1
|
Scrima S, Lambrughi M, Tiberti M, Fadda E, Papaleo E. ASM variants in the spotlight: A structure-based atlas for unraveling pathogenic mechanisms in lysosomal acid sphingomyelinase. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167260. [PMID: 38782304 DOI: 10.1016/j.bbadis.2024.167260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/30/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024]
Abstract
Lysosomal acid sphingomyelinase (ASM), a critical enzyme in lipid metabolism encoded by the SMPD1 gene, plays a crucial role in sphingomyelin hydrolysis in lysosomes. ASM deficiency leads to acid sphingomyelinase deficiency, a rare genetic disorder with diverse clinical manifestations, and the protein can be found mutated in other diseases. We employed a structure-based framework to comprehensively understand the functional implications of ASM variants, integrating pathogenicity predictions with molecular insights derived from a molecular dynamics simulation in a lysosomal membrane environment. Our analysis, encompassing over 400 variants, establishes a structural atlas of missense variants of lysosomal ASM, associating mechanistic indicators with pathogenic potential. Our study highlights variants that influence structural stability or exert local and long-range effects at functional sites. To validate our predictions, we compared them to available experimental data on residual catalytic activity in 135 ASM variants. Notably, our findings also suggest applications of the resulting data for identifying cases suited for enzyme replacement therapy. This comprehensive approach enhances the understanding of ASM variants and provides valuable insights for potential therapeutic interventions.
Collapse
Affiliation(s)
- Simone Scrima
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, 2100 Copenhagen, Denmark; Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Lambrughi
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, 2100 Copenhagen, Denmark
| | - Matteo Tiberti
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, 2100 Copenhagen, Denmark
| | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, co. Kildare, Ireland
| | - Elena Papaleo
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, 2100 Copenhagen, Denmark; Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark.
| |
Collapse
|
2
|
Wang R, Qin Z, Huang L, Luo H, Peng H, Zhou X, Zhao Z, Liu M, Yang P, Shi T. SMPD1 expression profile and mutation landscape help decipher genotype-phenotype association and precision diagnosis for acid sphingomyelinase deficiency. Hereditas 2023; 160:11. [PMID: 36907956 PMCID: PMC10009935 DOI: 10.1186/s41065-023-00272-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/28/2023] [Indexed: 03/14/2023] Open
Abstract
BACKGROUND Acid sphingomyelinase deficiency (ASMD) disorder, also known as Niemann-Pick disease (NPD) is a rare genetic disease caused by mutations in SMPD1 gene, which encodes sphingomyelin phosphodiesterase (ASM). Except for liver and spleen enlargement and lung disease, two subtypes (Type A and B) of NDP have different onset times, survival times, ASM activities, and neurological abnormalities. To comprehensively explore NPD's genotype-phenotype association and pathophysiological characteristics, we collected 144 NPD cases with strict quality control through literature mining. RESULTS The difference in ASM activity can differentiate NPD type A from other subtypes, with the ratio of ASM activity to the reference values being lower in type A (threshold 0.045 (4.45%)). Severe variations, such as deletion and insertion, can cause complete loss of ASM function, leading to type A, whereas relatively mild missense mutations generally result in type B. Among reported mutations, the p.Arg3AlafsX76 mutation is highly prevalent in the Chinese population, and the p.R608del mutation is common in Mediterranean countries. The expression profiles of SMPD1 from GTEx and single-cell RNA sequencing data of multiple fetal tissues showed that high expressions of SMPD1 can be observed in the liver, spleen, and brain tissues of adults and hepatoblasts, hematopoietic stem cells, STC2_TLX1-positive cells, mesothelial cells of the spleen, vascular endothelial cells of the cerebellum and the cerebrum of fetuses, indicating that SMPD1 dysfunction is highly likely to have a significant effect on the function of those cell types during development and the clinicians need pay attention to these organs or tissues as well during diagnosis. In addition, we also predicted 21 new pathogenic mutations in the SMPD1 gene that potentially cause the NPD, signifying that more rare cases will be detected with those mutations in SMPD1. Finally, we also analysed the function of the NPD type A cells following the extracellular milieu. CONCLUSIONS Our study is the first to elucidate the effects of SMPD1 mutation on cell types and at the tissue level, which provides new insights into the genotype-phenotype association and can help in the precise diagnosis of NPD.
