99951
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Yan Z, An J, Peng Y, Kong S, Liu Q, Yang M, He Q, Song S, Chen Y, Chen W, Li R, Qiao J, Yan L. DevOmics: an integrated multi-omics database of human and mouse early embryo. Brief Bioinform 2021; 22:6294163. [PMID: 34097004 DOI: 10.1093/bib/bbab208] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
Transcriptomic and epigenetic alterations during early embryo development have been proven to play essential roles in regulating the cell fate. Nowadays, advances in single-cell transcriptomics and epigenomics profiling techniques provide large volumes of data for understanding the molecular regulatory mechanisms in early embryos and facilitate the investigation of assisted reproductive technology as well as preimplantation genetic testing. However, the lack of integrated data collection and unified analytic procedures greatly limits their usage in scientific research and clinical application. Hence, it is necessary to establish a database integrating the regulatory information of human and mouse early embryos with unified analytic procedures. Here, we introduce DevOmics (http://devomics.cn/), which contains normalized gene expression, DNA methylation, histone modifications (H3K4me3, H3K9me3, H3K27me3, H3K27ac), chromatin accessibility and 3D chromatin architecture profiles of human and mouse early embryos spanning six developmental stages (zygote, 2cell, 4cell, 8cell, morula and blastocyst (ICM, TE)). The current version of DevOmics provides Search and Advanced Search for retrieving genes a researcher is interested in, Analysis Tools including the differentially expressed genes (DEGs) analysis for acquiring DEGs between different types of samples, allelic explorer for displaying allele-specific gene expression as well as epigenetic modifications and correlation analysis for showing the dynamic changes in different layers of data across developmental stages, as well as Genome Browser and Ortholog for visualization. DevOmics offers a user-friendly website for biologists and clinicians to decipher molecular regulatory mechanisms of human and mouse early embryos.
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Affiliation(s)
- Zhiqiang Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Jianting An
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Yong Peng
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Siming Kong
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Qiang Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Ming Yang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Qilong He
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Shi Song
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Yidong Chen
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Wei Chen
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Liying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
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99952
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Alves CS, Nogueira FTS. Plant Small RNA World Growing Bigger: tRNA-Derived Fragments, Longstanding Players in Regulatory Processes. Front Mol Biosci 2021; 8:638911. [PMID: 34164429 PMCID: PMC8215267 DOI: 10.3389/fmolb.2021.638911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/24/2021] [Indexed: 11/13/2022] Open
Abstract
In the past 2 decades, the discovery of a new class of small RNAs, known as tRNA-derived fragments (tRFs), shed light on a new layer of regulation implicated in many biological processes. tRFs originate from mature tRNAs and are classified according to the tRNA regions that they derive from, namely 3′tRF, 5′tRF, and tRF-halves. Additionally, another tRF subgroup deriving from tRNA precursors has been reported, the 3′U tRFs. tRF length ranges from 17 to 26 nt for the 3′and 5′tRFs, and from 30 to 40 nt for tRF-halves. tRF biogenesis is still not yet elucidated, although there is strong evidence that Dicer (and DICER-LIKE) proteins, as well as other RNases such as Angiogenin in mammal and RNS proteins family in plants, are responsible for processing specific tRFs. In plants, the abundance of those molecules varies among tissues, developmental stages, and environmental conditions. More recently, several studies have contributed to elucidate the role that these intriguing molecules may play in all organisms. Among the recent discoveries, tRFs were found to be involved in distinctive regulatory layers, such as transcription and translation regulation, RNA degradation, ribosome biogenesis, stress response, regulatory signaling in plant nodulation, and genome protection against transposable elements. Although tRF biology is still poorly understood, the field has blossomed in the past few years, and this review summarizes the most recent developments in the tRF field in plants.
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Affiliation(s)
- Cristiane S Alves
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Fabio T S Nogueira
- Laboratório de Genética Molecular do Desenvolvimento Vegetal, Departamento de Ciências Biológicas, ESALQ/USP, Piracicaba, Brazil
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99953
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Ma J, Xu LY, Sun QH, Wan XY, BingLi. Inhibition of miR-1298-5p attenuates sepsis lung injury by targeting SOCS6. Mol Cell Biochem 2021; 476:3745-3756. [PMID: 34100174 DOI: 10.1007/s11010-021-04170-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023]
Abstract
Sepsis is one of the leading causes of morbidity and mortality and a major cause of acute lung injury (ALI). carried by exosomes play a role in a variety of diseases. However,there are not many studies of exosomal miRNAs in sepsis and sepsis lung injury.miR-1298-5p and suppressor of cytokine signaling 6 (SOCS6) were silenced or overexpressed in human bronchial epithelial cells (BEAS-2B). PKH-67 Dye was used to trace exosome endocytosis. Cell permeability was evaluated by measuring trans-epithelial electrical resistance (TEER) and FITC dextran flux. ELISA kits were used for cytokine detection. Quantitative RT-PCR and western blots were used to evaluate gene expression. miR-1298-5p was elevated in exosomes from patients with sepsis lung injury (Sepsis_exo). Treatment of BEAS-2B cells using Sepsis_exo significantly inhibited cell proliferation, and induced cell permeability and inflammatory response. miR-1298-5p directly targeted SOCS6. Overexpressing SOCS6 reversed miR-1298-5p-induced cell permeability and inflammatory response. Inhibition of STAT3 blocked SOCS6-silencing caused significant increase of cell permeability and inflammation. Exosomes isolated from patients of sepsis lung injury increased cell permeability and inflammatory response in BEAS-2B cells through exosomal miR-1298-5p which targeted SOCS6 via STAT3 pathway. The findings highlight the importance of miR-1298-5p/SOCS6/STAT3 axis in sepsis lung injury and provide new insights into therapeutic strategies for sepsis lung injury.
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Affiliation(s)
- Jian Ma
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Doctor's Office, 10th floor, building 2, NO.507 Zhengmin Road, Yangpu District, Shanghai, 200433, P.R. China.
| | - Li-Yun Xu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Doctor's Office, 10th floor, building 2, NO.507 Zhengmin Road, Yangpu District, Shanghai, 200433, P.R. China
| | - Qiu-Hong Sun
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Doctor's Office, 10th floor, building 2, NO.507 Zhengmin Road, Yangpu District, Shanghai, 200433, P.R. China
| | - Xiao-Yu Wan
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Doctor's Office, 10th floor, building 2, NO.507 Zhengmin Road, Yangpu District, Shanghai, 200433, P.R. China
| | - BingLi
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Doctor's Office, 10th floor, building 2, NO.507 Zhengmin Road, Yangpu District, Shanghai, 200433, P.R. China
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99954
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Kim H, Son S, Ko Y, Lee JE, Kim S, Shin I. YAP, CTGF and Cyr61 are overexpressed in tamoxifen-resistant breast cancer and induce transcriptional repression of ERα. J Cell Sci 2021; 134:269035. [PMID: 34096606 DOI: 10.1242/jcs.256503] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/22/2021] [Indexed: 11/20/2022] Open
Abstract
About 70% of breast cancers overexpress estrogen receptor α (ERα, encoded by ESR1). Tamoxifen, a competitive inhibitor of estrogen that binds to ER, has been widely used as a treatment for ER-positive breast cancer. However, 20-30% of breast cancer is resistant to tamoxifen treatment. The mechanisms underlying tamoxifen resistance remain elusive. We found that Yes-associated protein (YAP; also known as YAP1), connective tissue growth factor (CTGF; also known as CCN2) and cysteine-rich angiogenic inducer 61 (Cyr61; also known as CCN1) are overexpressed, while ERα is downregulated in tamoxifen-resistant breast cancer. Inhibition of YAP, CTGF and Cyr61 restored ERα expression and increased sensitivity to tamoxifen. Overexpression of YAP, CTGF, and Cyr61 led to downregulation of ERα and conferred resistance to tamoxifen in ER-positive breast cancer cells. Mechanistically, CTGF and Cyr61 downregulated ERα expression at the transcriptional level by directly binding to the regulatory regions of the ERα-encoding gene, leading to increased tamoxifen resistance. Also, CTGF induced Glut3 (also known as SLC2A3) expression, leading to increased glycolysis, which enhanced cell proliferation and migration in tamoxifen-resistant cells. Together, these results demonstrate a novel role of YAP, CTGF and Cyr61 in tamoxifen resistance and provide a molecular basis for their function in tamoxifen-resistant breast cancer.
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Affiliation(s)
- Hyungjoo Kim
- Department of Life Science, Hanyang University, Seoul 04763, Korea
| | - Seogho Son
- Department of Life Science, Hanyang University, Seoul 04763, Korea
| | - Yunhyo Ko
- Department of Life Science, Hanyang University, Seoul 04763, Korea
| | - Jeong Eon Lee
- Department of Breast Cancer Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Sangmin Kim
- Department of Breast Cancer Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Incheol Shin
- Department of Life Science, Hanyang University, Seoul 04763, Korea.,Natural Science Institute, Hanyang University, Seoul 04763, Korea
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99955
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Nászai M, Bellec K, Yu Y, Román-Fernández A, Sandilands E, Johansson J, Campbell AD, Norman JC, Sansom OJ, Bryant DM, Cordero JB. RAL GTPases mediate EGFR-driven intestinal stem cell proliferation and tumourigenesis. eLife 2021; 10:e63807. [PMID: 34096503 PMCID: PMC8216719 DOI: 10.7554/elife.63807] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
RAS-like (RAL) GTPases function in Wnt signalling-dependent intestinal stem cell proliferation and regeneration. Whether RAL proteins work as canonical RAS effectors in the intestine and the mechanisms of how they contribute to tumourigenesis remain unclear. Here, we show that RAL GTPases are necessary and sufficient to activate EGFR/MAPK signalling in the intestine, via induction of EGFR internalisation. Knocking down Drosophila RalA from intestinal stem and progenitor cells leads to increased levels of plasma membrane-associated EGFR and decreased MAPK pathway activation. Importantly, in addition to influencing stem cell proliferation during damage-induced intestinal regeneration, this role of RAL GTPases impacts on EGFR-dependent tumourigenic growth in the intestine and in human mammary epithelium. However, the effect of oncogenic RAS in the intestine is independent from RAL function. Altogether, our results reveal previously unrecognised cellular and molecular contexts where RAL GTPases become essential mediators of adult tissue homeostasis and malignant transformation.
