1
|
Tan Y, Scornet AL, Yap MNF, Zhang D. Machine learning-based classification reveals distinct clusters of non-coding genomic allelic variations associated with Erm-mediated antibiotic resistance. mSystems 2024:e0043024. [PMID: 38953319 DOI: 10.1128/msystems.00430-24] [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: 03/25/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024] Open
Abstract
The erythromycin resistance RNA methyltransferase (erm) confers cross-resistance to all therapeutically important macrolides, lincosamides, and streptogramins (MLS phenotype). The expression of erm is often induced by the macrolide-mediated ribosome stalling in the upstream co-transcribed leader sequence, thereby triggering a conformational switch of the intergenic RNA hairpins to allow the translational initiation of erm. We investigated the evolutionary emergence of the upstream erm regulatory elements and the impact of allelic variation on erm expression and the MLS phenotype. Through systematic profiling of the upstream regulatory sequences across all known erm operons, we observed that specific erm subfamilies, such as ermB and ermC, have independently evolved distinct configurations of small upstream ORFs and palindromic repeats. A population-wide genomic analysis of the upstream ermB regions revealed substantial non-random allelic variation at numerous positions. Utilizing machine learning-based classification coupled with RNA structure modeling, we found that many alleles cooperatively influence the stability of alternative RNA hairpin structures formed by the palindromic repeats, which, in turn, affects the inducibility of ermB expression and MLS phenotypes. Subsequent experimental validation of 11 randomly selected variants demonstrated an impressive 91% accuracy in predicting MLS phenotypes. Furthermore, we uncovered a mixed distribution of MLS-sensitive and MLS-resistant ermB loci within the evolutionary tree, indicating repeated and independent evolution of MLS resistance. Taken together, this study not only elucidates the evolutionary processes driving the emergence and development of MLS resistance but also highlights the potential of using non-coding genomic allele data to predict antibiotic resistance phenotypes. IMPORTANCE Antibiotic resistance (AR) poses a global health threat as the efficacy of available antibiotics has rapidly eroded due to the widespread transmission of AR genes. Using Erm-dependent MLS resistance as a model, this study highlights the significance of non-coding genomic allelic variations. Through a comprehensive analysis of upstream regulatory elements within the erm family, we elucidated the evolutionary emergence and development of AR mechanisms. Leveraging population-wide machine learning (ML)-based genomic analysis, we transformed substantial non-random allelic variations into discernible clusters of elements, enabling precise prediction of MLS phenotypes from non-coding regions. These findings offer deeper insight into AR evolution and demonstrate the potential of harnessing non-coding genomic allele data for accurately predicting AR phenotypes.
Collapse
Affiliation(s)
- Yongjun Tan
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, USA
| | - Alexandre Le Scornet
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Mee-Ngan Frances Yap
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Dapeng Zhang
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, USA
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, Missouri, USA
| |
Collapse
|
2
|
Zhao D, Guan P, Wei L, Gao J, Guo L, Tian D, Li Q, Guo Z, Cui H, Li Y, Guo J. Comprehensive identification and expression analysis of FAR1/FHY3 genes under drought stress in maize ( Zea mays L.). PeerJ 2024; 12:e17684. [PMID: 38952979 PMCID: PMC11216215 DOI: 10.7717/peerj.17684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024] Open
Abstract
Background FAR1/FHY3 transcription factors are derived from transposase, which play important roles in light signal transduction, growth and development, and response to stress by regulating downstream gene expression. Although many FAR1/FHY3 members have been identified in various species, the FAR1/FHY3 genes in maize are not well characterized and their function in drought are unknown. Method The FAR1/FHY3 family in the maize genome was identified using PlantTFDB, Pfam, Smart, and NCBI-CDD websites. In order to investigate the evolution and functions of FAR1 genes in maize, the information of protein sequences, chromosome localization, subcellular localization, conserved motifs, evolutionary relationships and tissue expression patterns were analyzed by bioinformatics, and the expression patterns under drought stress were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Results A total of 24 ZmFAR members in maize genome, which can be divided into five subfamilies, with large differences in protein and gene structures among subfamilies. The promoter regions of ZmFARs contain abundant abiotic stress-responsive and hormone-respovensive cis-elements. Among them, drought-responsive cis-elements are quite abundant. ZmFARs were expressed in all tissues detected, but the expression level varies widely. The expression of ZmFARs were mostly down-regulated in primary roots, seminal roots, lateral roots, and mesocotyls under water deficit. Most ZmFARs were down-regulated in root after PEG-simulated drought stress. Conclusions We performed a genome-wide and systematic identification of FAR1/FHY3 genes in maize. And most ZmFARs were down-regulated in root after drought stress. These results indicate that FAR1/FHY3 transcription factors have important roles in drought stress response, which can lay a foundation for further analysis of the functions of ZmFARs in response to drought stress.
Collapse
Affiliation(s)
- Dongbo Zhao
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Peiyan Guan
- College of Life Science, Dezhou University, Dezhou, Shandong, China
| | - Longxue Wei
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Jiansheng Gao
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Lianghai Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Dianbin Tian
- Pingyuan County Rural Revitalization Service Center, Pingyuan, Shandong, China
| | - Qingfang Li
- Linyi County Agricultural and Rural Bureau, Linyi, Shandong, China
| | - Zhihui Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Huini Cui
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Yongjun Li
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Jianjun Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| |
Collapse
|
3
|
Tang Y, Sang S, Gao S, Xu W, Zhou H, Xia X. Mechanistic insights into super-enhancer-related genes as prognostic signatures in colon cancer. Aging (Albany NY) 2024; 16:9918-9932. [PMID: 38850524 PMCID: PMC11210223 DOI: 10.18632/aging.205906] [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: 11/14/2023] [Accepted: 05/03/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Colon cancer (CC) is the most frequently occurring digestive system malignancy and is associated with a dismal prognosis. While super-enhancer (SE) genes have been identified as prognostic markers in several cancers, their potential as practical prognostic markers for CC patients remains unexplored. METHODS We obtained super-enhancer-related genes (SERGs) from the Human Super-Enhancer Database (SEdb). Transcriptome and relevant clinical data for colon cancer (CC) were sourced from the Gene Expression Omnibus (GEO) database. Subsequently, we identified up-regulated SERGs by the Weighted Gene Co-expression Network Analysis (WGCNA). Prognostic signatures were constructed via univariate and multivariate Cox regression analysis. We then delved into the mechanisms of these predictive genes by examining immune infiltration. We also assessed differential sensitivities to chemotherapeutic drugs between high- and low-SERGs risk patients. The critical gene was further validated using external datasets and finally confirmed by qRT PCR. RESULTS We established a ten-gene risk score prognostic model (S100A11, LZTS2, CYP2S1, ZNF552, PSMG1, GJC1, NXN, and DCBLD2), which can effectively predict patient survival rates. This model demonstrated effective prediction capabilities in survival rates at 1, 3, and 5 years and was successfully validated using external datasets. Furthermore, we detected significant differences in immune cell infiltration between high- and low-SERGs risk groups. Notably, high-risk patients exhibited heightened sensitivity to four chemotherapeutic agents, suggesting potential benefits for precision therapy in CC patients. Finally, qRT-PCR validation revealed a significant upregulation of LZTS2 mRNA expression in CC cells. CONCLUSION These findings reveal that the SERGs model could effectively predict the prognosis of CC.
Collapse
Affiliation(s)
- Yini Tang
- Department of Endoscopy, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shuliu Sang
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shuang Gao
- Department of Anorectal Surgery, The Third Affiliated Hospital of Yunnan University of Traditional Chinese Medicine, Yunnan, China
| | - Weina Xu
- Department of TCM, Zhoujiadu Community Health Service of Shanghai Pudong New Area Center, Shanghai, China
| | - Hailun Zhou
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoting Xia
- Department of Oncology, Shanghai TCM-intergrated Hospital, Shanghai, China
| |
Collapse
|
4
|
Park YA, Chang Y, Lee DH, Kim JS, Park M, Choi SA, Song TJ, Gwak HS. Association between coenzyme Q 10-related genetic polymorphisms and statin-associated myotoxicity in Korean stroke patients. Front Pharmacol 2024; 15:1358567. [PMID: 38774208 PMCID: PMC11106472 DOI: 10.3389/fphar.2024.1358567] [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: 12/20/2023] [Accepted: 04/17/2024] [Indexed: 05/24/2024] Open
Abstract
Introduction The purpose of this study is to identify the relationship between coenzyme Q 10 (CoQ10)-related gene polymorphisms and statin-related myotoxicity (SRM). Methods We retrospectively analyzed prospectively collected samples from February to May 2021. To investigate the association between CoQ10-related genetic factors and SRM, we selected 37 single nucleotide polymorphisms from five genes (COQ2, COQ3, COQ5, COQ6, and COQ7). The odds ratio (OR) and adjusted OR with 95% confidence intervals (CI) were calculated for univariate and multivariable logistic regression analyses, respectively. Results A total of 688 stroke patients were included in the analysis, including 56 SRM cases. In the multivariable analysis, two models were constructed using demographic factors only in model I, and demographic and genetic factors in model II. Compared to other statins, atorvastatin decreased the SRM risk whereas ezetimibe use increased the SRM risk in model I and model II. Patients with COQ2 rs4693075 G allele, COQ3 rs11548336 TT genotype, and COQ5 rs10849757 A allele had a 2.9-fold (95% CI: 1.6-5.3), 1.9-fold (95% CI: 1.1-3.5), and 3.3-fold (95% CI: 1.5-8.3) higher risk of SRM, respectively. Conclusion This study could be utilized to develop a personalized medicine strategy in patients treated with statins.
Collapse
Affiliation(s)
- Yoon-A Park
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Yoonkyung Chang
- Department of Neurology, Mokdong Hospital, College of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Da Hoon Lee
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Jung Sun Kim
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Minju Park
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Seo-A Choi
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Tae-Jin Song
- Department of Neurology, Seoul Hospital, College of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Hye Sun Gwak
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| |
Collapse
|
5
|
Garcia IS, Silva-Vignato B, Cesar ASM, Petrini J, da Silva VH, Morosini NS, Goes CP, Afonso J, da Silva TR, Lima BD, Clemente LG, Regitano LCDA, Mourão GB, Coutinho LL. Novel putative causal mutations associated with fat traits in Nellore cattle uncovered by eQTLs located in open chromatin regions. Sci Rep 2024; 14:10094. [PMID: 38698200 PMCID: PMC11066111 DOI: 10.1038/s41598-024-60703-5] [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: 10/19/2023] [Accepted: 04/26/2024] [Indexed: 05/05/2024] Open
Abstract
Intramuscular fat (IMF) and backfat thickness (BFT) are critical economic traits impacting meat quality. However, the genetic variants controlling these traits need to be better understood. To advance knowledge in this area, we integrated RNA-seq and single nucleotide polymorphisms (SNPs) identified in genomic and transcriptomic data to generate a linkage disequilibrium filtered panel of 553,581 variants. Expression quantitative trait loci (eQTL) analysis revealed 36,916 cis-eQTLs and 14,408 trans-eQTLs. Association analysis resulted in three eQTLs associated with BFT and 24 with IMF. Functional enrichment analysis of genes regulated by these 27 eQTLs revealed noteworthy pathways that can play a fundamental role in lipid metabolism and fat deposition, such as immune response, cytoskeleton remodeling, iron transport, and phospholipid metabolism. We next used ATAC-Seq assay to identify and overlap eQTL and open chromatin regions. Six eQTLs were in regulatory regions, four in predicted insulators and possible CCCTC-binding factor DNA binding sites, one in an active enhancer region, and the last in a low signal region. Our results provided novel insights into the transcriptional regulation of IMF and BFT, unraveling putative regulatory variants.
Collapse
Affiliation(s)
- Ingrid Soares Garcia
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Bárbara Silva-Vignato
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Aline Silva Mello Cesar
- Department of Agroindustry, Food and Nutrition, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Juliana Petrini
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Vinicius Henrique da Silva
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Natália Silva Morosini
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Carolina Purcell Goes
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | | | - Thaís Ribeiro da Silva
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Beatriz Delcarme Lima
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Luan Gaspar Clemente
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | | | - Gerson Barreto Mourão
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil.
| |
Collapse
|
6
|
Zhang B, Yan L, Lin C, Liu Y, Zhao C, Wang P, Zhang B, Zhang Y, Qiu L. Asymmetric evolution of ISG15 homologs and the immune adaptation to LBUSV infection in spotted seabass (Lateolabrax maculatus). FISH & SHELLFISH IMMUNOLOGY 2024; 148:109441. [PMID: 38354965 DOI: 10.1016/j.fsi.2024.109441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/15/2024] [Accepted: 02/11/2024] [Indexed: 02/16/2024]
Abstract
The battle between host and viral is ubiquitous across all ecosystems. Despite this, research is scarce on the antiviral characteristics of fish, particularly in those that primarily rely on innate immune responses. This study, comprehensively explored the genetic and antiviral features of ISG15 in spotted seabass, focusing on its response to largemouth bass ulcerative syndrome virus (LBUSV). Through whole-genome BLAST and PCR cloning, two ISG15 homologs, namely LmISG15a and LmISG15b, were identified in spotted seabass, both encoding highly conserved proteins. However, a distinctive contrast emerged in their expression patterns, with LmISG15a exhibiting high expression in immune organs while LmISG15b remained largely silent across various organs. Regulatory elements analysis indicated an asymmetric evolution of the two ISG15s, with the minimal expression of LmISG15b may attribute to the loss of a necessary ISRE and an additional instability "ATTTA" motif. Association analysis demonstrated a significant correlation between LmISG15a expression and LBUSV infection. Subsequent antiviral activity detection revealed that LmISG15a interacted with LBUSV, inhibiting its replication by activating ISGylation and downstream pro-inflammatory mediators. In summary, this study unveils a distinct evolutionary strategy of fish antiviral gene ISG15 and delineates its kinetic characteristics in response to LBUSV infection.
