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Li M, Yan C, Jiao Y, Xu Y, Bai C, Miao R, Jiang J, Liu J. Site-directed RNA editing by harnessing ADARs: advances and challenges. Funct Integr Genomics 2022; 22:1089-1103. [DOI: 10.1007/s10142-022-00910-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/04/2022]
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Appleby BS, Shetty S, Elkasaby M. Genetic aspects of human prion diseases. Front Neurol 2022; 13:1003056. [PMID: 36277922 PMCID: PMC9579322 DOI: 10.3389/fneur.2022.1003056] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Human prion diseases are rapidly progressive and fatal neurodegenerative conditions caused by a disease-causing isoform of the native prion protein. The prion protein gene (PRNP) encodes for the cellular prion protein, which is the biological substrate for prion disease transmission and neurotoxicity. Human prion diseases have three etiologies: sporadic, genetic, and acquired. PRNP polymorphisms and pathogenic variants play a large role in the frequency, age at onset, and clinicopathologic phenotype of prion diseases. Genetic prion diseases will be covered in detail and information necessary for clinical care, predictive genetic testing, and genetic counseling will be reviewed. Because the prion protein is necessary for transmission and neurotoxicity, many experimental treatments targeting its production are being investigated and hold potential promise as a disease modifying treatment for all forms of prion disease, including asymptomatic mutation carriers. This article will review genetic aspects of human prion disease and their influence on epidemiology, clinicopathologic phenotype, diagnostics, clinical management, and potential treatment approaches.
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Affiliation(s)
- Brian S. Appleby
- Department of Pathology, National Prion Disease Pathology Surveillance Center, Case Western Reserve University, Cleveland, OH, United States
- Department of Neurology, University Hospitals Cleveland Medical Center/Case Western Reserve University, Cleveland, OH, United States
- *Correspondence: Brian S. Appleby
| | - Shashirekha Shetty
- Department of Pathology, National Prion Disease Pathology Surveillance Center, Case Western Reserve University, Cleveland, OH, United States
- Department of Pathology, Center for Human Genetics Laboratory, University Hospitals Cleveland Medical Center/Case Western Reserve University, Cleveland, OH, United States
| | - Mohamed Elkasaby
- Department of Neurology, University Hospitals Cleveland Medical Center/Case Western Reserve University, Cleveland, OH, United States
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Jo WS, Kim YC, Oem JK, Jeong BH. First report of structural characteristics and polymorphisms of the prion protein gene in raccoon dogs: The possibility of prion disease-resistance. Front Vet Sci 2022; 9:989352. [PMID: 36204297 PMCID: PMC9530392 DOI: 10.3389/fvets.2022.989352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Prion diseases are fatal degenerative encephalopathies caused by misfolded prion protein (PrPSc) converted from normal prion protein (PrPC). Previous studies have reported that genetic polymorphisms of the prion protein gene (PRNP) play a critical role in susceptibility to prion diseases. In addition, prion disease-resistant animals showed unique structural features of prion protein (PrP) related to species-specific amino acids. However, investigations of genetic polymorphisms of the PRNP gene and structural characteristics of PrP have not been performed in raccoon dogs thus far. We investigated genetic polymorphisms of PRNP in 87 raccoon dogs using amplicon sequencing and analyzed the genotype, allele, haplotype frequencies, and linkage disequilibrium (LD) using Haploview version 4.2. In addition, we performed phylogenetic analysis and multiple sequence alignment (MSA) using MEGA X version 10.1.8 and Clustal X version 2.1, respectively. We estimated the impact of raccoon dog and Canidae family-specific amino acids using PolyPhen-2, PROVEAN, and AMYCO. Furthermore, we analyzed the effect of raccoon dog and Canidae family-specific amino acids using the AlphaFold2 and Swiss-PdbViewer programs. We found 4 novel single nucleotide polymorphisms (SNPs) of the raccoon dog PRNP gene. In addition, the raccoon dog PrP showed 99.61% identity and the closest genetic distance to dog PrP. Among the substitutions of Canidae-specific amino acids with interspecific amino acids, D163N showed increased amyloidogenic propensity, and R181H showed alterations of hydrogen bonds. Furthermore, electrostatic potentials were changed according to the substitutions of D163N and R181H. By comparing PrP between raccoon dogs and raccoons, R168K and K224R were found to be related to changes in hydrogen bonds, and K224R altered the electrostatic potential of raccoon dog PrP. In the present study, we first reported 4 novel synonymous SNPs of the raccoon dog PRNP gene. We also identified that the PrP of raccoon dog has high homology (99.61%) with PrP of dog, which is a prion-resistant animal. In addition, raccoon dog PrP-specific amino acids are related to low amyloid propensity and inherent characteristics of 3D structure of raccoon dog PrP compared to the PrP of prion-susceptible species.
