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Roychowdhury S, Joshi D, Singh VK, Faruq M, Das P. Genetic and in silico analysis of Indian sporadic young onset patient with amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 2024; 25:589-599. [PMID: 38450645 DOI: 10.1080/21678421.2024.2324896] [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: 12/16/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is an old onset devastating neurodegenerative disorder. Young-onset ALS cases especially sporadic ones who are between 25 and 45 years are rarely affected by the disease. Despite the identification of numerous candidate genes associated with ALS, the etiology of the disease remains elusive due to extreme genetic and phenotypic variability. The advent of affordable whole exome sequencing (WES) has opened new avenues for unraveling the disease's pathophysiology better. METHODS AND RESULTS We aimed to determine the genetic basis of an Indian-origin, young onset sporadic ALS patient with very rapid deterioration of the disease course without any cognitive decline who was screened for mutations in major ALS candidate genes by WES. Variants detected were reconfirmed by Sanger sequencing. The clinicopathological features were investigated and two heterozygous missense variants were identified: R452W, not previously associated with ALS, present in one of the four conserved C terminal domains in ANXA11 and R208W in SIGMAR1, respectively. Both of these variants were predicted to be damaging by pathogenicity prediction tools and various in silico methods. CONCLUSION Our study revealed two potentially pathogenic variants in two ALS candidate genes. The genetic makeup of ALS patients from India has been the subject of a few prior studies, but none of them examined ANXA11 and SIGMAR1 genes so far. These results establish the framework for additional research into the pathogenic processes behind these variations that result in sporadic ALS disease and further our understanding of the genetic makeup of Indian ALS patients.
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Affiliation(s)
- Saileyee Roychowdhury
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Deepika Joshi
- Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Vinay Kumar Singh
- School of Biotechnology, Centre for Bioinformatics, Institute of Science, Banaras Hindu University, Varanasi, India, and
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Parimal Das
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, India
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Snyder A, Ryan VH, Hawrot J, Lawton S, Ramos DM, Qi YA, Johnson KR, Reed X, Johnson NL, Kollasch AW, Duffy MF, VandeVrede L, Cochran JN, Miller BL, Toro C, Bielekova B, Marks DS, Yokoyama JS, Kwan JY, Cookson MR, Ward ME. An ANXA11 P93S variant dysregulates TDP-43 and causes corticobasal syndrome. Alzheimers Dement 2024. [PMID: 38923692 DOI: 10.1002/alz.13915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 06/28/2024]
Abstract
INTRODUCTION Variants of uncertain significance (VUS) surged with affordable genetic testing, posing challenges for determining pathogenicity. We examine the pathogenicity of a novel VUS P93S in Annexin A11 (ANXA11) - an amyotrophic lateral sclerosis/frontotemporal dementia-associated gene - in a corticobasal syndrome kindred. Established ANXA11 mutations cause ANXA11 aggregation, altered lysosomal-RNA granule co-trafficking, and transactive response DNA binding protein of 43 kDa (TDP-43) mis-localization. METHODS We described the clinical presentation and explored the phenotypic diversity of ANXA11 variants. P93S's effect on ANXA11 function and TDP-43 biology was characterized in induced pluripotent stem cell-derived neurons alongside multiomic neuronal and microglial profiling. RESULTS ANXA11 mutations were linked to corticobasal syndrome cases. P93S led to decreased lysosome colocalization, neuritic RNA, and nuclear TDP-43 with cryptic exon expression. Multiomic microglial signatures implicated immune dysregulation and interferon signaling pathways. DISCUSSION This study establishes ANXA11 P93S pathogenicity, broadens the phenotypic spectrum of ANXA11 mutations, underscores neuronal and microglial dysfunction in ANXA11 pathophysiology, and demonstrates the potential of cellular models to determine variant pathogenicity. HIGHLIGHTS ANXA11 P93S is a pathogenic variant. Corticobasal syndrome is part of the ANXA11 phenotypic spectrum. Hybridization chain reaction fluorescence in situ hybridization (HCR FISH) is a new tool for the detection of cryptic exons due to TDP-43-related loss of splicing regulation. Microglial ANXA11 and related immune pathways are important drivers of disease. Cellular models are powerful tools for adjudicating variants of uncertain significance.