Collapse
Affiliation(s)
- Bo Zhang
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Sanya Tropical Fisheries Research Institute, Sanya, China.
| | - Lulu Yan
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Changhong Lin
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; College of Aqua-life Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yong Liu
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chao Zhao
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Pengfei Wang
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Bo Zhang
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Sanya Tropical Fisheries Research Institute, Sanya, China.
| | - Yanhong Zhang
- Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, China
| | - Lihua Qiu
- Key Laboratory of Aquatic Product Processing, Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Sanya Tropical Fisheries Research Institute, Sanya, China.
| |
Collapse
|
7
|
Recktenwald M, Hutt E, Davis L, MacAulay J, Daringer NM, Galie PA, Staehle MM, Vega SL. Engineering transcriptional regulation for cell-based therapies. SLAS Technol 2024; 29:100121. [PMID: 38340892 DOI: 10.1016/j.slast.2024.100121] [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: 11/30/2023] [Revised: 01/10/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
A major aim in the field of synthetic biology is developing tools capable of responding to user-defined inputs by activating therapeutically relevant cellular functions. Gene transcription and regulation in response to external stimuli are some of the most powerful and versatile of these cellular functions being explored. Motivated by the success of chimeric antigen receptor (CAR) T-cell therapies, transmembrane receptor-based platforms have been embraced for their ability to sense extracellular ligands and to subsequently activate intracellular signal transduction. The integration of transmembrane receptors with transcriptional activation platforms has not yet achieved its full potential. Transient expression of plasmid DNA is often used to explore gene regulation platforms in vitro. However, applications capable of targeting therapeutically relevant endogenous or stably integrated genes are more clinically relevant. Gene regulation may allow for engineered cells to traffic into tissues of interest and secrete functional proteins into the extracellular space or to differentiate into functional cells. Transmembrane receptors that regulate transcription have the potential to revolutionize cell therapies in a myriad of applications, including cancer treatment and regenerative medicine. In this review, we will examine current engineering approaches to control transcription in mammalian cells with an emphasis on systems that can be selectively activated in response to extracellular signals. We will also speculate on the potential therapeutic applications of these technologies and examine promising approaches to expand their capabilities and tighten the control of gene regulation in cellular therapies.
Collapse
Affiliation(s)
- Matthias Recktenwald
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Evan Hutt
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Leah Davis
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - James MacAulay
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Nichole M Daringer
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Peter A Galie
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Mary M Staehle
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Sebastián L Vega
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA; Department of Orthopaedic Surgery, Cooper Medical School of Rowan University, Camden, NJ 08103, USA.
| |
Collapse
|
8
|
Chen F, Zhang Y, Sedlazeck FJ, Creighton CJ. Germline structural variation globally impacts the cancer transcriptome including disease-relevant genes. Cell Rep Med 2024; 5:101446. [PMID: 38442712 PMCID: PMC10983041 DOI: 10.1016/j.xcrm.2024.101446] [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: 09/26/2023] [Revised: 01/01/2024] [Accepted: 02/06/2024] [Indexed: 03/07/2024]
Abstract
Germline variation and somatic alterations contribute to the molecular profile of cancers. We combine RNA with whole genome sequencing across 1,218 cancer patients to determine the extent germline structural variants (SVs) impact expression of nearby genes. For hundreds of genes, recurrent and common germline SV breakpoints within 100 kb associate with increased or decreased expression in tumors spanning various tissues of origin. A significant fraction of germline SV expression associations involves duplication of intergenic enhancers or 3' UTR disruption. Genes altered by both somatic and germline SVs include ATRX and CEBPA. Genes essential in cancer cell lines include BARD1 and IRS2. Genes with both expression and germline SV breakpoint patterns associated with patient survival include GCLM. Our results capture a class of phenotypic variation at work in the disease setting, including genes with cancer roles. Specific germline SVs represent potential cancer risk variants for genetic testing, including those involving genes with targeting implications.
Collapse
Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
9
|
Mobasher M, Ansari R, Castejon AM, Barar J, Omidi Y. Advanced nanoscale delivery systems for mRNA-based vaccines. Biochim Biophys Acta Gen Subj 2024; 1868:130558. [PMID: 38185238 DOI: 10.1016/j.bbagen.2024.130558] [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: 11/07/2023] [Revised: 12/24/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
The effectiveness of messenger RNA (mRNA) vaccines, especially those designed for COVID-19, relies heavily on sophisticated delivery systems that ensure efficient delivery of mRNA to target cells. A variety of nanoscale vaccine delivery systems (VDSs) have been explored for this purpose, including lipid nanoparticles (LNPs), liposomes, and polymeric nanoparticles made from biocompatible polymers such as poly(lactic-co-glycolic acid), as well as viral vectors and lipid-polymer hybrid complexes. Among these, LNPs are particularly notable for their efficiency in encapsulating and protecting mRNA. These nanoscale VDSs can be engineered to enhance stability and facilitate uptake by cells. The choice of delivery system depends on factors like the specific mRNA vaccine, target cell types, stability requirements, and desired immune response. In this review, we shed light on recent advances in delivery mechanisms for self-amplifying RNA (saRNA) vaccines, emphasizing groundbreaking studies on nanoscale delivery systems aimed at improving the efficacy and safety of mRNA/saRNA vaccines.
Collapse
Affiliation(s)
- Maha Mobasher
- Department of Pharmaceutical Sciences, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Rais Ansari
- Department of Pharmaceutical Sciences, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Ana M Castejon
- Department of Pharmaceutical Sciences, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Jaleh Barar
- Department of Pharmaceutical Sciences, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Yadollah Omidi
- Department of Pharmaceutical Sciences, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33328, USA.
| |
Collapse
|
10
|
Hafez M, Gourlie R, McDonald M, Telfer M, Carmona MA, Sautua FJ, Moffat CS, Moolhuijzen PM, See PT, Aboukhaddour R. Evolution of the Toxb Gene in Pyrenophora tritici-repentis and Related Species. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:327-337. [PMID: 37759383 DOI: 10.1094/mpmi-08-23-0114-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Pyrenophora tritici-repentis (tan spot) is a destructive foliar pathogen of wheat with global impact. This ascomycete fungus possesses a highly plastic open pangenome shaped by the gain and loss of effector genes. This study investigated the allelic variations in the chlorosis-encoding gene ToxB across 422 isolates representing all identified pathotypes and worldwide origins. To gain better insights into ToxB evolution, we examined its presence and variability in other Pyrenophora spp. A ToxB haplotype network was constructed, revealing the evolutionary relationships of this gene (20 haplotypes) across four Pyrenophora species. Notably, toxb, the homolog of ToxB, was detected for the first time in the barley pathogen Pyrenophora teres. The ToxB/toxb genes display evidence of selection that is characterized by loss of function, duplication, and diverse mutations. Within the ToxB/toxb open reading frame, 72 mutations were identified, including 14 synonymous, 55 nonsynonymous, and 3 indel mutations. Remarkably, a, ∼5.6-kb Copia-like retrotransposon, named Copia-1_Ptr, was found inserted in the toxb gene of a race 3 isolate. This insert disrupted the ToxB gene's function, a first case of effector gene disruption by a transposable element in P. tritici-repentis. Additionally, a microsatellite with 25 nucleotide repeats (0 to 10) in the upstream region of ToxB suggested a potential mechanism influencing ToxB expression and regulation. Exploring ToxB-like protein distribution in other ascomycetes revealed the presence of ToxB-like proteins in 19 additional species, including the Leotiomycetes class for the first time. The presence/absence pattern of ToxB-like proteins defied species relatedness compared with a phylogenetic tree, suggesting a past horizontal gene transfer event during the evolution of the ToxB gene. [Formula: see text] Copyright © 2024 His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food. This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Mohamed Hafez
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
- Botany and Microbiology Department, Faculty of Science, Suez University, Suez, Egypt
| | - Ryan Gourlie
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Megan McDonald
- School of Biosciences, University of Birmingham, Institute of Microbiology and Infection, Edgbaston, Birmingham, U.K
| | - Melissa Telfer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Marcelo A Carmona
- Cátedra de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Francisco J Sautua
- Cátedra de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Caroline S Moffat
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Australia
| | - Paula M Moolhuijzen
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Australia
| | - Pao Theen See
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Australia
| | - Reem Aboukhaddour
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| |
Collapse
|
11
|
Soni J, Chattopadhyay P, Mehta P, Mohite R, Tardalkar K, Joshi M, Pandey R. Dynamics of Whole Transcriptome Analysis (WTA) and Surface markers expression (AbSeq) in Immune Cells of COVID-19 Patients and Recovered captured through Single Cell Genomics. Front Med (Lausanne) 2024; 11:1297001. [PMID: 38357647 PMCID: PMC10864604 DOI: 10.3389/fmed.2024.1297001] [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: 09/19/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Single-cell multi-omics studies, such as multidimensional transcriptomics (whole transcriptomic analysis, WTA), and surface marker analysis (antibody sequencing, AbSeq), have turned out to be valuable techniques that offer inaccessible possibilities for single-cell profiling of mRNA, lncRNA, and proteins. Methods We used this technique to understand the dynamics of mRNA and protein-level differences in healthy, COVID-19-infected and recovered individuals using peripheral blood mononuclear cells (PBMCs). Our results demonstrate that compared to mRNA expression, protein abundance is a better indicator of the disease state. Results We demonstrate that compared to mRNA expression, protein abundance is a better indicator of the disease state. We observed high levels of cell identity and regulatory markers, CD3E, CD4, CD8A, CD5, CD7, GITR, and KLRB1 in healthy individuals, whereas markers related to cell activation, CD38, CD28, CD69, CD62L, CD14, and CD16 elevated in the SARS-CoV-2 infected patients at both WTA and AbSeq levels. Curiously, in recovered individuals, there was a high expression of cytokine and chemokine receptors (CCR5, CCR7, CCR4, CXCR3, and PTGRD2). We also observed variations in the expression of markers within cell populations under different states. Discussion Furthermore, our study emphasizes the significance of employing an oligo-based method (AbSeq) that can help in diagnosis, prognosis, and protection from disease/s by identifying cell surface markers that are unique to different cell types or states. It also allows simultaneous study of a vast array of markers, surpassing the constraints of techniques like FACS to query the vast repertoire of proteins.
Collapse
Affiliation(s)
- Jyoti Soni
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ramakant Mohite
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Kishore Tardalkar
- Department of Stem Cells & Regenerative Medicine, D. Y. Patil Education Society, Kolhapur, India
| | - Meghnad Joshi
- Department of Stem Cells & Regenerative Medicine, D. Y. Patil Education Society, Kolhapur, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
12
|
Abdel-Maksoud MA, Ullah S, Nadeem A, Shaikh A, Zia MK, Zakri AM, Almanaa TN, Alfuraydi AA, Mubarak A, Hameed Y. Unlocking the diagnostic, prognostic roles, and immune implications of BAX gene expression in pan-cancer analysis. Am J Transl Res 2024; 16:63-74. [PMID: 38322551 PMCID: PMC10839381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/20/2023] [Indexed: 02/08/2024]
Abstract
OBJECTIVES Cancer, a formidable disease, continues to challenge our understanding and therapeutic approaches. This study delves into the pan-cancer analysis of BCL2 Associated X (BAX) gene expression, seeking to unravel its significance in cancer development, prognosis, and potential therapeutic strategies. METHODS A combination of bioinformatics and molecular experiments. RESULTS Our pan-cancer investigation into BAX expression encompassed 33 distinct cancer types, revealing a remarkable and uniform increase in BAX expression. This groundbreaking finding emphasizes the potential universality of BAX's role in cancer development and progression. Further, our study explored the prognostic implications of BAX expression, highlighting a consistent association between up-regulated BAX and poor overall survival (OS) in Liver Hepatocellular Carcinoma (LIHC) and Skin Cutaneous Melanoma (SKCM). These results suggest that BAX may serve as an adverse prognostic indicator in these malignancies, emphasizing the importance of personalized treatment strategies. Epigenetic and genetic analyses of BAX provided valuable insights. Hypomethylation of the BAX promoter region was evident in LIHC and SKCM, which likely contributes to the up-regulation of BAX, while genetic mutations in the BAX gene itself were infrequent in these cancers. Our exploration of BAX-associated signaling pathways and the correlation between BAX expression and CD8+ T cell infiltration shed light on the intricate molecular landscape of cancer. BAX's interaction with key apoptotic and immune-related pathways reinforces its role as a central player in tumor development and the immune microenvironment. Moreover, our drug prediction analysis identified potential therapeutic agents for modulating BAX expression in the context of LIHC and SKCM, bridging the gap between research and clinical application. CONCLUSION In sum, our comprehensive BAX study not only enhances our understanding of its significance as a biomarker gene but also offers novel avenues for therapeutic interventions, contributing to the ongoing quest for more effective cancer treatments and improved patient care.
