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Kittaka M, Mizuno N, Morino H, Yoshimoto T, Zhu T, Liu S, Wang Z, Mayahara K, Iio K, Kondo K, Kondo T, Hayashi T, Coghlan S, Teno Y, Doan AAP, Levitan M, Choi RB, Matsuda S, Ouhara K, Wan J, Cassidy AM, Pelletier S, Nampoothiri S, Urtizberea AJ, Robling AG, Ono M, Kawakami H, Reichenberger EJ, Ueki Y. Loss-of-function OGFRL1 variants identified in autosomal recessive cherubism families. JBMR Plus 2024; 8:ziae050. [PMID: 38699440 PMCID: PMC11062026 DOI: 10.1093/jbmrpl/ziae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/01/2024] [Accepted: 03/24/2024] [Indexed: 05/05/2024] Open
Abstract
Cherubism (OMIM 118400) is a rare craniofacial disorder in children characterized by destructive jawbone expansion due to the growth of inflammatory fibrous lesions. Our previous studies have shown that gain-of-function mutations in SH3 domain-binding protein 2 (SH3BP2) are responsible for cherubism and that a knock-in mouse model for cherubism recapitulates the features of cherubism, such as increased osteoclast formation and jawbone destruction. To date, SH3BP2 is the only gene identified to be responsible for cherubism. Since not all patients clinically diagnosed with cherubism had mutations in SH3BP2, we hypothesized that there may be novel cherubism genes and that these genes may play a role in jawbone homeostasis. Here, using whole exome sequencing, we identified homozygous loss-of-function variants in the opioid growth factor receptor like 1 (OGFRL1) gene in 2 independent autosomal recessive cherubism families from Syria and India. The newly identified pathogenic homozygous variants were not reported in any variant databases, suggesting that OGFRL1 is a novel gene responsible for cherubism. Single cell analysis of mouse jawbone tissue revealed that Ogfrl1 is highly expressed in myeloid lineage cells. We generated OGFRL1 knockout mice and mice carrying the Syrian frameshift mutation to understand the in vivo role of OGFRL1. However, neither mouse model recapitulated human cherubism or the phenotypes exhibited by SH3BP2 cherubism mice under physiological and periodontitis conditions. Unlike bone marrow-derived M-CSF-dependent macrophages (BMMs) carrying the SH3BP2 cherubism mutation, BMMs lacking OGFRL1 or carrying the Syrian mutation showed no difference in TNF-ɑ mRNA induction by LPS or TNF-ɑ compared to WT BMMs. Osteoclast formation induced by RANKL was also comparable. These results suggest that the loss-of-function effects of OGFRL1 in humans differ from those in mice and highlight the fact that mice are not always an ideal model for studying rare craniofacial bone disorders.
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Affiliation(s)
- Mizuho Kittaka
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN 46202, United States
- Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, Indianapolis, IN 46202, United States
| | - Noriyoshi Mizuno
- Department of Periodontal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Hiroyuki Morino
- Department of Medical Genetics, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan
| | - Tetsuya Yoshimoto
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN 46202, United States
- Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, Indianapolis, IN 46202, United States
| | - Tianli Zhu
- Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, Indianapolis, IN 46202, United States
| | - Sheng Liu
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Ziyi Wang
- Department of Molecular Biology and Biochemistry, Okayama University Medical School, Okayama 700-8558, Japan
| | - Kotoe Mayahara
- Department of Orthodontics, Nihon University School of Dentistry, Tokyo 101-8310, Japan
| | - Kyohei Iio
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Kaori Kondo
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo 113-8677, Japan
| | - Toshio Kondo
- Department of Molecular Biology and Biochemistry, Okayama University Medical School, Okayama 700-8558, Japan
| | - Tatsuhide Hayashi
- Department of Dental Materials Science, School of Dentistry, Aichi Gakuin University, Aichi 464-8650, Japan
| | - Sarah Coghlan
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN 46202, United States
- Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, Indianapolis, IN 46202, United States
| | - Yayoi Teno
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN 46202, United States
- Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, Indianapolis, IN 46202, United States
| | - Andrew Anh Phung Doan
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN 46202, United States
- Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, Indianapolis, IN 46202, United States
| | - Marcus Levitan
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN 46202, United States
- Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, Indianapolis, IN 46202, United States
| | - Roy B Choi
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Shinji Matsuda
- Department of Periodontal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Kazuhisa Ouhara
- Department of Periodontal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Jun Wan
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Annelise M Cassidy
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Stephane Pelletier
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Kerala 682041, India
| | | | - Alexander G Robling
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Mitsuaki Ono
- Department of Molecular Biology and Biochemistry, Okayama University Medical School, Okayama 700-8558, Japan
| | - Hideshi Kawakami
- Department of Molecular Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Ernst J Reichenberger
- Department of Reconstructive Sciences, School of Dental Medicine, University of Connecticut Health, CT 06030, United States
| | - Yasuyoshi Ueki
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN 46202, United States
- Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, Indianapolis, IN 46202, United States
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Turgut GT, Altunoglu U, Gulec C, Sarac Sivrikoz T, Kalaycı T, Toksoy G, Avcı Ş, Yıldırım BT, Sayın GY, Kalelioglu IH, Karaman B, Has R, Başaran S, Yuksel A, Kayserili H, Uyguner ZO. Clinical and molecular characteristics of 26 fetuses with lethal multiple congenital contractures. Clin Genet 2024; 105:596-610. [PMID: 38278647 DOI: 10.1111/cge.14490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/03/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024]
Abstract
Multiple congenital contractures (MCC) due to fetal akinesia manifest across a broad spectrum of diseases, ranging from mild distal arthrogryposis to lethal fetal akinesia deformation sequence. We hereby present a series of 26 fetuses displaying severe MCC phenotypes from 18 families and describe detailed prenatal ultrasound findings, postmortem clinical evaluations, and genetic investigations. Most common prenatal findings were abnormal facial profile (65%), central nervous system abnormalities (62%), polyhydramnios (50%), increased nuchal translucency (50%), and fetal hydrops (35%). Postmortem examinations unveiled additional anomalies including facial dysmorphisms, dysplastic skeletal changes, ichthyosis, multiple pterygia, and myopathy, allowing preliminary diagnosis of particular Mendelian disorders in multiple patients. Evaluation of the parents revealed maternal grip myotonia in one family. By exome sequencing and targeted testing, we identified causative variants in ACTC1, CHST14, COG6, DMPK, DOK7, HSPG2, KLHL7, KLHL40, KIAA1109, NEB, PSAT1, RAPSN, USP14, and WASHC5 in 15 families, and one patient with a plausible diagnosis associated with biallelic NEB variants. Three patients received a dual diagnosis. Pathogenic alterations in newly discovered genes or in previously known genes recently linked to new MCC phenotypes were observed in 44% of the cohort. Our results provide new insights into the clinical and molecular landscape of lethal MCC phenotypes.
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Affiliation(s)
- Gozde Tutku Turgut
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Umut Altunoglu
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
- Department of Medical Genetics, Koç University School of Medicine (KUSoM), Istanbul, Turkey
| | - Cagri Gulec
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Tugba Sarac Sivrikoz
- Division of Perinatology, Department of Obstetrics and Gynecology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Tuğba Kalaycı
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Guven Toksoy
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Şahin Avcı
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
- Department of Medical Genetics, Koç University School of Medicine (KUSoM), Istanbul, Turkey
| | - Behiye Tuğçe Yıldırım
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Gözde Yeşil Sayın
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Ibrahim Halil Kalelioglu
- Division of Perinatology, Department of Obstetrics and Gynecology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Birsen Karaman
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
- Department of Pediatric Basic Sciences, Institute of Child Health, Istanbul University, Istanbul, Turkey
| | - Recep Has
- Division of Perinatology, Department of Obstetrics and Gynecology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Seher Başaran
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Atil Yuksel
- Division of Perinatology, Department of Obstetrics and Gynecology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Hülya Kayserili
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
- Department of Medical Genetics, Koç University School of Medicine (KUSoM), Istanbul, Turkey
| | - Zehra Oya Uyguner
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
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Hwang HW, Shin HT, An HY, Byun JW. Genomic progression for local invasion of cutaneous squamous cell carcinoma from the superficial to the deep portion. Int J Cancer 2024. [PMID: 38739001 DOI: 10.1002/ijc.34952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/29/2024] [Accepted: 03/19/2024] [Indexed: 05/14/2024]
Abstract
Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer. While many treatments exist, our understanding of its genomic progression, especially from the epidermis to the deep dermis, remains limited. This study aims to identify genetic mutations associated with the progression of cSCC into the deep dermis, providing insights into its aggressive behavior and high-risk features. We performed high-depth whole-exome sequencing on 12 cSCC tissues, along with paired normal tissues from six patients, using microdissection techniques. The mutational analysis focused on identifying alterations enriched during cSCC progression. Gene Ontology enrichment analysis, immunohistochemical assays, and external single-cell RNA data were utilized for validation. A total of 8863 non-synonymous somatic mutations were identified in 4092 genes across the superficial and deep portions of cSCCs. Analysis of deep portion mutations revealed a significant correlation with gene ontology biological processes, particularly cell junction organization, and cell-cell adhesion. Clonal mutations in these processes were more prevalent in the deep portions, indicating their impact on the cSCC mutation landscape. Genetic evolution analysis identified 29 causal genes associated with dermal invasion in cSCC. We highlight somatic mutations in cSCC, revealing heterogeneity between superficial and deep regions. Altered genes in cell junction organization and cell-cell adhesion emerged as pivotal in dermal invasion. We identified 29 causal genes primarily in deep tumor regions. Our findings emphasize analyzing multiple tumor regions to capture varied mutational landscapes. These insights advance our understanding of cSCC progression, emphasizing genetic and cellular changes during tumor evolution.
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Affiliation(s)
- Hye Won Hwang
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
| | - Hyun-Tae Shin
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
- Research Center for Controlling Intercellular Communication (RCIC), Inha University School of Medicine, Incheon, Republic of Korea
| | - Hye Young An
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
| | - Ji Won Byun
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
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Tanaka S, Akagawa H, Azuma K, Higuchi S, Ujiie A, Hashimoto K, Iwasaki N. High prevalence of copy number variations in the Japanese participants with suspected MODY. Clin Genet 2024. [PMID: 38733153 DOI: 10.1111/cge.14544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
Maturity-Onset Diabetes of the Young (MODY) is a diabetes mellitus subtype caused by a single gene. The detection rate of the responsible gene is 27% in the United Kingdom, indicating that the causative gene remains unknown in the majority of clinically diagnosed MODY cases. To improve the detection rate, we applied comprehensive genetic testing using whole exome sequencing (WES) followed by Multiplex Ligation-dependent Probe Amplification (MLPA) and functional analyses. Twenty-one unrelated Japanese participants with MODY were enrolled in the study. To detect copy number variations (CNVs), WES was performed first, followed by MLPA analysis for participants who were negative on the basis of WES. Undetermined variants were analyzed according to their functional properties. WES identified 7 pathogenic and 3 novel likely pathogenic variants in the 21 participants. Functional analyses revealed that 1 in 3 variants was pathogenic. MLPA analysis applied to the remaining 13 undetermined samples identified 4 cases with pathogenic CNVs: 3 in HNF4A and 1 in HNF1B. Pathogenic variants were identified in 12 participants (12/21, 57.1%) - relatively high rate reported to date. Notably, one-third of the participants had CNVs in HNF4A or HNF1B, indicating a limitation of WES-only screening.
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Affiliation(s)
- Satoshi Tanaka
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
- Diabetes and Metabolism, School of Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiroyuki Akagawa
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
- Department of Neurosurgery, Tokyo Women's Medical University Adachi Medical Center, Tokyo, Japan
| | - Kenkou Azuma
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| | - Sayaka Higuchi
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| | - Atsushi Ujiie
- Department of Diabetes, Endocrinology and Hematology, Dokkyo Medical University Saitama Medical Center, Saitama, Japan
| | - Koshi Hashimoto
- Department of Diabetes, Endocrinology and Hematology, Dokkyo Medical University Saitama Medical Center, Saitama, Japan
| | - Naoko Iwasaki
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
- Diabetes and Metabolism, School of Medicine, Tokyo Women's Medical University, Tokyo, Japan
- Division of Diabetes, Endocrinology and Metabolism, Tokyo Women's Medical University Yachiyo Medical Center, Chiba, Japan
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Muranishi Y, Kobori Y, Katoh-Fukui Y, Tamaoka S, Hattori A, Osaka A, Okada H, Nakabayashi K, Hata K, Kawai T, Ogata-Kawata H, Iwahata T, Saito K, Kon M, Shinohara N, Fukami M. Systematic molecular analyses for 115 karyotypically normal men with isolated non-obstructive azoospermia. Hum Reprod 2024; 39:1131-1140. [PMID: 38511217 DOI: 10.1093/humrep/deae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
STUDY QUESTION Do copy-number variations (CNVs) in the azoospermia factor (AZF) regions and monogenic mutations play a major role in the development of isolated (non-syndromic) non-obstructive azoospermia (NOA) in Japanese men with a normal 46, XY karyotype? SUMMARY ANSWER Deleterious CNVs in the AZF regions and damaging sequence variants in eight genes likely constitute at least 8% and approximately 8% of the genetic causes, respectively, while variants in other genes play only a minor role. WHAT IS KNOWN ALREADY Sex chromosomal abnormalities, AZF-linked microdeletions, and monogenic mutations have been implicated in isolated NOA. More than 160 genes have been reported as causative/susceptibility/candidate genes for NOA. STUDY DESIGN, SIZE, DURATION Systematic molecular analyses were conducted for 115 patients with isolated NOA and a normal 46, XY karyotype, who visited our hospital between 2017 and 2021. PARTICIPANTS/MATERIALS, SETTING, METHODS We studied 115 unrelated Japanese patients. AZF-linked CNVs were examined using sequence-tagged PCR and multiplex ligation-dependent probe amplification, and nucleotide variants were screened using whole exome sequencing (WES). An optimized sequence kernel association test (SKAT-O), a gene-based association study using WES data, was performed to identify novel disease-associated genes in the genome. The results were compared to those of previous studies and our in-house control data. MAIN RESULTS AND THE ROLE OF CHANCE Thirteen types of AZF-linked CNVs, including the hitherto unreported gr/gr triplication and partial AZFb deletion, were identified in 63 (54.8%) cases. When the gr/gr deletion, a common polymorphism in Japan, was excluded from data analyses, the total frequency of CNVs was 23/75 (30.7%). This frequency is higher than that of the reference data in Japan and China (11.1% and 14.7%, respectively). Known NOA-causative AZF-linked CNVs were found in nine (7.8%) cases. Rare damaging variants in known causative genes (DMRT1, PLK4, SYCP2, TEX11, and USP26) and hemizygous/multiple-heterozygous damaging variants in known spermatogenesis-associated genes (TAF7L, DNAH2, and DNAH17) were identified in nine cases (7.8% in total). Some patients carried rare damaging variants in multiple genes. SKAT-O detected no genes whose rare damaging variants were significantly accumulated in the patient group. LIMITATIONS, REASONS FOR CAUTION The number of participants was relatively small, and the clinical information of each patient was fragmentary. Moreover, the pathogenicity of identified variants was assessed only by in silico analyses. WIDER IMPLICATIONS OF THE FINDINGS This study showed that various AZF-linked CNVs are present in more than half of Japanese NOA patients. These results broadened the structural variations of AZF-linked CNVs, which should be considered for the molecular diagnosis of spermatogenic failure. Furthermore, the results of this study highlight the etiological heterogeneity and possible oligogenicity of isolated NOA. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by Grants from the Japan Society for the Promotion of Science (21K19283 and 21H0246), the Japan Agency for Medical Research and Development (22ek0109464h0003), the National Center for Child Health and Development, the Canon Foundation, the Japan Endocrine Society, and the Takeda Science Foundation. The results of this study were based on samples and patient data obtained from the International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan. The authors have no conflicts of interest to disclose. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Yuki Muranishi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Renal and Genitourinary Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Yoshitomo Kobori
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Yuko Katoh-Fukui
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Satoshi Tamaoka
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Atsushi Hattori
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akiyoshi Osaka
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Hiroshi Okada
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hiroko Ogata-Kawata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Toshiyuki Iwahata
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Kazuki Saito
- Department of Comprehensive Reproductive Medicine, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masafumi Kon
- Department of Renal and Genitourinary Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Nobuo Shinohara
- Department of Renal and Genitourinary Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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Jiang R, Qiu X, Han X, Ma Z. A novel mutation in ANOS1 in a Chinese family with Kallmann syndrome: Case report. Clin Case Rep 2024; 12:e8860. [PMID: 38736573 PMCID: PMC11082082 DOI: 10.1002/ccr3.8860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 01/23/2024] [Indexed: 05/14/2024] Open
Abstract
We reported a novel variant in Kallmann syndrome. It not only determines the clinical importance of whole exome sequencing for identification of genetic pathogenic variants, but also enriches the ANOS1 genetic spectrum of CHH patients in Chinese population.
