence implicating this important process as a new hallmark of ageing, which could be harnessed in the future to develop new senotherapeutic interventions for chronic disease.
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Sahin SB, Nalkiran I, Ayaz T, Irfan Guzel A, Eldes T, Calapoglu T, Sevim Nalkiran H. Genetic variations in OLR1 gene associated with PCOS and atherosclerotic risk factors. J Investig Med 2023; 71:113-123. [PMID: 36647317 DOI: 10.1177/10815589221141831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Polycystic ovary syndrome (PCOS) is the most common endocrinopathy in women of reproductive age. The aim of this study was to investigate the association of oxidized low-density lipoprotein receptor 1 (OLR1) gene variations with the susceptibility of PCOS and to examine the relationship between the frequencies of OLR1 gene variations and atherosclerotic risk factors. Genomic DNA was extracted from blood samples collected from 49 patients with PCOS and 43 healthy controls. The variants in the OLR1 gene were identified using next-generation sequencing (NGS). Heterozygous rs11053646 (K167N), rs11611438, rs11611453, and rs35688880 genotype frequencies were significantly higher in the PCOS group than that of control group. Single nucleotide polymorphism (SNP) rs34163097 minor A allele increased the PCOS risk by ∼10-fold (p = 0.03). SNPs rs11053646, rs11611438, rs11611453, rs34163097, and rs35688880 were positively correlated with body mass index (BMI). The logistic regression model (area under the curve: 0.770, p = 0.000) further revealed a combination of 2-h plasma glucose (PG-2 h), dehydroepiandrosterone sulfate (DHEAS), and rs11053646 as predictors of PCOS phenotype. This is the first study reporting the NGS data of OLR1 gene variants which might be associated with the pathogenesis of PCOS and several atherosclerotic risk factors, particularly higher BMI and DHEAS. To fully understand the genetic basis of PCOS and the contribution of OLR1 gene variants to PCOS pathogenesis, additional large-scale studies are warranted.
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Affiliation(s)
- Serap Baydur Sahin
- Department of Endocrinology and Metabolism Disease, Medistate Hospital, Istanbul, Turkey
| | - Ihsan Nalkiran
- Department of Medical Biology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
| | - Teslime Ayaz
- Department of Internal Medicine, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
| | - Ali Irfan Guzel
- Department of Medical Biology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
| | - Tugba Eldes
- Department of Radiology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
| | - Tugba Calapoglu
- Department of Pediatrics, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
| | - Hatice Sevim Nalkiran
- Department of Medical Biology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
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Zhang X, Cai M, Ma Y, Chen J, Huang S, Cai M, Ding Y, Ma D, Gao Q, Hu X, Zhu C, Yi L. Minigene Assay as an Effective Molecular Diagnostic Strategy in Determining the Pathogenicity of Noncanonical Splice-Site Variants in FLCN. J Mol Diagn 2023; 25:110-120. [PMID: 36410626 DOI: 10.1016/j.jmoldx.2022.10.005] [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: 05/03/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022] Open
Abstract
Primary spontaneous pneumothorax (PSP) or pulmonary cyst is one of the manifestations of Birt-Hogg-Dubé syndrome, which is caused by pathogenic variants in FLCN gene. Genetic testing in patients with PSP identifies a certain number of missense or intronic variants. These variants are usually considered as variants of uncertain significance, whose functional interpretations pose a challenge in clinical genetics. To improve recognition of pathogenic splice-altering variants in FLCN gene, computational tools are used to prioritize potential splice-altering variants and then a hybrid minigene assay is performed to verify the RNA splicing pattern. Herein, variants in FLCN exon 11 and its flanking sequence are focused. Eight variants detected in 11 patients with PSP are evaluated, and six variants are prioritized by in silico tools as potential splice-altering variants of uncertain significance. Four variants (c.1177-5_1177-3delCTC, c.1292_1300+4del, c.1300+4C>T, and c.1300+5G>A) are demonstrated by minigene assay to alter RNA splicing of FLCN, and the last three of them are novel. RT-PCR of patient-derived RNA gives consistent results. Genotype-phenotype correlation analysis in patients with PSP with these variants demonstrates good concordance. Our results underline the importance of RNA analysis, which could provide molecular evidence for pathogenicity of a variant, and provide essential information for the clinical interpretation of variants. Combining the clinical information, a definitive diagnosis could be made.
