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Hasegawa K, Fujimori H, Nakatani K, Takahashi M, Izumi Y, Bamba T, Nakamura‐Shima M, Shibuya‐Takahashi R, Mochizuki M, Wakui Y, Abue M, Iwai W, Fukushi D, Satoh K, Yamaguchi K, Shindo N, Yasuda J, Asano N, Imai T, Asada Y, Katori Y, Tamai K. Delta‐6 desaturase FADS2 is a tumor‐promoting factor in cholangiocarcinoma. Cancer Sci 2024. [DOI: 10.1111/cas.16306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 07/25/2024] [Indexed: 08/09/2024] Open
Abstract
AbstractCholangiocarcinoma is a fatal disease with limited therapeutic options. We screened genes required for cholangiocarcinoma tumorigenicity and identified FADS2, a delta‐6 desaturase. FADS2 depletion reduced in vivo tumorigenicity and cell proliferation. In clinical samples, FADS2 was expressed in cancer cells but not in stromal cells. FADS2 inhibition also reduced the migration and sphere‐forming ability of cells and increased apoptotic cell death and ferroptosis markers. Lipidome assay revealed that triglyceride and cholesterol ester levels were decreased in FADS2‐knockdown cells. The oxygen consumption ratio was also decreased in FADS2‐depleted cells. These data indicate that FADS2 depletion causes a reduction in lipid levels, resulting in decrease of energy production and attenuation of cancer cell malignancy.
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Affiliation(s)
- Kohsei Hasegawa
- Division of Cancer Stem Cell Miyagi Cancer Center Research Institute Natori Miyagi Japan
- Department of Head and Neck Surgery Miyagi Cancer Center Natori Miyagi Japan
- Department of Otolaryngology‐Head and Neck Surgery Tohoku University Graduate School of Medicine Sendai Miyagi Japan
| | - Haruna Fujimori
- Division of Cancer Stem Cell Miyagi Cancer Center Research Institute Natori Miyagi Japan
| | - Kohta Nakatani
- Division of Metabolomics, Medical Research Center for High Depth Omics Medical Institute of Bioregulation, Kyushu University Fukuoka Japan
| | - Masatomo Takahashi
- Division of Metabolomics, Medical Research Center for High Depth Omics Medical Institute of Bioregulation, Kyushu University Fukuoka Japan
| | - Yoshihiro Izumi
- Division of Metabolomics, Medical Research Center for High Depth Omics Medical Institute of Bioregulation, Kyushu University Fukuoka Japan
| | - Takeshi Bamba
- Division of Metabolomics, Medical Research Center for High Depth Omics Medical Institute of Bioregulation, Kyushu University Fukuoka Japan
| | - Mao Nakamura‐Shima
- Division of Cancer Stem Cell Miyagi Cancer Center Research Institute Natori Miyagi Japan
| | - Rie Shibuya‐Takahashi
- Division of Cancer Stem Cell Miyagi Cancer Center Research Institute Natori Miyagi Japan
| | - Mai Mochizuki
- Division of Cancer Stem Cell Miyagi Cancer Center Research Institute Natori Miyagi Japan
| | - Yuta Wakui
- Division of Gastroenterology Miyagi Cancer Center Natori Miyagi Japan
| | - Makoto Abue
- Division of Gastroenterology Miyagi Cancer Center Natori Miyagi Japan
| | - Wataru Iwai
- Division of Gastroenterology Miyagi Cancer Center Natori Miyagi Japan
| | - Daisuke Fukushi
- Division of Gastroenterology Tohoku Medical and Pharmaceutical University Sendai Miyagi Japan
| | - Kennichi Satoh
- Division of Gastroenterology Tohoku Medical and Pharmaceutical University Sendai Miyagi Japan
| | - Kazunori Yamaguchi
- Division of Molecular and Cellular Oncology Miyagi Cancer Center Research Institute Natori Miyagi Japan
| | - Norihisa Shindo
- Division of Cancer Chromosome Biology Unit Miyagi Cancer Center Research Institute Natori Miyagi Japan
| | - Jun Yasuda
- Division of Molecular and Cellular Oncology Miyagi Cancer Center Research Institute Natori Miyagi Japan
| | - Naoki Asano
- Division of Cancer Stem Cell Miyagi Cancer Center Research Institute Natori Miyagi Japan
- Division of Gastroenterology Tohoku University Graduate School of Medicine Sendai Japan
| | - Takayuki Imai
- Department of Head and Neck Surgery Miyagi Cancer Center Natori Miyagi Japan
| | - Yukinori Asada
- Department of Head and Neck Surgery Miyagi Cancer Center Natori Miyagi Japan
| | - Yukio Katori
- Department of Otolaryngology‐Head and Neck Surgery Tohoku University Graduate School of Medicine Sendai Miyagi Japan
| | - Keiichi Tamai
- Division of Cancer Stem Cell Miyagi Cancer Center Research Institute Natori Miyagi Japan
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Qianqian R, Peng Z, Licai Z, Ruizhi Z, Tianhe Y, Xiangwen X, Chuansheng Z, Fan Y. A longitudinal evaluation of oxidative stress - mitochondrial dysfunction - ferroptosis genes in anthracycline-induced cardiotoxicity. BMC Cardiovasc Disord 2024; 24:350. [PMID: 38987722 PMCID: PMC11234563 DOI: 10.1186/s12872-024-03967-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 05/30/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Antineoplastic medications, including doxorubicin, idarubicin, and epirubicin, have been found to adversely affect the heart due to oxidative stress - mitochondrial dysfunction - ferroptosis (ORMFs), which act as contributing attributes to anthracycline-induced cardiotoxicity. To better understand this phenomenon, the time-resolved measurements of ORMFS genes were analyzed in this study. METHODS The effect of three anthracycline drugs on ORMFs genes was studied using a human 3D cardiac microtissue cell model. Transcriptome data was collected over 14 days at two doses (therapeutic and toxic). WGCNA identified key module-related genes, and functional enrichment analysis investigated the biological processes quantified by ssGSEA, such as immune cell infiltration and angiogenesis. Biopsies were collected from heart failure patients and control subjects. GSE59672 and GSE2965 were collected for validation. Molecular docking was used to identify anthracyclines's interaction with key genes. RESULTS The ORMFs genes were screened in vivo or in vitro. Using WGCNA, six co-expressed gene modules were grouped, with MEblue emerging as the most significant module. Eight key genes intersecting the blue module with the dynamic response genes were obtained: CD36, CDH5, CHI3L1, HBA2, HSD11B1, OGN, RPL8, and VWF. Compared with control samples, all key genes except RPL8 were down-regulated in vitro ANT treatment settings, and their expression levels varied over time. According to functional analyses, the key module-related genes were engaged in angiogenesis and the immune system pathways. In all ANT-treated settings, ssGSEA demonstrated a significant down-regulation of angiogenesis score and immune cell activity, including Activated CD4 T cell, Immature B cell, Memory B cell, Natural killer cell, Type 1 T helper cell, and Type 2 T helper cell. Molecular docking revealed that RPL8 and CHI3L1 show significant binding affinity for anthracyclines. CONCLUSION This study focuses on the dynamic characteristics of ORMFs genes in both human cardiac microtissues and cardiac biopsies from ANT-treated patients. It has been highlighted that ORMFs genes may contribute to immune infiltration and angiogenesis in cases of anthracycline-induced cardiotoxicity. A thorough understanding of these genes could potentially lead to improved diagnosis and treatment of the disease.
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Affiliation(s)
- Ren Qianqian
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Zhu Peng
- Department of Hepatobiliary Surgery, Wuhan No. 1 Hospital, Wuhan, China
| | - Zhang Licai
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Zhang Ruizhi
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Ye Tianhe
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Xia Xiangwen
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China
| | - Zheng Chuansheng
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China.
| | - Yang Fan
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, 430022, China.
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Srivastava P, Benegas Coll M, Götz S, Nueda MJ, Conesa A. scMaSigPro: Differential Expression Analysis along Single-Cell Trajectories. Bioinformatics 2024; 40:btae443. [PMID: 38976653 PMCID: PMC11269465 DOI: 10.1093/bioinformatics/btae443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 06/27/2024] [Accepted: 07/04/2024] [Indexed: 07/10/2024] Open
Abstract
MOTIVATION Understanding the dynamics of gene expression across different cellular states is crucial for discerning the mechanisms underneath cellular differentiation. Genes that exhibit variation in mean expression as a function of Pseudotime and between branching trajectories are expected to govern cell fate decisions. We introduce scMaSigPro, a method for the identification of differential gene expression patterns along Pseudotime and branching paths simultaneously. RESULTS We assessed the performance of scMaSigPro using synthetic and public datasets. Our evaluation shows that scMaSigPro outperforms existing methods in controlling the False Positive Rate and is computationally efficient. AVAILABILITY AND IMPLEMENTATION scMaSigPro is available as a free R package (version 4.0 or higher) under the GPL(≥2) license on GitHub at 'github.com/BioBam/scMaSigPro' and archived with version 0.03 on Zenodo at 'zenodo.org/records/12568922'.
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Affiliation(s)
- Priyansh Srivastava
- BioBam Bioinformatics S.L., Valencia, 46024, Spain
- Department of Computer Science, University of Valencia, Valencia, 46100, Spain
| | | | - Stefan Götz
- BioBam Bioinformatics S.L., Valencia, 46024, Spain
| | - María José Nueda
- Mathematics Department, University of Alicante, Alicante, 03690, Spain
| | - Ana Conesa
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cientıficas (CSIC), Paterna, 46980, Spain
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Shen J, Sun H, Zhou S, Wang L, Dong C, Ren K, Du Q, Cao J, Wang Y, Sun J. Development of a screening system of gene sets for estimating the time of early skeletal muscle injury based on second-generation sequencing technology. Int J Legal Med 2024; 138:1629-1644. [PMID: 38532207 DOI: 10.1007/s00414-024-03210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
The present study is aimed to address the challenge of wound age estimation in forensic science by identifying reliable genetic markers using low-cost and high-precision second-generation sequencing technology. A total of 54 Sprague-Dawley rats were randomly assigned to a control group or injury groups, with injury groups being further divided into time points (4 h, 8 h, 12 h, 16 h, 20 h, 24 h, 28 h, and 32 h after injury, n = 6) to establish rat skeletal muscle contusion models. Gene expression data were obtained using second-generation sequencing technology, and differential gene expression analysis, weighted gene co-expression network analysis (WGCNA) and time-dependent expression trend analysis were performed. A total of six sets of biomarkers were obtained: differentially expressed genes at adjacent time points (127 genes), co-expressed genes most associated with wound age (213 genes), hub genes exhibiting time-dependent expression (264 genes), and sets of transcription factors (TF) corresponding to the above sets of genes (74, 87, and 99 genes, respectively). Then, random forest (RF), support vector machine (SVM) and multilayer perceptron (MLP), were constructed for wound age estimation from the above gene sets. The results estimated by transcription factors were all superior to the corresponding hub genes, with the transcription factor group of WGCNA performed the best, with average accuracy rates of 96% for three models' internal testing, and 91.7% for the highest external validation. This study demonstrates the advantages of the indicator screening system based on second-generation sequencing technology and transcription factor level for wound age estimation.
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Affiliation(s)
- Junyi Shen
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China
- Institute of Forensic Science Public Security Department of Shanxi, Taiyuan, China
| | - Hao Sun
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Shidong Zhou
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Liangliang Wang
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Chaoxiu Dong
- Institute of Forensic Science Public Security Department of Shanxi, Taiyuan, China
| | - Kang Ren
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Qiuxiang Du
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Jie Cao
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Yingyuan Wang
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China.
| | - Junhong Sun
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China.
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Tien NTN, Anh TT, Yen NTH, Anh NK, Nguyen HT, Kim HS, Oh JH, Kim DH, Long NP. Time-course cross-species transcriptomics reveals conserved hepatotoxicity pathways induced by repeated administration of cyclosporine A. Toxicol Mech Methods 2024:1-12. [PMID: 38937256 DOI: 10.1080/15376516.2024.2371894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
Cyclosporine A (CsA) has shown efficacy against immunity-related diseases despite its toxicity in various organs, including the liver, emphasizing the need to elucidate its underlying hepatotoxicity mechanism. This study aimed to capture the alterations in genome-wide expression over time and the subsequent perturbations of corresponding pathways across species. Six data from humans, mice, and rats, including animal liver tissue, human liver microtissues, and two liver cell lines exposed to CsA toxic dose, were used. The microtissue exposed to CsA for 10 d was analyzed to obtain dynamically differentially expressed genes (DEGs). Single-time points data at 1, 3, 5, 7, and 28 d of different species were used to provide additional evidence. Using liver microtissue-based longitudinal design, DEGs that were consistently up- or down-regulated over time were captured, and the well-known mechanism involved in CsA toxicity was elucidated. Thirty DEGs that consistently changed in longitudinal data were also altered in 28-d rat in-house data with concordant expression. Some genes (e.g. TUBB2A, PLIN2, APOB) showed good concordance with identified DEGs in 1-d and 7-d mouse data. Pathway analysis revealed up-regulations of protein processing, asparagine N-linked glycosylation, and cargo concentration in the endoplasmic reticulum. Furthermore, the down-regulations of pathways related to biological oxidations and metabolite and lipid metabolism were elucidated. These pathways were also enriched in single-time-point data and conserved across species, implying their biological significance and generalizability. Overall, the human organoids-based longitudinal design coupled with cross-species validation provides temporal molecular change tracking, aiding mechanistic elucidation and biologically relevant biomarker discovery.
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Affiliation(s)
- Nguyen Tran Nam Tien
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
| | - Trinh Tam Anh
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Thi Hai Yen
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Ky Anh
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Huy Truong Nguyen
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Ho-Sook Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
| | - Jung-Hwa Oh
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, Republic of Korea
| | - Dong-Hyun Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Phuoc Long
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea
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Gao Y, Liu GE, Ma L, Fang L, Li CJ, Baldwin RL. Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis. J Adv Res 2024:S2090-1232(24)00257-1. [PMID: 38925453 DOI: 10.1016/j.jare.2024.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/21/2024] [Indexed: 06/28/2024] Open
Abstract
During lactation, dairy cattle's digestive tract requires significant adaptations to meet the increased nutrient demands for milk production. As we attempt to improve milk-related traits through selective pressure, it is crucial to understand the biological functions of the epithelia of the rumen, small intestine, and colonic tissues in response to changes in physiological state driven by changes in nutrient demands for milk synthesis. In this study, we obtained a total of 108 transcriptome profiles from three tissues (epithelia of the colon, duodenum, and rumen) of five Holstein cows, spanning eight time points from the early, mid, late lactation periods to the dry period. On average 97.06% of reads were successfully mapped to the reference genome assembly ARS-UCD1.2. We analyzed 27,607 gene expression patterns at multiple periods, enabling direct comparisons within and among tissues during different lactation stages, including early and peak lactation. We identified 1645, 813, and 2187 stage-specific genes in the colon, duodenum, and rumen, respectively, which were enriched for common or specific biological functions among different tissues. Time series analysis categorized the expressed genes within each tissue into four clusters. Furthermore, when the three tissues were analyzed collectively, 36 clusters of similarly expressed genes were identified. By integrating other comprehensive approaches such as gene co-expression analyses, functional enrichment, and cell type deconvolution, we gained profound insights into cattle lactation, revealing tissue-specific characteristics of the gastrointestinal tract and shedding light on the intricate molecular adaptations involved in nutrient absorption, immune regulation, and cellular processes for milk synthesis during lactation.
