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Khanzode R, Soni G, Srivastava S, Pawar S, Wadapurkar R, Singh A. Combinative workflow for mRNA vaccine development. Biochem Biophys Rep 2024; 39:101766. [PMID: 39040540 PMCID: PMC11261026 DOI: 10.1016/j.bbrep.2024.101766] [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: 03/20/2024] [Accepted: 06/25/2024] [Indexed: 07/24/2024] Open
Abstract
Recently, mRNA has gained a lot of attention in the field of vaccines, gene therapy, and protein replacement therapies. Herein, we are demonstrating a comprehensive approach to designing, cloning, and characterizing an antigenic cassette for the development of mRNA vaccine for COVID-19. The gene encoding the antigenic spike protein of the SARS-CoV-2 Omicron variant (B.1.1.529) was designed using the databases, characterized by in-silico tools, and assembled using overlapping oligonucleotide-based assembly by PCR. Next, the gene was cloned, mRNA was synthesized, and characterized using orthogonal approaches (Capillary electrophoresis, Sanger DNA sequencing, Next-generation sequencing, HPLC, qPCR, etc.). Furthermore, the antigen expression was monitored in-vitro using an animal cell model by western blot, flow cytometer, and surface plasmon resonance. The demonstrated approach has also been followed for developing the mRNA vaccines for various other indications such as Malaria, Herpes, Dengue, HPV, etc.
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Affiliation(s)
| | | | - Shalini Srivastava
- Gennova Biopharmaceuticals Ltd, ITBT Park, Rajiv Gandhi Infotech Park, Hinjawadi, Phase-2, Pune, Maharashtra, 411057, India
| | - Sharad Pawar
- Gennova Biopharmaceuticals Ltd, ITBT Park, Rajiv Gandhi Infotech Park, Hinjawadi, Phase-2, Pune, Maharashtra, 411057, India
| | - Rucha Wadapurkar
- Gennova Biopharmaceuticals Ltd, ITBT Park, Rajiv Gandhi Infotech Park, Hinjawadi, Phase-2, Pune, Maharashtra, 411057, India
| | - Ajay Singh
- Gennova Biopharmaceuticals Ltd, ITBT Park, Rajiv Gandhi Infotech Park, Hinjawadi, Phase-2, Pune, Maharashtra, 411057, India
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Yu T, Ning J, Wang F, Liu G, Wang Q, Xu X, Wang C, Lu X. Whole-Genome Re-sequencing and Transcriptome Reveal Candidate Genes and Pathways Associated with Hybrid Sterility in Hermaphroditic Argopecten Scallops. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:891-906. [PMID: 37632589 DOI: 10.1007/s10126-023-10247-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/18/2023] [Indexed: 08/28/2023]
Abstract
The interspecific hybrid scallops generated from the hermaphroditic bay scallops (Argopecten irradians) and Peruvian scallops (Argopecten purpuratus) showed significant heterosis in growth. However, its sterility limits large-scale hybridization and hinders the development of the scallop breeding industry. Hybrid sterility is regulated by plenty of genes and involves a range of biochemical and physiological transformations. In this study, whole-genome re-sequencing and transcriptomic analysis were performed in sterile and fertile hybrid scallops. The potential genetic variations and abnormally expressed genes were detected to explore the mechanism underlying hybrid sterility in hermaphroditic Argopecten scallops. Compared with fertile hybrids, 24 differentially expressed genes (DEGs) with 246 variations were identified to be related to fertility regulation, which were mainly enriched in germarium-derived egg chamber formation, spermatogenesis, spermatid development, mismatch repair, mitotic and meiotic cell cycles, Wnt signaling pathway, MAPK signaling pathway, calcium modulating pathway, and notch signaling pathway. Specifically, variation and abnormal expression of these genes might inhibit the progress of mitosis and meiosis, promote cell apoptosis, and impede the genesis and maturation of gametes in sterile hybrid scallops. Eleven DEGs (XIAP, KAZN, CDC42, MEIS1, SETD1B, NOTCH2, TRPV5, M- EXO1, GGT1, SBDS, and TBCEL) were confirmed by qRT-PCR validation. Our findings may enrich the determination mechanism of hybrid sterility and provide new insights into the use of interspecific hybrids for extensive breeding.