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MESH Headings
- Animals
- Animals, Genetically Modified
- Breast Neoplasms/enzymology
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Cell Line, Tumor
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Drosophila melanogaster/enzymology
- Drosophila melanogaster/genetics
- Endocytosis
- ErbB Receptors/genetics
- ErbB Receptors/metabolism
- Female
- Humans
- Hyperplasia
- Intestinal Mucosa/metabolism
- Intestinal Mucosa/pathology
- Lung Neoplasms/enzymology
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Mammary Glands, Human/enzymology
- Mammary Glands, Human/pathology
- Mice, Inbred C57BL
- Mitogen-Activated Protein Kinases/metabolism
- Monomeric GTP-Binding Proteins/genetics
- Monomeric GTP-Binding Proteins/metabolism
- Receptors, Invertebrate Peptide/genetics
- Receptors, Invertebrate Peptide/metabolism
- Signal Transduction
- Stem Cells/metabolism
- Stem Cells/pathology
- ral GTP-Binding Proteins/genetics
- ral GTP-Binding Proteins/metabolism
- Mice
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Affiliation(s)
- Máté Nászai
- Wolfson Wohl Cancer Research CentreGlasgowUnited Kingdom
- Institute of Cancer Sciences, University of GlasgowGlasgowUnited Kingdom
| | - Karen Bellec
- Wolfson Wohl Cancer Research CentreGlasgowUnited Kingdom
- Institute of Cancer Sciences, University of GlasgowGlasgowUnited Kingdom
| | - Yachuan Yu
- Wolfson Wohl Cancer Research CentreGlasgowUnited Kingdom
- Institute of Cancer Sciences, University of GlasgowGlasgowUnited Kingdom
- Cancer Research UK Beatson InstituteGlasgowUnited Kingdom
| | - Alvaro Román-Fernández
- Institute of Cancer Sciences, University of GlasgowGlasgowUnited Kingdom
- Cancer Research UK Beatson InstituteGlasgowUnited Kingdom
| | - Emma Sandilands
- Institute of Cancer Sciences, University of GlasgowGlasgowUnited Kingdom
- Cancer Research UK Beatson InstituteGlasgowUnited Kingdom
| | - Joel Johansson
- Cancer Research UK Beatson InstituteGlasgowUnited Kingdom
| | | | - Jim C Norman
- Institute of Cancer Sciences, University of GlasgowGlasgowUnited Kingdom
- Cancer Research UK Beatson InstituteGlasgowUnited Kingdom
| | - Owen J Sansom
- Institute of Cancer Sciences, University of GlasgowGlasgowUnited Kingdom
- Cancer Research UK Beatson InstituteGlasgowUnited Kingdom
| | - David M Bryant
- Institute of Cancer Sciences, University of GlasgowGlasgowUnited Kingdom
- Cancer Research UK Beatson InstituteGlasgowUnited Kingdom
| | - Julia B Cordero
- Wolfson Wohl Cancer Research CentreGlasgowUnited Kingdom
- Institute of Cancer Sciences, University of GlasgowGlasgowUnited Kingdom
- Cancer Research UK Beatson InstituteGlasgowUnited Kingdom
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99956
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Groblewska M, Mroczko B. Pro- and Antiangiogenic Factors in Gliomas: Implications for Novel Therapeutic Possibilities. Int J Mol Sci 2021; 22:ijms22116126. [PMID: 34200145 PMCID: PMC8201226 DOI: 10.3390/ijms22116126] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
Angiogenesis, a complex, multistep process of forming new blood vessels, plays crucial role in normal development, embryogenesis, and wound healing. Malignant tumors characterized by increased proliferation also require new vasculature to provide an adequate supply of oxygen and nutrients for developing tumor. Gliomas are among the most frequent primary tumors of the central nervous system (CNS), characterized by increased new vessel formation. The processes of neoangiogenesis, necessary for glioma development, are mediated by numerous growth factors, cytokines, chemokines and other proteins. In contrast to other solid tumors, some biological conditions, such as the blood–brain barrier and the unique interplay between immune microenvironment and tumor, represent significant challenges in glioma therapy. Therefore, the objective of the study was to present the role of various proangiogenic factors in glioma angiogenesis as well as the differences between normal and tumoral angiogenesis. Another goal was to present novel therapeutic options in oncology approaches. We performed a thorough search via the PubMed database. In this paper we describe various proangiogenic factors in glioma vasculature development. The presented paper also reviews various antiangiogenic factors necessary in maintaining equilibrium between pro- and antiangiogenic processes. Furthermore, we present some novel possibilities of antiangiogenic therapy in this type of tumors.
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Affiliation(s)
- Magdalena Groblewska
- Department of Biochemical Diagnostics, University Hospital in Białystok, 15-269 Białystok, Poland;
| | - Barbara Mroczko
- Department of Biochemical Diagnostics, University Hospital in Białystok, 15-269 Białystok, Poland;
- Department of Neurodegeneration Diagnostics, Medical University of Białystok, 15-269 Białystok, Poland
- Correspondence: ; Tel.: +48-858318785
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99957
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Paul S, Jakhar R, Bhardwaj M, Chauhan AK, Kang SC. Fumonisin B1 induces poly (ADP-ribose) (PAR) polymer-mediated cell death (parthanatos) in neuroblastoma. Food Chem Toxicol 2021; 154:112326. [PMID: 34111490 DOI: 10.1016/j.fct.2021.112326] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/25/2022]
Abstract
Fumonisin B1 (FB1) is a well-known mycotoxin produced by Fusarium spp. and has a wide range of dose-dependent toxic effects, including nephrotoxicity, hepatotoxicity, and neurotoxicity. This research illustrated that FB1 exerts its toxicity in the neuroblastoma cell line through a distinct cell-death pathway called parthanatos. FB1 can cause excessive DNA strand breaks, leading to poly (ADP-ribose) polymerase-1 (PARP-1) overactivation and cell death. In this study, we used 50 μM FB1-treated SH-SY5Y neuroblastoma cells to elucidate the signaling pathway of FB1-induced parthanatos. We observed that FB1-induced cell death is caspase-independent and accompanied by rapid activation of PARP-1, c-Jun N-terminal kinase activation, reactive oxygen species (ROS) generation, and intracellular calcium increase. FB1 treatment also increased endoplasmic reticulum stress due to the rapid increase of calcium ions and ROS levels. In addition, FB1 induced massive DNA damage and chromatin decondensation. We also observed that apoptosis-inducing factor nuclear translocation and PAR accumulation were associated with the necroptosis signal.
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Affiliation(s)
- Souren Paul
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, USA; Department of Biotechnology, Daegu University, Kyoungsan, Kyoungbook, 38453, Republic of Korea
| | - Rekha Jakhar
- Department of Biotechnology, Daegu University, Kyoungsan, Kyoungbook, 38453, Republic of Korea
| | - Monika Bhardwaj
- Department of Biotechnology, Daegu University, Kyoungsan, Kyoungbook, 38453, Republic of Korea
| | - Anil Kumar Chauhan
- Department of Biotechnology, Daegu University, Kyoungsan, Kyoungbook, 38453, Republic of Korea
| | - Sun Chul Kang
- Department of Biotechnology, Daegu University, Kyoungsan, Kyoungbook, 38453, Republic of Korea.
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99958
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Nan K, Zhang Y, Zhang X, Li D, Zhao Y, Jing Z, Liu K, Shang D, Geng Z, Fan L. Exosomes from miRNA-378-modified adipose-derived stem cells prevent glucocorticoid-induced osteonecrosis of the femoral head by enhancing angiogenesis and osteogenesis via targeting miR-378 negatively regulated suppressor of fused (Sufu). Stem Cell Res Ther 2021; 12:331. [PMID: 34099038 PMCID: PMC8186190 DOI: 10.1186/s13287-021-02390-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/13/2021] [Indexed: 01/08/2023] Open
Abstract
Background Local ischemia and defective osteogenesis are implicated in the progression of glucocorticoid (GC)-induced osteonecrosis of the femoral head (ONFH). Recent studies have revealed that exosomes released from adipose-derived stem cells (ASCs) play important roles in ONFH therapy. The present study aimed to investigate whether exosomes derived from miR-378-overexpressing ASCs (miR-378-ASCs-Exos) could promote angiogenesis and osteogenesis in GC-induced ONFH. Methods In vitro, we investigated the osteogenic potential of miR-378-ASCs-Exos on bone marrow stromal cells (BMSCs) by alkaline phosphatase staining and western blotting. The angiogenic effects of miR-378-ASCs-Exos on human umbilical vein endothelial cells (HUVECs) were examined by evaluating their proliferation, migration, and tube-forming analyses. We identified the underlying mechanisms of miR-378 in osteogenic and angiogenic regulation. In addition, an ONFH rat model was established to explore the effects of miR-378-ASCs-Exos through histological and immunohistochemical staining and micro-CT in vivo. Results Administration of miR-378-ASCs-Exos improved the osteogenic and angiogenic potentials of BMSCs and HUVECs. miR-378 negatively regulated the suppressor of fused (Sufu) and activated Sonic Hedgehog (Shh) signaling pathway, and recombinant Sufu protein reduced the effects triggered by miR-378-ASCs-Exos. In vivo experiments indicated that miR-378-ASCs-Exos markedly accelerated bone regeneration and angiogenesis, which inhibited the progression of ONFH. Conclusion Our study indicated that miR-378-ASCs-Exos enhances osteogenesis and angiogenesis by targeting Sufu to upregulate the Shh signaling pathway, thereby attenuating GC-induced ONFH development.
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Affiliation(s)
- Kai Nan
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, Shaanxi Province, People's Republic of China
| | - Yuankai Zhang
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, Shaanxi Province, People's Republic of China
| | - Xin Zhang
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, Shaanxi Province, People's Republic of China
| | - Dong Li
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, Shaanxi Province, People's Republic of China
| | - Yan Zhao
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, Shaanxi Province, People's Republic of China
| | - Zhaopu Jing
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, Shaanxi Province, People's Republic of China
| | - Kang Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi Province, People's Republic of China
| | - Donglong Shang
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, Shaanxi Province, People's Republic of China
| | - Zilong Geng
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, Shaanxi Province, People's Republic of China
| | - Lihong Fan
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, Shaanxi Province, People's Republic of China.
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99959
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Repair pathway choice for double-strand breaks. Essays Biochem 2021; 64:765-777. [PMID: 32648897 DOI: 10.1042/ebc20200007] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/20/2022]
Abstract
Deoxyribonucleic acid (DNA) is at a constant risk of damage from endogenous substances, environmental radiation, and chemical stressors. DNA double-strand breaks (DSBs) pose a significant threat to genomic integrity and cell survival. There are two major pathways for DSB repair: nonhomologous end-joining (NHEJ) and homologous recombination (HR). The extent of DNA end resection, which determines the length of the 3' single-stranded DNA (ssDNA) overhang, is the primary factor that determines whether repair is carried out via NHEJ or HR. NHEJ, which does not require a 3' ssDNA tail, occurs throughout the cell cycle. 53BP1 and the cofactors PTIP or RIF1-shieldin protect the broken DNA end, inhibit long-range end resection and thus promote NHEJ. In contrast, HR mainly occurs during the S/G2 phase and requires DNA end processing to create a 3' tail that can invade a homologous region, ensuring faithful gene repair. BRCA1 and the cofactors CtIP, EXO1, BLM/DNA2, and the MRE11-RAD50-NBS1 (MRN) complex promote DNA end resection and thus HR. DNA resection is influenced by the cell cycle, the chromatin environment, and the complexity of the DNA end break. Herein, we summarize the key factors involved in repair pathway selection for DSBs and discuss recent related publications.
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99960
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Lu Y, Li Z, Lin C, Zhang J, Shen Z. Translation role of circRNAs in cancers. J Clin Lab Anal 2021; 35:e23866. [PMID: 34097315 PMCID: PMC8275004 DOI: 10.1002/jcla.23866] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 12/24/2022] Open
Abstract
Circular RNAs (circRNAs) constitute a class of covalently closed RNA molecules. With the continuous advancement of high‐throughput sequencing technology and bioinformatics tools, many circRNAs have been identified in various human tissues and cell lines. Notably, recent studies have indicated that some circRNAs have translational functions. Internal ribosome entry sites and the N6‐methyladenosine modification mediate cap‐independent translation. This review describes these two translation mechanisms and verification methods at the molecular level. Databases (including ORF Finder, Pfam, BLASTp, CircRNADb, CircBase, CircPro, CircCode, IRESite, IRESbase) were used to analyze whether circRNAs have the structural characteristic of translation. CircRNA minigene reporter system containing green fluorescent protein (GFP) confirmed the translation potential of circRNAs. Also, we briefly summarize the roles of proteins/peptides encoded by circRNAs (circFBXW7, circFNDC3B, circLgr4, circPPP1R12A, circMAPK1, circβ‐catenin, circGprc5a, circ‐SHPRH, circPINTexon2, circAKT3) that have been verified thus far in human cancers (triple‐negative breast cancer, colon cancer, gastric cancer, hepatocellular carcinoma, bladder cancer, glioblastoma). Those findings suggest circRNAs have a great implication in translation of the human genome.
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Affiliation(s)
- Yaqin Lu
- Ningbo University School of MedicineNingboChina
| | - Zhe Li
- Ningbo University School of MedicineNingboChina
| | - Chen Lin
- Ningbo University School of MedicineNingboChina
| | - Jian Zhang
- Li Huili Hospital Affiliated to Ningbo University SchoolNingboChina
| | - Zhisen Shen
- Li Huili Hospital Affiliated to Ningbo University SchoolNingboChina
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99961
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Almasabi S, Ahmed AU, Boyd R, Williams BRG. A Potential Role for Integrin-Linked Kinase in Colorectal Cancer Growth and Progression via Regulating Senescence and Immunity. Front Genet 2021; 12:638558. [PMID: 34163519 PMCID: PMC8216764 DOI: 10.3389/fgene.2021.638558] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/08/2021] [Indexed: 01/10/2023] Open
Abstract
Integrin-linked kinase (ILK) has been implicated as a molecular driver and mediator in both inflammation and tumorigenesis of the colon. ILK functions as an adaptor and mediator protein linking the extracellular matrix with downstream signaling pathways. ILK is broadly expressed in many human tissues and cells. It is also overexpressed in many cancers, including colorectal cancer (CRC). Inflammation, as evidenced by inflammatory bowel disease (IBD), is one of the highest risk factors for initiating CRC. This has led to the hypothesis that targeting ILK therapeutically could have potential in CRC, as it regulates different cellular processes associated with CRC development and progression as well as inflammation in the colon. A number of studies have indicated an ILK function in senescence, a cellular process that arrests the cell cycle while maintaining active metabolism and transcription. Senescent cells produce different secretions collectively known as the senescence-associated secretory phenotype (SASP). The SASP secretions influence infiltration of different immune cells, either positively for clearing senescent cells or negatively for promoting tumor growth, reflecting the dual role of senescence in cancer. However, a role for ILK in senescence and immunity in CRC remains to be determined. In this review, we discuss the possible role for ILK in senescence and immunity, paying particular attention to the relevance of ILK in CRC. We also examine how activating Toll-like receptors (TLRs) and their agonists in CRC could trigger immune responses against cancer, as a combination therapy with ILK inhibition.