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Affiliation(s)
- Woo-Sung Jo
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, South Korea
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Yong-Chan Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, South Korea
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Jae-Ku Oem
- Laboratory of Veterinary Infectious Diseases, College of Veterinary Medicine, Jeonbuk National University, Iksan, South Korea
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, South Korea
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, South Korea
- *Correspondence: Byung-Hoon Jeong
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The First Evaluation of Proteinase K-Resistant Prion Protein (PrPSc) in Korean Appendix Specimens. Medicina (B Aires) 2022; 58:medicina58070947. [PMID: 35888666 PMCID: PMC9321321 DOI: 10.3390/medicina58070947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/08/2022] [Accepted: 07/15/2022] [Indexed: 11/17/2022] Open
Abstract
Background and Objectives: Prion diseases are fatal neurodegenerative disorders caused by the abnormal proteinase K-resistant prion protein (PrPSc). Since variant Creutzfeldt–Jakob disease (CJD) was first reported in the United Kingdom (UK) in 1996, the occurrence of variant CJD has been reported in over 10 countries. To date, variant CJD has not been reported in Korea. However, the E211K somatic mutation in the prion protein gene (PRNP), which is related to bovine spongiform encephalopathy (BSE), was reported in Korean Holstein cattle, and atypical BSE, which is supposed to be sporadic BSE, has been occurring in many countries, including Japan and the USA. These results suggest that BSE may occur naturally in Korea. Thus, we performed a preemptive PrPSc test in appendix specimens to diagnose variant CJD in a Korean population. Materials and Methods: In the present study, we investigated CJD-related mutations and polymorphisms of the PRNP gene and carried out an examination on PrPSc in appendix specimens of Korean patients after appendectomy. Results: In all Korean appendix specimens tested, PrPSc bands were not detected. Conclusion: To the best of our knowledge, this was the first evaluation of PrPSc in Korean appendix specimens.
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Kim YC, Kim HH, Kim K, Kim AD, Jeong BH. Novel Polymorphisms and Genetic Characteristics of the Shadow of Prion Protein Gene ( SPRN) in Cats, Hosts of Feline Spongiform Encephalopathy. Viruses 2022; 14:v14050981. [PMID: 35632724 PMCID: PMC9148082 DOI: 10.3390/v14050981] [Citation(s) in RCA: 1] [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: 03/31/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 02/04/2023] Open
Abstract
Prion diseases are transmissible spongiform encephalopathies (TSEs) caused by pathogenic prion protein (PrPSc) originating from normal prion protein (PrPC) and have been reported in several types of livestock and pets. Recent studies have reported that the shadow of prion protein (Sho) encoded by the shadow of prion protein gene (SPRN) interacts with prion protein (PrP) and accelerates prion diseases. In addition, genetic polymorphisms in the SPRN gene are related to susceptibility to prion diseases. However, genetic polymorphisms in the feline SPRN gene and structural characteristics of the Sho have not been investigated in cats, a major host of feline spongiform encephalopathy (FSE). We performed amplicon sequencing to identify feline SPRN polymorphisms in the 623 bp encompassing the open reading frame (ORF) and a small part of the 3' untranslated region (UTR) of the SPRN gene. We analyzed the impact of feline SPRN polymorphisms on the secondary structure of SPRN mRNA using RNAsnp. In addition, to find feline-specific amino acids, we carried out multiple sequence alignments using ClustalW. Furthermore, we analyzed the N-terminal signal peptide and glycosylphosphatidylinositol (GPI)-anchor using SignalP and PredGPI, respectively. We identified three novel SNPs in the feline SPRN gene and did not find strong linkage disequilibrium (LD) among the three SNPs. We found four major haplotypes of the SPRN polymorphisms. Strong LD was not observed between PRNP and SPRN polymorphisms. In addition, we found alterations in the secondary structure and minimum free energy of the mRNA according to the haplotypes in the SPRN polymorphisms. Furthermore, we found four feline-specific amino acids in the feline Sho using multiple sequence alignments among several species. Lastly, the N-terminal signal sequence and cutting site of the Sho protein of cats showed similarity with those of other species. However, the feline Sho protein exhibited the shortest signal sequence and a unique amino acid in the omega-site of the GPI anchor. To the best of our knowledge, this is the first report on genetic polymorphisms of the feline SPRN gene.
