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Abdulnour-Nakhoul SM, Kolls JK, Flemington EK, Ungerleider NA, Nakhoul HN, Song K, Nakhoul NL. Alterations in gene expression and microbiome composition upon calcium-sensing receptor deletion in the mouse esophagus. Am J Physiol Gastrointest Liver Physiol 2024; 326:G438-G459. [PMID: 38193195 DOI: 10.1152/ajpgi.00066.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 12/17/2023] [Accepted: 12/23/2023] [Indexed: 01/10/2024]
Abstract
The calcium-sensing receptor (CaSR), a G protein-coupled receptor, regulates Ca2+ concentration in plasma by regulating parathyroid hormone secretion. In other tissues, it is reported to play roles in cellular differentiation and migration and in secretion and absorption. We reported previously that CaSR can be conditionally deleted in the mouse esophagus. This conditional knockout (KO) (EsoCaSR-/-) model showed a significant reduction in the levels of adherens and tight junction proteins and had a marked buildup of bacteria on the luminal esophageal surface. To further examine the role of CaSR, we used RNA sequencing to determine gene expression profiles in esophageal epithelia of control and EsoCaSR-/-mice RNA Seq data indicated upregulation of gene sets involved in DNA replication and cell cycle in EsoCaSR-/-. This is accompanied by the downregulation of gene sets involved in the innate immune response and protein homeostasis including peptide elongation and protein trafficking. Ingenuity pathway analysis (IPA) demonstrated that these genes are mapped to important biological networks including calcium and Ras homologus A (RhoA) signaling pathways. To further explore the bacterial buildup in EsoCaSR-/- esophageal tissue, 16S sequencing of the mucosal-associated bacterial microbiome was performed. Three bacterial species, g_Rodentibacter, s_Rodentibacter_unclassified, and s_Lactobacillus_hilgardi were significantly increased in EsoCaSR-/-. Furthermore, metagenomic analysis of 16S sequences indicated that pathways related to oxidative phosphorylation and metabolism were downregulated in EsoCaSR-/- tissues. These data demonstrate that CaSR impacts major pathways of cell proliferation, differentiation, cell cycle, and innate immune response in esophageal epithelium. The disruption of these pathways causes inflammation and significant modifications of the microbiome.NEW & NOTEWORTHY Calcium-sensing receptor (CaSR) plays a significant role in maintaining the barrier function of esophageal epithelium. Using RNA sequencing, we show that conditional deletion of CaSR from mouse esophagus causes upregulation of genes involved in DNA replication and cell cycle and downregulation of genes involved in the innate immune response, protein translation, and cellular protein synthesis. Pathway analysis shows disruption of signaling pathways of calcium and actin cytoskeleton. These changes caused inflammation and esophageal dysbiosis.
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Affiliation(s)
- Solange M Abdulnour-Nakhoul
- Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States
- Department of Physiology, Tulane University School of Medicine, New Orleans, Louisiana, United States
| | - Jay K Kolls
- Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States
- Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, Louisiana, United States
| | - Erik K Flemington
- Department of Pathology, Tulane University, New Orleans, Louisiana, United States
| | - Nathan A Ungerleider
- Department of Pathology, Tulane University, New Orleans, Louisiana, United States
| | - Hani N Nakhoul
- Department of Pathology, Tulane University, New Orleans, Louisiana, United States
| | - Kejing Song
- Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States
- Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, Louisiana, United States
| | - Nazih L Nakhoul
- Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States
- Department of Physiology, Tulane University School of Medicine, New Orleans, Louisiana, United States
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Niu R, Zhang X, Yu Y, Bao Z, Yang J, Yuan J, Li F. Identification of Growth-Related Gene BAMBI and Analysis of Gene Structure and Function in the Pacific White Shrimp Litopenaeus vannamei. Animals (Basel) 2024; 14:1074. [PMID: 38612313 PMCID: PMC11011141 DOI: 10.3390/ani14071074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/30/2024] [Accepted: 03/30/2024] [Indexed: 04/14/2024] Open
Abstract
As one of the most important aquaculture species in the world, the improvement of growth traits of the Pacific white shrimp (Litopenaeus vannamei), has always been a primary focus. In this study, we conducted SNP-specific locus analysis and identified a growth-related gene, BAMBI, in L. vannamei. We analyzed the structure and function of LvBAMBI using genomic, transcriptomic, metabolomic, and RNA interference (RNAi) assays. The LvBAMBI possessed highly conserved structural domains and widely expressed in various tissues. Knockdown of LvBAMBI significantly inhibited the gain of body length and weight of the shrimp, underscoring its role as a growth-promoting factor. Specifically, knockdown of LvBAMBI resulted in a significant downregulation of genes involved in lipid metabolism, protein synthesis, catabolism and transport, and immunity. Conversely, genes related to glucose metabolism exhibited significant upregulations. Analysis of differential metabolites (DMs) in metabolomics further revealed that LvBAMBI knockdown may primarily affect shrimp growth by regulating biological processes related to lipid and glucose metabolism. These results suggested that LvBAMBI plays a crucial role in regulating lipid metabolism, glucose metabolism, and protein transport in shrimp. This study provides valuable insights for future research and utilization of BAMBI genes in shrimp and crustaceans.
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Affiliation(s)
- Ruigang Niu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhenning Bao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junqing Yang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
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Zhang W, Liao Y, Shao P, Yang Y, Huang L, Du Z, Zhang C, Wang Y, Lin Y, Zhu J. Integrated analysis of differently expressed microRNAs and mRNAs at different postnatal stages reveals intramuscular fat deposition regulation in goats (Capra hircus). Anim Genet 2024; 55:238-248. [PMID: 38175181 DOI: 10.1111/age.13384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 11/18/2023] [Accepted: 11/23/2023] [Indexed: 01/05/2024]
Abstract
Intramuscular fat refers to the adipose tissue distributed in the muscle. It is an important indicator that affects the quality of goat meat, and can directly affect the tenderness and flavor of goat meat. Our previous study revealed the mRNA that may be crucial for intramuscular fat deposition during goat growth; however, how the microRNAs (miRNAs) are involved in the process is largely unclear. In the present study, a total of 401 known miRNAs and 120 goat novel miRNAs, including 110 differentially expressed (DE) miRNAs, were identified among longissimus dorsi from three growth stages (2, 9, and 24 months) by miRNA sequencing. Combining analysis of the DE mRNAs and DE miRNAs was then performed by miRDB and miRwalk, and miR-145-5p and FOXO1, miR-487b-3p, and PPARG coactivator 1 α (PPARGC1A), miR-345-3p, and solute carrier family 2 member 4 (SLC2A4), etc. were shown to closely associate with lipid metabolism, which was then validated by a correlation analysis. The final DE mRNAs were significantly enriched in fatty acid transmembrane transport, fatty acid homeostasis, apelin signaling pathway, glucagon signaling pathway, insulin signaling pathway, and AMPK signaling pathway by gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis. Besides, miR-145-5p showed a certain effect on goat intramuscular fat metabolism by acting on the possible target gene Forkhead Box O1 (FOXO1). These data provide some theoretical support for improving the quality of goat meat.
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Affiliation(s)
- Wenyang Zhang
- Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Yu Liao
- Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Peng Shao
- Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Yuling Yang
- Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Lian Huang
- Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Zhanyu Du
- Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Changhui Zhang
- Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Yong Wang
- Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Yaqiu Lin
- Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education, Chengdu, China
| | - Jiangjiang Zhu
- Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education, Chengdu, China
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104
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Raposo M, Hübener-Schmid J, Tagett R, Ferreira AF, Vieira Melo AR, Vasconcelos J, Pires P, Kay T, Garcia-Moreno H, Giunti P, Santana MM, Pereira de Almeida L, Infante J, van de Warrenburg BP, de Vries JJ, Faber J, Klockgether T, Casadei N, Admard J, Schöls L, Riess O, Costa MDC, Lima M. Blood and cerebellar abundance of ATXN3 splice variants in spinocerebellar ataxia type 3/Machado-Joseph disease. Neurobiol Dis 2024; 193:106456. [PMID: 38423193 DOI: 10.1016/j.nbd.2024.106456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/14/2023] [Accepted: 02/25/2024] [Indexed: 03/02/2024] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3)/Machado-Joseph disease (MJD) is a heritable proteinopathy disorder, whose causative gene, ATXN3, undergoes alternative splicing. Ataxin-3 protein isoforms differ in their toxicity, suggesting that certain ATXN3 splice variants may be crucial in driving the selective toxicity in SCA3. Using RNA-seq datasets we identified and determined the abundance of annotated ATXN3 transcripts in blood (n = 60) and cerebellum (n = 12) of SCA3 subjects and controls. The reference transcript (ATXN3-251), translating into an ataxin-3 isoform harbouring three ubiquitin-interacting motifs (UIMs), showed the highest abundance in blood, while the most abundant transcript in the cerebellum (ATXN3-208) was of unclear function. Noteworthy, two of the four transcripts that encode full-length ataxin-3 isoforms but differ in the C-terminus were strongly related with tissue expression specificity: ATXN3-251 (3UIM) was expressed in blood 50-fold more than in the cerebellum, whereas ATXN3-214 (2UIM) was expressed in the cerebellum 20-fold more than in the blood. These findings shed light on ATXN3 alternative splicing, aiding in the comprehension of SCA3 pathogenesis and providing guidance in the design of future ATXN3 mRNA-lowering therapies.
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Affiliation(s)
- Mafalda Raposo
- IBMC - Instituto de Biologia Molecular e Celular, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal.
| | - Jeannette Hübener-Schmid
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; Centre for Rare Diseases, University of Tübingen, Tübingen, Germany.
| | - Rebecca Tagett
- Bioinformatics Core, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Ana F Ferreira
- Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal
| | - Ana Rosa Vieira Melo
- Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal
| | - João Vasconcelos
- Serviço de Neurologia, Hospital do Divino Espírito Santo, Ponta Delgada, Portugal
| | - Paula Pires
- Serviço de Neurologia, Hospital do Santo Espírito da Ilha Terceira, Angra do Heroísmo, Portugal
| | - Teresa Kay
- Serviço de Genética Clínica, Hospital D. Estefânia, Lisboa, Portugal
| | - Hector Garcia-Moreno
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK; Department of Neurogenetics, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Paola Giunti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK; Department of Neurogenetics, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Magda M Santana
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal; Institute for Interdisciplinary Research, University of Coimbra (IIIUC), Coimbra, Portugal
| | - Luis Pereira de Almeida
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra (FFUC), Coimbra, Portugal
| | - Jon Infante
- Neurology Service, University Hospital Marqués de Valdecilla-IDIVAL, Universidad de Cantabria, Centro de Investigación en Red de Enfermedades Neurodegenerativas (CIBERNED), Santander, Spain
| | - Bart P van de Warrenburg
- Radboud University Medical Centre, Donders Institute for Brain, Cognition and Behaviour, Department of Neurology, Nijmegen, the Netherlands
| | - Jeroen J de Vries
- Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jennifer Faber
- Department of Neurology, University Hospital Bonn, Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Thomas Klockgether
- Department of Neurology, University Hospital Bonn, Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen, Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen, Tübingen, Germany
| | - Ludger Schöls
- Department for Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center for Neurology, University of Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; Centre for Rare Diseases, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen, Tübingen, Germany
| | - Maria do Carmo Costa
- Department of Neurology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA.
| | - Manuela Lima
- Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal.
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Gandhi N, Wills L, Akers K, Su Y, Niccum P, Murali TM, Rajagopalan P. Comparative transcriptomic and phenotypic analysis of induced pluripotent stem cell hepatocyte-like cells and primary human hepatocytes. Cell Tissue Res 2024; 396:119-139. [PMID: 38369646 DOI: 10.1007/s00441-024-03868-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
Abstract
Primary human hepatocytes (PHHs) are used extensively for in vitro liver cultures to study hepatic functions. However, limited availability and invasive retrieval prevent their widespread use. Induced pluripotent stem cells exhibit significant potential since they can be obtained non-invasively and differentiated into hepatic lineages, such as hepatocyte-like cells (iHLCs). However, there are concerns about their fetal phenotypic characteristics and their hepatic functions compared to PHHs in culture. Therefore, we performed an RNA-sequencing (RNA-seq) analysis to understand pathways that are either up- or downregulated in each cell type. Analysis of the RNA-seq data showed an upregulation in the bile secretion pathway where genes such as AQP9 and UGT1A1 were higher expressed in PHHs compared to iHLCs by 455- and 15-fold, respectively. Upon immunostaining, bile canaliculi were shown to be present in PHHs. The TCA cycle in PHHs was upregulated compared to iHLCs. Cellular analysis showed a 2-2.5-fold increase in normalized urea production in PHHs compared to iHLCs. In addition, drug metabolism pathways, including cytochrome P450 (CYP450) and UDP-glucuronosyltransferase enzymes, were upregulated in PHHs compared to iHLCs. Of note, CYP2E1 gene expression was significantly higher (21,810-fold) in PHHs. Acetaminophen and ethanol were administered to PHH and iHLC cultures to investigate differences in biotransformation. CYP450 activity of baseline and toxicant-treated samples was significantly higher in PHHs compared to iHLCs. Our analysis revealed that iHLCs have substantial differences from PHHs in critical hepatic functions. These results have highlighted the differences in gene expression and hepatic functions between PHHs and iHLCs to motivate future investigation.