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Affiliation(s)
- Saleh Almasabi
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Cartherics, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Clinical Laboratory Sciences, Applied Medical Sciences, Najran University, Najran, Saudi Arabia.,Department of Molecular and Translational Sciences, Faculty of Medicine Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Afsar U Ahmed
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Richard Boyd
- Cartherics, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Bryan R G Williams
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Faculty of Medicine Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
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99962
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Msn2/4 transcription factors positively regulate expression of Atg39 ER-phagy receptor. Sci Rep 2021; 11:11919. [PMID: 34099851 PMCID: PMC8184937 DOI: 10.1038/s41598-021-91480-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/27/2021] [Indexed: 12/18/2022] Open
Abstract
Selective autophagy requires the autophagy receptor specifically localizing to the target for degradation. In the budding yeast, Atg39 and Atg40 function as an autophagy receptor for the endoplasmic reticulum (ER)-selective autophagy, referred to as ER-phagy. The expression level of the ATG39 gene is increased in response to ER stress and nitrogen starvation. Under unstressed conditions, ATG39 transcription is repressed by Mig1/2 repressors. ER stress activates Snf1 AMP-activated protein kinase (AMPK), which negatively regulates Mig1/2 and consequently derepresses ATG39 transcription. However, ATG39 expression is still induced by ER stress and nitrogen starvation in the absence of Snf1, suggesting that additional molecules are involved in regulation of ATG39 expression. Here, we identify Msn2/4 transcription factors as an activator of ATG39 transcription. Not only ATG39 promoter activity but also ER-phagy are downregulated by loss of Msn2/4 and disruption of Msn2/4-binding consensus sequences located in the ATG39 promoter. We also find that the cAMP-dependent protein kinase pathway is involved in Msn2/4-mediated transcriptional regulation of ATG39. Our results suggest that yeast ER-phagy is appropriately controlled through modulation of the expression level of the ER-phagy receptor involving multiple signaling pathways and transcription factors.
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99963
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Lin Y, Zeng Y, Zhu Y, Shen J, Ye H, Jiang L. Plant Rho GTPase signaling promotes autophagy. MOLECULAR PLANT 2021; 14:905-920. [PMID: 33794369 DOI: 10.1016/j.molp.2021.03.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/27/2021] [Accepted: 03/25/2021] [Indexed: 05/06/2023]
Abstract
The roles of Rho family guanosine triphosphatases (GTPases) of plants (ROPs) in modulating plant growth and development have been well characterized. However, little is known about the roles of ROP signaling pathways in regulating plant autophagy and autophagosome formation. In this study, we identify a unique ROP signaling mechanism, which mediates developmental to autophagic transition under stress conditions in the model plant Arabidopsis. Loss-of-function mutants of ROP8 showed stress-induced hypersensitive phenotypes and compromised autophagic flux. Similar to other ROPs in the ROP/RAC family, ROP8 exhibits both plasma membrane and cytosolic punctate localization patterns. Upon autophagic induction, active ROP8 puncta colocalize with autophagosomal markers and are degraded inside the vacuole. In human cells, RalB, an RAS subfamily GTPase, engages its effector Exo84 for autophagosome assembly. However, a RalB counterpart is missing in the plant lineage. Intriguingly, we discovered that plant ROP8 promotes autophagy via its downstream effector Sec5. Live-cell super-resolution imaging showed that ROP8 and Sec5 reside on phagophores for autophagosome formation. Taken together, our findings highlight a previously unappreciated role of an ROP8-Sec5 signaling axis in autophagy promotion, providing new insights into how plants utilize versatile ROP signaling networks to coordinate developmental and autophagic responses depending on environmental changes.
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Affiliation(s)
- Youshun Lin
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China.
| | - Yonglun Zeng
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Ying Zhu
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Hao Ye
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; Institute of Plant Molecular Biology and Agricultural Biotechnology, CUHK, Hong Kong, China; CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Shenzhen, Hong Kong, 518057, China.
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99964
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Cao C, He K, Li S, Ge Q, Liu L, Zhang Z, Zhang H, Wang X, Sun X, Ding L. ITPRIP promotes glioma progression by linking MYL9 to DAPK1 inhibition. Cell Signal 2021; 85:110062. [PMID: 34111521 DOI: 10.1016/j.cellsig.2021.110062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/27/2021] [Accepted: 06/04/2021] [Indexed: 12/01/2022]
Abstract
Epigenetic gene silencing of the tumor suppressor death-associated protein kinase 1 (DAPK1) is implicated in the progression of malignant gliomas. However, the mechanism underlying the repression of DAPK1 in gliomas remains elusive. In this study, we identified the existence of DAPK1-inositol 1,4,5-trisphosphate receptor (IP3R)-interacting protein (ITPRIP) -myosin regulatory light polypeptide 9 (MYL9) complex in malignant glioma cells. Lentivirus co-infection and coimmunoprecipitation showed that ITPRIP bound with the death domain (DD) of DAPK1 in vitro. Further, dissociating ITPRIP-DAPK1 interaction inhibited glioma tumor growth in vitro but not in vivo. Moreover, knockdown of ITPRIP or DAPK1 impaired the ternary complex formation, whereas MYL9 knockdown did not affect ITPRIP-DAPK1 association. We further found that ITPRIP recruited MYL9 to the kinase domain (KD) of DAPK1, and in turn impeded the phosphorylation of MYL9. Accordingly, interference of ITPRIP enhanced the suppressive effects of DAPK1-KD on glioma progression both in vitro and in vivo. Our results demonstrate that ITPRIP plays a crucial role in the inhibition of DAPK1 and enhancement of tumorigenic properties of malignant glioma cells.
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Affiliation(s)
- Changchun Cao
- Department of Pharmacy, The Affiliated Huaian NO.1 People's Hospital of Nanjing Medical University, 1 Huanghe West Road, Huaian 223300, China.
| | - Kang He
- Department of Neurosurgery, The Affiliated Huaian NO.1 People's Hospital of Nanjing Medical University, 1 Huanghe West Road, Huaian 223300, China
| | - Shaoxun Li
- Department of Neurosurgery, The Affiliated Huaian NO.1 People's Hospital of Nanjing Medical University, 1 Huanghe West Road, Huaian 223300, China
| | - Qianqian Ge
- Department of Gynecology, The Affiliated Huaian NO.1 People's Hospital of Nanjing Medical University, 1 Huanghe West Road, Huaian 223300, China
| | - Lei Liu
- Department of Neurosurgery, The Affiliated Huaian NO.1 People's Hospital of Nanjing Medical University, 1 Huanghe West Road, Huaian 223300, China
| | - Zhengwei Zhang
- Department of Pathology, The Affiliated Huaian NO.1 People's Hospital of Nanjing Medical University, 1 Huanghe West Road, Huaian 223300, China
| | - Hui Zhang
- Department of Pathology, The Affiliated Huaian NO.1 People's Hospital of Nanjing Medical University, 1 Huanghe West Road, Huaian 223300, China
| | - Xinwen Wang
- Department of Pharmacy, The Affiliated Huaian NO.1 People's Hospital of Nanjing Medical University, 1 Huanghe West Road, Huaian 223300, China.
| | - Xiaoyang Sun
- Department of Neurosurgery, The Affiliated Huaian NO.1 People's Hospital of Nanjing Medical University, 1 Huanghe West Road, Huaian 223300, China.
| | - Lianshu Ding
- Department of Neurosurgery, The Affiliated Huaian NO.1 People's Hospital of Nanjing Medical University, 1 Huanghe West Road, Huaian 223300, China.
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99965
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Männik J, Teshima TF, Wolfrum B, Yang D. Lab-on-a-chip based mechanical actuators and sensors for single-cell and organoid culture studies. JOURNAL OF APPLIED PHYSICS 2021; 129:210905. [PMID: 34103765 PMCID: PMC8175090 DOI: 10.1063/5.0051875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/10/2021] [Indexed: 05/04/2023]
Abstract
All living cells constantly experience and respond to mechanical stresses. The molecular networks that activate in cells in response to mechanical stimuli are yet not well-understood. Our limited knowledge stems partially from the lack of available tools that are capable of exerting controlled mechanical stress to individual cells and at the same time observing their responses at subcellular to molecular resolution. Several tools such as rheology setups, micropipetes, and magnetic tweezers have been used in the past. While allowing to quantify short-time viscoelastic responses, these setups are not suitable for long-term observations of cells and most of them have low throughput. In this Perspective, we discuss lab-on-a-chip platforms that have the potential to overcome these limitations. Our focus is on devices that apply shear, compressive, tensile, and confinement derived stresses to single cells and organoid cultures. We compare different design strategies for these devices and highlight their advantages, drawbacks, and future potential. While the majority of these devices are used for fundamental research, some of them have potential applications in medical diagnostics and these applications are also discussed.
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Affiliation(s)
- Jaan Männik
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, Tennessee 37996, USA
- Author to whom correspondence should be addressed:
| | | | | | - Da Yang
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, Tennessee 37996, USA
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99966
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Yes-Associated Protein (Yap) Is Up-Regulated in Heart Failure and Promotes Cardiac Fibroblast Proliferation. Int J Mol Sci 2021; 22:ijms22116164. [PMID: 34200497 PMCID: PMC8201133 DOI: 10.3390/ijms22116164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/04/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023] Open
Abstract
Left ventricular (LV) heart failure (HF) is a significant and increasing cause of death worldwide. HF is characterized by myocardial remodeling and excessive fibrosis. Transcriptional co-activator Yes-associated protein (Yap), the downstream effector of HIPPO signaling pathway, is an essential factor in cardiomyocyte survival; however, its status in human LV HF is not entirely elucidated. Here, we report that Yap is elevated in LV tissue of patients with HF, and is associated with down-regulation of its upstream inhibitor HIPPO component large tumor suppressor 1 (LATS1) activation as well as upregulation of the fibrosis marker connective tissue growth factor (CTGF). Applying the established profibrotic combined stress of TGFβ and hypoxia to human ventricular cardiac fibroblasts in vitro increased Yap protein levels, down-regulated LATS1 activation, increased cell proliferation and collagen I production, and decreased ribosomal protein S6 and S6 kinase phosphorylation, a hallmark of mTOR activation, without any significant effect on mTOR and raptor protein expression or phosphorylation of mTOR or 4E-binding protein 1 (4EBP1), a downstream effector of mTOR pathway. As previously reported in various cell types, TGFβ/hypoxia also enhanced cardiac fibroblast Akt and ERK1/2 phosphorylation, which was similar to our observation in LV tissues from HF patients. Further, depletion of Yap reduced TGFβ/hypoxia-induced cardiac fibroblast proliferation and Akt phosphorylation at Ser 473 and Thr308, without any significant effect on TGFβ/hypoxia-induced ERK1/2 activation or reduction in S6 and S6 kinase activities. Taken together, these data demonstrate that Yap is a mediator that promotes human cardiac fibroblast proliferation and suggest its possible contribution to remodeling of the LV, opening the door to further studies to decipher the cell-specific roles of Yap signaling in human HF.
