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Adnan Awad S, Dufva O, Klievink J, Karjalainen E, Ianevski A, Pietarinen P, Kim D, Potdar S, Wolf M, Lotfi K, Aittokallio T, Wennerberg K, Porkka K, Mustjoki S. Integrated drug profiling and CRISPR screening identify BCR::ABL1-independent vulnerabilities in chronic myeloid leukemia. Cell Rep Med 2024; 5:101521. [PMID: 38653245 PMCID: PMC11148568 DOI: 10.1016/j.xcrm.2024.101521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/10/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024]
Abstract
BCR::ABL1-independent pathways contribute to primary resistance to tyrosine kinase inhibitor (TKI) treatment in chronic myeloid leukemia (CML) and play a role in leukemic stem cell persistence. Here, we perform ex vivo drug screening of CML CD34+ leukemic stem/progenitor cells using 100 single drugs and TKI-drug combinations and identify sensitivities to Wee1, MDM2, and BCL2 inhibitors. These agents effectively inhibit primitive CD34+CD38- CML cells and demonstrate potent synergies when combined with TKIs. Flow-cytometry-based drug screening identifies mepacrine to induce differentiation of CD34+CD38- cells. We employ genome-wide CRISPR-Cas9 screening for six drugs, and mediator complex, apoptosis, and erythroid-lineage-related genes are identified as key resistance hits for TKIs, whereas the Wee1 inhibitor AZD1775 and mepacrine exhibit distinct resistance profiles. KCTD5, a consistent TKI-resistance-conferring gene, is found to mediate TKI-induced BCR::ABL1 ubiquitination. In summary, we delineate potential mechanisms for primary TKI resistance and non-BCR::ABL1-targeting drugs, offering insights for optimizing CML treatment.
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MESH Headings
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Protein Kinase Inhibitors/pharmacology
- CRISPR-Cas Systems/genetics
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/drug effects
- Proto-Oncogene Proteins c-abl/metabolism
- Proto-Oncogene Proteins c-abl/genetics
- Proto-Oncogene Proteins c-abl/antagonists & inhibitors
- Cell Line, Tumor
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Affiliation(s)
- Shady Adnan Awad
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; Foundation for the Finnish Cancer Institute, 00290 Helsinki, Finland; Clinical Pathology Department, National Cancer Institute, Cairo University, 11796 Cairo, Egypt.
| | - Olli Dufva
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland
| | - Jay Klievink
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Ella Karjalainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Aleksandr Ianevski
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Paavo Pietarinen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland
| | - Daehong Kim
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Maija Wolf
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Kourosh Lotfi
- Department of Medical and Health Sciences, Faculty of Medicine and Health, Linköping University, 58183 Linköping, Sweden
| | - Tero Aittokallio
- Foundation for the Finnish Cancer Institute, 00290 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland; Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; Oslo Centre for Biostatistics and Epidemiology, University of Oslo, 0317 Oslo, Norway
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland; Biotech Research & Innovation Centre and Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kimmo Porkka
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland.
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2
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Yang X, Jiao Y, Zhang Y, Sun M, Gao Y, Zhou Y, Xiao H, Ren J, Zhou Z, Zhai Y, Song B, Zhang L, Kong P. Oseltamivir enhances 5-FU sensitivity in esophageal squamous carcinoma with high SPNS1. Biomed Pharmacother 2024; 173:116367. [PMID: 38460365 DOI: 10.1016/j.biopha.2024.116367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 03/11/2024] Open
Abstract
Sphingolipid transporter 1 (SPNS1) is a significant differentially expressed gene (DEGs) in esophageal squamous cell carcinoma (ESCC). According to 3 pairs clinic cohorts, transcriptomic (155 pairs of ESCC samples and GSE53624, and proteomic data from PXD021701 including 124 ESCC samples) we found that SPNS1 was significantly higher in ESCC tissues compared to adjacent normal esophagus tissues. ESCC patients with high SPNS1 had a significantly poorer clinical prognosis than those with low SPNS1. Knockdown of SPNS1 significantly inhibited the proliferation, migration, and invasion abilities of ESCC cells, while promoting apoptosis. And overexpression of SPNS1 exhibited opposite functions. Furthermore, ESCC cells became more sensitive to 5-fluorouracil (5-FU) when SPNS1 was knocked down. Transcriptome sequencing revealed that NEU1 was one significant DEG affected by SPNS1 and positively correlated with SPNS1 expression. Oseltamivir phosphate (OP), one NEU1 inhibitor, markedly reversed 5-FU resistance, migration, and proliferation induced by high expression of SPNS1 both in vivo and in vitro. Our findings indicated that SPNS1 might promote the progression of ESCC by upregulating NEU1 expression and influencing chemotherapy sensitivity. These results provide new perceptions into potential therapeutic targets for ESCC treatment. The present study aimed to investigate the role and underlying mechanism of SPNS1 in ESCC.
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Affiliation(s)
- Xin Yang
- Translational Medicine Research Center, Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, China; Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ye Jiao
- Translational Medicine Research Center, Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, China; Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yingying Zhang
- Translational Medicine Research Center, Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, China; Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Meng Sun
- Translational Medicine Research Center, Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, China; Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yingzhen Gao
- Translational Medicine Research Center, Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, China; Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yan Zhou
- Translational Medicine Research Center, Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, China; Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Heng Xiao
- Translational Medicine Research Center, Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, China; Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jing Ren
- Translational Medicine Research Center, Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, China; Department of Microbiology and Immunology, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Zhinan Zhou
- Translational Medicine Research Center, Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, China; Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yuanfang Zhai
- Translational Medicine Research Center, Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, China; Department of Human Anatomy, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Bin Song
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Shanxi, China
| | - Ling Zhang
- Translational Medicine Research Center, Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, China; Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China.
| | - Pengzhou Kong
- Translational Medicine Research Center, Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, China; Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, China; State Key Laboratory for Pneumoconiosis of National Health Commission, Key Laboratory of Prevention, Treatment and Fundamental Studies for Respiratory Diseases of Shanxi, Department of Respiratory and Critical Care Medicine, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China.