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Affiliation(s)
- Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; State Key Laboratory of Livestock and Poultry Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark
| | - Cong-Jun Li
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Ransom L Baldwin
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.
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Fletcher P, Clancy CS, O’Donnell KL, Doratt BM, Malherbe DC, Rhoderick JF, Feldmann F, Hanley PW, Takada A, Messaoudi I, Marzi A. Pathogenic differences of cynomolgus macaques after Taï Forest virus infection depend on the viral stock propagation. PLoS Pathog 2024; 20:e1012290. [PMID: 38861571 PMCID: PMC11195944 DOI: 10.1371/journal.ppat.1012290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/24/2024] [Accepted: 05/24/2024] [Indexed: 06/13/2024] Open
Abstract
Taï Forest virus (TAFV) is a negative-sense RNA virus in the Filoviridae family. TAFV has caused only a single human infection, but several disease outbreaks in chimpanzees have been linked to this virus. Limited research has been done on this human-pathogenic virus. We sought to establish an animal model to assess TAFV disease progression and pathogenicity at our facility. We had access to two different viral stock preparations from different institutions, both originating from the single human case. Type I interferon receptor knockout mice were inoculated with TAFV stock 1 or stock 2 by the intraperitoneal route. Inoculation resulted in 100% survival with no disease regardless of viral stock preparation or infectious dose. Next, cynomolgus macaques were inoculated with TAFV stock 1 or stock 2. Inoculation with TAFV stock 1 resulted in 100% survival and robust TAFV glycoprotein-specific IgG responses including neutralizing antibodies. In contrast, macaques infected with TAFV stock 2 developed disease and were euthanized 8-11 days after infection exhibiting viremia, thrombocytopenia, and increased inflammatory mediators identified by transcriptional analysis. Histopathologic analysis of tissue samples collected at necropsy confirmed classic filovirus disease in numerous organs. Genomic differences in both stock preparations were mapped to several viral genes which may have contributed to disease severity. Taken together, we demonstrate that infection with the two TAFV stocks resulted in no disease in mice and opposing disease phenotypes in cynomolgus macaques, highlighting the impact of viral stock propagation on pathogenicity in animal models.
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Affiliation(s)
- Paige Fletcher
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Chad S. Clancy
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Kyle L. O’Donnell
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Brianna M. Doratt
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, United States of America
| | - Delphine C. Malherbe
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, United States of America
| | - Joseph F. Rhoderick
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Patrick W. Hanley
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, United States of America
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
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Fujimori H, Shima‐Nakamura M, Kanno S, Shibuya‐Takahashi R, Mochizuki M, Mizuma M, Unno M, Wakui Y, Abue M, Iwai W, Fukushi D, Satoh K, Yamaguchi K, Shindo N, Yasuda J, Tamai K. FAXC interacts with ANXA2 and SRC in mitochondria and promotes tumorigenesis in cholangiocarcinoma. Cancer Sci 2024; 115:1896-1909. [PMID: 38480477 PMCID: PMC11145136 DOI: 10.1111/cas.16140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 06/04/2024] Open
Abstract
Cholangiocarcinoma (CCA) is one of the most difficult malignancies to treat as the therapeutic options are limited. Although several driver genes have been identified, most remain unknown. In this study, we identified a failed axon connection homolog (FAXC), whose function is unknown in mammals, by analyzing serially passaged CCA xenograft models. Knockdown of FAXC reduced subcutaneous tumorigenicity in mice. FAXC was bound to annexin A2 (ANXA2) and c-SRC, which are tumor-promoting genes. The FAXC/ANXA2/c-SRC complex forms in the mitochondria. FAXC enhances SRC-dependent ANXA2 phosphorylation at tyrosine-24, and the C-terminal amino acid residues (351-375) of FAXC are required for ANXA2 phosphorylation. Transcriptome data from a xenografted CCA cell line revealed that FAXC correlated with epithelial-mesenchymal transition, hypoxia, and KRAS signaling genes. Collectively, these findings advance our understanding of CCA tumorigenesis and provide candidate therapeutic targets.
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Affiliation(s)
- Haruna Fujimori
- Division of Cancer Stem CellMiyagi Cancer Center Research InstituteNatoriJapan
| | - Mao Shima‐Nakamura
- Division of Cancer Stem CellMiyagi Cancer Center Research InstituteNatoriJapan
| | - Shin‐Ichiro Kanno
- IDAC Fellow Research Group for DNA Repair and Dynamic Proteome Institute of Development, Aging and Cancer (IDAC)Tohoku UniversitySendaiJapan
| | | | - Mai Mochizuki
- Division of Cancer Stem CellMiyagi Cancer Center Research InstituteNatoriJapan
| | - Masamichi Mizuma
- Department of SurgeryTohoku University Graduate School of MedicineSendaiJapan
| | - Michiaki Unno
- Department of SurgeryTohoku University Graduate School of MedicineSendaiJapan
| | - Yuta Wakui
- Department of GastroenterologyMiyagi Cancer CenterNatoriJapan
| | - Makoto Abue
- Department of GastroenterologyMiyagi Cancer CenterNatoriJapan
| | - Wataru Iwai
- Department of GastroenterologyMiyagi Cancer CenterNatoriJapan
| | - Daisuke Fukushi
- Division of GastroenterologyTohoku Medical and Pharmaceutical UniversitySendaiJapan
| | - Kennich Satoh
- Division of GastroenterologyTohoku Medical and Pharmaceutical UniversitySendaiJapan
| | - Kazunori Yamaguchi
- Division of Molecular and Cellular OncologyMiyagi Cancer Center Research InstituteNatoriJapan
| | - Norihisa Shindo
- Cancer Chromosome Biology UnitMiyagi Cancer Center Research InstituteNatoriJapan
| | - Jun Yasuda
- Division of Molecular and Cellular OncologyMiyagi Cancer Center Research InstituteNatoriJapan
| | - Keiichi Tamai
- Division of Cancer Stem CellMiyagi Cancer Center Research InstituteNatoriJapan
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Ek CJ, Alkmark M, Baburamani AA, Supramaniam VG, Sood S, Melchiotti R, de Rinaldis E, Hagberg H, Mallard C. Novel biomarkers of preterm brain injury from blood transcriptome in sheep model of intrauterine asphyxia. Pediatr Res 2024:10.1038/s41390-024-03224-1. [PMID: 38822135 DOI: 10.1038/s41390-024-03224-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 03/06/2024] [Accepted: 04/02/2024] [Indexed: 06/02/2024]
Abstract
BACKGROUND Infants born preterm have a higher incidence of neurological deficits. A key step in finding effective treatments is to identify biomarkers that reliably predict outcome. METHODS Following umbilical cord occlusion (UCO) in pregnant sheep, whole fetal blood RNA was sequenced pre- and post-UCO, brain injury outcome was determined by battery of neuropathology scoring and the transcriptome signature correlated to the degree of brain injury. Additionally, we developed a novel analytical procedure to deduce cell blood composition over time. RESULTS Sixty-one genes were identified with significant altered expression after UCO. In pre-UCO blood, the level of three mRNAs (Trex2, Znf280b, novel miRNA) and in post-UCO, four mRNAs (Fam184a, Angptl2, novel lincRNA and an unknown protein-coding gene) were associated to brain injury (FDR < 0.01). Several of these mRNAs are related to inflammation and angiogenesis. Pathway analysis highlighted genes playing a role in perinatal death and growth failure. Results also indicate that several leukocyte populations undergo significant changes after UCO. CONCLUSION We have used a whole transcriptomic approach to uncover novel biomarkers in fetal blood that correlate to neuropathology in the preterm sheep brain. The current data forms a basis for future studies to investigate mechanisms of these mRNAs in the injury progression. IMPACT Trend analysis of genes following asphyxia reveal a group of genes associated with perinatal death and growth failure. Several pre-asphyxia transcripts were associated to brain injury severity suggesting genomic susceptibility to injury. Several post-asphyxia transcripts were correlated to brain injury severity, thus, serve as potential novel biomarkers of injury outcome. Successfully adaptation of cell profiling algorithms suggests significant changes in blood cell composition following asphyxia.
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Affiliation(s)
- C Joakim Ek
- Centre for Perinatal Medicine and Health, Institutes of Neuroscience and Physiology & Clinical Sciences, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden.
| | - Mårten Alkmark
- Centre for Perinatal Medicine and Health, Institutes of Neuroscience and Physiology & Clinical Sciences, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Ana A Baburamani
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, School of Biomedical Engineering and Imaging Sciences, King's Health Partners, St Thomas' Hospital, London, SE1 7EH, UK
| | - Veena G Supramaniam
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, School of Biomedical Engineering and Imaging Sciences, King's Health Partners, St Thomas' Hospital, London, SE1 7EH, UK
| | - Sanjana Sood
- Department of Cancer Epidemiology and Population Health, King's College London, London, UK
| | - Rossella Melchiotti
- Department of Cancer Epidemiology and Population Health, King's College London, London, UK
| | - Emanuele de Rinaldis
- Department of Cancer Epidemiology and Population Health, King's College London, London, UK
| | - Henrik Hagberg
- Centre for Perinatal Medicine and Health, Institutes of Neuroscience and Physiology & Clinical Sciences, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, School of Biomedical Engineering and Imaging Sciences, King's Health Partners, St Thomas' Hospital, London, SE1 7EH, UK
| | - Carina Mallard
- Centre for Perinatal Medicine and Health, Institutes of Neuroscience and Physiology & Clinical Sciences, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
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10
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Shen L, Zeng H, Fu Y, Ma W, Guo X, Luo G, Hua R, Wang X, Shi X, Wu B, Luo C, Quan S. Specific plasma microRNA profiles could be potential non-invasive biomarkers for biochemical pregnancy loss following embryo transfer. BMC Pregnancy Childbirth 2024; 24:351. [PMID: 38720272 PMCID: PMC11080217 DOI: 10.1186/s12884-024-06488-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 04/07/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Plasma microRNAs act as biomarkers for predicting and diagnosing diseases. Reliable non-invasive biomarkers for biochemical pregnancy loss have not been established. We aim to analyze the dynamic microRNA profiles during the peri-implantation period and investigate if plasma microRNAs could be non-invasive biomarkers predicting BPL. METHODS In this study, we collected plasma samples from patients undergoing embryo transfer (ET) on ET day (ET0), 11 days after ET (ET11), and 14 days after ET (ET14). Patients were divided into the NP (negative pregnancy), BPL (biochemical pregnancy loss), and CP (clinical pregnancy) groups according to serum hCG levels at day11~14 and ultrasound at day28~35 following ET. MicroRNA profiles at different time-points were detected by miRNA-sequencing. We analyzed plasma microRNA signatures for BPL at the peri-implantation stage, we characterized the dynamic microRNA changes during the implantation period, constructed a microRNA co-expression network, and established predictive models for BPL. Finally, the sequencing results were confirmed by Taqman RT-qPCR. RESULTS BPL patients have distinct plasma microRNA profiles compared to CP patients at multiple time-points during the peri-implantation period. Machine learning models revealed that plasma microRNAs could predict BPL. RT-qPCR confirmed that miR-181a-2-3p, miR-9-5p, miR-150-3p, miR-150-5p, and miR-98-5p, miR-363-3p were significantly differentially expressed between patients with different reproductive outcomes. CONCLUSION Our study highlights the non-invasive value of plasma microRNAs in predicting BPL.
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Affiliation(s)
- Lang Shen
- Reproductive Center of Gynecology and Obstetrics Department, NanFang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Hong Zeng
- Reproductive Center of Gynecology and Obstetrics Department, NanFang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Reproductive Medicine Center, Foshan Maternal and Child Health Care Hospital, Southern Medical University, Foshan, 528000, China
| | - Yu Fu
- Reproductive Center of Gynecology and Obstetrics Department, NanFang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Wenmin Ma
- Department of Reproductive Medicine Center, Foshan Maternal and Child Health Care Hospital, Southern Medical University, Foshan, 528000, China
| | - Xiaoling Guo
- Department of Reproductive Medicine Center, Foshan Maternal and Child Health Care Hospital, Southern Medical University, Foshan, 528000, China
| | - Guoqun Luo
- Department of Reproductive Medicine Center, Foshan Maternal and Child Health Care Hospital, Southern Medical University, Foshan, 528000, China
| | - Rui Hua
- Reproductive Center of Gynecology and Obstetrics Department, NanFang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaocong Wang
- Reproductive Center of Gynecology and Obstetrics Department, NanFang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiao Shi
- Reproductive Center of Gynecology and Obstetrics Department, NanFang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Biao Wu
- Reproductive Center of Gynecology and Obstetrics Department, NanFang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Chen Luo
- Reproductive Center of Gynecology and Obstetrics Department, NanFang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Song Quan
- Reproductive Center of Gynecology and Obstetrics Department, NanFang Hospital, Southern Medical University, Guangzhou, 510515, China.
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11
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Lorenzo MG, Fernandes GDR, Latorre-Estivalis JM. Local age-dependent neuromodulation in Rhodnius prolixus antennae. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22106. [PMID: 38597092 DOI: 10.1002/arch.22106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
Kissing bugs do not respond to host cues when recently molted and only exhibit robust host-seeking several days after ecdysis. Behavioral plasticity has peripheral correlates in antennal gene expression changes through the week after ecdysis. The mechanisms regulating these peripheral changes are still unknown, but neuropeptide, G-protein coupled receptor, nuclear receptor, and takeout genes likely modulate peripheral sensory physiology. We evaluated their expression in antennal transcriptomes along the first week postecdysis of Rhodnius prolixus 5th instar larvae. Besides, we performed clustering and co-expression analyses to reveal relationships between neuromodulatory (NM) and sensory genes. Significant changes in transcript abundance were detected for 50 NM genes. We identified 73 sensory-related and NM genes that were assigned to nine clusters. According to their expression patterns, clusters were classified into four groups: two including genes up or downregulated immediately after ecdysis; and two with genes with expression altered at day 2. Several NM genes together with sensory genes belong to the first group, suggesting functional interactions. Co-expression network analysis revealed a set of genes that seem to connect with sensory system maturation. Significant expression changes in NM components were described in the antennae of R. prolixus after ecdysis, suggesting that a local NM system acts on antennal physiology. These changes may modify the sensitivity of kissing bugs to host cues during this maturation interval.