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Affiliation(s)
- Xinxin Zhang
- Department of Histology and Embryology, School of Medicine, Southeast University, Nanjing, China
| | - Minghui Cai
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Yuanchun Ma
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Jie Chen
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Shaoping Huang
- Department of Histology and Embryology, School of Medicine, Southeast University, Nanjing, China
| | - Mengru Cai
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Yibing Ding
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Dehua Ma
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Qian Gao
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Xiaowen Hu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Chengchu Zhu
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China.
| | - Long Yi
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China; Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China.
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Boro H, Bundela V, Mannar V, Nagendra L, Jain V, Jain B, Kumar S, Agstam S. Novel homozygous leptin receptor mutation in an infant with monogenic obesity. Pediatr Endocrinol Diabetes Metab 2023; 29:118-123. [PMID: 37728464 PMCID: PMC10411088 DOI: 10.5114/pedm.2023.129344] [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: 12/21/2022] [Accepted: 01/17/2023] [Indexed: 09/21/2023]
Abstract
Monogenic obesity can be caused by a mutation in one of the single genes involved in hunger and satiety. The most common mutations affect melanocortin 4 (MC4) followed by the leptin gene and its receptor. Leptin receptor (LEPR) gene mutation is an extremely rare endocrine disease characterized by early-onset obesity, hyperphagia in addition to pituitary hormone deficiency, and metabolic abnormalities. We report the case of a 12-month-old male infant born of a non-consanguineous marriage. He presented to us with rapid weight gain from 2 months of age along with hyperphagia. Biochemistry revealed a deranged lipid profile, elevated transaminases, and markedly raised serum leptin levels. On genetic analysis, a novel mutation was detected, which was a homozygous variation In exon 12 of the LEPR gene (chr1:g.65608901G>A) that resulted in the synonymous amino acid change of lysine at codon 584 proximal to donor splice site (p.Lys584). The in silico prediction of the variant was 'damaging' by MutationTaster2. The mutation was classified as a 'variant of uncertain significance' due to a lack of published literature and had to be correlated carefully with the clinical symptoms. It was recommended to do Sanger sequencing of the parents and other family members. However, due to financial constraints, the family could not afford the same. At the time of writing, funds were being arranged for procuring setmelanotide, which is a novel and effective therapy for monogenic obesity due to LepR mutation.
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Affiliation(s)
- Hiya Boro
- Endocrinology and Metabolism, Aadhar Health Institute, India
| | | | | | | | | | - Bimal Jain
- Pediatrics, Aadhar Health Institute, India
| | - Senthil Kumar
- Scientific Affairs Team, MedGenome Laboratory, India
| | - Sourabh Agstam
- Cardiology, Vardhman Mahavir Medical College and Safdarjung Hospital, India
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Rowane MJ, Stewart-Bates BC, Doll RJ, Meyerson HJ, Venglarcik JS, Callahan M, Fill L, Saab R, Ochs HD, Hostoffer RW. CD5 B-Cell Predominant Primary Immunodeficiency: Part of the Spectrum of MAGT1 Deficiency. THERAPEUTIC ADVANCES IN ALLERGY AND RHINOLOGY 2023; 14:27534030231199675. [PMID: 37706151 PMCID: PMC10496486 DOI: 10.1177/27534030231199675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/22/2023] [Indexed: 09/15/2023]
Abstract