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Affiliation(s)
- Rong Jiang
- Endocrinology DepartmentThe Affiliated Suzhou Hospital of Nanjing University Medical SchoolSuzhouJiangsuChina
| | - Xueting Qiu
- Endocrinology DepartmentThe Affiliated Suzhou Hospital of Nanjing University Medical SchoolSuzhouJiangsuChina
| | - Xingfa Han
- Endocrinology DepartmentThe Affiliated Suzhou Hospital of Nanjing University Medical SchoolSuzhouJiangsuChina
| | - Zhimin Ma
- Endocrinology DepartmentThe Affiliated Suzhou Hospital of Nanjing University Medical SchoolSuzhouJiangsuChina
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Zhao M, Meng X, Wang J, Wang T. Corrigendum: Novel FOXL2 variants in two Chinese families with blepharophimosis, ptosis, and epicanthus inversus syndrome. Front Genet 2024; 15:1414939. [PMID: 38742166 PMCID: PMC11089390 DOI: 10.3389/fgene.2024.1414939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fgene.2024.1343411.].
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Affiliation(s)
- Mingyu Zhao
- The Department of Facial and Neck Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaolu Meng
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiaqi Wang
- The Department of Facial and Neck Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tailing Wang
- The Department of Facial and Neck Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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De Sousa SMC, McCormack A, Orsmond A, Shen A, Yates CJ, Clifton-Bligh R, Santoreneos S, King J, Feng J, Toubia J, Torpy DJ, Scott HS. Increased prevalence of germline pathogenic CHEK2 variants in individuals with pituitary adenomas. J Clin Endocrinol Metab 2024:dgae268. [PMID: 38651569 DOI: 10.1210/clinem/dgae268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
CONTEXT CHEK2 is a cell cycle checkpoint regulator gene with a long-established role as a clinically relevant, moderate risk breast cancer predisposition gene, with greater risk ascribed to truncating variants than missense variants. METHODS We assessed 165 individuals with pituitary adenomas for CHEK2 variants. The study consisted of a primary cohort of 29 individuals who underwent germline and tumour whole exome sequencing, and a second, independent cohort of 136 individuals who had a targeted next-generation sequencing panel performed on both germline and tumour DNA (n=52) or germline DNA alone (n=84). RESULTS We identified rare, coding, non-synonymous germline CHEK2 variants amongst 3/29 (10.3%) patients in our primary cohort and 5/165 (3.0%) patients overall, with affected patients having a range of hormone secretion types (prolactinoma, thyrotrophinoma, somatotrophinoma and non-functioning pituitary adenoma). No somatic variants were identified. Two variants were definitive null variants (c.1100delC, c.444+1G>A), classified as pathogenic. Two variants were missense variants (p.Asn186His, p.Thr476Met), classified as likely pathogenic. Even when considering the null variants only, the rate of CHEK2 variants was higher in our cohort compared to national control data (1.8% vs. 0.5%, P=0.049). CONCLUSIONS This is the first study to suggest a role for the breast cancer predisposition gene, CHEK2, in pituitary tumorigenesis, with pathogenic/likely pathogenic variants found in 3% of patients with pituitary adenomas. As pituitary adenomas are relatively common and typically lack classical autosomal dominant family histories, risk alleles - such as these variants found in CHEK2 - might be a significant contributor to pituitary adenoma risk in the general population.
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Affiliation(s)
- Sunita M C De Sousa
- Endocrine & Metabolic Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia
- South Australian Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Ann McCormack
- Department of Endocrinology, St Vincent's Hospital, Sydney, NSW, Australia
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Andreas Orsmond
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Angeline Shen
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher J Yates
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Roderick Clifton-Bligh
- Cancer Genetics Laboratory, Kolling Institute, Royal North Shore Hospital, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
- Department of Endocrinology, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Stephen Santoreneos
- Department of Neurosurgery, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - James King
- Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Jinghua Feng
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, South Australia, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - John Toubia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, South Australia, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - David J Torpy
- Endocrine & Metabolic Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Hamish S Scott
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, South Australia, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
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Komlosi K, Glocker C, Hsu-Rehder HH, Alter S, Kopp J, Hotz A, Zimmer AD, Hausser-Siller I, Sandhoff R, Oji V, Fischer J. Autosomal dominant lamellar ichthyosis due to a missense mutation in the gene NKPD1. J Invest Dermatol 2024:S0022-202X(24)00303-8. [PMID: 38642798 DOI: 10.1016/j.jid.2024.03.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/23/2024] [Accepted: 03/08/2024] [Indexed: 04/22/2024]
Abstract
The identification of monogenic causes for cornification disorders has enhanced our understanding of epidermal differentiation and skin barrier function. Autosomal dominant lamellar ichthyosis (ADLI) is a rare condition, and ASPRV1 was the only gene linked to ADLI to date. We identified a heterozygous variant (ENST00000686631.1:c.1372G>T, p.(Val458Phe)) in the NKPD1 gene in seven individuals from a four-generation German pedigree with generalized lamellar ichthyosis by whole exome sequencing. Segregation analysis confirmed its presence in affected individuals, resulting in a LOD score of 3.31. NKPD1 encodes the NTPase KAP Family P-Loop Domain-Containing Protein 1, implicated in the plasma membrane, its role in human disease is as yet unknown. Skin histology showed moderate acanthosis and compact orthohyperkeratosis, and the ultrastructure differed clearly from that in ASPRV1-ADLI. While NKPD1 mRNA expression increased during keratinocyte differentiation, stratum corneum ceramides exhibited no significant changes. However, affected individuals showed an elevated ratio of protein-bound ceramides to omega-esterified ceramides. This highlights NKPD1's role in ADLI, impacting ceramide metabolism and skin lipid barrier formation, as demonstrated through functional characterization.
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Affiliation(s)
- Katalin Komlosi
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center For Rare Diseases, University of Freiburg, Freiburg, Germany.
| | - Cristina Glocker
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center For Rare Diseases, University of Freiburg, Freiburg, Germany.
| | - Hao-Hsiang Hsu-Rehder
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center For Rare Diseases, University of Freiburg, Freiburg, Germany.
| | - Svenja Alter
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center For Rare Diseases, University of Freiburg, Freiburg, Germany.
| | - Julia Kopp
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center For Rare Diseases, University of Freiburg, Freiburg, Germany.
| | - Alrun Hotz
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center For Rare Diseases, University of Freiburg, Freiburg, Germany.
| | - Andreas David Zimmer
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center For Rare Diseases, University of Freiburg, Freiburg, Germany.
| | | | - Roger Sandhoff
- Lipid Pathobiochemistry Group, German Cancer Research Center, Heidelberg, Germany.
| | - Vinzenz Oji
- Department of Dermatology, University Hospital Münster, Münster, Germany.
| | - Judith Fischer
- Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center For Rare Diseases, University of Freiburg, Freiburg, Germany.
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10
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Yang S, Li Z. FBN2 pathogenic variants in congenital contractural arachnodactyly with severe cardiovascular manifestations. Connect Tissue Res 2024:1-12. [PMID: 38602424 DOI: 10.1080/03008207.2024.2340004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
PURPOSE Congenital contractural arachnodactyly (CCA) is an extremely rare autosomal dominant connective tissue genetic disorder caused by pathogenic variants in FBN2. CCA is characterized by arachnodactyly, camptodactyly, contracture of major joints, scoliosis, pectus deformities, and crumpled ears, but rarely with lethal cardiovascular manifestations as in Marfan syndrome. It is imperative to conduct a comprehensive analysis and review of the pathogenesis of CCA resulting from pathogenic variants in FBN2 gene. MATERIALS AND METHODS Using whole-exome sequencing and Sanger sequencing, we identified a novel pathogenic splice-altering variant (c.4472-3C>A) in intron 34 of FBN2 gene in a CCA pedigree. The transcriptional result of the splicing-altering variant was analyzed by RNA sequencing. We systematically analyzed the clinical manifestations of all reported cases of CCA caused by splicing-altering pathogenic variants and focused on all the pathogenic variants in FBN2 gene that are associated with severe cardiovascular manifestations. RESULTS The splice-altering variant (c.4472-3C>A) in FBN2 was demonstrated to result in the exon 35 skipping and cause an in-frame deletion. Furthermore, we identified exons 31 to 35 may be a hotspot region in FBN2 gene associated with severe cardiovascular phenotype. CONCLUSIONS This study enriched the pathogenic spectrum of CCA and identified a hotspot region in FBN2 gene associated with severe cardiovascular manifestations. We recommend that patients carrying pathogenic variants in exons 31 to 35 of FBN2 pay more attention to cardiac evaluation.
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Affiliation(s)
- Shulin Yang
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zongzhe Li
- Division of Cardiology, Departments of Internal Medicine and Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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11
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Veerappa A, Guda C. Coordination among frequent genetic variants imparts substance use susceptibility and pathogenesis. Front Neurosci 2024; 18:1332419. [PMID: 38660223 PMCID: PMC11041639 DOI: 10.3389/fnins.2024.1332419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
Determining the key genetic variants is a crucial step to comprehensively understand substance use disorders (SUDs). In this study, utilizing whole exome sequences of five multi-generational pedigrees with SUDs, we used an integrative omics-based approach to uncover candidate genetic variants that impart susceptibility to SUDs and influence addition traits. We identified several SNPs and rare, protein-function altering variants in genes, GRIA3, NCOR1, and SHANK1; compound heterozygous variants in LNPEP, LRP1, and TBX2, that play a significant role in the neurotransmitter-neuropeptide axis, specifically in the dopaminergic circuits. We also noted a greater frequency of heterozygous and recessive variants in genes involved in the structural and functional integrity of synapse receptors, CHRNA4, CNR2, GABBR1, DRD4, NPAS4, ADH1B, ADH1C, OPRM1, and GABBR2. Variant analysis in upstream promoter regions revealed regulatory variants in NEK9, PRRX1, PRPF4B, CELA2A, RABGEF1, and CRBN, crucial for dopamine regulation. Using family-and pedigree-based data, we identified heterozygous recessive alleles in LNPEP, LRP1 (4 frameshift deletions), and TBX2 (2 frameshift deletions) linked to SUDs. GWAS overlap identified several SNPs associated with SUD susceptibility, including rs324420 and rs1229984. Furthermore, miRNA variant analysis revealed notable variants in mir-548 U and mir-532. Pathway studies identified the presence of extensive coordination among these genetic variants to impart substance use susceptibility and pathogenesis. This study identified variants that were found to be overrepresented among genes of dopaminergic circuits participating in the neurotransmitter-neuropeptide axis, suggesting pleiotropic influences in the development and sustenance of chronic substance use. The presence of a diverse set of haploinsufficient variants in varying frequencies demonstrates the existence of extraordinary coordination among them in attributing risk and modulating severity to SUDs.
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Affiliation(s)
- Avinash Veerappa
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
- Center for Biomedical Informatics Research and Innovation, University of Nebraska Medical Center, Omaha, NE, United States
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12
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Shao Y, Yang S, Li J, Cheng L, Kang J, Liu J, Ma J, Duan J, Zhang Y. Compound heterozygous mutation of the SNX14 gene causes autosomal recessive spinocerebellar ataxia 20. Front Genet 2024; 15:1379366. [PMID: 38655056 PMCID: PMC11035801 DOI: 10.3389/fgene.2024.1379366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
Objective: The article aims to provide genetic counseling to a family with two children who were experiencing growth and developmental delays. Methods: Clinical information of the proband was collected. Peripheral blood was collected from core family members to identify the initial reason for growth and developmental delays by whole exome sequencing (WES) and Sanger sequencing. To ascertain the consequences of the newly discovered variants, details of the variants detected were analyzed by bioinformatic tools. Furthermore, we performed in vitro experimentation targeting SNX14 gene expression to confirm whether the variants could alter the expression of SNX14. Results: The proband had prenatal ultrasound findings that included flattened frontal bones, increased interocular distance, widened bilateral cerebral sulci, and shortened long bones, which resulted in subsequent postnatal developmental delays. The older sister also displayed growth developmental delays and poor muscle tone. WES identified compound heterozygous variants of c.712A>T (p.Arg238Ter) and .2744A>T (p.Gln915Leu) in the SNX14 gene in these two children. Both are novel missense variant that originates from the father and mother, respectively. Sanger sequencing confirmed this result. Following the guideline of the American College of Medical Genetics and Genomics (ACMG), the SNX14 c.712A>T (p.Arg238Ter) variant was predicted to be pathogenic (P), while the SNX14 c.2744A>T (p.Gln915Leu) variant was predicted to be a variant of uncertain significance (VUS). The structural analysis revealed that the c.2744A>T (p.Gln915Leu) variant may impact the stability of the SNX14 protein. In vitro experiments demonstrated that both variants reduced SNX14 expression. Conclusion: The SNX14 gene c.712A>T (p.Arg238Ter) and c.2744A>T (p.Gln915Leu) were identified as the genetic causes of growth and developmental delay in two affected children. This conclusion was based on the clinical presentations of the children, structural analysis of the mutant protein, and in vitro experimental validation. This discovery expands the range of SNX14 gene variants and provides a foundation for genetic counseling and guidance for future pregnancies in the affected children's families.