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Affiliation(s)
- Yong-Chan Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Jeonbuk, Korea; (Y.-C.K.); (H.-H.K.)
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Jeonbuk, Korea
| | - Hyeon-Ho Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Jeonbuk, Korea; (Y.-C.K.); (H.-H.K.)
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Jeonbuk, Korea
| | - Kiwon Kim
- Haemalken Animal Hospital, Yangju 11492, Gyeonggi, Korea;
| | - An-Dang Kim
- Cool-Pet Animal Hospital, Anyang 14066, Gyeonggi, Korea;
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Jeonbuk, Korea; (Y.-C.K.); (H.-H.K.)
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Jeonbuk, Korea
- Correspondence: ; Tel.: +82-63-900-4040; Fax: +82-63-900-4012
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Roh IS, Kim YC, Won SY, Jeong MJ, Park KJ, Park HC, Lee YR, Kang HE, Sohn HJ, Jeong BH. The first report of a strong association between genetic polymorphisms of the prion protein gene (PRNP) and susceptibility to chronic wasting disease (CWD) in sika deer (Cervus nippon). Transbound Emerg Dis 2022; 69:e2073-e2083. [PMID: 35349210 DOI: 10.1111/tbed.14543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/16/2022] [Accepted: 03/27/2022] [Indexed: 11/28/2022]
Abstract
Prion diseases are incurable neurodegenerative disorders caused by proteinase K-resistant prion protein (PrPSc ) derived from normal prion protein (PrPC ) encoded by the prion protein gene (PRNP). Although the cervid PRNP gene plays a pivotal role in the pathological mechanism of chronic wasting disease (CWD), there is no existing association analysis between susceptibility to CWD and genetic polymorphisms of the PRNP gene in sika deer. We investigated genetic polymorphisms of the PRNP gene using amplicon sequencing in sika deer. In addition, to identify a genetic susceptibility factor, we compared genotype, allele and haplotype frequencies of the PRNP gene between CWD-positive and CWD-negative sika deer. Furthermore, to assess the effect of the genetic polymorphisms on sika deer prion protein (PrP), we performed in silico analysis using PolyPhen-2, PROVEAN and AMYCO. Finally, we analyzed the tertiary structure and electrostatic potential of sika deer PrP based on single nucleotide polymorphisms (SNPs) using the SWISS-MODEL and Swiss-PdbViewer programs. We found a total of 24 SNPs of the PRNP gene including 22 novel SNPs (10 synonymous SNPs and 12 non-synonymous SNPs) in sika deer. Among the non-synonymous SNPs, we found a strong association of the susceptibility to CWD with c.56G>A (Ser19Asn). In addition, we found that c.56G>A (Ser19Asn), c.296A>T (His99Leu) and c.560T>A (Val187Asp) were predicted to have damaging effects on sika deer PrP. Furthermore, we observed significant alterations in the electrostatic potential of sika deer PrP by genetic polymorphisms of the 187Asp allele. To the best of our knowledge, this was the first association study between genetic polymorphisms of the PRNP gene and susceptibility to CWD in sika deer. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- In-Soon Roh
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - Yong-Chan Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea.,Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Sae-Young Won
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea.,Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Min-Ju Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea.,Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Kyung-Je Park
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - Hoo-Chang Park
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - Yu-Ran Lee
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - Hae-Eun Kang
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - Hyun-Joo Sohn
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea.,Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, 54896, Republic of Korea
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