Background Selective anti-polysaccharide antibody deficiency (SPAD) with CD5 B-cell predominance and autoimmune phenomena was identified in a male cohort first reported by Antall et al in 1999. The phenotypically likewise and genotypically identical X-linked immunodeficiency with magnesium defect, Epstein-Barr Virus infection, and neoplasia (XMEN) disease was defined as a novel primary immunodeficiency (PID) in 2011. Recent studies of the magnesium transporter 1 (MAGT1) gene mutation reveal glycosylation defects contributing to more phenotypic variance than the "XMEN" title pathologies. The updated title, "X-linked MAGT1 deficiency with increased susceptibility to EBV-infection and N-linked glycosylation defect," was proposed in 2020. Objectives To reflect the patient population more accurately, a prospective classification update may consider MAGT1 glycobiological errors contributing to phenotypic variance but also pre-genetic testing era reports with CD5 B-cell predominance. Methods Patient 1 from Antall et al presented at 28 years of age for further immunological evaluation of his CD5/CD19 B-cell predominance diagnosed at 5 years old. Design Immune re-evaluation done through flow cytometry and next-generation sequencing. Results Flow cytometry B-cell phenotyping revealed persistent CD5+CD19+ (93%). Flow cytometric histogram quantified reduced activator CD16+CD56+ natural killer and CD8+ T-cell receptor, Group 2, Member D (NKG2D) glycoprotein expression. A c.923-1_934 deletion loss of function mutation was identified in the MAGT1 gene. Conclusion We suggest the novel PID XMEN, based on its CD5 B-cell predominance, had been discovered and reported over a decade earlier as CD5+ PID based on the MAGT1 mutation found in the same. We encourage consideration of combining these labels and recent findings to offer the most accurate classification of this disease.
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Affiliation(s)
- Marija J. Rowane
- Children's Hospital of St. Francis at Oklahoma State University, Tulsa, Oklahoma
| | | | - Rayna J. Doll
- Spokane Allergy & Asthma Clinic, Spokane, Washington
| | - Howard J. Meyerson
- Division of Clinical Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - John S. Venglarcik
- Department of Pediatrics, Northeast Ohio Medical University, Rootstown, Ohio
| | - Meghan Callahan
- Lake Erie College of Osteopathic Medicine, Erie, Pennsylvania
| | - Lauren Fill
- Allergy/Immunology Associates, Inc., Mayfield Heights, Ohio
| | - Remie Saab
- University Hospitals Community Consortium Geauga, Geauga, Ohio
| | - Hans D. Ochs
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington
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El Younsi M, Trabelsi M, Ben Youssef S, Ouertani I, Hammi Y, Achour A, Maazoul F, Kharrat M, Gargah T, M'rad R. Clinical and genetic characteristics of Tunisian children with infantile nephropathic cystinosis. Pediatr Nephrol 2023; 38:119-129. [PMID: 35445972 DOI: 10.1007/s00467-022-05525-1] [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: 09/28/2021] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Nephropathic cystinosis is an autosomal recessive disease caused by a mutation in the CTNS gene which encodes cystinosin, a lysosomal cystine transporter. The spectrum of mutations in the CTNS gene is not well defined in the North African population. Here, we investigated twelve patients with nephropathic cystinosis belonging to eight Tunisian families in order to analyze the clinical and genetic characteristics of Tunisian children with infantile nephropathic cystinosis. METHODS Clinical data were collected retrospectively. Molecular analysis of the CTNS gene was performed by Sanger sequencing. RESULTS We describe a new splicing mutation c.971-1G > C in the homozygous state in 6/12 patients which seems to be a founder mutation. The