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Affiliation(s)
- Neeti Gandhi
- Department of Chemical Engineering, Virginia Tech, 333 Kelly Hall, Blacksburg, VA, 24061, USA
| | - Lauren Wills
- School of Biomedical Engineering and Sciences, Virginia Tech, Blacksburg, USA
| | - Kyle Akers
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA, USA
| | - Yiqi Su
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Parker Niccum
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA, USA
| | - T M Murali
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Padmavathy Rajagopalan
- Department of Chemical Engineering, Virginia Tech, 333 Kelly Hall, Blacksburg, VA, 24061, USA.
- School of Biomedical Engineering and Sciences, Virginia Tech, Blacksburg, USA.
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106
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Chen M, Wan Q, Xu M, Chen Z, Guo S. Transcriptome Analysis of Host Anti-Vibrio harveyi Infection Revealed the Pathogenicity of V. harveyi to American Eel (Anguilla rostrata). Mar Biotechnol (NY) 2024; 26:306-323. [PMID: 38367180 DOI: 10.1007/s10126-024-10298-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 02/12/2024] [Indexed: 02/19/2024]
Abstract
Vibrio harveyi, a recently discovered pathogenic bacterium isolated from American eels (Anguilla rostrata), poses uncertainties regarding its pathogenesis in American eel and the molecular mechanisms underlying host defense against V. harveyi infection. This study aimed to determine the LD50 of V. harveyi in American eel and assess the bacterial load in the liver, spleen, and kidney post-infection with the LD50 dose. The results showed that the LD50 of V. harveyi via intraperitoneal injection in American eels over a 14d period was determined to be 1.24 × 103 cfu/g body weight (6.2 × 104 cfu/fish). The peak bacterial load occurred at 36 h post-infection (hpi) in all three organs examined. Histopathology analysis revealed hepatic vein congestion and thrombi, tubular vacuolar degeneration, and splenic bleeding. Moreover, quantitative reverse transcription polymerase chain reaction (qRT-PCR) results indicated significant up or downregulation of 18 host immune- or anti-infection-related genes post 12 to 60 hpi following the infection. Additionally, RNA sequencing (RNA-seq) unveiled 7 hub differentially expressed genes (DEGs) and 11 encoded proteins play crucial roles in the anti-V. harveyi response in American eels. This study firstly represents the comprehensive report on the pathogenicity of V. harveyi to American eels and RNA-seq of host's response to V. harveyi infection. These findings provide valuable insights into V. harveyi pathogenesis and the strategies employed by the host's immune system at the transcriptomic level to combat V. harveyi infection.
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Affiliation(s)
- Minxia Chen
- Fisheries College, Jimei University, Xiamen, 361021, China
- Engineering Research Center of the Modern Industry Technology for Eel. Ministry of Education of PRC, Xiamen, 361021, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, 361021, China
| | - Qijuan Wan
- Fisheries College, Jimei University, Xiamen, 361021, China
- Engineering Research Center of the Modern Industry Technology for Eel. Ministry of Education of PRC, Xiamen, 361021, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, 361021, China
| | - Ming Xu
- Fisheries College, Jimei University, Xiamen, 361021, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, 361021, China
| | - Zihao Chen
- Fisheries College, Jimei University, Xiamen, 361021, China
- Engineering Research Center of the Modern Industry Technology for Eel. Ministry of Education of PRC, Xiamen, 361021, China
| | - Songlin Guo
- Fisheries College, Jimei University, Xiamen, 361021, China.
- Engineering Research Center of the Modern Industry Technology for Eel. Ministry of Education of PRC, Xiamen, 361021, China.
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, 361021, China.
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107
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Wu J, Liu S, Banerjee O, Shi H, Xue B, Ding Z. Disturbed flow impairs MerTK-mediated efferocytosis in aortic endothelial cells during atherosclerosis. Theranostics 2024; 14:2427-2441. [PMID: 38646649 PMCID: PMC11024847 DOI: 10.7150/thno.93036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/18/2024] [Indexed: 04/23/2024] Open
Abstract
Background: MER proto-oncogene tyrosine kinase (MerTK) is a key receptor for efferocytosis, a process for the clearance of apoptotic cells. MerTK is mainly expressed in macrophages and immature dendritic cells. There are very limited reports focused on MerTK biology in aortic endothelial cells (ECs). It remains unclear for the role of blood flow patterns in regulating MerTK-mediated efferocytosis in aortic ECs. This study was designed to investigate whether endothelial MerTK and EC efferocytosis respond to blood flow patterns during atherosclerosis. Methods: Big data analytics, RNA-seq and proteomics combined with our in vitro and in vivo studies were applied to reveal the potential molecular mechanisms. Partial carotid artery ligation combined with AAV-PCSK9 and high fat diet were used to set up acute atherosclerosis in 4 weeks. Results: Our data showed that MerTK is sensitive to blood flow patterns and is inhibited by disturbed flow and oscillatory shear stress in primary human aortic ECs (HAECs). The RNA-seq data in HAECs incubated with apoptotic cells showed that d-flow promotes pro-inflammatory pathway and senescence pathway. Our in vivo data of proteomics and immunostaining showed that, compared with WT group, MerTK-/- aggravates atherosclerosis in d-flow areas through upregulation of endothelial dysfunction markers (e.g. IL-1β, NF-κB, TLR4, MAPK signaling, vWF, VCAM-1 and p22phox) and mitochondrial dysfunction. Interestingly, MerTK-/-induces obvious abnormal endothelial thickening accompanied with decreased endothelial efferocytosis, promoting the development of atherosclerosis. Conclusions: Our data suggests that blood flow patterns play an important role in regulating MerTK-mediated efferocytosis in aortic ECs, revealing a new promising therapeutic strategy with EC efferocytosis restoration to against atherosclerosis.
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Affiliation(s)
| | | | | | | | | | - Zufeng Ding
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
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108
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Zhang Y, Li H, Liu X, Li H, Lan Q, Wu H, Wang Y, Zhang J, Zhao X. Nuclear Receptor FTZ-F1 Controls Locust Molt by Regulating the Molting Process of Locusta migratoria. Insects 2024; 15:237. [PMID: 38667367 PMCID: PMC11050008 DOI: 10.3390/insects15040237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024]
Abstract
Fushi-tarazu factor 1 (FTZ-F1) is a class of transcription factors belonging to the nuclear receptor superfamily and an important molting regulator in insects; however, its detailed function in the molting process of Locusta migratoria is still unclear. This study identified two FTZ-F1 transcripts (LmFTZ-F1-X1 and LmFTZ-F1-X2) in L. migratoria. The classical domains of FTZ-F1 were present in their protein sequences and distinguished based on their variable N-terminal domains. Reverse-transcription quantitative polymerase chain reaction analysis revealed that LmFTZ-F1-X1 and LmFTZ-F1-X2 were highly expressed in the integument. RNA interference (RNAi) was used to explore the function of LmFTZ-F1s in the molting of the third-instar nymph. Separate LmFTZ-F1-X1 or LmFTZ-F1-X2 silencing did not affect the normal development of third-instar nymphs; however, the simultaneous RNAi of LmFTZ-F1-X1 and LmFTZ-F1-X2 caused the nymphs to be trapped in the third instar stage and finally die. Furthermore, the hematoxylin-eosin and chitin staining of the cuticle showed that the new cuticles were thickened after silencing the LmFTZ-F1s compared to the controls. RNA-seq analysis showed that genes encoding four cuticle proteins, two chitin synthesis enzymes, and cytochrome P450 303a1 were differentially expressed between dsGFP- and dsLmFTZ-F1s-injected groups. Taken together, LmFTZ-F1-X1 and LmFTZ-F1-X2 are involved in the ecdysis of locusts, possibly by regulating the expression of genes involved in cuticle formation, chitin synthesis, and other key molting processes.
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Affiliation(s)
- Yichao Zhang
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, China
- Shanxi Key Laboratory of Nucleic Acid Biopesticides, Taiyuan 030006, China
| | - Hongjing Li
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, China
- Shanxi Key Laboratory of Nucleic Acid Biopesticides, Taiyuan 030006, China
- College of Life Science, Shanxi University, Taiyuan 030006, China
| | - Xiaoman Liu
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, China
- Shanxi Key Laboratory of Nucleic Acid Biopesticides, Taiyuan 030006, China
- College of Life Science, Shanxi University, Taiyuan 030006, China
| | - Hongli Li
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, China
- Shanxi Key Laboratory of Nucleic Acid Biopesticides, Taiyuan 030006, China
- College of Life Science, Shanxi University, Taiyuan 030006, China
| | - Qiuyan Lan
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, China
- Shanxi Key Laboratory of Nucleic Acid Biopesticides, Taiyuan 030006, China
- College of Life Science, Shanxi University, Taiyuan 030006, China
| | - Haihua Wu
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, China
- Shanxi Key Laboratory of Nucleic Acid Biopesticides, Taiyuan 030006, China
| | - Yanli Wang
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, China
- Shanxi Key Laboratory of Nucleic Acid Biopesticides, Taiyuan 030006, China
| | - Jianzhen Zhang
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, China
- Shanxi Key Laboratory of Nucleic Acid Biopesticides, Taiyuan 030006, China
| | - Xiaoming Zhao
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, China
- Shanxi Key Laboratory of Nucleic Acid Biopesticides, Taiyuan 030006, China
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109
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Hirose A, Nakamura G, Nikaido M, Fujise Y, Kato H, Kishida T. Localized Expression of Olfactory Receptor Genes in the Olfactory Organ of Common Minke Whales. Int J Mol Sci 2024; 25:3855. [PMID: 38612665 PMCID: PMC11012115 DOI: 10.3390/ijms25073855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Baleen whales (Mysticeti) possess the necessary anatomical structures and genetic elements for olfaction. Nevertheless, the olfactory receptor gene (OR) repertoire has undergone substantial degeneration in the cetacean lineage following the divergence of the Artiodactyla and Cetacea. The functionality of highly degenerated mysticete ORs within their olfactory epithelium remains unknown. In this study, we extracted total RNA from the nasal mucosae of common minke whales (Balaenoptera acutorostrata) to investigate ORs' localized expression. All three sections of the mucosae examined in the nasal chamber displayed comparable histological structure. However, the posterior portion of the frontoturbinal region exhibited notably high OR expression. Neither the olfactory bulb nor the external skin exhibited the expression of these genes. Although this species possesses four intact non-class-2 ORs, all the ORs expressed in the nasal mucosae belong to class-2, implying the loss of aversion to specific odorants. These anatomical and genomic analyses suggest that ORs are still responsible for olfaction within the nasal region of baleen whales, enabling them to detect desirable scents such as prey and potential mating partners.
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Affiliation(s)
- Ayumi Hirose
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan;
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Gen Nakamura
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan;
| | | | - Hidehiro Kato
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
- The Institute of Cetacean Research, Tokyo 104-0055, Japan
| | - Takushi Kishida
- Museum of Natural and Environmental History, Shizuoka 422-8017, Japan;
- College of Bioresource Sciences, Nihon University, Fujisawa 252-0880, Japan
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110
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Cerav EN, Wu N, Akkaya MS. Transcriptome-Wide N6-Methyladenosine (m 6A) Methylation Analyses in a Compatible Wheat- Puccinia striiformis f. sp. tritici Interaction. Plants (Basel) 2024; 13:982. [PMID: 38611510 PMCID: PMC11013425 DOI: 10.3390/plants13070982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
N6-methyladenosine (m6A) is a prevalent internal modification in eukaryotic mRNA, tRNA, miRNA, and long non-coding RNA. It is also known for its role in plant responses to biotic and abiotic stresses. However, a comprehensive m6A transcriptome-wide map for Puccinia striiformis f. sp. tritici (Pst) infections in wheat (Triticum aestivum) is currently unavailable. Our study is the first to profile m6A modifications in wheat infected with a virulent Pst race. Analysis of RNA-seq and MeRIP-seq data revealed that the majority of differentially expressed genes are up-regulated and hyper-methylated. Some of these genes are enriched in the plant-pathogen interaction pathway. Notably, genes related to photosynthesis showed significant down-regulation and hypo-methylation, suggesting a potential mechanism facilitating successful Pst invasion by impairing photosynthetic function. The crucial genes, epitomizing the core molecular constituents that fortify plants against pathogenic assaults, were detected with varying expression and methylation levels, together with a newly identified methylation motif. Additionally, m6A regulator genes were also influenced by m6A modification, and their expression patterns varied at different time points of post-inoculation, with lower expression at early stages of infection. This study provides insights into the role of m6A modification regulation in wheat's response to Pst infection, establishing a foundation for understanding the potential function of m6A RNA methylation in plant resistance or susceptibility to pathogens.