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Affiliation(s)
- Marcelo Gustavo Lorenzo
- Instituto de Investigaciones en Biodiversidad y Biotecnología, CONICET, Mar del Plata, Buenos Aires, Argentina
- Vector Behaviour and Pathogen Interaction Group, Instituto René Rachou-FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
| | | | - Jose Manuel Latorre-Estivalis
- Laboratorio de Insectos Sociales, Instituto de Fisiología, Biología Molecular y Neurociencias, Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina
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12
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Zhu P, Ren Q, Zhang R, Zhang L, Xia X, Zheng C, Ye T. Exploring the effects of calycosin on anthracycline-induced cardiotoxicity: a network pharmacology, molecular docking, and experimental study. Front Cardiovasc Med 2024; 11:1286620. [PMID: 38576421 PMCID: PMC10991710 DOI: 10.3389/fcvm.2024.1286620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 03/11/2024] [Indexed: 04/06/2024] Open
Abstract
Background Chemotherapy with anthracyclines can cause cardiotoxicity, possibly leading to stopping treatment in some cancer patients. In cardio-oncology research, preventing and minimizing anthracycline-induced cardiotoxicity (AIC) is a hot issue. For the treatment of AIC, calycosin (CA), an isoflavone component in astragali radix (AR), has become a research focus. However, the elaborate mechanisms of calycosin treating AIC remain to be unrevealed. Aim of the study To explore the effects of CA on AIC through multiple dimensions concerning network pharmacology, molecular docking, and experimental evaluations. Methods The study evaluated calycosin's potential targets and mechanisms for treating AIC using network pharmacology and molecular docking. The candidate genes/targets of CA and AIC were screened using the online-available database. Protein-protein interactions (PPI) between the common targets were constructed using the STRING platform, and the results were then visualized using Cytoscape. Molecular docking was used to evaluate the strength of the binding force between CA and the common targets. The possible pharmacological mechanisms of CA were explained by pathway enrichment and GSEA. Subsequently, the candidate targets were identified in vitro experiments. Results Network pharmacology effectively discovered the CA's multitarget intervention in AIC, including TNF, ABCC1, TOP2A, ABCB1, and XDH. CA binds to the ATP-binding cassette subfamily B member 1(ABCB1) had the highest binding energy (-7.5 kcal/mol) according to the molecular docking analysis and was selected and visualized for subsequent analysis. In vitro experiments showed that ABCB1 exhibited significant time-curve changes under different doses of doxorubicin (DOX) compared with DMSO control experiments. The anti-AIC pharmacological mechanism of CA were revealed by highlighting the biological processes of oxidative stress (OR) and inflammation. Conclusions We employed a practicable bioinformatics method to connect network and molecular docking to determine the calycosin's therapeutic mechanism against AIC and identified some bioinformatics results in in vitro experiments. The results presented show that CA may represent an encouraging treatment for AIC.
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Affiliation(s)
- Peng Zhu
- Department of Hepatobiliary Surgery, Wuhan No.1 Hospital, Wuhan, China
| | - Qianqian Ren
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, China
| | - Ruizhi Zhang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, China
| | - Licai Zhang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, China
| | - Xiangwen Xia
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, China
| | - Chuansheng Zheng
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, China
| | - Tianhe Ye
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, China
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13
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Scharl T, Grün B. A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models. BMC Bioinformatics 2024; 25:90. [PMID: 38429687 PMCID: PMC10905927 DOI: 10.1186/s12859-024-05717-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/21/2024] [Indexed: 03/03/2024] Open
Abstract
RNA sequencing of time-course experiments results in three-way count data where the dimensions are the genes, the time points and the biological units. Clustering RNA-seq data allows to extract groups of co-expressed genes over time. After standardisation, the normalised counts of individual genes across time points and biological units have similar properties as compositional data. We propose the following procedure to suitably cluster three-way RNA-seq data: (1) pre-process the RNA-seq data by calculating the normalised expression profiles, (2) transform the data using the additive log ratio transform to map the composition in the D-part Aitchison simplex to a D - 1 -dimensional Euclidean vector, (3) cluster the transformed RNA-seq data using matrix-variate Gaussian mixture models and (4) assess the quality of the overall cluster solution and of individual clusters based on cluster separation in the transformed space using density-based silhouette information and on compactness of the cluster in the original space using cluster maps as a suitable visualisation. The proposed procedure is illustrated on RNA-seq data from fission yeast and results are also compared to an analogous two-way approach after flattening out the biological units.
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Affiliation(s)
- Theresa Scharl
- Institute of Statistics, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Bettina Grün
- Institute for Statistics and Mathematics, Vienna University of Economics and Business, Vienna, Austria
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14
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Coschiera A, Yoshihara M, Lauter G, Ezer S, Pucci M, Li H, Kavšek A, Riedel CG, Kere J, Swoboda P. Primary cilia promote the differentiation of human neurons through the WNT signaling pathway. BMC Biol 2024; 22:48. [PMID: 38413974 PMCID: PMC10900739 DOI: 10.1186/s12915-024-01845-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Primary cilia emanate from most human cell types, including neurons. Cilia are important for communicating with the cell's immediate environment: signal reception and transduction to/from the ciliated cell. Deregulation of ciliary signaling can lead to ciliopathies and certain neurodevelopmental disorders. In the developing brain cilia play well-documented roles for the expansion of the neural progenitor cell pool, while information about the roles of cilia during post-mitotic neuron differentiation and maturation is scarce. RESULTS We employed ciliated Lund Human Mesencephalic (LUHMES) cells in time course experiments to assess the impact of ciliary signaling on neuron differentiation. By comparing ciliated and non-ciliated neuronal precursor cells and neurons in wild type and in RFX2 -/- mutant neurons with altered cilia, we discovered an early-differentiation "ciliary time window" during which transient cilia promote axon outgrowth, branching and arborization. Experiments in neurons with IFT88 and IFT172 ciliary gene knockdowns, leading to shorter cilia, confirm these results. Cilia promote neuron differentiation by tipping WNT signaling toward the non-canonical pathway, in turn activating WNT pathway output genes implicated in cyto-architectural changes. CONCLUSIONS We provide a mechanistic entry point into when and how ciliary signaling coordinates, promotes and translates into anatomical changes. We hypothesize that ciliary alterations causing neuron differentiation defects may result in "mild" impairments of brain development, possibly underpinning certain aspects of neurodevelopmental disorders.
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Affiliation(s)
- Andrea Coschiera
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba, Japan
- Chiba University, Chiba, Japan
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala, Sweden
- Uppsala University, Uppsala, Sweden
| | - Sini Ezer
- University of Helsinki, Stem Cells and Metabolism Research Program, and Folkhälsan Research Center, Helsinki, Finland
| | - Mariangela Pucci
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Bioscience and Technology for Food, Agriculture and Environment, Teramo, Italy
- University of Teramo, Teramo, Italy
| | - Haonan Li
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Alan Kavšek
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Christian G Riedel
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- University of Helsinki, Stem Cells and Metabolism Research Program, and Folkhälsan Research Center, Helsinki, Finland
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
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15
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Xu Z, Liu Q, Ning C, Yang M, Zhu Q, Li D, Wang T, Li F. miRNA profiling of chicken follicles during follicular development. Sci Rep 2024; 14:2212. [PMID: 38278859 PMCID: PMC10817932 DOI: 10.1038/s41598-024-52716-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 01/23/2024] [Indexed: 01/28/2024] Open
Abstract
MicroRNAs (miRNAs) play a crucial role as transcription regulators in various aspects of follicular development, including steroidogenesis, ovulation, apoptosis, and gene regulation in poultry. However, there is a paucity of studies examining the specific impact of miRNAs on ovarian granulosa cells (GCs) across multiple grades in laying hens. Consequently, this study aims to investigate the roles of miRNAs in chicken GCs. By constructing miRNA expression profiles of GCs at 10 different time points, encompassing 4 pre-hierarchical, 5 preovulatory, and 1 postovulatory follicles stage, we identified highly expressed miRNAs involved in GC differentiation (miR-148a-3p, miR-143-3p), apoptosis (let7 family, miR-363-3p, miR-30c-5p, etc.), and autophagy (miR-128-3p, miR-21-5p). Furthermore, we discovered 48 developmentally dynamic miRNAs (DDMs) that target 295 dynamic differentially expressed genes (DDGs) associated with follicular development and selection (such as oocyte meiosis, progesterone-mediated oocyte maturation, Wnt signaling pathway, TGF-β signaling pathway) as well as follicular regression (including autophagy and cellular senescence). These findings contribute to a more comprehensive understanding of the intricate mechanisms underlying follicle recruitment, selection, and degeneration, aiming to enhance poultry's reproductive capacity.
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Affiliation(s)
- Zhongxian Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, China
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qian Liu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, China
| | - Chunyou Ning
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Maosen Yang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qing Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Diyan Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Tao Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, China.
| | - Feng Li
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, China.
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16
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Vural-Ozdeniz M, Calisir K, Acar R, Yavuz A, Ozgur MM, Dalgıc E, Konu O. CAP-RNAseq: an integrated pipeline for functional annotation and prioritization of co-expression clusters. Brief Bioinform 2024; 25:bbad536. [PMID: 38279653 PMCID: PMC10818169 DOI: 10.1093/bib/bbad536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/04/2023] [Accepted: 12/21/2024] [Indexed: 01/28/2024] Open
Abstract
Cluster analysis is one of the most widely used exploratory methods for visualization and grouping of gene expression patterns across multiple samples or treatment groups. Although several existing online tools can annotate clusters with functional terms, there is no all-in-one webserver to effectively prioritize genes/clusters using gene essentiality as well as congruency of mRNA-protein expression. Hence, we developed CAP-RNAseq that makes possible (1) upload and clustering of bulk RNA-seq data followed by identification, annotation and network visualization of all or selected clusters; and (2) prioritization using DepMap gene essentiality and/or dependency scores as well as the degree of correlation between mRNA and protein levels of genes within an expression cluster. In addition, CAP-RNAseq has an integrated primer design tool for the prioritized genes. Herein, we showed using comparisons with the existing tools and multiple case studies that CAP-RNAseq can uniquely aid in the discovery of co-expression clusters enriched with essential genes and prioritization of novel biomarker genes that exhibit high correlations between their mRNA and protein expression levels. CAP-RNAseq is applicable to RNA-seq data from different contexts including cancer and available at http://konulabapps.bilkent.edu.tr:3838/CAPRNAseq/ and the docker image is downloadable from https://hub.docker.com/r/konulab/caprnaseq.
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Affiliation(s)
| | - Kubra Calisir
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Türkiye
| | - Rana Acar
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Türkiye
| | - Aysenur Yavuz
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Türkiye
| | - Mustafa M Ozgur
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Türkiye
| | - Ertugrul Dalgıc
- Department of Medical Biology, School of Medicine, Zonguldak Bülent Ecevit University, Zonguldak, Türkiye
| | - Ozlen Konu
- Department of Neuroscience, Bilkent University, Ankara, Türkiye
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Türkiye
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17
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Raja R, Khanum S, Aboulmouna L, Maurya MR, Gupta S, Subramaniam S, Ramkrishna D. Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach. Biophys J 2024; 123:221-234. [PMID: 38102827 PMCID: PMC10808046 DOI: 10.1016/j.bpj.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 09/18/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023] Open
Abstract
Quantitative understanding of cellular processes, such as cell cycle and differentiation, is impeded by various forms of complexity ranging from myriad molecular players and their multilevel regulatory interactions, cellular evolution with multiple intermediate stages, lack of elucidation of cause-effect relationships among the many system players, and the computational complexity associated with the profusion of variables and parameters. In this paper, we present a modeling framework based on the cybernetic concept that biological regulation is inspired by objectives embedding rational strategies for dimension reduction, process stage specification through the system dynamics, and innovative causal association of regulatory events with the ability to predict the evolution of the dynamical system. The elementary step of the modeling strategy involves stage-specific objective functions that are computationally determined from experiments, augmented with dynamical network computations involving endpoint objective functions, mutual information, change-point detection, and maximal clique centrality. We demonstrate the power of the method through application to the mammalian cell cycle, which involves thousands of biomolecules engaged in signaling, transcription, and regulation. Starting with a fine-grained transcriptional description obtained from RNA sequencing measurements, we develop an initial model, which is then dynamically modeled using the cybernetic-inspired method, based on the strategies described above. The cybernetic-inspired method is able to distill the most significant interactions from a multitude of possibilities. In addition to capturing the complexity of regulatory processes in a mechanistically causal and stage-specific manner, we identify the functional network modules, including novel cell cycle stages. Our model is able to predict future cell cycles consistent with experimental measurements. We posit that this innovative framework has the promise to extend to the dynamics of other biological processes, with a potential to provide novel mechanistic insights.
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Affiliation(s)
- Rubesh Raja
- The Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana
| | - Sana Khanum
- The Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana
| | - Lina Aboulmouna
- Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Mano R Maurya
- Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Shakti Gupta
- Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Shankar Subramaniam
- Department of Bioengineering, University of California San Diego, La Jolla, California; Departments of Computer Science and Engineering, Cellular and Molecular Medicine, San Diego Supercomputer Center, and the Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, California.
| | - Doraiswami Ramkrishna
- The Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana.
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18
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VanKuren NW, Sheikh SI, Massardo D, Lu W, Kronforst MR. Supergene evolution via gain of auto-regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574839. [PMID: 38260248 PMCID: PMC10802445 DOI: 10.1101/2024.01.09.574839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The development of complex phenotypes requires the coordinated action of many genes across space and time, yet many species have evolved the ability to develop multiple discrete, alternate phenotypes1-3. Such polymorphisms are often controlled by supergenes, sets of tightly-linked mutations in one or more loci that function together to produce a complex phenotype4. Although theories of supergene evolution are well-established, the mutations that cause functional differences between supergene alleles remain essentially unknown. doublesex is the master regulator of insect sexual differentiation but functions as a supergene in multiple Papilio swallowtail butterflies, where divergent dsx alleles control development of discrete non-mimetic or mimetic female wing color patterns5-7. Here we demonstrate that the functional elements of the mimetic allele in Papilio alphenor are six new cis-regulatory elements (CREs) spread across 150 kb that are bound by DSX itself. Our findings provide experimental support to classic supergene theory and suggest that the evolution of auto-regulation may provide a simple route to supergene origination and to the co-option of pleiotropic genes into new developmental roles.
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Affiliation(s)
| | - Sofia I. Sheikh
- Department of Ecology & Evolution, The University of Chicago, Chicago IL USA
| | - Darli Massardo
- Department of Ecology & Evolution, The University of Chicago, Chicago IL USA
| | - Wei Lu
- Department of Ecology & Evolution, The University of Chicago, Chicago IL USA
| | - Marcus R. Kronforst
- Department of Ecology & Evolution, The University of Chicago, Chicago IL USA
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19
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Cheng S, You Y, Wang X, Yi C, Zhang W, Xie Y, Xiu L, Luo F, Lu Y, Wang J, Hu W. Dynamic profiles of lncRNAs reveal a functional natural antisense RNA that regulates the development of Schistosoma japonicum. PLoS Pathog 2024; 20:e1011949. [PMID: 38285715 PMCID: PMC10878521 DOI: 10.1371/journal.ppat.1011949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/20/2024] [Accepted: 01/06/2024] [Indexed: 01/31/2024] Open
Abstract
Schistosomes are flatworm parasites that undergo a complex life cycle involving two hosts. The regulation of the parasite's developmental processes relies on both coding RNAs and non-coding RNAs. However, the roles of non-coding RNAs, including long non-coding RNAs (lncRNAs) in schistosomes remain largely unexplored. Here we conduct advanced RNA sequencing on male and female S. japonicum during their pairing and reproductive development, resulting in the identification of nearly 8,000 lncRNAs. This extensive dataset enables us to construct a comprehensive co-expression network of lncRNAs and mRNAs, shedding light on their interactions during the crucial reproductive stages within the mammalian host. Importantly, we have also revealed a specific lncRNA, LNC3385, which appears to play a critical role in the survival and reproduction of the parasite. These findings not only enhance our understanding of the dynamic nature of lncRNAs during the reproductive phase of schistosomes but also highlight LNC3385 as a potential therapeutic target for combating schistosomiasis.
