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Karamali F, Behtaj S, Babaei-Abraki S, Hadady H, Atefi A, Savoj S, Soroushzadeh S, Najafian S, Nasr Esfahani MH, Klassen H. Potential therapeutic strategies for photoreceptor degeneration: the path to restore vision. J Transl Med 2022; 20:572. [PMID: 36476500 PMCID: PMC9727916 DOI: 10.1186/s12967-022-03738-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/29/2022] [Indexed: 12/12/2022] Open
Abstract
Photoreceptors (PRs), as the most abundant and light-sensing cells of the neuroretina, are responsible for converting light into electrical signals that can be interpreted by the brain. PR degeneration, including morphological and functional impairment of these cells, causes significant diminution of the retina's ability to detect light, with consequent loss of vision. Recent findings in ocular regenerative medicine have opened promising avenues to apply neuroprotective therapy, gene therapy, cell replacement therapy, and visual prostheses to the challenge of restoring vision. However, successful visual restoration in the clinical setting requires application of these therapeutic approaches at the appropriate stage of the retinal degeneration. In this review, firstly, we discuss the mechanisms of PR degeneration by focusing on the molecular mechanisms underlying cell death. Subsequently, innovations, recent developments, and promising treatments based on the stage of disorder progression are further explored. Then, the challenges to be addressed before implementation of these therapies in clinical practice are considered. Finally, potential solutions to overcome the current limitations of this growing research area are suggested. Overall, the majority of current treatment modalities are still at an early stage of development and require extensive additional studies, both pre-clinical and clinical, before full restoration of visual function in PR degeneration diseases can be realized.
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Affiliation(s)
- Fereshteh Karamali
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Sanaz Behtaj
- grid.1022.10000 0004 0437 5432Clem Jones Centre for Neurobiology and Stem Cell Research, Griffith University, Queensland, Australia ,grid.1022.10000 0004 0437 5432Menzies Health Institute Queensland, Griffith University, Southport, QLD 4222 Australia
| | - Shahnaz Babaei-Abraki
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Hanieh Hadady
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Atefeh Atefi
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Soraya Savoj
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Sareh Soroushzadeh
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Samaneh Najafian
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Hossein Nasr Esfahani
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Henry Klassen
- grid.266093.80000 0001 0668 7243Gavin Herbert Eye Institute, Irvine, CA USA
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Zhao P, Zheng X, Yu Y, Hou Z, Diao C, Wang H, Kang H, Ning C, Li J, Feng W, Wang W, Liu GE, Li B, Smith J, Chamba Y, Liu JF. Mining Unknown Porcine Protein Isoforms by Tissue-based Map of Proteome Enhances Pig Genome Annotation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:772-786. [PMID: 33631433 PMCID: PMC9170766 DOI: 10.1016/j.gpb.2021.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 09/05/2019] [Accepted: 11/29/2019] [Indexed: 11/29/2022]
Abstract
A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical model. In this study, we developed a tissue-based proteome map using 34 major normal pig tissues. A total of 5841 unknown protein isoforms were identified and systematically characterized, including 2225 novel protein isoforms, 669 protein isoforms from 460 genes symbolized beginning with LOC, and 2947 protein isoforms without clear NCBI annotation in the current pig reference genome. These newly identified protein isoforms were functionally annotated through profiling the pig transcriptome with high-throughput RNA sequencing of the same pig tissues, further improving the genome annotation of the corresponding protein-coding genes. Combining the well-annotated genes that have parallel expression pattern and subcellular witness, we predicted the tissue-related subcellularlocations and potential functions for these unknown proteins. Finally, we mined 3081 orthologous genes for 52.7% of unknown protein isoforms across multiple species, referring to 68 KEGG pathways as well as 23 disease signaling pathways. These findings provide valuable insights and a rich resource for enhancing studies of pig genomics and biology, as well as biomedical model application to human medicine.
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Affiliation(s)
- Pengju Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ying Yu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhuocheng Hou
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chenguang Diao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Haifei Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huimin Kang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chao Ning
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Junhui Li
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wen Feng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Bugao Li
- Department of Animal Sciences and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Yangzom Chamba
- Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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Feng W, Zhao P, Zheng X, Hu Z, Liu J. Profiling Novel Alternative Splicing within Multiple Tissues Provides Useful Insights into Porcine Genome Annotation. Genes (Basel) 2020; 11:genes11121405. [PMID: 33255998 PMCID: PMC7760890 DOI: 10.3390/genes11121405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing (AS) is a process during gene expression that results in a single gene coding for different protein variants. AS contributes to transcriptome and proteome diversity. In order to characterize AS in pigs, genome-wide transcripts and AS events were detected using RNA sequencing of 34 different tissues in Duroc pigs. In total, 138,403 AS events and 29,270 expressed genes were identified. An alternative donor site was the most common AS form and accounted for 44% of the total AS events. The percentage of the other three AS forms (exon skipping, alternative acceptor site, and intron retention) was approximately 19%. The results showed that the most common AS events involving alternative donor sites could produce different transcripts or proteins that affect the biological processes. The expression of genes with tissue-specific AS events showed that gene functions were consistent with tissue functions. AS increased proteome diversity and resulted in novel proteins that gained or lost important functional domains. In summary, these findings extend porcine genome annotation and highlight roles that AS could play in determining tissue identity.