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3
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Ha HT, Liu S, Nguyen XT, Vo LK, Leong NC, Nguyen DT, Balamurugan S, Lim PY, Wu Y, Seong E, Nguyen TQ, Oh J, Wenk MR, Cazenave-Gassiot A, Yapici Z, Ong WY, Burmeister M, Nguyen LN. Lack of SPNS1 results in accumulation of lysolipids and lysosomal storage disease in mouse models. JCI Insight 2024; 9:e175462. [PMID: 38451736 PMCID: PMC11141868 DOI: 10.1172/jci.insight.175462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/05/2024] [Indexed: 03/09/2024] Open
Abstract
Accumulation of sphingolipids, especially sphingosines, in the lysosomes is a key driver of several lysosomal storage diseases. The transport mechanism for sphingolipids from the lysosome remains unclear. Here, we identified SPNS1, which shares the highest homology to SPNS2, a sphingosine-1-phosphate (S1P) transporter, functions as a transporter for lysolipids from the lysosome. We generated Spns1-KO cells and mice and employed lipidomic and metabolomic approaches to reveal SPNS1 ligand identity. Global KO of Spns1 caused embryonic lethality between E12.5 and E13.5 and an accumulation of sphingosine, lysophosphatidylcholines (LPC), and lysophosphatidylethanolamines (LPE) in the fetal livers. Similarly, metabolomic analysis of livers from postnatal Spns1-KO mice presented an accumulation of sphingosines and lysoglycerophospholipids including LPC and LPE. Subsequently, biochemical assays showed that SPNS1 is required for LPC and sphingosine release from lysosomes. The accumulation of these lysolipids in the lysosomes of Spns1-KO mice affected liver functions and altered the PI3K/AKT signaling pathway. Furthermore, we identified 3 human siblings with a homozygous variant in the SPNS1 gene. These patients suffer from developmental delay, neurological impairment, intellectual disability, and cerebellar hypoplasia. These results reveal a critical role of SPNS1 as a promiscuous lysolipid transporter in the lysosomes and link its physiological functions with lysosomal storage diseases.
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Affiliation(s)
- Hoa T.T. Ha
- Department of Biochemistry, Yong Loo Lin School of Medicine
| | - SiYi Liu
- Department of Biochemistry, Yong Loo Lin School of Medicine
| | | | - Linh K. Vo
- Department of Biochemistry, Yong Loo Lin School of Medicine
| | | | - Dat T. Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine
| | | | - Pei Yen Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, and
| | - YaJun Wu
- Department of Anatomy, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore
| | - Eunju Seong
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, USA
| | - Toan Q. Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine
| | - Jeongah Oh
- Department of Biochemistry, Yong Loo Lin School of Medicine
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, and
| | - Markus R. Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, and
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, Yong Loo Lin School of Medicine
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, and
| | - Zuhal Yapici
- Department of Neurology, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Wei-Yi Ong
- Department of Anatomy, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore
| | - Margit Burmeister
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, USA
- Departments of Computational Medicine and Biochemistry, Psychiatry, and Human Genetics, University of Michigan, Ann Arbor, USA
| | - Long N. Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, and
- Cardiovascular Disease Research (CVD) Programme, Yong Loo Lin School of Medicine
- Immunology Program, Life Sciences Institute, and
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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4
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Gadi S, Niture S, Hoang H, Qi Q, Hatcher C, Huang X, Haider J, Norford DC, Leung T, Levine KE, Kumar D. Deficiency of spns1 exacerbates per- and polyfluoroalkyl substances mediated hepatic toxicity and steatosis in zebrafish (Danio rerio). Toxicology 2023; 499:153641. [PMID: 37806615 DOI: 10.1016/j.tox.2023.153641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are man-made long-lasting chemical compounds that are found in everyday household items. Today they occur in the environment as a major group of pollutants. These compounds are broadly used in commercial product preparation such as, for food packaging, nonstick coatings, and firefighting foam. In humans, PFAS can cause immune disorders, impaired fetal development, abnormal skeletal tissue development, osteoarthritis, thyroid dysfunctions, cholesterol changes, affect insulin regulation and lipid metabolism, and are also involved in the development of fatty liver disease. In the current study, we investigated the effect of low, but physiologically relevant, concentrations of perfluorooctanoic acid (PFOA), heptafluorobutyric acid (HFBA), and perfluorotetradecanoic acid (PFTA) on gene expression markers of an inflammatory response (tnfa, il-1b, il-6, rplp0, edem1, and dnajc3a), unfolded protein response (UPR) (bip, atf4a, atf6, xbp1, and ddit3), senescence (p21, pai1, smp30, mdm2, and baxa), lipogenesis (scd1, acc, srebp1, pparγ, and fasn) and autophagy (p62, atg3, atg7, rab7, lc3b, and becn1) in AB wild-type (+/+), spns1-wt sibling (+/+), (+/-) and spns1 homozygous mutant (-/-) zebrafish embryos. Exposure to PFOA and HFBA (50 and 100 nM) specifically modulated inflammatory, UPR, senescence, lipogenic, and autophagy signaling in spns1-wt (+/+), (+/-), and spns1-mutant (-/-) zebrafish embryos. Furthermore, PFOA, but not HFBA, upregulated lipogenic-related gene expression and enhanced hepatic steatosis in spns1-wt (+/+), (+/-) zebrafish embryos. Combined exposure to PFOA, HFBA, and PFTA differentially expressed inflammatory, senescence, lipogenic, and autophagy-associated gene expression in spns1-mutant (-/-) zebrafish embryos compared with spns1-wt (+/+), (+/-) and AB-wt (+/+) zebrafish embryos. In addition, chronic exposure (∼2 months) to PFOA (120-600 nM) upregulated the expression of hepatic lipogenic and steatosis biomarkers in AB-wt (+/+) zebrafish. Collectively, our data suggest that acute/chronic physiologically relevant concentrations of PFOA upregulate inflammatory, UPR, senescence, and lipogenic signaling in spns1-wt (+/+), (+/-) and spns1-mutant (-/-) zebrafish embryos as well as in two-month-old AB-wt zebrafish, by targeting autophagy and hence induces toxicity that could promote nonalcoholic fatty liver disease.