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Affiliation(s)
- Allison Snyder
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Veronica H Ryan
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA
- National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - James Hawrot
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Sydney Lawton
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA
| | - Y Andy Qi
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA
| | - Kory R Johnson
- Intramural Bioinformatics Core, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Xylena Reed
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA
| | - Nicholas L Johnson
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA
- DataTecnica LLC, Washington, District of Columbia, USA
| | - Aaron W Kollasch
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Megan F Duffy
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Lawren VandeVrede
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
| | | | - Bruce L Miller
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
| | - Camilo Toro
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Bibiana Bielekova
- Neuroimmunological Diseases Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Justin Y Kwan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark R Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael E Ward
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
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Dudas EF, Tully MD, Foldes T, Kelly G, Tartaglia GG, Pastore A. The structural properties of full-length annexin A11. Front Mol Biosci 2024; 11:1347741. [PMID: 38516187 PMCID: PMC10955470 DOI: 10.3389/fmolb.2024.1347741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 03/23/2024] Open
Abstract
Annexin A11 (ANXA11) is a calcium-dependent phospholipid-binding protein belonging to the annexin protein family and implicated in the neurodegenerative amyotrophic lateral sclerosis. Structurally, ANXA11 contains a conserved calcium-binding C-terminal domain common to all annexins and a putative intrinsically unfolded N-terminus specific for ANXA11. Little is known about the structure and functions of this region of the protein. By analogy with annexin A1, it was suggested that residues 38 to 59 within the ANXA11 N-terminus could form a helical region that would be involved in interactions. Interestingly, this region contains residues that, when mutated, may lead to clinical manifestations. In the present study, we have studied the structural features of the full-length protein with special attention to the N-terminal region using a combination of biophysical techniques which include nuclear magnetic resonance and small angle X-ray scattering. We show that the N-terminus is intrinsically disordered and that the overall features of the protein are not markedly affected by the presence of calcium. We also analyzed the 38-59 helix hypothesis using synthetic peptides spanning both the wild-type sequence and clinically relevant mutations. We show that the peptides have a remarkable character typical of a native helix and that mutations do not alter the behaviour suggesting that they are required for interactions rather than being structurally important. Our work paves the way to a more thorough understanding of the ANXA11 functions.
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Affiliation(s)
- Erika F. Dudas
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- European Synchrotron Radiation Facility, Grenoble, France
| | - Mark D. Tully
- European Synchrotron Radiation Facility, Grenoble, France
| | - Tamas Foldes
- University College London, Department of Physics and Astronomy, University College London, London, United Kingdom
- Institut de Biologie Structurale (IBS), Institut Laue-Langevin, University Grenoble Alpes, Grenoble, France
| | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, London, United Kingdom
| | | | - Annalisa Pastore
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- European Synchrotron Radiation Facility, Grenoble, France
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Snyder A, Ryan VH, Hawrot J, Lawton S, Ramos DM, Qi YA, Johnson K, Reed X, Johnson NL, Kollasch AW, Duffy M, VandeVrede L, Cochran JN, Miller BL, Toro C, Bielekova B, Yokoyama JS, Marks DS, Kwan JY, Cookson MR, Ward ME. An ANXA11 P93S variant dysregulates TDP-43 and causes corticobasal syndrome. RESEARCH SQUARE 2023:rs.3.rs-3462973. [PMID: 37886540 PMCID: PMC10602153 DOI: 10.21203/rs.3.rs-3462973/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