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Sun Y, Li W, Li J, Wang Z, Bai J, Xu L, Xing B, Yang W, Wang Z, Wang L, He W, Chen F. Genetic and clinical findings of panel-based targeted exome sequencing in a northeast Chinese cohort with retinitis pigmentosa. Mol Genet Genomic Med 2020; 8:e1184. [PMID: 32100970 PMCID: PMC7196472 DOI: 10.1002/mgg3.1184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/15/2020] [Accepted: 01/31/2020] [Indexed: 12/18/2022] Open
Abstract
Background Panel‐based targeted exome sequencing was used to analyze the genetic and clinical findings of targeted genes in a cohort of northeast Chinese with retinitis pigmentosa. Methods A total of 87 subjects, comprising 23 probands and their family members (total patients: 32) with confirmed retinitis pigmentosa were recruited in the study. Panel‐based targeted exome sequencing was used to sequence the patients and family members, all subjects with retinitis pigmentosa underwent a complete ophthalmologic examination. Results Of the 23 probands, the clinical manifestations include night blindness, narrowing of vision, secondary cataracts, choroidal atrophy, color blindness, and high myopia, the average age of onset of night blindness is 12.9 ± 14 (range, 0–65; median, 8). Posterior subcapsular opacities is the most common forms of secondary cataracts (nine cases, 39.1%), and peripheral choroidal atrophy is the most common form of secondary choroidal atrophy (12 cases, 52.2%). Of these probands with complication peripheral choroidal atrophy, there were eight probands (66.7%, 8/12) caused by the pathogenic variation in USH2A gene. A total of 17 genes and 45 variants were detected in 23 probands. Among these genes, the commonest genes were USH2A (40%; 18/45), RP1 (15.6%; 7/45), and EYS (8.9%; 4/45), and the top three genes account for 56.5% (13/23) of diagnostic probands. Among these variants, comprising 22 (48.9%) pathogenic variants, 14 (31%) likely pathogenic variants, and nine (20%) uncertain clinical significance variants, and 22 variants was discovered first time. Most of the mutations associated with RP were missense (53.3%, 24/45), and the remaining mutation types include frameshift (35.6%, 16/45), nonsense (6.7%, 3/45), and spliceSite (4.4%, 2/45). Among the probands with mutations detected, compound heterozygous forms was detected in 13 (56.5%, 13/23) probands, and digenic inheritance (DI) forms was detected in five (21.7%, 5/23) probands. Conclusion Panel‐based targeted exome sequencing revealed 23 novel mutations, recognized different combinations forms of variants, and extended the mutational spectrum of retinitis pigmentosa and depicted common variants in northeast China.
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Affiliation(s)
- Yan Sun
- Shenyang He Eye Specialist HospitalShenyangChina
- He UniversityShenyangChina
| | - Wei Li
- He UniversityShenyangChina
- BGI Education CenterUniversity of Chinese Academy of SciencesShenzhenChina
- BGI‐ShenzhenShenzhenChina
| | - Jian‐kang Li
- BGI‐ShenzhenShenzhenChina
- Department of Computer ScienceCity University of Hong KongKowloonHong Kong
- Guangdong Provincial Key Laboratory of Human Disease Genomics Shenzhen Key Laboratory of GenomicsBGI-ShenzhenShenzhenChina
| | - Zhuo‐shi Wang
- Shenyang He Eye Specialist HospitalShenyangChina
- He UniversityShenyangChina
| | - Jin‐yue Bai
- School of Basic MedicineQingdao UniversityQingdaoChina
| | - Ling Xu
- Shenyang He Eye Specialist HospitalShenyangChina
- He UniversityShenyangChina
| | - Bo Xing
- School of Basic MedicineQingdao UniversityQingdaoChina
| | - Wen Yang
- BGI‐ShenzhenShenzhenChina
- Department of Computer ScienceCity University of Hong KongKowloonHong Kong
| | - Zi‐wei Wang
- BGI Education CenterUniversity of Chinese Academy of SciencesShenzhenChina
- BGI‐ShenzhenShenzhenChina
| | - Lu‐sheng Wang
- BGI‐ShenzhenShenzhenChina
- Department of Computer ScienceCity University of Hong KongKowloonHong Kong
| | - Wei He
- Shenyang He Eye Specialist HospitalShenyangChina
- He UniversityShenyangChina
| | - Fang Chen
- BGI‐ShenzhenShenzhenChina
- Guangdong Provincial Key Laboratory of Human Disease Genomics Shenzhen Key Laboratory of GenomicsBGI-ShenzhenShenzhenChina
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Heterozygous RHO p.R135W missense mutation in a large Han-Chinese family with retinitis pigmentosa and different refractive errors. Biosci Rep 2019; 39:BSR20182198. [PMID: 31239368 PMCID: PMC6629948 DOI: 10.1042/bsr20182198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/28/2019] [Accepted: 06/24/2019] [Indexed: 12/14/2022] Open
Abstract
Retinitis pigmentosa (RP), the most common type of inherited retinal degeneration causing blindness, initially manifests as severely impaired rod function followed by deteriorating cone function. Mutations in the rhodopsin gene (RHO) are the most common cause of autosomal dominant RP (adRP). The present study aims to identify the disease-causing mutation in a numerous, four-generation Han-Chinese family with adRP detected by whole exome sequencing and Sanger sequencing. Afflicted family members present classic adRP along with heterogeneous clinical phenotypes including differing refractive errors, cataracts, astigmatism and epiretinal membranes. A missense mutation, c.403C>T (p.R135W), in the RHO gene was identified in nine subjects and it co-segregated with family members. The mutation is predicted to be disease-causing and results in rhodopsin protein abnormalities. The present study extends the genotype-phenotype relationship between RHO gene mutations and adRP clinical findings. The results have implications for familial genetic counseling, clinical management and developing RP target gene therapy strategies.