reported deletion of 23nt c.771_793 Del (p.Gly258Serfs*30) was detected in a homozygous state in one patient and in a heterozygous compound state with the c.971-1G > C mutation in 3/12 patients. Two of 12 patients have a deletion of exons 4 and 5 of the CTNS gene. None of our patients had the most common 57-kb deletion. CONCLUSIONS The mutational spectrum in the Tunisian population is different from previously described populations. Thus, a molecular diagnostic strategy must be implemented in Tunisia, by targeting as a priority the common mutations described in this country. Such a strategy will allow a cost-effective diagnosis confirmation as well as early administration of treatment with oral cysteamine. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Mariem El Younsi
- Laboratoire de Génétique Humaine, LR99ES10, Faculté de Médecine de Tunis, Université de Tunis El Manar, 1007, Tunis, Tunisia
| | - Médiha Trabelsi
- Service des Maladies Congénitales et Héréditaires, Hôpital Charles Nicolle, Bab Souika, 1006, Tunis, Tunisia
| | - Sandra Ben Youssef
- Service de Pédiatrie Néphrologique Hôpital Charles Nicolle, Bab Souika, 1006, Tunis, Tunisia
| | - Inès Ouertani
- Service des Maladies Congénitales et Héréditaires, Hôpital Charles Nicolle, Bab Souika, 1006, Tunis, Tunisia
| | - Yousra Hammi
- Service de Pédiatrie Néphrologique Hôpital Charles Nicolle, Bab Souika, 1006, Tunis, Tunisia
| | - Ahlem Achour
- Service des Maladies Congénitales et Héréditaires, Hôpital Charles Nicolle, Bab Souika, 1006, Tunis, Tunisia
| | - Faouzi Maazoul
- Service des Maladies Congénitales et Héréditaires, Hôpital Charles Nicolle, Bab Souika, 1006, Tunis, Tunisia
| | - Maher Kharrat
- Laboratoire de Génétique Humaine, LR99ES10, Faculté de Médecine de Tunis, Université de Tunis El Manar, 1007, Tunis, Tunisia
| | - Tahar Gargah
- Service de Pédiatrie Néphrologique Hôpital Charles Nicolle, Bab Souika, 1006, Tunis, Tunisia
| | - Ridha M'rad
- Laboratoire de Génétique Humaine, LR99ES10, Faculté de Médecine de Tunis, Université de Tunis El Manar, 1007, Tunis, Tunisia. .,Service des Maladies Congénitales et Héréditaires, Hôpital Charles Nicolle, Bab Souika, 1006, Tunis, Tunisia.
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Zhou J, Zhang Q, Zhao Y, Song Y, Leng Y, Chen M, Zhou S, Wang Z. The regulatory role of alternative splicing in inflammatory bowel disease. Front Immunol 2023; 14:1095267. [PMID: 37153612 PMCID: PMC10160418 DOI: 10.3389/fimmu.2023.1095267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
Inflammatory bowel disease (IBD) mainly includes Crohn's disease and ulcerative colitis. These diseases have a progressive course of chronic relapse and remission and affect a large number of children and adults worldwide. The burden of IBD is rising worldwide, with levels and trends varying greatly in countries and regions. Like most chronic diseases, the costs associated with IBD are high, including hospitalizations, outpatient and emergency visits, surgeries, and pharmacotherapies. However, there is no radical cure for it yet, and its therapeutic targets still need further study. Currently, the pathogenesis of IBD remains unclear. It is generally assumed that the occurrence and development of IBD are related to the environmental factors, gut microbiota, immune imbalance, and genetic susceptibility. Alternative splicing contributes to a various diseases, such as spinal muscular atrophy, liver diseases, and cancers. In the past, it has been reported that alternative splicing events, splicing factors, and splicing mutations were associated with IBD, but there were no reports on the practical application for clinical diagnosis and treatment of IBD using splicing-related methods. Therefore, this article reviews research progress on alternative splicing events, splicing factors, and splicing mutations associated with IBD.