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Affiliation(s)
| | | | - Mahinur S. Akkaya
- School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China; (E.N.C.); (N.W.)
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111
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Eid SA, Elzinga SE, Guo K, Hinder LM, Hayes JM, Pacut CM, Koubek EJ, Hur J, Feldman EL. Transcriptomic profiling of sciatic nerves and dorsal root ganglia reveals site-specific effects of prediabetic neuropathy. Transl Res 2024; 270:24-41. [PMID: 38556110 DOI: 10.1016/j.trsl.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/01/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
Peripheral neuropathy (PN) is a severe and frequent complication of obesity, prediabetes, and type 2 diabetes characterized by progressive distal-to-proximal peripheral nerve degeneration. However, a comprehensive understanding of the mechanisms underlying PN, and whether these mechanisms change during PN progression, is currently lacking. Here, gene expression data were obtained from distal (sciatic nerve; SCN) and proximal (dorsal root ganglia; DRG) injury sites of a high-fat diet (HFD)-induced mouse model of obesity/prediabetes at early and late disease stages. Self-organizing map and differentially expressed gene analyses followed by pathway enrichment analysis identified genes and pathways altered across disease stage and injury site. Pathways related to immune response, inflammation, and glucose and lipid metabolism were consistently dysregulated with HFD-induced PN, irrespective of injury site. However, regulation of oxidative stress was unique to the SCN while dysregulated Hippo and Notch signaling were only observed in the DRG. The role of the immune system and inflammation in disease progression was supported by an increase in the percentage of immune cells in the SCN with PN progression. Finally, when comparing these data to transcriptomic signatures from human patients with PN, we observed conserved pathways related to metabolic dysregulation across species, highlighting the translational relevance of our mouse data. Our findings demonstrate that PN is associated with distinct site-specific molecular re-programming in the peripheral nervous system, identifying novel, clinically relevant therapeutic targets.
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Affiliation(s)
- Stéphanie A Eid
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place 5017 AAT-BSRB, Ann Arbor, MI 48109, USA
| | - Sarah E Elzinga
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place 5017 AAT-BSRB, Ann Arbor, MI 48109, USA
| | - Kai Guo
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place 5017 AAT-BSRB, Ann Arbor, MI 48109, USA
| | - Lucy M Hinder
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place 5017 AAT-BSRB, Ann Arbor, MI 48109, USA
| | - John M Hayes
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place 5017 AAT-BSRB, Ann Arbor, MI 48109, USA
| | - Crystal M Pacut
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place 5017 AAT-BSRB, Ann Arbor, MI 48109, USA
| | - Emily J Koubek
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place 5017 AAT-BSRB, Ann Arbor, MI 48109, USA
| | - Junguk Hur
- Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, 1301 N Columbia Rd. Stop 9037. Rm 130W, Grand Forks, ND 58202, USA
| | - Eva L Feldman
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place 5017 AAT-BSRB, Ann Arbor, MI 48109, USA.
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112
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Costa FG, Mills KB, Crosby HA, Horswill AR. The Staphylococcus aureus regulatory program in a human skin-like environment. mBio 2024:e0045324. [PMID: 38546267 DOI: 10.1128/mbio.00453-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/04/2024] [Indexed: 04/09/2024] Open
Abstract
Staphylococcus aureus is a Gram-positive pathogen responsible for the majority of skin and soft tissue infections (SSTIs). S. aureus colonizes the anterior nares of approximately 20%-30% of the population and transiently colonizes the skin, thereby increasing the risk of developing SSTIs and more serious infections. Current laboratory models that mimic the skin surface environment are expensive, require substantial infrastructure, and limit the scope of bacterial physiology studies under human skin conditions. To overcome these limitations, we developed a cost-effective, open-source, chemically defined media recipe termed skin-like medium (SLM) that incorporates key aspects of the human skin surface environment and supports growth of several staphylococcal species. We utilized SLM to investigate the transcriptional response of methicillin-resistant Staphylococcus aureus (MRSA) following growth in SLM compared to a commonly used laboratory media. Through RNA-seq analysis, we observed the upregulation of several virulence factors, including genes encoding functions involved in adhesion, proteolysis, and cytotoxicity. To further explore these findings, we conducted quantitative reverse transcription-PCR (qRT-PCR) experiments to determine the influence of media composition, pH, and temperature on the transcriptional response of key factors involved in adhesion and virulence. We also demonstrated that MRSA primed in SLM adhered better to human corneocytes and demonstrated adhesin-specific phenotypes that previously required genetic manipulation. This improved adherence to corneocytes was dependent on both acidic pH and growth in SLM. These results support the potential utility of SLM as an in vitro model for assessing staphylococcal physiology and metabolism on human skin. IMPORTANCE Staphylococcus aureus is the major cause of skin diseases, and its increased prevalence in skin colonization and infections present a need to understand its physiology in this environment. The work presented here outlines S. aureus upregulation of colonization and virulence factors using a newly developed medium that strives to replicate the human skin surface environment and demonstrates roles for adhesins clumping factor A (ClfA), serine-rich repeat glycoprotein adhesin (SraP), and the fibronectin binding proteins (Fnbps) in human corneocyte adherence.
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Affiliation(s)
- Flavia G Costa
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Krista B Mills
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Heidi A Crosby
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alexander R Horswill
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Veterans Affairs, Eastern Colorado Healthcare System, Aurora, Colorado, USA
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113
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Holden AC, Cohen H, Berry HM, Rickett DV, Aharoni A, Fraser PD. Carotenoid retention during post-harvest storage of Capsicum annuum: the role of the fruit surface structure. J Exp Bot 2024; 75:1997-2012. [PMID: 38064717 DOI: 10.1093/jxb/erad482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 12/01/2023] [Indexed: 03/28/2024]
Abstract
In this study, a chilli pepper (Capsicum annuum) panel for post-harvest carotenoid retention was studied to elucidate underlying mechanisms associated with this commercial trait of interest. Following drying and storage, some lines within the panel had an increase in carotenoids approaching 50% compared with the initial content at the fresh fruit stage. Other lines displayed a 25% loss of carotenoids. The quantitative determination of carotenoid pigments with concurrent cellular analysis indicated that in most cases, pepper fruit with thicker (up to 4-fold) lipid exocarp layers and smooth surfaces exhibit improved carotenoid retention properties. Total cutin monomer content increased in medium/high carotenoid retention fruits and subepidermal cutin deposits were responsible for the difference in exocarp thickness. Cutin biosynthesis and cuticle precursor transport genes were differentially expressed between medium/high and low carotenoid retention genotypes, and this supports the hypothesis that the fruit cuticle can contribute to carotenoid retention. Enzymatic degradation of the cuticle and cell wall suggests that in Capsicum the carotenoids (capsanthin and its esters) are embedded in the lipidic exocarp layer. This was not the case in tomato. Collectively, the data suggest that the fruit cuticle could provide an exploitable resource for the enhancement of fruit quality.
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Affiliation(s)
- Alexandra C Holden
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Hagai Cohen
- Nella and Leon Benoziyo Building for Biological Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Harriet M Berry
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Daniel V Rickett
- Syngenta Ltd, Jealott's Hill International Research Centre, Bracknell RG42 6EY, UK
| | - Asaph Aharoni
- Nella and Leon Benoziyo Building for Biological Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
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114
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Brooks TG, Lahens NF, Mrčela A, Sarantopoulou D, Nayak S, Naik A, Sengupta S, Choi PS, Grant GR. BEERS2: RNA-Seq simulation through high fidelity in silico modeling. Brief Bioinform 2024; 25:bbae164. [PMID: 38605641 PMCID: PMC11009461 DOI: 10.1093/bib/bbae164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/26/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully length messenger RNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.
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Affiliation(s)
- Thomas G Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Soumyashant Nayak
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: Statistics and Mathematics Unit, Indian Statistical Institute, Bengaluru, Karnataka, India
| | - Amruta Naik
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shaon Sengupta
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Peter S Choi
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology & Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
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115
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Kilfeather P, Khoo JH, Wagner K, Liang H, Caiazza MC, An Y, Zhang X, Chen X, Connor-Robson N, Shang Z, Wade-Martins R. Single-cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging, and disease. Cell Rep 2024; 43:113784. [PMID: 38386560 DOI: 10.1016/j.celrep.2024.113784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 11/14/2023] [Accepted: 01/27/2024] [Indexed: 02/24/2024] Open
Abstract
The brain is spatially organized and contains unique cell types, each performing diverse functions and exhibiting differential susceptibility to neurodegeneration. This is exemplified in Parkinson's disease with the preferential loss of dopaminergic neurons of the substantia nigra pars compacta. Using a Parkinson's transgenic model, we conducted a single-cell spatial transcriptomic and dopaminergic neuron translatomic analysis of young and old mouse brains. Through the high resolving capacity of single-cell spatial transcriptomics, we provide a deep characterization of the expression features of dopaminergic neurons and 27 other cell types within their spatial context, identifying markers of healthy and aging cells, spanning Parkinson's relevant pathways. We integrate gene enrichment and genome-wide association study data to prioritize putative causative genes for disease investigation, identifying CASR as a regulator of dopaminergic calcium handling. These datasets represent the largest public resource for the investigation of spatial gene expression in brain cells in health, aging, and disease.
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Affiliation(s)
- Peter Kilfeather
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | | | - Katherina Wagner
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | | | - Maria Claudia Caiazza
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Yanru An
- BGI Research, 49276 Riga, Latvia
| | | | | | - Natalie Connor-Robson
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | | | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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116
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Kahar G, Haxim Y, Waheed A, Bozorov TA, Liu X, Wen X, Zhao M, Zhang D. Multi-Omics Approaches Provide New Insights into the Identification of Putative Fungal Effectors from Valsa mali. Microorganisms 2024; 12:655. [PMID: 38674600 PMCID: PMC11051974 DOI: 10.3390/microorganisms12040655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Pathogenic fungi secrete numerous effectors into host cells to manipulate plants' defense mechanisms. Valsa mali, a necrotrophic fungus, severely impacts apple production in China due to the occurrence of Valsa canker. Here, we predicted 210 candidate effector protein (CEP)-encoding genes from V. mali. The transcriptome analysis revealed that 146 CEP-encoding genes were differentially expressed during the infection of the host, Malus sieversii. Proteome analysis showed that 27 CEPs were differentially regulated during the infection stages. Overall, 25 of the 146 differentially expressed CEP-encoding genes were randomly selected to be transiently expressed in Nicotiana benthamiana. Pathogenicity analysis showed that the transient expression of VM1G-05058 suppressed BAX-triggered cell death while the expression of VM1G-10148 and VM1G-00140 caused cell death in N. benthamiana. In conclusion, by using multi-omics analysis, we identified potential effector candidates for further evaluation in vivo. Our results will provide new insights into the investigation of virulent mechanisms of V. mali.
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Affiliation(s)
- Gulnaz Kahar
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yakupjan Haxim
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Abdul Waheed
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Tohir A. Bozorov
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Laboratory of Molecular and Biochemical Genetics, Institute of Genetics and Plants Experimental Biology, Uzbek Academy of Sciences, Yukori-Yuz, Kibray 111226, Tashkent Region, Uzbekistan
| | - Xiaojie Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Xuejing Wen
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Mingqi Zhao
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
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Erdogdu B, Varabyou A, Hicks SC, Salzberg SL, Pertea M. Detecting differential transcript usage in complex diseases with SPIT. Cell Rep Methods 2024; 4:100736. [PMID: 38508189 PMCID: PMC10985272 DOI: 10.1016/j.crmeth.2024.100736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/21/2023] [Accepted: 02/27/2024] [Indexed: 03/22/2024]
Abstract
Differential transcript usage (DTU) plays a crucial role in determining how gene expression differs among cells, tissues, and developmental stages, contributing to the complexity and diversity of biological systems. In abnormal cells, it can also lead to deficiencies in protein function and underpin disease pathogenesis. Analyzing DTU via RNA sequencing (RNA-seq) data is vital, but the genetic heterogeneity in populations with complex diseases presents an intricate challenge due to diverse causal events and undetermined subtypes. Although the majority of common diseases in humans are categorized as complex, state-of-the-art DTU analysis methods often overlook this heterogeneity in their models. We therefore developed SPIT, a statistical tool that identifies predominant subgroups in transcript usage within a population along with their distinctive sets of DTU events. This study provides comprehensive assessments of SPIT's methodology and applies it to analyze brain samples from individuals with schizophrenia, revealing previously unreported DTU events in six candidate genes.