Collapse
Affiliation(s)
- Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | | | - Amun Nadeem
- Department of Pathology, Gujranwala Medical College Teaching Hospital GujranwalaPakistan
| | | | - Muhammad Khurram Zia
- Department of Surgery, Liaquat College of Medicine and Dentistry and Darul Sehat HospitalKarachi, Pakistan
| | - Adel M Zakri
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud UniversityRiyadh 11451, Saudi Arabia
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Akram A Alfuraydi
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ayman Mubarak
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Yasir Hameed
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of BahawalpurBahawalpur 63100, Pakistan
| |
Collapse
|
13
|
Qu A, Han B, Hua M, Wang C, Li T. SF3B4 downregulation restrains lung adenocarcinoma tumorigenesis via 5' alternative splicing of KAT2A. Sci Rep 2024; 14:30. [PMID: 38168564 PMCID: PMC10762244 DOI: 10.1038/s41598-023-50606-2] [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: 03/29/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Aberrant expression of splicing factors, including SF3B4, plays a vital role in lung adenocarcinoma (LUAD). However, the impact of SF3B4 in the progression of LUAD has not been studied well. Here, we demonstrated the effects of SF3B4 in LUAD via apoptosis, proliferation, migration assays, etc. Gene manipulations confirmed the role of SF3B4 via KAT2A. SF3B4 was found to promote LUAD growth. Further studies found that, upon SF3B4 knockdown in LUAD cells, an alternative splice site occurred at the 5'-UTR of KAT2A, which led to the downregulation of KAT2A at both RNA and protein levels. Furthermore, the decrease in KAT2A expression partially reversed the effect of SF3B4 in promoting tumorigenesis. The axis SF3B4/ KAT2A was identified as a significant player in LUAD progression, shedding light on the therapeutic development in LUAD.
Collapse
Affiliation(s)
- Ailin Qu
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China
| | - Bo Han
- Department of Pathology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Mengmeng Hua
- Department of Oral and Maxillofacial Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Institute of Stomatology, Shandong University, Jinan, Shandong, China
| | - Chune Wang
- Department of Oral and Maxillofacial Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Institute of Stomatology, Shandong University, Jinan, Shandong, China
| | - Tao Li
- Department of Respiratory Diseases, Qilu Hospital of Shandong University, No. 107, Culture West Road, Jinan, China.
| |
Collapse
|
14
|
Zhang Y, Yan Z, Nan N, Qin G, Sang N. Circadian rhythm disturbances involved in ozone-induced glucose metabolism disorder in mouse liver. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167316. [PMID: 37742977 DOI: 10.1016/j.scitotenv.2023.167316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
Ozone (O3) is a key environmental factor for developing diabetes. Nevertheless, the underlying mechanisms remain unclear. This study aimed to investigate alterations of glycometabolism in mice after O3 exposure and the role of circadian rhythms in this process. C57BL/6 male mice were randomly assigned to O3 (0.5 ppm) or filtered air for four weeks (4 h/day). Then, hepatic tissues of mice were collected at 4 h intervals within 24 h after O3 exposure to test. The results showed that hepatic circadian rhythm genes oscillated abnormally, mainly at zeitgeber time (ZT)8 and ZT20 after O3 exposure. Furthermore, detection of glycometabolism (metabolites, enzymes, and genes) revealed that O3 caused change in the daily oscillations of glycometabolism. The serum glucose content decreased at ZT4 and ZT20, while hepatic glucose enhanced at ZT16 and ZT24(0). Both G6pc and Pck1, which are associated with hepatic gluconeogenesis, significantly increased at ZT20. O3 exposure disrupted glycometabolism by increasing gluconeogenesis and decreasing glycolysis in mice liver. Finally, correlation analysis showed that the association between Bmal1 and O3-induced disruption of glycometabolism was the strongest. The findings emphasized the interaction between adverse outcomes of circadian rhythms and glycometabolism following O3 exposure.
Collapse
Affiliation(s)
- Yaru Zhang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China
| | - Zhipeng Yan
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China
| | - Nan Nan
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China
| | - Guohua Qin
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China.
| | - Nan Sang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China
| |
Collapse
|
15
|
Lu C, Li S, Li Y, Zhang X, Chi J, Jiang Q, Ma Y, Shi X, Wang L, Li J. Associations between polymorphisms in the cannabinoid receptor 1 gene, cognitive impairments and tardive dyskinesia in a Chinese population with schizophrenia. Brain Res 2023; 1821:148579. [PMID: 37739333 DOI: 10.1016/j.brainres.2023.148579] [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: 07/25/2023] [Revised: 09/03/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023]
Abstract
OBJECTIVE Tardive dyskinesia (TD) is a medically induced movement disorder that occurs as a result of long-term use of antipsychotic medications, commonly seen in patients with schizophrenia (SCZ). The study aimed to investigate the relationship between single nucleotide polymorphisms (SNPs) of the CNR1 gene, TD and cognitive impairments in a Chinese population with SCZ. METHODS A total of 216 SCZ patients were recruited. The participants were divided into TD and without TD (WTD) groups using the Schooler-Kane International Diagnostic Criteria. The severity of TD was assessed using the Abnormal Involuntary Movement Scale (AIMS). Cognitive function was assessed using the Repeatable Battery for Assessment of Neuropsychological Status (RBANS) scale. Hardy-Weinberg equilibrium tests, chained disequilibrium analyses and haplotype analyses were performed using SHE-sis software. To explore the main effects of TD diagnosis, genotype and cognitive function, as well as interaction effects, analysis of covariance (ANCOVA) was employed. RESULTS The prevalence of TD was approximately 27.3%. Significant differences were observed in the rs806368 CT genotype and rs806370 TC genotype within the hypercongenic pattern between the male TD and WTD groups (OR = 2.508, 95% CI: 1.055-5.961, p = 0.037; OR = 2.552, 95% CI: 1.073-6.069, p = 0.034). Among TD patients, those carrying the rs806368 CC genotype exhibited higher limb trunk scores (p < 0.05). Moreover, there was a statistically significant difference in visuospatial/construction between the TD and WTD groups (p = 0.04), and a borderline significant difference in visuospatial/construction when considering the interaction between TD diagnosis and genotype at the rs806368 locus (p = 0.05). CONCLUSION CNR1 rs806368 and rs806370 polymorphisms may play a role in TD susceptibility. Additionally, CNR1 gene polymorphisms were associated with the severity of involuntary movements and cognitive impairments in TD patients.
Collapse
Affiliation(s)
- Chenghao Lu
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Shen Li
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Yanzhe Li
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Xiaofei Zhang
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Jinghui Chi
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Qiaona Jiang
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Yanyan Ma
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Xiaomei Shi
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Lili Wang
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China.
| | - Jie Li
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China.
| |
Collapse
|
16
|
Abuzahra M, Sumantri C, Uddin MJ, Gunawan A. Association and expression study of SEPW1 and JAML as preliminary candidate genes related to lamb odor and flavor. Anim Biotechnol 2023; 34:4247-4255. [PMID: 36485018 DOI: 10.1080/10495398.2022.2141763] [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] [Indexed: 12/13/2022]
Abstract
The current study aimed to identify the SEPW1 and JAML genes in lamb as candidate genes related to lamb odor and flavor. The polymorphism study showed that the SEPW1 gene was polymorphic at the BanI restriction site with three genotypes (AA, AG, and GG), whereas the JAML gene was monomorphic at HhaI with genotype (GG). The association of SEPW1 between genotype and lamb odor and flavor (BCFAs and skatole) was analyzed using GLM (General Linear Model). MNA (4-methylnonanoic) was significantly associated (p < 0.05) with lamb odor and flavor. AA genotype has a lower level of MNA than AG and GG, while MOA (4-methyloctanoic), EOA(4-ethyloctanoic), MI (3-methylindole) and MP (3-methylphenol) was not significantly associated with lamb odor and flavor (p > 0.05). Furthermore, to analyze the mRNA expression of SEPW1 in liver tissues, the lambs were divided into three groups based on the genotypes AA, AG, and GG, however, mRNA expression was not differentially expressed between AA, AG, and GG (p > 0.05). These results will enhance the understanding of the functions of SEPW1 gene relation to odor and flavor traits and will shed light on the polymorphism of SEPW1 gene in lamb as a candidate gene for reducing MNA in lamb.
Collapse
Affiliation(s)
- Mutasem Abuzahra
- Graduate School of Animal Production and Technology, IPB, Bogor, Indonesia
| | - C Sumantri
- Department of Animal Production and Technology, IPB, Bogor, Indonesia
| | - M J Uddin
- School of Veterinary Medicine, Murdoch University, Murdoch, Australia
| | - A Gunawan
- Department of Animal Production and Technology, IPB, Bogor, Indonesia
| |
Collapse
|
17
|
Garza EA, Bielinski VA, Espinoza JL, Orlandi K, Alfaro JR, Bolt TM, Beeri K, Weyman PD, Dupont CL. Validating a Promoter Library for Application in Plasmid-Based Diatom Genetic Engineering. ACS Synth Biol 2023; 12:3215-3228. [PMID: 37857380 PMCID: PMC10661051 DOI: 10.1021/acssynbio.3c00163] [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: 03/21/2023] [Indexed: 10/21/2023]
Abstract
While diatoms are promising synthetic biology platforms, there currently exists a limited number of validated genetic regulatory parts available for genetic engineering. The standard method for diatom transformation, nonspecific introduction of DNA into chromosomes via biolistic particle bombardment, is low throughput and suffers from clonal variability and epigenetic effects. Recent developments in diatom engineering have demonstrated that autonomously replicating episomal plasmids serve as stable expression platforms for diverse gene expression technologies. These plasmids are delivered via bacterial conjugation and, when combined with modular DNA assembly technologies, provide a flexibility and speed not possible with biolistic-mediated strain generation. In order to expand the current toolbox for plasmid-based engineering in the diatom Phaeodactylum tricornutum, a conjugation-based forward genetics screen for promoter discovery was developed, and application to a diatom genomic DNA library defined 252 P. tricornutum promoter elements. From this library, 40 promoter/terminator pairs were delivered via conjugation on episomal plasmids, characterized in vivo, and ranked across 4 orders of magnitude difference in reporter gene expression levels.
Collapse
Affiliation(s)
- Erin A. Garza
- J. Craig Venter Institute, La Jolla, California 92037, United States
| | | | - Josh L. Espinoza
- J. Craig Venter Institute, La Jolla, California 92037, United States
| | | | | | | | | | | | | |
Collapse
|
18
|
Li J, Wang Y, Yang K, Wang X, Wang Y, Zhang H, Huang H, Su X, Yao B, Luo H, Qin X. Development of an efficient protein expression system in the thermophilic fungus Myceliophthora thermophila. Microb Cell Fact 2023; 22:236. [PMID: 37974259 PMCID: PMC10652509 DOI: 10.1186/s12934-023-02245-5] [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: 07/07/2023] [Accepted: 11/05/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Thermophilic fungus Myceliophthora thermophila has been widely used in industrial applications due to its ability to produce various enzymes. However, the lack of an efficient protein expression system has limited its biotechnological applications. RESULTS In this study, using a laccase gene reporting system, we developed an efficient protein expression system in M. thermophila through the selection of strong constitutive promoters, 5'UTRs and signal peptides. The expression of the laccase was confirmed by enzyme activity assays. The results showed that the Mtpdc promoter (Ppdc) was able to drive high-level expression of the target protein in M. thermophila. Manipulation of the 5'UTR also has significant effects on protein expression and secretion. The best 5'UTR (NCA-7d) was identified. The transformant containing the laccase gene under the Mtpdc promoter, NCA-7d 5'UTR and its own signal peptide with the highest laccase activity (1708 U/L) was obtained. In addition, the expression system was stable and could be used for the production of various proteins, including homologous proteins like MtCbh-1, MtGh5-1, MtLPMO9B, and MtEpl1, as well as a glucoamylase from Trichoderma reesei. CONCLUSIONS An efficient protein expression system was established in M. thermophila for the production of various proteins. This study provides a valuable tool for protein production in M. thermophila and expands its potential for biotechnological applications.
Collapse
Affiliation(s)
- Jinyang Li
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Yidi Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Kun Yang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Honglian Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China.
| | - Xing Qin
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10093, China.
| |
Collapse
|
19
|
Cutter AD. Sexual conflict, heterochrony and tissue specificity as evolutionary problems of adaptive plasticity in development. Proc Biol Sci 2023; 290:20231854. [PMID: 37817601 PMCID: PMC10565415 DOI: 10.1098/rspb.2023.1854] [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: 08/16/2023] [Accepted: 09/15/2023] [Indexed: 10/12/2023] Open
Abstract
Differential gene expression represents a fundamental cause and manifestation of phenotypic plasticity. Adaptive phenotypic plasticity in gene expression as a trait evolves when alleles that mediate gene regulation serve to increase organismal fitness by improving the alignment of variation in gene expression with variation in circumstances. Among the diverse circumstances that a gene encounters are distinct cell types, developmental stages and sexes, as well as an organism's extrinsic ecological environments. Consequently, adaptive phenotypic plasticity provides a common framework to consider diverse evolutionary problems by considering the shared implications of alleles that produce context-dependent gene expression. From this perspective, adaptive plasticity represents an evolutionary resolution to conflicts of interest that arise from any negatively pleiotropic effects of expression of a gene across ontogeny, among tissues, between the sexes, or across extrinsic environments. This view highlights shared properties within the general relation of fitness, trait expression and context that may nonetheless differ substantively in the grain of selection within and among generations to influence the likelihood of adaptive plasticity as an evolutionary response. Research programmes that historically have focused on these separate issues may use the insights from one another by recognizing their shared dependence on context-dependent gene regulatory evolution.
