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Zhang L, Shen M, Shu X, Zhou J, Ding J, Zhong C, Pan B, Wang B, Zhang C, Guo W. Intronic position +9 and -9 are potentially splicing sites boundary from intronic variants analysis of whole exome sequencing data. BMC Med Genomics 2023; 16:146. [PMID: 37365551 DOI: 10.1186/s12920-023-01542-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/12/2023] [Indexed: 06/28/2023] Open
Abstract
Whole exome sequencing (WES) can also detect some intronic variants, which may affect splicing and gene expression, but how to use these intronic variants, and the characteristics about them has not been reported. This study aims to reveal the characteristics of intronic variant in WES data, to further improve the clinical diagnostic value of WES. A total of 269 WES data was analyzed, 688,778 raw variants were called, among these 367,469 intronic variants were in intronic regions flanking exons which was upstream/downstream region of the exon (default is 200 bps). Contrary to expectation, the number of intronic variants with quality control (QC) passed was the lowest at the +2 and -2 positions but not at the +1 and -1 positions. The plausible explanation was that the former had the worst effect on trans-splicing, whereas the latter did not completely abolish splicing. And surprisingly, the number of intronic variants that passed QC was the highest at the +9 and -9 positions, indicating a potential splicing site boundary. The proportion of variants which could not pass QC filtering (false variants) in the intronic regions flanking exons generally accord with "S"-shaped curve. At +5 and -5 positions, the number of variants predicted damaging by software was most. This was also the position at which many pathogenic variants had been reported in recent years. Our study revealed the characteristics of intronic variant in WES data for the first time, we found the +9 and -9 positions might be a potentially splicing sites boundary and +5 and -5 positions were potentially important sites affecting splicing or gene expression, the +2 and -2 positions seem more important splicing site than +1 and -1 positions, and we found variants in intronic regions flanking exons over ± 50 bps may be unreliable. This result can help researchers find more useful variants and demonstrate that WES data is valuable for intronic variants analysis.
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Affiliation(s)
- Li Zhang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Minna Shen
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xianhong Shu
- Department of Echocardiography, Zhongshan Hospital, Shanghai Institute of Cardiovascular Diseases, Shanghai Institute of Medical Imaging, Fudan University, Shanghai, China
| | - Jingmin Zhou
- Department of Cardiology Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jing Ding
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunjiu Zhong
- Department of Neurology, Zhongshan Hospital, State Key Laboratory, Fudan University, Shanghai, China
| | - Baishen Pan
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Beili Wang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunyan Zhang
- Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China.
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China.
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Zhang X, Young C, Liao XH, Refetoff S, Torres M, Tomer Y, Stefan-Lifshitz M, Zhang H, Larkin D, Fang D, Qi L, Arvan P. Perturbation of endoplasmic reticulum proteostasis triggers tissue injury in the thyroid gland. JCI Insight 2023; 8:e169937. [PMID: 37345654 PMCID: PMC10371246 DOI: 10.1172/jci.insight.169937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
Defects in endoplasmic reticulum (ER) proteostasis have been linked to diseases in multiple organ systems. Here we examined the impact of perturbation of ER proteostasis in mice bearing thyrocyte-specific knockout of either HRD1 (to disable ER-associated protein degradation [ERAD]) or ATG7 (to disable autophagy) in the absence or presence of heterozygous expression of misfolded mutant thyroglobulin (the most highly expressed thyroid gene product, synthesized in the ER). Misfolding-inducing thyroglobulin mutations are common in humans but are said to yield only autosomal-recessive disease - perhaps because misfolded thyroglobulin protein might undergo disposal by ERAD or ER macroautophagy. We find that as single defects, neither ERAD, nor autophagy, nor heterozygous thyroglobulin misfolding altered circulating thyroxine levels, and neither defective ERAD nor defective autophagy caused any gross morphological change in an otherwise WT thyroid gland. However, heterozygous expression of misfolded thyroglobulin itself triggered significant ER stress and individual thyrocyte death while maintaining integrity of the surrounding thyroid epithelium. In this context, deficiency of ERAD (but not autophagy) resulted in patchy whole-follicle death with follicular collapse and degeneration, accompanied by infiltration of bone marrow-derived macrophages. Perturbation of thyrocyte ER proteostasis is thus a risk factor for both cell death and follicular demise.