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Affiliation(s)
- Shaoyun Cheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yanmin You
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaoling Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Cun Yi
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wei Zhang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuxiang Xie
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Lei Xiu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Fang Luo
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jipeng Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wei Hu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, China
- College of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia Autonomous Region, China
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
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20
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Prator CA, Dorratt BM, O’Donnell KL, Lack J, Pinski AN, Ricklefs S, Martens CA, Messaoudi I, Marzi A. Transcriptional profiling of immune responses in NHPs after low-dose, VSV-based vaccination against Marburg virus. Emerg Microbes Infect 2023; 12:2252513. [PMID: 37616377 PMCID: PMC10498809 DOI: 10.1080/22221751.2023.2252513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 08/26/2023]
Abstract
Infection with Marburg virus (MARV), the causative agent of Marburg virus disease (MVD), results in haemorrhagic disease and high case fatality rates (>40%) in humans. Despite its public health relevance, there are no licensed vaccines or therapeutics to prevent or treat MVD. A vesicular stomatitis virus (VSV)-based vaccine expressing the MARV glycoprotein (VSV-MARV) is currently in clinical development. Previously, a single 10 million PFU dose of VSV-MARV administered 1-5 weeks before lethal MARV challenge conferred uniform protection in nonhuman primates (NHPs), demonstrating fast-acting potential. Additionally, our group recently demonstrated that even a low dose VSV-MARV (1000 PFU) protected NHPs when given 7 days before MARV challenge. In this study, we longitudinally profiled the transcriptional responses of NHPs vaccinated with this low dose of VSV-MARV either 14 or 7 days before lethal MARV challenge. NHPs vaccinated 14 days before challenge presented with transcriptional changes consistent with an antiviral response before challenge. Limited gene expression changes were observed in the group vaccinated 7 days before challenge. After challenge, genes related to lymphocyte-mediated immunity were only observed in the group vaccinated 14 days before challenge, indicating that the length of time between vaccination and challenge influenced gene expression. Our results indicate that a low dose VSV-MARV elicits distinct immune responses that correlate with protection against MVD. A low dose of VSV-MARV should be evaluated in clinical rails as it may be an option to deliver beneficial public health outcomes to more people in the event of future outbreaks.
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Affiliation(s)
- Cecilia A. Prator
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Brianna M. Dorratt
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Kyle L. O’Donnell
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amanda N. Pinski
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Stacy Ricklefs
- Research Technology Branch, Division of Intramural Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Craig A. Martens
- Research Technology Branch, Division of Intramural Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
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21
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Langston PK, Sun Y, Ryback BA, Mueller AL, Spiegelman BM, Benoist C, Mathis D. Regulatory T cells shield muscle mitochondria from interferon-γ-mediated damage to promote the beneficial effects of exercise. Sci Immunol 2023; 8:eadi5377. [PMID: 37922340 PMCID: PMC10860652 DOI: 10.1126/sciimmunol.adi5377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/02/2023] [Indexed: 11/05/2023]
Abstract
Exercise enhances physical performance and reduces the risk of many disorders such as cardiovascular disease, type 2 diabetes, dementia, and cancer. Exercise characteristically incites an inflammatory response, notably in skeletal muscles. Although some effector mechanisms have been identified, regulatory elements activated in response to exercise remain obscure. Here, we have addressed the roles of Foxp3+CD4+ regulatory T cells (Tregs) in the healthful activities of exercise via immunologic, transcriptomic, histologic, metabolic, and biochemical analyses of acute and chronic exercise models in mice. Exercise rapidly induced expansion of the muscle Treg compartment, thereby guarding against overexuberant production of interferon-γ and consequent metabolic disruptions, particularly mitochondrial aberrancies. The performance-enhancing effects of exercise training were dampened in the absence of Tregs. Thus, exercise is a natural Treg booster with therapeutic potential in disease and aging contexts.
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Affiliation(s)
- P. Kent Langston
- Department of Immunology, Harvard Medical School; Boston, 02115, USA
| | - Yizhi Sun
- Department of Cancer Biology, Dana-Farber Cancer Institute; Boston, 02115, USA
- Department of Cell Biology, Harvard Medical School; Boston, 02115, USA
| | - Birgitta A. Ryback
- Department of Cancer Biology, Dana-Farber Cancer Institute; Boston, 02115, USA
| | - Amber L. Mueller
- Department of Genetics, Harvard Medical School; Boston, 02115, USA
| | - Bruce M. Spiegelman
- Department of Cancer Biology, Dana-Farber Cancer Institute; Boston, 02115, USA
- Department of Cell Biology, Harvard Medical School; Boston, 02115, USA
| | | | - Diane Mathis
- Department of Immunology, Harvard Medical School; Boston, 02115, USA
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22
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Paull RE, Ksouri N, Kantar M, Zerpa‐Catanho D, Chen NJ, Uruu G, Yue J, Guo S, Zheng Y, Wai CMJ, Ming R. Differential gene expression during floral transition in pineapple. PLANT DIRECT 2023; 7:e541. [PMID: 38028646 PMCID: PMC10644199 DOI: 10.1002/pld3.541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 12/01/2023]
Abstract
Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 h to 8 days after treatment, 7961 genes were found to exhibit differential expression (DE) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up-regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS-like 3 (CO), a WUSCHEL gene, two APETALA1/FRUITFULL (AP1/FUL) genes, an epidermal patterning gene, and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up-regulated within a day of treatment, their predicted targets being the up-regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS-like APETELAR (AP2), and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up-regulated at the apex and not at the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads act directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP, and AP2. A model based on AP2/ERTF DE and predicted DE target genes was developed to give focus to future research. The identified candidate genes are potential targets for genetic manipulation to determine their molecular role in flower transition.
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Affiliation(s)
- Robert E. Paull
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Najla Ksouri
- Laboratory of Genomics, Genetics and Breeding of Fruits and Grapevine, Experimental Aula Dei‐CSICZaragozaSpain
| | - Michael Kantar
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | | | - Nancy Jung Chen
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Gail Uruu
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Jingjing Yue
- Center for Genomics and BiotechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Shiyong Guo
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational MedicineKunming University of Science and TechnologyKunmingYunnanChina
| | - Yun Zheng
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational MedicineKunming University of Science and TechnologyKunmingYunnanChina
| | | | - Ray Ming
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Center for Genomics and BiotechnologyFujian Agriculture and Forestry UniversityFuzhouChina
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23
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Rodríguez-Lorenzo M, Mauri N, Royo C, Rambla JL, Diretto G, Demurtas O, Hilbert G, Renaud C, Tobar V, Huete J, Delrot S, Granell A, Martínez-Zapater JM, Carbonell-Bejerano P. The flavour of grape colour: anthocyanin content tunes aroma precursor composition by altering the berry microenvironment. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6369-6390. [PMID: 37294268 PMCID: PMC10627162 DOI: 10.1093/jxb/erad223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 06/07/2023] [Indexed: 06/10/2023]
Abstract
Anthocyaninless (white) instead of black/red (coloured) fruits develop in grapevine cultivars without functional VviMYBA1 and VviMYBA2 genes, and this conditions the colour of wines that can be produced. To evaluate whether this genetic variation has additional consequences on fruit ripening and composition, we performed comparisons of microenvironment, transcriptomics, and metabolomics of developing grapes between near-isogenic white- and black-berried somatic variants of Garnacha and Tempranillo cultivars. Berry temperature was as much as 3.5 ºC lower in white- compared to black-berried Tempranillo. An RNA-seq study combined with targeted and untargeted metabolomics revealed that ripening fruits of white-berried variants were characterized by the up-regulation of photosynthesis-related and other light-responsive genes and by their higher accumulation of specific terpene aroma precursors, fatty acid-derived aldehyde volatiles, and phenylpropanoid precursor amino acids. MYBA1-MYBA2 function proved essential for flavonol trihydroxylation in black-berried somatic variants, which were also characterized by enhanced expression of pathogen defence genes in the berry skin and increased accumulation of C6-derived alcohol and ester volatiles and γ-aminobutyric acid. Collectively, our results indicate that anthocyanin depletion has side-effects on grape composition by altering the internal microenvironment of the berry and the partitioning of the phenylpropanoid pathway. Our findings show how fruit colour can condition other fruit features, such as flavour potential and stress homeostasis.
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Affiliation(s)
- Maite Rodríguez-Lorenzo
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, 26007 Logroño, Spain
| | - Nuria Mauri
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, 26007 Logroño, Spain
| | - Carolina Royo
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, 26007 Logroño, Spain
| | - José L Rambla
- Instituto de Biología Molecular y Celular de Plantas, IBMCP, CSIC - Universidad Politécnica de Valencia, 46011 Valencia, Spain
- Universitat Jaume I, Departamento de Biología, Bioquímica y Ciencias Naturales, 12071 Castellón de la Plana, Spain
| | - Gianfranco Diretto
- Italian National Agency for New Technologies Energy and Sustainable Development, Casaccia Research Centre, 00123 Rome, Italy
| | - Olivia Demurtas
- Italian National Agency for New Technologies Energy and Sustainable Development, Casaccia Research Centre, 00123 Rome, Italy
| | - Ghislaine Hilbert
- EGFV, Bordeaux Sciences Agro, INRA - Université de Bordeaux, ISVV, 33140 Villenave d’Ornon, France
| | - Christel Renaud
- EGFV, Bordeaux Sciences Agro, INRA - Université de Bordeaux, ISVV, 33140 Villenave d’Ornon, France
| | - Vanessa Tobar
- Servicio de Información Agroclimática de La Rioja (SIAR). Consejería de Agricultura, Ganadería y Medio Ambiente, Gobierno de La Rioja, 26007 Logroño, Spain
| | - Joaquín Huete
- Servicio de Información Agroclimática de La Rioja (SIAR). Consejería de Agricultura, Ganadería y Medio Ambiente, Gobierno de La Rioja, 26007 Logroño, Spain
| | - Serge Delrot
- EGFV, Bordeaux Sciences Agro, INRA - Université de Bordeaux, ISVV, 33140 Villenave d’Ornon, France
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, IBMCP, CSIC - Universidad Politécnica de Valencia, 46011 Valencia, Spain
| | - José Miguel Martínez-Zapater
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, 26007 Logroño, Spain
| | - Pablo Carbonell-Bejerano
- Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC - Universidad de La Rioja - Gobierno de La Rioja, 26007 Logroño, Spain
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24
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Wang Z, Tian W, Wang D, Guo Y, Cheng Z, Zhang Y, Li X, Zhi Y, Li D, Li Z, Jiang R, Li G, Tian Y, Kang X, Li H, Dunn IC, Liu X. Comparative analyses of dynamic transcriptome profiles highlight key response genes and dominant isoforms for muscle development and growth in chicken. Genet Sel Evol 2023; 55:73. [PMID: 37872550 PMCID: PMC10591418 DOI: 10.1186/s12711-023-00849-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Modern breeding strategies have resulted in significant differences in muscle mass between indigenous chicken and specialized broiler. However, the molecular regulatory mechanisms that underlie these differences remain elusive. The aim of this study was to identify key genes and regulatory mechanisms underlying differences in breast muscle development between indigenous chicken and specialized broiler. RESULTS Two time-series RNA-sequencing profiles of breast muscles were generated from commercial Arbor Acres (AA) broiler (fast-growing) and Chinese indigenous Lushi blue-shelled-egg (LS) chicken (slow-growing) at embryonic days 10, 14, and 18, and post-hatching day 1 and weeks 1, 3, and 5. Principal component analysis of the transcriptome profiles showed that the top four principal components accounted for more than 80% of the total variance in each breed. The developmental axes between the AA and LS chicken overlapped at the embryonic stages but gradually separated at the adult stages. Integrative investigation of differentially-expressed transcripts contained in the top four principal components identified 44 genes that formed a molecular network associated with differences in breast muscle mass between the two breeds. In addition, alternative splicing analysis revealed that genes with multiple isoforms always had one dominant transcript that exhibited a significantly higher expression level than the others. Among the 44 genes, the TNFRSF6B gene, a mediator of signal transduction pathways and cell proliferation, harbored two alternative splicing isoforms, TNFRSF6B-X1 and TNFRSF6B-X2. TNFRSF6B-X1 was the dominant isoform in both breeds before the age of one week. A switching event of the dominant isoform occurred at one week of age, resulting in TNFRSF6B-X2 being the dominant isoform in AA broiler, whereas TNFRSF6B-X1 remained the dominant isoform in LS chicken. Gain-of-function assays demonstrated that both isoforms promoted the proliferation of chicken primary myoblasts, but only TNFRSF6B-X2 augmented the differentiation and intracellular protein content of chicken primary myoblasts. CONCLUSIONS For the first time, we identified several key genes and dominant isoforms that may be responsible for differences in muscle mass between slow-growing indigenous chicken and fast-growing commercial broiler. These findings provide new insights into the regulatory mechanisms underlying breast muscle development in chicken.
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Affiliation(s)
- Zhang Wang
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Weihua Tian
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Dandan Wang
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Yulong Guo
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Zhimin Cheng
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Yanyan Zhang
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Xinyan Li
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Yihao Zhi
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Donghua Li
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China.
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China.
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China.
| | - Ian C Dunn
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK.
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China.
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China.
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China.
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25
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Khajuria DK, Reider I, Kamal F, Norbury CC, Elbarbary RA. Distinct defects in early innate and late adaptive immune responses typify impaired fracture healing in diet-induced obesity. Front Immunol 2023; 14:1250309. [PMID: 37854593 PMCID: PMC10579581 DOI: 10.3389/fimmu.2023.1250309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/25/2023] [Indexed: 10/20/2023] Open
Abstract
Bone fractures, the most common musculoskeletal injuries, heal through three main phases: inflammatory, repair, and remodeling. Around 10% of fracture patients suffer from impaired healing that requires surgical intervention, a huge burden on the healthcare system. The rate of impaired healing increases with metabolic diseases such as obesity-associated hyperglycemia/type 2 diabetes (T2D), an increasing concern given the growing incidence of obesity/T2D. Immune cells play pivotal roles in fracture healing, and obesity/T2D is associated with defective immune-cell functions. However, there is a gap in knowledge regarding the stoichiometry of immune cells that populate the callus and how that population changes during different phases of healing. Here, we used complementary global and single-cell techniques to characterize the repertoire of immune cells in the fracture callus and to identify populations specifically enriched in the fracture callus relative to the unfractured bone or bone marrow. Our analyses identified two clear waves of immune-cell infiltration into the callus: the first wave occurs during the early inflammatory phase of fracture healing, while the second takes place during the late repair/early remodeling phase, which is consistent with previous publications. Comprehensive analysis of each wave revealed that innate immune cells were activated during the early inflammatory phase, but in later phases they returned to homeostatic numbers and activation levels. Of the innate immune cells, distinct subsets of activated dendritic cells were particularly enriched in the inflammatory healing hematoma. In contrast to innate cells, lymphocytes, including B and T cells, were enriched and activated in the callus primarily during the late repair phase. The Diet-Induced Obesity (DIO) mouse, an established model of obesity-associated hyperglycemia and insulin resistance, suffers from multiple healing defects. Our data demonstrate that DIO mice exhibit dysregulated innate immune responses during the inflammatory phase, and defects in all lymphocyte compartments during the late repair phase. Taken together, our data characterize, for the first time, immune populations that are enriched/activated in the callus during two distinct phases of fracture healing and identify defects in the healing-associated immune response in DIO mice, which will facilitate future development of immunomodulatory therapeutics for impaired fracture healing.