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Affiliation(s)
- Yuqi Shao
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, China
| | - Saisai Yang
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, China
| | - Jiafu Li
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lin Cheng
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, China
| | - Jiawei Kang
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, China
| | - Juan Liu
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, China
| | - Jianhong Ma
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, China
| | - Jie Duan
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, China
| | - Yuanzhen Zhang
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, China
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13
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Budak B, Arga KY. Tumor Mutation Burden as a Cornerstone in Precision Oncology Landscapes: Effect of Panel Size and Uncertainty in Cutoffs. OMICS 2024; 28:193-203. [PMID: 38657109 DOI: 10.1089/omi.2024.0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Tumor mutation burden (TMB) has profound implications for personalized cancer therapy, particularly immunotherapy. However, the size of the panel and the cutoff values for an accurate determination of TMB are still controversial. In this study, a pan-cancer analysis was performed on 22 cancer types from The Cancer Genome Atlas. The efficiency of gene panels of different sizes and the effect of cutoff values in accurate TMB determination was assessed on a large cohort using Whole Exome Sequencing data (n = 9929 patients) as the gold standard. Gene panels of four different sizes (i.e., 0.44-2.54 Mb) were selected for comparative analyses. The heterogeneity of TMB within and between cancer types is observed to be very high, and it becomes possible to obtain the exact TMB value as the size of the panel increases. In panels with limited size, it is particularly difficult to recognize patients with low TMB. In addition, the use of a general TMB cutoff can be quite misleading. The optimal cutoff value varies between 5 and 20, depending on the TMB distribution of the different tumor types. The use of comprehensive gene panels and the optimization of TMB cutoff values for different cancer types can make TMB a robust biomarker in precision oncology. Moreover, optimization of TMB can help accelerate translational medicine research, and by extension, delivery of personalized cancer care in the future.
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Affiliation(s)
- Betul Budak
- Department of Genetics and Bioengineering, Istanbul Bilgi University, Istanbul, Türkiye
- Department of Bioengineering, Marmara University, Istanbul, Türkiye
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, Istanbul, Türkiye
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Türkiye
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Türkiye
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14
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Pérez-Sayáns M, Chamorro-Petronacci CM, Bravo SB, Padín-Iruegas ME, Guitián-Fernández E, Barros-Angueira F, Quintas-Rey R, García-García A. Genetic linkage analysis of head and neck cancer in a Spanish family. Oral Dis 2024; 30:1032-1039. [PMID: 37026679 DOI: 10.1111/odi.14572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 04/08/2023]
Abstract
OBJECTIVES To describe the genetic variants that may be associated with the development of head and neck cancer (HNC) and functionally validating the molecular implications. MATERIALS AND METHODS A prospective observational study was carried out on a family of 3 generations in which 3 members had developed HNC. Peripheral blood sample was taken in a routine procedure for exome sequencing in one relative and genotyping in the remaining twelve relatives. For the functional analysis all-trans retinoic acid (atRA) was extracted from saliva and serum and measured using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The presence of HPV-DNA. RESULTS None of the patients smoked or consumed alcohol. The presence of HPV DNA was not detected in any of the biopsied samples. A total amount of 6 members out of 13 (46.15%) carried out the same mutation of CYP26B1 (2p13.2; G>T). The mean plasma concentration of atRA was 3.3109 ± 1.4791 pg/mL for the study family and 4.7370 ± 1.5992 pg/mL for the controls (p = 0.042). CONCLUSION Lower levels of atRA were confirmed in the study family, which may open the way to the possible relationship between the polymorphism CYP26B1 (2p13.2; G>T) and HNC.
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Affiliation(s)
- Mario Pérez-Sayáns
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Santiago de Compostela University, Santiago de Compostela, Spain
- Institute of Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Cintia M Chamorro-Petronacci
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Santiago de Compostela University, Santiago de Compostela, Spain
- Institute of Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Susana B Bravo
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, Santiago de Compostela, Spain
| | - María E Padín-Iruegas
- Department of Functional Biology and Health Sciences, Faculty of Physiotherapy, Human Anatomy and Embryology Area, Vigo University, Pontevedra, Spain
| | - Esteban Guitián-Fernández
- Mass Spectrometry and Proteomics Unit, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco Barros-Angueira
- Molecular Medicine Unit - Galician Public Foundation of Genomic Medicine, Consultation Building, Floor -2, University Hospital Complex of Santiago, Santiago de Compostela, Spain
| | - Rita Quintas-Rey
- Molecular Medicine Unit - Galician Public Foundation of Genomic Medicine, Consultation Building, Floor -2, University Hospital Complex of Santiago, Santiago de Compostela, Spain
| | - Abel García-García
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Santiago de Compostela University, Santiago de Compostela, Spain
- Institute of Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
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15
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Dufresne A, Attignon V, Ferrari A, Tonon L, Boyault S, Tabone‐Eglinger S, Cassier P, Trédan O, Corradini N, Vinceneux A, Swalduz A, Viari A, Chabaud S, Pérol D, Blay JY, Saintigny P. Added value of whole-exome and RNA sequencing in advanced and refractory cancer patients with no molecular-based treatment recommendation based on a 90-gene panel. Cancer Med 2024; 13:e7115. [PMID: 38553950 PMCID: PMC10980928 DOI: 10.1002/cam4.7115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 02/21/2024] [Accepted: 03/04/2024] [Indexed: 04/02/2024] Open
Abstract
INTRODUCTION The objective was to determine the added value of comprehensive molecular profile by whole-exome and RNA sequencing (WES/RNA-Seq) in advanced and refractory cancer patients who had no molecular-based treatment recommendation (MBTR) based on a more limited targeted gene panel (TGP) plus array-based comparative genomic hybridization (aCGH). MATERIALS AND METHODS In this retrospective analysis, we selected 50 patients previously included in the PROFILER trial (NCT01774409) for which no MBT could be recommended based on a targeted 90-gene panel and aCGH. For each patient, the frozen tumor sample mirroring the FFPE sample used for TGP/aCGH analysis were processed for WES and RNA-Seq. Data from TGP/aCGH were reanalyzed, and together with WES/RNA-Seq, findings were simultaneously discussed at a new molecular tumor board (MTB). RESULTS After exclusion of variants of unknown significance, a total of 167 somatic molecular alterations were identified in 50 patients (median: 3 [1-10]). Out of these 167 relevant molecular alterations, 51 (31%) were common to both TGP/aCGH and WES/RNA-Seq, 19 (11%) were identified by the TGP/aCGH only and 97 (58%) were identified by WES/RNA-Seq only, including two fusion transcripts in two patients. A MBTR was provided in 4/50 (8%) patients using the information from TGP/aCGH versus 9/50 (18%) patients using WES/RNA-Seq findings. Three patients had similar recommendations based on TGP/aCGH and WES/RNA-Seq. CONCLUSIONS In advanced and refractory cancer patients in whom no MBTR was recommended from TGP/aCGH, WES/RNA-Seq allowed to identify more alterations which may in turn, in a limited fraction of patients, lead to new MBTR.
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Affiliation(s)
| | | | - Anthony Ferrari
- Platform of Bioinformatics Gilles‐ThomasCentre Léon BérardLyonFrance
| | - Laurie Tonon
- Platform of Bioinformatics Gilles‐ThomasCentre Léon BérardLyonFrance
| | | | | | | | - Olivier Trédan
- Department of Medical OncologyCentre Léon BérardLyonFrance
| | - Nadège Corradini
- Department of Pediatric Oncology, Institute of Pediatric Hematology and OncologyCentre Leon BérardLyonFrance
| | | | | | - Alain Viari
- Platform of Bioinformatics Gilles‐ThomasCentre Léon BérardLyonFrance
| | - Sylvie Chabaud
- Department of Clinical ResearchCentre Léon BérardLyonFrance
| | - David Pérol
- Department of Clinical ResearchCentre Léon BérardLyonFrance
| | - Jean Yves Blay
- Department of Medical OncologyCentre Léon BérardLyonFrance
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon BérardCancer Research Center of LyonLyonFrance
| | - Pierre Saintigny
- Department of Medical OncologyCentre Léon BérardLyonFrance
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon BérardCancer Research Center of LyonLyonFrance
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Nazmina G, Khan A, Jiang J, Miao Z, Khan SN, Khan MI, Shah AH, Shah AH, Khisroon M, Haack TB. Exome sequencing identifies homozygous variants in MBOAT7 associated with neurodevelopmental disorder. Clin Genet 2024; 105:423-429. [PMID: 38088234 DOI: 10.1111/cge.14469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 02/24/2024]
Abstract
Intellectual disability (ID) is a large group of neurodevelopmental disorders characterized by a congenital limitation in intellectual functioning (reasoning, learning, and problem solving), adaptive behavior (conceptual, social, and practical skills), originated at birth and manifested before the age of 18. By whole exome sequencing of five consanguineous Pakistani families presenting hallmark features of ID, global developmental delay, aggressive and self-injurious behaviors, microcephaly, febrile seizures and facial dysmorphic features, we identified three novel homozygous missense variants (NM_024298.5: c.588G > T; p.Trp196Cys, c.736 T > C; p.Tyr246His and c.524A > C; p. Asp175Ala) and one rare homozygous in-frame deletion variant (c.758_778del;p.Glu253_Ala259del) in membrane-bound O-acyltransferase family member 7 (MBOAT7) gene previously associated with autosomal recessive neurodevelopmental disorder. The segregation of the variants was validated by Sanger sequencing in all family members. In silico homology modeling of wild-type and mutated proteins revealed substantial changes in the structure of both proteins, indicating a possible effect on function. The identification and validation of new pathogenic MBOAT7 variants in five cases of autosomal recessive ID further highlight the importance of this genes in proper brain function and development.
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Affiliation(s)
- Gul Nazmina
- Department of Zoology, University of Peshawar, Peshawar, Pakistan
| | - Amjad Khan
- Faculty of Biological Sciences, Department of Zoology, University of Lakki Marwat, Khyber Pakhtunkhwa, Pakistan
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Alexander von Humboldt Fellowship Foundation, Berlin, Germany
| | - Jiuhong Jiang
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Zhichao Miao
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shahid Niaz Khan
- Department of Zoology, Kohat University of Science and Technology, Kohat, Pakistan
| | | | - Abdul Haleem Shah
- Institute of Biological sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Ayesha Haleem Shah
- Institute of Biological sciences, Gomal University, Dera Ismail Khan, Pakistan
| | | | - Tobias B Haack
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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Jelin AC, Wohler E, Martin R, Di Carlo H, Isaacs W, Ko J, Michaud J, Blakemore K, Valle D, Sobreira N, Gearhart J. De novo variants identified by trio whole exome sequencing of bladder exstrophy epispadias complex. Am J Med Genet A 2024; 194:e63501. [PMID: 38082334 PMCID: PMC10939865 DOI: 10.1002/ajmg.a.63501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/15/2023] [Accepted: 11/28/2023] [Indexed: 03/10/2024]
Abstract
Bladder exstrophy epispadias complex (BEEC) encompasses a spectrum of conditions ranging from mild epispadias to the most severe form: omphalocele-bladder exstrophy-imperforate anus-spinal defects (OEIS). BEEC involves abnormalities related to anatomical structures that are proposed to have a similar underlying etiology and pathogenesis. In general, BEEC, is considered to arise from a sequence of events in embryonic development and is believed to be a multi-etiological disease with contributions from genetic and environmental factors. Several genes have been implicated and mouse models have been generated, including a knockout model of p63, which is involved in the synthesis of stratified epithelium. Mice lacking p63 have undifferentiated ventral urothelium. MNX1 has also been implicated. In addition, cigarette smoking, diazepam and clomid have been implied as environmental factors due to their relative association. By in large, the etiology and pathogenesis of human BEEC is unknown. We performed de novo analysis of whole exome sequencing (WES) of germline samples from 31 unrelated trios where the probands have a diagnosis of BEEC syndrome. We also evaluated the DECIPHER database to identify copy number variants (CNVs) in genes in individuals with the search terms "bladder exstrophy" in an attempt to identify additional candidate genes within these regions. Several de novo variants were identified; however, a candidate gene is still unclear. This data further supports the multi-etiological nature of BEEC.
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Affiliation(s)
- Angie C Jelin
- Department of Gynecology and Obstetrics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Renan Martin
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Heather Di Carlo
- Department of Pediatric Urology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - William Isaacs
- Department of Pediatric Urology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Joan Ko
- Department of Pediatric Urology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Jason Michaud
- Department of Pediatric Urology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Karin Blakemore
- Department of Gynecology and Obstetrics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - David Valle
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - John Gearhart
- Department of Pediatric Urology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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Sepulveda‐Falla D, Vélez JI, Acosta‐Baena N, Baena A, Moreno S, Krasemann S, Lopera F, Mastronardi CA, Arcos‐Burgos M. Genetic modifiers of cognitive decline in PSEN1 E280A Alzheimer's disease. Alzheimers Dement 2024; 20:2873-2885. [PMID: 38450831 PMCID: PMC11032577 DOI: 10.1002/alz.13754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
INTRODUCTION Rate of cognitive decline (RCD) in Alzheimer's disease (AD) determines the degree of impairment for patients and of burden for caretakers. We studied the association of RCD with genetic variants in AD. METHODS RCD was evaluated in 62 familial AD (FAD) and 53 sporadic AD (SAD) cases, and analyzed by whole-exome sequencing for association with common exonic functional variants. Findings were validated in post mortem brain tissue. RESULTS One hundred seventy-two gene variants in FAD, and 227 gene variants in SAD associated with RCD. In FAD, performance decline of the immediate recall of the Rey-Osterrieth figure test associated with 122 genetic variants. Olfactory receptor OR51B6 showed the highest number of associated variants. Its expression was detected in temporal cortex neurons. DISCUSSION Impaired olfactory function has been associated with cognitive impairment in AD. Genetic variants in these or other genes could help to identify risk of faster memory decline in FAD and SAD patients.