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99967
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You C, Zhang Y, Yang S, Wang X, Yao W, Jin W, Wang W, Hu X, Yang H. Proteomic Analysis of Generative and Vegetative Nuclei Reveals Molecular Characteristics of Pollen Cell Differentiation in Lily. FRONTIERS IN PLANT SCIENCE 2021; 12:641517. [PMID: 34163497 PMCID: PMC8215658 DOI: 10.3389/fpls.2021.641517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/01/2021] [Indexed: 06/13/2023]
Abstract
In plants, the cell fates of a vegetative cell (VC) and generative cell (GC) are determined after the asymmetric division of the haploid microspore. The VC exits the cell cycle and grows a pollen tube, while the GC undergoes further mitosis to produce two sperm cells for double fertilization. However, our understanding of the mechanisms underlying their fate differentiation remains limited. One major advantage of the nuclear proteome analysis is that it is the only method currently able to uncover the systemic differences between VC and GC due to GC being engulfed within the cytoplasm of VC, limiting the use of transcriptome. Here, we obtained pure preparations of the vegetative cell nuclei (VNs) and generative cell nuclei (GNs) from germinating lily pollens. Utilizing these high-purity VNs and GNs, we compared the differential nucleoproteins between them using state-of-the-art quantitative proteomic techniques. We identified 720 different amount proteins (DAPs) and grouped the results in 11 fate differentiation categories. Among them, we identified 29 transcription factors (TFs) and 10 cell fate determinants. Significant differences were found in the molecular activities of vegetative and reproductive nuclei. The TFs in VN mainly participate in pollen tube development. In comparison, the TFs in GN are mainly involved in cell differentiation and male gametogenesis. The identified novel TFs may play an important role in cell fate differentiation. Our data also indicate differences in nuclear pore complexes and epigenetic modifications: more nucleoporins synthesized in VN; more histone variants and chaperones; and structural maintenance of chromosome (SMC) proteins, chromatin remodelers, and DNA methylation-related proteins expressed in GN. The VC has active macromolecular metabolism and mRNA processing, while GC has active nucleic acid metabolism and translation. Moreover, the members of unfolded protein response (UPR) and programmed cell death accumulate in VN, and DNA damage repair is active in GN. Differences in the stress response of DAPs in VN vs. GN were also found. This study provides a further understanding of pollen cell differentiation mechanisms and also a sound basis for future studies of the molecular mechanisms behind cell fate differentiation.
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Affiliation(s)
- Chen You
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- College of Life Science, Henan Normal University, Xinxiang, China
| | - YuPing Zhang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - ShaoYu Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Xu Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wen Yao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - WeiHuan Jin
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - XiuLi Hu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Hao Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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99968
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Yuan Y, Wang Z, Chen M, Jing Y, Shu W, Xie Z, Li Z, Xu J, He F, Jiao P, Wang J, Xu J, Xia Y, Liu S, Du H, Li H, Dai L, Dai Y, Zhang Y. Macrophage-Derived Exosomal miR-31-5p Promotes Oral Squamous Cell Carcinoma Tumourigenesis Through the Large Tumor Suppressor 2-Mediated Hippo Signalling Pathway. J Biomed Nanotechnol 2021; 17:822-837. [PMID: 34082869 DOI: 10.1166/jbn.2021.3066] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Tumour-associated macrophages (TAMs) are thought to contribute to oral squamous cell carcinoma (OSCC) initiation and progression. However, the underlying mechanism through which TAMs foster OSCC progression is still unclear. This study intended to determine whether there are exclusively exosomal miRNAs-derived macrophages that are functionally necessary for OSCC progression. The phenotype of TAM recruitment in OSCC tissue samples was assessed, subsequently identifying the influence of M2 macrophages and exosomes derived from M2 macrophages on OSCC proliferation and tumorigenesis in vitro and in vivo. CD68 and CD163, the specific markers of M2 type macrophages, were upregulated in TAMs presented in intra-cancer tissues. M2 macrophages and M2 macrophage-derived exosomes (M2 exos) both can promote OSCC growth and tumorigenicity. An exosomal RNA-seq analysis was conducted to predict regulatory exosomal miRNAs related to OSCC growth, which determined miR-31-5p and LATS2 for subsequent experiments. Mechanistically, miR-31-5p was delivered to recipient OSCC cells through M2 exos and complementary pairing with the large tumor suppressor 2 (LATS2) coding sequence, thus suppressing the expression of LATS2 and inactivation the Hippo signaling pathway to support OSCC growth. Collectively, our findings demonstrate that M2 macrophage-derived exosomal miR- 31-5p can make tumor suppressor LATS2 gene inhibited and facilitate the progression of OSCC via inhibiting the Hippo signaling pathway, which possibly provides new targets for the molecular therapy of OSCC.
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Affiliation(s)
- Yi Yuan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, Jiangsu, PR China
| | - Zeyu Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, Jiangsu, PR China
| | - Mengqi Chen
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, Jiangsu, PR China
| | - Yang Jing
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, Jiangsu, PR China
| | - Wei Shu
- Department of Stomatology, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing 210029, Jiangsu, PR China
| | - Zhuoying Xie
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, Jiangsu, PR China
| | - Zhiyang Li
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008
| | - Juanyong Xu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, Jiangsu, PR China
| | - Feng He
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, Jiangsu, PR China
| | - Pengfei Jiao
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, Jiangsu, PR China
| | - Jiaqing Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, Jiangsu, PR China
| | - Jiamin Xu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, Jiangsu, PR China
| | - Yan Xia
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, Jiangsu, PR China
| | - Siyu Liu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, Jiangsu, PR China
| | - Hongming Du
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, Jiangsu, PR China
| | - Hongwei Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, Jiangsu, PR China
| | - Lu Dai
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, Jiangsu, PR China
| | - Youjin Dai
- Key Laboratory of Model Animal Research, Animal Core Facility of Nanjing Medical University, Nanjing Medical University, Nanjing 211166, Jiangsu, PR China
| | - Yaqin Zhang
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing 211166, Jiangsu, PR China
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99969
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Chen L, Hong W, Ren W, Xu T, Qian Z, He Z. Recent progress in targeted delivery vectors based on biomimetic nanoparticles. Signal Transduct Target Ther 2021; 6:225. [PMID: 34099630 PMCID: PMC8182741 DOI: 10.1038/s41392-021-00631-2] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 02/05/2023] Open
Abstract
Over the past decades, great interest has been given to biomimetic nanoparticles (BNPs) since the rise of targeted drug delivery systems and biomimetic nanotechnology. Biological vectors including cell membranes, extracellular vesicles (EVs), and viruses are considered promising candidates for targeted delivery owing to their biocompatibility and biodegradability. BNPs, the integration of biological vectors and functional agents, are anticipated to load cargos or camouflage synthetic nanoparticles to achieve targeted delivery. Despite their excellent intrinsic properties, natural vectors are deliberately modified to endow multiple functions such as good permeability, improved loading capability, and high specificity. Through structural modification and transformation of the vectors, they are pervasively utilized as more effective vehicles that can deliver contrast agents, chemotherapy drugs, nucleic acids, and genes to target sites for refractory disease therapy. This review summarizes recent advances in targeted delivery vectors based on cell membranes, EVs, and viruses, highlighting the potential applications of BNPs in the fields of biomedical imaging and therapy industry, as well as discussing the possibility of clinical translation and exploitation trend of these BNPs.
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Affiliation(s)
- Li Chen
- Department of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Weiqi Hong
- Department of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wenyan Ren
- Department of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ting Xu
- Department of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Zhiyong Qian
- Department of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhiyao He
- Department of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China.
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99970
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Kamalesh K, Scher N, Biton T, Schejter ED, Shilo BZ, Avinoam O. Exocytosis by vesicle crumpling maintains apical membrane homeostasis during exocrine secretion. Dev Cell 2021; 56:1603-1616.e6. [PMID: 34102104 PMCID: PMC8191493 DOI: 10.1016/j.devcel.2021.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/17/2021] [Accepted: 05/06/2021] [Indexed: 12/14/2022]
Abstract
Exocrine secretion commonly employs micron-scale vesicles that fuse to a limited apical surface, presenting an extreme challenge for maintaining membrane homeostasis. Using Drosophila melanogaster larval salivary glands, we show that the membranes of fused vesicles undergo actomyosin-mediated folding and retention, which prevents them from incorporating into the apical surface. In addition, the diffusion of proteins and lipids between the fused vesicle and the apical surface is limited. Actomyosin contraction and membrane crumpling are essential for recruiting clathrin-mediated endocytosis to clear the retained vesicular membrane. Finally, we also observe membrane crumpling in secretory vesicles of the mouse exocrine pancreas. We conclude that membrane sequestration by crumpling followed by targeted endocytosis of the vesicular membrane, represents a general mechanism of exocytosis that maintains membrane homeostasis in exocrine tissues that employ large secretory vesicles.
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Affiliation(s)
- Kumari Kamalesh
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel; Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Nadav Scher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tom Biton
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel; Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal D Schejter
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ben-Zion Shilo
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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99971
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Multi-target mode of action of silver against Staphylococcus aureus endows it with capability to combat antibiotic resistance. Nat Commun 2021; 12:3331. [PMID: 34099682 PMCID: PMC8184742 DOI: 10.1038/s41467-021-23659-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
The rapid emergence of drug resistant Staphylococcus aureus (S. aureus) poses a serious threat to public health globally. Silver (Ag)-based antimicrobials are promising to combat antibiotic resistant S. aureus, yet their molecular targets are largely elusive. Herein, we separate and identify 38 authentic Ag+-binding proteins in S. aureus at the whole-cell scale. We then capture the molecular snapshot on the dynamic action of Ag+ against S. aureus and further validate that Ag+ could inhibit a key target 6-phosphogluconate dehydrogenase through binding to catalytic His185 by X-ray crystallography. Significantly, the multi-target mode of action of Ag+ (and nanosilver) endows its sustainable antimicrobial efficacy, leading to enhanced efficacy of conventional antibiotics and resensitization of MRSA to antibiotics. Our study resolves the long-standing question of the molecular targets of silver in S. aureus and offers insights into the sustainable bacterial susceptibility of silver, providing a potential approach for combating antimicrobial resistance. Silver (Ag) has been used as an antimicrobial agent since a long time, but its molecular mechanism of action was not elucidated due to technical challenges. Here, the authors develop a mass spectrometric approach to identify the Ag-proteome in Staphylococcus aureus, and capture a molecular snapshot of the dynamic bactericidal mode of action of Ag through targeting multiple biological pathways.
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99972
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Garcia LR, Tenev T, Newman R, Haich RO, Liccardi G, John SW, Annibaldi A, Yu L, Pardo M, Young SN, Fitzgibbon C, Fernando W, Guppy N, Kim H, Liang LY, Lucet IS, Kueh A, Roxanis I, Gazinska P, Sims M, Smyth T, Ward G, Bertin J, Beal AM, Geddes B, Choudhary JS, Murphy JM, Aurelia Ball K, Upton JW, Meier P. Ubiquitylation of MLKL at lysine 219 positively regulates necroptosis-induced tissue injury and pathogen clearance. Nat Commun 2021; 12:3364. [PMID: 34099649 PMCID: PMC8184782 DOI: 10.1038/s41467-021-23474-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 04/29/2021] [Indexed: 12/19/2022] Open
Abstract
Necroptosis is a lytic, inflammatory form of cell death that not only contributes to pathogen clearance but can also lead to disease pathogenesis. Necroptosis is triggered by RIPK3-mediated phosphorylation of MLKL, which is thought to initiate MLKL oligomerisation, membrane translocation and membrane rupture, although the precise mechanism is incompletely understood. Here, we show that K63-linked ubiquitin chains are attached to MLKL during necroptosis and that ubiquitylation of MLKL at K219 significantly contributes to the cytotoxic potential of phosphorylated MLKL. The K219R MLKL mutation protects animals from necroptosis-induced skin damage and renders cells resistant to pathogen-induced necroptosis. Mechanistically, we show that ubiquitylation of MLKL at K219 is required for higher-order assembly of MLKL at membranes, facilitating its rupture and necroptosis. We demonstrate that K219 ubiquitylation licenses MLKL activity to induce lytic cell death, suggesting that necroptotic clearance of pathogens as well as MLKL-dependent pathologies are influenced by the ubiquitin-signalling system.
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Affiliation(s)
- Laura Ramos Garcia
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Tencho Tenev
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Richard Newman
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rachel O Haich
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Gianmaria Liccardi
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Institute of Biochemistry I, Medical Faculty, Joseph-Stelzmann-Str. 44, University of Cologne, Cologne, Germany
| | - Sidonie Wicky John
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Alessandro Annibaldi
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Lu Yu
- Functional Proteomics Group, The Institute of Cancer Research, London, UK
| | - Mercedes Pardo
- Functional Proteomics Group, The Institute of Cancer Research, London, UK
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Cheree Fitzgibbon
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Winnie Fernando
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Hyojin Kim
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Lung-Yu Liang
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Isabelle S Lucet
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Andrew Kueh
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Patrycja Gazinska
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | | | | | - John Bertin
- Innate Immunity Research Unit, GlaxoSmithKline, Collegeville, PA, USA
- Immunology and Inflammation Research Therapeutic Area at Sanofi, Cambridge, MA, USA
| | - Allison M Beal
- Innate Immunity Research Unit, GlaxoSmithKline, Collegeville, PA, USA
| | - Brad Geddes
- Innate Immunity Research Unit, GlaxoSmithKline, Collegeville, PA, USA
| | - Jyoti S Choudhary
- Functional Proteomics Group, The Institute of Cancer Research, London, UK
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - K Aurelia Ball
- Department of Chemistry, Skidmore College, Saratoga Springs, NY, USA
| | - Jason W Upton
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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99973
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Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle. Sci Rep 2021; 11:11897. [PMID: 34099805 PMCID: PMC8184995 DOI: 10.1038/s41598-021-91373-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/26/2021] [Indexed: 11/12/2022] Open
Abstract
Water holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.