Collapse
Affiliation(s)
- Asher D. Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| |
Collapse
|
20
|
Wozniak J, Loba W, Wysocka A, Dzimira S, Przadka P, Switonski M, Nowacka-Woszuk J. Altered Transcript Levels of MMP13 and VIT Genes in the Muscle and Connective Tissue of Pigs with Umbilical Hernia. Genes (Basel) 2023; 14:1903. [PMID: 37895252 PMCID: PMC10606093 DOI: 10.3390/genes14101903] [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: 09/01/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Umbilical hernia (UH) and inguinal hernia (IH) are among the most common defects in pigs, affecting their welfare and resulting in economic losses. In this study, we aimed to verify the association of previously reported differences in transcript levels of the ACAN, COL6A5, MMP13, and VIT genes with the occurrence of UH and IH. We examined mRNA levels in muscle and connective tissue from 68 animals-34 affected by UH and 34 controls. In a second cohort, we examined inguinal channel samples from 46 pigs (in four groups). We determined DNA methylation levels in muscle tissue for the UH and control animals. The transcript level of MMP13 changed in the UH cases, being upregulated and downregulated in muscle and connective tissue, respectively, and the VIT gene also showed an increased muscular mRNA level. The transcript of the ACAN gene significantly decreased in old pigs with IH. We further observed an increased DNA methylation level for one CpG site within the MMP13 gene in UH individuals. We conclude that these alterations in gene mRNA levels in the UH animals depend on the tissue and can sometimes be a consequence of, not a cause of, the affected phenotype.
Collapse
Affiliation(s)
- Jakub Wozniak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.W.); (W.L.); (A.W.); (M.S.)
| | - Weronika Loba
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.W.); (W.L.); (A.W.); (M.S.)
| | - Alicja Wysocka
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.W.); (W.L.); (A.W.); (M.S.)
| | - Stanislaw Dzimira
- Department of Pathology, Wroclaw University of Environmental and Life Sciences, C.K. Norwida 31, 50-375 Wroclaw, Poland;
| | - Przemyslaw Przadka
- Department of Surgery, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 51, 50-366 Wroclaw, Poland;
| | - Marek Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.W.); (W.L.); (A.W.); (M.S.)
| | - Joanna Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.W.); (W.L.); (A.W.); (M.S.)
| |
Collapse
|
21
|
Hao S, Zhang L, Zhao D, Zhou J, Ye C, Qu H, Li QQ. Inhibitor AN3661 reveals biological functions of Arabidopsis CLEAVAGE and POLYADENYLATION SPECIFICITY FACTOR 73. PLANT PHYSIOLOGY 2023; 193:537-554. [PMID: 37335917 DOI: 10.1093/plphys/kiad352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/09/2023] [Accepted: 05/21/2023] [Indexed: 06/21/2023]
Abstract
Cleavage and polyadenylation specificity factor (CPSF) is a protein complex that plays an essential biochemical role in mRNA 3'-end formation, including poly(A) signal recognition and cleavage at the poly(A) site. However, its biological functions at the organismal level are mostly unknown in multicellular eukaryotes. The study of plant CPSF73 has been hampered by the lethality of Arabidopsis (Arabidopsis thaliana) homozygous mutants of AtCPSF73-I and AtCPSF73-II. Here, we used poly(A) tag sequencing to investigate the roles of AtCPSF73-I and AtCPSF73-II in Arabidopsis treated with AN3661, an antimalarial drug with specificity for parasite CPSF73 that is homologous to plant CPSF73. Direct seed germination on an AN3661-containing medium was lethal; however, 7-d-old seedlings treated with AN3661 survived. AN3661 targeted AtCPSF73-I and AtCPSF73-II, inhibiting growth through coordinating gene expression and poly(A) site choice. Functional enrichment analysis revealed that the accumulation of ethylene and auxin jointly inhibited primary root growth. AN3661 affected poly(A) signal recognition, resulted in lower U-rich signal usage, caused transcriptional readthrough, and increased the distal poly(A) site usage. Many microRNA targets were found in the 3' untranslated region lengthened transcripts; these miRNAs may indirectly regulate the expression of these targets. Overall, this work demonstrates that AtCPSF73 plays important part in co-transcriptional regulation, affecting growth, and development in Arabidopsis.
Collapse
Affiliation(s)
- Saiqi Hao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Lidan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Danhui Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Jiawen Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Haidong Qu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA 91766, USA
| |
Collapse
|
22
|
Chinnappan R, Ramadan Q, Zourob M. Isolation and Detection of Exosomal Mir210 Using Carbon Nanomaterial-Coated Magnetic Beads. J Funct Biomater 2023; 14:441. [PMID: 37754855 PMCID: PMC10531929 DOI: 10.3390/jfb14090441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/28/2023] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that are found in various cellular compartments and play an important role in regulating gene expression. Extracellular miRNAs, such as those found within extracellular vesicles such as exosomes are involved in cell-to-cell communication. The intercellular transfer of miRNAs has been implicated in various diseases' pathogenesis including cancer and has been studied extensively as potential cancer biomarkers. However, the extraction of miRNA from exosomes is still a challenging task. The current nucleic acid extraction assays are expensive and labor-intensive. In this study, we demonstrated a microfluidic device for aptamer-based magnetic separation of the exosomes and subsequent detection of the miRNA using a fluorescence switching assay, which was enabled by carbon nanomaterials coated on magnetic beads. In the OFF state, the fluorophore-labelled cDNA is quenched using carbon nanomaterials. However, when the target miRNA210 is introduced, the cDNA detaches from the bead's surface, which leads to an increase in the fluorescence intensity (ON state). This increment was found to be proportional to miRNA concentration within the dynamic range of 0-100 nM with a detection limit of 5 pM. The assay was validated with spiked miRNA using the standard RT-PCR method. No notable cross-reactivity with other closely related miRNAs was observed. The developed method can be utilized for the minimally invasive detection of cancer biomarkers.
Collapse
Affiliation(s)
| | - Qasem Ramadan
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia;
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia;
| |
Collapse
|
23
|
Swart PC, Du Plessis M, Rust C, Womersley JS, van den Heuvel LL, Seedat S, Hemmings SMJ. Identifying genetic loci that are associated with changes in gene expression in PTSD in a South African cohort. J Neurochem 2023; 166:705-719. [PMID: 37522158 PMCID: PMC10953375 DOI: 10.1111/jnc.15919] [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: 01/18/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
The molecular mechanisms underlying posttraumatic stress disorder (PTSD) are yet to be fully elucidated, especially in underrepresented population groups. Expression quantitative trait loci (eQTLs) are DNA sequence variants that influence gene expression, in a local (cis-) or distal (trans-) manner, and subsequently impact cellular, tissue, and system physiology. This study aims to identify genetic loci associated with gene expression changes in a South African PTSD cohort. Genome-wide genotype and RNA-sequencing data were obtained from 32 trauma-exposed controls and 35 PTSD cases of mixed-ancestry, as part of the SHARED ROOTS project. The first approach utilised 108 937 single-nucleotide polymorphisms (SNPs) (MAF > 10%) and 11 312 genes with Matrix eQTL to map potential eQTLs, while controlling for covariates as appropriate. The second analysis was focused on 5638 SNPs related to a previously calculated PTSD polygenic risk score for this cohort. SNP-gene pairs were considered eQTLs if they surpassed Bonferroni correction and had a false discovery rate <0.05. We did not identify eQTLs that significantly influenced gene expression in a PTSD-dependent manner. However, several known cis-eQTLs, independent of PTSD diagnosis, were observed. rs8521 (C > T) was associated with TAGLN and SIDT2 expression, and rs11085906 (C > T) was associated with ZNF333 expression. This exploratory study provides insight into the molecular mechanisms associated with PTSD in a non-European, admixed sample population. This study was limited by the cross-sectional design and insufficient statistical power. Overall, this study should encourage further multi-omics approaches towards investigating PTSD in diverse populations.
Collapse
Affiliation(s)
- Patricia C. Swart
- Department of Psychiatry, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders UnitCape TownSouth Africa
| | - Morne Du Plessis
- Department of Psychiatry, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders UnitCape TownSouth Africa
| | - Carlien Rust
- Department of Psychiatry, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders UnitCape TownSouth Africa
| | - Jacqueline S. Womersley
- Department of Psychiatry, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders UnitCape TownSouth Africa
| | - Leigh L. van den Heuvel
- Department of Psychiatry, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders UnitCape TownSouth Africa
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders UnitCape TownSouth Africa
| | - Sian M. J. Hemmings
- Department of Psychiatry, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders UnitCape TownSouth Africa
| |
Collapse
|
24
|
Pourzand P, Tabasi F, Fayazbakhsh F, Sarhadi S, Bahari G, Mohammadi M, Jomepour S, Nafeli M, Mosayebi F, Heravi M, Taheri M, Hashemi M, Ghavami S. The Reticulon-4 3-bp Deletion/Insertion Polymorphism Is Associated with Structural mRNA Changes and the Risk of Breast Cancer: A Population-Based Case-Control Study with Bioinformatics Analysis. Life (Basel) 2023; 13:1549. [PMID: 37511924 PMCID: PMC10381770 DOI: 10.3390/life13071549] [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: 05/10/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Breast cancer (BC) is a complex disease caused by molecular events that disrupt cellular survival and death. Discovering novel biomarkers is still required to better understand and treat BC. The reticulon-4 (RTN4) gene, encoding Nogo proteins, plays a critical role in apoptosis and cancer development, with genetic variations affecting its function. We investigated the rs34917480 in RTN4 and its association with BC risk in an Iranian population sample. We also predicted the rs34917480 effect on RTN4 mRNA structure and explored the RTN4's protein-protein interaction network (PPIN) and related pathways. In this case-control study, 437 women (212 BC and 225 healthy) were recruited. The rs34917480 was genotyped using AS-PCR, mRNA secondary structure was predicted with RNAfold, and PPIN was constructed using the STRING database. Our findings revealed that this variant was associated with a decreased risk of BC in heterozygous (p = 0.012), dominant (p = 0.015), over-dominant (p = 0.017), and allelic (p = 0.035) models. Our prediction model showed that this variant could modify RTN4's mRNA thermodynamics and potentially its translation. RTN4's PPIN also revealed a strong association with apoptosis regulation and key signaling pathways highly implicated in BC. Consequently, our findings, for the first time, demonstrate that rs34917480 could be a protective factor against BC in our cohort, probably via preceding mechanisms.
Collapse
Affiliation(s)
- Pouria Pourzand
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 9816743463, Iran
| | - Farhad Tabasi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 9816743463, Iran
- Department of Physiology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
| | - Fariba Fayazbakhsh
- School of Medicine, Zahedan University of Medical Science, Zahedan 9816743463, Iran
| | - Shamim Sarhadi
- Faculty of Advanced Medical Sciences, Department of Medical Biotechnology, Tabriz University of Medical Sciences, Tabriz 5166616471, Iran
| | - Gholamreza Bahari
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 9816743463, Iran
- Children and Adolescent Health Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan 9816743463, Iran
| | - Mohsen Mohammadi
- School of Medicine, Zahedan University of Medical Science, Zahedan 9816743463, Iran
| | - Sahar Jomepour
- Department of Cardiology, Cardiovascular Research Center, School of Medicine, Hormozgan University of Medical Science, Bandar Abbas 7916613885, Iran
| | - Mohammad Nafeli
- School of Medicine, Zahedan University of Medical Science, Zahedan 9816743463, Iran
| | - Fatemeh Mosayebi
- Tehran Heart Center, Tehran University of Medical Science, Tehran 1416634793, Iran
| | - Mehrdad Heravi
- School of Medicine, Zahedan University of Medical Science, Zahedan 9816743463, Iran
| | - Mohsen Taheri
- Genetics of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan 9816743463, Iran
- Department of Genetics, School of Medicine, Zahedan University of Medical Sciences, Zahedan 9816743463, Iran
| | - Mohammad Hashemi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 9816743463, Iran
- Genetics of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan 9816743463, Iran
| | - Saeid Ghavami
- Research Institute of Oncology and Hematology, Cancer Care Manitoba-University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Biology of Breathing Theme, Children Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Faculty of Medicine in Zabrze, University of Technology in Katowice, 41-800 Zabrze, Poland
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| |
Collapse
|
25
|
Yuan X, Hou M, Wang Y, Zhang S, Li L, Mi Y, Du H, Yu S, Nan Y. Mitofusin-2 gene polymorphisms and metabolic dysfunction associated fatty liver disease: a case-control study in a Chinese population. J Int Med Res 2023; 51:3000605231187953. [PMID: 37522325 PMCID: PMC10392247 DOI: 10.1177/03000605231187953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023] Open
Abstract
OBJECTIVES Mitofusion-2 (Mfn2) may have a role in mitochondrial oxidative stress and insulin resistance that can promote the development of metabolic dysfunction associated fatty liver disease (MAFLD). This retrospective and case control study aimed to explore the relationships between common Mfn2 single nucleotide polymorphisms (SNPs) and MAFLD in a northern Han Chinese population. METHODS Six Mfn2 SNPs (rs2336384, rs873458, rs873457, rs4846085, rs2878677, and rs2236057) were genotyped using the ligase detection reaction in 466 MAFLD patients and 423 healthy controls. Genotype and allele frequencies were calculated, along with haplotype analysis and pairwise linkage disequilibrium. RESULTS The genotype distribution of rs2336384, rs2878677, and rs2236057 among the MAFLD patients showed a significantly different pattern from that of healthy controls. The data showed that an increased risk of MAFLD was significantly correlated with patients carrying the GG genotype of rs2336384, CC genotype of rs873457, TT genotype of rs4846085, TT genotype of rs2878677, and the AA genotype of rs2236057. Moreover, The GGCTTA haplotype was found to be adversely linked with MAFLD by haplotype analysis. CONCLUSION The current findings suggest a strong link between certain Mfn2 gene polymorphisms and MAFLD.