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Affiliation(s)
- Diego Sepulveda‐Falla
- Institute of NeuropathologyUniversity Medical Center Hamburg‐EppendorfHamburgGermany
- Grupo de Neurociencias de AntioquiaUniversidad de AntioquiaMedellínColombia
| | - Jorge I. Vélez
- Grupo de Neurociencias de AntioquiaUniversidad de AntioquiaMedellínColombia
- Universidad del NorteBarranquillaColombia
| | | | - Ana Baena
- Grupo de Neurociencias de AntioquiaUniversidad de AntioquiaMedellínColombia
| | - Sonia Moreno
- Grupo de Neurociencias de AntioquiaUniversidad de AntioquiaMedellínColombia
| | - Susanne Krasemann
- Institute of NeuropathologyUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Francisco Lopera
- Grupo de Neurociencias de AntioquiaUniversidad de AntioquiaMedellínColombia
| | - Claudio A. Mastronardi
- Genomics and Predictive Medicine GroupDepartment of Genome SciencesJohn Curtin School of Medical ResearchThe Australian National UniversityCanberraAustralia
- INPAC Research Group, Fundación Universitaria SanitasBogotáColombia
| | - Mauricio Arcos‐Burgos
- Grupo de Investigación en Psiquiatría (GIPSI)Departamento de PsiquiatríaFacultad de MedicinaInstituto de Investigaciones MédicasUniversidad de AntioquiaMedellínColombia
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19
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Bai T, Shen Y, Yang Y, Dai S, Liu H. Maternal CHD7 gonosomal mosaicism in a fetus with CHARGE syndrome. Am J Med Genet A 2024; 194:e63491. [PMID: 38057991 DOI: 10.1002/ajmg.a.63491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
Parental mosaicism is important in families with de novo mutations. Herein, we report a case of fetal CHARGE syndrome (CS) with a CHD7 variant inherited from maternal CHD7 gonosomal mosaicism. The variant was detected through trio-based whole-exome sequencing and Sanger sequencing. High-depth whole-exome sequencing was performed for the identification of parental mosaicism. A novel heterozygous CHD7 nonsense mutation (c.5794G>T/ p.E1932*) was detected in the tissue from the aborted fetus. The parents were wild-type, indicating that the mutation was a de novo variant. The mutation was suspected to be the cause of the fetal CS. However, high-depth whole-exome sequencing revealed maternal gonosomal mosaicism at a variant allele frequency of 3.2%-23.3%. The variant was identified in various tissues (peripheral blood, hair follicles, buccal epithelia, and pharyngeal epithelia) from the asymptomatic mother. We confirmed maternal CHD7 gonosomal mosaicism as a genetic cause of fetal CS. Our results emphasize the importance of clinical analysis in accurately determining the parents' status in detecting the CHD7 de novo variant in fetal CS, as this analysis has vital implications for evaluating the recurrence risk for genetic counseling.
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Affiliation(s)
- Ting Bai
- Department of Medical Genetics, 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
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Ying Shen
- Department of Obstetrics/Gynecology, Joint Laboratory of Reproductive Medicine (SCU-CUHK), Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yanting Yang
- Department of Medical Genetics, 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
| | - Siyu Dai
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Hongqian Liu
- Department of Medical Genetics, 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
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
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20
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Alfayyadh MM, Maksemous N, Sutherland HG, Lea RA, Griffiths LR. Unravelling the Genetic Landscape of Hemiplegic Migraine: Exploring Innovative Strategies and Emerging Approaches. Genes (Basel) 2024; 15:443. [PMID: 38674378 PMCID: PMC11049430 DOI: 10.3390/genes15040443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Migraine is a severe, debilitating neurovascular disorder. Hemiplegic migraine (HM) is a rare and debilitating neurological condition with a strong genetic basis. Sequencing technologies have improved the diagnosis and our understanding of the molecular pathophysiology of HM. Linkage analysis and sequencing studies in HM families have identified pathogenic variants in ion channels and related genes, including CACNA1A, ATP1A2, and SCN1A, that cause HM. However, approximately 75% of HM patients are negative for these mutations, indicating there are other genes involved in disease causation. In this review, we explored our current understanding of the genetics of HM. The evidence presented herein summarises the current knowledge of the genetics of HM, which can be expanded further to explain the remaining heritability of this debilitating condition. Innovative bioinformatics and computational strategies to cover the entire genetic spectrum of HM are also discussed in this review.
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Affiliation(s)
| | | | | | | | - Lyn R. Griffiths
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD 4059, Australia; (M.M.A.); (N.M.); (H.G.S.); (R.A.L.)
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21
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Wei T, Zhang B, Tang W, Li X, Shuai Z, Tang T, Zhang Y, Deng L, Liu Q. A de novo PKD1 mutation in a Chinese family with autosomal dominant polycystic kidney disease. Medicine (Baltimore) 2024; 103:e27853. [PMID: 38552045 PMCID: PMC10977567 DOI: 10.1097/md.0000000000027853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 11/02/2021] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND PKD1, which has a relatively high mutation rate, is highly polymorphic, and the role of PKD1 is incompletely defined. In the current study, in order to determine the molecular etiology of a family with autosomal dominant polycystic kidney disease, the pathogenicity of an frameshift mutation in the PKD1 gene, c.9484delC, was evaluated. METHODS The family clinical data were collected. Whole exome sequencing analysis determined the level of this mutation in the proband's PKD1, and Sanger sequencing and bioinformatics analysis were performed. SIFT, Polyphen2, and MutationTaster were used to evaluate the conservation of the gene and pathogenicity of the identified mutations. SWISS-MODEL was used to predict and map the protein structure of PKD1 and mutant neonate proteins. RESULTS A novel c.9484delC (p.Arg3162Alafs*154) mutation of the PKD1 gene was identified by whole exome sequencing in the proband, which was confirmed by Sanger sequencing in his sister (II7). The same mutation was not detected in the healthy pedigree members. Random screening of 100 normal and end-stage renal disease patients did not identify the c.9484delC mutation. Bioinformatics analysis suggested that the mutation caused the 3162 nd amino acid substitution of arginine by alanine and a shift in the termination codon. As a result, the protein sequence was shortened from 4302 amino acids to 3314 amino acids, the protein structure was greatly changed, and the PLAT/LH2 domain was destroyed. Clustal analysis indicated that the altered amino acids were highly conserved in mammals. CONCLUSION A novel mutation in the PKD1 gene has been identified in an affected Chinese family. The mutation is probably responsible for a range of clinical manifestations for which reliable prenatal diagnosis and genetic counseling may be provided.
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Affiliation(s)
- Ting Wei
- Department of Medical Laboratory, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China
- Department of Medical Laboratory, North Sichuan Medical College, Nanchong, China
| | - Bing Zhang
- Department of Medical Laboratory, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China
| | - Wei Tang
- Department of Medical Laboratory, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China
| | - Xin Li
- Department of Medical Laboratory, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China
| | - Zhuang Shuai
- Department of Cardiology Medicine, the Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Tao Tang
- Department of Medical Laboratory, North Sichuan Medical College, Nanchong, China
| | - Yueyang Zhang
- Department of Medical Laboratory, North Sichuan Medical College, Nanchong, China
| | - Lin Deng
- Department of Medical Laboratory, North Sichuan Medical College, Nanchong, China
| | - Qingsong Liu
- Department of Prenatal Diagnosis, Chengdu Women’s and Children’s Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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Uddin MS, Alradhi AY, Alqathani FMN, Alessa OS, Alshammari ANM, Tripathy R, Alomari MA. A Rare Case of Neonatal Hypomagnesemia with Secondary Hypocalcemia Caused by a Novel Homozygous TRPM6 Gene Variant. Am J Case Rep 2024; 25:e942498. [PMID: 38528672 PMCID: PMC10985420 DOI: 10.12659/ajcr.942498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 02/22/2024] [Accepted: 02/13/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND Familial hypomagnesemia with secondary hypocalcemia (HSH) is a rare autosomal recessive disorder (OMIM# 602014) caused by mutations in the gene encoding transient receptor potential melastatin 6 (TRPM6)) on chromosome 9q22, a channel involved in epithelial magnesium resorption. While a plethora of studies have delineated various clinical manifestations pertinent to this mutation, the literature is devoid of connections between TRPM6 mutations and bleeding diathesis, or sudden infant death syndrome (SIDS). This report presents a case of familial HSH associated with the novel homozygous TRPM6 gene variant c.5281C>G p. (Arg1761Gly) chr9: 77354845. CASE REPORT This report details a 26-day-old neonate, born full term with optimal Apgar scores, who experienced an abrupt emergence of apnea, cyanosis, bilateral nasal bleeding, and diminished alertness. Despite the neonate's initially unremarkable clinical birth indicators, a meticulous assessment unveiled a pronounced family history of SIDS, including a sibling previously diagnosed with hypomagnesemia. Laboratory examination of the infant demonstrated severe hypomagnesemia and hypocalcemia, conditions which were promptly ameliorated following intravenous administration of magnesium and calcium. Whole-exome sequencing identified a homozygous TRPM6 gene mutation c.5281C>G p. (Arg1761Gly) at chr9: 77354845. This gene is crucial for magnesium regulation. The mutation involves a cytosine-to-guanine shift, resulting in an arginine to glycine amino acid substitution at position 1761 of the TRPM6 protein. CONCLUSIONS This report has highlighted that infantile hypomagnesemia may be associated with symptoms and signs that can mimic infection, or it can present with seizures. Although familial HSH is a rare genetic disorder that can be identified by genetic testing, correction of hypomagnesemia is the most important and immediate clinical management strategy.
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Affiliation(s)
- Mohammed Shahab Uddin
- Department of Pediatrics, Ministry of National Guard Health Affairs, Dammam, Saudi Arabia
| | - AlZahra Y. Alradhi
- Department of Pediatrics, Ministry of National Guard Health Affairs, Dammam, Saudi Arabia
| | | | - Othman Saleh Alessa
- Department of Pediatrics, Ministry of National Guard Health Affairs, Dammam, Saudi Arabia
| | | | - Ratna Tripathy
- Department of Human Genetics, Bioscientia Institute for Medical Diagnostics GmbH, Ingelheim, Germany
| | - Mohammed Ahmed Alomari
- Department of Pediatrics, Ministry of National Guard Health Affairs, Dammam, Saudi Arabia
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23
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Li H, Hu X, Ning MS, Fuller GN, Stewart JM, Gilliam JC, Wu J, Le X, Vaporciyan AA, Lee JJ, Gibbons DL, Heymach JV, Futreal A, Zhang J. Case report: Molecular profiling facilitates the diagnosis of a challenging case of lung cancer with choriocarcinoma features. Front Oncol 2024; 14:1324057. [PMID: 38590653 PMCID: PMC10999639 DOI: 10.3389/fonc.2024.1324057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/29/2024] [Indexed: 04/10/2024] Open
Abstract
Accurate diagnoses are crucial in determining the most effective treatment across different cancers. In challenging cases, morphology-based traditional pathology methods have important limitations, while molecular profiling can provide valuable information to guide clinical decisions. We present a 35-year female with lung cancer with choriocarcinoma features. Her disease involved the right lower lung, brain, and thoracic lymph nodes. The pathology from brain metastasis was reported as "metastatic choriocarcinoma" (a germ cell tumor) by local pathologists. She initiated carboplatin and etoposide, a regimen for choriocarcinoma. Subsequently, her case was assessed by pathologists from an academic cancer center, who gave the diagnosis of "adenocarcinoma with aberrant expression of β-hCG" and finally pathologists at our hospital, who gave the diagnosis of "poorly differentiated carcinoma with choriocarcinoma features". Genomic profiling detected a KRAS G13R mutation and transcriptomics profiling was suggestive of lung origin. The patient was treated with carboplatin/paclitaxel/ipilimumab/nivolumab followed by consolidation radiation therapy. She had no evidence of progression to date, 16 months after the initial presentation. The molecular profiling could facilitate diagnosing of challenging cancer cases. In addition, chemoimmunotherapy and local consolidation radiation therapy may provide promising therapeutic options for patients with lung cancer exhibiting choriocarcinoma features.
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Affiliation(s)
- Hui Li
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Matthew S. Ning
- Department of Thoracic Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Gregory N. Fuller
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - John M. Stewart
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Jia Wu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ara A. Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - J. Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Don L. Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - John V. Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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Pantalone G, Mancardi MM, Rossi A, Romanelli R, Marasco E, Carla M. A de novo frameshift variant in MED13 gene in a patient with autism spectrum disorder and magnetic resonance imaging abnormalities mimicking tuberous sclerosis. Am J Med Genet A 2024:e63611. [PMID: 38528425 DOI: 10.1002/ajmg.a.63611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/09/2024] [Accepted: 03/13/2024] [Indexed: 03/27/2024]
Abstract
The mediator complex subunit 13 (MED13) gene is implicated in neurodevelopmental disorders including autism spectrum disorder (ASD), intellectual disability, and speech delay with varying severity and course. Additional, extra central nervous system, features include eye or vision problems, hypotonia, congenital heart abnormalities, and dysmorphisms. We describe a 7-year- and 4-month-old girl evaluated for ASD whose brain magnetic resonance imaging was suggestive of multiple cortical tubers. The exome sequencing (ES - trio analysis) uncovered a unique, de novo, frameshift variant in the MED13 gene (c.4880del, D1627Vfs*17), with a truncating effect on the protein. This case report thus expands the phenotypic spectrum of MED13-related disorders to include brain abnormalities.
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Affiliation(s)
- Gloria Pantalone
- Child Neurology and Psychiatry Unit, "G. Salesi" Children's Hospital, Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | - Maria Margherita Mancardi
- Unit of Child Neuropsychiatry, EpiCARE Member for Rare Diseases, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Andrea Rossi
- Neuroradiology Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | | | | | - Marini Carla
- Child Neurology and Psychiatry Unit, "G. Salesi" Children's Hospital, Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
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Wilson GN, Tonk VS. Clinical-Genomic Analysis of 1261 Patients with Ehlers-Danlos Syndrome Outlines an Articulo-Autonomic Gene Network (Entome). Curr Issues Mol Biol 2024; 46:2620-2643. [PMID: 38534782 DOI: 10.3390/cimb46030166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/08/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
Systematic evaluation of 80 history and 40 history findings diagnosed 1261 patients with Ehlers-Danlos syndrome (EDS) by direct or online interaction, and 60 key findings were selected for their relation to clinical mechanisms and/or management. Genomic testing results in 566 of these patients supported EDS relevance by their differences from those in 82 developmental disability patients and by their association with general rather than type-specific EDS findings. The 437 nuclear and 79 mitochondrial DNA changes included 71 impacting joint matrix (49 COL5), 39 bone (30 COL1/2/9/11), 22 vessel (12 COL3/8VWF), 43 vessel-heart (17FBN1/11TGFB/BR), 59 muscle (28 COL6/12), 56 neural (16 SCN9A/10A/11A), and 74 autonomic (13 POLG/25porphyria related). These genes were distributed over all chromosomes but the Y, a network analogized to an 'entome' where DNA change disrupts truncal mechanisms (skin constraint, neuromuscular support, joint vessel flexibility) and produces a mirroring cascade of articular and autonomic symptoms. The implied sequences of genes from nodal proteins to hypermobility to branching tissue laxity or dysautonomia symptoms would be ideal for large language/artificial intelligence analyses.