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Affiliation(s)
- Beril Erdogdu
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA.
| | - Ales Varabyou
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Stephanie C Hicks
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA
| | - Steven L Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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118
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Kaplan HG, Dowdell AK, Berry AB, Shimol RB, Robinson FL, Carney CA, Piening BD. Multi-omic profiling of simultaneous ductal carcinoma in situ and invasive breast cancer. Breast Cancer Res Treat 2024:10.1007/s10549-024-07270-5. [PMID: 38523186 DOI: 10.1007/s10549-024-07270-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/24/2024] [Indexed: 03/26/2024]
Abstract
PURPOSE The progression of ductal carcinoma in situ (DCIS) to invasive breast carcinoma (IBC) in humans is highly variable. To better understand the relationship between them, we performed a multi-omic characterization of co-occurring DCIS and IBC lesions in a cohort of individuals. METHODS Formalin-fixed paraffin-embedded tissue samples from 50 patients with co-occurring DCIS and IBC lesions were subjected to DNA-seq and whole transcriptome RNA-seq. Paired DCIS and IBC multi-omics profiles were then interrogated for DNA mutations, gene expression profiles and pathway analysis. RESULTS Most small variants and copy number variations were shared between co-occurring DCIS and IBC lesions, with IBC exhibiting on average a higher degree of additional mutations. However, 36% of co-occurring lesions shared no common mutations and 49% shared no common copy number variations. The most frequent genomic variants in both DCIS and IBC were PIK3CA, TP53, KMT2C, MAP3K1, GATA3 and SF3B1, with KMT2C being more frequent in DCIS and TP53 and MAP3K1 more frequent in IBC, though the numbers are too small for definitive conclusions. The most frequent copy number variations were seen in MCL1, CKSB1 and ERBB2. ERBB2 changes were not seen in IBC unless present in the corresponding DCIS. Transcriptional profiles were highly distinct between DCIS and IBC, with DCIS exhibiting upregulation of immune-related signatures, while IBC showed significant overexpression in genes and pathways associated with cell division and proliferation. Interestingly, DCIS and IBC exhibited significant differential expression of different components of extracellular matrix (ECM) formation and regulation, with DCIS showing overexpression of ECM-membrane interaction components while IBC showed upregulation of genes associated with fibronectin and invadopodia. CONCLUSION While most co-occurring DCIS and IBC were mutationally similar and suggestive of a common clonal progenitor, transcriptionally the lesions are highly distinct, with IBC expressing key pathways that facilitate invasion and proliferation. These results are suggestive of additional levels of regulation, epigenetic or other, that facilitate the acquisition of invasive properties during tumor evolution.
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Affiliation(s)
- Henry G Kaplan
- Swedish Cancer Institute, 1221 Madison St., Suite 920, Seattle, WA, 98104, USA.
| | - Alexa K Dowdell
- Earle A. Chiles Research Institute, Providence Health, Portland, OR, 97213, USA
| | - Anna B Berry
- Swedish Cancer Institute, 1221 Madison St., Suite 920, Seattle, WA, 98104, USA
| | - Racheli Ben Shimol
- Earle A. Chiles Research Institute, Providence Health, Portland, OR, 97213, USA
| | - Fred L Robinson
- Earle A. Chiles Research Institute, Providence Health, Portland, OR, 97213, USA
| | | | - Brian D Piening
- Earle A. Chiles Research Institute, Providence Health, Portland, OR, 97213, USA
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Ito T, Rojasawasthien T, Takeuchi SY, Okamoto H, Okumura N, Shirakawa T, Matsubara T, Kawamoto T, Kokabu S. Royal Jelly Enhances the Ability of Myoblast C2C12 Cells to Differentiate into Multilineage Cells. Molecules 2024; 29:1449. [PMID: 38611729 PMCID: PMC11013243 DOI: 10.3390/molecules29071449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Royal jelly (RJ) is recognized as beneficial to mammalian health. Multilineage differentiation potential is an important property of mesenchymal stem cells (MSCs). C2C12 cells have an innate ability to differentiate into myogenic cells. Like MSCs, C2C12 cells can also differentiate into osteoblast- and adipocyte-lineage cells. We recently reported that RJ enhances the myogenic differentiation of C2C12 cells. However, the effect of RJ on osteoblast or adipocyte differentiation is still unknown. Here in this study, we have examined the effect of RJ on the osteoblast and adipocyte differentiation of C2C12 cells. Protease-treated RJ was used to reduce the adverse effects caused by RJ supplementation. To induce osteoblast or adipocyte differentiation, cells were treated with bone morphogenetic proteins (BMP) or peroxisome proliferator-activated receptor γ (PPARγ) agonist, respectively. RNA-seq was used to analyze the effect of RJ on gene expression. We found that RJ stimulates osteoblast and adipocyte differentiation. RJ regulated 279 genes. RJ treatment upregulated glutathione-related genes. Glutathione, the most abundant antioxidative factor in cells, has been shown to promote osteoblast differentiation in MSC and MSC-like cells. Therefore, RJ may promote osteogenesis, at least in part, through the antioxidant effects of glutathione. RJ enhances the differentiation ability of C2C12 cells into multiple lineages, including myoblasts, osteoblasts, and adipocytes.
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Affiliation(s)
- Takumi Ito
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Fukuoka 803-8580, Japan; (T.I.); (T.R.); (S.Y.T.); (T.M.)
- Division of Orofacial Functions and Orthodontics, Kyushu Dental University, Fukuoka 803-8580, Japan; (T.S.); (T.K.)
| | - Thira Rojasawasthien
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Fukuoka 803-8580, Japan; (T.I.); (T.R.); (S.Y.T.); (T.M.)
| | - Sachiko Yamashita Takeuchi
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Fukuoka 803-8580, Japan; (T.I.); (T.R.); (S.Y.T.); (T.M.)
| | - Hideto Okamoto
- Institute for Bee Products and Health Science, Yamada Bee Company, Inc., Okayama 708-0393, Japan; (H.O.); (N.O.)
| | - Nobuaki Okumura
- Institute for Bee Products and Health Science, Yamada Bee Company, Inc., Okayama 708-0393, Japan; (H.O.); (N.O.)
| | - Tomohiko Shirakawa
- Division of Orofacial Functions and Orthodontics, Kyushu Dental University, Fukuoka 803-8580, Japan; (T.S.); (T.K.)
| | - Takuma Matsubara
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Fukuoka 803-8580, Japan; (T.I.); (T.R.); (S.Y.T.); (T.M.)
| | - Tatsuo Kawamoto
- Division of Orofacial Functions and Orthodontics, Kyushu Dental University, Fukuoka 803-8580, Japan; (T.S.); (T.K.)
| | - Shoichiro Kokabu
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Fukuoka 803-8580, Japan; (T.I.); (T.R.); (S.Y.T.); (T.M.)
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Papanikolaou AS, Papaefthimiou D, Matekalo D, Karakousi CV, Makris AM, Kanellis AK. Chemical and transcriptomic analysis of leaf trichomes from Cistus creticus subsp. creticus reveal the biosynthetic pathways of certain labdane-type diterpenoids and their acetylated forms. J Exp Bot 2024:erae098. [PMID: 38520311 DOI: 10.1093/jxb/erae098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Indexed: 03/25/2024]
Abstract
Labdane-related diterpenoids (LRDs), a subgroup of terpenoids, exhibit structural diversity and significant commercial and pharmacological potential. LRDs share the characteristic decalin-labdanic core structure that derives from the cycloisomerization of geranylgeranyl diphosphate (GGPP). Labdanes derive their name from the oleoresin known as "Labdanum," "Ladano" or "Aladano, used since ancient Greek times. Acetylated labdanes, rarely identified in plants, are associated with enhanced biological activities. Chemical analysis of C. creticus subsp. creticus revealed labda-7,13(Ε)-dien-15-yl acetate and labda-7,13(Ε)-dien-15-ol as major constituents. In addition, novel labdanes such as cis-abienol, neoabienol, ent-copalol, and one yet unidentified labdane-type diterpenoid were detected for the first time. These compounds exhibit developmental regulation, with higher accumulation observed in young leaves. Using RNA-sequencing (RNA-seq) analysis of young leaf trichomes, it was possible to identify, clone, and eventually functionally characterize labdane-type diterpenoid synthase (diTPS) genes, encoding proteins responsible for the production of labda-7,13(Ε)-dien-15-yl diphosphate (endo-7,13-CPP), labda-7,13(Ε)-dien-15-yl acetate, and labda-13(Ε)-ene-8α-ol-15-yl acetate. Moreover, the reconstitution of labda-7,13(Ε)-dien-15-yl acetate and labda-13(Ε)-ene-8α-ol-15-yl acetate production in yeast is presented. Finally, the accumulation of LRDs in different plant tissues showed correlation with the expression profiles of the corresponding genes.
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Affiliation(s)
- Antigoni S Papanikolaou
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Macedonia, Greece
| | - Dimitra Papaefthimiou
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Macedonia, Greece
| | - Dragana Matekalo
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Macedonia, Greece
| | - Christina-Vasiliki Karakousi
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Macedonia, Greece
| | - Antonios M Makris
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), 57001 Thessaloniki, Macedonia, Greece
| | - Angelos K Kanellis
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Macedonia, Greece
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Zhao S, Zhang Q, Xiao W, Chen D, Hu J, Gao N, Huang M, Ye X. Comparison of Transcriptome Differences between Two Rice Cultivars Differing in Cadmium Translocation from Spike-Neck to Grain. Int J Mol Sci 2024; 25:3592. [PMID: 38612404 PMCID: PMC11011891 DOI: 10.3390/ijms25073592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
At present, the mechanism of varietal differences in cadmium (Cd) accumulation in rice is not well understood. Two rice cultivars, ZZY (high translocation-high grain Cd) and SJ18 (low translocation-low grain Cd), were used to analyze transcriptome differences in the spike-neck tissue in field trials. The results showed that, compared with ZZY, 22,367 differentially expressed genes (DEGs) were identified in SJ18, including 2941 upregulated and 19,426 downregulated genes. GO analysis enriched 59 downregulated terms, concerning 24 terms enriched for more than 1000 DEGs, including cellular and metabolic processes, biological regulation, localization, catalytic activity, transporter activity, signaling, etc. KEGG enrichment identified 21 significant downregulated pathways, regarding the ribosome, metabolic pathways, biosynthesis of secondary metabolism, signaling transduction, cell membrane and cytoskeleton synthesis, genetic information transfer, amino acid synthesis, etc. Weighted gene co-expression network analysis (WGCNA) revealed that these DEGs could be clustered into five modules. Among them, the yellow module was significantly related to SJ18 with hub genes related to OsHMA and OsActin, whereas the brown module was significantly related to ZZY with hub genes related to mitogen-activated protein kinase (MAPK), CBS, and glutaredoxin. This suggests that different mechanisms are involved in the process of spike-neck-grain Cd translocation among varieties. This study provides new insights into the mechanisms underlying differences in Cd transport among rice varieties.
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Affiliation(s)
| | | | | | | | | | | | | | - Xuezhu Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.Z.); (Q.Z.); (W.X.); (D.C.); (J.H.); (N.G.); (M.H.)
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Lv Z, Lan G, Bai B, Yu P, Wang C, Zhang H, Zhong C, Zhao X, Yu H. Identification of candidate genes associated with peanut pod length by combined analysis of QTL-seq and RNA-seq. Genomics 2024; 116:110835. [PMID: 38521201 DOI: 10.1016/j.ygeno.2024.110835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 03/25/2024]
Abstract
Pod length (PL) is one of the major traits determining pod size and yield of peanut. Discovering the quantitative trait loci (QTL) and identifying candidate genes associated with PL are essential for breeding high-yield peanut. In this study, quantitative trait loci sequencing (QTL-seq) was performed using the F2 population constructed by a short-pod variety Tifrunner (Tif) and a long-pod line Lps, and a 0.77 Mb genomic region on chromosome 07 was identified as the candidate region for PL. Then, the candidate region was narrowed to a 265.93 kb region by traditional QTL approach. RNA-seq analysis showed that there were four differentially expressed genes (DEGs) in the candidate region, among which Arahy.PF2L6F (AhCDC48) and Arahy.P4LK2T (AhTAA1) were speculated to be PL-related candidate genes. These results were informative for the elucidation of the underlying regulatory mechanism in peanut pod length and would facilitate further identification of valuable target genes.
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Affiliation(s)
- Zhenghao Lv
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Guohu Lan
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Baiyi Bai
- College of Agriculture and Horticulture, Liaoning Agriculture Ovcational and Technical College, Yingkou 115009, China
| | - Penghao Yu
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Chuantang Wang
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; Shandong Peanut Research Institute, Qingdao 266100, China
| | - He Zhang
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Chao Zhong
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Xinhua Zhao
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Haiqiu Yu
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; College of Agriculture and Horticulture, Liaoning Agriculture Ovcational and Technical College, Yingkou 115009, China.