Collapse
Affiliation(s)
- Xiwei Yuan
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Mengmeng Hou
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yiqi Wang
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Siyu Zhang
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lu Li
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yingjun Mi
- School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Huijuan Du
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Songhao Yu
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yuemin Nan
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| |
Collapse
|
26
|
Yanaizu M, Adachi H, Araki M, Kontani K, Kino Y. Translational regulation and protein-coding capacity of the 5' untranslated region of human TREM2. Commun Biol 2023; 6:616. [PMID: 37291187 PMCID: PMC10250343 DOI: 10.1038/s42003-023-04998-6] [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: 09/08/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
TREM2 is a transmembrane receptor expressed in microglia and macrophages. Elevated TREM2 levels in these cells are associated with age-related pathological conditions, including Alzheimer's disease. However, the regulatory mechanism underlying the protein expression of TREM2 remains unclear. In this study, we uncover the role of the 5' untranslated region (5'-UTR) of human TREM2 in translation. An upstream start codon (uAUG) in the 5'-UTR of TREM2 is specific to some primates, including humans. The expression of the conventional TREM2 protein, starting from the downstream AUG (dTREM2), is repressed by the 5'-UTR in a uAUG-mediated manner. We also detect a TREM2 protein isoform starting from uAUG (uTREM2) that is largely degraded by proteasomes. Finally, the 5'-UTR is essential for the downregulation of dTREM2 expression in response to amino acid starvation. Collectively, our study identifies a species-specific regulatory role of the 5'-UTR in TREM2 translation.
Collapse
Affiliation(s)
- Motoaki Yanaizu
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
- Department of RNA Pathobiology and Therapeutics, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Haruka Adachi
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Makoto Araki
- Department of Biochemistry, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Kenji Kontani
- Department of Biochemistry, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Yoshihiro Kino
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan.
- Department of RNA Pathobiology and Therapeutics, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan.
| |
Collapse
|
27
|
Nihei M, Kawaguchi S, Mineyama A, Sato T. Transcriptional Mechanism of the Mouse β4-Galactosyltransferase 6 Gene in Mouse Neuroblastoma Cell Line Neuro-2a. Biol Pharm Bull 2023; 46:741-745. [PMID: 36928041 DOI: 10.1248/bpb.b23-00122] [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] [Indexed: 03/14/2023]
Abstract
Lactosylceramide (Lac-Cer) constitutes the backbone structure of various gangliosides whose abnormal expression is associated with malignancy of neuroblastoma. The understanding of the regulatory mechanism of Lac-Cer contributes to the development of neuroblastoma therapy. In this study, the transcriptional mechanism of mouse β4-galactosyltransferase (β4GalT) 6, which is one of Lac-Cer synthase, was analyzed using mouse neuroblastoma cell line Neuro-2a. The -226 to -13 region relative to the most downstream transcriptional start site was determined to be the promoter region by luciferase assay using the 5'-deletion constructs. The mutation into the activating protein (AP) 4-binding site -110/-101 drastically decreased the promoter activity, indicating that this site is mainly implicated in the transcription. Furthermore, the mutation into the GATA-binding site -210/-201 or another AP4-binding site -202/-193 partially decreased the promoter activity. The study suggests that the mouse β4GalT6 gene is transcriptionally regulated by AP4 in cooperation with GATA family transcription factor in neuroblastoma.
Collapse
Affiliation(s)
- Masanobu Nihei
- Laboratory of Glycobiology, Department of Bioengineering, Nagaoka University of Technology
| | - Saori Kawaguchi
- Laboratory of Glycobiology, Department of Bioengineering, Nagaoka University of Technology
| | - Anri Mineyama
- Laboratory of Glycobiology, Department of Bioengineering, Nagaoka University of Technology
| | - Takeshi Sato
- Laboratory of Glycobiology, Department of Bioengineering, Nagaoka University of Technology
| |
Collapse
|
28
|
Choi GH, Cho SH, An HJ, Park HS, Lee JY, Ko EJ, Oh SH, Kim OJ, Kim NK. Association between PAI-1 Polymorphisms and Ischemic Stroke in a South Korean Case-Control Cohort. Int J Mol Sci 2023; 24:8041. [PMID: 37175749 PMCID: PMC10178745 DOI: 10.3390/ijms24098041] [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: 03/19/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Stroke is the second leading cause of death in the world. Approximately 80% of strokes are ischemic in origin. Many risk factors have been linked to stroke, including an increased level of plasminogen activator inhibitor-1 (PAI-1). PAI-1 levels increase and remain elevated in blood during the acute phase of ischemic stroke, which can impair fibrinolytic activity, leading to coronary artery disease and arterial thrombotic disorders. Here, we present a case-control study of 574 stroke patients and 425 controls seen for routine health examination or treatment for nonspecific dizziness, nonorganic headache, or anxiety for positive family history of stroke at the Bundang Medical Center in South Korea. Polymorphisms in PAI-1 were identified by polymerase chain reaction/restriction fragment length polymorphism analysis using genomic DNA. Specifically, three variations (-675 4G>5G, 10692T>C, and 12068G>A) were linked to a higher overall prevalence of stroke as well as a higher prevalence of certain stroke subtypes. Haplotype analyses also revealed combinations of these variations (-844G>A, -675 4G>5G, 43G>A, 9785A>G, 10692T>C, 11053T>G, and 12068G>A) that were significantly associated with a higher prevalence of ischemic stroke. To the best of our knowledge, this is the first strong evidence that polymorphic sites in PAI-1 promoter and 3'-UTR regions are associated with higher ischemic stroke risk. Furthermore, the PAI-1 genotypes and haplotypes identified here have potential as clinical biomarkers of ischemic stroke and could improve the prognosis and future management of stroke patients.
Collapse
Affiliation(s)
- Gun Ho Choi
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Sung Hwan Cho
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- College of Medicine, Konyang University, 158 Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Hui Jeong An
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- College of Life Science, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung 25457, Republic of Korea
| | - Han Sung Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Jeong Yong Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Eun Ju Ko
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Seung Hun Oh
- Department of Neurology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13496, Republic of Korea
| | - Ok Joon Kim
- Department of Neurology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13496, Republic of Korea
| | - Nam Keun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| |
Collapse
|
29
|
Aghaei S, Farrokhi E, Saffari-Chaleshtori J, Hoseinzadeh M, Molavi N, Hashemipour M, Rostampour N, Asgharzadeh S, Tabatabaiefar MA. New molecular insights into the A218V variant impact on the steroidogenic acute regulatory protein (STAR) associated with 46, XY disorders of sexual development. Mol Genet Genomics 2023; 298:693-708. [PMID: 37004560 DOI: 10.1007/s00438-023-02006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/07/2023] [Indexed: 04/04/2023]
Abstract
Disorders of sexual development (DSD) are an abnormal congenital conditions associated with atypical development of the urogenital tract and external genital structures. The steroidogenic acute regulatory (STAR) gene, associated with congenital lipoid adrenal hyperplasia (CLAH), is included in the targeted gene panel for the DSD diagnosis. Therefore, the genetic alterations of the STAR gene and their molecular effect were examined in the CLAH patients affected with DSD. Ten different Iranian families including twelve male pseudo-hermaphroditism patients with CLAH phenotype were studied using genetic linkage screening and STAR gene sequencing in the linked families to the STAR locus. Furthermore, the structural, dynamical, and functional impacts of the variants on the STAR in silico were analyzed. Sanger sequencing showed the pathogenic variant p.A218V in STAR gene, as the first report in Iranian population. Moreover, modeling and simulation analysis were performed using tools such as radius of gyration, root mean square deviation (RMSD), root mean square fluctuation (RMSF), and molecular docking showed that p.A218V variant affects the residues interaction in cholesterol-binding site and the proper folding of STAR through increasing H-bound and the amount of α-Helix, deceasing total flexibility and changing fluctuations in some residues, resulting in reduced steroidogenic activity of the STAR protein. The study characterized the structural and functional changes of STAR caused by pathogenic variant p.A218V. It leads to limited cholesterol-binding activity of STAR, ultimately leading to the CLAH disease. Molecular dynamics simulation of STAR variants could help explain different clinical manifestations of CLAH disease.
Collapse
Affiliation(s)
- Shahrzad Aghaei
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Effat Farrokhi
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Javad Saffari-Chaleshtori
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Marziyeh Hoseinzadeh
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Newsha Molavi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahin Hashemipour
- Metabolic Liver Disease Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Noushin Rostampour
- Metabolic Liver Disease Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Samira Asgharzadeh
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
- Department of Genetics and Molecular Biology, School of Medicine and Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran.
| |
Collapse
|
30
|
Zhou Z, Wang J, Yu Q, Lan H. Promoter activity and transcriptome analyses decipher functions of CgbHLH001 gene (Chenopodium glaucum L.) in response to abiotic stress. BMC PLANT BIOLOGY 2023; 23:116. [PMID: 36849913 PMCID: PMC9969703 DOI: 10.1186/s12870-023-04128-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Our previous studies revealed that CgbHLH001 transcription factor (TF) played an important role in abiotic stress tolerance, suggesting that its promoter was a potential target in response to stress signals. In addition, the regulatory mechanism of CgbHLH001 TF is still limited. RESULTS In the present study, a 1512 bp of 5'-flanking sequence of CgbHLH001 gene was identified, and the sequence carried quite a few of cis-acting elements. The gene promoter displayed strong activity and was induced by multiple abiotic stress. A series of 5'-deletions of the promoter sequence resulted in a gradual decrease in its activity, especially, the 5' untranslated region (UTR) was necessary to drive promoter activity. Further, CgbHLH001 promoter drove its own gene overexpression ectopically at the transcriptional and translational levels, which in turn conferred the stress tolerance to transgenic Arabidopsis. Transcriptome analysis showed that salt stress induced a large number of genes involved in multiple biological regulatory processes. Differentially expressed genes (DEGs) that mediate phytohormone signal transduction and mitogen-activated protein kinase (MAPK) signaling pathway were widely induced and mostly upregulated under salt stress, and the transcription levels in PbHLH::bHLH-overexpressing transgenic lines were higher than that of 35S::bHLH overexpression. CONCLUSIONS The CgbHLH001 promoter exhibited a positive response to abiotic stress and its 5' UTR sequence enhanced the regulation of gene expression to stress. A few important pathways and putative key genes involved in salt tolerance were identified, which can be used to elucidate the mechanism of salt tolerance and decipher the regulatory mechanism of promoters to develop an adaptation strategy for desert halophytes.
Collapse
Affiliation(s)
- Zixin Zhou
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830017, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Haiyan Lan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830017, China.
| |
Collapse
|
31
|
Genomic Survey of Flavin Monooxygenases in Wild and Cultivated Rice Provides Insight into Evolution and Functional Diversities. Int J Mol Sci 2023; 24:ijms24044190. [PMID: 36835601 PMCID: PMC9960948 DOI: 10.3390/ijms24044190] [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: 12/06/2022] [Revised: 01/08/2023] [Accepted: 01/12/2023] [Indexed: 02/22/2023] Open
Abstract
The flavin monooxygenase (FMO) enzyme was discovered in mammalian liver cells that convert a carcinogenic compound, N-N'-dimethylaniline, into a non-carcinogenic compound, N-oxide. Since then, many FMOs have been reported in animal systems for their primary role in the detoxification of xenobiotic compounds. In plants, this family has diverged to perform varied functions like pathogen defense, auxin biosynthesis, and S-oxygenation of compounds. Only a few members of this family, primarily those involved in auxin biosynthesis, have been functionally characterized in plant species. Thus, the present study aims to identify all the members of the FMO family in 10 different wild and cultivated Oryza species. Genome-wide analysis of the FMO family in different Oryza species reveals that each species has multiple FMO members in its genome and that this family is conserved throughout evolution. Taking clues from its role in pathogen defense and its possible function in ROS scavenging, we have also assessed the involvement of this family in abiotic stresses. A detailed in silico expression analysis of the FMO family in Oryza sativa subsp. japonica revealed that only a subset of genes responds to different abiotic stresses. This is supported by the experimental validation of a few selected genes using qRT-PCR in stress-sensitive Oryza sativa subsp. indica and stress-sensitive wild rice Oryza nivara. The identification and comprehensive in silico analysis of FMO genes from different Oryza species carried out in this study will serve as the foundation for further structural and functional studies of FMO genes in rice as well as other crop types.