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Affiliation(s)
- Xiaohan Zhang
- Division of Metabolism, Endocrinology & Diabetes and
| | - Crystal Young
- Division of Metabolism, Endocrinology & Diabetes and
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Samuel Refetoff
- Department of Medicine
- Department of Pediatrics, and Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, Illinois, USA
| | - Mauricio Torres
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yaron Tomer
- Department of Medicine, Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, New York, New York, USA
| | - Mihaela Stefan-Lifshitz
- Department of Medicine, Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, New York, New York, USA
| | - Hao Zhang
- Division of Metabolism, Endocrinology & Diabetes and
| | - Dennis Larkin
- Division of Metabolism, Endocrinology & Diabetes and
| | - Deyu Fang
- Department of Pathology, Feinberg School of Medicine, Northwestern Medicine, Chicago, Illinois, USA
| | - Ling Qi
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter Arvan
- Division of Metabolism, Endocrinology & Diabetes and
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
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Matsuyama M, Sawada H, Inoue S, Hishinuma A, Sekiya R, Sato Y, Moritake H. Goiter in a 6-year-old patient with novel thyroglobulin gene variant (Gly145Glu) causing intracellular thyroglobulin transport disorder: Correlation between goiter size and the free T3 to free T4 ratio. Clin Pediatr Endocrinol 2022; 31:185-191. [PMID: 35928386 PMCID: PMC9297170 DOI: 10.1297/cpe.2022-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 04/12/2022] [Indexed: 11/04/2022] Open
Affiliation(s)
- Misayo Matsuyama
- Division of Pediatrics, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Hirotake Sawada
- Department of Fundamental Nursing, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Shinobu Inoue
- Division of Pediatrics, National Hospital Organization Miyazaki Higashi Hospital, Miyazaki, Japan
| | - Akira Hishinuma
- Department of Infection Control and Clinical Laboratory Medicine, Dokkyo Medical University, Mibu, Japan
| | - Ryo Sekiya
- Division of Surgery, Miyazaki Zenjinkai Hospital, Miyazaki, Japan
| | - Yuichiro Sato
- Departoment of Diagnostic Pathology, University of Miyazaki Hospital, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Hiroshi Moritake
- Division of Pediatrics, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
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Pio MG, Siffo S, Scheps KG, Molina MF, Adrover E, Abelleyro MM, Rivolta CM, Targovnik HM. Curating the gnomAD database: Report of novel variants in the thyrogobulin gene using in silico bioinformatics algorithms. Mol Cell Endocrinol 2021; 534:111359. [PMID: 34119605 DOI: 10.1016/j.mce.2021.111359] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 01/09/2023]
Abstract
Thyroglobulin (TG) is a large glycosylated protein of 2767 amino acids, secreted by the thyrocytes into the follicular lumen. It plays an essential role in the process of thyroid hormone synthesis. TG gene variants lead to permanent congenital hypothyroidism. In the present work, we report a detailed population and bioinformatic prediction analyses of the TG variants indexed in the Genome Aggregation Database (gnomAD). The results showed a clear predominance of nonsense variants in the European (Finnish), European (Non-Finnish) and Ashkenazi Jewish ethnic groups, whereas the splice site variants predominate in South Asian and African/African-American populations. In total, 282 novel TG variants were described (47 missense involving the wild-type cysteine residues, 177 missense located in the ChEL domain and 58 splice site variants) which were not reported in the literature and that would have deleterious effects in prediction programs. In the gnomAD population, the estimated prevalence of heterozygous carriers of the potentially damaging variants was 1:320. In conclusion, we provide an updated and curated reference source for the diagnosis of thyroid disease, mainly to congenital hypothyroidism due to TG deficiency. The identification and characterization of TG variants is undoubtedly a valuable approach to study the TG structure/function relations and an important tool for clinical diagnosis and genetic counseling.
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Affiliation(s)
- Mauricio Gomes Pio
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Sofia Siffo
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Karen G Scheps
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Maricel F Molina
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Ezequiela Adrover
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Miguel M Abelleyro
- CONICET-Academia Nacional de Medicina, Instituto de Medicina Experimental (IMEX), Buenos Aires, Argentina
| | - Carina M Rivolta
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Héctor M Targovnik
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina.