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Affiliation(s)
- Golder N Wilson
- Department of Pediatrics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- KinderGenome Genetics Private Practice, 5347 W Mockingbird, Dallas, TX 75209, USA
| | - Vijay S Tonk
- Director of Medical Genetics and the Cytogenomic Laboratory, Department of Pediatrics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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Shrivastava A, Magani SKJ, Lokhande KB, Chintakhindi M, Singh A. Exploring the role of TLK2 mutation in tropical calcific pancreatitis: an in silico and molecular dynamics simulation study. J Biomol Struct Dyn 2024:1-20. [PMID: 38500246 DOI: 10.1080/07391102.2024.2329797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
Tropical calcific pancreatitis (TCP) is a juvenile form of non-alcoholic chronic pancreatitis seen exclusively in tropical countries. The disease poses a high risk of complications, including pancreatic diabetes and cancer, leading to significant mortality due to poor diagnosis and ineffective treatments. This study employed whole exome sequencing (WES) of 5 TCP patient samples to identify genetic variants associated with TCP. Advanced computational techniques were used to gain atomic-level insights into disease progression, including microsecond-scale long MD simulations and essential dynamics. In silico virtual screening was performed to identify potential therapeutic compounds targeting the mutant protein using the Asinex and DrugBank compound library. WES analysis predicted several single nucleotide variants (SNVs) associated with TCP, including a novel missense variant (c.T1802A or p.V601E) in the TLK2 gene. Computational analysis revealed that the p.V601E mutation significantly affected the structure of the TLK2 kinase domain and its conformational dynamics, altering the interaction profile between ATP and the binding pocket. These changes could impact TLK2's kinase activity and functions, potentially correlating with TCP progression. Promising lead compounds that selectively bind to the TLK2 mutant protein were identified, offering potential for therapeutic interventions in TCP. These findings hold great potential for future research.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ashish Shrivastava
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Sri Krishna Jayadev Magani
- Cancer Biology Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Kiran Bharat Lokhande
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | | | - Ashutosh Singh
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
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Yeo NKW, Lim CK, Yaung KN, Khoo NKH, Arkachaisri T, Albani S, Yeo JG. Genetic interrogation for sequence and copy number variants in systemic lupus erythematosus. Front Genet 2024; 15:1341272. [PMID: 38501057 PMCID: PMC10944961 DOI: 10.3389/fgene.2024.1341272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/20/2024] Open
Abstract
Early-onset systemic lupus erythematosus presents with a more severe disease and is associated with a greater genetic burden, especially in patients from Black, Asian or Hispanic ancestries. Next-generation sequencing techniques, notably whole exome sequencing, have been extensively used in genomic interrogation studies to identify causal disease variants that are increasingly implicated in the development of autoimmunity. This Review discusses the known casual variants of polygenic and monogenic systemic lupus erythematosus and its implications under certain genetic disparities while suggesting an age-based sequencing strategy to aid in clinical diagnostics and patient management for improved patient care.
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Affiliation(s)
- Nicholas Kim-Wah Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Che Kang Lim
- Duke-NUS Medical School, Singapore, Singapore
- Department of Clinical Translation Research, Singapore General Hospital, Singapore, Singapore
| | - Katherine Nay Yaung
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Nicholas Kim Huat Khoo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Thaschawee Arkachaisri
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Salvatore Albani
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Joo Guan Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
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Wu S, Han J, Duan G, Xue J, Huang R, Wu L, Yan X, Pi H, Yang X. Prenatal Diagnosis of Fetal Micrognathia at 11-20 Weeks of Gestation: A Prospective Observation Study. J Ultrasound Med 2024; 43:491-499. [PMID: 38164991 DOI: 10.1002/jum.16379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 01/03/2024]
Abstract
OBJECTIVE To prospectively evaluate the prognosis of fetuses diagnosed with micrognathia using prenatal ultrasound screening. METHODS Between January 2019 and December 2022, a normal range of IFA to evaluate the facial profile in fetuses with micrognathia in a Chinese population between 11 and 20 gestational weeks was established, and the pregnancy outcomes of fetal micrognathia were described. The medical records of these pregnancies were collected, including family history, maternal demographics, sonographic findings, genetic testing results, and pregnancy outcomes. RESULTS Ultrasound identified 25 patients with fetal micrognathia, with a mean IFA value of 43.6°. All cases of isolated fetal micrognathia in the initial scans were non-isolated in the following scans. A total of 78.9% (15/19) cases had a genetic cause confirmed, including 12 with chromosomal abnormalities and 3 with monogenic disorders. Monogenic disorders were all known causes of micrognathia, including two cases of campomelic dysplasia affected by SOX9 mutations and one case of mandibulofacial dysostosis with an EFTUD2 mutation. In the end, 19 cases were terminated, 1 live birth was diagnosed as Pierre Robin syndrome, and 5 cases were lost to follow-up. CONCLUSION IFA is a useful indicator and three-dimensional ultrasound is a significant support technique for fetal micrognathia prenatal diagnosis. Repeat ultrasound monitoring and genetic testing are crucial, with CMA recommended and Whole exome sequencing performed when normal arrays are reported. Isolated fetal micrognathia may be an early manifestation of monogenic disorders.
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Affiliation(s)
- Siqi Wu
- Department of Medical Genetics and Prenatal Diagnosis, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Jin Han
- Department of Prenatal Diagnosis, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Guanhua Duan
- Department of Ultrasonics, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Jiaxin Xue
- Department of Obstetrics, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Ruchun Huang
- Department of Medical Genetics and Prenatal Diagnosis, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Liping Wu
- Department of Medical Genetics and Prenatal Diagnosis, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Xiuyan Yan
- Department of Medical Genetics and Prenatal Diagnosis, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Huichun Pi
- Department of Medical Genetics and Prenatal Diagnosis, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Xin Yang
- Department of Medical Genetics and Prenatal Diagnosis, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
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Mao B, Yang J, Zhao X, Jia X, Shi X, Zhao L, Banerjee S, Zhang L, Ma X. Identification and functional characterization of a novel heterozygous splice‑site mutation in the calpain 3 gene causes rare autosomal dominant limb‑girdle muscular dystrophy. Exp Ther Med 2024; 27:97. [PMID: 38356676 PMCID: PMC10865457 DOI: 10.3892/etm.2024.12385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/03/2023] [Indexed: 02/16/2024] Open
Abstract
Limb-girdle muscular dystrophies are a group of extremely heterogenous neuromuscular disorders that manifest with gradual and progressive weakness of both proximal and distal muscles. Autosomal dominant limb-girdle muscular dystrophy (LGMDD4) or calpainopathy is a very rare form of myopathy characterized by weakness and atrophy of both proximal and distal muscles with a variable age of onset. LGMDD4 is caused by germline heterozygous mutations of the calpain 3 (CAPN3) gene. Patients with LGMDD4 often show extreme phenotypic heterogeneity; however, most patients present with gait difficulties, increased levels of serum creatine kinase, myalgia and back pain. In the present study, a 16-year-old male patient, clinically diagnosed with LGMDD4, was investigated. The proband had been suffering from weakness and atrophy of both of their proximal and distal muscles, and had difficulty walking and standing independently. The serum creatine kinase levels (4,754 IU/l; normal, 35-232 IU/l) of the patient were markedly elevated. The younger sister and mother of the proband were also clinically diagnosed with LGMDD4, while the father was phenotypically normal. Whole exome sequencing identified a heterozygous novel splice-site (c.2440-1G>A) mutation in intron 23 of the CAPN3 gene in the proband. Sanger sequencing confirmed that this mutation was also present in both the younger sister and mother of the proband, but the father was not a carrier of this mutation. This splice-site (c.2440-1G>A) mutation causes aberrant splicing of CAPN3 mRNA, leading to the skipping of the last exon (exon 24) of CAPN3 mRNA and resulting in the removal of eight amino acids from the C-terminal of domain IV of the CAPN3 protein. Hence, this splice site mutation causes the formation of a truncated CAPN3 protein (p.Trp814*) of 813 amino acids instead of the wild-type CAPN3 protein that consists of 821 amino acids. This mutation causes partial loss of domain IV (PEF domain) in the CAPN3 protein, which is involved in calcium binding and homodimerization; therefore, this is a loss-of-function mutation. Relative expression of the mutated CAPN3 mRNA was reduced in comparison with the wild-type CAPN3 mRNA in the proband, and their younger sister and mother. This mutation was also not present in 100 normal healthy control individuals of the same ethnicity. The present study reported the first case of CAPN3 gene-associated LGMDD4 in the Chinese population.
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Affiliation(s)
- Bin Mao
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Jie Yang
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Xiaodong Zhao
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Xueling Jia
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Xin Shi
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Lihui Zhao
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Santasree Banerjee
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Lili Zhang
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Xiaoling Ma
- The Reproductive Medicine Centre, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
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Frolov A, Guzman MA, Hayat G, Martin JR. Two Cases of Sporadic Amyotrophic Lateral Sclerosis With Contrasting Clinical Phenotypes: Genetic Insights. Cureus 2024; 16:e56023. [PMID: 38606235 PMCID: PMC11008550 DOI: 10.7759/cureus.56023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2024] [Indexed: 04/13/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neuromuscular disease that affects individuals of diverse racial and ethnic backgrounds. There is currently no cure for ALS, and the number of efficient disease-modifying drugs for ALS is limited to a few, despite the large number of clinical trials conducted in recent years. The latter could be attributed to the significant heterogeneity of ALS clinical phenotypes even in their familial forms. To address this issue, we conducted postmortem genetic screening of two female patients with sporadic ALS (sALS) and contrasting clinical phenotypes. The results demonstrated that despite their contrasting clinical phenotypes, both patients had rare pathologic/deleterious mutations in five genes: ACSM5, BBS12, HLA-DQB1, MUC20, and OBSCN, with mutations in three of those genes being identical: BBS12, HLA-DQB1, and MUC20. Additional groups of mutated genes linked to ALS, other neurologic disorders, and ALS-related pathologies were also identified. These data are consistent with a hypothesis that an individual could be primed for ALS via mutations in a specific set of genes not directly linked to ALS. The disease could be initiated by a concerted action of several mutated genes linked to ALS and the disease's clinical phenotype will evolve further through accessory gene mutations associated with other neurological disorders and ALS-related pathologies.
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Affiliation(s)
- Andrey Frolov
- Center for Anatomical Science and Education, Saint Louis University School of Medicine, Saint Louis, USA
| | - Miguel A Guzman
- Department of Pathology, Saint Louis University School of Medicine, Saint Louis, USA
| | - Ghazala Hayat
- Department of Neurology, Saint Louis University School of Medicine, Saint Louis, USA
- ALS Center of Excellence, Saint Louis University School of Medicine, Saint Louis, USA
| | - John R Martin
- Center for Anatomical Science and Education, Saint Louis University School of Medicine, Saint Louis, USA
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Ochoa JP, Lalaguna L, Mirelis JG, Dominguez F, Gonzalez-Lopez E, Salas C, Roustan G, McGurk KA, Zheng SL, Barton PJ, Ware JS, Gómez-Gaviro MV, Lara-Pezzi E, Garcia-Pavia P. Biallelic Loss of Function Variants in Myocardial Zonula Adherens Protein Gene (MYZAP) Cause a Severe Recessive Form of Dilated Cardiomyopathy. Circ Heart Fail 2024; 17:e011226. [PMID: 38436102 PMCID: PMC10942163 DOI: 10.1161/circheartfailure.123.011226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Affiliation(s)
- Juan Pablo Ochoa
- Hospital Universitario Puerta de Hierro Majadahonda, IDIPHISA, Madrid, Spain (J.P.O., J.G.M., F.D., E.G.-L., C.S., G.R., P.G.-P.)
- CIBERCV, Instituto de Salud Carlos III, Madrid, Spain (J.P.O., F.D., E.G.-L., C.S., E.L.-P., P.G.-P.)
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.P.O., L.L., F.D., E.G.-L., E.L.-P., P.G.-P.)
| | - Laura Lalaguna
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.P.O., L.L., F.D., E.G.-L., E.L.-P., P.G.-P.)
| | - Jesús G. Mirelis
- Hospital Universitario Puerta de Hierro Majadahonda, IDIPHISA, Madrid, Spain (J.P.O., J.G.M., F.D., E.G.-L., C.S., G.R., P.G.-P.)
| | - Fernando Dominguez
- Hospital Universitario Puerta de Hierro Majadahonda, IDIPHISA, Madrid, Spain (J.P.O., J.G.M., F.D., E.G.-L., C.S., G.R., P.G.-P.)
- CIBERCV, Instituto de Salud Carlos III, Madrid, Spain (J.P.O., F.D., E.G.-L., C.S., E.L.-P., P.G.-P.)
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.P.O., L.L., F.D., E.G.-L., E.L.-P., P.G.-P.)
| | - Esther Gonzalez-Lopez
- Hospital Universitario Puerta de Hierro Majadahonda, IDIPHISA, Madrid, Spain (J.P.O., J.G.M., F.D., E.G.-L., C.S., G.R., P.G.-P.)
- CIBERCV, Instituto de Salud Carlos III, Madrid, Spain (J.P.O., F.D., E.G.-L., C.S., E.L.-P., P.G.-P.)
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.P.O., L.L., F.D., E.G.-L., E.L.-P., P.G.-P.)
| | - Clara Salas
- Hospital Universitario Puerta de Hierro Majadahonda, IDIPHISA, Madrid, Spain (J.P.O., J.G.M., F.D., E.G.-L., C.S., G.R., P.G.-P.)
- CIBERCV, Instituto de Salud Carlos III, Madrid, Spain (J.P.O., F.D., E.G.-L., C.S., E.L.-P., P.G.-P.)
| | - Gaston Roustan
- Hospital Universitario Puerta de Hierro Majadahonda, IDIPHISA, Madrid, Spain (J.P.O., J.G.M., F.D., E.G.-L., C.S., G.R., P.G.-P.)
| | - Kathryn A. McGurk
- National Heart and Lung Institute (K.A.M, S.L.Z., P.J.R.B., J.S.W.), Imperial College London, United Kingdom
- MRC London Institute of Medical Sciences (K.A.M., S.L.Z., P.J.R.B., J.S.W.), Imperial College London, United Kingdom
| | - Sean L. Zheng
- National Heart and Lung Institute (K.A.M, S.L.Z., P.J.R.B., J.S.W.), Imperial College London, United Kingdom
- MRC London Institute of Medical Sciences (K.A.M., S.L.Z., P.J.R.B., J.S.W.), Imperial College London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St Thomas’ Hospital NHS Trust, London, UK (S.L.Z., P.J.R.B., J.S.W.)
| | - Paul J.R. Barton
- National Heart and Lung Institute (K.A.M, S.L.Z., P.J.R.B., J.S.W.), Imperial College London, United Kingdom
- MRC London Institute of Medical Sciences (K.A.M., S.L.Z., P.J.R.B., J.S.W.), Imperial College London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St Thomas’ Hospital NHS Trust, London, UK (S.L.Z., P.J.R.B., J.S.W.)
| | - James S. Ware
- National Heart and Lung Institute (K.A.M, S.L.Z., P.J.R.B., J.S.W.), Imperial College London, United Kingdom
- MRC London Institute of Medical Sciences (K.A.M., S.L.Z., P.J.R.B., J.S.W.), Imperial College London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St Thomas’ Hospital NHS Trust, London, UK (S.L.Z., P.J.R.B., J.S.W.)
| | - María Victoria Gómez-Gaviro
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain (M.V.G.-G.)