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99974
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Zhu CL, Yao RQ, Li LX, Li P, Xie J, Wang JF, Deng XM. Mechanism of Mitophagy and Its Role in Sepsis Induced Organ Dysfunction: A Review. Front Cell Dev Biol 2021; 9:664896. [PMID: 34164394 PMCID: PMC8215549 DOI: 10.1164/rccm.202111-2484oc+10.3389/fcell.2021.664896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/18/2021] [Indexed: 01/17/2024] Open
Abstract
Autophagy, an evolutionarily conserved process, plays an important role in maintaining cellular homeostasis under physiological and pathophysiological conditions. It is widely believed that mitochondria influence the development of disease by regulating cellular metabolism. When challenged by different stimuli, mitochondria may experience morphological disorders and functional abnormalities, leading to a selective form of autophagy-mitophagy, which can clear damaged mitochondria to promote mitochondrial quality control. Sepsis is a complex global problem with multiple organ dysfunction, often accompanied by manifold mitochondrial damage. Recent studies have shown that autophagy can regulate both innate and acquired immune processes to protect against organ dysfunction in sepsis. Sepsis-induced mitochondrial dysfunction may play a pathophysiological role in the initiation and progression of sepsis-induced organ failure. Mitophagy is reported to be beneficial for sepsis by eliminating disabled mitochondria and maintaining homeostasis to protect against organ failure. In this review, we summarize the recent findings and mechanisms of mitophagy and its involvement in septic organ dysfunction as a potential therapeutic target.
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Affiliation(s)
- Cheng-long Zhu
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Ren-qi Yao
- Trauma Research Center, Fourth Medical Center of the Chinese PLA General Hospital, Beijing, China
- Department of Burn Surgery, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Lu-xi Li
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Peng Li
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Jian Xie
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Jia-feng Wang
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Xiao-ming Deng
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
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99975
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Abstract
Septins, a conserved family of GTP-binding proteins, are widely recognized as an essential cytoskeletal component, playing important roles in a variety of biological processes, including division, polarity, and membrane remodeling, in different eukaryotes. Although the roles played by septins were identified in the model organism Saccharomyces cerevisiae, their importance in other fungi, especially pathogenic fungi, have recently been determined. In this review, we summarize the functions of septins in pathogenic fungi in the cell cycle, autophagy, endocytosis and invasion host-microbe interactions that were reported in the last two years in the field of septin cell biology. These new discoveries may be expanded to investigate the functions of septin proteins in fungal pathogenesis and may be of wide interest to the readers of Microbiology and Molecular Pathology.
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Affiliation(s)
- Lin Li
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xue-Ming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhen-Zhu Su
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Maurizio Del Poeta
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA.,Division of Infectious Diseases, Stony Brook University, Stony Brook, New York, USA.,Veterans Affairs Medical Center, Northport, New York, USA
| | - Xiao-Hong Liu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Fu-Cheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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99976
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Fernandes SG, Shah P, Khattar E. Recent Advances in Therapeutic Application of DNA Damage Response Inhibitors against Cancer. Anticancer Agents Med Chem 2021; 22:469-484. [PMID: 34102988 DOI: 10.2174/1871520621666210608105735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/02/2021] [Accepted: 02/22/2021] [Indexed: 11/22/2022]
Abstract
DNA integrity is continuously challenged by intrinsic cellular processes and environmental agents. To overcome this genomic damage, cells have developed multiple signaling pathways collectively named as DNA damage response (DDR) and composed of three components: (i) sensor proteins, which detect DNA damage, (ii) mediators that relay the signal downstream and recruit the repair machinery, and (iii) the repair proteins, which restore the damaged DNA. A flawed DDR and failure to repair the damage lead to the accumulation of genetic lesions and increased genomic instability, which is recognized as a hallmark of cancer. Cancer cells tend to harbor increased mutations in DDR genes and often have fewer DDR pathways than normal cells. This makes cancer cells more dependent on particular DDR pathways and thus become more susceptible to compounds inhibiting those pathways compared to normal cells, which have all the DDR pathways intact. Understanding the roles of different DDR proteins in the DNA damage response and repair pathways and identification of their structures have paved the way for the development of their inhibitors as targeted cancer therapy. In this review, we describe the major participants of various DDR pathways, their significance in carcinogenesis, and focus on the inhibitors developed against several key DDR proteins.
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Affiliation(s)
- Stina George Fernandes
- Sunandan Divatia School of Science, SVKM's NMIMS (Deemed to be) University, Mumbai, India
| | - Prachi Shah
- Sunandan Divatia School of Science, SVKM's NMIMS (Deemed to be) University, Mumbai, India
| | - Ekta Khattar
- Sunandan Divatia School of Science, SVKM's NMIMS (Deemed to be) University, Mumbai, India
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99977
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Quintarelli C, Camera A, Ciccone R, Alessi I, Del Bufalo F, Carai A, Del Baldo G, Mastronuzzi A, De Angelis B. Innovative and Promising Strategies to Enhance Effectiveness of Immunotherapy for CNS Tumors: Where Are We? Front Immunol 2021; 12:634031. [PMID: 34163465 PMCID: PMC8216238 DOI: 10.3389/fimmu.2021.634031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
Although there are several immunotherapy approaches for the treatment of Central Nervous System (CNS) tumors under evaluation, currently none of these approaches have received approval from the regulatory agencies. CNS tumors, especially glioblastomas, are tumors characterized by highly immunosuppressive tumor microenvironment, limiting the possibility of effectively eliciting an immune response. Moreover, the peculiar anatomic location of these tumors poses relevant challenges in terms of safety, since uncontrolled hyper inflammation could lead to cerebral edema and cranial hypertension. The most promising strategies of immunotherapy in neuro-oncology consist of the use of autologous T cells redirected against tumor cells through chimeric antigen receptor (CAR) constructs or genetically modified T-cell receptors. Trials based on native or genetically engineered oncolytic viruses and on vaccination with tumor-associated antigen peptides are also under evaluation. Despite some sporadic complete remissions achieved in clinical trials, the outcome of patients with CNS tumors treated with different immunotherapeutic approaches remains poor. Based on the lessons learned from these unsatisfactory experiences, novel immune-therapy approaches aimed at overcoming the profound immunosuppressive microenvironment of these diseases are bringing new hope to reach the cure for CNS tumors.
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Affiliation(s)
- Concetta Quintarelli
- Department Onco-Hematology, Cell and Gene Therapy, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy.,Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Antonio Camera
- Department Onco-Hematology, Cell and Gene Therapy, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - Roselia Ciccone
- Department Onco-Hematology, Cell and Gene Therapy, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - Iside Alessi
- Department Onco-Hematology, Cell and Gene Therapy, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesca Del Bufalo
- Department Onco-Hematology, Cell and Gene Therapy, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - Andrea Carai
- Neurosurgery Unit, Department of Neurological and Psychiatric Sciences, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Giada Del Baldo
- Department Onco-Hematology, Cell and Gene Therapy, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - Angela Mastronuzzi
- Department Onco-Hematology, Cell and Gene Therapy, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - Biagio De Angelis
- Department Onco-Hematology, Cell and Gene Therapy, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
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99978
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Bridges AE, Ramachandran S, Tamizhmani K, Parwal U, Lester A, Rajpurohit P, Morera DS, Hasanali SL, Arjunan P, Jedeja RN, Patel N, Martin PM, Korkaya H, Singh N, Manicassamy S, Prasad PD, Lokeshwar VB, Lokeshwar BL, Ganapathy V, Thangaraju M. RAD51AP1 Loss Attenuates Colorectal Cancer Stem Cell Renewal and Sensitizes to Chemotherapy. Mol Cancer Res 2021; 19:1486-1497. [PMID: 34099522 DOI: 10.1158/1541-7786.mcr-20-0780] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 03/25/2021] [Accepted: 06/02/2021] [Indexed: 11/16/2022]
Abstract
DNA damage, induced by either chemical carcinogens or environmental pollutants, plays an important role in the initiation of colorectal cancer. DNA repair processes, however, are involved in both protecting against cancer formation, and also contributing to cancer development, by ensuring genomic integrity and promoting the efficient DNA repair in tumor cells, respectively. Although DNA repair pathways have been well exploited in the treatment of breast and ovarian cancers, the role of DNA repair processes and their therapeutic efficacy in colorectal cancer is yet to be appreciably explored. To understand the role of DNA repair, especially homologous recombination (HR), in chemical carcinogen-induced colorectal cancer growth, we unraveled the role of RAD51AP1 (RAD51-associated protein 1), a protein involved in HR, in genotoxic carcinogen (azoxymethane, AOM)-induced colorectal cancer. Although AOM treatment alone significantly increased RAD51AP1 expression, the combination of AOM and dextran sulfate sodium (DSS) treatment dramatically increased by several folds. RAD51AP1 expression is found in mouse colonic crypt and proliferating cells. RAD51AP1 expression is significantly increased in majority of human colorectal cancer tissues, including BRAF/KRAS mutant colorectal cancer, and associated with reduced treatment response and poor prognosis. Rad51ap1-deficient mice were protected against AOM/DSS-induced colorectal cancer. These observations were recapitulated in a genetically engineered mouse model of colorectal cancer (ApcMin /+ ). Furthermore, chemotherapy-resistant colorectal cancer is associated with increased RAD51AP1 expression. This phenomenon is associated with reduced cell proliferation and colorectal cancer stem cell (CRCSC) self-renewal. Overall, our studies provide evidence that RAD51AP1 could be a novel diagnostic marker for colorectal cancer and a potential therapeutic target for colorectal cancer prevention and treatment. IMPLICATIONS: This study provides first in vivo evidence that RAD51AP1 plays a critical role in colorectal cancer growth and drug resistance by regulating CRCSC self-renewal.
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Affiliation(s)
- Allison E Bridges
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Sabarish Ramachandran
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia.,Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Kavin Tamizhmani
- Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Utkarsh Parwal
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Adrienne Lester
- Department of Undergraduate Health Professions, College of Allied Health Sciences, Augusta University, Augusta, Georgia
| | - Pragya Rajpurohit
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Daley S Morera
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Sarrah L Hasanali
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Pachiappan Arjunan
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia.,Department of Periodontics, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Ravirajsinh N Jedeja
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Nikhil Patel
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Pamela M Martin
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia.,Department of Opthalmology, Medical College of Georgia, Augusta University, Augusta, Georgia.,James and Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Hasan Korkaya
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia.,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Nagendra Singh
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia.,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Santhakumar Manicassamy
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia.,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Puttur D Prasad
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia.,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Vinata B Lokeshwar
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia.,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Bal L Lokeshwar
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia.,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Vadivel Ganapathy
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia.,Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Muthusamy Thangaraju
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia. .,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia
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99979
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Robert A, Schöll M, Vogels T. Tau Seeding Mouse Models with Patient Brain-Derived Aggregates. Int J Mol Sci 2021; 22:6132. [PMID: 34200180 PMCID: PMC8201271 DOI: 10.3390/ijms22116132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/23/2022] Open
Abstract
Tauopathies are a heterogeneous class of neurodegenerative diseases characterized by intracellular inclusions of aggregated tau proteins. Tau aggregates in different tauopathies have distinct structural features and can be found in different cell types. Transgenic animal models overexpressing human tau have been used for over two decades in the research of tau pathology. However, these models poorly recapitulate the heterogeneity of tauopathies found in human brains. Recent findings demonstrate that injection of purified tau aggregates from the brains of human tauopathy patients recapitulates both the structural features and cell-type specificity of the tau pathology of the donor tauopathy. These models may therefore have unique translational value in the study of functional consequences of tau pathology, tau-based diagnostics, and tau targeting therapeutics. This review provides an update of the literature relating to seeding-based tauopathy and their potential applications.
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Affiliation(s)
- Aiko Robert
- Department of Neurodegenerative Disease, UCL Queen Square, Institute of Neurology, University College London, London WC1N 3BG, UK; (A.R.); (M.S.)
| | - Michael Schöll
- Department of Neurodegenerative Disease, UCL Queen Square, Institute of Neurology, University College London, London WC1N 3BG, UK; (A.R.); (M.S.)