Collapse
|
32
|
Elangovan A, Venkatesan D, Selvaraj P, Pasha MY, Babu HWS, Iyer M, Narayanasamy A, Subramaniam MD, Valsala Gopalakrishnan A, Kumar NS, Vellingiri B. miRNA in Parkinson's disease: From pathogenesis to theranostic approaches. J Cell Physiol 2023; 238:329-354. [PMID: 36502506 DOI: 10.1002/jcp.30932] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/22/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Parkinson's disease (PD) is an age associated neurological disorder which is specified by cardinal motor symptoms such as tremor, stiffness, bradykinesia, postural instability, and non-motor symptoms. Dopaminergic neurons degradation in substantia nigra region and aggregation of αSyn are the classic signs of molecular defects noticed in PD pathogenesis. The discovery of microRNAs (miRNA) predicted to have a pivotal part in various processes regarding regularizing the cellular functions. Studies on dysregulation of miRNA in PD pathogenesis has recently gained the concern where our review unravels the role of miRNA expression in PD and its necessity in clinical validation for therapeutic development in PD. Here, we discussed how miRNA associated with ageing process in PD through molecular mechanistic approach of miRNAs on sirtuins, tumor necrosis factor-alpha and interleukin-6, dopamine loss, oxidative stress and autophagic dysregulation. Further we have also conferred the expression of miRNAs affected by SNCA gene expression, neuronal differentiation and its therapeutic potential with PD. In conclusion, we suggest more rigorous studies should be conducted on understanding the mechanisms and functions of miRNA in PD which will eventually lead to discovery of novel and promising therapeutics for PD.
Collapse
Affiliation(s)
- Ajay Elangovan
- Department of Human Genetics and Molecular Biology, Human Molecular Cytogenetics and Stem Cell Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India
| | - Dhivya Venkatesan
- Department of Human Genetics and Molecular Biology, Human Molecular Cytogenetics and Stem Cell Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India
| | - Priyanka Selvaraj
- Department of Human Genetics and Molecular Biology, Human Molecular Cytogenetics and Stem Cell Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India
| | - Md Younus Pasha
- Department of Human Genetics and Molecular Biology, Human Molecular Cytogenetics and Stem Cell Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India
| | - Harysh Winster Suresh Babu
- Department of Human Genetics and Molecular Biology, Human Molecular Cytogenetics and Stem Cell Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India.,Department of Zoology, Disease Proteomics Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India
| | - Mahalaxmi Iyer
- Livestock Farming, & Bioresources Technology, Tamil Nadu, India
| | - Arul Narayanasamy
- Department of Zoology, Disease Proteomics Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India
| | - Mohana Devi Subramaniam
- Department of Genetics and Molecular Biology, Vision Research Foundation, Tamil Nadu, Chennai, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Bioscience and Technology, Vellore Institute of Technology (VIT), Tamil Nadu, Vellore, India
| | | | - Balachandar Vellingiri
- Department of Human Genetics and Molecular Biology, Human Molecular Cytogenetics and Stem Cell Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India.,Stem cell and Regenerative Medicine/Translational Research, Department of Zoology, School of Basic Sciences, Central University of Punjab, Punjab, Bathinda, India
| |
Collapse
|
33
|
Kharel P, Fay M, Manasova EV, Anderson PJ, Kurkin AV, Guo JU, Ivanov P. Stress promotes RNA G-quadruplex folding in human cells. Nat Commun 2023; 14:205. [PMID: 36639366 PMCID: PMC9839774 DOI: 10.1038/s41467-023-35811-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Guanine (G)-rich nucleic acids can fold into G-quadruplex (G4) structures under permissive conditions. Although many RNAs contain sequences that fold into RNA G4s (rG4s) in vitro, their folding and functions in vivo are not well understood. In this report, we showed that the folding of putative rG4s in human cells into rG4 structures is dynamically regulated under stress. By using high-throughput dimethylsulfate (DMS) probing, we identified hundreds of endogenous stress-induced rG4s, and validated them by using an rG4 pull-down approach. Our results demonstrate that stress-induced rG4s are enriched in mRNA 3'-untranslated regions and enhance mRNA stability. Furthermore, stress-induced rG4 folding is readily reversible upon stress removal. In summary, our study revealed the dynamic regulation of rG4 folding in human cells and suggested that widespread rG4 motifs may have a global regulatory impact on mRNA stability and cellular stress response.
Collapse
Affiliation(s)
- Prakash Kharel
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marta Fay
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Ekaterina V Manasova
- Chemistry Department of Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Paul J Anderson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, 02115, USA
| | - Alexander V Kurkin
- Chemistry Department of Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Junjie U Guo
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06520, USA.
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, 02115, USA.
| |
Collapse
|
34
|
Paukszto Ł, Wiśniewska J, Liszewska E, Majewska M, Jastrzębski J, Jankowski J, Ciereszko A, Słowińska M. Specific expression of alternatively spliced genes in the turkey (Meleagris gallopavo) reproductive tract revealed their function in spermatogenesis and post-testicular sperm maturation. Poult Sci 2023; 102:102484. [PMID: 36709584 PMCID: PMC9922982 DOI: 10.1016/j.psj.2023.102484] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023] Open
Abstract
The tissue-specific profile of alternatively spliced genes (ASGs) and their involvement in reproduction processes characteristic of turkey testis, epididymis, and ductus deferens were investigated for the first time in birds. Deep sequencing of male turkey reproductive tissue RNA samples (n = 6) was performed using Illumina RNA-Seq with 2 independent methods, rMATs and SUPPA2, for differential alternative splicing (DAS) event prediction. The expression of selected ASGs was validated using quantitative real-time reverse transcriptase-polymerase chain reaction. The testis was found to be the site of the highest number of posttranscriptional splicing events within the reproductive tract, and skipping exons were the most frequently occurring class of alternative splicing (AS) among the reproductive tract. Statistical analysis revealed 86, 229, and 6 DAS events in the testis/epididymis, testis/ductus deferens, and epididymis/ductus deferens comparison, respectively. Alternative splicing was found to be a mechanism of gene expression regulation within the turkey reproduction tract. In testis, modification was observed for spermatogenesis specific genes; the changes in 5' UTR could act as regulator of MEIG1 expression (a player during spermatocytes meiosis), and modification of 3' UTR led to diversification of CREM mRNA (modulator of gene expression related to the structuring of mature spermatozoa). Sperm tail formation can be regulated by changes in the 5' UTR of testicular SLC9A3R1 and gene silencing by producing dysfunctional variants of ODF2 in the testis and ATP1B3 in the epididymis. Predicted differentially ASGs in the turkey reproductive tract seem to be involved in the regulation of spermatogenesis, including acrosome formation and sperm tail formation and binding of sperm to the zona pellucida. Several ASGs were classified as cilia by actin and microtubule cytoskeleton organization. Such genes may play a role in the organization of sperm flagellum and post-testicular motility development. To our knowledge, this is the first functional investigation of alternatively spliced genes associated with tissue-specific processes in the turkey reproductive tract.
Collapse
Affiliation(s)
- Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology; University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Joanna Wiśniewska
- Department of Biological Function of Food, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, 10-748, Olsztyn, Poland
| | - Ewa Liszewska
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, 10-748, Olsztyn, Poland
| | - Marta Majewska
- Department of Human Physiology and Pathophysiology, School of Medicine, Collegium Medicum; University of Warmia and Mazury in Olsztyn, 10-561 Olsztyn, Poland
| | - Jan Jastrzębski
- Department of Plant Physiology, Genetics, and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Jan Jankowski
- Department of Poultry Science, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Andrzej Ciereszko
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, 10-748, Olsztyn, Poland
| | - Mariola Słowińska
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, 10-748, Olsztyn, Poland.
| |
Collapse
|
35
|
Hu C, Xu B, Wang X, Wan W, Lu J, Kong D, Jin Y, You W, Sun H, Mu X, Feng D, Chen Y. Gut microbiota-derived short-chain fatty acids regulate group 3 innate lymphoid cells in HCC. Hepatology 2023; 77:48-64. [PMID: 35262957 PMCID: PMC9970019 DOI: 10.1002/hep.32449] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND AND AIMS Type 3 innate lymphoid cells (ILC3s) are essential for host defense against infection and tissue homeostasis. However, their role in the development of HCC has not been adequately confirmed. In this study, we investigated the immunomodulatory role of short-chain fatty acids (SCFAs) derived from intestinal microbiota in ILC3 regulation. APPROACH AND RESULTS We report that Lactobacillus reuteri was markedly reduced in the gut microbiota of mice with HCC, accompanied by decreased SCFA levels, especially acetate. Additionally, transplantation of fecal bacteria from wild-type mice or L. reuteri could promote an anticancer effect, elevate acetate levels, and reduce IL-17A secretion in mice with HCC. Mechanistically, acetate reduced the production of IL-17A in hepatic ILC3s by inhibiting histone deacetylase activity, increasing the acetylation of SRY (sex-determining region Y)-box transcription factor 13 (Sox13) at site K30, and decreasing expression of Sox13. Moreover, the combination of acetate with programmed death 1/programmed death ligand 1 blockade significantly enhanced antitumor immunity. Consistently, tumor-infiltrating ILC3s correlated with negative prognosis in patients with HCC, which could be functionally mediated by acetate. CONCLUSIONS These findings suggested that modifying bacteria, changing SCFAs, reducing IL-17A-producing ILC3 infiltration, and combining with immune checkpoint inhibitors will contribute to the clinical treatment of HCC.
Collapse
Affiliation(s)
- Chupeng Hu
- Department of Immunology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Gusu School, Nanjing Medical University, Nanjing, Jiangsu, China
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Bingqing Xu
- Department of Immunology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Gusu School, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Ultrasound, Children’s Hospital of Soochow University, Suzhou, China
| | - Xiaodong Wang
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Wen‐Hua Wan
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory 8 of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat‐sen University, Guangzhou, China
| | - Jinying Lu
- Department of Immunology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Gusu School, Nanjing Medical University, Nanjing, Jiangsu, China
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Deyuan Kong
- Department of Immunology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Gusu School, Nanjing Medical University, Nanjing, Jiangsu, China
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu Jin
- Department of Immunology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Gusu School, Nanjing Medical University, Nanjing, Jiangsu, China
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wenhua You
- Department of Immunology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Gusu School, Nanjing Medical University, Nanjing, Jiangsu, China
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hua Sun
- Department of Immunology, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Xiaoxin Mu
- Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Dongju Feng
- Department of Immunology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Gusu School, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yun Chen
- Department of Immunology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Gusu School, Nanjing Medical University, Nanjing, Jiangsu, China
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| |
Collapse
|
36
|
Kircher M, Ludwig KU. Systematic assays and resources for the functional annotation of non-coding variants. MED GENET-BERLIN 2022; 34:275-286. [PMID: 37034418 PMCID: PMC10081529 DOI: 10.1515/medgen-2022-2161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abstract
Identification of genetic variation in individual genomes is now a routine procedure in human genetic research and diagnostics. For many variants, however, insufficient evidence is available to establish a pathogenic effect, particularly for variants in non-coding regions. Furthermore, the sheer number of candidate variants renders testing in individual assays virtually impossible. While scalable approaches are being developed, the selection of methods and resources and the application of a given framework to a particular disease or trait remain major challenges. This limits the translation of results from both genome-wide association studies and genome sequencing. Here, we discuss computational and experimental approaches available for functional annotation of non-coding variation.
Collapse
Affiliation(s)
- Martin Kircher
- Institute of Human Genetics , University of Lübeck , Lübeck , Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin , Berlin , Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University Hospital Bonn , University of Bonn , Venusberg-Campus 1, Building 76 , Bonn , Germany
| |
Collapse
|
37
|
The potential of cold-shock promoters for the expression of recombinant proteins in microbes and mammalian cells. J Genet Eng Biotechnol 2022; 20:173. [PMID: 36580173 PMCID: PMC9800685 DOI: 10.1186/s43141-022-00455-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/15/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Low-temperature expression of recombinant proteins may be advantageous to support their proper folding and preserve bioactivity. The generation of expression vectors regulated under cold conditions can improve the expression of some target proteins that are difficult to express in different expression systems. The cspA encodes the major cold-shock protein from Escherichia coli (CspA). The promoter of cspA has been widely used to develop cold shock-inducible expression platforms in E. coli. Moreover, it is often necessary to employ expression systems other than bacteria, particularly when recombinant proteins require complex post-translational modifications. Currently, there are no commercial platforms available for expressing target genes by cold shock in eukaryotic cells. Consequently, genetic elements that respond to cold shock offer the possibility of developing novel cold-inducible expression platforms, particularly suitable for yeasts, and mammalian cells. CONCLUSIONS This review covers the importance of the cellular response to low temperatures and the prospective use of cold-sensitive promoters to direct the expression of recombinant proteins. This concept may contribute to renewing interest in applying white technologies to produce recombinant proteins that are difficult to express.