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Affiliation(s)
- Jianli Zhou
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Qiao Zhang
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yuzhen Zhao
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yuchen Song
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yanan Leng
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Moxian Chen
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
| | - Shaoming Zhou
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
| | - Zhaoxia Wang
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
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Bergougnoux A, Billet A, Ka C, Heller M, Degrugillier F, Vuillaume ML, Thoreau V, Sasorith S, Bareil C, Thèze C, Ferec C, Gac GL, Bienvenu T, Bieth E, Gaston V, Lalau G, Pagin A, Malinge MC, Dufernez F, Lemonnier L, Koenig M, Fergelot P, Claustres M, Taulan-Cadars M, Kitzis A, Reboul MP, Becq F, Fanen P, Mekki C, Audrezet MP, Girodon E, Raynal C. The multi-faceted nature of 15 CFTR exonic variations: Impact on their functional classification and perspectives for therapy. J Cyst Fibros 2022:S1569-1993(22)01423-0. [PMID: 36567205 DOI: 10.1016/j.jcf.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/30/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND The majority of variants of unknown clinical significance (VUCS) in the CFTR gene are missense variants. While change on the CFTR protein structure or function is often suspected, impact on splicing may be neglected. Such undetected splicing default of variants may complicate the interpretation of genetic analyses and the use of an appropriate pharmacotherapy. METHODS We selected 15 variants suspected to impact CFTR splicing after in silico predictions on 319 missense variants (214 VUCS), reported in the CFTR-France database. Six specialized laboratories assessed the impact of nucleotide substitutions on splicing (minigenes), mRNA expression levels (quantitative PCR), synthesis and maturation (western blot), cellular localization (immunofluorescence) and channel function (patch clamp) of the CFTR protein. We also studied maturation and function of the truncated protein, consecutive to in-frame aberrant splicing, on additional plasmid constructs. RESULTS Six of the 15 variants had a major impact on CFTR splicing by in-frame (n = 3) or out-of-frame (n = 3) exon skipping. We reclassified variants into: splicing variants; variants causing a splicing defect and the impairment of CFTR folding and/or function related to the amino acid substitution; deleterious missense variants that impair CFTR folding and/or function; and variants with no consequence on the different processes tested. CONCLUSION The 15 variants have been reclassified by our comprehensive approach of in vitro experiments that should be used to properly interpret very rare exonic variants of the CFTR gene. Targeted therapies may thus be adapted to the molecular defects regarding the results of laboratory experiments.
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Affiliation(s)
- A Bergougnoux
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France; Université de Montpellier, Montpellier, France
| | - A Billet
- Laboratoire STIM, Université de Poitiers, Poitiers, France
| | - C Ka
- Service de génétique moléculaire, CHRU Brest, Brest, France; Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - M Heller
- Service de Médecine Génomique des Maladies de Système et d'Organe, APHP Centre - Université de Paris, Hôpital Cochin, Paris, France
| | - F Degrugillier
- Université Paris-Est Créteil, INSERM, IMRB, Créteil F-94010, France
| | - M-L Vuillaume
- Génétique Moléculaire, CHU Bordeaux, Bordeaux, France
| | - V Thoreau
- Laboratoire NEUVACOD-3808, Université de Poitiers, Poitiers, France
| | - S Sasorith
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France
| | - C Bareil
- Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - C Thèze
- Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - C Ferec
- Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - G Le Gac
- Service de génétique moléculaire, CHRU Brest, Brest, France; Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - T Bienvenu
- Service de Médecine Génomique des Maladies de Système et d'Organe, APHP Centre - Université de Paris, Hôpital Cochin, Paris, France
| | - E Bieth
- Génétique Médicale, CHU Toulouse, Toulouse, France
| | - V Gaston
- Génétique Médicale, CHU Toulouse, Toulouse, France
| | - G Lalau
- Biochimie et Biologie Moléculaire, CHU Lille, Lille, France
| | - A Pagin
- Biochimie et Biologie Moléculaire, CHU Lille, Lille, France
| | - M-C Malinge
- Biochimie et Génétique, CHU Angers, Angers, France
| | - F Dufernez
- Génétique, CHU Poitiers, Poitiers, France
| | - L Lemonnier
- Association Vaincre la Mucoviscidose, Paris, France
| | - M Koenig
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France; Université de Montpellier, Montpellier, France
| | - P Fergelot
- MRGM, INSERM UMR 1211 Université de Bordeaux, Bordeaux, France
| | - M Claustres
- Université de Montpellier, Montpellier, France
| | - M Taulan-Cadars
- PhyMedExp, INSERM, CNRS UMR, Montpellier, France; Université de Montpellier, Montpellier, France
| | - A Kitzis
- Génétique, CHU Poitiers, Poitiers, France
| | - M-P Reboul
- Génétique Moléculaire, CHU Bordeaux, Bordeaux, France
| | - F Becq
- Laboratoire STIM, Université de Poitiers, Poitiers, France
| | - P Fanen
- AP-HP, Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, Hôpital Henri Mondor, Créteil F-94010, France
| | - C Mekki
- AP-HP, Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, Hôpital Henri Mondor, Créteil F-94010, France
| | - M-P Audrezet
- Service de génétique moléculaire, CHRU Brest, Brest, France; Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - E Girodon
- Service de Médecine Génomique des Maladies de Système et d'Organe, APHP Centre - Université de Paris, Hôpital Cochin, Paris, France; INSERM U1151, Institut Necker Enfants Malades, Université de Paris, Paris, France
| | - C Raynal
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France.