- Centro de Investigación Biomédica en Red de Salud Mental, Madrid, Spain (M.V.G.-G.)
| | - Enrique Lara-Pezzi
- CIBERCV, Instituto de Salud Carlos III, Madrid, Spain (J.P.O., F.D., E.G.-L., C.S., E.L.-P., P.G.-P.)
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.P.O., L.L., F.D., E.G.-L., E.L.-P., P.G.-P.)
| | - Pablo Garcia-Pavia
- Hospital Universitario Puerta de Hierro Majadahonda, IDIPHISA, Madrid, Spain (J.P.O., J.G.M., F.D., E.G.-L., C.S., G.R., P.G.-P.)
- CIBERCV, Instituto de Salud Carlos III, Madrid, Spain (J.P.O., F.D., E.G.-L., C.S., E.L.-P., P.G.-P.)
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.P.O., L.L., F.D., E.G.-L., E.L.-P., P.G.-P.)
- Universidad Francisco de Vitoria, Pozuelo de Alarcón, Spain (P.G.-P.)
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Niu J, Teng X, Zhang J. Aberrant splicing caused by a novel KMT2A variant in Wiedemann-Steiner syndrome. Mol Genet Genomic Med 2024; 12:e2415. [PMID: 38488438 PMCID: PMC10941593 DOI: 10.1002/mgg3.2415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 03/18/2024] Open
Abstract
INTRODUCTION Wiedemann-Steiner syndrome (WSS) is a rare autosomal-dominant disorder caused by KMT2A variants. The aim of this study was to characterize a novel KMT2A variant in a child with WSS and demonstrate integrated diagnostic approaches. METHODS A 3-year-old female with developmental delay, distinctive facial features, and anal fistula underwent whole exome sequencing (WES). RNA analysis was performed to assess splicing effects caused by a novel variant. RESULTS WES identified novel heterozygous KMT2A c.5664+6T>C variant initially classified as a variant of uncertain significance. RNA analysis provided evidence of aberrant splicing (exon 20 skipping), allowing reclassification to likely pathogenic. The patient exhibited typical WSS features along with a potential novel finding of anal fistula. CONCLUSION This report describes a novel non-canonical splice site variant in KMT2A associated with WSS. RNA analysis was critical for variant reclassification. Detailed phenotypic evaluation revealed common and expanded WSS manifestations. This case highlights the importance of combining clinical assessment, DNA testing, and RNA functional assays for the diagnosis of rare genetic disorders.
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Affiliation(s)
- Jianing Niu
- Reproductive Medicine Center, Shanghai First Maternity and Infant Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Obstetrics and Gynecology, Jiaxing Maternity and Child Health Care Hospital, College of MedicineJiaxing UniversityJiaxingChina
| | - Xiaoming Teng
- Reproductive Medicine Center, Shanghai First Maternity and Infant Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Junyu Zhang
- Reproductive Medicine Center, Shanghai First Maternity and Infant Hospital, School of MedicineTongji UniversityShanghaiChina
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Wu Z, Gu T, Xiong C, Shi J, Wang J, Guo T, Xing X, Pang F, He N, Miao R, Shan F, Zhou Y, Li Z, Ji J. Genomic characterization of peritoneal lavage cytology-positive gastric cancer. Chin J Cancer Res 2024; 36:66-77. [PMID: 38455368 PMCID: PMC10915641 DOI: 10.21147/j.issn.1000-9604.2024.01.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/04/2024] [Indexed: 03/09/2024] Open
Abstract
Objective Positive peritoneal lavege cytology (CY1) gastric cancer is featured by dismal prognosis, with high risks of peritoneal metastasis. However, there is a lack of evidence on pathogenic mechanism and signature of CY1 and there is a continuous debate on CY1 therapy. Therefore, exploring the mechanism of CY1 is crucial for treatment strategies and targets for CY1 gastric cancer. Methods In order to figure out specific driver genes and marker genes of CY1 gastric cancer, and ultimately offer clues for potential marker and risk assessment of CY1, 17 cytology-positive gastric cancer patients and 31 matched cytology-negative gastric cancer patients were enrolled in this study. The enrollment criteria were based on the results of diagnostic laparoscopy staging and cytology inspection of exfoliated cells. Whole exome sequencing was then performed on tumor samples to evaluate genomic characterization of cytology-positive gastric cancer. Results Least absolute shrinkage and selection operator (LASSO) algorithm identified 43 cytology-positive marker genes, while MutSigCV identified 42 cytology-positive specific driver genes. CD3G and CDKL2 were both driver and marker genes of CY1. Regarding mutational signatures, driver gene mutation and tumor subclone architecture, no significant differences were observed between CY1 and negative peritoneal lavege cytology (CY0). Conclusions There might not be distinct differences between CY1 and CY0, and CY1 might represent the progression of CY0 gastric cancer rather than constituting an independent subtype. This genomic analysis will thus provide key molecular insights into CY1, which may have a direct effect on treatment recommendations for CY1 and CY0 patients, and provides opportunities for genome-guided clinical trials and drug development.
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Affiliation(s)
- Zhouqiao Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Tingfei Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Changxian Xiong
- Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Jinyao Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jingpu Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Ting Guo
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xiaofang Xing
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Fei Pang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Ning He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Rulin Miao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Fei Shan
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yuan Zhou
- Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Ziyu Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jiafu Ji
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
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Lin ZJ, Long JY, Li J, Wang FN, Chu W, Zhu L, Li YL, Fan LL. Case report: Whole exome sequencing identified a novel mutation (p.Y301H) of MAF in a Chinese family with congenital cataracts. Front Med (Lausanne) 2024; 11:1332992. [PMID: 38487030 PMCID: PMC10937461 DOI: 10.3389/fmed.2024.1332992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 02/07/2024] [Indexed: 03/17/2024] Open
Abstract
Background Congenital cataracts stand as the primary cause of childhood blindness globally, characterized by clouding of the eye's lens at birth or shortly thereafter. Previous investigations have unveiled that a variant in the V-MAF avian musculoaponeurotic-fibrosarcoma oncogene homolog (MAF) gene can result in Ayme-Gripp syndrome and solitary cataract. Notably, MAF mutations have been infrequently reported in recent years. Methods In this investigation, we recruited a Chinese family with non-syndromic cataracts. Whole exome sequencing and Sanger sequencing were applied to scrutinize the genetic anomaly within the family. Results Through whole exome sequencing and subsequent data filtration, a new mutation (NM_005360, c.901T>C/p.Y301H) in the MAF gene was detected. Sanger sequencing validated the presence of this mutation in another affected individual. The p.Y301H mutation, situated in an evolutionarily preserved locus, was not detected in our 200 local control cohorts and various public databases. Additionally, multiple bioinformatic programs predicted that the mutation was deleterious and disrupted the bindings between MAF and its targets. Conclusion Hence, we have documented a new MAF mutation within a Chinese family exhibiting isolated congenital cataracts. Our study has the potential to broaden the spectrum of MAF mutations, offering insights into the mechanisms underlying cataract formation and facilitating genetic counseling and early diagnosis for congenital cataract patients.
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Affiliation(s)
- Zhao-Jing Lin
- Department of Anesthesiology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jie-Yi Long
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Juan Li
- Department of Reproductive Genetics, Hebei General Hospital, Shijiazhuang, China
| | - Fang-Na Wang
- Department of Reproductive Genetics, Hebei General Hospital, Shijiazhuang, China
| | - Wei Chu
- Department of Reproductive Genetics, Hebei General Hospital, Shijiazhuang, China
| | - Lei Zhu
- Department of Obstetrics and Gynecology, Ordos Central Hospital, Ordos, China
| | - Ya-Li Li
- Department of Reproductive Genetics, Hebei General Hospital, Shijiazhuang, China
| | - Liang-Liang Fan
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
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Lin Y, Zhang Y, Ma J, Liu S, Liu Y, Yang C, Zeng C, Luo X. Two Chinese Patients of Auriculocondylar Syndrome 2: A Novel PLCB4 Splicing Variant and 5-Year Follow-up. Cleft Palate Craniofac J 2024:10556656241234575. [PMID: 38414442 DOI: 10.1177/10556656241234575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Abstract
OBJECTIVE Auriculocondylar syndrome (ARCND) is a set of rare craniofacial malformations characterized by variable micrognathia, ear malformations, and mandibular condyle hypoplasia, and other accompanying features with phenotypic complexity. ARCND2 caused by pathogenic variants in the PLCB4 gene is a very rare disease with less than 50 patients reported and only 36 different variants of the PLCB4 gene recorded in HGMD. This study aims to enrich the patient resources, clinical data and mutational spectrum of ARCND2. DESIGN Case series study. SETTING Guangzhou Women and Children's Medical Center and Guangdong Women and Children Hospital. PATIENTS Two Chinese patients with ARCND2. MAIN OUTCOME MEASURES Clinical, radiological and molecular findings. RESULTS Both the two patients presented with craniofacial and ear malformations, and feeding difficulties. Whole exome sequencing identified two different variants of the PLCB4 gene in these two patients with a heterozygous allele and a de novo mode of inheritance respectively. Patient 1 carried a known pathogenic c.1861C > T(p.Arg621Cys) missense variant, whereas Patient 2 had a novel c.225 + 1G > A splicing variant. Sanger sequencing confirmed the presence of PLCB4 variants in the proband and absence in the unaffected parents. These two PLCB4 variants were suggested as disease-causing candidates for these two patients. During a 5-year follow-up, Patient 2 gradually manifested crowded teeth, underweight, motor delay and intellectual disability. CONCLUSIONS In this study, we report two Chinese patients with ARCND2, describe their clinical and mutational features, and share a 5-year follow-up of one patient. Our study adds two additional patients to ARCND2, reveals a novel PLCB4 variant, and expands the phenotypic and genotypic spectrum.
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Affiliation(s)
- Yunting Lin
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
| | - Ye Zhang
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Guangdong Women and Children Hospital, Guangzhou 511442, China
| | - Jian Ma
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou 511442, China
| | - Shu Liu
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Guangdong Women and Children Hospital, Guangzhou 511442, China
| | - Yongxi Liu
- Department of Radiology, Guangdong Women and Children Hospital, Guangzhou 511442, China
| | - Chaoxiang Yang
- Department of Radiology, Guangdong Women and Children Hospital, Guangzhou 511442, China
| | - Chunhua Zeng
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
| | - Xianqiong Luo
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Guangdong Women and Children Hospital, Guangzhou 511442, China
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Wang MT, Weng KP, Chang SK, Huang WC, Chen LW. Hemodynamic and Clinical Profiles of Pulmonary Arterial Hypertension Patients with GDF2 and BMPR2 Variants. Int J Mol Sci 2024; 25:2734. [PMID: 38473983 DOI: 10.3390/ijms25052734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Asians have a higher carrier rate of pulmonary arterial hypertension (PAH)-related genetic variants than Caucasians do. This study aimed to identify PAH-related genetic variants using whole exome sequencing (WES) in Asian idiopathic and heritable PAH cohorts. A WES library was constructed, and candidate variants were further validated by polymerase chain reaction and Sanger sequencing in the PAH cohort. In a total of 69 patients, the highest incidence of variants was found in the BMPR2, ATP13A3, and GDF2 genes. Regarding the BMPR2 gene variants, there were two nonsense variants (c.994C>T, p. Arg332*; c.1750C>T, p. Arg584*), one missense variant (c.1478C>T, p. Thr493Ile), and one novel in-frame deletion variant (c.877_888del, p. Leu293_Ser296del). Regarding the GDF2 variants, there was one likely pathogenic nonsense variant (c.259C>T, p. Gln87*) and two missense variants (c.1207G>A, p. Val403Ile; c.38T>C, p. Leu13Pro). The BMPR2 and GDF2 variant subgroups had worse hemodynamics. Moreover, the GDF2 variant patients were younger and had a significantly lower GDF2 value (135.6 ± 36.2 pg/mL, p = 0.002) in comparison to the value in the non-BMPR2/non-GDF2 mutant group (267.8 ± 185.8 pg/mL). The BMPR2 variant carriers had worse hemodynamics compared to the patients with the non-BMPR2/non-GDF2 mutant group. Moreover, there was a significantly lower GDF2 value in the GDF2 variant carriers compared to the control group. GDF2 may be a protective or corrected modifier in certain genetic backgrounds.
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Affiliation(s)
- Mei-Tzu Wang
- Institute of Emergency and Critical Care Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Department of Critical Care Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
| | - Ken-Pen Weng
- Congenital Structural Heart Disease Center, Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
| | | | - Wei-Chun Huang
- Department of Critical Care Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
- Department of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Department of Physical Therapy, Fooyin University, Kaohsiung 813, Taiwan
| | - Lee-Wei Chen
- Institute of Emergency and Critical Care Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung 813, Taiwan
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Lorente-Bermúdez R, Pan-Lizcano R, Núñez L, López-Vázquez D, Rebollal-Leal F, Vázquez-Rodríguez JM, Hermida-Prieto M. Analysis of the Association between Copy Number Variation and Ventricular Fibrillation in ST-Elevation Acute Myocardial Infarction. Int J Mol Sci 2024; 25:2548. [PMID: 38473795 DOI: 10.3390/ijms25052548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/15/2024] [Accepted: 02/07/2024] [Indexed: 03/14/2024] Open
Abstract
Sudden cardiac death due to ventricular fibrillation (VF) during ST-elevation acute myocardial infarction (STEAMI) significantly contributes to cardiovascular-related deaths. Although VF has been linked to genetic factors, variations in copy number variation (CNV), a significant source of genetic variation, have remained largely unexplored in this context. To address this knowledge gap, this study performed whole exome sequencing analysis on a cohort of 39 patients with STEAMI who experienced VF, aiming to elucidate the role of CNVs in this pathology. The analysis revealed CNVs in the form of duplications in the PARP2 and TTC5 genes as well as CNVs in the form of deletions in the MUC15 and PPP6R1 genes, which could potentially serve as risk indicators for VF during STEAMI. The analysis also underscores notable CNVs with an average gene copy number equal to or greater than four in DEFB134, FCGR2C, GREM1, PARM1, SCG5, and UNC79 genes. These findings provide further insight into the role of CNVs in VF in the context of STEAMI.