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Affiliation(s)
- Sashi Gadi
- The Julius L. Chambers Biomedical/Biotechnology Research Institute (JLC-BBRI), North Carolina Central University (NCCU), Durham, NC, USA
| | - Suryakant Niture
- The Julius L. Chambers Biomedical/Biotechnology Research Institute (JLC-BBRI), North Carolina Central University (NCCU), Durham, NC, USA; NCCU-RTI Center for Applied Research in Environmental Sciences (CARES), RTI International, Research Triangle Park, Durham, NC, USA.
| | - Hieu Hoang
- The Julius L. Chambers Biomedical/Biotechnology Research Institute (JLC-BBRI), North Carolina Central University (NCCU), Durham, NC, USA
| | - Qi Qi
- The Julius L. Chambers Biomedical/Biotechnology Research Institute (JLC-BBRI), North Carolina Central University (NCCU), Durham, NC, USA
| | - Charles Hatcher
- The Julius L. Chambers Biomedical/Biotechnology Research Institute (JLC-BBRI), North Carolina Central University (NCCU), Durham, NC, USA
| | - Xiaoyan Huang
- The NCCU, JLC-BBRI North Carolina Research Campus, Kannapolis, NC, USA
| | - Jamil Haider
- The NCCU, JLC-BBRI North Carolina Research Campus, Kannapolis, NC, USA
| | - Derek C Norford
- The Julius L. Chambers Biomedical/Biotechnology Research Institute (JLC-BBRI), North Carolina Central University (NCCU), Durham, NC, USA
| | - TinChung Leung
- The NCCU, JLC-BBRI North Carolina Research Campus, Kannapolis, NC, USA
| | - Keith E Levine
- NCCU-RTI Center for Applied Research in Environmental Sciences (CARES), RTI International, Research Triangle Park, Durham, NC, USA
| | - Deepak Kumar
- The Julius L. Chambers Biomedical/Biotechnology Research Institute (JLC-BBRI), North Carolina Central University (NCCU), Durham, NC, USA; NCCU-RTI Center for Applied Research in Environmental Sciences (CARES), RTI International, Research Triangle Park, Durham, NC, USA.
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5
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Xu J, Si H, Zeng Y, Wu Y, Zhang S, Shen B. Transcriptome-wide association study reveals candidate causal genes for lumbar spinal stenosis. Bone Joint Res 2023; 12:387-396. [PMID: 37356815 DOI: 10.1302/2046-3758.126.bjr-2022-0160.r1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/27/2023] Open
Abstract
Aims Lumbar spinal stenosis (LSS) is a common skeletal system disease that has been partly attributed to genetic variation. However, the correlation between genetic variation and pathological changes in LSS is insufficient, and it is difficult to provide a reference for the early diagnosis and treatment of the disease. Methods We conducted a transcriptome-wide association study (TWAS) of spinal canal stenosis by integrating genome-wide association study summary statistics (including 661 cases and 178,065 controls) derived from Biobank Japan, and pre-computed gene expression weights of skeletal muscle and whole blood implemented in FUSION software. To verify the TWAS results, the candidate genes were furthered compared with messenger RNA (mRNA) expression profiles of LSS to screen for common genes. Finally, Metascape software was used to perform enrichment analysis of the candidate genes and common genes. Results TWAS identified 295 genes with permutation p-values < 0.05 for skeletal muscle and 79 genes associated for the whole blood, such as RCHY1 (PTWAS = 0.001). Those genes were enriched in 112 gene ontology (GO) terms and five Kyoto Encyclopedia of Genes and Genomes pathways, such as 'chemical carcinogenesis - reactive oxygen species' (LogP value = -2.139). Further comparing the TWAS significant genes with the differentially expressed genes identified by mRNA expression profiles of LSS found 18 overlapped genes, such as interleukin 15 receptor subunit alpha (IL15RA) (PTWAS = 0.040, PmRNA = 0.010). Moreover, 71 common GO terms were detected for the enrichment results of TWAS and mRNA expression profiles, such as negative regulation of cell differentiation (LogP value = -2.811). Conclusion This study revealed the genetic mechanism behind the pathological changes in LSS, and may provide novel insights for the early diagnosis and intervention of LSS.