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Xiao Y, Qin T, He S, Chen Y, Li H, He Q, Wang X, Yang S. Systematic investigation of TetR-family transcriptional regulators and their roles on lignocellulosic inhibitor acetate tolerance in Zymomonas mobilis. Front Bioeng Biotechnol 2024; 12:1385519. [PMID: 38585710 PMCID: PMC10998469 DOI: 10.3389/fbioe.2024.1385519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/14/2024] [Indexed: 04/09/2024] Open
Abstract
TetR-family transcriptional regulators are widely distributed among bacteria and involved in various cellular processes such as multidrug and inhibitor resistance. Zymomonas mobilis is a industrial bacterium for lignocellulosic ethanol production. Although TetR-family regulators and their associated RND-family efflux pumps in Z. mobilis have been identified to be differentially expressed under various inhibitors and stressful conditions, there are no systematic investigation yet. In this study, bioinformatic analyses indicated that there are three TetR-family transcriptional regulators (ZMO0281, ZMO0963, ZMO1547) and two RND-family efflux pumps (ZMO0282-0285, ZMO0964-0966) adjacent to corresponding TetR-family regulators of ZMO0281 and ZMO0963 in Z. mobilis. Genetics studies were then carried out with various mutants of TetR-family regulators constructed, and ZMO0281 was characterized to be related to acetate tolerance. Combining transcriptomics and dual-reporter gene system, this study demonstrated that three TetR-family regulators repressed their adjacent genes specifically. Moreover, TetR-family regulator ZMO0281 might also be involved in other cellular processes in the presence of acetate. In addition, the upregulation of RND-family efflux pumps due to ZMO0281 deletion might lead to an energy imbalance and decreased cell growth in Z. mobilis under acetate stress. The systematic investigation of all three TetR-family regulators and their roles on a major lignocellulosic inhibitor acetate tolerance in Z. mobilis thus not only unravels the molecular mechanisms of TetR-family regulators and their potential cross-talks on regulating RND-family efflux pumps and other genes in Z. mobilis, but also provides guidance on understanding the roles of multiple regulators of same family in Z. mobilis and other microorganisms for efficient lignocellulosic biochemical production.
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Affiliation(s)
- Yubei Xiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Tongjia Qin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
- Chinese Medicine College, Guangdong Yunfu Vocational College of Chinese Medicine, Guangzhou, Guangdong, China
| | - Shuche He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Yunhao Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Han Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Qiaoning He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Xia Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
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Agrawal S, Tran MT, Jennings TSK, Soliman MMH, Heo S, Sasson B, Rahmatpanah F, Agrawal A. Changes in the innate immune response to SARS-CoV-2 with advancing age in humans. Immun Ageing 2024; 21:21. [PMID: 38515147 PMCID: PMC10956333 DOI: 10.1186/s12979-024-00426-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/12/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND Advancing age is a major risk factor for respiratory viral infections. The infections are often prolonged and difficult to resolve resulting hospitalizations and mortality. The recent COVID-19 pandemic has highlighted this as elderly subjects have emerged as vulnerable populations that display increased susceptibility and severity to SARS-CoV-2. There is an urgent need to identify the probable mechanisms underlying this to protect against future outbreaks of such nature. Innate immunity is the first line of defense against viruses and its decline impacts downstream immune responses. This is because dendritic cells (DCs) and macrophages are key cellular elements of the innate immune system that can sense and respond to viruses by producing inflammatory mediators and priming CD4 and CD8 T-cell responses. RESULTS We investigated the changes in innate immune responses to SARS-CoV-2 as a function of age. Our results using human PBMCs from aged, middle-aged, and young subjects indicate that the activation of DCs and monocytes in response to SARS-CoV-2 is compromised with age. The impairment is most apparent in pDCs where both aged and middle-aged display reduced responses. The secretion of IL-29 that confers protection against respiratory viruses is also decreased in both aged and middle-aged subjects. In contrast, inflammatory mediators associated with severe COVID-19 including CXCL-8, TREM-1 are increased with age. This is also apparent in the gene expression data where pathways related host defense display an age dependent decrease with a concomitant increase in inflammatory pathways. Not only are the inflammatory pathways and mediators increased after stimulation with SARS-CoV-2 but also at homeostasis. In keeping with reduced DC activation, the induction of cytotoxic CD8 T cells is also impaired in aged subjects. However, the CD8 T cells from aged subjects display increased baseline activation in accordance with the enhanced baseline inflammation. CONCLUSIONS Our results demonstrate a decline in protective anti-viral immune responses and increase in damaging inflammatory responses with age indicating that dysregulated innate immune responses play a significant role in the increased susceptibility of aged subjects to COVID-19. Furthermore, the dysregulation in immune responses develops early on as middle-aged demonstrate several of these changes.
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Affiliation(s)
- Sudhanshu Agrawal
- Division of Basic and Clinical Immunology, Department of Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Michelle Thu Tran
- Division of Basic and Clinical Immunology, Department of Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | | | - Marlaine Maged Hosny Soliman
- Division of Basic and Clinical Immunology, Department of Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Sally Heo
- Division of Basic and Clinical Immunology, Department of Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Bobby Sasson
- Department of Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Farah Rahmatpanah
- Department of Pathology, University of California Irvine, Irvine, CA, 92697, USA
| | - Anshu Agrawal
- Division of Basic and Clinical Immunology, Department of Medicine, University of California Irvine, Irvine, CA, 92697, USA.
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Travisano SI, Lien CL. Protocol for the isolation and single-nuclei multiomic analyses of the human fetal epicardium. STAR Protoc 2024; 5:102973. [PMID: 38517898 PMCID: PMC10978535 DOI: 10.1016/j.xpro.2024.102973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/18/2024] [Accepted: 03/04/2024] [Indexed: 03/24/2024] Open
Abstract
The characterization of cell populations that reside in the outer layer of the heart has been hindered by difficulties in their isolation. Here, we present a protocol for isolation and single-nuclei multiomic analyses of the human fetal epicardium. We describe steps for microdissection, isolation, and enrichment of epicardial cells by mechanical dissociations and direct lysis. We then detail procedures for integrating transcriptome and chromatin accessibility datasets. This approach allows the analysis of diverse cell populations, marked by unique cis-regulatory elements. For complete details on the use and execution of this protocol, please refer to Travisano et al.1.
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Affiliation(s)
| | - Ching-Ling Lien
- The Saban Research Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Departments of Surgery, Biochemistry, and Molecular Medicine, Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Pressl C, Mätlik K, Kus L, Darnell P, Luo JD, Paul MR, Weiss AR, Liguore W, Carroll TS, Davis DA, McBride J, Heintz N. Selective vulnerability of layer 5a corticostriatal neurons in Huntington's disease. Neuron 2024; 112:924-941.e10. [PMID: 38237588 DOI: 10.1016/j.neuron.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/18/2023] [Accepted: 12/13/2023] [Indexed: 01/30/2024]
Abstract
The properties of the cell types that are selectively vulnerable in Huntington's disease (HD) cortex, the nature of somatic CAG expansions of mHTT in these cells, and their importance in CNS circuitry have not been delineated. Here, we employed serial fluorescence-activated nuclear sorting (sFANS), deep molecular profiling, and single-nucleus RNA sequencing (snRNA-seq) of motor-cortex samples from thirteen predominantly early stage, clinically diagnosed HD donors and selected samples from cingulate, visual, insular, and prefrontal cortices to demonstrate loss of layer 5a pyramidal neurons in HD. Extensive mHTT CAG expansions occur in vulnerable layer 5a pyramidal cells, and in Betz cells, layers 6a and 6b neurons that are resilient in HD. Retrograde tracing experiments in macaque brains identify layer 5a neurons as corticostriatal pyramidal cells. We propose that enhanced somatic mHTT CAG expansion and altered synaptic function act together to cause corticostriatal disconnection and selective neuronal vulnerability in HD cerebral cortex.
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Affiliation(s)
- Christina Pressl
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Kert Mätlik
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Laura Kus
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Paul Darnell
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Alison R Weiss
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, USA
| | - William Liguore
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - David A Davis
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jodi McBride
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Nathaniel Heintz
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA.
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127
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Iguchi A, Hayashi M, Yorifuji M, Nishijima M, Gibu K, Kunishima T, Bell T, Suzuki A, Ono T. Whole transcriptome analysis of demersal fish eggs reveals complex responses to ocean deoxygenation and acidification. Sci Total Environ 2024; 917:169484. [PMID: 38302347 DOI: 10.1016/j.scitotenv.2023.169484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 11/20/2023] [Accepted: 12/16/2023] [Indexed: 02/03/2024]
Abstract
Ocean acidification and deoxygenation co-occur in marine environments, causing deterioration of marine ecosystems. However, effects of compound stresses on marine organisms and their physiological coping mechanisms are largely unknown. Here, we show how high pCO2 and low dissolved oxygen (DO) cause transcriptomic changes in eggs of a demersal fish (Sillago japonica), which are fully exposed to such stresses in natural environment. Overall gene expression was affected more strongly by low DO than by high pCO2. Enrichment analysis detected significant stress responses such as glycolytic processes in response to low DO. Increased expression of a group of glycolytic genes under low DO conditions is presumably because oxygen depletion disables the electron transfer pathway, complementing ATP production in the glycolytic pathway. Contrary to expectations, apparent mitigation of gene expression changes was dominant under combined stress conditions, and may represent an innate fish adaptive trait for severe environments.
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Affiliation(s)
- Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan; Research Laboratory on Environmentally-conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan.
| | - Masahiro Hayashi
- Demonstration Laboratory, Marine Ecology Research Institute, 4-7-17 Arahama, Kashiwazaki, Niigata 945-0017, Japan
| | - Makiko Yorifuji
- Demonstration Laboratory, Marine Ecology Research Institute, 4-7-17 Arahama, Kashiwazaki, Niigata 945-0017, Japan
| | - Miyuki Nishijima
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Kodai Gibu
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Taiga Kunishima
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan; Laboratory of Marine Biology, Division of Applied Biological Science, Faculty of Agriculture, Setsunan University, Hirakata, Japan
| | - Tomoko Bell
- Division of Science and Mathmatics, Newman University, Wichita 67213, KS, USA
| | - Atsushi Suzuki
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan; Research Laboratory on Environmentally-conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan
| | - Tsuneo Ono
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
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128
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Williams-Simon PA, Oster C, Moaton JA, Ghidey R, Ng'oma E, Middleton KM, King EG. Naturally segregating genetic variants contribute to thermal tolerance in a Drosophila melanogaster model system. Genetics 2024:iyae040. [PMID: 38506092 DOI: 10.1093/genetics/iyae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/11/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Thermal tolerance is a fundamental physiological complex trait for survival in many species. For example, everyday tasks such as foraging, finding a mate, and avoiding predation, are highly dependent on how well an organism can tolerate extreme temperatures. Understanding the general architecture of the natural variants within the genes that control this trait is of high importance if we want to better comprehend thermal physiology. Here, we take a multipronged approach to further dissect the genetic architecture that controls thermal tolerance in natural populations using the Drosophila Synthetic Population Resource (DSPR) as a model system. First, we used quantitative genetics and Quantitative Trait Loci (QTL) mapping to identify major effect regions within the genome that influences thermal tolerance, then integrated RNA-sequencing to identify differences in gene expression, and lastly, we used the RNAi system to 1) alter tissue-specific gene expression and 2) functionally validate our findings. This powerful integration of approaches not only allows for the identification of the genetic basis of thermal tolerance but also the physiology of thermal tolerance in a natural population, which ultimately elucidates thermal tolerance through a fitness-associated lens.
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Affiliation(s)
- Patricka A Williams-Simon
- Postdoctoral Research Associate, University of Pennsylvania, 433 S University Ave., 226 Leidy Laboratories, Philadelphia, PA 19104, USA
| | - Camille Oster
- Habitat Restoration Specialist, Ash Creek Forest Management, 2796 SE 73rd Ave., Hillsboro, OR 97123, USA
| | - Jordyn A Moaton
- Research Assistant, University of Missouri, 2035 W Wellington Ave., Chicago, IL 60618, USA
| | - Ronel Ghidey
- Biostatistician, ECHO Data Analysis Center, Johns Hopkins Bloomberg School of Public Health, 504 Cathedral St., Baltimore, MD 2120, USA
| | - Enoch Ng'oma
- Assistant Professor of Biological Sciences, University of Missouri, Division of Biology, 226 Tucker Hall, Columbia, MO 65211, USA
| | - Kevin M Middleton
- Associate Professor of Biological Sciences, University of Missouri, 222 Tucker Hall, Columbia, MO 65211, USA
| | - Elizabeth G King
- Associate Professor of Biological Sciences, University of Missouri, 401 Tucker Hall, Columbia, MO 65211, USA
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129
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Ganesan S, Cortés-López M, Swett AD, Dai X, Hickey S, Chamely P, Hawkins AG, Juul S, Landau DA, Gaiti F. GoT-Splice protocol for multi-omics profiling of gene expression, cell-surface proteins, mutational status, and RNA splicing in human cells. STAR Protoc 2024; 5:102966. [PMID: 38512867 DOI: 10.1016/j.xpro.2024.102966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/25/2024] [Accepted: 03/04/2024] [Indexed: 03/23/2024] Open
Abstract
Studying RNA splicing factor mutations is challenging due to difficulties in distinguishing wild-type and mutant cells within complex human tissues and inaccuracies associated with reconstructing splicing signals from short-read sequencing data. Here, we present Genotyping of Transcriptomes (GoT)-Splice, a protocol that overcomes these limitations by combining GoT with enhanced long-read single-cell transcriptome and cell-surface proteomics profiling. We describe steps for long-read library preparation and analysis, followed by cDNA re-amplification, enrichment of mutation of interest, sample indexing, and GoT library preparation. For complete details on the use and execution of this protocol, please refer to Cortés-López et al.1.