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Affiliation(s)
- Deepak Kumar Khajuria
- Department of Orthopaedics and Rehabilitation, The Pennsylvania State University College of Medicine, Hershey, PA, United States
- Center for Orthopaedic Research and Translational Science (CORTS), The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Irene Reider
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Fadia Kamal
- Department of Orthopaedics and Rehabilitation, The Pennsylvania State University College of Medicine, Hershey, PA, United States
- Center for Orthopaedic Research and Translational Science (CORTS), The Pennsylvania State University College of Medicine, Hershey, PA, United States
- Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Christopher C. Norbury
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Reyad A. Elbarbary
- Department of Orthopaedics and Rehabilitation, The Pennsylvania State University College of Medicine, Hershey, PA, United States
- Center for Orthopaedic Research and Translational Science (CORTS), The Pennsylvania State University College of Medicine, Hershey, PA, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, United States
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, State College, PA, United States
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26
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Huang P, Li C, Lin F, Liu Y, Zong Y, Li B, Zheng Y. Chromosome-level genome assembly and population genetic analysis of a near-threatened rosewood species ( Dalbergia cultrata Pierre Graham ex Benth) provide insights into its evolutionary and cold stress responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1212967. [PMID: 37810393 PMCID: PMC10552272 DOI: 10.3389/fpls.2023.1212967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/28/2023] [Indexed: 10/10/2023]
Abstract
Dalbergia cultrata Pierre Graham ex Benth (D. cultrata) is a precious rosewood tree species that grows in the tropical and subtropical regions of Asia. In this study, we used PacBio long-reading sequencing technology and Hi-C assistance to sequence and assemble the reference genome of D. cultrata. We generated 171.47 Gb PacBio long reads and 72.43 Gb Hi-C data and yielded an assembly of 10 pseudochromosomes with a total size of 690.99 Mb and Scaffold N50 of 65.76 Mb. The analysis of specific genes revealed that the triterpenoids represented by lupeol may play an important role in D. cultrata's potential medicinal value. Using the new reference genome, we analyzed the resequencing of 19 Dalbergia accessions and found that D. cultrata and D. cochinchinensis have the latest genetic relationship. Transcriptome sequencing of D. cultrata leaves grown under cold stress revealed that MYB transcription factor and E3 ubiquitin ligase may be playing an important role in the cold response of D. cultrata. Genome resources and identified genetic variation, especially those genes related to the biosynthesis of phytochemicals and cold stress response, will be helpful for the introduction, domestication, utilization, and further breeding of Dalbergia species.
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Affiliation(s)
- Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Changhong Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Furong Lin
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yu Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, Zhejiang, China
| | - Yichen Zong
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bin Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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27
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Calviño C, Ceballos C, Alfonso A, Jauregui P, Calleja-Cervantes ME, San Martin-Uriz P, Rodriguez-Marquez P, Martin-Mallo A, Iglesias E, Abizanda G, Rodriguez-Diaz S, Martinez-Turrillas R, Illarramendi J, Viguria MC, Redondo M, Rifon J, Villar S, Lasarte JJ, Inoges S, Lopez-Diaz de Cerio A, Hernaez M, Prosper F, Rodriguez-Madoz JR. Optimization of universal allogeneic CAR-T cells combining CRISPR and transposon-based technologies for treatment of acute myeloid leukemia. Front Immunol 2023; 14:1270843. [PMID: 37795087 PMCID: PMC10546312 DOI: 10.3389/fimmu.2023.1270843] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
Despite the potential of CAR-T therapies for hematological malignancies, their efficacy in patients with relapse and refractory Acute Myeloid Leukemia has been limited. The aim of our study has been to develop and manufacture a CAR-T cell product that addresses some of the current limitations. We initially compared the phenotype of T cells from AML patients and healthy young and elderly controls. This analysis showed that T cells from AML patients displayed a predominantly effector phenotype, with increased expression of activation (CD69 and HLA-DR) and exhaustion markers (PD1 and LAG3), in contrast to the enriched memory phenotype observed in healthy donors. This differentiated and more exhausted phenotype was also observed, and corroborated by transcriptomic analyses, in CAR-T cells from AML patients engineered with an optimized CAR construct targeting CD33, resulting in a decreased in vivo antitumoral efficacy evaluated in xenograft AML models. To overcome some of these limitations we have combined CRISPR-based genome editing technologies with virus-free gene-transfer strategies using Sleeping Beauty transposons, to generate CAR-T cells depleted of HLA-I and TCR complexes (HLA-IKO/TCRKO CAR-T cells) for allogeneic approaches. Our optimized protocol allows one-step generation of edited CAR-T cells that show a similar phenotypic profile to non-edited CAR-T cells, with equivalent in vitro and in vivo antitumoral efficacy. Moreover, genomic analysis of edited CAR-T cells revealed a safe integration profile of the vector, with no preferences for specific genomic regions, with highly specific editing of the HLA-I and TCR, without significant off-target sites. Finally, the production of edited CAR-T cells at a larger scale allowed the generation and selection of enough HLA-IKO/TCRKO CAR-T cells that would be compatible with clinical applications. In summary, our results demonstrate that CAR-T cells from AML patients, although functional, present phenotypic and functional features that could compromise their antitumoral efficacy, compared to CAR-T cells from healthy donors. The combination of CRISPR technologies with transposon-based delivery strategies allows the generation of HLA-IKO/TCRKO CAR-T cells, compatible with allogeneic approaches, that would represent a promising option for AML treatment.
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MESH Headings
- Animals
- Humans
- Aged
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- T-Lymphocytes/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Acute/metabolism
- Immunotherapy, Adoptive/methods
- Disease Models, Animal
- Hematopoietic Stem Cell Transplantation
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Affiliation(s)
- Cristina Calviño
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Candela Ceballos
- Hematology Department, Hospital Universitario de Navarra, IdiSNA, Pamplona, Spain
| | - Ana Alfonso
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
| | - Patricia Jauregui
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Maria E. Calleja-Cervantes
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Computational Biology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | | | - Paula Rodriguez-Marquez
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Angel Martin-Mallo
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Elena Iglesias
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Gloria Abizanda
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | | | - Rebeca Martinez-Turrillas
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Jorge Illarramendi
- Hematology Department, Hospital Universitario de Navarra, IdiSNA, Pamplona, Spain
| | - Maria C. Viguria
- Hematology Department, Hospital Universitario de Navarra, IdiSNA, Pamplona, Spain
| | - Margarita Redondo
- Hematology Department, Hospital Universitario de Navarra, IdiSNA, Pamplona, Spain
| | - Jose Rifon
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
| | - Sara Villar
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Juan J. Lasarte
- Immunology and Immunotherapy Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Susana Inoges
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Immunology and Immunotherapy Department, Clinica Universidad de Navarra, Pamplona, Spain
| | - Ascension Lopez-Diaz de Cerio
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Immunology and Immunotherapy Department, Clinica Universidad de Navarra, Pamplona, Spain
| | - Mikel Hernaez
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- Computational Biology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Data Science and Artificial Intelligence Institute (DATAI), Universidad de Navarra, Pamplona, Spain
| | - Felipe Prosper
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Juan R. Rodriguez-Madoz
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
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Eckold C, van Doorn CLR, Ruslami R, Ronacher K, Riza A, van Veen S, Lee J, Kumar V, Kerry‐Barnard S, Malherbe ST, Kleynhans L, Stanley K, Joosten SA, Critchley JA, Hill PC, van Crevel R, Wijmenga C, Haks MC, Ioana M, Alisjahbana B, Walzl G, Ottenhoff THM, Dockrell HM, Vianello E, Cliff JM. Impaired resolution of blood transcriptomes through tuberculosis treatment with diabetes comorbidity. Clin Transl Med 2023; 13:e1375. [PMID: 37649224 PMCID: PMC10468587 DOI: 10.1002/ctm2.1375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND People with diabetes are more likely to develop tuberculosis (TB) and to have poor TB-treatment outcomes than those without. We previously showed that blood transcriptomes in people with TB-diabetes (TB-DM) co-morbidity have excessive inflammatory and reduced interferon responses at diagnosis. It is unknown whether this persists through treatment and contributes to the adverse outcomes. METHODS Pulmonary TB patients recruited in South Africa, Indonesia and Romania were classified as having TB-DM, TB with prediabetes, TB-related hyperglycaemia or TB-only, based on glycated haemoglobin concentration at TB diagnosis and after 6 months of TB treatment. Gene expression in blood at diagnosis and intervals throughout treatment was measured by unbiased RNA-Seq and targeted Multiplex Ligation-dependent Probe Amplification. Transcriptomic data were analysed by longitudinal mixed-model regression to identify whether genes were differentially expressed between clinical groups through time. Predictive models of TB-treatment response across groups were developed and cross-tested. RESULTS Gene expression differed between TB and TB-DM patients at diagnosis and was modulated by TB treatment in all clinical groups but to different extents, such that differences remained in TB-DM relative to TB-only throughout. Expression of some genes increased through TB treatment, whereas others decreased: some were persistently more highly expressed in TB-DM and others in TB-only patients. Genes involved in innate immune responses, anti-microbial immunity and inflammation were significantly upregulated in people with TB-DM throughout treatment. The overall pattern of change was similar across clinical groups irrespective of diabetes status, permitting models predictive of TB treatment to be developed. CONCLUSIONS Exacerbated transcriptome changes in TB-DM take longer to resolve during TB treatment, meaning they remain different from those in uncomplicated TB after treatment completion. This may indicate a prolonged inflammatory response in TB-DM, requiring prolonged treatment or host-directed therapy for complete cure. Development of transcriptome-based biomarker signatures of TB-treatment response should include people with diabetes for use across populations.
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Affiliation(s)
- Clare Eckold
- Department of Infection Biology and TB CentreLondon School of Hygiene & Tropical MedicineLondonUK
| | | | - Rovina Ruslami
- Department of Biomedical SciencesFaculty of MedicineUniversitas PadjadjaranBandungIndonesia
| | - Katharina Ronacher
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis ResearchSouth African Medical Research Council Centre for Tuberculosis ResearchDivision of Molecular Biology and Human GeneticsDepartment of Biomedical SciencesFaculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- Mater Research InstituteFaculty of MedicineTranslational Research InstituteThe University of QueenslandBrisbaneQLDAustralia
| | - Anca‐Lelia Riza
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
- Human Genomics LaboratoryDepartment of Diagnostics and TreatmentUniversity of Medicine and Pharmacy of CraiovaCraiovaRomania
- Regional Centre for Human Genetics – DoljEmergency Clinical County Hospital CraiovaCraiovaRomania
| | - Suzanne van Veen
- Department of Infectious DiseasesLeiden University Medical CenterLeidenThe Netherlands
| | - Ji‐Sook Lee
- Department of Infection Biology and TB CentreLondon School of Hygiene & Tropical MedicineLondonUK
| | - Vinod Kumar
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
- Department of GeneticsUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | | | - Stephanus T. Malherbe
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis ResearchSouth African Medical Research Council Centre for Tuberculosis ResearchDivision of Molecular Biology and Human GeneticsDepartment of Biomedical SciencesFaculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
| | - Léanie Kleynhans
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis ResearchSouth African Medical Research Council Centre for Tuberculosis ResearchDivision of Molecular Biology and Human GeneticsDepartment of Biomedical SciencesFaculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
| | - Kim Stanley
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis ResearchSouth African Medical Research Council Centre for Tuberculosis ResearchDivision of Molecular Biology and Human GeneticsDepartment of Biomedical SciencesFaculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
| | - Simone A. Joosten
- Department of Infectious DiseasesLeiden University Medical CenterLeidenThe Netherlands
| | - Julia A Critchley
- Population Health Research InstituteSt George'sUniversity of LondonLondonUK
| | - Philip C. Hill
- Division of Health SciencesCentre for International HealthUniversity of OtagoDunedinNew Zealand
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
- Nuffield Department of MedicineCentre for Tropical Medicine and Global HealthUniversity of OxfordOxfordUK
| | - Cisca Wijmenga
- Department of GeneticsUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Mariëlle C. Haks
- Department of Infectious DiseasesLeiden University Medical CenterLeidenThe Netherlands
| | - Mihai Ioana
- Human Genomics LaboratoryDepartment of Diagnostics and TreatmentUniversity of Medicine and Pharmacy of CraiovaCraiovaRomania
- Regional Centre for Human Genetics – DoljEmergency Clinical County Hospital CraiovaCraiovaRomania
| | - Bachti Alisjahbana
- Internal Medicine DepartmentHasan Sadikin General HospitalBandungIndonesia
- Research Center for Care and Control of Infectious DiseasesUniversitas PadjadjaranBandungIndonesia
| | - Gerhard Walzl
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis ResearchSouth African Medical Research Council Centre for Tuberculosis ResearchDivision of Molecular Biology and Human GeneticsDepartment of Biomedical SciencesFaculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
| | - Tom H. M. Ottenhoff
- Department of Infectious DiseasesLeiden University Medical CenterLeidenThe Netherlands
| | - Hazel M. Dockrell
- Department of Infection Biology and TB CentreLondon School of Hygiene & Tropical MedicineLondonUK
| | - Eleonora Vianello
- Department of Infectious DiseasesLeiden University Medical CenterLeidenThe Netherlands
| | - Jacqueline M. Cliff
- Department of Infection Biology and TB CentreLondon School of Hygiene & Tropical MedicineLondonUK
- Department of Life SciencesCentre for Inflammation Research and Translational MedicineBrunel University LondonLondonUK
| | - the TANDEM Consortium$
- Department of Infection Biology and TB CentreLondon School of Hygiene & Tropical MedicineLondonUK
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29
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VanKuren NW, Doellman MM, Sheikh SI, Palmer Droguett DH, Massardo D, Kronforst MR. Acute and Long-Term Consequences of Co-opted doublesex on the Development of Mimetic Butterfly Color Patterns. Mol Biol Evol 2023; 40:msad196. [PMID: 37668300 PMCID: PMC10498343 DOI: 10.1093/molbev/msad196] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/28/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023] Open
Abstract
Novel phenotypes are increasingly recognized to have evolved by co-option of conserved genes into new developmental contexts, yet the process by which co-opted genes modify existing developmental programs remains obscure. Here, we provide insight into this process by characterizing the role of co-opted doublesex in butterfly wing color pattern development. dsx is the master regulator of insect sex differentiation but has been co-opted to control the switch between discrete nonmimetic and mimetic patterns in Papilio alphenor and its relatives through the evolution of novel mimetic alleles. We found dynamic spatial and temporal expression pattern differences between mimetic and nonmimetic butterflies throughout wing development. A mimetic color pattern program is switched on by a pulse of dsx expression in early pupal development that causes acute and long-term differential gene expression, particularly in Wnt and Hedgehog signaling pathways. RNAi suggested opposing, novel roles for these pathways in mimetic pattern development. Importantly, Dsx co-option caused Engrailed, a primary target of Hedgehog signaling, to gain a novel expression domain early in pupal wing development that is propagated through mid-pupal development to specify novel mimetic patterns despite becoming decoupled from Dsx expression itself. Altogether, our findings provide multiple views into how co-opted genes can both cause and elicit changes to conserved networks and pathways to result in development of novel, adaptive phenotypes.