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Affiliation(s)
- Jiawen Xu
- Orthopedic Research Institute, Department of Orthopedics, Sichuan University West China Hospital, Chengdu, China
| | - Haibo Si
- Orthopedic Research Institute, Department of Orthopedics, Sichuan University West China Hospital, Chengdu, China
| | - Yi Zeng
- Orthopedic Research Institute, Department of Orthopedics, Sichuan University West China Hospital, Chengdu, China
| | - Yuangang Wu
- Orthopedic Research Institute, Department of Orthopedics, Sichuan University West China Hospital, Chengdu, China
| | - Shaoyun Zhang
- Orthopedic Research Institute, Department of Orthopedics, Sichuan University West China Hospital, Chengdu, China
| | - Bin Shen
- Orthopedic Research Institute, Department of Orthopedics, Sichuan University West China Hospital, Chengdu, China
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Scharenberg SG, Dong W, Ghoochani A, Nyame K, Levin-Konigsberg R, Krishnan AR, Rawat ES, Spees K, Bassik MC, Abu-Remaileh M. An SPNS1-dependent lysosomal lipid transport pathway that enables cell survival under choline limitation. SCIENCE ADVANCES 2023; 9:eadf8966. [PMID: 37075117 PMCID: PMC10115416 DOI: 10.1126/sciadv.adf8966] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Lysosomes degrade macromolecules and recycle their nutrient content to support cell function and survival. However, the machineries involved in lysosomal recycling of many nutrients remain to be discovered, with a notable example being choline, an essential metabolite liberated via lipid degradation. Here, we engineered metabolic dependency on lysosome-derived choline in pancreatic cancer cells to perform an endolysosome-focused CRISPR-Cas9 screen for genes mediating lysosomal choline recycling. We identified the orphan lysosomal transmembrane protein SPNS1 as critical for cell survival under choline limitation. SPNS1 loss leads to intralysosomal accumulation of lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE). Mechanistically, we reveal that SPNS1 is a proton gradient-dependent transporter of LPC species from the lysosome for their re-esterification into phosphatidylcholine in the cytosol. Last, we establish that LPC efflux by SPNS1 is required for cell survival under choline limitation. Collectively, our work defines a lysosomal phospholipid salvage pathway that is essential under nutrient limitation and, more broadly, provides a robust platform to deorphan lysosomal gene function.
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Affiliation(s)
- Samantha G. Scharenberg
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Stanford Medical Scientist Training Program, Stanford University, Stanford, CA 94305, USA
- Stanford Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Wentao Dong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Ali Ghoochani
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Kwamina Nyame
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Aswini R. Krishnan
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Stanford Medical Scientist Training Program, Stanford University, Stanford, CA 94305, USA
| | - Eshaan S. Rawat
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Kaitlyn Spees
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Michael C. Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
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7
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Spns1 is a lysophospholipid transporter mediating lysosomal phospholipid salvage. Proc Natl Acad Sci U S A 2022; 119:e2210353119. [PMID: 36161949 DOI: 10.1073/pnas.2210353119] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The lysosome is central to the degradation of proteins, carbohydrates, and lipids and their salvage back to the cytosol for reutilization. Lysosomal transporters for amino acids, sugars, and cholesterol have been identified, and the metabolic fates of these molecules in the cytoplasm have been elucidated. Remarkably, it is not known whether lysosomal salvage exists for glycerophospholipids, the major constituents of cellular membranes. By using a transport assay screen against orphan lysosomal transporters, we identified the major facilitator superfamily protein Spns1 that is ubiquitously expressed in all tissues as a proton-dependent lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE) transporter, with LPC and LPE being the lysosomal breakdown products of the most abundant eukaryotic phospholipids, phosphatidylcholine and phosphatidylethanolamine, respectively. Spns1 deficiency in cells, zebrafish embryos, and mouse liver resulted in lysosomal accumulation of LPC and LPE species with pathological consequences on lysosomal function. Flux analysis using stable isotope-labeled phospholipid apolipoprotein E nanodiscs targeted to lysosomes showed that LPC was transported out of lysosomes in an Spns1-dependent manner and re-esterified back into the cytoplasmic pools of phosphatidylcholine. Our findings identify a phospholipid salvage pathway from lysosomes to the cytosol that is dependent on Spns1 and critical for maintaining normal lysosomal function.
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Ni J, Wang P, Yin KJ, Yang XK, Cen H, Sui C, Wu GC, Pan HF. Novel insight into the aetiology of rheumatoid arthritis gained by a cross-tissue transcriptome-wide association study. RMD Open 2022; 8:e002529. [PMID: 37582060 PMCID: PMC9462377 DOI: 10.1136/rmdopen-2022-002529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/23/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Although genome-wide association studies (GWASs) have identified more than 100 loci associated with rheumatoid arthritis (RA) susceptibility, the causal genes and biological mechanisms remain largely unknown. METHODS A cross-tissue transcriptome-wide association study (TWAS) using the unified test for molecular signaturestool was performed to integrate GWAS summary statistics from 58 284 individuals (14 361 RA cases and 43 923 controls) with gene-expression matrix in the Genotype-Tissue Expression project. Subsequently, a single tissue by using FUSION software was conducted to validate the significant associations. We also compared the TWAS with different gene-based methodologies, including Summary Data Based Mendelian Randomization (SMR) and Multimarker Analysis of Genomic Annotation (MAGMA). Further in silico analyses (conditional and joint analysis, differential expression analysis and gene-set enrichment analysis) were used to deepen our understanding of genetic architecture and comorbidity aetiology of RA. RESULTS We identified a total of 47 significant candidate genes for RA in both cross-tissue and single-tissue test after multiple testing correction, of which 40 TWAS-identified genes were verified by SMR or MAGMA. Among them, 13 genes were situated outside of previously reported significant loci by RA GWAS. Both TWAS-based and MAGMA-based enrichment analyses illustrated the shared genetic determinants among autoimmune thyroid disease, asthma, type I diabetes mellitus and RA. CONCLUSION Our study unveils 13 new candidate genes whose predicted expression is associated with risk of RA, providing new insights into the underlying genetic architecture of RA.