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Affiliation(s)
- Saravanan Ganesan
- New York Genome Center, New York, NY 10013, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Mariela Cortés-López
- New York Genome Center, New York, NY 10013, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ariel D Swett
- New York Genome Center, New York, NY 10013, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Xiaoguang Dai
- Oxford Nanopore Technologies Inc., New York, NY 10013, USA
| | - Scott Hickey
- Oxford Nanopore Technologies Inc., Alameda, CA 94501-1170, USA
| | - Paulina Chamely
- New York Genome Center, New York, NY 10013, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Allegra G Hawkins
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation for Childhood Cancer, Wynnewood, PA 19096, USA
| | - Sissel Juul
- Oxford Nanopore Technologies Inc., New York, NY 10013, USA
| | - Dan A Landau
- New York Genome Center, New York, NY 10013, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Federico Gaiti
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON M5G 0A3, Canada; University of Toronto, Medical Biophysics, Toronto, ON M5G 1L7, Canada.
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130
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Zhang X, Zhang M, Li Y, Jiang Y. Comprehensive transcriptional analysis of early dorsal skin development in pigs. Gene 2024; 899:148141. [PMID: 38184019 DOI: 10.1016/j.gene.2024.148141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/11/2023] [Accepted: 01/03/2024] [Indexed: 01/08/2024]
Abstract
Porcine skin is similar to human skin in physiology, anatomy and histology and is often used as a model animal for human skin research. There are few studies on the transcriptome aspects of pig skin during the embryonic period. In this study, RNA sequencing was performed on the dorsal skin of Chenghua sows at embryonic day 56 (E56), embryonic day 76 (E76), embryonic day 105 (E105), and 3 days after birth (D3) to explore RNA changes in pig dorsal skin at four ages. A number of skin-related differential genes were identified by intercomparison between RNAs at four time points, and KEGG functional analysis showed that these differential genes were mainly enriched in metabolic and developmental, immune, and disease pathways, and the pathways enriched in GO analysis were highly overlapping. Collagen is an important part of the skin, with type I collagen making up the largest portion. In this study, collagen type I alpha 1 (COL1A1) and collagen type I alpha 2 (COL1A2) were significantly upregulated at four time points. In addition, lncRNA-miRNA-mRNA and miRNA-circRNA coexpression networks were constructed. The data obtained may help to explain age-related changes in transcriptional patterns during skin development and provide further references for understanding human skin development at the molecular level.
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Affiliation(s)
- Xinyue Zhang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an 625014, Sichuan, China
| | - Mei Zhang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an 625014, Sichuan, China
| | - Yujing Li
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an 625014, Sichuan, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
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131
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Li X, Cai J, Zhang H, Sun S, Zhao S, Wang Z, Nie X, Xu C, Zhang Y, Xiao H. A Trisulfide Bond Containing Biodegradable Polymer Delivering Pt(IV) Prodrugs to Deplete Glutathione and Donate H 2S to Boost Chemotherapy and Antitumor Immunity. ACS Nano 2024; 18:7852-7867. [PMID: 38437513 DOI: 10.1021/acsnano.3c06194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
The clinical application of cisplatin (CisPt) is limited by its dose-dependent toxicity. To overcome this, we developed reduction-responsive nanoparticles (NP(3S)s) for the targeted delivery of a platinum(IV) (Pt(IV)) prodrug to improve efficacy and reduce the toxicity. NP(3S)s could release Pt(II) and hydrogen sulfide (H2S) upon encountering intracellular glutathione, leading to potent anticancer effects. Notably, NP(3S)s induced DNA damage and activated the STING pathway, which is a known promoter for T cell activation. Comparative RNA profiling revealed that NP(3S)s outperformed CisPt in enhancing T cell immunity, antitumor immunity, and oxidative stress pathways. In vivo experiments showed that NP(3S)s accumulated in tumors, promoting CD8+ T cell infiltration and boosting antitumor immunity. Furthermore, NP(3S)s exhibited robust in vivo anticancer efficacy while minimizing the CisPt-induced liver toxicity. Overall, the results indicate NP(3S)s hold great promise for clinical translation due to their low toxicity profile and potent anticancer activity.
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Affiliation(s)
- Xinyi Li
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jing Cai
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hanchen Zhang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si Sun
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Simei Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zehua Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xiu Nie
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Chun Xu
- School of Dentistry, The University of Queensland, Brisbane 4006, Australia
| | - Yuan Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, University of Chinese Academy of Sciences, Beijing 100049, China
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132
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Xiong X, Xie C, Li S, Wang Y, Jiang J, Xie D, Chen S, Xiong Y, Gan L. PvGeneExpDB: An integrative gene expression database for in-depth understanding on the Pacific white shrimp (Litopenaeus vannamei). Comp Biochem Physiol Part D Genomics Proteomics 2024; 50:101227. [PMID: 38518736 DOI: 10.1016/j.cbd.2024.101227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/27/2024] [Accepted: 03/17/2024] [Indexed: 03/24/2024]
Abstract
The Pacific white shrimp (Litopenaeus vannamei) is a high-valued economic farming species. With the development of high-throughput sequencing technology, cumulative large-scale transcriptomic studies have been revealing molecular landscape of various biological conditions including genetic selection, breeding, evolution, disease landscape, etc. However, no single experiment or databases allow thorough investigations of transcriptomic dynamics for these progressions. Meanwhile, the available datasets are often scattered and lack management. Here, we have established PvGeneExpDB, the first gene expression database for L. vannamei (www.bio-marine-scau.com/pv_ex/), which encompasses gene expression profiles, differential expression, and co-expression analyses under various biological conditions. Based on the analyses of 7 datasets, which include 53 samples with accurate and detailed records, PvGeneExpDB identifies 20,599 novel transcripts, shows expression profiles of a total of 20,817 genes, and implements Gene Ontology (GO) reconstruction of 76.7 % of these genes. Besides, 26 co-expressed groups were first identified by large-scale, cross-sample Weighted Gene Co-expression Network Analysis (WGCNA). By integrating the gene expression data in the database, our goal is to deepen the biological understanding of L. vannamei.
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Affiliation(s)
- Xi Xiong
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China
| | - Chun Xie
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Sijun Li
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun-Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Yanzhi Wang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun-Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Junyang Jiang
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China
| | - Dizhi Xie
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China
| | - Shijun Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China.
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun-Yat-sen University, Guangzhou, Guangdong 510006, China.
| | - Lian Gan
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China.
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133
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Singh M, Chandra D, Jagdish S, Nandi D. Global transcriptome analysis reveals Salmonella Typhimurium employs nitrate metabolism to combat bile stress. FEBS Lett 2024. [PMID: 38503554 DOI: 10.1002/1873-3468.14853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/21/2024]
Abstract
Salmonella Typhimurium is an enteric pathogen that is highly tolerant to bile. Next-generation mRNA sequencing was performed to analyze the adaptive responses to bile in two S. Typhimurium strains: wild type (WT) and a mutant lacking cold shock protein E (ΔcspE). CspE is an RNA chaperone which is crucial for survival of S. Typhimurium during bile stress. This study identifies transcriptional responses in bile-tolerant WT and bile-sensitive ΔcspE. Upregulation of several genes involved in nitrate metabolism was observed, including fnr, a global regulator of nitrate metabolism. Notably, Δfnr was susceptible to bile stress. Also, complementation with fnr lowered reactive oxygen species and enhanced the survival of bile-sensitive ΔcspE. Importantly, intracellular nitrite amounts were highly induced in bile-treated WT compared to ΔcspE. Also, the WT strain pre-treated with nitrate displayed better growth with bile. These results demonstrate that nitrate-dependent metabolism promotes adaptation of S. Typhimurium to bile.
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Affiliation(s)
- Madhulika Singh
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Deepti Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sirisha Jagdish
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Dipankar Nandi
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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134
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Hosseinzadeh S, Hasanpur K. Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress. Sci Rep 2024; 14:6544. [PMID: 38503864 PMCID: PMC10951342 DOI: 10.1038/s41598-024-56757-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) are functional bridges connecting the genome with phenotypes by interacting with DNA, mRNA, and proteins. Using publically available acute heat stress (AHS)-related RNA-seq data, we discovered novel lncRNAs and tested their association with AHS along with ~ 8800 known lncRNAs and ~ 28,000 mRNA transcripts. Our pipeline discovered a total of 145 potentially novel-lncRNAs. One of them (Fishcomb_p-value = 0.06) along with another novel transcript (annotated as protein-coding; Fishcomb_p-value = 0.03) were identified as significantly associated with AHS. We found five known-lncRNAs and 134 mRNAs transcripts that were significantly associated with AHS. Four novel lncRNAs interact cis-regulated with 12 mRNA transcripts and are targeted by 11 miRNAs. Also six meta-lncRNAs associate with 134 meta-mRNAs through trans-acting co-expression, each targeted by 15 and 216 miRNAs, respectively. Three of the known-lncRNAs significantly co-expressed with almost 97 of the significant mRNAs (Pearson correlation p-value < 0.05). We report the mentioned three known-lncRNAs (ENSGALT00000099876, ENSGALT00000107573, and ENSGALT00000106323) as the most, significantly regulatory elements of AHS in chicken. It can be concluded that in order to alleviate the adverse effects of AHS on chicken, the manipulation of the three regulatory lncRNAs could lead to a more desirable result than the manipulation of the most significant mRNAs.
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Affiliation(s)
- Sevda Hosseinzadeh
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Karim Hasanpur
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
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135
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Hasan MS, McElroy KE, Audino JA, Serb JM. Opsin expression varies across larval development and taxa in pteriomorphian bivalves. Front Neurosci 2024; 18:1357873. [PMID: 38562306 PMCID: PMC10982516 DOI: 10.3389/fnins.2024.1357873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Many marine organisms have a biphasic life cycle that transitions between a swimming larva with a more sedentary adult form. At the end of the first phase, larvae must identify suitable sites to settle and undergo a dramatic morphological change. Environmental factors, including photic and chemical cues, appear to influence settlement, but the sensory receptors involved are largely unknown. We targeted the protein receptor, opsin, which belongs to large superfamily of transmembrane receptors that detects environmental stimuli, hormones, and neurotransmitters. While opsins are well-known for light-sensing, including vision, a growing number of studies have demonstrated light-independent functions. We therefore examined opsin expression in the Pteriomorphia, a large, diverse clade of marine bivalves, that includes commercially important species, such as oysters, mussels, and scallops. Methods Genomic annotations combined with phylogenetic analysis show great variation of opsin abundance among pteriomorphian bivalves, including surprisingly high genomic abundance in many species that are eyeless as adults, such as mussels. Therefore, we investigated the diversity of opsin expression from the perspective of larval development. We collected opsin gene expression in four families of Pteriomorphia, across three distinct larval stages, i.e., trochophore, veliger, and pediveliger, and compared those to adult tissues. Results We found larvae express all opsin types in these bivalves, but opsin expression patterns are largely species-specific across development. Few opsins are expressed in the adult mantle, but many are highly expressed in adult eyes. Intriguingly, opsin genes such as retinochrome, xenopsins, and Go-opsins have higher levels of expression in the later larval stages when substrates for settlement are being tested, such as the pediveliger. Conclusion Investigating opsin gene expression during larval development provides crucial insights into their intricate interactions with the surroundings, which may shed light on how opsin receptors of these organisms respond to various environmental cues that play a pivotal role in their settlement process.
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Affiliation(s)
- Md Shazid Hasan
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Kyle E. McElroy
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Jorge A. Audino
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
- Department of Zoology, University of São Paulo, São Paulo, Brazil
| | - Jeanne M. Serb
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
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136
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Lykke-Andersen S, Rouvière JO, Schmid M, Gockert M, Jensen TH. Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR package. STAR Protoc 2024; 5:102960. [PMID: 38502686 DOI: 10.1016/j.xpro.2024.102960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/11/2023] [Accepted: 02/29/2024] [Indexed: 03/21/2024] Open
Abstract
The widespread usage of next-generation sequencing methods for functional genomics studies requires standardized tools for consistent visualization of the associated data. Here, we present seqNdisplayR, an R package for plotting standard sequencing data coverage within a genomic region of interest in a customizable and reproducible manner. We describe steps for installing software, preparing data files, choosing options, and plotting data. This tool is readily available for users with no prior experience with R through the "Shiny app" interface. For complete details on the use and execution of this protocol, please refer to Lykke-Andersen et al.,1 Gockert et al.,2 and Rouviere et al.3.
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Affiliation(s)
- Søren Lykke-Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark.
| | - Jérôme O Rouvière
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark
| | - Maria Gockert
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark.