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Affiliation(s)
- Tieying Yu
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junhao Ning
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China
| | - Fukai Wang
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Guilong Liu
- Yantai Spring-Sea AquaSeed, Ltd., Yantai, 264006, China
| | - Quanchao Wang
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China
| | - Xin Xu
- Yantai Spring-Sea AquaSeed, Ltd., Yantai, 264006, China
| | - Chunde Wang
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xia Lu
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China.
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Fang T, Wang F, Zhang R, Du ZQ, Yang CX. Single-cell RNA sequencing reveals blastomere heterogeneity of 2-cell embryos in pigs. Reprod Domest Anim 2023; 58:1393-1403. [PMID: 37568261 DOI: 10.1111/rda.14454] [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: 05/23/2023] [Revised: 07/17/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023]
Abstract
In mammals, single blastomeres from as early as 2-cell embryos demonstrate heterogeneous developmental capacity and fate decision into different cell lineages. However, mechanisms underlying blastomere heterogeneity of 2-cell embryos remain largely unresolved. Here, we analysed the molecular heterogeneity of full-length mRNAs and their 3'UTR regions, based on the single-cell RNA-seq data of pig 2-cell embryos generated from in vivo fertilization (in vivo), in vitro fertilization (in vitro) and parthenogenetic activation (PA), respectively. First, unsupervised clustering helped discover two different groups of blastomeres for 2-cell pig embryos. Between these two groups of blastomeres in pig 2-cell embryos, 35, 301 and 428 full-length mRNAs respectively in in vivo, in vitro and PA embryo types were identified to be differentially expressed (padj ≤ .05 and |log2 [fold change]| ≥1) (DE mRNAs), while 92, 89 and 42 mRNAs were shown to be with significantly different 3'UTR lengths (3'UTR DE) (padj ≤ .05). Gene enrichment for both DE mRNAs and 3'UTR DE mRNAs found multiple signalling pathways, including cell cycle, RNA processing. Few numbers of common DE mRNAs and 3'UTR DE mRNAs existed between in vitro and in vivo blastomeres derived from 2-cell embryos, indicating the larger differences between in vitro and in vivo fertilized embryos. Integrative genomics viewer analysis further identified that 3'UTRs of HSDL2 and SGTA (in vivo), FAM204A and phosphoserine phosphatase (in vitro), PRPF40A and RPIA (PA) had >100 nt average length changes. Moreover, numbers and locations of regulatory elements (polyadenylation site, cytoplasmic polyadenylation element and microRNA binding sites) within 3'UTRs of these DE mRNAs were predicted. These results indicate that molecular heterogeneity existed among blastomeres from different types of pig 2-cell embryos, providing useful information and novel insights into future functional investigation on its relationship with the subsequent embryo development and differentiation.
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Affiliation(s)
- Ting Fang
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Fang Wang
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Rong Zhang
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Zhi-Qiang Du
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Cai-Xia Yang
- College of Animal Science, Yangtze University, Jingzhou, China
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Wang Y, Wu ZW, Mou Q, Chen L, Fang T, Zhang YQ, Yin Z, Du ZQ, Yang CX. Global 3'-UTRome of porcine immature Sertoli cells altered by acute heat stress. Theriogenology 2023; 196:79-87. [PMID: 36401935 DOI: 10.1016/j.theriogenology.2022.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 10/30/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
Alternative polyadenylation (APA) affects the composition of cis-elements in 3'-untranslated region (3'-UTR), to regulate gene expression and localization, and subsequently the downstream biological processes. Acute heat stress could change rapidly the cellular transcriptome, however the underlying molecular changes are less explored. Here, we systematically catalogued the global 3'-UTRome dynamics, by analyzing our previously reported transcriptome sequencing data of porcine immature Sertoli (iST) cells before (Control group), acute heat stress treatment at 43 °C for 0.5h (HS0.5 group), and 36h recovery culture (HS0.5-R36h group) after acute heat stress treatment. After three group comparisons (HS0.5 vs. Control, HS0.5-R36 vs. HS0.5, and HS0.5-R36 vs. Control), DaPars (dynamic analysis of alternative polyadenylation) identified 639, 464 and 290 mRNAs, and APAtrap (a tool to identify APA sites and detect changes of APA site usage) identified 713, 518 and 321 mRNAs, with significantly different 3'-UTRs (Padj.≤0.05), respectively. These genes with different 3'-UTR patterns were mainly enriched in P53, glycolysis/gluconeogenesis, HIF-1, apoptosis, PI3K-Akt and AMPK signaling pathways. Further analysis identified that average 3'-UTR lengths of Acss2, Inpp1 and Nr1h4 were more than 140 nt longer (HS0.5-R36 vs. HS0.5), and contained different cis-elements (PAS, CPE and microRNA binding sites). Moreover, Hsp70.2, Inhbb and Dhrs were identified to have extremely different 3'-UTR abundances. Further 3'RACE assays validated several 3'-UTRs of Nr1h4, and RT-qPCR confirmed the abundance changes of different 3'-UTR isoforms for Nr1h4 and Hsp70.2. Our findings provide useful information and resources to further uncover the molecular role of 3'-UTR, in regulating the response of porcine iST cells to acute heat stress.