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Affiliation(s)
- Jing Ni
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Peng Wang
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, China
| | - Kang-Jia Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Xiao-Ke Yang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Han Cen
- Department of Preventive Medicine, Ningbo University Medical School, Ningbo, Zhejiang, China
| | - Cong Sui
- Department of Orthopedics Trauma, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Guo-Cui Wu
- Department of Obstetrics and Gynecological Nursing, School of Nursing, Anhui Medical University, Hefei, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
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9
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Phagosomal Acidification Is Required to Kill Streptococcus pneumoniae in a Zebrafish Model. Cell Microbiol 2022. [DOI: 10.1155/2022/9429516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Streptococcus pneumoniae (the pneumococcus) is a major human pathogen causing invasive disease, including community-acquired bacteraemia, and remains a leading cause of global mortality. Understanding the role of phagocytes in killing bacteria is still limited, especially in vivo. In this study, we established a zebrafish model to study the interaction between intravenously administered pneumococci and professional phagocytes such as macrophages and neutrophils, to unravel bacterial killing mechanisms employed by these immune cells. Our model confirmed the key role of polysaccharide capsule in promoting pneumococcal virulence through inhibition of phagocytosis. Conversely, we show pneumococci lacking a capsule are rapidly internalised by macrophages. Low doses of encapsulated S. pneumoniae cause near 100% mortality within 48 hours postinfection (hpi), while 50 times higher doses of unencapsulated pneumococci are easily cleared. Time course analysis of in vivo bacterial numbers reveals that while encapsulated pneumococcus proliferates to levels exceeding 105 CFU at the time of host death, unencapsulated bacteria are unable to grow and are cleared within 20 hpi. Using genetically induced macrophage depletion, we confirmed an essential role for macrophages in bacterial clearance. Additionally, we show that upon phagocytosis by macrophages, phagosomes undergo rapid acidification. Genetic and chemical inhibition of vacuolar ATPase (v-ATPase) prevents intracellular bacterial killing and induces host death indicating a key role of phagosomal acidification in immunity to invading pneumococci. We also show that our model can be used to study the efficacy of antimicrobials against pneumococci in vivo. Collectively, our data confirm that larval zebrafish can be used to dissect killing mechanisms during pneumococcal infection in vivo and highlight key roles for phagosomal acidification in macrophages for pathogen clearance.
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Lysosomal Function Impacts the Skeletal Muscle Extracellular Matrix. J Dev Biol 2021; 9:jdb9040052. [PMID: 34842731 PMCID: PMC8629007 DOI: 10.3390/jdb9040052] [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: 09/24/2021] [Revised: 11/05/2021] [Accepted: 11/13/2021] [Indexed: 12/18/2022] Open
Abstract
Muscle development and homeostasis are critical for normal muscle function. A key aspect of muscle physiology during development, growth, and homeostasis is modulation of protein turnover, the balance between synthesis and degradation of muscle proteins. Protein degradation depends upon lysosomal pH, generated and maintained by proton pumps. Sphingolipid transporter 1 (spns1), a highly conserved gene encoding a putative late endosome/lysosome carbohydrate/H+ symporter, plays a pivotal role in maintaining optimal lysosomal pH and spns1−/− mutants undergo premature senescence. However, the impact of dysregulated lysosomal pH on muscle development and homeostasis is not well understood. We found that muscle development proceeds normally in spns1−/− mutants prior to the onset of muscle degeneration. Dysregulation of the extracellular matrix (ECM) at the myotendinous junction (MTJ) coincided with the onset of muscle degeneration in spns1−/− mutants. Expression of the ECM proteins laminin 111 and MMP-9 was upregulated. Upregulation of laminin 111 mitigated the severity of muscle degeneration, as inhibition of adhesion to laminin 111 exacerbated muscle degeneration in spns1−/− mutants. MMP-9 upregulation was induced by tnfsf12 signaling, but abrogation of MMP-9 did not impact muscle degeneration in spns1−/− mutants. Taken together, these data indicate that dysregulated lysosomal pH impacts expression of ECM proteins at the myotendinous junction.
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11
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Pant DC, Nazarko TY. Selective autophagy: the rise of the zebrafish model. Autophagy 2021; 17:3297-3305. [PMID: 33228439 PMCID: PMC8632090 DOI: 10.1080/15548627.2020.1853382] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/16/2020] [Indexed: 12/31/2022] Open
Abstract
Selective autophagy is a specific elimination of certain intracellular substrates by autophagic pathways. The most studied macroautophagy pathway involves tagging and recognition of a specific cargo by the autophagic membrane (phagophore) followed by the complete sequestration of targeted cargo from the cytosol by the double-membrane vesicle, autophagosome. Until recently, the knowledge about selective macroautophagy was minimal, but now there is a panoply of links elucidating how phagophores engulf their substrates selectively. The studies of selective autophagy processes have further stressed the importance of using the in vivo models to validate new in vitro findings and discover the physiologically relevant mechanisms. However, dissecting how the selective autophagy occurs yet remains difficult in living organisms, because most of the organelles are relatively inaccessible to observation and experimental manipulation in mammals. In recent years, zebrafish (Danio rerio) is widely recognized as an excellent model for studying autophagic processes in vivo because of its optical accessibility, genetic manipulability and translational potential. Several selective autophagy pathways, such as mitophagy, xenophagy, lipophagy and aggrephagy, have been investigated using zebrafish and still need to be studied further, while other selective autophagy pathways, such as pexophagy or reticulophagy, could also benefit from the use of the zebrafish model. In this review, we shed light on how zebrafish contributed to our understanding of these selective autophagy processes by providing the in vivo platform to study them at the organismal level and highlighted the versatility of zebrafish model in the selective autophagy field.Abbreviations: AD: Alzheimer disease; ALS: amyotrophic lateral sclerosis; Atg: autophagy-related; CMA: chaperone-mediated autophagy; CQ: chloroquine; HsAMBRA1: human AMBRA1; KD: knockdown; KO: knockout; LD: lipid droplet; MMA: methylmalonic acidemia; PD: Parkinson disease; Tg: transgenic.