Collapse
Affiliation(s)
- Ruisong Wang
- College of Life and Environmental Sciences, Hunan University of Arts and Science, 3150 Dongting Ave., Changde, 415000, Hunan Province, People's Republic of China
- Affiliated Hospital of Hunan University of Arts and Science (the Maternal and Child Health Hospital), Medical college, 3150 Dongting Ave., Changde, Hunan Province, People's Republic of China, 415000
| | - Ziyi Qin
- College of Life and Environmental Sciences, Hunan University of Arts and Science, 3150 Dongting Ave., Changde, 415000, Hunan Province, People's Republic of China
| | - Long Huang
- College of Life and Environmental Sciences, Hunan University of Arts and Science, 3150 Dongting Ave., Changde, 415000, Hunan Province, People's Republic of China
| | - Huiling Luo
- College of Life and Environmental Sciences, Hunan University of Arts and Science, 3150 Dongting Ave., Changde, 415000, Hunan Province, People's Republic of China
| | - Han Peng
- College of Life and Environmental Sciences, Hunan University of Arts and Science, 3150 Dongting Ave., Changde, 415000, Hunan Province, People's Republic of China
| | - Xinyu Zhou
- College of Life and Environmental Sciences, Hunan University of Arts and Science, 3150 Dongting Ave., Changde, 415000, Hunan Province, People's Republic of China
| | - Zhixiang Zhao
- College of Life and Environmental Sciences, Hunan University of Arts and Science, 3150 Dongting Ave., Changde, 415000, Hunan Province, People's Republic of China
| | - Mingyao Liu
- College of Life and Environmental Sciences, Hunan University of Arts and Science, 3150 Dongting Ave., Changde, 415000, Hunan Province, People's Republic of China
- Changde Research Centre for Artificial Intelligence and Biomedicine, 3150 Dongting Ave., Changde, 415000, Hunan Province, People's Republic of China
| | - Pinhong Yang
- College of Life and Environmental Sciences, Hunan University of Arts and Science, 3150 Dongting Ave., Changde, 415000, Hunan Province, People's Republic of China.
- Changde Research Centre for Artificial Intelligence and Biomedicine, 3150 Dongting Ave., Changde, 415000, Hunan Province, People's Republic of China.
| | - Tieliu Shi
- College of Life and Environmental Sciences, Hunan University of Arts and Science, 3150 Dongting Ave., Changde, 415000, Hunan Province, People's Republic of China.
- Changde Research Centre for Artificial Intelligence and Biomedicine, 3150 Dongting Ave., Changde, 415000, Hunan Province, People's Republic of China.
| |
Collapse
|
3
|
Dursun FE, Özen F. SMPD1 gene variants in patients with β-Thalassemia major. Mol Biol Rep 2023; 50:3355-3363. [PMID: 36725747 PMCID: PMC10042979 DOI: 10.1007/s11033-023-08275-x] [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: 08/22/2022] [Accepted: 01/11/2023] [Indexed: 02/03/2023]
Abstract
BACKGROUND β-thalassemia major and Niemann-Pick diseases have similar clinical and laboratory findings. We aimed to investigate the effects of sphingomyelin phosphodiesterase 1 (SMPD1) gene variants on the clinical and laboratory findings in patients with β-thalassemia major. METHODS AND RESULTS This study included 45 patients who were followed up for β-thalassemia major in our clinic. Plasma chitotriosidase, leukocyte acid sphingomyelinase, liver enzymes, ferritin, hemogram, biochemical parameters, SMPD1 gene variant analysis, cardiac T2* MRI, and liver R2 MRI were assessed in all patients. The SMPD1 gene c.132_143del, p.A46_L49del (c.108GCTGGC[4] (p.38AL[4])) (rs3838786) variant was detected in 9 of 45 (20.0%) patients. Plasma chitotriosidase, ferritin, acetyl aminotransferase, and alanine aminotransferase levels were significantly higher in patients with the gene variant than in those without (p < 0.05). Leukocyte acid sphingomyelinase levels were significantly lower in patients with the gene variant than in those without (p < 0.05). CONCLUSION These results imply that the clinical and laboratory findings and some features of disease progression in patients with β-thalassemia major are similar to those of Niemann-Pick disease. They also suggest that SMPD1 gene c.132_143del, p.A46_L49del (c.108GCTGGC[4] (p.38AL[4])) (rs3838786) variant may underlie these clinical findings in patients with β-thalassemia major.