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5
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Zhang X, Kellogg AP, Citterio CE, Zhang H, Larkin D, Morishita Y, Targovnik HM, Balbi VA, Arvan P. Thyroid hormone synthesis continues despite biallelic thyroglobulin mutation with cell death. JCI Insight 2021; 6:148496. [PMID: 33914707 PMCID: PMC8262357 DOI: 10.1172/jci.insight.148496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/28/2021] [Indexed: 11/17/2022] Open
Abstract
Complete absence of thyroid hormone is incompatible with life in vertebrates. Thyroxine is synthesized within thyroid follicles upon iodination of thyroglobulin conveyed from the endoplasmic reticulum (ER), via the Golgi complex, to the extracellular follicular lumen. In congenital hypothyroidism from biallelic thyroglobulin mutation, thyroglobulin is misfolded and cannot advance from the ER, eliminating its secretion and triggering ER stress. Nevertheless, untreated patients somehow continue to synthesize sufficient thyroxine to yield measurable serum levels that sustain life. Here, we demonstrate that TGW2346R/W2346R humans, TGcog/cog mice, and TGrdw/rdw rats exhibited no detectable ER export of thyroglobulin, accompanied by severe thyroidal ER stress and thyroid cell death. Nevertheless, thyroxine was synthesized, and brief treatment of TGrdw/rdw rats with antithyroid drug was lethal to the animals. When untreated, remarkably, thyroxine was synthesized on the mutant thyroglobulin protein, delivered via dead thyrocytes that decompose within the follicle lumen, where they were iodinated and cannibalized by surrounding live thyrocytes. As the animals continued to grow goiters, circulating thyroxine increased. However, when TGrdw/rdw rats age, they cannot sustain goiter growth that provided the dying cells needed for ongoing thyroxine synthesis, resulting in profound hypothyroidism. These results establish a disease mechanism wherein dead thyrocytes support organismal survival.
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Affiliation(s)
- Xiaohan Zhang
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA
| | - Aaron P Kellogg
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA
| | - Cintia E Citterio
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo, Buenos Aires, Argentina
| | - Hao Zhang
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA
| | - Dennis Larkin
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA
| | - Yoshiaki Morishita
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA.,Division of Diabetes, Department of Internal Medicine, Aichi Medical University, Nagakute, Japan
| | - Héctor M Targovnik
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Inmunología, Genética y Metabolismo, Buenos Aires, Argentina
| | - Viviana A Balbi
- Department of Endocrinology and Growth, Hospital de Niños Sor María Ludovica, La Plata, Argentina
| | - Peter Arvan
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA
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6
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Citterio CE, Rivolta CM, Targovnik HM. Structure and genetic variants of thyroglobulin: Pathophysiological implications. Mol Cell Endocrinol 2021; 528:111227. [PMID: 33689781 DOI: 10.1016/j.mce.2021.111227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/22/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Thyroglobulin (TG) plays a main role in the biosynthesis of thyroid hormones (TH), and, thus, it is involved in a wide range of vital functions throughout the life cycle of all vertebrates. Deficiency of TH production due to TG genetic variants causes congenital hypothyroidism (CH), with devastating consequences such as intellectual disability and impaired growth if untreated. To this day, 229 variations in the human TG gene have been identified while the 3D structure of TG has recently appeared. Although TG deficiency is thought to be of autosomal recessive inheritance, the introduction of massive sequencing platforms led to the identification of a variety of monoallelic TG variants (combined with mutations in other thyroid gene products) opening new questions regarding the possibility of oligogenic inheritance of the disease. In this review we discuss remarkable advances in the understanding of the TG architecture and the pathophysiology of CH associated with TG defects, providing new insights for the management of congenital disorders as well as counseling benefits for families with a history of TG abnormalities. Moreover, we summarize relevant aspects of TH synthesis within TG and offer an updated analysis of animal and cellular models of TG deficiency for pathophysiological studies of thyroid dyshormonogenesis while highlighting perspectives for new investigations. All in all, even though there has been sustained progress in understanding the role of TG in thyroid pathophysiology during the past 50 years, functional characterization of TG variants remains an important area of study for future advancement in the field.
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Affiliation(s)
- Cintia E Citterio
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Carina M Rivolta
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Héctor M Targovnik
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina.
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