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Affiliation(s)
- Nicholas W VanKuren
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA
| | - Meredith M Doellman
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA
| | - Sofia I Sheikh
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA
| | | | - Darli Massardo
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA
| | - Marcus R Kronforst
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA
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30
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Fletcher P, O'Donnell KL, Doratt BM, Malherbe DC, Clancy CS, Rhoderick JF, Feldmann F, Hanley PW, Ksiazek TG, Geisbert TW, Messaoudi I, Marzi A. Single-dose VSV-based vaccine protects cynomolgus macaques from disease after Taï Forest virus infection. Emerg Microbes Infect 2023:2239950. [PMID: 37470396 PMCID: PMC10392270 DOI: 10.1080/22221751.2023.2239950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Taï Forest virus (TAFV) is a lesser-known ebolavirus that causes lethal infections in chimpanzees and is responsible for a single human case. Limited research has been done on this human pathogen; however, with the recent emergence of filoviruses in West Africa, further investigation and countermeasure development against this virus is warranted.We developed a vesicular stomatitis virus (VSV)-based vaccine expressing the TAFV glycoprotein as the viral antigen and assessed it for protective efficacy in nonhuman primates (NHPs). Following a single high-dose vaccination, NHPs developed antigen-specific binding and neutralizing antibodies as well as modest T cell responses. Importantly, all vaccinated NHPs were uniformly protected from disease after lethal TAFV challenge while the naïve control group succumbed to the disease. Histopathologic lesions consistent with filovirus disease were present in control NHPs but were not observed in vaccinated NHPs. Transcriptional analysis of whole blood samples obtained after vaccination and challenge was performed to gain insight into molecular underpinnings conferring protection. Differentially expressed genes (DEG) detected 7 days post-vaccination were enriched to processes associated with innate immunity and antiviral responses. Only a small number of DEG was detected in vaccinated NHPs post-challenge while over 1,000 DEG were detected in control NHPs at end-stage disease which mapped to gene ontology terms indicative of defense responses and inflammation. Taken together, this data demonstrates the effective single-dose protection of the VSV-TAFV vaccine, and its potential for use in outbreaks.
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Affiliation(s)
- Paige Fletcher
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kyle L O'Donnell
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Brianna M Doratt
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Delphine C Malherbe
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Chad S Clancy
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Joseph F Rhoderick
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Patrick W Hanley
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Thomas G Ksiazek
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Thomas W Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
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Zhou W, Li W, Wang S, Salovska B, Hu Z, Tao B, Di Y, Punyamurtula U, Turk BE, Sessa WC, Liu Y. An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells. Nat Commun 2023; 14:3803. [PMID: 37365174 PMCID: PMC10293293 DOI: 10.1038/s41467-023-39514-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
The serine/threonine kinase AKT is a central node in cell signaling. While aberrant AKT activation underlies the development of a variety of human diseases, how different patterns of AKT-dependent phosphorylation dictate downstream signaling and phenotypic outcomes remains largely enigmatic. Herein, we perform a systems-level analysis that integrates methodological advances in optogenetics, mass spectrometry-based phosphoproteomics, and bioinformatics to elucidate how different intensity, duration, and pattern of Akt1 stimulation lead to distinct temporal phosphorylation profiles in vascular endothelial cells. Through the analysis of ~35,000 phosphorylation sites across multiple conditions precisely controlled by light stimulation, we identify a series of signaling circuits activated downstream of Akt1 and interrogate how Akt1 signaling integrates with growth factor signaling in endothelial cells. Furthermore, our results categorize kinase substrates that are preferably activated by oscillating, transient, and sustained Akt1 signals. We validate a list of phosphorylation sites that covaried with Akt1 phosphorylation across experimental conditions as potential Akt1 substrates. Our resulting dataset provides a rich resource for future studies on AKT signaling and dynamics.
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Affiliation(s)
- Wenping Zhou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06511, USA
- Vascular Biology & Therapeutics Program, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Wenxue Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, 06516, USA
| | - Shisheng Wang
- Department of Pulmonary and Critical Care Medicine, and Proteomics-Metabolomics Analysis Platform, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Barbora Salovska
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, 06516, USA
| | - Zhenyi Hu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, 06516, USA
| | - Bo Tao
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Vascular Biology & Therapeutics Program, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Yi Di
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, 06516, USA
| | - Ujwal Punyamurtula
- Master of Biotechnology ScM Program, Brown University, Providence, RI, 02912, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - William C Sessa
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA.
- Vascular Biology & Therapeutics Program, Yale University School of Medicine, New Haven, CT, 06520, USA.
| | - Yansheng Liu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA.
- Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, 06516, USA.
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Morimoto S, Takahashi S, Ito D, Daté Y, Okada K, Kato C, Nakamura S, Ozawa F, Chyi CM, Nishiyama A, Suzuki N, Fujimori K, Kondo T, Takao M, Hirai M, Kabe Y, Suematsu M, Jinzaki M, Aoki M, Fujiki Y, Sato Y, Suzuki N, Nakahara J, Okano H. Phase 1/2a clinical trial in ALS with ropinirole, a drug candidate identified by iPSC drug discovery. Cell Stem Cell 2023; 30:766-780.e9. [PMID: 37267913 DOI: 10.1016/j.stem.2023.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 01/12/2023] [Accepted: 04/24/2023] [Indexed: 06/04/2023]
Abstract
iPSC-based drug discovery led to a phase 1/2a trial of ropinirole in ALS. 20 participants with sporadic ALS received ropinirole or placebo for 24 weeks in the double-blind period to evaluate safety, tolerability, and therapeutic effects. Adverse events were similar in both groups. During the double-blind period, muscle strength and daily activity were maintained, but a decline in the ALSFRS-R, which assesses the functional status of ALS patients, was not different from that in the placebo group. However, in the open-label extension period, the ropinirole group showed significant suppression of ALSFRS-R decline and an additional 27.9 weeks of disease-progression-free survival. iPSC-derived motor neurons from participants showed dopamine D2 receptor expression and a potential involvement of the SREBP2-cholesterol pathway in therapeutic effects. Lipid peroxide represents a clinical surrogate marker to assess disease progression and drug efficacy. Limitations include small sample sizes and high attrition rates in the open-label extension period, requiring further validation.
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Affiliation(s)
- Satoru Morimoto
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Neurology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Shinichi Takahashi
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Neurology, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Neurology and Stroke, Saitama Medical University International Medical Center, Saitama 350-1298, Japan
| | - Daisuke Ito
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Neurology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yugaku Daté
- Department of Neurology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kensuke Okada
- Department of Neurology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Chris Kato
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Shiho Nakamura
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Fumiko Ozawa
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Chai Muh Chyi
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan; Keio University Global Research Institute, Tokyo 108-8345, Japan
| | - Ayumi Nishiyama
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Naoki Suzuki
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Koki Fujimori
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Tosho Kondo
- Research Center of Neurology, ONO Pharmaceutical Co., Ltd., Osaka 541-8564, Japan
| | - Masaki Takao
- Department of Clinical Laboratory, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-0031, Japan; Department of Neurology, Mihara Memorial Hospital, Isesaki, Gunmma 372-0006, Japan
| | - Miwa Hirai
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yasuaki Kabe
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masahiro Jinzaki
- Department of Radiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masashi Aoki
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Yuto Fujiki
- Keio University Hospital Clinical and Translational Research Center, Tokyo 160-8582, Japan
| | - Yasunori Sato
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Norihiro Suzuki
- Department of Neurology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Jin Nakahara
- Department of Neurology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan.
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Wang Y, Wang X, Luo Y, Zhang J, Lin Y, Wu J, Zeng B, Liu L, Yan P, Liang J, Guo H, Jin L, Tang Q, Long K, Li M. Spatio-temporal transcriptome dynamics coordinate rapid transition of core crop functions in 'lactating' pigeon. PLoS Genet 2023; 19:e1010746. [PMID: 37289658 DOI: 10.1371/journal.pgen.1010746] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 04/14/2023] [Indexed: 06/10/2023] Open
Abstract
Pigeons (Columba livia) are among a select few avian species that have developed a specialized reproductive mode wherein the parents produce a 'milk' in their crop to feed newborn squabs. Nonetheless, the transcriptomic dynamics and role in the rapid transition of core crop functions during 'lactation' remain largely unexplored. Here, we generated a de novo pigeon genome assembly to construct a high resolution spatio-temporal transcriptomic landscape of the crop epithelium across the entire breeding stage. This multi-omics analysis identified a set of 'lactation'-related genes involved in lipid and protein metabolism, which contribute to the rapid functional transitions in the crop. Analysis of in situ high-throughput chromatin conformation capture (Hi-C) sequencing revealed extensive reorganization of promoter-enhancer interactions linked to the dynamic expression of these 'lactation'-related genes between stages. Moreover, their expression is spatially localized in specific epithelial layers, and can be correlated with phenotypic changes in the crop. These results illustrate the preferential de novo synthesis of 'milk' lipids and proteins in the crop, and provides candidate enhancer loci for further investigation of the regulatory elements controlling pigeon 'lactation'.
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Affiliation(s)
- Yujie Wang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xun Wang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yi Luo
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiaman Zhang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yu Lin
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jie Wu
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bo Zeng
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Lei Liu
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Peiqi Yan
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiyuan Liang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hongrui Guo
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Long Jin
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Qianzi Tang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Keren Long
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Mingzhou Li
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
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Kanellis DC, Zisi A, Skrott Z, Lemmens B, Espinoza JA, Kosar M, Björkman A, Li X, Arampatzis S, Bartkova J, Andújar-Sánchez M, Fernandez-Capetillo O, Mistrik M, Lindström MS, Bartek J. Actionable cancer vulnerability due to translational arrest, p53 aggregation and ribosome biogenesis stress evoked by the disulfiram metabolite CuET. Cell Death Differ 2023:10.1038/s41418-023-01167-4. [PMID: 37142656 DOI: 10.1038/s41418-023-01167-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/06/2023] Open
Abstract
Drug repurposing is a versatile strategy to improve current therapies. Disulfiram has long been used in the treatment of alcohol dependency and multiple clinical trials to evaluate its clinical value in oncology are ongoing. We have recently reported that the disulfiram metabolite diethyldithiocarbamate, when combined with copper (CuET), targets the NPL4 adapter of the p97VCP segregase to suppress the growth of a spectrum of cancer cell lines and xenograft models in vivo. CuET induces proteotoxic stress and genotoxic effects, however important issues concerning the full range of the CuET-evoked tumor cell phenotypes, their temporal order, and mechanistic basis have remained largely unexplored. Here, we have addressed these outstanding questions and show that in diverse human cancer cell models, CuET causes a very early translational arrest through the integrated stress response (ISR), later followed by features of nucleolar stress. Furthermore, we report that CuET entraps p53 in NPL4-rich aggregates leading to elevated p53 protein and its functional inhibition, consistent with the possibility of CuET-triggered cell death being p53-independent. Our transcriptomics profiling revealed activation of pro-survival adaptive pathways of ribosomal biogenesis (RiBi) and autophagy upon prolonged exposure to CuET, indicating potential feedback responses to CuET treatment. The latter concept was validated here by simultaneous pharmacological inhibition of RiBi and/or autophagy that further enhanced CuET's tumor cytotoxicity, using both cell culture and zebrafish in vivo preclinical models. Overall, these findings expand the mechanistic repertoire of CuET's anti-cancer activity, inform about the temporal order of responses and identify an unorthodox new mechanism of targeting p53. Our results are discussed in light of cancer-associated endogenous stresses as exploitable tumor vulnerabilities and may inspire future clinical applications of CuET in oncology, including combinatorial treatments and focus on potential advantages of using certain validated drug metabolites, rather than old, approved drugs with their, often complex, metabolic profiles.
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Affiliation(s)
- Dimitris C Kanellis
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden.
| | - Asimina Zisi
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
| | - Zdenek Skrott
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Bennie Lemmens
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
| | - Jaime A Espinoza
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
| | - Martin Kosar
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
| | - Andrea Björkman
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
| | - Xuexin Li
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
| | | | - Jirina Bartkova
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
- Danish Cancer Society Research Center, DK-2100, Copenhagen, Denmark
| | - Miguel Andújar-Sánchez
- Pathology Department, Complejo Hospitalario Universitario Insular, Las Palmas, Gran Canaria, Spain
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Martin Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Mikael S Lindström
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden
| | - Jiri Bartek
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden.
- Danish Cancer Society Research Center, DK-2100, Copenhagen, Denmark.
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35
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Zlobina K, Malekos E, Chen H, Gomez M. Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data. BMC Bioinformatics 2023; 24:166. [PMID: 37098473 PMCID: PMC10127407 DOI: 10.1186/s12859-023-05295-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 04/17/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Wound healing involves careful coordination among various cell types carrying out unique or even multifaceted functions. The abstraction of this complex dynamic process into four primary wound stages is essential to the study of wound care for timing treatment and tracking wound progression. For example, a treatment that may promote healing in the inflammatory stage may prove detrimental in the proliferative stage. Additionally, the time scale of individual responses varies widely across and within the same species. Therefore, a robust method to assess wound stages can help advance translational work from animals to humans. RESULTS In this work, we present a data-driven model that robustly identifies the dominant wound healing stage using transcriptomic data from biopsies gathered from mouse and human wounds, both burn and surgical. A training dataset composed of publicly available transcriptomic arrays is used to derive 58 shared genes that are commonly differentially expressed. They are divided into 5 clusters based on temporal gene expression dynamics. The clusters represent a 5-dimensional parametric space containing the wound healing trajectory. We then create a mathematical classification algorithm in the 5-dimensional space and demonstrate that it can distinguish between the four stages of wound healing: hemostasis, inflammation, proliferation, and remodeling. CONCLUSIONS In this work, we present an algorithm for wound stage detection based on gene expression. This work suggests that there are universal characteristics of gene expression in wound healing stages despite the seeming disparities across species and wounds. Our algorithm performs well for human and mouse wounds of both burn and surgical types. The algorithm has the potential to serve as a diagnostic tool that can advance precision wound care by providing a way of tracking wound healing progression with more accuracy and finer temporal resolution compared to visual indicators. This increases the potential for preventive action.
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Affiliation(s)
| | | | - Han Chen
- University of California, Santa Cruz, CA, USA
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36
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Hanna BS, Wang G, Galván-Peña S, Mann AO, Ramirez RN, Muñoz-Rojas AR, Smith K, Wan M, Benoist C, Mathis D. The gut microbiota promotes distal tissue regeneration via RORγ + regulatory T cell emissaries. Immunity 2023; 56:829-846.e8. [PMID: 36822206 PMCID: PMC10101925 DOI: 10.1016/j.immuni.2023.01.033] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 12/22/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023]
Abstract
Specific microbial signals induce the differentiation of a distinct pool of RORγ+ regulatory T (Treg) cells crucial for intestinal homeostasis. We discovered highly analogous populations of microbiota-dependent Treg cells that promoted tissue regeneration at extra-gut sites, notably acutely injured skeletal muscle and fatty liver. Inflammatory meditators elicited by tissue damage combined with MHC-class-II-dependent T cell activation to drive the accumulation of gut-derived RORγ+ Treg cells in injured muscle, wherein they regulated the dynamics and tenor of early inflammation and helped balance the proliferation vs. differentiation of local stem cells. Reining in IL-17A-producing T cells was a major mechanism underlying the rheostatic functions of RORγ+ Treg cells in compromised tissues. Our findings highlight the importance of gut-trained Treg cell emissaries in controlling the response to sterile injury of non-mucosal tissues.