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Affiliation(s)
- Devesh C. Pant
- Department of Biology, Georgia State University, Atlanta, GA, USA
| | - Taras Y. Nazarko
- Department of Biology, Georgia State University, Atlanta, GA, USA
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12
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Al-Bari MAA, Ito Y, Ahmed S, Radwan N, Ahmed HS, Eid N. Targeting Autophagy with Natural Products as a Potential Therapeutic Approach for Cancer. Int J Mol Sci 2021; 22:9807. [PMID: 34575981 PMCID: PMC8467030 DOI: 10.3390/ijms22189807] [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: 07/15/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 02/07/2023] Open
Abstract
Macro-autophagy (autophagy) is a highly conserved eukaryotic intracellular process of self-digestion caused by lysosomes on demand, which is upregulated as a survival strategy upon exposure to various stressors, such as metabolic insults, cytotoxic drugs, and alcohol abuse. Paradoxically, autophagy dysfunction also contributes to cancer and aging. It is well known that regulating autophagy by targeting specific regulatory molecules in its machinery can modulate multiple disease processes. Therefore, autophagy represents a significant pharmacological target for drug development and therapeutic interventions in various diseases, including cancers. According to the framework of autophagy, the suppression or induction of autophagy can exert therapeutic properties through the promotion of cell death or cell survival, which are the two main events targeted by cancer therapies. Remarkably, natural products have attracted attention in the anticancer drug discovery field, because they are biologically friendly and have potential therapeutic effects. In this review, we summarize the up-to-date knowledge regarding natural products that can modulate autophagy in various cancers. These findings will provide a new position to exploit more natural compounds as potential novel anticancer drugs and will lead to a better understanding of molecular pathways by targeting the various autophagy stages of upcoming cancer therapeutics.
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Affiliation(s)
| | - Yuko Ito
- Department of General and Gastroenterological Surgery, Osaka Medical and Pharmaceutical University, 2–7 Daigaku-machi, Takatsuki 569-8686, Osaka, Japan;
| | - Samrein Ahmed
- Department of Biosciences and Chemistry, College of Health and Wellbeing and Life Sciences, Sheffield Hallam University, City Campus, Howard Street, Sheffield S1 1WB, UK;
| | - Nada Radwan
- Department of Anatomy, College of Medicine & Health Sciences, United Arab Emirates University, Al Ain 17666, United Arab Emirates;
| | - Hend S. Ahmed
- Department of Hematology and Blood Transfusion, Faculty of Medical Laboratory Science, Omdurman Ahlia University, Khartoum 786, Sudan;
| | - Nabil Eid
- Department of Anatomy, College of Medicine & Health Sciences, United Arab Emirates University, Al Ain 17666, United Arab Emirates;
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13
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Dong Z, Qiu T, Zhang J, Sha S, Han X, Kang J, Shi X, Sun X, Jiang L, Yang G, Yao X, Ma Y. Perfluorooctane sulfonate induces autophagy-dependent lysosomal membrane permeabilization by weakened interaction between tyrosinated alpha-tubulin and spinster 1. Food Chem Toxicol 2021; 157:112540. [PMID: 34500008 DOI: 10.1016/j.fct.2021.112540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/15/2021] [Accepted: 09/05/2021] [Indexed: 10/20/2022]
Abstract
Perfluorooctane sulfonate (PFOS) is one kind of persistent organic pollutants. In previous study, we found that PFOS induced autophagy-dependent lysosomal membrane permeabilization (LMP) in hepatocytes, and siRNA against lysosomal permease spinster 1 (SPNS1) relieved PFOS-induced LMP. However, whether and how SPNS1 functioned as the link between autophagy and LMP was still not defined. In this study, we constructed a stable cell line expressing high levels of SPNS1. We found that SPNS1 interacted specifically with α-tubulin of tyrosinated isotype by pull-down assay. After treatment with PFOS, the level of tyrosinated α-tubulin was autophagy-dependently decreased. SPNS1-tyrosinated α-tubulin interaction was disrupted subsequently, which led to LMP eventually. We also found that stable high-expression of SPNS1 in hepatocytes accelerated lysosomal acidification, and deteriorated PFOS-induced LMP. This study pointed out that SPNS1-tyrosinated α-tubulin interaction mediated the cross-talk between autophagy and LMP induced by PFOS, shedding new light on the mechanism of PFOS hepatotoxicity.
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Affiliation(s)
- Zhanchen Dong
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China.
| | - Tianming Qiu
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Jingyuan Zhang
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Shanshan Sha
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Xiuyan Han
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Jian Kang
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Xiaoxia Shi
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Xiance Sun
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Liping Jiang
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Guang Yang
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China
| | - Xiaofeng Yao
- Department of Preventive Medicine, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China.
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W Lushun South Road, Dalian, 116044, PR China.