- Wallenberg Centre for Molecular and Translational Medicine and the Department of Psychiatry and Neurochemistry, University of Gothenburg, 413 45 Gothenburg, Sweden
- Department of Psychiatry and Neurochemistry, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Thomas Vogels
- Department of Neurodegenerative Disease, UCL Queen Square, Institute of Neurology, University College London, London WC1N 3BG, UK; (A.R.); (M.S.)
- Department of Psychiatry and Neurochemistry, University of Gothenburg, 413 45 Gothenburg, Sweden
- Sylics (Synaptologics B.V.), 3721 MA Bilthoven, The Netherlands
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99980
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Ng HL, Quail E, Cruickshank MN, Ulgiati D. To Be, or Notch to Be: Mediating Cell Fate from Embryogenesis to Lymphopoiesis. Biomolecules 2021; 11:biom11060849. [PMID: 34200313 PMCID: PMC8227657 DOI: 10.3390/biom11060849] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/29/2021] [Accepted: 06/04/2021] [Indexed: 12/11/2022] Open
Abstract
Notch signaling forms an evolutionarily conserved juxtacrine pathway crucial for cellular development. Initially identified in Drosophila wing morphogenesis, Notch signaling has since been demonstrated to play pivotal roles in governing mammalian cellular development in a large variety of cell types. Indeed, abolishing Notch constituents in mouse models result in embryonic lethality, demonstrating that Notch signaling is critical for development and differentiation. In this review, we focus on the crucial role of Notch signaling in governing embryogenesis and differentiation of multiple progenitor cell types. Using hematopoiesis as a diverse cellular model, we highlight the role of Notch in regulating the cell fate of common lymphoid progenitors. Additionally, the influence of Notch through microenvironment interplay with lymphoid cells and how dysregulation influences disease processes is explored. Furthermore, bi-directional and lateral Notch signaling between ligand expressing source cells and target cells are investigated, indicating potentially novel therapeutic options for treatment of Notch-mediated diseases. Finally, we discuss the role of cis-inhibition in regulating Notch signaling in mammalian development.
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Affiliation(s)
- Han Leng Ng
- Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK;
- School of Biomedical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (E.Q.); (M.N.C.)
| | - Elizabeth Quail
- School of Biomedical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (E.Q.); (M.N.C.)
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Mark N. Cruickshank
- School of Biomedical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (E.Q.); (M.N.C.)
| | - Daniela Ulgiati
- School of Biomedical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (E.Q.); (M.N.C.)
- Correspondence: ; Tel.: +61-8-6457-1076
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99981
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Majtnerova P, Capek J, Petira F, Handl J, Rousar T. Quantitative spectrofluorometric assay detecting nuclear condensation and fragmentation in intact cells. Sci Rep 2021; 11:11921. [PMID: 34099803 PMCID: PMC8184882 DOI: 10.1038/s41598-021-91380-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/21/2021] [Indexed: 12/17/2022] Open
Abstract
At present, nuclear condensation and fragmentation have been estimated also using Hoechst probes in fluorescence microscopy and flow cytometry. However, none of the methods used the Hoechst probes for quantitative spectrofluorometric assessment. Therefore, the aim of the present study was to develop a spectrofluorometric assay for detection of nuclear condensation and fragmentation in the intact cells. We used human hepatoma HepG2 and renal HK-2 cells cultured in 96-well plates treated with potent apoptotic inducers (i.e. cisplatin, staurosporine, camptothecin) for 6-48 h. Afterwards, the cells were incubated with Hoechst 33258 (2 µg/mL) and the increase of fluorescence after binding of the dye to DNA was measured. The developed spectrofluorometric assay was capable to detect nuclear changes caused by all tested apoptotic inducers. Then, we compared the outcomes of the spectrofluorometric assay with other methods detecting cell impairment and apoptosis (i.e. WST-1 and glutathione tests, TUNEL, DNA ladder, caspase activity, PARP-1 and JNKs expressions). We found that our developed spectrofluorometric assay provided results of the same sensitivity as the TUNEL assay but with the advantages of being fast processing, low-cost and a high throughput. Because nuclear condensation and fragmentation can be typical markers of cell death, especially in apoptosis, we suppose that the spectrofluorometric assay could become a routinely used method for characterizing cell death processes.
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Affiliation(s)
- Pavlina Majtnerova
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10, Pardubice, Czech Republic
| | - Jan Capek
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10, Pardubice, Czech Republic
| | - Filip Petira
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10, Pardubice, Czech Republic
| | - Jiri Handl
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10, Pardubice, Czech Republic
| | - Tomas Rousar
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10, Pardubice, Czech Republic.
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99982
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Abstract
When attempting to propagate infections, bacterial pathogens encounter phagocytes that encase them in vacuoles called phagosomes. Within phagosomes, bacteria are bombarded with a plethora of stresses that often lead to their demise. However, pathogens have evolved numerous strategies to counter those host defenses and facilitate survival. Given the importance of phagosome-bacteria interactions to infection outcomes, they represent a collection of targets that are of interest for next-generation antibacterials. To facilitate such therapies, different approaches can be employed to increase understanding of phagosome-bacteria interactions, and these can be classified broadly as top down (starting from intact systems and breaking down the importance of different parts) or bottom up (developing a knowledge base on simplified systems and progressively increasing complexity). Here we review knowledge of phagosomal compositions and bacterial survival tactics useful for bottom-up approaches, which are particularly relevant for the application of reaction engineering to quantify and predict the time evolution of biochemical species in these death-dealing vacuoles. Further, we highlight how understanding in this area can be built up through the combination of immunology, microbiology, and engineering.
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Affiliation(s)
- Darshan M Sivaloganathan
- Program in Quantitative and Computational Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA;
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99983
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Carissimi C, Laudadio I, Lorefice E, Azzalin G, De Paolis V, Fulci V. Bisulphite miRNA-seq reveals widespread CpG and non-CpG 5-(hydroxy)methyl-Cytosine in human microRNAs. RNA Biol 2021; 18:2226-2235. [PMID: 33980133 DOI: 10.1080/15476286.2021.1927423] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In the last decade, the field of epitranscriptomics highlighted a wide array of post-transcriptional modifications in human RNAs, including microRNAs (miRNAs). Recent reports showed that human miRNAs undergo cytosine methylation. We describe the first high-throughput NGS-based method (BS-miRNA-seq) and an analysis pipeline (MAmBA) to attain high-resolution mapping of (hydroxy)-methyl-5-cytosine ((h)m5C) modifications in human miRNAs. Our method uncovers that miRNAs undergo widespread cytosine modification in various sequence contexts.Furthermore, validation of our data with specific antibodies reveals both m5C and hm5C residues in human mature miRNAs. BS-miRNA-seq and MAmBA may contribute to the precise mapping of (h)m5C on miRNAs in various cell types and tissues, a key achievement towards the understanding of the functional implications of this modification in miRNAs. MAmBA is available for download at https://github.com/flcvlr/MAmBA.
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Affiliation(s)
- Claudia Carissimi
- Dipartimento Di Medicina Molecolare, Sapienza Università Di Roma, Rome, Italy
| | - Ilaria Laudadio
- Dipartimento Di Medicina Molecolare, Sapienza Università Di Roma, Rome, Italy
| | - Elisa Lorefice
- Dipartimento Di Medicina Molecolare, Sapienza Università Di Roma, Rome, Italy
| | - Gianluca Azzalin
- Dipartimento di Biotecnologie Cellulari Ed Ematologia, Sapienza Università di Roma, Rome, Italy
| | - Veronica De Paolis
- Dipartimento Di Medicina Molecolare, Sapienza Università Di Roma, Rome, Italy
| | - Valerio Fulci
- Dipartimento Di Medicina Molecolare, Sapienza Università Di Roma, Rome, Italy
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99984
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Pojer JM, Saiful Hilmi AJ, Kondo S, Harvey KF. Crumbs and the apical spectrin cytoskeleton regulate R8 cell fate in the Drosophila eye. PLoS Genet 2021; 17:e1009146. [PMID: 34097697 PMCID: PMC8211197 DOI: 10.1371/journal.pgen.1009146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 06/17/2021] [Accepted: 05/11/2021] [Indexed: 12/31/2022] Open
Abstract
The Hippo pathway is an important regulator of organ growth and cell fate. In the R8 photoreceptor cells of the Drosophila melanogaster eye, the Hippo pathway controls the fate choice between one of two subtypes that express either the blue light-sensitive Rhodopsin 5 (Hippo inactive R8 subtype) or the green light-sensitive Rhodopsin 6 (Hippo active R8 subtype). The degree to which the mechanism of Hippo signal transduction and the proteins that mediate it are conserved in organ growth and R8 cell fate choice is currently unclear. Here, we identify Crumbs and the apical spectrin cytoskeleton as regulators of R8 cell fate. By contrast, other proteins that influence Hippo-dependent organ growth, such as the basolateral spectrin cytoskeleton and Ajuba, are dispensable for the R8 cell fate choice. Surprisingly, Crumbs promotes the Rhodopsin 5 cell fate, which is driven by Yorkie, rather than the Rhodopsin 6 cell fate, which is driven by Warts and the Hippo pathway, which contrasts with its impact on Hippo activity in organ growth. Furthermore, neither the apical spectrin cytoskeleton nor Crumbs appear to regulate the Hippo pathway through mechanisms that have been observed in growing organs. Together, these results show that only a subset of Hippo pathway proteins regulate the R8 binary cell fate decision and that aspects of Hippo signalling differ between growing organs and post-mitotic R8 cells.
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Affiliation(s)
- Jonathan M. Pojer
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Abdul Jabbar Saiful Hilmi
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Shu Kondo
- Laboratory of Invertebrate Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kieran F. Harvey
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- * E-mail:
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99985
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Spiliotis ET, McMurray MA. Masters of asymmetry - lessons and perspectives from 50 years of septins. Mol Biol Cell 2021; 31:2289-2297. [PMID: 32991244 PMCID: PMC7851956 DOI: 10.1091/mbc.e19-11-0648] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Septins are a unique family of GTPases, which were discovered 50 years ago as essential genes for the asymmetric cell shape and division of budding yeast. Septins assemble into filamentous nonpolar polymers, which associate with distinct membrane macrodomains and subpopulations of actin filaments and microtubules. While structurally a cytoskeleton-like element, septins function predominantly as spatial regulators of protein localization and interactions. Septin scaffolds and barriers have provided a long-standing paradigm for the generation and maintenance of asymmetry in cell membranes. Septins also promote asymmetry by regulating the spatial organization of the actin and microtubule cytoskeleton, and biasing the directionality of membrane traffic. In this 50th anniversary perspective, we highlight how septins have conserved and adapted their roles as effectors of membrane and cytoplasmic asymmetry across fungi and animals. We conclude by outlining principles of septin function as a module of symmetry breaking, which alongside the monomeric small GTPases provides a core mechanism for the biogenesis of molecular asymmetry and cell polarity.
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Affiliation(s)
| | - Michael A McMurray
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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99986
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Unexpected localization of AQP3 and AQP4 induced by migration of primary cultured IMCD cells. Sci Rep 2021; 11:11930. [PMID: 34099798 PMCID: PMC8185088 DOI: 10.1038/s41598-021-91369-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/13/2021] [Indexed: 12/18/2022] Open
Abstract
Aquaporin-2-4 (AQP) are expressed in the principal cells of the renal collecting duct (CD). Beside their role in water transport across membranes, several studies showed that AQPs can influence the migration of cells. It is unknown whether this also applies for renal CD cells. Another fact is that the expression of these AQPs is highly modulated by the external osmolality. Here we analyzed the localization of AQP2-4 in primary cultured renal inner medullary CD (IMCD) cells and how osmolality influences the migration behavior of these cells. The primary IMCD cells showed a collective migration behavior and there were no differences in the migration speed between cells cultivated either at 300 or 600 mosmol/kg. Acute increase from 300 to 600 mosmol/kg led to a marked reduction and vice versa an acute decrease from 600 to 300 mosmol/kg to a marked increase in migration speed. Interestingly, none of the analyzed AQPs were localized at the leading edge. While AQP3 disappeared within the first 2-3 rows of cells, AQP4 was enriched at the rear end. Further analysis indicated that migration induced lysosomal degradation of AQP3. This could be prevented by activation of the protein kinase A, inducing localization of AQP3 and AQP2 at the leading edge and increasing the migration speed.