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Affiliation(s)
- Bola S Hanna
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Gang Wang
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Silvia Galván-Peña
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Alexander O Mann
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ricardo N Ramirez
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Andrés R Muñoz-Rojas
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kathleen Smith
- Internal Medicine Research Unit, Worldwide Research, Development & Medical, Pfizer Inc., Cambridge, MA, USA
| | - Min Wan
- Internal Medicine Research Unit, Worldwide Research, Development & Medical, Pfizer Inc., Cambridge, MA, USA
| | - Christophe Benoist
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
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37
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Fontugne J, Wong J, Cabel L, Neyret-Kahn H, Karboul N, Maillé P, Rapinat A, Gentien D, Nicolas A, Baulande S, Sibony M, Bernard-Pierrot I, Radvanyi F, Allory Y. Progression-associated molecular changes in basal/squamous and sarcomatoid bladder carcinogenesis. J Pathol 2023; 259:455-467. [PMID: 36695554 DOI: 10.1002/path.6060] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/13/2022] [Accepted: 01/23/2023] [Indexed: 01/26/2023]
Abstract
The aggressive basal/squamous (Ba/Sq) bladder cancer (BLCA) subtype is often diagnosed at the muscle-invasive stage and can progress to the sarcomatoid variant. Identification of molecular changes occurring during progression from non-muscle-invasive BLCA (NMIBC) to Ba/Sq muscle-invasive BLCA (MIBC) is thus challenging in human disease. We used the N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN) mouse model of Ba/Sq MIBC to study longitudinally the molecular changes leading to the Ba/Sq phenotype and to the sarcomatoid variant using IHC and microdissection followed by RNA-seq at all stages of progression. A shift to the Ba/Sq phenotype started in early progression stages. Pathway analysis of gene clusters with coordinated expression changes revealed Shh signaling loss and a shift from fatty acid metabolism to glycolysis. An upregulated cluster, appearing early in carcinogenesis, showed relevance to human disease, identifying NMIBC patients at risk of progression. Similar to the human counterpart, sarcomatoid BBN tumors displayed a Ba/Sq phenotype and epithelial-mesenchymal transition (EMT) features. An EGFR/FGFR1 signaling switch occurred with sarcomatoid dedifferentiation and correlated with EMT. BLCA cell lines with high EMT were the most sensitive to FGFR1 knockout and resistant to EGFR knockout. Taken together, these findings provide insights into the underlying biology of Ba/Sq BLCA progression and sarcomatoid dedifferentiation with potential clinical implications. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Jacqueline Fontugne
- Institut Curie, CNRS, UMR144, Equipe labellisée Ligue Contre le Cancer, PSL Research University, Paris, France.,Department of Pathology, Institut Curie, Saint-Cloud, France.,Université Paris-Saclay, Université Versailles St-Quentin, Montigny-le-Bretonneux, France
| | - Jennifer Wong
- Institut Curie, CNRS, UMR144, Equipe labellisée Ligue Contre le Cancer, PSL Research University, Paris, France.,Department of Genetics, Institut Curie, Paris, France
| | - Luc Cabel
- Institut Curie, CNRS, UMR144, Equipe labellisée Ligue Contre le Cancer, PSL Research University, Paris, France
| | - Hélène Neyret-Kahn
- Institut Curie, CNRS, UMR144, Equipe labellisée Ligue Contre le Cancer, PSL Research University, Paris, France
| | - Narjesse Karboul
- Institut Curie, CNRS, UMR144, Equipe labellisée Ligue Contre le Cancer, PSL Research University, Paris, France
| | - Pascale Maillé
- Department of Pathology, Institut Curie, Saint-Cloud, France
| | - Audrey Rapinat
- Genomics Core Facility, Translational Research Department, PSL Research University, Institut Curie, Paris, France
| | - David Gentien
- Genomics Core Facility, Translational Research Department, PSL Research University, Institut Curie, Paris, France
| | - André Nicolas
- Department of Pathology, Institut Curie, Paris, France
| | - Sylvain Baulande
- Genomics of Excellence (ICGex) Platform, Institut Curie, PSL Research University, Paris, France
| | | | - Isabelle Bernard-Pierrot
- Institut Curie, CNRS, UMR144, Equipe labellisée Ligue Contre le Cancer, PSL Research University, Paris, France
| | - François Radvanyi
- Institut Curie, CNRS, UMR144, Equipe labellisée Ligue Contre le Cancer, PSL Research University, Paris, France
| | - Yves Allory
- Institut Curie, CNRS, UMR144, Equipe labellisée Ligue Contre le Cancer, PSL Research University, Paris, France.,Department of Pathology, Institut Curie, Saint-Cloud, France.,Université Paris-Saclay, Université Versailles St-Quentin, Montigny-le-Bretonneux, France
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38
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Teng X, Dai Y, Li K, Wu Y, Hou H, Li J. LiveG4ID-Seq for Profiling the Dynamic Landscape of Chromatin G-Quadruplexes During Cell Cycle in Living Cells. SMALL METHODS 2023; 7:e2201487. [PMID: 36739600 DOI: 10.1002/smtd.202201487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/11/2023] [Indexed: 06/18/2023]
Abstract
G-quadruplex (G4) structures exist in the single-stranded DNA of chromatin and regulate genome function. However, the native chromatin G4 landscape in living cells has yet to be fully characterized. Herein, a genetic-encoded live-cell G4 identifier probe (LiveG4ID) is constructed and its cellular localization, biocompatibility, and G4-binding specificity is evaluated. By coupling LiveG4ID with cleavage under targets and tagmentation (CUT&Tag), LiveG4ID-seq, a method for mapping native chromatin G4 landscape in living cells with high accuracy is established. Compared to the conventional G4 CUT&Tag method, LiveG4ID-seq can identify more chromatin G4 signals and have a higher ratio of true positive signals. Using LiveG4ID-seq, the dynamic landscape of chromatin G4 structures during the cell cycle is profiled. It is discovered that chromatin G4 structures are prevalent in the promoter regions of cell cycle-specific genes, even in the early M phase when the chromatin is condensed. These data demonstrate the capacity of LiveG4ID-seq to profile a more accurate G4 landscape in living cells and promote future studies on chromatin G4 structures.
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Affiliation(s)
- Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Yicong Dai
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Ke Li
- Novoprotein Scientific Inc., Shanghai, 201210, China
| | - Yuncong Wu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Hongwei Hou
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, 450001, China
- Beijing Institute of Life Science and Technology, Beijing, 100101, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China
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39
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Sidhaye J, Trepte P, Sepke N, Novatchkova M, Schutzbier M, Dürnberger G, Mechtler K, Knoblich JA. Integrated transcriptome and proteome analysis reveals posttranscriptional regulation of ribosomal genes in human brain organoids. eLife 2023; 12:85135. [PMID: 36989136 PMCID: PMC10059687 DOI: 10.7554/elife.85135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
During development of the human cerebral cortex, multipotent neural progenitors generate excitatory neurons and glial cells. Investigations of the transcriptome and epigenome have revealed important gene regulatory networks underlying this crucial developmental event. However, the posttranscriptional control of gene expression and protein abundance during human corticogenesis remains poorly understood. We addressed this issue by using human telencephalic brain organoids grown using a dual reporter cell line to isolate neural progenitors and neurons and performed cell class and developmental stage-specific transcriptome and proteome analysis. Integrating the two datasets revealed modules of gene expression during human corticogenesis. Investigation of one such module uncovered mTOR-mediated regulation of translation of the 5'TOP element-enriched translation machinery in early progenitor cells. We show that in early progenitors partial inhibition of the translation of ribosomal genes prevents precocious translation of differentiation markers. Overall, our multiomics approach proposes novel posttranscriptional regulatory mechanisms crucial for the fidelity of cortical development.
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Affiliation(s)
- Jaydeep Sidhaye
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Philipp Trepte
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Natalie Sepke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | | | | | - Karl Mechtler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Department of Neurology, Medical University of Vienna, Vienna, Austria
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Bartsch D, Kalamkar K, Ahuja G, Lackmann JW, Hescheler J, Weber T, Bazzi H, Clamer M, Mendjan S, Papantonis A, Kurian L. mRNA translational specialization by RBPMS presets the competence for cardiac commitment in hESCs. SCIENCE ADVANCES 2023; 9:eade1792. [PMID: 36989351 PMCID: PMC10058251 DOI: 10.1126/sciadv.ade1792] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/01/2023] [Indexed: 06/19/2023]
Abstract
The blueprints of developing organs are preset at the early stages of embryogenesis. Transcriptional and epigenetic mechanisms are proposed to preset developmental trajectories. However, we reveal that the competence for the future cardiac fate of human embryonic stem cells (hESCs) is preset in pluripotency by a specialized mRNA translation circuit controlled by RBPMS. RBPMS is recruited to active ribosomes in hESCs to control the translation of essential factors needed for cardiac commitment program, including Wingless/Integrated (WNT) signaling. Consequently, RBPMS loss specifically and severely impedes cardiac mesoderm specification, leading to patterning and morphogenetic defects in human cardiac organoids. Mechanistically, RBPMS specializes mRNA translation, selectively via 3'UTR binding and globally by promoting translation initiation. Accordingly, RBPMS loss causes translation initiation defects highlighted by aberrant retention of the EIF3 complex and depletion of EIF5A from mRNAs, thereby abrogating ribosome recruitment. We demonstrate how future fate trajectories are programmed during embryogenesis by specialized mRNA translation.
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Affiliation(s)
- Deniz Bartsch
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Kaustubh Kalamkar
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Gaurav Ahuja
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Jan-Wilm Lackmann
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Jürgen Hescheler
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
| | - Timm Weber
- Laboratory of Experimental Immunology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany
| | - Hisham Bazzi
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
- Department of Dermatology and Venereology, Medical Faculty, University of Cologne, Cologne 50931, Germany
| | | | - Sasha Mendjan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, Vienna 1030, Austria
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, Göttingen 37075, Germany
| | - Leo Kurian
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
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Wang Y, Xiao N, Hu L, Deng M, Zong F, Zhang Z, Su D, Zhou D, Yang H, Dai E. Mechanism of pulmonary plague biphasic syndrome: inhibition or activation of NF-κB signaling pathway. Future Microbiol 2023; 18:267-286. [PMID: 36971082 DOI: 10.2217/fmb-2023-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Background: Pneumonic plague is a fatal respiratory disease caused by Yersinia pestis. Time-course transcriptome analysis on the mechanism of pneumonic plague biphasic syndrome is lacking in the literature. Materials & methods: This study documented the disease course through bacterial load, histopathology, cytokine levels and flow cytometry. RNA-sequencing technology was used to investigate the global transcriptome profile of lung tissue in mice infected with Y. pestis. Results: Inflammation-related genes were significantly upregulated at 48 h post-infection, while genes related to cell adhesion and cytoskeletal structure were downregulated. Conclusion: NOD-like receptor and TNF signaling pathways play a plausible role in pneumonic plague biphasic syndrome and lung injury by controlling the activation and inhibition of the NF-κB signaling pathway.
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Raja R, Khanum S, Aboulmouna L, Maurya MR, Gupta S, Subramaniam S, Ramkrishna D. Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533676. [PMID: 36993235 PMCID: PMC10055344 DOI: 10.1101/2023.03.21.533676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Quantitative understanding of cellular processes, such as cell cycle and differentiation, is impeded by various forms of complexity ranging from myriad molecular players and their multilevel regulatory interactions, cellular evolution with multiple intermediate stages, lack of elucidation of cause-effect relationships among the many system players, and the computational complexity associated with the profusion of variables and parameters. In this paper, we present an elegant modeling framework based on the cybernetic concept that biological regulation is inspired by objectives embedding entirely novel strategies for dimension reduction, process stage specification through the system dynamics, and innovative causal association of regulatory events with the ability to predict the evolution of the dynamical system. The elementary step of the modeling strategy involves stage-specific objective functions that are computationally-determined from experiments, augmented with dynamical network computations involving end point objective functions, mutual information, change point detection, and maximal clique centrality. We demonstrate the power of the method through application to the mammalian cell cycle, which involves thousands of biomolecules engaged in signaling, transcription, and regulation. Starting with a fine-grained transcriptional description obtained from RNA sequencing measurements, we develop an initial model, which is then dynamically modeled using the cybernetic-inspired method (CIM), utilizing the strategies described above. The CIM is able to distill the most significant interactions from a multitude of possibilities. In addition to capturing the complexity of regulatory processes in a mechanistically causal and stage-specific manner, we identify the functional network modules, including novel cell cycle stages. Our model is able to predict future cell cycles consistent with experimental measurements. We posit that this state-of-the-art framework has the promise to extend to the dynamics of other biological processes, with a potential to provide novel mechanistic insights. STATEMENT OF SIGNIFICANCE Cellular processes like cell cycle are overly complex, involving multiple players interacting at multiple levels, and explicit modeling of such systems is challenging. The availability of longitudinal RNA measurements provides an opportunity to "reverse-engineer" for novel regulatory models. We develop a novel framework, inspired using goal-oriented cybernetic model, to implicitly model transcriptional regulation by constraining the system using inferred temporal goals. A preliminary causal network based on information-theory is used as a starting point, and our framework is used to distill the network to temporally-based networks containing essential molecular players. The strength of this approach is its ability to dynamically model the RNA temporal measurements. The approach developed paves the way for inferring regulatory processes in many complex cellular processes.
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Chen H, Liu C, Li Y, Wang X, Pan X, Wang F, Zhang Q. Developmental dynamic transcriptome and systematic analysis reveal the major genes underlying isoflavone accumulation in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1014349. [PMID: 36959940 PMCID: PMC10027745 DOI: 10.3389/fpls.2023.1014349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Soy isoflavone, a class of polyphenolic compounds exclusively occurred in legumes, is an important bioactive compound for both plants and human beings. The outline of isoflavones biosynthesis pathway has been drawn up basically in the previous research. However, research on the subject has been mostly restricted to investigate the static regulation of isoflavone content in soybean, rather than characterize its dynamic variation and modulation network in developing seeds. METHODS In this study, by using eight recombinant inbred lines (RIL), the contents of six isoflavone components in the different stages of developing soybean seeds were determined to characterize the dynamic variation of isoflavones, and the isoflavones accumulation pattern at physiological level was investigated. Meanwhile, we integrated and analyzed the whole genome expression profile of four lines and 42 meta-transcriptome data, based on the multiple algorithms. RESULTS This study: 1) obtained 4 molecular modules strongly correlated with isoflavone accumulation; 2) identified 28 novel major genes that could affect the accumulation of isoflavones in developing seeds free from the limitation of environments; 3) discussed the dynamic molecular patterns regulating isoflavones accumulation in developing seed; 4) expanded the isoflavone biosynthesis pathway. DISCUSSION The results not only promote the understandings on the biosynthesis and regulation of isoflavones at physiological and molecular level, but also facilitate to breed elite soybean cultivars with high isoflavone contents.