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Affiliation(s)
- Roberto Lorente-Bermúdez
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), GRINCAR-Universidade da Coruña (UDC), 15006 A Coruña, Spain
| | - Ricardo Pan-Lizcano
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), GRINCAR-Universidade da Coruña (UDC), 15006 A Coruña, Spain
| | - Lucía Núñez
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), GRINCAR-Universidade da Coruña (UDC), 15006 A Coruña, Spain
- GRINCAR Research Group, Departamento de Ciencias de la Salud, Universidade da Coruña, 15403 A Coruña, Spain
| | - Domingo López-Vázquez
- Servicio de Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), Universidade da Coruña (UDC), 15006 A Coruña, Spain
| | - Fernando Rebollal-Leal
- Servicio de Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), Universidade da Coruña (UDC), 15006 A Coruña, Spain
| | - José Manuel Vázquez-Rodríguez
- Servicio de Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), Universidade da Coruña (UDC), 15006 A Coruña, Spain
- Centro de Investigación Biomédica en Red Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Manuel Hermida-Prieto
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), GRINCAR-Universidade da Coruña (UDC), 15006 A Coruña, Spain
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Fielding D, Lakis V, Dalley AJ, Chittoory H, Newell F, Koufariotis LT, Patch AM, Kazakoff S, Bashirzadeh F, Son JH, Ryan K, Steinfort D, Williamson JP, Bint M, Pahoff C, Nguyen PT, Twaddell S, Arnold D, Grainge C, Pattison A, Fairbairn D, Gune S, Christie J, Holmes O, Leonard C, Wood S, Pearson JV, Lakhani SR, Waddell N, Simpson PT, Nones K. Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing. Cancers (Basel) 2024; 16:785. [PMID: 38398180 PMCID: PMC10887389 DOI: 10.3390/cancers16040785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is often the only source of tumor tissue from patients with advanced, inoperable lung cancer. EBUS-TBNA aspirates are used for the diagnosis, staging, and genomic testing to inform therapy options. Here we extracted DNA and RNA from 220 EBUS-TBNA aspirates to evaluate their suitability for whole genome (WGS), whole exome (WES), and comprehensive panel sequencing. For a subset of 40 cases, the same nucleic acid extraction was sequenced using WGS, WES, and the TruSight Oncology 500 assay. Genomic features were compared between sequencing platforms and compared with those reported by clinical testing. A total of 204 aspirates (92.7%) had sufficient DNA (100 ng) for comprehensive panel sequencing, and 109 aspirates (49.5%) had sufficient material for WGS. Comprehensive sequencing platforms detected all seven clinically reported tier 1 actionable mutations, an additional three (7%) tier 1 mutations, six (15%) tier 2-3 mutations, and biomarkers of potential immunotherapy benefit (tumor mutation burden and microsatellite instability). As expected, WGS was more suited for the detection and discovery of emerging novel biomarkers of treatment response. WGS could be performed in half of all EBUS-TBNA aspirates, which points to the enormous potential of EBUS-TBNA as source material for large, well-curated discovery-based studies for novel and more effective predictors of treatment response. Comprehensive panel sequencing is possible in the vast majority of fresh EBUS-TBNA aspirates and enhances the detection of actionable mutations over current clinical testing.
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Affiliation(s)
- David Fielding
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia; (F.B.); (J.H.S.); (K.R.)
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Andrew J. Dalley
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
| | - Haarika Chittoory
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Lambros T. Koufariotis
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Stephen Kazakoff
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Farzad Bashirzadeh
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia; (F.B.); (J.H.S.); (K.R.)
| | - Jung Hwa Son
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia; (F.B.); (J.H.S.); (K.R.)
| | - Kimberley Ryan
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia; (F.B.); (J.H.S.); (K.R.)
| | - Daniel Steinfort
- Department of Respiratory and Sleep Medicine, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia; (D.S.); (J.C.)
| | - Jonathan P. Williamson
- Department of Thoracic Medicine, Liverpool Hospital Sydney, Sydney, NSW 2170, Australia;
| | - Michael Bint
- Department of Respiratory and Sleep Medicine, Sunshine Coast University Hospital, Birtinya, QLD 4575, Australia; (M.B.); (A.P.)
| | - Carl Pahoff
- Department of Thoracic Medicine, Gold Coast University Hospital, Southport, QLD 4215, Australia;
| | - Phan Tien Nguyen
- Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, SA 5000, Australia;
| | - Scott Twaddell
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW 2305, Australia; (S.T.); (D.A.); (C.G.)
| | - David Arnold
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW 2305, Australia; (S.T.); (D.A.); (C.G.)
| | - Christopher Grainge
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW 2305, Australia; (S.T.); (D.A.); (C.G.)
| | - Andrew Pattison
- Department of Respiratory and Sleep Medicine, Sunshine Coast University Hospital, Birtinya, QLD 4575, Australia; (M.B.); (A.P.)
| | - David Fairbairn
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia;
| | - Shailendra Gune
- NSW Health Pathology South, Liverpool Hospital, Sydney, NSW 2170, Australia;
| | - Jemma Christie
- Department of Respiratory and Sleep Medicine, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia; (D.S.); (J.C.)
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - John V. Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia;
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Peter T. Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4067, Australia
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Abid R, Nisar H, Chaudhary SU, Hamid M, Sahibzada KI, Firdous S, Mudassar M, Sadaf S. Association of epilepsy and neurological impairments with homozygous recessive missense mutations found in the genes responsible for ganglioside biosynthesis ( ST3GAL5) and calcium voltage-gated channels ( CACNA1H) - insights through molecular dynamic simulations. J Biomol Struct Dyn 2024:1-12. [PMID: 38356142 DOI: 10.1080/07391102.2024.2314751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024]
Abstract
With over 2.2 million cases, the incidence rate of epilepsy in Pakistan is far higher than the rest of the world due primarily to the frequent, traditionally imposed cousin marriages. In the present study, comprehensive whole exome sequencing (WES) analyses of a three-generation family with four affected members presenting 'unexplained' childhood absence epilepsy (CAE), seizures and dementia, was performed in a quest to identify heritable, epilepsy-causal gene variants to better aid in carrier screening and genetic counselling. The WES data was generated, analyzed, and validated through Sanger's sequencing, molecular dynamic simulation (MDS) analysis, and molecular mechanics with generalized Born and surface area solvation (MM/GBSA) studies. Two homozygous recessive, missense mutations in ST3GAL5 (c.311A > G, p. His104Arg) and CACNA1H (c.6230G > A, p. Arg2077His) genes, earlier regarded as benign or of uncertain significance, have been identified as a potential etiology. Comparative MDS and free binding energy calculations revealed substantial structural perturbations in mutant forms of ST3GAL5 leading to decreased binding and reduced catalytic activity of the p.His104Arg and two other functional variants (p.Val74Glu and p.Arg288Ter) when compared with wild type. Our findings reinforce that WES analyses may uncover 'hidden', heritable variants and together with MDS and MM/GBSA may provide plausible clues to answer the unexplained causes of epilepsy for an effective management and better patient outcome. Further, revisit of epilepsy-associated mutational landscape in population context is imperative as the variants with 'benign' tags may turn out to be 'non-benign', when exist in combination with other benign.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rizwan Abid
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Haseeb Nisar
- Department of Life-Sciences, University of Management and Technology, Lahore, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics & Engineering Research Laboratory, Department of Life-Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Maham Hamid
- Biomedical Informatics & Engineering Research Laboratory, Department of Life-Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Kashif Iqbal Sahibzada
- Department of Health Professional Technologies, The University of Lahore, Lahore, Pakistan
| | - Safia Firdous
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- Faculty of Rehabilitation and Allied Health Sciences, Riphah International University, Lahore, Pakistan
| | | | - Saima Sadaf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
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Zhang H, Liao Y, Zhu Z, Liu H, Li D, Wang S. Assistance of next-generation sequencing for diagnosis of disseminated Bacillus Calmette-Guerin disease with X-SCID in an infant: a case report and literature review. Front Cell Infect Microbiol 2024; 14:1341236. [PMID: 38410723 PMCID: PMC10894915 DOI: 10.3389/fcimb.2024.1341236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
Bacille Calmette-Guérin (BCG) is a live strain of Mycobacterium bovis (M.bovis) for use as an attenuated vaccine to prevent tuberculosis (TB) infection, while it could also lead to an infection in immunodeficient patients. M.bovis could infect patients with immunodeficiency via BCG vaccination. Disseminated BCG disease (BCGosis) is extremely rare and has a high mortality rate. This article presents a case of a 3-month-old patient with disseminated BCG infection who was initially diagnosed with hemophagocytic syndrome (HPS) and eventually found to have X-linked severe combined immunodeficiency (X-SCID). M.bovis and its drug resistance genes were identified by metagenomics next-generation sequencing (mNGS) combined with targeted next-generation sequencing (tNGS) in blood and cerebrospinal fluid. Whole exome sequencing (WES) revealed a pathogenic variant in the common γ-chain gene (IL2RG), confirming X-SCID. Finally, antituberculosis therapy and umbilical cord blood transplantation were given to the patient. He was successfully cured of BCGosis, and his immune function was restored. The mNGS combined with the tNGS provided effective methods for diagnosing rare BCG infections in children. Their combined application significantly improved the sensitivity and specificity of the detection of M.bovis.
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Affiliation(s)
- Haiyang Zhang
- Department of Pediatrics, 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
| | - Yi Liao
- 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
| | - Zhensheng Zhu
- Depertment of Bioinformation, Hugobiotech Co., Ltd., Beijing, China
| | - Hanmin Liu
- Department of Pediatrics, 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
| | - Deyuan Li
- Department of Pediatrics, 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
| | - Sisi Wang
- Department of Pediatrics, 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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Zhao M, Meng X, Wang J, Wang T. Novel FOXL2 variants in two Chinese families with blepharophimosis, ptosis, and epicanthus inversus syndrome. Front Genet 2024; 15:1343411. [PMID: 38410153 PMCID: PMC10894958 DOI: 10.3389/fgene.2024.1343411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
Introduction: Blepharophimosis, ptosis, and epicanthus inversus syndrome (BPES) is a rare inherited disorder. This study was aimed to identify and functionally validate FOXL2 variants in two Chinese families with BPES. Methods: The proband and his family members were subjected to whole-exome sequencing to identify disease-associated variants. Several bioinformatic tools were used to computationally predict altered proteins. In vitro functional assays were conducted by transfecting wild-type and mutant FOXL2 cDNAs into HEK-293 cells, followed by subcellular localization assays, luciferase reporter gene assays, and quantitative real-time polymerase chain reaction. Results: The clinical features of BPES, including small palpebral fissures, ptosis, telecanthus, and epicanthus inversus, were present in all affected patients. Two novel mutations were detected, c.292T>A and c.383G>T. Whole-exome sequencing analysis and prediction software suggested that these mutations were pathogenic. Functional studies showed that these two point mutations decreased FOXL2 protein expression, resulting in subcellular mislocalization and aberrant transcriptional activity of the steroidogenic acute regulatory protein gene promoter. Conclusion: Our results add to the current understanding of known FOXL2 variants in, and our in vitro experiments provide reference data and insights into the etiology of BPES. Further studies are needed to identify the possible mechanisms underlying the action of this mutation on the development of BPES.
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Affiliation(s)
- Mingyu Zhao
- The Department of Facial and Neck Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaolu Meng
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiaqi Wang
- The Department of Facial and Neck Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tailing Wang
- The Department of Facial and Neck Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Huang Y, Du Z, Kan A, He M, Li H, Lai Z, Wen D, Huang L, Li Q, Xu L, Shi M. Clinical and biomarker analyses of hepatic arterial infusion chemotherapy plus lenvatinib and PD-1 inhibitor for patients with advanced intrahepatic cholangiocarcinoma. Front Immunol 2024; 15:1260191. [PMID: 38384459 PMCID: PMC10880187 DOI: 10.3389/fimmu.2024.1260191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024] Open
Abstract
Background Intrahepatic cholangiocarcinoma (iCCA) is a highly aggressive cancer with a dismal prognosis and few effective therapeutic approaches. This study aimed to investigate the efficacy, safety, and predictive biomarkers of hepatic arterial infusion chemotherapy (FOLFOX-HAIC) in combination with lenvatinib and PD-1 inhibitor for patients with advanced iCCA. Methods Locally advanced or metastatic iCCA patients receiving the triple combination therapy of lenvatinib, PD-1 inhibitor, and FOLFOX-HAIC were included in this retrospective study. Primary endpoint was the progression-free survival, evaluated using the RECIST criterion. The secondary endpoints included overall survival, objective response rate, and safety. Whole exome and RNA sequencing of tumor biopsy tissues were performed for biomarker exploration. Results Between May, 2019 and December 2022, a total of 46 patients were included in this study. The primary endpoint showed a median progression-free survival of 9.40 months (95% CI: 5.28-13.52), with a 6-month progression-free survival rate of 76.1%. The median overall survival was 16.77 months (95% CI, 14.20-19.33), with an objective response rate of 47.8% and disease control rate of 91.3% per RECIST. In addition, 4.3% and 8.7% of patients achieved complete response of all lesions and intrahepatic target lesions per mRECIST, respectively. The most common treatment-related adverse events were neutropenia, thrombocytopenia, elevated aspartate aminotransferase and alanine aminotransferase level. Furthermore, integrated analysis of genetic, transcriptomic, and immunohistochemistry data revealed that pre-existing immunity (high expression level of immune-related signatures and intra-tumoral CD8+ T cell density) in baseline tumor tissues was associated with superior clinical benefits. However, the evaluation of tumor mutation burden did not show potential predictive value in this triple combination. Conclusion FOLFOX-HAIC in combination with lenvatinib and PD-1 inhibitor demonstrated a promising antitumor activity with manageable safety profiles in patients with advanced iCCA. Moreover, our study also revealed new perspectives on potential biomarkers for clinical efficacy.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Li Xu
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Ming Shi
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
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Khan F, Khan S, Rana N, Rahim T, Arshad A, Khan I, Ogaly HA, Ahmed DAEM, Dera AA, Zaib S. Mutational analysis of consanguineous families and their targeted therapy against dwarfism. J Biomol Struct Dyn 2024:1-18. [PMID: 38321911 DOI: 10.1080/07391102.2024.2307446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024]
Abstract
Dwarfism is a medical term used to describe individuals with a height-vertex measurement that falls below two standard deviations (-2SD) or the third percentile for their gender and age. Normal development of growth is a complicated dynamic procedure that depends upon the coordination of different aspects involving diet, genetics, and biological aspects like hormones in equilibrium. Any severe or acute pathologic procedure may disturb the individual's normal rate of growth. In this research, we examined four (A-D) Pakistani consanguineous families that exhibited syndromic dwarfism, which was inherited in an autosomal recessive pattern. The genomic DNA of each family member was extracted by using phenol-chloroform and Kit methods. Whole Exome Sequencing (WES) of affected family members (IV-11, III-5, IV-4 and III-13) from each group was performed at the Department of Medical Genetics, University of Antwerp, Belgium. After filtering the exome data, the mutations in PPM1F, FGFR3, ERCC2, and PCNT genes were determined by Sanger sequencing of each gene by using specific primers. Afterward, FGFR3 was found to be a suitable drug target among all the mutations to treat achondroplasia also known as disproportionate dwarfism. BioSolveIT softwares were used to discover the lead active inhibitory molecule against FGFR3. This research will not only provide short knowledge to the concerned pediatricians, researchers, and family physicians for the preliminary assessment and management of the disorder but also provide a lead inhibitor for the treatment of disproportionate dwarfism.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Feroz Khan
- Department of Zoology Wild Life and Fishries, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Sarmir Khan
- Center of Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Nehal Rana
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Tariq Rahim
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Abida Arshad
- Department of Zoology Wild Life and Fishries, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Imtiaz Khan
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Hanan A Ogaly
- Chemistry Department, College of Science, King Khalid University, Abha, Saudi Arabia
| | | | - Ayed A Dera
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Sumera Zaib
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
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Pivirotto A, Peles N, Hey J. Allele age estimators designed for whole genome datasets show only a modest decrease in accuracy when applied to whole exome datasets. bioRxiv 2024:2024.02.01.578465. [PMID: 38370640 PMCID: PMC10871225 DOI: 10.1101/2024.02.01.578465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Personalized genomics in the healthcare system is becoming increasingly accessible as the costs of sequencing decreases. With the increase in number of genomes, larger numbers of rare variants are being discovered and much work is being done to identify their functional impacts in relation to disease phenotypes. One way to characterize these variants is to estimate the time the mutation entered the population. However, allele age estimators such as Relate, Genealogical Estimator of Variant Age, and time of coalescence, were developed based on the assumption that datasets include the entire genome. We examined the performance of each of these estimators on simulated exome data under a neutral constant population size model and found that each provides usable estimates of allele age from whole-exome datasets. To test the robustness of these methods, analyses were undertaken to simulate data under a population expansion model and background selection. Relate performs the best amongst all three estimators with Pearson coefficients of 0.64 and 0.68 (neutral constant and expansion population model) with a 17 percent and 15 percent drop in accuracy between whole genome and whole exome estimations. Of the three estimators, Relate is best able to parallelize to yield quick results with little resources, however even Relate is only able to scale to thousands of samples making it unable to match the hundreds of thousands of samples being currently released. While more work is needed to expand the capabilities of current methods of estimating allele age, these methods estimate the age of mutations with a modest decrease in performance.