As genetic testing has become more accessible and affordable, variants of uncertain significance (VUS) are increasingly identified, and determining whether these variants play causal roles in disease is a major challenge. The known disease-associated Annexin A11 (ANXA11) mutations result in ANXA11 aggregation, alterations in lysosomal-RNA granule co-trafficking, and TDP-43 mis-localization and present as amyotrophic lateral sclerosis or frontotemporal dementia. We identified a novel VUS in ANXA11 (P93S) in a kindred with corticobasal syndrome and unique radiographic features that segregated with disease. We then queried neurodegenerative disorder clinic databases to identify the phenotypic spread of ANXA11 mutations. Multi-modal computational analysis of this variant was performed and the effect of this VUS on ANXA11 function and TDP-43 biology was characterized in iPSC-derived neurons. Single-cell sequencing and proteomic analysis of iPSC-derived neurons and microglia were used to determine the multiomic signature of this VUS. Mutations in ANXA11 were found in association with clinically diagnosed corticobasal syndrome, thereby establishing corticobasal syndrome as part of ANXA11 clinical spectrum. In iPSC-derived neurons expressing mutant ANXA11, we found decreased colocalization of lysosomes and decreased neuritic RNA as well as decreased nuclear TDP-43 and increased formation of cryptic exons compared to controls. Multiomic assessment of the P93S variant in iPSC-derived neurons and microglia indicates that the pathogenic omic signature in neurons is modest compared to microglia. Additionally, omic studies reveal that immune dysregulation and interferon signaling pathways in microglia are central to disease. Collectively, these findings identify a new pathogenic variant in ANXA11, expand the range of clinical syndromes caused by ANXA11 mutations, and implicate both neuronal and microglia dysfunction in ANXA11 pathophysiology. This work illustrates the potential for iPSC-derived cellular models to revolutionize the variant annotation process and provides a generalizable approach to determining causality of novel variants across genes.
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Affiliation(s)
- Allison Snyder
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke
| | - Veronica H Ryan
- Center for Alzheimer's and Related Dementias, National Institutes of Health
| | - James Hawrot
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke
| | - Sydney Lawton
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias, National Institutes of Health
| | - Y Andy Qi
- Center for Alzheimer's and Related Dementias, National Institutes of Health
| | - Kory Johnson
- Intramural Bioinformatics, National Institute of Neurological Disorders and Stroke
| | - Xylena Reed
- Center for Alzheimer's and Related Dementias, National Institutes of Health
| | | | | | - Megan Duffy
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging
| | - Lawren VandeVrede
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco
| | | | - Bruce L Miller
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco
| | - Camilo Toro
- Undiagnosed Diseases Program, National Human Genome Research Institute
| | - Bibiana Bielekova
- Neuroimmunological Diseases Section, National Institute of Allergy and Infectious Disease
| | - Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston
| | - Justin Y Kwan
- Office of the Clinical Director, National Institute of Neurological Disorders and Stroke
| | - Mark R Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging
| | - Michael E Ward
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke
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Yang J, Pei T, Su G, Duan P, Liu X. AnnexinA6: a potential therapeutic target gene for extracellular matrix mineralization. Front Cell Dev Biol 2023; 11:1201200. [PMID: 37727505 PMCID: PMC10506415 DOI: 10.3389/fcell.2023.1201200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/10/2023] [Indexed: 09/21/2023] Open
Abstract
The mineralization of the extracellular matrix (ECM) is an essential and crucial process for physiological bone formation and pathological calcification. The abnormal function of ECM mineralization contributes to the worldwide risk of developing mineralization-related diseases; for instance, vascular calcification is attributed to the hyperfunction of ECM mineralization, while osteoporosis is due to hypofunction. AnnexinA6 (AnxA6), a Ca2+-dependent phospholipid-binding protein, has been extensively reported as an essential target in mineralization-related diseases such as osteoporosis, osteoarthritis, atherosclerosis, osteosarcoma, and calcific aortic valve disease. To date, AnxA6, as the largest member of the Annexin family, has attracted much attention due to its significant contribution to matrix vesicles (MVs) production and release, MVs-ECM interaction, cytoplasmic Ca2+ influx, and maturation of hydroxyapatite, making it an essential target in ECM mineralization. In this review, we outlined the recent advancements in the role of AnxA6 in mineralization-related diseases and the potential mechanisms of AnxA6 under normal and mineralization-related pathological conditions. AnxA6 could promote ECM mineralization for bone regeneration in the manner described previously. Therefore, AnxA6 may be a potential osteogenic target for ECM mineralization.