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14
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Khan A, Zaman T, Fahad TM, Akther T, Hasan MF, Naz T, Kishi S. Carbofuran affects cellular autophagy and developmental senescence through the impairment of Nrf2 signalling. J Cell Mol Med 2021; 26:35-47. [PMID: 34240810 PMCID: PMC8742233 DOI: 10.1111/jcmm.16774] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 05/24/2021] [Accepted: 06/19/2021] [Indexed: 12/14/2022] Open
Abstract
Carbofuran is a broad-spectrum synthetic pesticide. Its exposure to non-target mammals affects the biological system through the induction of oxidative stress. Since oxidative stress is a major contributing factor to cellular autophagy and senescence, our present investigation determined the impacts of carbofuran-induced oxidative stress on cellular autophagy and senescence. A transmembrane protein, Spinster homolog 1 (Spns1), is involved in autophagic lysosomal metabolism. Its mutation accelerates the cellular senescence and shortens the lifespan. Using a transgenic zebrafish line, expressing fluorescent microtubules-associated protein 1 light chain 3 (EGFP-LC3) at the membrane of the autophagosome, we found that carbofuran affects autophagic lysosomal biogenesis in wild-type zebrafish and exacerbates autophagic defect in spns1-mutant zebrafish. In real-time mortality study, carbofuran has shortened the lifespan of wild-type fish. Nrf2 is a stress-responsive transcription factor that regulates the expression of antioxidant genes (such as gstp1) in the prevention of oxidative stress-mediated cellular damage. To assess the effect of carbofuran on Nrf2 signalling, we established a dual-monitoring transgenic zebrafish line, expressing gstp1 promoter-driven EGFP and mCherry-tagged Neh2 domain of Nrf2. Our results suggested that the exposure of carbofuran has down-regulated both Nrf2 and Gstp1 expressions. Overall, carbofuran affects cellular autophagy and accelerates senescence by enervating the Nrf2 signalling.
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Affiliation(s)
- Alam Khan
- Department of Pharmacy, University of Rajshahi, Rajshahi, Bangladesh.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Tanjeena Zaman
- Department of Fisheries, University of Rajshahi, Rajshahi, Bangladesh.,Department of Biology, University of Hail, Hail, Kingdom of Saudi Arabia
| | | | - Tanjima Akther
- Department of Pharmacy, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Faruk Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Tarannum Naz
- Department of Pharmacy, University of Rajshahi, Rajshahi, Bangladesh
| | - Shuji Kishi
- S&J Kishi Research Corporation, Jupiter, FL, USA
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15
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Joy J, Barrio L, Santos-Tapia C, Romão D, Giakoumakis NN, Clemente-Ruiz M, Milán M. Proteostasis failure and mitochondrial dysfunction leads to aneuploidy-induced senescence. Dev Cell 2021; 56:2043-2058.e7. [PMID: 34216545 DOI: 10.1016/j.devcel.2021.06.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 03/03/2021] [Accepted: 06/11/2021] [Indexed: 01/10/2023]
Abstract
Aneuploidy, an unbalanced number of chromosomes, is highly deleterious at the cellular level and leads to senescence, a stress-induced response characterized by permanent cell-cycle arrest and a well-defined associated secretory phenotype. Here, we use a Drosophila epithelial model to delineate the pathway that leads to the induction of senescence as a consequence of the acquisition of an aneuploid karyotype. Whereas aneuploidy induces, as a result of gene dosage imbalance, proteotoxic stress and activation of the major protein quality control mechanisms, near-saturation functioning of autophagy leads to compromised mitophagy, accumulation of dysfunctional mitochondria, and the production of radical oxygen species (ROS). We uncovered a role of c-Jun N-terminal kinase (JNK) in driving senescence as a consequence of dysfunctional mitochondria and ROS. We show that activation of the major protein quality control mechanisms and mitophagy dampens the deleterious effects of aneuploidy, and we identify a role of senescence in proteostasis and compensatory proliferation for tissue repair.
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Affiliation(s)
- Jery Joy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Lara Barrio
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Celia Santos-Tapia
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Daniela Romão
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Nikolaos Nikiforos Giakoumakis
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Marta Clemente-Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Marco Milán
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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16
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Metabolomic profiling of single enlarged lysosomes. Nat Methods 2021; 18:788-798. [PMID: 34127857 DOI: 10.1038/s41592-021-01182-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/10/2021] [Indexed: 02/05/2023]
Abstract
Lysosomes are critical for cellular metabolism and are heterogeneously involved in various cellular processes. The ability to measure lysosomal metabolic heterogeneity is essential for understanding their physiological roles. We therefore built a single-lysosome mass spectrometry (SLMS) platform integrating lysosomal patch-clamp recording and induced nano-electrospray ionization (nanoESI)/mass spectrometry (MS) that enables concurrent metabolic and electrophysiological profiling of individual enlarged lysosomes. The accuracy and reliability of this technique were validated by supporting previous findings, such as the transportability of lysosomal cationic amino acids transporters such as PQLC2 and the lysosomal trapping of lysosomotropic, hydrophobic weak base drugs such as lidocaine. We derived metabolites from single lysosomes in various cell types and classified lysosomes into five major subpopulations based on their chemical and biological divergence. Senescence and carcinoma altered metabolic profiles of lysosomes in a type-specific manner. Thus, SLMS can open more avenues for investigating heterogeneous lysosomal metabolic changes during physiological and pathological processes.