Collapse
Affiliation(s)
- Fadime Ersoy Dursun
- Department of Hematology, Prof. Dr. Süleyman Yalçın City Hospital, Eğitim mah, Dr. Erkin Cd. No:161/1, 34722, Kadıköy, İstanbul, Turkey.
| | - Filiz Özen
- Department of Medical Genetics, Prof. Dr. Süleyman Yalçın City Hospital, Kadıköy, İstanbul, Turkey
| |
Collapse
|
4
|
Wang NL, Lin J, Chen L, Lu Y, Xie XB, Abuduxikuer K, Wang JS. Neonatal cholestasis is an early liver manifestation of children with acid sphingomyelinase deficiency. BMC Gastroenterol 2022; 22:227. [PMID: 35534800 PMCID: PMC9088046 DOI: 10.1186/s12876-022-02310-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/25/2022] [Indexed: 11/12/2022] Open
Abstract
Background Patients with acid sphingomyelinase deficiency (ASMD) may be referred to a hepatologist for liver manifestations. This study summarized the liver manifestations of patients with ASMD in the early disease course. Methods This study enrolled ASMD patients diagnosed by genetic tests between July 2016 and December 2020 in a national pediatric liver center. The significance of low High-density lipoprotein cholesterol (HDL-C) for aid diagnosis of ASMD in infancy was explored by reviewing 160 consecutive infants with liver manifestations, who underwent both genetic tests and lipid profile studies, between January 2020 and December 2020. Results A total of 7 patients were diagnosed as ASMD, and 10 known disease-causing variants were identified. Hepatosplenomegaly, elevated transaminases, and liver foam cells were observed in all the 7 patients at age ranging from 4 to 31 months. Low HDL-C was detected in 5 patients, cherry red spot in 4 patients, development delay in 3 patients, and interstitial lung diseases in 1 patient. Three ASMD patients developed cholestasis around 1 month of age, and bilirubin levels normalized at age ranging from 3 to 10 months. They had persistently elevated transaminases and hepatosplenomegaly, and died within 4 years of age. Among the 160 infants with liver manifestations, 125 (78.1%) had low HDL-C. Fifty-four had both low HDL-C and splenomegaly, including 48 cholestatic infants, but only 1 (1.9%, 1/54) infant without cholestasis was diagnosed as ASMD. Conclusions ASMD can manifest as neonatal cholestasis in the early disease course. Cholestasis is a pitfall when low HDL-C is used for aid diagnosis of ASMD in infants with splenomegaly.
Collapse
Affiliation(s)
- Neng-Li Wang
- Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Jing Lin
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lian Chen
- Department of Pathology, Children's Hospital of Fudan University, Shanghai, China
| | - Yi Lu
- Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Xin-Bao Xie
- Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | | | - Jian-She Wang
- Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China.
| |
Collapse
|
5
|
Potter JHT, Davies KTJ, Yohe LR, Sanchez MKR, Rengifo EM, Struebig M, Warren K, Tsagkogeorga G, Lim BK, dos Reis M, Dávalos LM, Rossiter SJ. Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution. Mol Biol Evol 2021; 38:3864-3883. [PMID: 34426843 PMCID: PMC8382914 DOI: 10.1093/molbev/msab028] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dietary adaptation is a major feature of phenotypic and ecological diversification, yet the genetic basis of dietary shifts is poorly understood. Among mammals, Neotropical leaf-nosed bats (family Phyllostomidae) show unmatched diversity in diet; from a putative insectivorous ancestor, phyllostomids have radiated to specialize on diverse food sources including blood, nectar, and fruit. To assess whether dietary diversification in this group was accompanied by molecular adaptations for changing metabolic demands, we sequenced 89 transcriptomes across 58 species and combined these with published data to compare ∼13,000 protein coding genes across 66 species. We tested for positive selection on focal lineages, including those inferred to have undergone dietary shifts. Unexpectedly, we found a broad signature of positive selection in the ancestral phyllostomid branch, spanning genes implicated in the metabolism of all major macronutrients, yet few positively selected genes at the inferred switch to plantivory. Branches corresponding to blood- and nectar-based diets showed selection in loci underpinning nitrogenous waste excretion and glycolysis, respectively. Intriguingly, patterns of selection in metabolism genes were mirrored by those in loci implicated in craniofacial remodeling, a trait previously linked to phyllostomid dietary specialization. Finally, we show that the null model of the widely-used branch-site test is likely to be misspecified, with the implication that the test is too conservative and probably under-reports true cases of positive selection. Our findings point to a complex picture of adaptive radiation, in which the evolution of new dietary specializations has been facilitated by early adaptations combined with the generation of new genetic variation.
Collapse
Affiliation(s)
- Joshua H T Potter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Department of Earth and Planetary Science, Yale University, 210 Whitney Ave, New Haven, CT, USA
| | - Miluska K R Sanchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, Peru
| | - Edgardo M Rengifo
- Escola Superior de Agricultura ‘Luiz de Queiroz,’ Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
- Centro de Investigación Biodiversidad Sostenible (BioS), Lima, Peru
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Kim Warren
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Mario dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| |
Collapse
|