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Affiliation(s)
| | | | | | | | - Xiaoheng Liu
- Institute of Biomedical Engineering, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
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Varabyou A, Erdogdu B, Salzberg SL, Pertea M. Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage. NATURE COMPUTATIONAL SCIENCE 2023; 3:700-708. [PMID: 38098813 PMCID: PMC10718564 DOI: 10.1038/s43588-023-00496-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 12/17/2023]
Abstract
ORFanage is a system designed to assign open reading frames (ORFs) to known and novel gene transcripts while maximizing similarity to annotated proteins. The primary intended use of ORFanage is the identification of ORFs in the assembled results of RNA sequencing experiments, a capability that most transcriptome assembly methods do not have. Our experiments demonstrate how ORFanage can be used to find novel protein variants in RNA-seq datasets, and to improve the annotations of ORFs in tens of thousands of transcript models in the human annotation databases. Through its implementation of a highly accurate and efficient pseudo-alignment algorithm, ORFanage is substantially faster than other ORF annotation methods, enabling its application to very large datasets. When used to analyze transcriptome assemblies, ORFanage can aid in the separation of signal from transcriptional noise and the identification of likely functional transcript variants, ultimately advancing our understanding of biology and medicine.
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Affiliation(s)
- Ales Varabyou
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Beril Erdogdu
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Steven L. Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
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Patil SS, Panchal V, Røstbø T, Romanyuk S, Hollås H, Brenk R, Grindheim AK, Vedeler A. RNA-binding is an ancient trait of the Annexin family. Front Cell Dev Biol 2023; 11:1161588. [PMID: 37397259 PMCID: PMC10311354 DOI: 10.3389/fcell.2023.1161588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/25/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction: The regulation of intracellular functions in mammalian cells involves close coordination of cellular processes. During recent years it has become evident that the sorting, trafficking and distribution of transport vesicles and mRNA granules/complexes are closely coordinated to ensure effective simultaneous handling of all components required for a specific function, thereby minimizing the use of cellular energy. Identification of proteins acting at the crossroads of such coordinated transport events will ultimately provide mechanistic details of the processes. Annexins are multifunctional proteins involved in a variety of cellular processes associated with Ca2+-regulation and lipid binding, linked to the operation of both the endocytic and exocytic pathways. Furthermore, certain Annexins have been implicated in the regulation of mRNA transport and translation. Since Annexin A2 binds specific mRNAs via its core structure and is also present in mRNP complexes, we speculated whether direct association with RNA could be a common property of the mammalian Annexin family sharing a highly similar core structure. Methods and results: Therefore, we performed spot blot and UV-crosslinking experiments to assess the mRNA binding abilities of the different Annexins, using annexin A2 and c-myc 3'UTRs as well as c-myc 5'UTR as baits. We supplemented the data with immunoblot detection of selected Annexins in mRNP complexes derived from the neuroendocrine rat PC12 cells. Furthermore, biolayer interferometry was used to determine the KD of selected Annexin-RNA interactions, which indicated distinct affinities. Amongst these Annexins, Annexin A13 and the core structures of Annexin A7, Annexin A11 bind c-myc 3'UTR with KDs in the nanomolar range. Of the selected Annexins, only Annexin A2 binds the c-myc 5'UTR indicating some selectivity. Discussion: The oldest members of the mammalian Annexin family share the ability to associate with RNA, suggesting that RNA-binding is an ancient trait of this protein family. Thus, the combined RNA- and lipid-binding properties of the Annexins make them attractive candidates to participate in coordinated long-distance transport of membrane vesicles and mRNAs regulated by Ca2+. The present screening results can thus pave the way for studies of the multifunctional Annexins in a novel cellular context.