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Qian Y, Chen B, Wang Z, Peng Y. Genetic association between the PTPN22, IRF5 and TYK2 gene variants and susceptibility to juvenile idiopathic arthritis. Exp Ther Med 2022; 24:756. [PMID: 36605568 PMCID: PMC9808742 DOI: 10.3892/etm.2022.11692] [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: 07/22/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022] Open
Abstract
Juvenile idiopathic arthritis (JIA) refers to a group of chronic childhood arthropathies of unknown etiology. In the present study, the genetic association between the variants in PTPN22, IRF5 and TYK2 genes and susceptibility to JIA was investigated. The distributions of 16 variants in PTPN22, IRF5 and TYK2 genes were analyzed by direct sequencing in 378 patients with JIA and 378 healthy controls. Odds ratios and 95% confidence intervals were used to evaluate the association between the gene variants and JIA. The gene-gene interactions were investigated using multifactor dimensionality reduction. All allelic and dominant models of PTPN22 rs1214414, rs1214418, rs1746853, rs3765598 and rs3811021 were significantly associated with JIA risk (P<0.05). IRF5 rs10954213 in both allelic and dominant models, as well as the allelic model of rs2004640, was significantly related to JIA risk (P<0.05). In addition, the allelic, recessive and dominant models of TYK2 rs280500, rs280519, rs2304256 and rs12720270 were significantly related to JIA risk (P<0.05). In addition, three haplotypes (HC A G T C C, HC A G T T C and HC G T T C T ) in PTPN22 gene, three haplotypes (HD T A A, HI T A C and HD T G C) in IRF5 gene and two haplotypes (HA G G A T and HG A G G T) in TYK2 gene were associated with the risk of JIA (P<0.05). Furthermore, a three-way interaction between IRF5 rs10954213, rs2004640 and PTPN22 rs1214414 was shown to be associated with JIA risk. In conclusion, PTPN22 rs1214418, rs1746853, rs3765598, IRF5 rs2004640, TYK2 rs280500, rs2304256 and a three-way interaction between IRF5 rs10954213, rs2004640 and PTPN22 rs1214414 may be risk factors for JIA.