Collapse
|
38
|
Rei N, Valente CA, Vaz SH, Farinha-Ferreira M, Ribeiro JA, Sebastião AM. Changes in adenosine receptors and neurotrophic factors in the SOD1G93A mouse model of amyotrophic lateral sclerosis: Modulation by chronic caffeine. PLoS One 2022; 17:e0272104. [PMID: 36516126 PMCID: PMC9749988 DOI: 10.1371/journal.pone.0272104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/13/2022] [Indexed: 12/15/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by the progressive degeneration of corticospinal tract motor neurons. Previous studies showed that adenosine-mediated neuromodulation is disturbed in ALS and that vascular endothelial growth factor (VEGF) has a neuroprotective function in ALS mouse models. We evaluated how adenosine (A1R and A2AR) and VEGF (VEGFA, VEGFB, VEGFR-1 and VEGFR-2) system markers are altered in the cortex and spinal cord of pre-symptomatic and symptomatic SOD1G93A mice. We then assessed if/how chronic treatment of SOD1G93A mice with a widely consumed adenosine receptor antagonist, caffeine, modulates VEGF system and/or the levels of Brain-derived Neurotrophic Factor (BDNF), known to be under control of A2AR. We found out decreases in A1R and increases in A2AR levels even before disease onset. Concerning the VEGF system, we detected increases of VEGFB and VEGFR-2 levels in the spinal cord at pre-symptomatic stage, which reverses at the symptomatic stage, and decreases of VEGFA levels in the cortex, in very late disease states. Chronic treatment with caffeine rescued cortical A1R levels in SOD1G93A mice, bringing them to control levels, while rendering VEGF signaling nearly unaffected. In contrast, BDNF levels were significantly affected in SOD1G93A mice treated with caffeine, being decreased in the cortex and increased in spinal the cord. Altogether, these findings suggest an early dysfunction of the adenosinergic system in ALS and highlights the possibility that the negative influence of caffeine previously reported in ALS animal models results from interference with BDNF rather than with the VEGF signaling molecules.
Collapse
Affiliation(s)
- Nádia Rei
- Faculdade de Medicina, Instituto de Farmacologia e Neurociências, Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Cláudia A. Valente
- Faculdade de Medicina, Instituto de Farmacologia e Neurociências, Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Sandra H. Vaz
- Faculdade de Medicina, Instituto de Farmacologia e Neurociências, Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel Farinha-Ferreira
- Faculdade de Medicina, Instituto de Farmacologia e Neurociências, Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Joaquim A. Ribeiro
- Faculdade de Medicina, Instituto de Farmacologia e Neurociências, Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Ana M. Sebastião
- Faculdade de Medicina, Instituto de Farmacologia e Neurociências, Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
- * E-mail:
| |
Collapse
|
39
|
de Lima LC, Cruz ÁA, Costa RDS, Silva HDS, Coelho RS, Teixeira HM, Oliveira PR, Barnes KC, Figueiredo CA, Carneiro VL. TSLP and IL25 variants are related to asthma and atopy. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
40
|
5′ Untranslated mRNA Regions Allow Bypass of Host Cell Translation Inhibition by Legionella pneumophila. Infect Immun 2022; 90:e0017922. [DOI: 10.1128/iai.00179-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Legionella pneumophila
grows within membrane-bound vacuoles in alveolar macrophages during human disease. Pathogen manipulation of the host cell is driven by bacterial proteins translocated through a type IV secretion system (T4SS).
Collapse
|
41
|
Bocher O, Ludwig TE, Oglobinsky MS, Marenne G, Deleuze JF, Suryakant S, Odeberg J, Morange PE, Trégouët DA, Perdry H, Génin E. Testing for association with rare variants in the coding and non-coding genome: RAVA-FIRST, a new approach based on CADD deleteriousness score. PLoS Genet 2022; 18:e1009923. [PMID: 36112662 PMCID: PMC9518893 DOI: 10.1371/journal.pgen.1009923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 09/28/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022] Open
Abstract
Rare variant association tests (RVAT) have been developed to study the contribution of rare variants widely accessible through high-throughput sequencing technologies. RVAT require to aggregate rare variants in testing units and to filter variants to retain only the most likely causal ones. In the exome, genes are natural testing units and variants are usually filtered based on their functional consequences. However, when dealing with whole-genome sequence (WGS) data, both steps are challenging. No natural biological unit is available for aggregating rare variants. Sliding windows procedures have been proposed to circumvent this difficulty, however they are blind to biological information and result in a large number of tests. We propose a new strategy to perform RVAT on WGS data: “RAVA-FIRST” (RAre Variant Association using Functionally-InfoRmed STeps) comprising three steps. (1) New testing units are defined genome-wide based on functionally-adjusted Combined Annotation Dependent Depletion (CADD) scores of variants observed in the gnomAD populations, which are referred to as “CADD regions”. (2) A region-dependent filtering of rare variants is applied in each CADD region. (3) A functionally-informed burden test is performed with sub-scores computed for each genomic category within each CADD region. Both on simulations and real data, RAVA-FIRST was found to outperform other WGS-based RVAT. Applied to a WGS dataset of venous thromboembolism patients, we identified an intergenic region on chromosome 18 enriched for rare variants in early-onset patients. This region that was missed by standard sliding windows procedures is included in a TAD region that contains a strong candidate gene. RAVA-FIRST enables new investigations of rare non-coding variants in complex diseases, facilitated by its implementation in the R package Ravages.
Collapse
Affiliation(s)
- Ozvan Bocher
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
- Institute of Translational Genomics, Helmholtz Zentrum München, Munich, Germany
- * E-mail:
| | - Thomas E. Ludwig
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
- CHU Brest, Brest, France
| | | | | | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine CNRGH, Institut de Biologie François Jacob, Université Paris Saclay, CEA, Evry, France
| | - Suryakant Suryakant
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team ELEANOR, UMR 1219, Bordeaux, France
| | - Jacob Odeberg
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Tromsö, Tromsö, Norway
| | | | - David-Alexandre Trégouët
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team ELEANOR, UMR 1219, Bordeaux, France
| | - Hervé Perdry
- CESP Inserm, U1018, UFR Médecine, Univ Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Emmanuelle Génin
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
- CHU Brest, Brest, France
| |
Collapse
|
42
|
Singh S, Shyamal S, Panda AC. Detecting RNA-RNA interactome. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1715. [PMID: 35132791 DOI: 10.1002/wrna.1715] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/27/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
The last decade has seen a robust increase in various types of novel RNA molecules and their complexity in gene regulation. RNA molecules play a critical role in cellular events by interacting with other biomolecules, including protein, DNA, and RNA. It has been established that RNA-RNA interactions play a critical role in several biological processes by regulating the biogenesis and function of RNA molecules. Interestingly, RNA-RNA interactions regulate the biogenesis of diverse RNA molecules, including mRNAs, microRNAs, tRNAs, and circRNAs, through splicing or backsplicing. Structured RNAs like rRNA, tRNA, and snRNAs achieve their functional conformation by intramolecular RNA-RNA interactions. In addition, functional consequences of many intermolecular RNA-RNA interactions have been extensively studied in the regulation of gene expression. Hence, it is essential to understand the mechanism and functions of RNA-RNA interactions in eukaryotes. Conventionally, RNA-RNA interactions have been identified through diverse biochemical methods for decades. The advent of high-throughput RNA-sequencing technologies has revolutionized the identification of global RNA-RNA interactome in cells and their importance in RNA structure and function in gene expression regulation. Although these technologies revealed tens of thousands of intramolecular and intermolecular RNA-RNA interactions, we further look forward to future unbiased and quantitative high-throughput technologies for detecting transcriptome-wide RNA-RNA interactions. With the ability to detect RNA-RNA interactome, we expect that future studies will reveal the higher-order structures of RNA molecules and multi-RNA hybrids impacting human health and diseases. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
Collapse
Affiliation(s)
- Suman Singh
- Institute of Life Sciences, Nalco Square, Bhubaneswar, India
- Regional Center for Biotechnology, Faridabad, India
| | | | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, India
| |
Collapse
|
43
|
Anqi Y, Saina Y, Chujie C, Yanfei Y, Xiangwei T, Jiajia M, Jiaojiao X, Maoliang R, Bin C. Regulation of DNA methylation during the testicular development of Shaziling pigs. Genomics 2022; 114:110450. [PMID: 35995261 DOI: 10.1016/j.ygeno.2022.110450] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/21/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022]
Abstract
DNA methylation is one of the key epigenetic regulatory mechanisms in development and spermatogenesis. However, the dynamic regulatory mechanisms of genome-wide DNA methylation during testicular development remain largely unknown. Herein, we generated a single-base resolution DNA methylome and transcriptome atlas of precocious porcine testicular tissues across three developmental stages (1, 75, and 150 days old). The results showed that the dynamic methylation patterns were directly related to the expression of the DNMT3A gene. Conjoint analysis revealed a negative regulatory pattern between promoter methylation and the positive regulation of 3'-untranslated region (3'UTR) methylation. Mechanistically, the decrease in promoter methylation affected the upregulation of meiosis-related genes, such as HORMAD1, SPO11, and SYCE1. Demethylation in the 3'UTR induced the downregulation of the INHBA gene and knockdown of INHBA inhibited cell proliferation by reducing the synthesis of activin A. These findings contribute to exploring the regulatory mechanisms of DNA methylation in testicular development.
Collapse
Affiliation(s)
- Yang Anqi
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Yan Saina
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Chen Chujie
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Yin Yanfei
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Tang Xiangwei
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Ma Jiajia
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Xiang Jiaojiao
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Ran Maoliang
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China.
| | - Chen Bin
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China.
| |
Collapse
|
44
|
Investigation of the multi-targeted protection potential of tannic acid against doxorubicin-induced kidney damage in rats. Chem Biol Interact 2022; 365:110111. [PMID: 35987278 DOI: 10.1016/j.cbi.2022.110111] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/20/2022]
Abstract
Doxorubicin (DOX) is an antitumor drug that is powerful but can cause worse outcomes, including nephrotoxicity, and therefore has limited clinical use. Therefore, it is necessary to identify safer agents that can minimize the damage caused by the drug without shifting the treatment performance, in addition to clarifying the underlying mechanisms of DOX-induced aberrant in vivo renal activation. In this study, we tested the prophylactic capacity and mechanisms of action of tannic acid (TA) against DOX-mediated kidney damage in rats and evaluated the nephrotoxic activity of DOX when used with TA. Rats were treated during the two weeks with cumulative (18 mg/kg with six different injections) DOX, daily TA (50 mg/kg), and the DOX + TA combination. Changes in major metabolites and components involved in antioxidant metabolism were evaluated in the kidney tissues of all animals. Further, the gene expression levels of regulatory factors that have critical importance in cell metabolism, inflammation, and apoptosis were investigated. Both biochemical and molecular examinations showed that TA improved DOX-induced dysregulations at both protein and gene levels in the kidneys. Increased lipid peroxidation and decreased glutathione levels were reversed. Consistent with oxidative stress marker metabolites, suppressed antioxidant enzyme activities and transcript levels of antioxidant system members were restored. Of note, combination treatment with TA could overcome doxorubicin-induced gene expressions markedly altered by DOX, suggesting that nephroprotection conferred by TA involved the remodeling of stress resistance, cell metabolism, inflammation, and apoptosis. Collectively, the present in vivo study suggests that TA could be used as a multitarget and effective agent for the mitigation of doxorubicin-induced nephrotoxicity without changing the therapeutic efficacy of the drug.
Collapse
|
45
|
Schipper M, Posthuma D. "Demystifying non-coding GWAS variants: an overview of computational tools and methods.". Hum Mol Genet 2022; 31:R73-R83. [PMID: 35972862 PMCID: PMC9585674 DOI: 10.1093/hmg/ddac198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 02/01/2023] Open
Abstract
Genome-wide association studies (GWAS) have found the majority of disease-associated variants to be non-coding. Major efforts into the charting of the non-coding regulatory landscapes have allowed for the development of tools and methods which aim to aid in the identification of causal variants and their mechanism of action. In this review, we give an overview of current tools and methods for the analysis of non-coding GWAS variants in disease. We provide a workflow that allows for the accumulation of in silico evidence to generate novel hypotheses on mechanisms underlying disease and prioritize targets for follow-up study using non-coding GWAS variants. Lastly, we discuss the need for comprehensive benchmarks and novel tools for the analysis of non-coding variants.