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Affiliation(s)
- Sudarshan S. Patil
- Neurotargeting Group, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Vipul Panchal
- Biorecognition Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Trude Røstbø
- Neurotargeting Group, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Sofya Romanyuk
- Neurotargeting Group, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Hanne Hollås
- Neurotargeting Group, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ruth Brenk
- Biorecognition Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ann Kari Grindheim
- Neurotargeting Group, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Anni Vedeler
- Neurotargeting Group, Department of Biomedicine, University of Bergen, Bergen, Norway
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Varabyou A, Erdogdu B, Salzberg SL, Pertea M. Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533704. [PMID: 36993373 PMCID: PMC10055401 DOI: 10.1101/2023.03.23.533704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
ORFanage is a system designed to assign open reading frames (ORFs) to both known and novel gene transcripts while maximizing similarity to annotated proteins. The primary intended use of ORFanage is the identification of ORFs in the assembled results of RNA sequencing (RNA-seq) experiments, a capability that most transcriptome assembly methods do not have. Our experiments demonstrate how ORFanage can be used to find novel protein variants in RNA-seq datasets, and to improve the annotations of ORFs in tens of thousands of transcript models in the RefSeq and GENCODE human annotation databases. Through its implementation of a highly accurate and efficient pseudo-alignment algorithm, ORFanage is substantially faster than other ORF annotation methods, enabling its application to very large datasets. When used to analyze transcriptome assemblies, ORFanage can aid in the separation of signal from transcriptional noise and the identification of likely functional transcript variants, ultimately advancing our understanding of biology and medicine.
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Affiliation(s)
- Ales Varabyou
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Beril Erdogdu
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Steven L Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
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Hollås H, Ramirez J, Nominé Y, Kostmann C, Toto A, Gianni S, Travé G, Vedeler A. The cooperative folding of annexin A2 relies on a transient nonnative intermediate. Biophys J 2022; 121:4492-4504. [PMID: 36325614 PMCID: PMC9748365 DOI: 10.1016/j.bpj.2022.10.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/29/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022] Open
Abstract
Annexins (Anxs) are a family of highly homologous proteins that bind and aggregate lipid vesicles in the presence of calcium. All members of the family contain a variable N-terminus determining specific functions, followed by a conserved core region responsible for the general calcium-dependent lipid-binding property. The core structure consists of four homologous domains (DI-DIV), each consisting of a right-handed super-helix of five α-helices. We present data from a combination of site-directed mutagenesis, NMR, and circular dichroism showing that the G25-D34 region of the N-terminus as well as the contacts between residues D38A, R63A, and Q67A of AnxA2-DI are crucial for the autonomous folding and stability of DI of AnxA2. However, we also show that the folding of the full-length protein is very robust in that mutations and truncations that disrupted the folding of AnxA2-DI did not abolish the folding of full-length AnxA2, only lowering its thermal stability. This robustness of the folding of full-length AnxA2 is likely to be mediated by the existence of at least one transient nonnative intermediate as suggested by our kinetic data using stopped-flow fluorescence experiments. We also show that hydrophobic amino acids in AnxA2-DI involved in interfacial contacts with AnxA2-DIV are important for the cooperative folding and stability of the full-length protein. Mutating all of the V57E-V98R-G101Y residues in AnxA2-DI did not affect the folding of the domain, only its stability, but prevented the cooperative folding of the full-length protein. Our collective results favor a highly cooperative and robust folding process mediated by alternative intermediate steps. Since AnxA2 is a multifunctional protein involved in several steps of the progression of cell transformation, these data on structure and folding pathways are therefore crucial to designing anticancer drugs targeting AnxA2.
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Affiliation(s)
- Hanne Hollås
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Juan Ramirez
- Équipe Labellisée Ligue 2015, Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Yves Nominé
- Équipe Labellisée Ligue 2015, Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Camille Kostmann
- Équipe Labellisée Ligue 2015, Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Angelo Toto
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Stefano Gianni
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Gilles Travé
- Équipe Labellisée Ligue 2015, Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France.
| | - Anni Vedeler
- Department of Biomedicine, University of Bergen, Bergen, Norway.
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Jiang Q, Lin J, Wei Q, Li C, Hou Y, Cao B, Zhang L, Ou R, Liu K, Yang T, Xiao Y, Shang H. Genetic analysis of and clinical characteristics associated with ANXA11 variants in a Chinese cohort with amyotrophic lateral sclerosis. Neurobiol Dis 2022; 175:105907. [DOI: 10.1016/j.nbd.2022.105907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
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