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99987
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The Hippo Pathway: A Master Regulatory Network Important in Cancer. Cells 2021; 10:cells10061416. [PMID: 34200285 PMCID: PMC8226666 DOI: 10.3390/cells10061416] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 12/11/2022] Open
Abstract
The Hippo pathway is pervasively activated and has been well recognized to play critical roles in human cancer. The deregulation of Hippo signaling involved in cancer development, progression, and resistance to cancer treatment have been confirmed in several human cancers. Its biological significance and deregulation in cancer have drawn increasing interest in the past few years. A fundamental understanding of the complexity of the Hippo pathway in cancer is crucial for improving future clinical interventions and therapy for cancers. In this review, we try to clarify the complex regulation and function of the Hippo signaling network in cancer development, including its role in signal transduction, metabolic regulation, and tumor development, as well as tumor therapies targeting the Hippo pathway.
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99988
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Sadhukhan S, Nandi SK. Theory and simulation for equilibrium glassy dynamics in cellular Potts model of confluent biological tissue. Phys Rev E 2021; 103:062403. [PMID: 34271700 DOI: 10.1103/physreve.103.062403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 05/14/2021] [Indexed: 01/23/2023]
Abstract
Glassy dynamics in a confluent monolayer is indispensable in morphogenesis, wound healing, bronchial asthma, and many others; a detailed theoretical framework for such a system is, therefore, important. Vertex-model (VM) simulations have provided crucial insights into the dynamics of such systems, but their nonequilibrium nature makes theoretical development difficult. The cellular Potts model (CPM) of confluent monolayers provides an alternative model for such systems with a well-defined equilibrium limit. We combine numerical simulations of the CPM and an analytical study based on one of the most successful theories of equilibrium glass, the random first-order transition theory, and develop a comprehensive theoretical framework for a confluent glassy system. We find that the glassy dynamics within the CPM is qualitatively similar to that in the VM. Our study elucidates the crucial role of geometric constraints in bringing about two distinct regimes in the dynamics, as the target perimeter P_{0} is varied. The unusual sub-Arrhenius relaxation results from the distinctive interaction potential arising from the perimeter constraint in such systems. The fragility of the system decreases with increasing P_{0} in the low-P_{0} regime, whereas the dynamics is independent of P_{0} in the other regime. The rigidity transition, found in the VM, is absent within the CPM; this difference seems to come from the nonequilibrium nature of the former. We show that the CPM captures the basic phenomenology of glassy dynamics in a confluent biological system via comparison of our numerical results with existing experiments on different systems.
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Affiliation(s)
- Souvik Sadhukhan
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Saroj Kumar Nandi
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500046, India
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99989
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Zhu CL, Yao RQ, Li LX, Li P, Xie J, Wang JF, Deng XM. Mechanism of Mitophagy and Its Role in Sepsis Induced Organ Dysfunction: A Review. Front Cell Dev Biol 2021; 9:664896. [PMID: 34164394 PMCID: PMC8215549 DOI: 10.1164/rccm.202111-2484oc 10.3389/fcell.2021.664896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Autophagy, an evolutionarily conserved process, plays an important role in maintaining cellular homeostasis under physiological and pathophysiological conditions. It is widely believed that mitochondria influence the development of disease by regulating cellular metabolism. When challenged by different stimuli, mitochondria may experience morphological disorders and functional abnormalities, leading to a selective form of autophagy-mitophagy, which can clear damaged mitochondria to promote mitochondrial quality control. Sepsis is a complex global problem with multiple organ dysfunction, often accompanied by manifold mitochondrial damage. Recent studies have shown that autophagy can regulate both innate and acquired immune processes to protect against organ dysfunction in sepsis. Sepsis-induced mitochondrial dysfunction may play a pathophysiological role in the initiation and progression of sepsis-induced organ failure. Mitophagy is reported to be beneficial for sepsis by eliminating disabled mitochondria and maintaining homeostasis to protect against organ failure. In this review, we summarize the recent findings and mechanisms of mitophagy and its involvement in septic organ dysfunction as a potential therapeutic target.
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Affiliation(s)
- Cheng-long Zhu
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Ren-qi Yao
- Trauma Research Center, Fourth Medical Center of the Chinese PLA General Hospital, Beijing, China,Department of Burn Surgery, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Lu-xi Li
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Peng Li
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Jian Xie
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Jia-feng Wang
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China,*Correspondence: Jia-feng Wang,
| | - Xiao-ming Deng
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China,Xiao-ming Deng,
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99990
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Long noncoding RNA DGCR5 involves in tumorigenesis of esophageal squamous cell carcinoma via SRSF1-mediated alternative splicing of Mcl-1. Cell Death Dis 2021; 12:587. [PMID: 34099633 PMCID: PMC8184765 DOI: 10.1038/s41419-021-03858-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) emerge as essential roles in the regulation of alternative splicing (AS) in various malignancies. Serine- and arginine-rich splicing factor 1 (SRSF1)-mediated AS events are the most important molecular hallmarks in cancer. Nevertheless, the biological mechanism underlying tumorigenesis of lncRNAs correlated with SRSF1 in esophageal squamous cell carcinoma (ESCC) remains elusive. In this study, we found that lncRNA DiGeorge syndrome critical region gene 5 (DGCR5) was upregulated in ESCC clinical samples, which associated with poor prognosis. Through RNA interference and overexpression approaches, we confirmed that DGCR5 contributed to promote ESCC cell proliferation, migration, and invasion while inhibited apoptosis in vitro. Mechanistically, DGCR5 could directly bind with SRSF1 to increase its stability and thus stimulate alternative splicing events. Furthermore, we clarified that SRSF1 regulated the aberrant splicing of myeloid cell leukemia-1 (Mcl-1) and initiated a significant Mcl-1L (antiapoptotic) isoform switch, which contributed to the expression of the full length of Mcl-1. Moreover, the cell-derived xenograft (CDX) model was validated that DGCR5 could facilitate the tumorigenesis of ESCC in vivo. Collectively, our findings identified that the key biological role of lncRNA DGCR5 in alternative splicing regulation and emphasized DGCR5 as a potential biomarker and therapeutic target for ESCC.
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99991
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Kazimierczyk M, Wrzesinski J. Long Non-Coding RNA Epigenetics. Int J Mol Sci 2021; 22:6166. [PMID: 34200507 PMCID: PMC8201194 DOI: 10.3390/ijms22116166] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs exceeding a length of 200 nucleotides play an important role in ensuring cell functions and proper organism development by interacting with cellular compounds such as miRNA, mRNA, DNA and proteins. However, there is an additional level of lncRNA regulation, called lncRNA epigenetics, in gene expression control. In this review, we describe the most common modified nucleosides found in lncRNA, 6-methyladenosine, 5-methylcytidine, pseudouridine and inosine. The biosynthetic pathways of these nucleosides modified by the writer, eraser and reader enzymes are important to understanding these processes. The characteristics of the individual methylases, pseudouridine synthases and adenine-inosine editing enzymes and the methods of lncRNA epigenetics for the detection of modified nucleosides, as well as the advantages and disadvantages of these methods, are discussed in detail. The final sections are devoted to the role of modifications in the most abundant lncRNAs and their functions in pathogenic processes.
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Affiliation(s)
| | - Jan Wrzesinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland;
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99992
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Cardona Gloria Y, Bernhart SH, Fillinger S, Wolz OO, Dickhöfer S, Admard J, Ossowski S, Nahnsen S, Siebert R, Weber ANR. Absence of Non-Canonical, Inhibitory MYD88 Splice Variants in B Cell Lymphomas Correlates With Sustained NF-κB Signaling. Front Immunol 2021; 12:616451. [PMID: 34163463 PMCID: PMC8215704 DOI: 10.3389/fimmu.2021.616451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
Gain-of-function mutations of the TLR adaptor and oncoprotein MyD88 drive B cell lymphomagenesis via sustained NF-κB activation. In myeloid cells, both short and sustained TLR activation and NF-κB activation lead to the induction of inhibitory MYD88 splice variants that restrain prolonged NF-κB activation. We therefore sought to investigate whether such a negative feedback loop exists in B cells. Analyzing MYD88 splice variants in normal B cells and different primary B cell malignancies, we observed that MYD88 splice variants in transformed B cells are dominated by the canonical, strongly NF-κB-activating isoform of MYD88 and contain at least three novel, so far uncharacterized signaling-competent splice isoforms. Sustained TLR stimulation in B cells unexpectedly reinforces splicing of NF-κB-promoting, canonical isoforms rather than the 'MyD88s', a negative regulatory isoform reported to be typically induced by TLRs in myeloid cells. This suggests that an essential negative feedback loop restricting TLR signaling in myeloid cells at the level of alternative splicing, is missing in B cells when they undergo proliferation, rendering B cells vulnerable to sustained NF-κB activation and eventual lymphomagenesis. Our results uncover MYD88 alternative splicing as an unappreciated promoter of B cell lymphomagenesis and provide a rationale why oncogenic MYD88 mutations are exclusively found in B cells.
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Affiliation(s)
- Yamel Cardona Gloria
- Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Stephan H. Bernhart
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany
- Transcriptome Bioinformatics, Leipzig Research Center for Civilization Diseases (LIFE), University of Leipzig, Leipzig, Germany
| | - Sven Fillinger
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Olaf-Oliver Wolz
- Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Sabine Dickhöfer
- Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Alexander N. R. Weber
- Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Deutsches Konsortium für Translationale Krebsforschung (DKTK; German Cancer Consortium), Partner Site Tübingen, Department of Immunology, University of Tübingen, Tübingen, Germany
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99993
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Sezaki M, Biswas S, Nakata S, Oshima M, Koide S, Ho NPY, Okamoto N, Miyamoto T, Iwama A, Takizawa H. CD271 +CD51 +PALLADIN - Human Mesenchymal Stromal Cells Possess Enhanced Ossicle-Forming Potential. Stem Cells Dev 2021; 30:725-735. [PMID: 33926240 DOI: 10.1089/scd.2021.0021] [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: 11/13/2022] Open
Abstract
Human mesenchymal stem/stromal cells (hMSCs), when engrafted into immunodeficient mice, can form ectopic bone organs with hematopoietic stem cell (HSC) supportive functions. However, the ability to do so, through a cartilage intermediate, appears limited to 30% of donor bone marrow samples. In this study, we characterize the heterogeneous nature of hMSCs and their ability to efficiently form humanized ossicles observed in "good donors" to correlate with the frequency and functionality of chondrocyte progenitors. Flow cytometry of putative hMSC markers was enriched in the CD271+CD51+ stromal cell subset, which also possessed enhanced hMSC activity as assessed by single-cell colony-forming unit fibroblast (CFU-F) and undifferentiated mesensphere formation. Transcriptome analysis of CD271+ cells presented upregulation of chondrogenesis-/osteogenesis-related genes and HSC/niche maintenance factors such as C-X-C motif chemokine 12 (CXCL12) and ANGIOPOIETIN 1. Among the candidate genes selected to enrich for subsets with greater chondrogenic ability, cells negative for the actin cross-linker PALLADIN displayed the greatest CFU-F potential. Our study contributes to a better characterization of ossicle-forming hMSCs and their efficient isolation for the optimized engineering of human bone organs.
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Affiliation(s)
- Maiko Sezaki
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Subinoy Biswas
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Sayuri Nakata
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Motohiko Oshima
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shuhei Koide
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Nicole Pui Yu Ho
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Nobukazu Okamoto
- Department of Orthopaedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takeshi Miyamoto
- Department of Orthopaedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Atsushi Iwama
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hitoshi Takizawa
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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99994
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Zhu CL, Yao RQ, Li LX, Li P, Xie J, Wang JF, Deng XM. Mechanism of Mitophagy and Its Role in Sepsis Induced Organ Dysfunction: A Review. Front Cell Dev Biol 2021; 9:664896. [PMID: 34164394 PMCID: PMC8215549 DOI: 10.3389/fcell.2021.664896] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Autophagy, an evolutionarily conserved process, plays an important role in maintaining cellular homeostasis under physiological and pathophysiological conditions. It is widely believed that mitochondria influence the development of disease by regulating cellular metabolism. When challenged by different stimuli, mitochondria may experience morphological disorders and functional abnormalities, leading to a selective form of autophagy-mitophagy, which can clear damaged mitochondria to promote mitochondrial quality control. Sepsis is a complex global problem with multiple organ dysfunction, often accompanied by manifold mitochondrial damage. Recent studies have shown that autophagy can regulate both innate and acquired immune processes to protect against organ dysfunction in sepsis. Sepsis-induced mitochondrial dysfunction may play a pathophysiological role in the initiation and progression of sepsis-induced organ failure. Mitophagy is reported to be beneficial for sepsis by eliminating disabled mitochondria and maintaining homeostasis to protect against organ failure. In this review, we summarize the recent findings and mechanisms of mitophagy and its involvement in septic organ dysfunction as a potential therapeutic target.