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137
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Mao YX, Li Y, Yang Z, Xu N, Zhang S, Wang X, Yang X, Sun Q, Mao Y. Comparative transcriptome analysis between rhesus macaques ( Macaca mulatta) and crab-eating macaques ( M. fascicularis). Zool Res 2024; 45:299-310. [PMID: 38485500 PMCID: PMC11017088 DOI: 10.24272/j.issn.2095-8137.2023.322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/28/2023] [Indexed: 03/19/2024] Open
Abstract
Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques ( Macaca mulatta, MMU) and crab-eating macaques ( M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from 84 samples (41 MFA samples and 43 MMU samples) encompassing 14 common tissues. Our findings revealed a small fraction of genes (3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover, 19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary, this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.
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Affiliation(s)
- Yu-Xiang Mao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yamei Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zikun Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ning Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xuankai Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiangyu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Qiang Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, Yunnan 650201, China. E-mail:
| | - Yafei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China
- Center for Genomic Research, International Institutes of Medicine, Fourth Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang 322000, China. E-mail:
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138
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Sharip A, Rakhimova S, Molkenov A, Ashenova A, Kozhamkulov U, Akhmetollayev I, Zinovyev A, Zhukov Y, Omarov M, Tuleutaev M, Rakhmetova V, Terwilliger JD, Lee JH, Zhumadilov Z, Akilzhanova A, Kairov U. Transcriptome profiling and analysis of patients with esophageal squamous cell carcinoma from Kazakhstan. Front Genet 2024; 15:1249751. [PMID: 38562378 PMCID: PMC10982404 DOI: 10.3389/fgene.2024.1249751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is the predominant subtype of esophageal cancer in Central Asia, often diagnosed at advanced stages. Understanding population-specific patterns of ESCC is crucial for tailored treatments. This study aimed to unravel ESCC's genetic basis in Kazakhstani patients and identify potential biomarkers for early diagnosis and targeted therapies. ESCC patients from Kazakhstan were studied. We analyzed histological subtypes and conducted in-depth transcriptome sequencing. Differential gene expression analysis was performed, and significantly dysregulated pathways were identified using KEGG pathway analysis (p-value < 0.05). Protein-protein interaction networks were constructed to elucidate key modules and their functions. Among Kazakhstani patients, ESCC with moderate dysplasia was the most prevalent subtype. We identified 42 significantly upregulated and two significantly downregulated KEGG pathways, highlighting molecular mechanisms driving ESCC pathogenesis. Immune-related pathways, such as viral protein interaction with cytokines, rheumatoid arthritis, and oxidative phosphorylation, were elevated, suggesting immune system involvement. Conversely, downregulated pathways were associated with extracellular matrix degradation, crucial in cancer invasion and metastasis. Protein-protein interaction network analysis revealed four distinct modules with specific functions, implicating pathways in esophageal cancer development. High-throughput transcriptome sequencing elucidated critical molecular pathways underlying esophageal carcinogenesis in Kazakhstani patients. Insights into dysregulated pathways offer potential for early diagnosis and precision treatment strategies for ESCC. Understanding population-specific patterns is essential for personalized approaches to ESCC management.
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Affiliation(s)
- Aigul Sharip
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Saule Rakhimova
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Askhat Molkenov
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Ainur Ashenova
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Ulan Kozhamkulov
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | | | | | - Yuri Zhukov
- Multidisciplinary Medical Center, Astana, Kazakhstan
| | - Marat Omarov
- Multidisciplinary Medical Center, Astana, Kazakhstan
| | | | - Venera Rakhmetova
- Department of Internal Diseases, Astana Medical University, Astana, Kazakhstan
| | - Joseph D. Terwilliger
- Sergiеvsky Center, Columbia University, New York, NY, United States
- Division of Medical Genetics, New York State Psychiatric Institute, New York, NY, United States
- Department of Psychiatry and Department of Genetics and Development, Columbia University, New York, NY, United States
| | - Joseph H. Lee
- Sergiеvsky Center, Columbia University, New York, NY, United States
- Departments of Epidemiology and Neurology, Columbia University, New York, NY, United States
| | - Zhaxybay Zhumadilov
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Ainur Akilzhanova
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Ulykbek Kairov
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
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139
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Li X, Wang Z, Wu Q, Klaunig JE. Evaluating the mode of action of perfluorooctanoic acid-induced liver tumors in male Sprague-Dawley rats using a toxicogenomic approach. J Environ Sci Health C Toxicol Carcinog 2024:1-25. [PMID: 38494990 DOI: 10.1080/26896583.2024.2327969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The mode of action (MOA) underlying perfluorooctanoic acid (PFOA)-induced liver tumors in rats is proposed to involve peroxisome proliferator-activated receptor α (PPARα) agonism. Despite clear PPARα activation evidence in rodent livers, the mechanisms driving cell growth remain elusive. Herein, we used dose-responsive apical endpoints and transcriptomic data to examine the proposed MOA. Male Sprague-Dawley rats were treated with 0, 1, 5, and 15 mg/kg PFOA for 7, 14, and 28 days via oral gavage. We showed PFOA induced hepatomegaly along with hepatocellular hypertrophy in rats. PPARα was activated in a dose-dependent manner. Toxicogenomic analysis revealed six early biomarkers (Cyp4a1, Nr1d1, Acot1, Acot2, Ehhadh, and Vnn1) in response to PPARα activation. A transient rise in hepatocellular DNA synthesis was demonstrated while Ki-67 labeling index showed no change. Transcriptomic analysis indicated no significant enrichment in pathways related to DNA synthesis, apoptosis, or the cell cycle. Key cyclins including Ccnd1, Ccnb1, Ccna2, and Ccne2 were dose-dependently suppressed by PFOA. Oxidative stress and the nuclear factor-κB signaling pathway were unaffected. Overall, evidence for PFOA-induced hepatocellular proliferation was transient within the studied timeframe. Our findings underscore the importance of considering inter-species differences and chemical-specific effects when evaluating the carcinogenic risk of PFOA in humans.
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Affiliation(s)
- Xilin Li
- Laboratory of Investigative Toxicology and Pathology, Department of Environmental and Occupational Health, Indiana University, Bloomington, IN, USA
| | - Zemin Wang
- Laboratory of Investigative Toxicology and Pathology, Department of Environmental and Occupational Health, Indiana University, Bloomington, IN, USA
| | - Qiangen Wu
- Laboratory of Investigative Toxicology and Pathology, Department of Environmental and Occupational Health, Indiana University, Bloomington, IN, USA
| | - James E Klaunig
- Laboratory of Investigative Toxicology and Pathology, Department of Environmental and Occupational Health, Indiana University, Bloomington, IN, USA
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140
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Rios KT, McGee JP, Sebastian A, Moritz RL, Feric M, Absalon S, Swearingen KE, Lindner SE. Global Release of Translational Repression Across Plasmodium's Host-to-Vector Transmission Event. bioRxiv 2024:2024.02.01.577866. [PMID: 38352447 PMCID: PMC10862809 DOI: 10.1101/2024.02.01.577866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Malaria parasites must be able to respond quickly to changes in their environment, including during their transmission between mammalian hosts and mosquito vectors. Therefore, before transmission, female gametocytes proactively produce and translationally repress mRNAs that encode essential proteins that the zygote requires to establish a new infection. This essential regulatory control requires the orthologues of DDX6 (DOZI), LSM14a (CITH), and ALBA proteins to form a translationally repressive complex in female gametocytes that associates with many of the affected mRNAs. However, while the release of translational repression of individual mRNAs has been documented, the details of the global release of translational repression have not. Moreover, the changes in spatial arrangement and composition of the DOZI/CITH/ALBA complex that contribute to translational control are also not known. Therefore, we have conducted the first quantitative, comparative transcriptomics and DIA-MS proteomics of Plasmodium parasites across the host-to-vector transmission event to document the global release of translational repression. Using female gametocytes and zygotes of P. yoelii, we found that nearly 200 transcripts are released for translation soon after fertilization, including those with essential functions for the zygote. However, we also observed that some transcripts remain repressed beyond this point. In addition, we have used TurboID-based proximity proteomics to interrogate the spatial and compositional changes in the DOZI/CITH/ALBA complex across this transmission event. Consistent with recent models of translational control, proteins that associate with either the 5' or 3' end of mRNAs are in close proximity to one another during translational repression in female gametocytes and then dissociate upon release of repression in zygotes. This observation is cross-validated for several protein colocalizations in female gametocytes via ultrastructure expansion microscopy and structured illumination microscopy. Moreover, DOZI exchanges its interaction from NOT1-G in female gametocytes to the canonical NOT1 in zygotes, providing a model for a trigger for the release of mRNAs from DOZI. Finally, unenriched phosphoproteomics revealed the modification of key translational control proteins in the zygote. Together, these data provide a model for the essential translational control mechanisms used by malaria parasites to promote their efficient transmission from their mammalian host to their mosquito vector.
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Affiliation(s)
- Kelly T. Rios
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802
| | - James P. McGee
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802
| | - Aswathy Sebastian
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802
| | | | - Marina Feric
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
| | - Sabrina Absalon
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202
| | | | - Scott E. Lindner
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802
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141
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Nguyen HD, Lin CC. Viscoelastic stiffening of gelatin hydrogels for dynamic culture of pancreatic cancer spheroids. Acta Biomater 2024; 177:203-215. [PMID: 38354874 PMCID: PMC10958777 DOI: 10.1016/j.actbio.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
The tumor microenvironment (TME) in pancreatic adenocarcinoma (PDAC) is a complex milieu of cellular and non-cellular components. Pancreatic cancer cells (PCC) and cancer-associated fibroblasts (CAF) are two major cell types in PDAC TME, whereas the non-cellular components are enriched with extracellular matrices (ECM) that contribute to high stiffness and fast stress-relaxation. Previous studies have suggested that higher matrix rigidity promoted aggressive phenotypes of tumors, including PDAC. However, the effects of dynamic viscoelastic matrix properties on cancer cell fate remain largely unexplored. The focus of this work was to understand the effects of such dynamic matrix properties on PDAC cell behaviors, particularly in the context of PCC/CAF co-culture. To this end, we engineered gelatin-norbornene (GelNB) based hydrogels with a built-in mechanism for simultaneously increasing matrix elastic modulus and viscoelasticity. Two GelNB-based macromers, namely GelNB-hydroxyphenylacetic acid (GelNB-HPA) and GelNB-boronic acid (GelNB-BA), were modularly mixed and crosslinked with 4-arm poly(ethylene glycol)-thiol (PEG4SH) to form elastic hydrogels. Treating the hybrid hydrogels with tyrosinase not only increased the elastic moduli of the gels (due to HPA dimerization) but also concurrently produced 1,2-diols that formed reversible boronic acid-diol bonding with the BA groups on GelNB-BA. We employed patient-derived CAF and a PCC cell line COLO-357 to demonstrate the effect of increasing matrix stiffness and viscoelasticity on CAF and PCC cell fate. Our results indicated that in the stiffened environment, PCC underwent epithelial-mesenchymal transition. In the co-culture PCC and CAF spheroid, CAF enhanced PCC spreading and stimulated collagen 1 production. Through mRNA-sequencing, we further showed that stiffened matrices, regardless of the degree of stress-relaxation, heightened the malignant phenotype of PDAC cells. STATEMENT OF SIGNIFICANCE: The pancreatic cancer microenvironment is a complex milieu composed of various cell types and extracellular matrices. It has been suggested that stiffer matrices could promote aggressive behavior in pancreatic cancer, but the effect of dynamic stiffening and matrix stress-relaxation on cancer cell fate remains largely undefined. This study aimed to explore the impact of dynamic changes in matrix viscoelasticity on pancreatic ductal adenocarcinoma (PDAC) cell behavior by developing a hydrogel system capable of simultaneously increasing stiffness and stress-relaxation on demand. This is achieved by crosslinking two gelatin-based macromers through orthogonal thiol-norbornene photochemistry and post-gelation stiffening with mushroom tyrosinase. The results revealed that higher matrix stiffness, regardless of the degree of stress relaxation, exacerbated the malignant characteristics of PDAC cells.
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Affiliation(s)
- Han D Nguyen
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Chien-Chi Lin
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA; Department of Biomedical Engineering, Purdue School of Engineering & Technology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA.
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142
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Najafi A, Jolly MK, George JT. Protocol for inferring epithelial-to-mesenchymal transition trajectories from single-cell RNA sequencing data using R. STAR Protoc 2024; 5:102819. [PMID: 38183653 PMCID: PMC10789639 DOI: 10.1016/j.xpro.2023.102819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/18/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024] Open
Abstract
The epithelial-to-mesenchymal transition (EMT) provides crucial insights into the metastatic process and possesses prognostic value within the cancer context. Here, we present COMET, an R package for inferring EMT trajectories and inter-state transition rates from single-cell RNA sequencing data. We describe steps for finding the optimal number of EMT genes for a specific context, estimating EMT-related trajectories, optimal fitting of continuous-time Markov chain to inferred trajectories, and estimating inter-state transition rates.