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Affiliation(s)
- Yi Wang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Zi-Wei Wu
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Qiao Mou
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Lu Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Ting Fang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yu-Qing Zhang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Zhi-Qiang Du
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Cai-Xia Yang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China.
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Li S, Wang J, Li J, Yue M, Liu C, Ma L, Liu Y. Integrative analysis of transcriptome complexity in pig granulosa cells by long-read isoform sequencing. PeerJ 2022; 10:e13446. [PMID: 35637716 PMCID: PMC9147391 DOI: 10.7717/peerj.13446] [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: 02/03/2022] [Accepted: 04/26/2022] [Indexed: 01/14/2023] Open
Abstract
Background In intensive and large-scale farms, abnormal estradiol levels in sows can cause reproductive disorders. The high incidence rate of reproductive disturbance will induce the elimination of productive sows in large quantities, and the poor management will bring great losses to the pig farms. The change in estradiol level has an important effect on follicular development and estrus of sows. To solve this practical problem and improve the productive capacity of sows, it is significant to further clarify the regulatory mechanism of estradiol synthesis in porcine granulosa cells (GCs). The most important function of granulosa cells is to synthesize estradiol. Thus, the studies about the complex transcriptome in porcine GCs are significant. As for precursor-messenger RNAs (pre-mRNAs), their post-transcriptional modification, such as alternative polyadenylation (APA) and alternative splicing (AS), together with long non-coding RNAs (lncRNAs), may regulate the functions of granulosa cells. However, the above modification events and their function are unclear within pig granulosa cells. Methods Combined PacBio long-read isoform sequencing (Iso-Seq) was conducted in this work for generating porcine granulosa cells' transcriptomic data. We discovered new transcripts and possible gene loci via comparison against reference genome. Later, combined Iso-Seq data were adopted to uncover those post-transcriptional modifications such as APA or AS, together with lncRNA within porcine granulosa cells. For confirming that the Iso-Seq data were reliable, we chose four AS genes and analyzed them through RT-PCR. Results The present article illustrated that pig GCs had a complex transcriptome, which gave rise to 8,793 APA, 3,465 AS events, 703 candidate new gene loci, as well as 92 lncRNAs. The results of this study revealed the complex transcriptome in pig GCs. It provided a basis for the interpretation of the molecular mechanism in GCs.
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Affiliation(s)
- Shuxin Li
- School of Life Science and Technology, Inner Mongolia University of Science & Technology, Baotou, Inner Mongolia, China
| | - Jiarui Wang
- School of Life Science and Technology, Inner Mongolia University of Science & Technology, Baotou, Inner Mongolia, China
| | - Jiale Li
- School of Life Science and Technology, Inner Mongolia University of Science & Technology, Baotou, Inner Mongolia, China
| | - Meihong Yue
- School of Life Science and Technology, Inner Mongolia University of Science & Technology, Baotou, Inner Mongolia, China
| | - Chuncheng Liu
- School of Life Science and Technology, Inner Mongolia University of Science & Technology, Baotou, Inner Mongolia, China
| | - Libing Ma
- School of Life Science and Technology, Inner Mongolia University of Science & Technology, Baotou, Inner Mongolia, China
| | - Ying Liu
- School of Life Science and Technology, Inner Mongolia University of Science & Technology, Baotou, Inner Mongolia, China
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