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Affiliation(s)
- Yufeng Qian
- Department of Orthopedics, Changshu Hospital Affiliated to Soochow University, First People's Hospital of Changshu City, Changshu, Jiangsu 215500, P.R. China,Correspondence to: Mr Yufeng Qian, Department of Orthopedics, Changshu Hospital Affiliated to Soochow University, First People's Hospital of Changshu City, 1 Shuyuan Street, Changshu, Jiangsu 215500, P.R. China
| | - Bingqian Chen
- Department of Orthopedics, Changshu Hospital Affiliated to Soochow University, First People's Hospital of Changshu City, Changshu, Jiangsu 215500, P.R. China
| | - Zhengfei Wang
- Department of Orthopedics, Changshu Hospital Affiliated to Soochow University, First People's Hospital of Changshu City, Changshu, Jiangsu 215500, P.R. China
| | - Yuqin Peng
- Department of Orthopedics, Changshu Hospital Affiliated to Soochow University, First People's Hospital of Changshu City, Changshu, Jiangsu 215500, P.R. China
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Cho S, Park S, Lee JS, Ju YS, Choi YJ, Lee S. Adenosine Deaminase 2 Deficiency Caused by Biallele Variants Including Splicing Variant: The First Case in Korea. JOURNAL OF RHEUMATIC DISEASES 2022; 29:254-260. [PMID: 37476427 PMCID: PMC10351412 DOI: 10.4078/jrd.21.0046] [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: 09/27/2021] [Revised: 10/30/2021] [Accepted: 11/04/2021] [Indexed: 07/22/2023]
Abstract
Deficiency of adenosine deaminase 2 (DADA2) is an autoinflammatory disease caused by pathogenic variants of the ADA2 gene and has similar clinical features to polyarteritis nodosa (PAN). We, herein, report a case of DADA2 in Korea that was diagnosed in a patient with childhood-onset PAN. The patient had a truncal ataxia and facial palsy caused by thalamic infarction at 34 months of age. Livedo reticularis with Raynaud phenomenon and abdominal pain with fever were followed. Radiologic examination showed multiple infarctions in brain and kidney. She was diagnosed with PAN using skin biopsy and angiography. She had severe hemorrhagic strokes despite medical treatments. Her disease activity was controlled after adding a tumor necrosis factor-α inhibitor. Molecular analysis revealed compound heterozygous pathogenic variants of ADA2 gene. This is the first case of DADA2 in Korea. Genetic analysis for ADA2 gene should be considered in patients with childhood-onset PAN.
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Affiliation(s)
- Sun Cho
- Department of Pediatrics, Seoul National University Hospital, Seoul, Korea
| | | | | | - Young Seok Ju
- GENOME INSIGHT Inc., Daejeon, Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Yun Jung Choi
- Department of Pediatrics, Seoul National University Hospital, Seoul, Korea
- Hospital Medicine Center, Seoul National University Hospital, Seoul, Korea
| | - Soyoung Lee
- Department of Pediatrics, Seoul National University Hospital, Seoul, Korea
- GENOME INSIGHT Inc., Daejeon, Korea
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Integrative Functional Genomic Analysis in Multiplex Autism Families from Kazakhstan. DISEASE MARKERS 2022; 2022:1509994. [PMID: 36199823 PMCID: PMC9529466 DOI: 10.1155/2022/1509994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/21/2022] [Accepted: 09/06/2022] [Indexed: 12/14/2022]
Abstract
The study of extended pedigrees containing autism spectrum disorder- (ASD-) related broader autism phenotypes (BAP) offers a promising approach to the search for ASD candidate variants. Here, a total of 650,000 genetic markers were tested in four Kazakhstani multiplex families with ASD and BAP to obtain data on de novo mutations (DNMs), common, and rare inherited variants that may contribute to the genetic risk for developing autistic traits. The variants were analyzed in the context of gene networks and pathways. Several previously well-described enriched pathways were identified, including ion channel activity, regulation of synaptic function, and membrane depolarization. Perhaps these pathways are crucial not only for the development of ASD but also for ВАР. The results also point to several additional biological pathways (circadian entrainment, NCAM and BTN family interactions, and interaction between L1 and Ankyrins) and hub genes (CFTR, NOD2, PPP2R2B, and TTR). The obtained results suggest that further exploration of PPI networks combining ASD and BAP risk genes can be used to identify novel or overlooked ASD molecular mechanisms.