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Affiliation(s)
- Annice Najafi
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India.
| | - Jason T George
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA; Intercollegiate School of Engineering Medicine, Texas A&M University, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
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143
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Gulko A, Essene A, Belmont-Rausch DM, Veregge M, Pant D, Tenen D, Kapel BS, Emont MP, Pers TH, Rosen ED, Tsai LT. Protocol for flow cytometry-assisted single-nucleus RNA sequencing of human and mouse adipose tissue with sample multiplexing. STAR Protoc 2024; 5:102893. [PMID: 38416649 PMCID: PMC10909897 DOI: 10.1016/j.xpro.2024.102893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/27/2023] [Accepted: 01/30/2024] [Indexed: 03/01/2024] Open
Abstract
Adipocyte size and fragility and commercial kit costs impose significant limitations on single-cell RNA sequencing of adipose tissue. Accordingly, we developed a workflow to isolate and sample-barcode nuclei from individual adipose tissue samples, integrating flow cytometry for quality control, counting, and precise nuclei pooling for direct loading onto the popular 10× Chromium controller. This approach can eliminate batch confounding, and significantly reduces poor-quality nuclei, ambient RNA contamination, and droplet loading-associated reagent waste, resulting in pronounced improvements in information content and cost efficiency.
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Affiliation(s)
- Anton Gulko
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Boston Nutrition and Obesity Research Center/Boston Area Diabetes and Endocrinology Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Adam Essene
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Boston Nutrition and Obesity Research Center/Boston Area Diabetes and Endocrinology Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | | | - Molly Veregge
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Boston Nutrition and Obesity Research Center/Boston Area Diabetes and Endocrinology Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Deepti Pant
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Boston Nutrition and Obesity Research Center/Boston Area Diabetes and Endocrinology Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Danielle Tenen
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Boston Nutrition and Obesity Research Center/Boston Area Diabetes and Endocrinology Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Benedicte Schultz Kapel
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Margo P Emont
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Tune H Pers
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Evan D Rosen
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Boston Nutrition and Obesity Research Center/Boston Area Diabetes and Endocrinology Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA
| | - Linus T Tsai
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Boston Nutrition and Obesity Research Center/Boston Area Diabetes and Endocrinology Research Center Functional Genomics and Bioinformatics Core, Boston, MA, USA.
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144
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Liao Y, Rao Z, Huang S, Zhao D. Protocol to analyze immune cells in the tumor microenvironment by transcriptome using machine learning. STAR Protoc 2024; 5:102684. [PMID: 38219153 PMCID: PMC10826422 DOI: 10.1016/j.xpro.2023.102684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/15/2023] [Accepted: 10/10/2023] [Indexed: 01/16/2024] Open
Abstract
Immunotherapy is a promising strategy to treat cancer. Here, we present a protocol for analyzing the transcriptome-based phenotypic alterations and immune cell infiltration in the tumor microenvironment. We describe steps for integrating single-cell RNA sequencing (scRNA-seq) data, comparing phenotypes and origins of mononuclear phagocytes, inferring the differentiation trajectory and infiltration process, and identifying infiltration-associated genes using machine learning. We then detail procedures for exploring the impact of these genes in prognosis through the integrated microarray and bulk RNA-seq data to obtain potential drug targets. For complete details on the use and execution of this protocol, please refer to Liao et al.1.
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Affiliation(s)
- Yunxi Liao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Ziyan Rao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Shaodong Huang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Dongyu Zhao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China; State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China.
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145
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Nguyen AD, Haines C, Price MJ, Dalton TE, Baëta CD, Hockenberry HA, Goodwin CR. Single-cell RNA sequencing comparison of the human metastatic prostate spine tumor microenvironment. STAR Protoc 2024; 5:102805. [PMID: 38341849 PMCID: PMC10867439 DOI: 10.1016/j.xpro.2023.102805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/20/2023] [Accepted: 12/13/2023] [Indexed: 02/13/2024] Open
Abstract
Spinal column tumors can be difficult to process for single-cell omic studies, given the heterogeneity in tissue. Here, we present a protocol for operating room-to-benchtop single-cell processing of clinical specimens from a prostate cancer patient. We describe steps for sample homogenization, red blood cell lysis, cryopreservation, and single-cell sequencing analysis. This protocol can be used to identify prognostic markers and therapeutic targets for patients with osseous spine metastases and better inform eligibility for clinical trials.
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Affiliation(s)
- Annee D Nguyen
- Department of Neurosurgery, Duke University Medical Center, 200 Trent Dr, Durham, NC 27710, USA
| | - Corinne Haines
- Department of Molecular Genetics, Ohio State University, 1060 Carmack Road, Columbus, OH 43210, USA
| | - Meghan J Price
- Department of Medicine, John Hopkins Hospital, 1800 Orleans St, Baltimore, MD 21287, USA
| | - Tara E Dalton
- Department of Neurosurgery, Duke University Medical Center, 200 Trent Dr, Durham, NC 27710, USA
| | - César D Baëta
- Center for Population Health Sciences, Stanford University, 1701 Page Mill Road, Palo Alto, CA 94304, USA
| | - Harrison A Hockenberry
- Department of Neurosurgery, Duke University Medical Center, 200 Trent Dr, Durham, NC 27710, USA
| | - C Rory Goodwin
- Department of Neurosurgery, Duke University Medical Center, 200 Trent Dr, Durham, NC 27710, USA.
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146
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Sun N, Shao H, Zhang Y, Ci B, Yao H, Bai B, Tan T. Establishing a 3D culture system for early organogenesis of monkey embryos ex vivo and single-cell transcriptome analysis of cultured embryos. STAR Protoc 2024; 5:102835. [PMID: 38224493 PMCID: PMC10826423 DOI: 10.1016/j.xpro.2023.102835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/17/2024] Open
Abstract
Creating in vitro culture platforms for monkey embryos is crucial for understanding the initial 4 weeks of early primate embryogenesis. Here, we present a protocol to culture cynomolgus monkey embryos in vitro for 25 days post-fertilization and to delineate the key developmental events of gastrulation and early organogenesis. We describe steps for culturing with a 3D system, immunofluorescence analysis, single-cell RNA sequencing, and bioinformatic analysis. For complete details on the use and execution of this protocol, please refer to Gong et al. (2023).1.
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Affiliation(s)
- Nianqin Sun
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
| | - Honglian Shao
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Youyue Zhang
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Baiquan Ci
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Hui Yao
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Bing Bai
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
| | - Tao Tan
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
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147
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Liu D, Gou L, Sun T, Liu J, Fan TP, Deng H, Cai Y. Characterization and Application of a Stationary Phase Promoter Library from Serratia marcescens. ACS Synth Biol 2024; 13:969-972. [PMID: 38340070 DOI: 10.1021/acssynbio.3c00687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Serratia marcescens has garnered increasing attention as a promising host for valuable compound production. However, the lack of an efficient gene regulation toolkit severely hampers its applications. Here, a library of stationary phase promoters was screened in S. marcescens HBA7 using RNA-seq and RT-qPCR, revealing a 43-fold regulatory range with the red fluorescent protein mKate2 as the reporter. The β-galactosidase was employed to demonstrate the universality in driving the expression of different proteins. The wide-ranging utility of these promoters in different hosts was demonstrated in Escherichia coli. Moreover, to assess their potential application, the strongest promoter, P2, was employed to express the swrW gene, resulting in a roughly 20-fold increase in serrawettin W1 production in S. marcescens HBQA7ΔswrW. In summary, this study successfully constructed a gradient-strength stationary phase promoter library, providing an effective toolkit for gene regulation and secondary metabolite production in diverse prokaryotes, including S. marcescens and E. coli.
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Affiliation(s)
- Di Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Linbo Gou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Tingting Sun
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Jie Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1TN, U.K
| | - Huaxiang Deng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, No.1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
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148
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Qi Y, Cai G, Yang W. Protocol for in situ visualization of mitochondrial ROS and apoptosis in spatially confined cells and sample preparation for biochemical analysis. STAR Protoc 2024; 5:102802. [PMID: 38159272 PMCID: PMC10787287 DOI: 10.1016/j.xpro.2023.102802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/30/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024] Open
Abstract
Locomotion through spatially confining spaces is an important in vivo migration mode. Here, we present a protocol for in situ visualization of mitochondrial reactive oxygen species and apoptosis in cancer cells during confined migration. We then detail sample preparation of confined cells for transcriptome and immunoblotting analysis by using transwell chambers. This approach allows in situ evaluation of a variety of cellular functions during confined migration and preparation of the samples of confined cells for further biochemical analysis. For complete details on the use and execution of this protocol, please refer to Cai et al.1.
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Affiliation(s)
- Yijun Qi
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Guoqing Cai
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Weiwei Yang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
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149
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Li Z, Li S, Wu Q, Gao X, Zhu L. Physiological responses and removal mechanisms of ciprofloxacin in freshwater microalgae. J Hazard Mater 2024; 466:133519. [PMID: 38278073 DOI: 10.1016/j.jhazmat.2024.133519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/02/2024] [Accepted: 01/10/2024] [Indexed: 01/28/2024]
Abstract
Antibiotics, such as ciprofloxacin (CIP), are frequently detected in various environmental compartments, posing significant risks to ecosystems and human health. In this study, the physiological responses and elimination mechanisms of CIP in Chlorella sorokiniana and Scenedesmus dimorphus were determined. The exposure CIP had a minimal impact on the growth of microalgae, with maximum inhibit efficiency (IR) of 5.14% and 22.74 for C. sorokiniana and S. dimorphus, respectively. Notably, the photorespiration in S. dimorphus were enhanced. Both microalgae exhibited efficient CIP removal, predominantly through bioaccumulation and biodegradation processes. Intermediates involved in photolysis and biodegradation were analyzed through Liquid Chromatography High Resolution Mass Spectrometer (HPLC-MS/MS), providing insights into degradation pathways of CIP. Upregulation of key enzymes, such as dioxygenase, oxygenase and cytochrome P450, indicated their involvement in the biodegradation of CIP. These findings enhance our understanding of the physiological responses, removal mechanisms, and pathways of CIP in microalgae, facilitating the advancement of microalgae-based wastewater treatment approaches, particularly in antibiotic-contaminated environments.
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Affiliation(s)
- Zhuo Li
- School of Resources & Environmental Science, Hubei International Scientific and Technological Cooperation Base of Sustainable Resource and Energy, Hubei Key Laboratory of Biomass-Resources Chemistry and Environmental Biotechnology, Wuhan University, Wuhan 430079, PR China
| | - Shuangxi Li
- School of Resources & Environmental Science, Hubei International Scientific and Technological Cooperation Base of Sustainable Resource and Energy, Hubei Key Laboratory of Biomass-Resources Chemistry and Environmental Biotechnology, Wuhan University, Wuhan 430079, PR China
| | - Qirui Wu
- School of Resources & Environmental Science, Hubei International Scientific and Technological Cooperation Base of Sustainable Resource and Energy, Hubei Key Laboratory of Biomass-Resources Chemistry and Environmental Biotechnology, Wuhan University, Wuhan 430079, PR China
| | - Xinxin Gao
- School of Resources & Environmental Science, Hubei International Scientific and Technological Cooperation Base of Sustainable Resource and Energy, Hubei Key Laboratory of Biomass-Resources Chemistry and Environmental Biotechnology, Wuhan University, Wuhan 430079, PR China
| | - Liandong Zhu
- School of Resources & Environmental Science, Hubei International Scientific and Technological Cooperation Base of Sustainable Resource and Energy, Hubei Key Laboratory of Biomass-Resources Chemistry and Environmental Biotechnology, Wuhan University, Wuhan 430079, PR China.
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150
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Yamada K, Menon JA, Kim Y, Cheng C, Chen W, Shih JA, Villasenor-Altamirano AB, Chen X, Tamura T, Merriam LT, Kim EY, Weissman AJ. Protocol for immunophenotyping out-of-hospital cardiac arrest patients. STAR Protoc 2024; 5:102874. [PMID: 38310512 PMCID: PMC10850743 DOI: 10.1016/j.xpro.2024.102874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/28/2023] [Accepted: 01/19/2024] [Indexed: 02/06/2024] Open
Abstract
Immunophenotyping of out-of-hospital cardiac arrest (OHCA) patients is of increasing interest but has challenges. Here, we describe steps for the design of the clinical cohort, planning patient enrollment and sample collection, and ethical review of the study protocol. We detail procedures for blood sample collection and cryopreservation of peripheral blood mononuclear cells (PBMCs). We detail steps to modulate immune checkpoints in OHCA PBMC ex vivo. This protocol also has relevance for immunophenotyping other types of critical illness. For complete details on the use and execution of this protocol, please refer to Tamura et al. (2023).1.
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Affiliation(s)
- Kohei Yamada
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
| | - Jaivardhan A Menon
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Yaunghyun Kim
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Changde Cheng
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jenny A Shih
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Ana B Villasenor-Altamirano
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Tomoyoshi Tamura
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Emergency and Critical Care Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Louis T Merriam
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Edy Y Kim
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
| | - Alexandra J Weissman
- Department of Emergency Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
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