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Affiliation(s)
- Heng Chen
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Changkai Liu
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Yansheng Li
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Xue Wang
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Xiangwen Pan
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Feifei Wang
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Qiuying Zhang
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, China
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Wang Q, Thiam M, Barreto Sánchez AL, Wang Z, Zhang J, Li Q, Wen J, Zhao G. Gene Co-Expression Network Analysis Reveals the Hub Genes and Key Pathways Associated with Resistance to Salmonella Enteritidis Colonization in Chicken. Int J Mol Sci 2023; 24:ijms24054824. [PMID: 36902251 PMCID: PMC10003191 DOI: 10.3390/ijms24054824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/16/2023] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
Salmonella negatively impacts the poultry industry and threatens animals' and humans' health. The gastrointestinal microbiota and its metabolites can modulate the host's physiology and immune system. Recent research demonstrated the role of commensal bacteria and short-chain fatty acids (SCFAs) in developing resistance to Salmonella infection and colonization. However, the complex interactions among chicken, Salmonella, host-microbiome, and microbial metabolites remain unelucidated. Therefore, this study aimed to explore these complex interactions by identifying the driver and hub genes highly correlated with factors that confer resistance to Salmonella. Differential gene expression (DEGs) and dynamic developmental genes (DDGs) analyses and weighted gene co-expression network analysis (WGCNA) were performed using transcriptome data from the cecum of Salmonella Enteritidis-infected chicken at 7 and 21 days after infection. Furthermore, we identified the driver and hub genes associated with important traits such as the heterophil/lymphocyte (H/L) ratio, body weight post-infection, bacterial load, propionate and valerate cecal contents, and Firmicutes, Bacteroidetes, and Proteobacteria cecal relative abundance. Among the multiple genes detected in this study, EXFABP, S100A9/12, CEMIP, FKBP5, MAVS, FAM168B, HESX1, EMC6, and others were found as potential candidate gene and transcript (co-) factors for resistance to Salmonella infection. In addition, we found that the PPAR and oxidative phosphorylation (OXPHOS) metabolic pathways were also involved in the host's immune response/defense against Salmonella colonization at the earlier and later stage post-infection, respectively. This study provides a valuable resource of transcriptome profiles from chicken cecum at the earlier and later stage post-infection and mechanistic understanding of the complex interactions among chicken, Salmonella, host-microbiome, and associated metabolites.
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Wang Y, Liu C, Qiao X, Han X, Liu ZP. PKI: A bioinformatics method of quantifying the importance of nodes in gene regulatory network via a pseudo knockout index. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194911. [PMID: 36804477 DOI: 10.1016/j.bbagrm.2023.194911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/09/2023] [Accepted: 01/30/2023] [Indexed: 02/18/2023]
Abstract
BACKGROUND Gene regulatory network (GRN) is a model that characterizes the complex relationships between genes and thereby provides an informatics environment to measure the importance of nodes. The evaluation of important nodes in a GRN can effectively refer to their functional implications severing as key players in particular biological processes, such as master regulator and driver gene. Currently, it is mainly based on network topological parameters and focuses only on evaluating a single node individually. However, genes and products play their functions by interacting with each other. It is worth noting that the effects of gene combinations in GRN are not simply additive. Key combinations discovery is of significance in revealing gene sets with important functions. Recently, with the development of single-cell RNA-sequencing (scRNA-seq) technology, we can quantify gene expression profiles of individual cells that provide the potential to identify crucial nodes in gene regulations regarding specific condition, e.g., stem cell differentiation. RESULTS In this paper, we propose a bioinformatics method, called Pseudo Knockout Importance (PKI), to quantify the importance of node and node sets in a specific GRN structure using time-course scRNA-seq data. First, we construct ordinary differential equations to approach the gene regulations during cell differentiation. Then we design gene pseudo knockout experiments and define PKI score evaluation criteria based on the coefficient of determination. The importance of nodes can be described as the influence on the ODE system of removing variables. For key gene combinations, PKI is derived as a combinatorial optimization problem of quantifying the in silico gene knockout effects. CONCLUSIONS Here, we focus our analyses on the specific GRN of embryonic stem cells with time series gene expression profile. To verify the effectiveness and advantage of PKI method, we compare its node importance rankings with other twelve kinds of centrality-based methods, such as degree and Latora closeness. For key node combinations, we compare the results with the method based on minimum dominant set. Moreover, the famous combinations of transcription factors in induced pluripotent stem cell are also employed to verify the vital gene combinations identified by PKI. These results demonstrate the reliability and superiority of the proposed method.
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Affiliation(s)
- Yijuan Wang
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China
| | - Chao Liu
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Xu Qiao
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China
| | - Xianhua Han
- Faculty of Science, Yamaguchi University, Yamaguchi 753-8511, Japan
| | - Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China.
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Paul I, Bolzan D, Youssef A, Gagnon KA, Hook H, Karemore G, Oliphant MUJ, Lin W, Liu Q, Phanse S, White C, Padhorny D, Kotelnikov S, Chen CS, Hu P, Denis GV, Kozakov D, Raught B, Siggers T, Wuchty S, Muthuswamy SK, Emili A. Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT. Nat Commun 2023; 14:688. [PMID: 36755019 PMCID: PMC9908882 DOI: 10.1038/s41467-023-36122-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
A proper understanding of disease etiology will require longitudinal systems-scale reconstruction of the multitiered architecture of eukaryotic signaling. Here we combine state-of-the-art data acquisition platforms and bioinformatics tools to devise PAMAF, a workflow that simultaneously examines twelve omics modalities, i.e., protein abundance from whole-cells, nucleus, exosomes, secretome and membrane; N-glycosylation, phosphorylation; metabolites; mRNA, miRNA; and, in parallel, single-cell transcriptomes. We apply PAMAF in an established in vitro model of TGFβ-induced epithelial to mesenchymal transition (EMT) to quantify >61,000 molecules from 12 omics and 10 timepoints over 12 days. Bioinformatics analysis of this EMT-ExMap resource allowed us to identify; -topological coupling between omics, -four distinct cell states during EMT, -omics-specific kinetic paths, -stage-specific multi-omics characteristics, -distinct regulatory classes of genes, -ligand-receptor mediated intercellular crosstalk by integrating scRNAseq and subcellular proteomics, and -combinatorial drug targets (e.g., Hedgehog signaling and CAMK-II) to inhibit EMT, which we validate using a 3D mammary duct-on-a-chip platform. Overall, this study provides a resource on TGFβ signaling and EMT.
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Affiliation(s)
- Indranil Paul
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA
| | - Dante Bolzan
- Department of Computer Science, University of Miami, 1356 Memorial Drive, Coral Gables, FL, 33146, USA
| | - Ahmed Youssef
- Graduate Program in Bioinformatics, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA
| | - Keith A Gagnon
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Heather Hook
- Department of Biology, Boston University, 24 Cummington Mall, Boston, MA, 02115, USA
- Biological Design Center, Boston University, 610 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Gopal Karemore
- Advanced Analytics, Novo Nordisk A/S, 2760, Måløv, Denmark
| | - Michael U J Oliphant
- Cancer Research Institute, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Weiwei Lin
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA
| | - Qian Liu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Sadhna Phanse
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA
| | - Carl White
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, 11794, Stony Brook, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Sergei Kotelnikov
- Department of Applied Mathematics and Statistics, Stony Brook University, 11794, Stony Brook, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Christopher S Chen
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Pingzhao Hu
- Department of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Gerald V Denis
- Boston Medical Center Cancer Center, Boston University, Boston University, 72 East Concord Street, Boston, MA, 02118, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, 11794, Stony Brook, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Brian Raught
- Discovery Tower (TMDT), 101 College St, Rm. 9-701A, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Trevor Siggers
- Department of Biology, Boston University, 24 Cummington Mall, Boston, MA, 02115, USA
- Biological Design Center, Boston University, 610 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, 1356 Memorial Drive, Coral Gables, FL, 33146, USA
| | - Senthil K Muthuswamy
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA.
- Department of Biology, Charles River Campus, Boston University, Life Science & Engineering (LSEB-602), 24 Cummington Mall, Boston, MA, 02215, USA.
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University, Portland, USA.
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Li W, Salovska B, Fornasiero EF, Liu Y. Toward a hypothesis-free understanding of how phosphorylation dynamically impacts protein turnover. Proteomics 2023; 23:e2100387. [PMID: 36422574 PMCID: PMC10964180 DOI: 10.1002/pmic.202100387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
The turnover measurement of proteins and proteoforms has been largely facilitated by workflows coupling metabolic labeling with mass spectrometry (MS), including dynamic stable isotope labeling by amino acids in cell culture (dynamic SILAC) or pulsed SILAC (pSILAC). Very recent studies including ours have integrated themeasurement of post-translational modifications (PTMs) at the proteome level (i.e., phosphoproteomics) with pSILAC experiments in steady state systems, exploring the link between PTMs and turnover at the proteome-scale. An open question in the field is how to exactly interpret these complex datasets in a biological perspective. Here, we present a novel pSILAC phosphoproteomic dataset which was obtained during a dynamic process of cell starvation using data-independent acquisition MS (DIA-MS). To provide an unbiased "hypothesis-free" analysis framework, we developed a strategy to interrogate how phosphorylation dynamically impacts protein turnover across the time series data. With this strategy, we discovered a complex relationship between phosphorylation and protein turnover that was previously underexplored. Our results further revealed a link between phosphorylation stoichiometry with the turnover of phosphorylated peptidoforms. Moreover, our results suggested that phosphoproteomic turnover diversity cannot directly explain the abundance regulation of phosphorylation during cell starvation, underscoring the importance of future studies addressing PTM site-resolved protein turnover.
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Affiliation(s)
- Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Barbora Salovska
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Eugenio F. Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
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Circadian rhythm disruption is associated with skeletal muscle dysfunction within the blind Mexican Cavefish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525368. [PMID: 36747688 PMCID: PMC9900830 DOI: 10.1101/2023.01.25.525368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Circadian control of physiology and metabolism is pervasive throughout nature, with circadian disruption contributing to premature aging, neurodegenerative disease, and type 2 diabetes (Musiek et al. 2016; Panda, 2016). It has become increasingly clear that peripheral tissues, such as skeletal muscle, possess cell-autonomous clocks crucial for metabolic homeostasis (Gabriel et al. 2021). In fact, disruption of the skeletal muscle circadian rhythm results in insulin resistance, sarcomere disorganization, and muscle weakness in both vertebrates and non-vertebrates - indicating that maintenance of a functional muscle circadian rhythm provides an adaptive advantage. We and others have found that cavefish possess a disrupted central circadian rhythm and, interestingly, a skeletal muscle phenotype strikingly similar to circadian knock-out mutants; namely, muscle loss, muscle weakness, and insulin resistance (Olsen et al. 2022; Riddle et al. 2018; Mack et al. 2021). However, whether the cavefish muscle phenotype results from muscle-specific circadian disruption remains untested. To this point, we investigated genome-wide, circadian-regulated gene expression within the skeletal muscle of the Astyanax mexicanus - comprised of the river-dwelling surface fish and troglobitic cavefish - providing novel insights into the evolutionary consequence of circadian disruption on skeletal muscle physiology.
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Lyu J, Liu Y, Gong L, Chen M, Madanat YF, Zhang Y, Cai F, Gu Z, Cao H, Kaphle P, Kim YJ, Kalkan FN, Stephens H, Dickerson KE, Ni M, Chen W, Patel P, Mims AS, Borate U, Burd A, Cai SF, Yin CC, You MJ, Chung SS, Collins RH, DeBerardinis RJ, Liu X, Xu J. Disabling Uncompetitive Inhibition of Oncogenic IDH Mutations Drives Acquired Resistance. Cancer Discov 2023; 13:170-193. [PMID: 36222845 PMCID: PMC9827114 DOI: 10.1158/2159-8290.cd-21-1661] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 08/31/2022] [Accepted: 10/04/2022] [Indexed: 01/16/2023]
Abstract
Mutations in IDH genes occur frequently in acute myeloid leukemia (AML) and other human cancers to generate the oncometabolite R-2HG. Allosteric inhibition of mutant IDH suppresses R-2HG production in a subset of patients with AML; however, acquired resistance emerges as a new challenge, and the underlying mechanisms remain incompletely understood. Here we establish isogenic leukemia cells containing common IDH oncogenic mutations by CRISPR base editing. By mutational scanning of IDH single amino acid variants in base-edited cells, we describe a repertoire of IDH second-site mutations responsible for therapy resistance through disabling uncompetitive enzyme inhibition. Recurrent mutations at NADPH binding sites within IDH heterodimers act in cis or trans to prevent the formation of stable enzyme-inhibitor complexes, restore R-2HG production in the presence of inhibitors, and drive therapy resistance in IDH-mutant AML cells and patients. We therefore uncover a new class of pathogenic mutations and mechanisms for acquired resistance to targeted cancer therapies. SIGNIFICANCE Comprehensive scanning of IDH single amino acid variants in base-edited leukemia cells uncovers recurrent mutations conferring resistance to IDH inhibition through disabling NADPH-dependent uncompetitive inhibition. Together with targeted sequencing, structural, and functional studies, we identify a new class of pathogenic mutations and mechanisms for acquired resistance to IDH-targeting cancer therapies. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Junhua Lyu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yuxuan Liu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Lihu Gong
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Mingyi Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yazan F. Madanat
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Feng Cai
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Zhimin Gu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Hui Cao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Pranita Kaphle
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yoon Jung Kim
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Fatma N. Kalkan
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Helen Stephens
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Kathryn E. Dickerson
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Min Ni
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Weina Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Prapti Patel
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Alice S. Mims
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Uma Borate
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health and Science University, Portland, Oregon
| | - Amy Burd
- The Leukemia & Lymphoma Society, Rye Brook, New York
| | - Sheng F. Cai
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - C. Cameron Yin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - M. James You
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen S. Chung
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Robert H. Collins
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ralph J. DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Xin Liu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jian Xu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
- Corresponding Author: Jian Xu, Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75235. Phone: 214-648-6125; E-mail:
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Thomas KT, Vermare A, Egleston SO, Wang YD, Mishra A, Lin T, Peng J, Zakharenko SS. MicroRNA 3' ends shorten during adolescent brain maturation. Front Mol Neurosci 2023; 16:1168695. [PMID: 37122627 PMCID: PMC10140418 DOI: 10.3389/fnmol.2023.1168695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/21/2023] [Indexed: 05/02/2023] Open
Abstract
MicroRNA (miRNA) dysregulation is well-documented in psychiatric disease, but miRNA dynamics remain poorly understood during adolescent and early adult brain maturation, when symptoms often first appear. Here, we use RNA sequencing to examine miRNAs and their mRNA targets in cortex and hippocampus from early-, mid-, and late-adolescent and adult mice. Furthermore, we use quantitative proteomics by tandem mass tag mass spectrometry (TMT-MS) to examine protein dynamics in cortex from the same subjects. We found that ~25% of miRNAs' 3' ends shorten with age due to increased 3' trimming and decreased U tailing. Particularly, shorter but functionally competent isoforms (isomiRs) of miR-338-3p increase up to 10-fold during adolescence and only in brain. MiRNAs that undergo 3' shortening exhibit stronger negative correlations with targets that decrease with age and stronger positive correlations with targets that increase with age, than miRNAs with stable 3' ends. Increased 3' shortening with age was also observed in available mouse and human miRNA-seq data sets, and stronger correlations between miRNAs that undergo shortening and their mRNA targets were observed in two of the three available data sets. We conclude that age-associated miRNA 3' shortening is a well-conserved feature of postnatal brain maturation.
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Affiliation(s)
- Kristen T. Thomas
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Anaïs Vermare
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Suzannah O. Egleston
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Ashutosh Mishra
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Tong Lin
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Stanislav S. Zakharenko
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- *Correspondence: Stanislav S. Zakharenko,
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