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Rodríguez-Salgado LE, Silva-Aldana CT, Medina-Méndez E, Bareño-Silva J, Arcos-Burgos M, Silgado-Guzmán DF, Restrepo CM. Frequency of actionable Exomic secondary findings in 160 Colombian patients: Impact in the healthcare system. Gene 2022; 838:146699. [PMID: 35803546 DOI: 10.1016/j.gene.2022.146699] [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: 10/05/2021] [Revised: 06/11/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION By 2021, the American College of Medical Genetics and Genomics (ACMG) published the last version of their secondary findings (SF) reporting recommendations for cases in which a person receives a genetic test. OBJECTIVE To determine in a sample of the Colombian population the prevalence of SF for the 59 genes on the ACMG SF v2.0 list associated with 27 genetic diseases. MATERIALS AND METHODS An analytical cross-sectional study was developed by examining the sequences of 160 exomes. Based on the ACMG guidelines, a variant classification algorithm was designed to filter and select reportable SF. RESULTS Eleven pathogenic variants were identified in 13/160 (8.13%) patients in genes APOB, BRCA2, CACNA1S, COL3A1, LDLR, MYBPC3, PCSK9, PKP2, PMS2 and RYR2. No association was found between the sociodemographic variables and the SF to report (P > 0,05). CONCLUSION We reported the first approach of actionable pathogenic variants spectrum in the Colombian population. Given the frequency found in this study and the clinical impact of genomic variants on health, it is essential to actively search for SF having the opportunity to receive genetic counselling, prevention and clinical management.
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Affiliation(s)
| | | | | | - José Bareño-Silva
- School of Medicine, Mental Health Research Group, CES University, Medellin, Colombia
| | - Mauricio Arcos-Burgos
- Research Group on Psychiatric Disorders (GIPSI), Department of Psychiatry, Institute of Medical Research, School of Medicine, University of Antioquia, Medellín, Colombia
| | | | - Carlos M Restrepo
- Center for Research in Genetics and Genomics (CIGGUR), GeniURos Research Group, School of Medicine and Health Sciences, University of Rosario, Bogotá, Colombia.
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50
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Zhang H, Lianto P, Li W, Xu M, Moore JB, Thorne JL. Associations between liver X receptor polymorphisms and blood lipids: A systematic review and meta-analysis. Steroids 2022; 185:109057. [PMID: 35679909 DOI: 10.1016/j.steroids.2022.109057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/07/2022] [Accepted: 06/02/2022] [Indexed: 12/22/2022]
Abstract
Genetic susceptibility to dyslipidaemia remains incompletely understood. The liver X receptors (LXRs), members of the nuclear receptor superfamily of ligand dependent transcription factors, are homeostatic regulators of lipid metabolism. Multiple single nucleotide polymorphisms (SNPs)have been identified previously in the coding and regulatory regions of the LXRs. The aim of this systematic review and meta-analysis was to summarise associations between SNPs of LXRs (α and β isoforms) with blood lipid and lipoprotein traits. Five databases (PubMed, Ovid Embase, Scopus, Web of Science, and the Cochrane Library) were systematically searched for population-based studies that assessed associations between one or more blood lipid/lipoprotein traits and LXR SNPs. Of seventeen articles included in the qualitative synthesis, ten were eligible for meta-analysis. Nine LXRα SNPs and five LXRβ SNPs were identified, and the three most studied LXRα SNPs were quantitatively summarised. Carriers of the minor allele A of LXRα rs12221497 (-115G>A) had higher triglyceride levels than GG homozygotes (0.13 mmol/L; 95%CI: [0.03, 0.23], P = 0.01). Heterozygote carriers of LXRα rs2279238 (297C/T) had higher total cholesterol levels (0.12 mmol/L; (95%CI: [0.01, 0.23], P = 0.04) than either CC or TT homozygotes. For LXRα rs11039155 (-6G>A), no significant differences in blood levels of either triglyceride (P = 0.39) or HDL-C (P = 0.98) were detected between genotypes in meta-analyses. In addition, there were no strong associations for other SNPs of LXRα and LXRβ. This study provides the evidence of an association between LXRα, but not LXRβ, SNPs and blood-lipid traits. Systematic review registration: PROSPERO No. CRD42021246158.
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Affiliation(s)
- Huifeng Zhang
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK; Clinical Nutrition Department, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China
| | - Priscilia Lianto
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
| | - Weiming Li
- Clinical Nutrition Department, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China
| | - Mengfan Xu
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
| | - J Bernadette Moore
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
| | - James L Thorne
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK.
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