Collapse
Affiliation(s)
- Marijn Schipper
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1105 1081HV Amsterdam, The Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1105 1081HV Amsterdam, The Netherlands
| |
Collapse
|
46
|
Neefjes M, Housmans BAC, Thielen NGM, van Beuningen HM, Vitters EL, van den Akker GGH, Welting TJM, van Caam APM, van der Kraan PM. An improved diagnostic tool to predict cartilage formation in an osteoarthritic joint environment. Tissue Eng Part A 2022; 28:907-917. [PMID: 35943880 DOI: 10.1089/ten.tea.2022.0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Osteoarthritis (OA) is a degenerative joint disease with progressive articular cartilage loss. Due to the chondrogenic potential of human mesenchymal stromal cells (MSCs), MSC-based therapies are promising treatment strategies for cartilage loss. However, the local joint microenvironment has a great impact on the success of cartilage formation by MSCs. This local joint environment is different between patients and therefore the outcome of MSC therapies is uncertain. We previously developed gene promoter-based reporter assays as a novel tool to predict the effect of a patient's OA joint microenvironment on the success of MSC-based cartilage formation. Here we describe an improved version of this molecular tool with increased prediction accuracy. For this, we generated fourteen stable cell lines using transcription factor (TF) binding elements (AP1, ARE, CRE, GRE, ISRE, NFAT5, NFκB, PPRE, SBE, SIE, SOX9, SRE, SRF, TCF/LEF) to drive luciferase reporter gene expression, and evaluated the cell lines for their responsiveness to an osteoarthritic microenvironment by stimulation with OA synovium-conditioned medium (OAs-cm; n=31). To study the effect of this OA microenvironment on MSC-based cartilage formation, MSCs were cultured in a three-dimensional pellet culture model while stimulated with OAs-cm. Cartilage formation was assessed histologically and by quantifying sulfated glycosaminoglycan (sGAG) production. Six TF reporters correlated significantly with the effect of OAs-cm on cartilage formation. We validated the predictive value of these TF reporters with an independent cohort of OAs-cm (n=22) and compared the prediction accuracy between our previous and the current new tool. Furthermore, we investigated which combination of reporters could predict the effect of the OA microenvironment on cartilage repair with the highest accuracy. A combination between the TF (NFκB) and the promoter-based (IL6) reporter proved to reach a more accurate prediction compared to the tools separately. These developments are an important step towards a diagnostic tool that can be used for personalized cartilage repair strategies for OA patients.
Collapse
Affiliation(s)
- Margot Neefjes
- Radboudumc, Experimental Rheumatology, Geert Grooteplein 28, Nijmegen, Netherlands, 6500 HB;
| | - Bas A C Housmans
- Maastricht University, Department of Orthopedic Surgery, Maastricht, Limburg, Netherlands;
| | | | | | - Elly L Vitters
- Radboudumc, Experimental Rheumatology, Nijmegen, Netherlands;
| | - Guus G H van den Akker
- Maastricht University, Department of Orthopedic Surgery, Maastricht, Limburg, Netherlands;
| | - Tim J M Welting
- University Hospital Maastricht, Department of Orthopaedic Surgery, P Debyelaan 25, Maastricht, Limburg, Netherlands, 6202 AZ;
| | | | | |
Collapse
|
47
|
Thind AS, Ashford B, Strbenac D, Mitchell J, Lee J, Mueller SA, Minaei E, Perry JR, Ch’ng S, Iyer NG, Clark JR, Gupta R, Ranson M. Whole genome analysis reveals the genomic complexity in metastatic cutaneous squamous cell carcinoma. Front Oncol 2022; 12:919118. [PMID: 35982973 PMCID: PMC9379253 DOI: 10.3389/fonc.2022.919118] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022] Open
Abstract
Metastatic cutaneous squamous cell carcinoma (CSCC) is a highly morbid disease requiring radical surgery and adjuvant therapy, which is associated with a poor prognosis. Yet, compared to other advanced malignancies, relatively little is known of the genomic landscape of metastatic CSCC. We have previously reported the mutational signatures and mutational patterns of CCCTC-binding factor (CTCF) regions in metastatic CSCC. However, many other genomic components (indel signatures, non-coding drivers, and structural variants) of metastatic CSCC have not been reported. To this end, we performed whole genome sequencing on lymph node metastases and blood DNA from 25 CSCC patients with regional metastases of the head and neck. We designed a multifaceted computational analysis at the whole genome level to provide a more comprehensive perspective of the genomic landscape of metastatic CSCC. In the non-coding genome, 3′ untranslated region (3′UTR) regions of EVC (48% of specimens), PPP1R1A (48% of specimens), and ABCA4 (20% of specimens) along with the tumor-suppressing long non-coding RNA (lncRNA) LINC01003 (64% of specimens) were significantly functionally altered (Q-value < 0.05) and represent potential non-coding biomarkers of CSCC. Recurrent copy number loss in the tumor suppressor gene PTPRD was observed. Gene amplification was much less frequent, and few genes were recurrently amplified. Single nucleotide variants driver analyses from three tools confirmed TP53 and CDKN2A as recurrently mutated genes but also identified C9 as a potential novel driver in this disease. Furthermore, indel signature analysis highlighted the dominance of ID signature 13 (ID13) followed by ID8 and ID9. ID9 has previously been shown to have no association with skin melanoma, unlike ID13 and ID8, suggesting a novel pattern of indel variation in metastatic CSCC. The enrichment analysis of various genetically altered candidates shows enrichment of “TGF-beta regulation of extracellular matrix” and “cell cycle G1 to S check points.” These enriched terms are associated with genetic instability, cell proliferation, and migration as mechanisms of genomic drivers of metastatic CSCC.
Collapse
Affiliation(s)
- Amarinder Singh Thind
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Bruce Ashford
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- Illawarra Shoalhaven Local Health District, Wollongong, NSW, Australia
- *Correspondence: Bruce Ashford,
| | - Dario Strbenac
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Jenny Mitchell
- Illawarra Shoalhaven Local Health District, Wollongong, NSW, Australia
| | - Jenny Lee
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Department of Clinical Medicine, Macquarie University, Sydney, NSW, Australia
| | - Simon A. Mueller
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Department of Otorhinolaryngology, Head and Neck Surgery, Zurich University Hospital and University of Zurich, Zurich, Switzerland
| | - Elahe Minaei
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Jay R. Perry
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Sydney Ch’ng
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
| | - N. Gopalakrishna Iyer
- Department of Head and Neck Surgery, National Cancer Center, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Jonathan R. Clark
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Royal Prince Alfred Institute of Academic Surgery, Sydney Local Health District, Sydney, NSW, Australia
| | - Ruta Gupta
- Anatomical Pathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Marie Ranson
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| |
Collapse
|
48
|
Suhorukova AV, Tyurin AA, Pavlenko OS, Mustafayev ON, Sinelnikov IG, Goldenkova-Pavlova IV. Development of dual reporter vector system for estimating translational activity of regulatory elements. BMC PLANT BIOLOGY 2022; 22:356. [PMID: 35864445 PMCID: PMC9306140 DOI: 10.1186/s12870-022-03735-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND For the needs of modern biotechnology, a quantitative approach to the control of regulatory elements at all stages of gene expression has long become indispensable. Such a control regime is impossible without a quantitative analysis of the role of each regulatory element or pattern used. Therefore, it seems important to modify and develop the accuracy, reproducibility, and availability of methods for quantifying the contribution of each regulatory code to the implementation of genetic information. RESULTS A new vector system for transient expression in plants is described; this system is intended for quantitative analysis of the contribution of regulatory elements to transcription and translation efficiencies. The proposed vector comprises two expression cassettes carrying reporter genes (of the Clostridium thermocellum thermostable lichenase and E. coli β-glucuronidase) under the control of different promoters. Herewith we also propose a new method for quantification of the effect of tested regulatory elements on expression, which relies on assessment of the enzyme activities of reporter proteins taking into account the transcription of their genes. CONCLUSIONS In our view, this approach makes it possible to precisely determine the amounts of reporter proteins and their transcripts at all stages of expression. The efficiency of the proposed system has been validated by the analysis of the roles of known translation enhancers at the stages of transcription and translation.
Collapse
Affiliation(s)
- Aleksandra V. Suhorukova
- Laboratory of functional genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander A. Tyurin
- Laboratory of functional genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Olga S. Pavlenko
- Laboratory of functional genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Orkhan N. Mustafayev
- Genetic resources institute, Azerbaijan National Academy of Sciences, Baku, Azerbaijan
| | - Igor G. Sinelnikov
- Laboratory of enzyme biotechnology, Federal Research Centre “Fundamentals of Biotechnology”, Russian Academy of Sciences, Moscow, Russia
| | - Irina V. Goldenkova-Pavlova
- Laboratory of functional genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
49
|
Zhou Y, Fang W, Pang Z, Chen LY, Cai H, Ain NU, Chang MC, Ming R. AP1G2 Affects Mitotic Cycles of Female and Male Gametophytes in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:924417. [PMID: 35873977 PMCID: PMC9301471 DOI: 10.3389/fpls.2022.924417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
During sexual reproduction in flowering plants, haploid spores are formed from meiosis of spore mother cells. The spores then undergo mitosis, develop into female and male gametophytes, and give rise to seeds after fertilization. We identified a female sterile mutant ap1g2-4 from EMS mutagenesis, and analyses of two T-DNA insertion mutants, ap1g2-1 +/- and ap1g2-3 -/-, and detected a partial female and male sterility. The ap1g2 mutant gametophyte development was arrested at one nuclear stage. A complementation test using a genomic sequence of AP1G2 with its native promoter restored the function in the three ap1g2 mutant lines. Transcriptome profiling of ap1g2 ovules revealed that four genes encoding clathrin assembly proteins PICALM5A/B and PICALM9A/B, which were involved in endocytosis, were downregulated, which were confirmed to interact with AP1G2 through yeast two-hybrid assays and BIFC analysis. Our result also demonstrated that RALFL4-8-15-19-26 CML16 and several calcium-dependent protein kinases, including CPK14-16-17, were all downregulated in the ovules of ap1g2-1 +/-. Moreover, Ca2+ concentration was low in impaired gametophytes. Therefore, we proposed that through interaction with PICALM5A/B and PICALM9A/B, AP1G2 may mediate gametogenesis accompanied by Ca2+ signaling in Arabidopsis. Our findings revealed a crucial role of AP1G2 in female and male gametogenesis in Arabidopsis and enhanced our understanding of the molecular mechanisms underpinning sexual reproduction in flowering plants.
Collapse
Affiliation(s)
- Yongmei Zhou
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenqin Fang
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ziqin Pang
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li-Yu Chen
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hanyang Cai
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Noor-Ul- Ain
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Men-Chi Chang
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| |
Collapse
|
50
|
Liao TJ, Pan B, Hong H, Hayashi P, Rule JA, Ganger D, Lee WM, Rakela J, Chen M. Whole Exome Sequencing Reveals Genetic Variants in HLA Class II Genes Associated With Transplant-free Survival of Indeterminate Acute Liver Failure. Clin Transl Gastroenterol 2022; 13:e00502. [PMID: 35905417 PMCID: PMC10476814 DOI: 10.14309/ctg.0000000000000502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/17/2022] [Indexed: 09/06/2023] Open
Abstract
INTRODUCTION Indeterminate acute liver failure (IND-ALF) is a rare clinical syndrome with a high mortality rate. Lacking a known etiology makes rapid evaluation and treatment difficult, with liver transplantation often considered as the only therapeutic option. Our aim was to identify genetic variants from whole exome sequencing data that might be associated with IND-ALF clinical outcomes. METHODS Bioinformatics analysis was performed on whole exome sequencing data for 22 patients with IND-ALF. A 2-tier approach was used to identify significant single-nucleotide polymorphisms (SNPs) associated with IND-ALF clinical outcomes. Tier 1 identified the SNPs with a higher relative risk in the IND-ALF population compared with those identified in control populations. Tier 2 determined the SNPs connected to transplant-free survival and associated with model for end-stage liver disease serum sodium and Acute Liver Failure Study Group prognostic scores. RESULTS Thirty-one SNPs were found associated with a higher relative risk in the IND-ALF population compared with those in controls, of which 11 belong to the human leukocyte antigen (HLA) class II genes but none for the class I. Further analysis showed that 5 SNPs: rs796202376, rs139189937, and rs113473719 of HLA-DRB5; rs9272712 of HLA-DQA1; and rs747397929 of IDO1 were associated with a higher probability of IND-ALF transplant-free survival. Using 3 selected SNPs, a model for the polygenic risk score was developed to predict IND-ALF prognoses, which are comparable with those by model for end-stage liver disease serum sodium and Acute Liver Failure Study Group prognostic scores. DISCUSSION Certain gene variants in HLA-DRB5, HLA-DQA1, and IDO1 were found associated with IND-ALF transplant-free survival. Once validated, these identified SNPs may help elucidate the mechanism of IND-ALF and assist in its diagnosis and management.
Collapse
Affiliation(s)
- Tsung-Jen Liao
- Division of Bioinformatics and Biostatistics, U.S. Food and Drug Administration (FDA) National Center for Toxicological Research, Jefferson, Arkansas, USA;
| | - Bohu Pan
- Division of Bioinformatics and Biostatistics, U.S. Food and Drug Administration (FDA) National Center for Toxicological Research, Jefferson, Arkansas, USA;
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, U.S. Food and Drug Administration (FDA) National Center for Toxicological Research, Jefferson, Arkansas, USA;
| | - Paul Hayashi
- Division of Hepatology and Nutrition, Office of New Drugs, FDA Center for Drug Evaluation and Research, Silver Spring, Maryland, USA;
| | - Jody A. Rule
- Division of Gastroenterology and Hepatology, University of Texas Southwestern, Dallas, Texas, USA;
| | - Daniel Ganger
- Division of Gastroenterology and Hepatology, Northwestern University, Chicago, Illinois, USA;
| | - William M. Lee
- Division of Gastroenterology and Hepatology, University of Texas Southwestern, Dallas, Texas, USA;
| | - Jorge Rakela
- Division of Gastroenterology and Hepatology, Mayo Clinic, Phoenix, Arizona, USA.
| | - Minjun Chen
- Division of Bioinformatics and Biostatistics, U.S. Food and Drug Administration (FDA) National Center for Toxicological Research, Jefferson, Arkansas, USA;
| |
Collapse
|