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Yu Y, Xia X, Li H, Zhang Y, Zhou X, Jiang H. A new rhodopsin R135W mutation induces endoplasmic reticulum stress and apoptosis in retinal pigment epithelial cells. J Cell Physiol 2019; 234:14100-14108. [PMID: 30635925 DOI: 10.1002/jcp.28100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/07/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Yixin Yu
- Department of Ophthalmology Xiangya Hospital, Central South University Changsha China
| | - Xiaobo Xia
- Department of Ophthalmology Xiangya Hospital, Central South University Changsha China
| | - Haibo Li
- Department of Ophthalmology Xiangya Hospital, Central South University Changsha China
| | - Yangzhou Zhang
- Department of Ophthalmology Xiangya Hospital, Central South University Changsha China
| | - Xiaoyun Zhou
- Department of Ophthalmology Xiangya Hospital, Central South University Changsha China
| | - Haibo Jiang
- Department of Ophthalmology Xiangya Hospital, Central South University Changsha China
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Chapman NH, Bernier RA, Webb SJ, Munson J, Blue EM, Chen DH, Heigham E, Raskind WH, Wijsman EM. Replication of a rare risk haplotype on 1p36.33 for autism spectrum disorder. Hum Genet 2018; 137:807-815. [PMID: 30276537 PMCID: PMC6309233 DOI: 10.1007/s00439-018-1939-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/22/2018] [Indexed: 01/15/2023]
Abstract
Hundreds of genes have been implicated in autism spectrum disorders (ASDs). In genetically heterogeneous conditions, large families with multiple affected individuals provide strong evidence implicating a rare variant, and replication of the same variant in multiple families is unusual. We previously published linkage analyses and follow-up exome sequencing in seven large families with ASDs, implicating 14 rare exome variants. These included rs200195897, which was transmitted to four affected individuals in one family. We attempted replication of those variants in the MSSNG database. MSSNG is a unique resource for replication of ASD risk loci, containing whole genome sequence (WGS) on thousands of individuals diagnosed with ASDs and family members. For each exome variant, we obtained all carriers and their relatives in MSSNG, using a TDT test to quantify evidence for transmission and association. We replicated the transmission of rs200195897 to four affected individuals in three additional families. rs200195897 was also present in three singleton affected individuals, and no unaffected individuals other than transmitting parents. We identified two additional rare variants (rs566472488 and rs185038034) transmitted with rs200195897 on 1p36.33. Sanger sequencing confirmed the presence of these variants in the original family segregating rs200195897. To our knowledge, this is the first example of a rare haplotype being transmitted with ASD in multiple families. The candidate risk variants include a missense mutation in SAMD11, an intronic variant in NOC2L, and a regulatory region variant close to both genes. NOC2L is a transcription repressor, and several genes involved in transcription regulation have been previously associated with ASDs.
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Affiliation(s)
- N H Chapman
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA
| | - R A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Center on Human Development and Disability, University of Washington, Seattle, WA, 98195, USA
| | - S J Webb
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Center on Human Development and Disability, University of Washington, Seattle, WA, 98195, USA
| | - J Munson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Center on Human Development and Disability, University of Washington, Seattle, WA, 98195, USA
| | - E M Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA
| | - D-H Chen
- Department of Neurology, University of Washington, Seattle, WA, 98195, USA
| | - E Heigham
- Department of Neurology, University of Washington, Seattle, WA, 98195, USA
| | - W H Raskind
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Ellen M Wijsman
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA.
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