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Affiliation(s)
- Cheng-Long Zhu
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Ren-Qi Yao
- Trauma Research Center, Fourth Medical Center of the Chinese PLA General Hospital, Beijing, China.,Department of Burn Surgery, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Lu-Xi Li
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Peng Li
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Jian Xie
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Jia-Feng Wang
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
| | - Xiao-Ming Deng
- Department of Anesthesiology and Intensive Care, Changhai Hospital, The Naval Medical University, Shanghai, China
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99995
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Yin T, Zhao D, Yao S. Identification of a Genome Instability-Associated LncRNA Signature for Prognosis Prediction in Colon Cancer. Front Genet 2021; 12:679150. [PMID: 34163531 PMCID: PMC8215581 DOI: 10.3389/fgene.2021.679150] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/14/2021] [Indexed: 02/05/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) were reported to have the potential in maintaining genome instability, but the identification of lncRNAs related to genome instability and their prognostic value have not been largely explored in colon cancer. In this study, we obtained 155 genome instability-associated lncRNAs based on somatic mutation profiles in colon cancer from The Cancer Genome Atlas (TCGA) database. Functional enrichment analysis revealed the possible roles of genes co-expressed with those lncRNAs involved in some cancer, genome instability and immune related biological processes. Combined with overall survival data, a seven-lncRNA signature was established for prognosis prediction. According to the risk score calculated by this signature, high-risk patients characterized by high somatic mutation count, high microsatellite instability, significantly poorer clinical outcomes and specific tumor immune infiltration status compared with low-risk patients. The lncRNA signature was validated to be an independent prognostic indicator with good predictive performance in TCGA cohort. Furthermore, the prognostic value of the ZNF503-AS1 in lncRNA signature was confirmed in another independent dataset from Gene Expression Omnibus database. In summary, the genome instability-associated lncRNA signature in this study could be a promising tool for effectively predicting survival outcomes in colon cancer.
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Affiliation(s)
- Tengfei Yin
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Dongyan Zhao
- Graduate School, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Shukun Yao
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China.,Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
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99996
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Sahin M, Wong W, Zhan Y, Van Deynze K, Koche R, Leslie CS. HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. Nat Commun 2021; 12:3366. [PMID: 34099725 PMCID: PMC8184932 DOI: 10.1038/s41467-021-23749-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 05/14/2021] [Indexed: 11/18/2022] Open
Abstract
Recent genome-wide chromosome conformation capture assays such as Hi-C and HiChIP have vastly expanded the resolution and throughput with which we can study 3D genomic architecture and function. Here, we present HiC-DC+, a software tool for Hi-C/HiChIP interaction calling and differential analysis using an efficient implementation of the HiC-DC statistical framework. HiC-DC+ integrates with popular preprocessing and visualization tools and includes topologically associating domain (TAD) and A/B compartment callers. We found that HiC-DC+ can more accurately identify enhancer-promoter interactions in H3K27ac HiChIP, as validated by CRISPRi-FlowFISH experiments, compared to existing methods. Differential HiC-DC+ analyses of published HiChIP and Hi-C data sets in settings of cellular differentiation and cohesin perturbation systematically and quantitatively recovers biological findings, including enhancer hubs, TAD aggregation, and the relationship between promoter-enhancer loop dynamics and gene expression changes. HiC-DC+ therefore provides a principled statistical analysis tool to empower genome-wide studies of 3D chromatin architecture and function. The genome-wide investigation of chromatin organization enables insights into global gene expression control. Here, the authors present a computationally efficient method for the analysis of chromatin organization data and use it to recover principles of 3D organization across conditions.
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Affiliation(s)
- Merve Sahin
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - Wilfred Wong
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - Yingqian Zhan
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kinsey Van Deynze
- Bioinformatics Program, University of California at San Diego, San Diego, CA, USA
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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99997
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Indo Y, Kitahara S, Tomokiyo M, Araki S, Islam MA, Zhou B, Albarracin L, Miyazaki A, Ikeda-Ohtsubo W, Nochi T, Takenouchi T, Uenishi H, Aso H, Takahashi H, Kurata S, Villena J, Kitazawa H. Ligilactobacillus salivarius Strains Isolated From the Porcine Gut Modulate Innate Immune Responses in Epithelial Cells and Improve Protection Against Intestinal Viral-Bacterial Superinfection. Front Immunol 2021; 12:652923. [PMID: 34163470 PMCID: PMC8215365 DOI: 10.3389/fimmu.2021.652923] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/20/2021] [Indexed: 12/29/2022] Open
Abstract
Previously, we constructed a library of Ligilactobacillus salivarius strains from the intestine of wakame-fed pigs and reported a strain-dependent capacity to modulate IFN-β expression in porcine intestinal epithelial (PIE) cells. In this work, we further characterized the immunomodulatory activities of L. salivarius strains from wakame-fed pigs by evaluating their ability to modulate TLR3- and TLR4-mediated innate immune responses in PIE cells. Two strains with a remarkable immunomodulatory potential were selected: L. salivarius FFIG35 and FFIG58. Both strains improved IFN-β, IFN-λ and antiviral factors expression in PIE cells after TLR3 activation, which correlated with an enhanced resistance to rotavirus infection. Moreover, a model of enterotoxigenic E. coli (ETEC)/rotavirus superinfection in PIE cells was developed. Cells were more susceptible to rotavirus infection when the challenge occurred in conjunction with ETEC compared to the virus alone. However, L. salivarius FFIG35 and FFIG58 maintained their ability to enhance IFN-β, IFN-λ and antiviral factors expression in PIE cells, and to reduce rotavirus replication in the context of superinfection. We also demonstrated that FFIG35 and FFIG58 strains regulated the immune response of PIE cells to rotavirus challenge or ETEC/rotavirus superinfection through the modulation of negative regulators of the TLR signaling pathway. In vivo studies performed in mice models confirmed the ability of L. salivarius FFIG58 to beneficially modulate the innate immune response and protect against ETEC infection. The results of this work contribute to the understanding of beneficial lactobacilli interactions with epithelial cells and allow us to hypothesize that the FFIG35 or FFIG58 strains could be used for the development of highly efficient functional feed to improve immune health status and reduce the severity of intestinal infections and superinfections in weaned piglets.
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Affiliation(s)
- Yuhki Indo
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shugo Kitahara
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Mikado Tomokiyo
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shota Araki
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Md. Aminul Islam
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Binghui Zhou
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Leonardo Albarracin
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Scientific Computing Laboratory, Computer Science Department, Faculty of Exact Sciences and Technology, National University of Tucuman, Tucuman, Argentina
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli, (CERELA-CONICET), Tucuman, Argentina
| | - Ayako Miyazaki
- Viral Diseases and Epidemiology Research Division, National Institute of Animal Health, NARO, Tsukuba, Japan
| | - Wakako Ikeda-Ohtsubo
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Tomonori Nochi
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Laboratory of Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Takato Takenouchi
- Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Hirohide Uenishi
- Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Hisashi Aso
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Laboratory of Animal Health Science, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Hideki Takahashi
- Laboratory of Plant Pathology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Plant Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shoichiro Kurata
- Laboratory of Molecular Genetics, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Julio Villena
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli, (CERELA-CONICET), Tucuman, Argentina
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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99998
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Abstract
Export from the ER is COPII-dependent. However, there is disagreement on the nature of the cargo-containing carriers that exit the ER. Two new studies from Shomron et al. (2021. J. Cell Biol.https://doi.org/10.1083/jcb.201907224) and Weigel et al. (2021. Cell. https://doi.org/10.1016/j.cell.2021.03.035) present a new model, where COPII helps to select secretory cargo but does not coat the carriers leaving the ER.
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Affiliation(s)
- Santosh Phuyal
- Institute of Pathophysiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Hesso Farhan
- Institute of Pathophysiology, Medical University of Innsbruck, Innsbruck, Austria
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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99999
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Inomata M, Horie T, Into T. Effect of the Antimicrobial Peptide LL-37 on Gene Expression of Chemokines and 29 Toll-like Receptor-Associated Proteins in Human Gingival Fibroblasts Under Stimulation with Porphyromonas gingivalis Lipopolysaccharide. Probiotics Antimicrob Proteins 2021; 12:64-72. [PMID: 31686299 DOI: 10.1007/s12602-019-09600-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The antimicrobial peptide LL-37 neutralizes the biological activity of lipopolysaccharide (LPS), while it upregulates the expression of several immune-related genes. We investigated the effect of LL-37 on gene regulation of human gingival fibroblasts (HGFs), stimulated with or without Porphyromonas gingivalis-derived LPS, a ligand for Toll-like receptor (TLR). LL-37 was non-toxic to HGFs up to a concentration of 10 μg/ml. P. gingivalis LPS upregulated the expression of IL8, CXCL10, and CCL2, whereas LL-37 reduced this upregulation. In absence of LPS, LL-37 itself upregulated the expression of IL8 and CCL2. LL-37 increased the expression of P2X7, which was constitutively expressed in HGFs. The P2X7 antagonist A-438079 suppressed the cytotoxicity and upregulatory effect of LL-37 on chemokine response, but not its downregulatory effect on P. gingivalis LPS-induced chemokine response. Whether LL-37 alters the expression of 29 genes that encode TLR-associated proteins, including TLRs, co-receptors, signaling molecules, and negative regulators, in HGFs, under stimulation with LPS, was examined. Among TLRs, P. gingivalis LPS upregulated the level of TLR4, whereas LL-37 reduced it. In co-receptors, LL-37 downregulated the level of CD14. Among signaling molecules, LL-37 augmented the LPS-upregulated expression of IRAK1. Similar effects were observed in the specific negative regulators TNFAIP3, RNF216, TOLLIP, and SIGIRR. Our results suggest that LL-37 exerts cytotoxicity and upregulation of chemokine response via the P2X7 receptor, while it induces downregulation of P. gingivalis LPS-induced chemokine response through alteration in the expression of 7 specific TLR-associated genes: downregulation of TLR4 and CD14 and upregulation of IRAK1, TNFAIP3, RNF216, TOLLIP, and SIGIRR.
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Affiliation(s)
- Megumi Inomata
- Department of Oral Microbiology, Division of Oral Infections and Health Sciences, Asahi University School of Dentistry, Mizuho, Gifu, 501-0296, Japan.
| | - Toshi Horie
- Department of Oral Microbiology, Division of Oral Infections and Health Sciences, Asahi University School of Dentistry, Mizuho, Gifu, 501-0296, Japan
| | - Takeshi Into
- Department of Oral Microbiology, Division of Oral Infections and Health Sciences, Asahi University School of Dentistry, Mizuho, Gifu, 501-0296, Japan.
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100000
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Liu H, Li R, Liao HK, Min Z, Wang C, Yu Y, Shi L, Dan J, Hayek A, Martinez Martinez L, Nuñez Delicado E, Izpisua Belmonte JC. Chemical combinations potentiate human pluripotent stem cell-derived 3D pancreatic progenitor clusters toward functional β cells. Nat Commun 2021; 12:3330. [PMID: 34099664 PMCID: PMC8184986 DOI: 10.1038/s41467-021-23525-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 05/02/2021] [Indexed: 11/09/2022] Open
Abstract
Human pluripotent stem cell (hPSC)-derived pancreatic β cells are an attractive cell source for treating diabetes. However, current derivation methods remain inefficient, heterogeneous, and cell line dependent. To address these issues, we first devised a strategy to efficiently cluster hPSC-derived pancreatic progenitors into 3D structures. Through a systematic study, we discovered 10 chemicals that not only retain the pancreatic progenitors in 3D clusters but also enhance their potentiality towards NKX6.1+/INS+ β cells. We further systematically screened signaling pathway modulators in the three steps from pancreatic progenitors toward β cells. The implementation of all these strategies and chemical combinations resulted in generating β cells from different sources of hPSCs with high efficiency. The derived β cells are functional and can reverse hyperglycemia in mice within two weeks. Our protocol provides a robust platform for studying human β cells and developing hPSC-derived β cells for cell replacement therapy.
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Affiliation(s)
- Haisong Liu
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Ronghui Li
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Hsin-Kai Liao
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Zheying Min
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Chao Wang
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Yang Yu
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Lei Shi
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Jiameng Dan
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Alberto Hayek
- Department of Pediatrics, UCSD-Medical School, La Jolla, California, USA
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