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Affiliation(s)
- Alyssa Pivirotto
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA USA
| | - Noah Peles
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA USA
| | - Jody Hey
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA USA
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Jiménez-Morales S, Rojas-Martinez A, Barbany G. Editorial: Decoding the genome of acute lymphoblastic leukemia through genomic and transcriptomic approaches. Front Oncol 2024; 14:1368676. [PMID: 38380367 PMCID: PMC10877064 DOI: 10.3389/fonc.2024.1368676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Affiliation(s)
- Silvia Jiménez-Morales
- Laboratorio de Innovación y Medicina de Precisión, Núcleo “A”, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, The Institute for Obesity Research and Escuela de Medicina y Ciencias de la Salud, Monterrey, Nuevo León, Mexico
| | - Gisela Barbany
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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Chen C, An G, Yu X, Wang S, Lin P, Yuan J, Zhuang Y, Lu X, Bai Y, Zhang G, Su J, Qu J, Xu L, Wang H. Screening Mutations of the Monogenic Syndromic High Myopia by Whole Exome Sequencing From MAGIC Project. Invest Ophthalmol Vis Sci 2024; 65:9. [PMID: 38315492 PMCID: PMC10851780 DOI: 10.1167/iovs.65.2.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/17/2024] [Indexed: 02/07/2024] Open
Abstract
Purpose This observational study aimed to identify mutations in monogenic syndromic high myopia (msHM) using data from reported samples (n = 9370) of the Myopia Associated Genetics and Intervention Consortium (MAGIC) project. Methods The targeted panel containing 298 msHM-related genes was constructed and screening of clinically actionable variants was performed based on whole exome sequencing. Capillary sequencing was used to verify the identified gene mutations in the probands and perform segregation analysis with their relatives. Results A total of 381 candidate variants in 84 genes and 85 eye diseases were found to contribute to msHM in 3.6% (335/9370) of patients with HM. Among them, the 22 genes with the most variations accounted for 62.7% of the diagnostic cases. In the genotype-phenotype association analysis, 60% (201/335) of suspected msHM cases were recalled and 25 patients (12.4%) received a definitive genetic diagnosis. Pathogenic variants were distributed in 18 msHM-related diseases, mainly involving retinal dystrophy genes (e.g. TRPM1, CACNA1F, and FZD4), connective tissue disease genes (e.g. FBN1 and COL2A1), corneal or lens development genes (HSF4, GJA8, and MIP), and other genes (TEK). The msHM gene mutation types were allocated to four categories: nonsense mutations (36%), missense mutations (36%), frameshift mutations (20%), and splice site mutations (8%). Conclusions This study highlights the importance of thorough molecular subtyping of msHM to provide appropriate genetic counselling and multispecialty care for children and adolescents with HM.
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Affiliation(s)
- Chong Chen
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou, China
| | - Gang An
- Institute of PSI Genomics Co., Ltd., Wenzhou, China
| | - Xiaoguang Yu
- Institute of PSI Genomics Co., Ltd., Wenzhou, China
| | - Siyu Wang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Peng Lin
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jian Yuan
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Youyuan Zhuang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xiaoyan Lu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yu Bai
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou, China
| | - Guosi Zhang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jianzhong Su
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jia Qu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou, China
| | - Liangde Xu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou, China
| | - Hong Wang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou, China
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Issa MY, Hafez MA, Mounir SM, Abdel Ghafar SF, Zaki MS, Abdel-Hamid MS. Refining the phenotypic spectrum of CCDC88A-related PEHO-like syndrome. Am J Med Genet A 2024; 194:226-232. [PMID: 37798908 DOI: 10.1002/ajmg.a.63425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/31/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023]
Abstract
Progressive encephalopathy with edema, hypsarrhythmia, and optic atrophy (PEHO) and PEHO-like syndromes are very rare infantile disorders characterized by profound intellectual disability, hypotonia, convulsions, optic, and progressive brain atrophy. Many causative genes for PEHO and PEHO-like syndromes have been identified including CCDC88A. So far, only five patients from two unrelated families with biallelic CCDC88A variants have been reported in the literature. Herein, we describe a new family from Egypt with a lethal epileptic encephalopathy. Our patient was the youngest child born to a highly consanguineous couple and had a family history of five deceased sibs with the same condition. She presented with postnatal microcephaly, poor visual responsiveness, and epilepsy. Her brain MRI showed abnormal cortical gyration with failure of opercularization of the insula, hypogenesis of corpus callosum, colpocephaly, reduced white matter, hypoplastic vermis, and brain stem. Whole exome sequencing identified a new homozygous frameshift variant in CCDC88A gene (c.1795_1798delACAA, p.Thr599ValfsTer4). Our study presents the third reported family with this extremely rare disorder. We also reviewed all described cases to better refine the phenotypic spectrum associated with biallelic loss of function variants in the CCDC88A gene.
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Affiliation(s)
- Mahmoud Y Issa
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Mona A Hafez
- Radiology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Samir M Mounir
- Pediatrics Department, Faculty of Medicine, Minia University, Minia, Egypt
| | - Sherif F Abdel Ghafar
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Mohamed S Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
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Lu Z, Zhang W, Mao X, Li D, Chen X, Liu L, Lin Y. The third case of Marbach-Rustad progeroid syndrome caused by a de novo LEMD2 variant. Clin Genet 2024; 105:209-213. [PMID: 37867468 DOI: 10.1111/cge.14441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/05/2023] [Accepted: 10/08/2023] [Indexed: 10/24/2023]
Abstract
Marbach-Rustad progeroid syndrome is an extremely rare disease caused by a heterozygous variant in the LEMD2 gene. To date, only two patients and one LEMD2 pathogenic variant have been reported in Marbach-Rustad progeroid syndrome. Here we describe the third case of Marbach-Rustad progeroid syndrome worldwide, which is also the first case in China. The proband was affected with premature birth, failed to thrive, facial abnormalities, feeding difficulties, skull defects and delayed motor milestones, but had a normal intelligence and speech. Whole exome sequencing (WES) initially did not find a phenotype-causing variant when the proband was 1 year of age. The reanalysis of WES data 4 years later revealed the proband harbored a de novo heterozygous c.1436C>T(p.Ser479Phe) variant in the LEMD2 gene, which is known responsible for Marbach-Rustad progeroid syndrome. Sanger sequencing confirmed the presence of this variant in the proband and absence in his parents and two elder sisters. Our study provides accurate clinical diagnosis for the proband and adds a new patient with Marbach-Rustad progeroid syndrome. Our study suggests the LEMD2 c.1436C>T(p.Ser479Phe) variant as a hotspot. Our work also indicates reanalysis of WES data of negative cases might identify pathogenic variant and improve diagnostic efficiency.
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Affiliation(s)
- Zhikun Lu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Wen Zhang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Xiaojian Mao
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Duan Li
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Xiaodan Chen
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Li Liu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Yunting Lin
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
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Li H, Qi Z, Xie L, Hao C, Li W. The first Chinese intellectual developmental disorder, autosomal recessive 57 patient with two novel MBOAT7 variants. Mol Genet Genomic Med 2024; 12:e2391. [PMID: 38407511 PMCID: PMC10844841 DOI: 10.1002/mgg3.2391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/27/2024] Open
Abstract
BACKGROUND Intellectual disability (ID) is a con neurodevelopmental disorder in children. The genetic etiology of ID is complex, but more subtypes are defined due to the broad application of next-generation sequencing. METHODS Whole-exome sequencing (WES) and Sanger sequencing was applied in a family with ID. RESULTS We report a Chinese 7.5-year-old boy, born to non-consanguineous parents. He showed severe intellectual disability, seizures and autistic features. Two previously unreported variants in MBOAT7, c.669C>G (p.(Tyr223*)) and c.1095C>G (p.(Ser365Arg)) were identified by trio-WES. His mother is a heterozygous carrier of the c.1095C>G variant. The c.669C>G variant is a de novo variant which was undetected in his parents. By construction of the full-length cDNA of the patient's MBOAT7, we verified that these two variants were trans-compound heterozygous variants, which support the genetic etiology of this patient. CONCLUSION This patient is the first Chinese case of intellectual developmental disorder (IDD), autosomal recessive 57 (OMIM:617188) with two unreported MBOAT7 variants.
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Affiliation(s)
- Huimin Li
- Department of Genetics and Reproductive MedicineShunyi Maternal and Children's Hospital of Beijing Children's HospitalBeijingChina
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; Rare Disease Center, National Center for Children's Health; MOE Key Laboratory of Major Diseases in ChildrenBeijing Children's Hospital, Capital Medical UniversityBeijingChina
| | - Zhan Qi
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; Rare Disease Center, National Center for Children's Health; MOE Key Laboratory of Major Diseases in ChildrenBeijing Children's Hospital, Capital Medical UniversityBeijingChina
| | - Limin Xie
- Department of Genetics and Reproductive MedicineShunyi Maternal and Children's Hospital of Beijing Children's HospitalBeijingChina
| | - Chanjuan Hao
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; Rare Disease Center, National Center for Children's Health; MOE Key Laboratory of Major Diseases in ChildrenBeijing Children's Hospital, Capital Medical UniversityBeijingChina
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; Rare Disease Center, National Center for Children's Health; MOE Key Laboratory of Major Diseases in ChildrenBeijing Children's Hospital, Capital Medical UniversityBeijingChina
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Liu F, Tian S, Liu Q, Deng Y, He Q, Shi Q, Chen G, Xu X, Yuan J, Nakamura S, Karube K, Wang Z. Comparison of genomic alterations in Epstein-Barr virus-positive and Epstein-Barr virus-negative diffuse large B-cell lymphoma. Cancer Med 2024; 13:e6995. [PMID: 38457199 PMCID: PMC10922027 DOI: 10.1002/cam4.6995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/30/2023] [Accepted: 01/26/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Epstein-Barr virus (EBV)-positive diffuse large B-cell lymphoma (EBV-posDLBCL) is an aggressive B-cell lymphoma that often presents similar morphological and immune phenotype features to that of EBV-negative DLBCL (EBV-negDLBCL). AIMS AND METHODS To better understand their difference in genomic landscape, we performed whole-exome sequencing (WES) of EBV-posDLBCL and EBV-negDLBCL. RESULTS This analysis revealed a new mutational signature 17 (unknown) and signature 29 (smoking) in EBV-posDLBCL as well as a specific mutational signature 24 (associated with aflatoxin) in EBV-negDLBCL. Compared with EBV-negDLBCL, more somatic copy number alterations (CNAs) and deletions were detected in EBV-posDLBCL (p = 0.01). The most frequent CNAs specifically detected in EBV-posDLBCL were gains at 9p24.1 (PDL1 and JAK2), 8q22.2-q24.23 (DEPTOR and MYC), and 7q31.31-q32.2 (MET), which were validated in additional EBV-posDLBCL cases. Overall, 53.7% (22/41) and 62.9% (22/35) of the cases expressed PD-L1 and c-MET, respectively, in neoplastic cells, whereas only 15.4% (4/26) expressed c-MYC. Neoplastic c-MET expression was positively correlated with PD-L1 (p < 0.001) and MYC expression (p = 0.016). However, EBV-posDLBCL cases did not show any differences in overall survival between PD-L1-, c-MET-, or c-MYC-positive and -negative cases or between age-related groups. Analysis of the association between somatic mutation load and EBV status showed no difference in the distribution of tumor mutant burden between the two lymphomas (p = 0.41). Recurrent mutations in EBV-posDLBCL implicated several genes, including DCAF8L1, KLF2, and NOL9, while in EBV-negDLBCL, ANK2, BPTF, and CNIH3 were more frequently mutated. Additionally, PIM1 is the most altered gene in all the WES-detected cases. CONCLUSIONS Our results confirm that genomic alteration differs significantly between EBV-posDLBCL and EBV-negDLBCL, and reveal new genetic alterations in EBV-posDLBCL. The positive correlation of c-MET and PD-L1/c-Myc expression may be involved in the pathogenesis of EBV-posDLBCL, which is should be explored prospectively in trials involving MET-directed therapies.
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Affiliation(s)
- Fang Liu
- Department of PathologyThe First People's Hospital of FoshanFoshanGuangdongChina
| | - Sufang Tian
- Department of Pathology and Molecular Diagnostics, Zhongnan HospitalWuhan UniversityWuhanHubeiChina
| | - Qing Liu
- Department of PathologyThe First People's Hospital of FoshanFoshanGuangdongChina
| | - Yuanfei Deng
- Department of PathologyThe First People's Hospital of FoshanFoshanGuangdongChina
| | - Qingyan He
- Department of PathologyThe First People's Hospital of FoshanFoshanGuangdongChina
| | - Qianyun Shi
- Department of Pathology, Nanjing Drum Tower HospitalNanjing University Medical SchoolNanjingJiangsuChina
| | - Gang Chen
- Department of PathologyFujian Province Cancer CenterFuzhouFujianChina
| | - Xiuli Xu
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing HospitalFourth Military Medical UniversityXi'anShannxiChina
| | - Jiayin Yuan
- Department of PathologyThe First People's Hospital of FoshanFoshanGuangdongChina
| | - Shigeo Nakamura
- Department of Pathology and Clinical LaboratoriesNagoya University HospitalNagoyaJapan
| | - Kennosuke Karube
- Department of Pathology and Clinical LaboratoriesNagoya University HospitalNagoyaJapan
| | - Zhe Wang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing HospitalFourth Military Medical UniversityXi'anShannxiChina
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