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17
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Lauri A, Fasano G, Venditti M, Dallapiccola B, Tartaglia M. In vivo Functional Genomics for Undiagnosed Patients: The Impact of Small GTPases Signaling Dysregulation at Pan-Embryo Developmental Scale. Front Cell Dev Biol 2021; 9:642235. [PMID: 34124035 PMCID: PMC8194860 DOI: 10.3389/fcell.2021.642235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/12/2021] [Indexed: 12/24/2022] Open
Abstract
While individually rare, disorders affecting development collectively represent a substantial clinical, psychological, and socioeconomic burden to patients, families, and society. Insights into the molecular mechanisms underlying these disorders are required to speed up diagnosis, improve counseling, and optimize management toward targeted therapies. Genome sequencing is now unveiling previously unexplored genetic variations in undiagnosed patients, which require functional validation and mechanistic understanding, particularly when dealing with novel nosologic entities. Functional perturbations of key regulators acting on signals' intersections of evolutionarily conserved pathways in these pathological conditions hinder the fine balance between various developmental inputs governing morphogenesis and homeostasis. However, the distinct mechanisms by which these hubs orchestrate pathways to ensure the developmental coordinates are poorly understood. Integrative functional genomics implementing quantitative in vivo models of embryogenesis with subcellular precision in whole organisms contribute to answering these questions. Here, we review the current knowledge on genes and mechanisms critically involved in developmental syndromes and pediatric cancers, revealed by genomic sequencing and in vivo models such as insects, worms and fish. We focus on the monomeric GTPases of the RAS superfamily and their influence on crucial developmental signals and processes. We next discuss the effectiveness of exponentially growing functional assays employing tractable models to identify regulatory crossroads. Unprecedented sophistications are now possible in zebrafish, i.e., genome editing with single-nucleotide precision, nanoimaging, highly resolved recording of multiple small molecules activity, and simultaneous monitoring of brain circuits and complex behavioral response. These assets permit accurate real-time reporting of dynamic small GTPases-controlled processes in entire organisms, owning the potential to tackle rare disease mechanisms.
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Affiliation(s)
- Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | | | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
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18
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Eldakhakhny BM, Al Sadoun H, Choudhry H, Mobashir M. In-Silico Study of Immune System Associated Genes in Case of Type-2 Diabetes With Insulin Action and Resistance, and/or Obesity. Front Endocrinol (Lausanne) 2021; 12:641888. [PMID: 33927693 PMCID: PMC8078136 DOI: 10.3389/fendo.2021.641888] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/08/2021] [Indexed: 12/11/2022] Open
Abstract
Type-2 diabetes and obesity are among the leading human diseases and highly complex in terms of diagnostic and therapeutic approaches and are among the most frequent and highly complex and heterogeneous in nature. Based on epidemiological evidence, it is known that the patients suffering from obesity are considered to be at a significantly higher risk of type-2 diabetes. There are several pieces of evidence that support the hypothesis that these diseases interlinked and obesity may aggravate the risk(s) of type-2 diabetes. Multi-level unwanted alterations such as (epi-) genetic alterations, changes at the transcriptional level, and altered signaling pathways (receptor, cytoplasmic, and nuclear level) are the major sources that promote several complex diseases, and such a heterogeneous level of complexity is considered as a major barrier in the development of therapeutics. With so many known challenges, it is critical to understand the relationships and the shared causes between type-2 diabetes and obesity, and these are difficult to unravel and understand. For this purpose, we have selected publicly available datasets of gene expression for obesity and type-2 diabetes, have unraveled the genes and the pathways associated with the immune system, and have also focused on the T-cell signaling pathway and its components. We have applied a simplified computational approach to understanding differential gene expression and patterns and the enriched pathways for obesity and type-2 diabetes. Furthermore, we have also analyzed genes by using network-level understanding. In the analysis, we observe that there are fewer genes that are commonly differentially expressed while a comparatively higher number of pathways are shared between them. There are only 4 pathways that are associated with the immune system in case of obesity and 10 immune-associated pathways in case of type-2 diabetes, and, among them, only 2 pathways are commonly altered. Furthermore, we have presented SPNS1, PTPN6, CD247, FOS, and PIK3R5 as the overexpressed genes, which are the direct components of TCR signaling.
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Affiliation(s)
- Basmah Medhat Eldakhakhny
- Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hadeel Al Sadoun
- Stem Cell Unit, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hani Choudhry
- Cancer and Mutagenesis Unit, Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Mobashir
- SciLifeLab, Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
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19
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Zebrafish as an animal model for biomedical research. Exp Mol Med 2021; 53:310-317. [PMID: 33649498 PMCID: PMC8080808 DOI: 10.1038/s12276-021-00571-5] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
Zebrafish have several advantages compared to other vertebrate models used in modeling human diseases, particularly for large-scale genetic mutant and therapeutic compound screenings, and other biomedical research applications. With the impactful developments of CRISPR and next-generation sequencing technology, disease modeling in zebrafish is accelerating the understanding of the molecular mechanisms of human genetic diseases. These efforts are fundamental for the future of precision medicine because they provide new diagnostic and therapeutic solutions. This review focuses on zebrafish disease models for biomedical research, mainly in developmental disorders, mental disorders, and metabolic diseases.
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20
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Lu JW, Tseng YS, Lo YS, Lin YM, Yeh CM, Lin SH. Prognostic Significance of Cytoplasmic SPNS2 Expression in Patients with Oral Squamous Cell Carcinoma. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:164. [PMID: 33673355 PMCID: PMC7917906 DOI: 10.3390/medicina57020164] [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] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 01/09/2023]
Abstract
Background and Objectives: Oral squamous cell carcinoma (OSCC) is a malignant disease with a particularly high incidence in Taiwan. Our objective in this study was to elucidate the involvement of sphingolipid transporter 2 (SPNS2) expression and SPNS2 protein expression in the clinicopathological indexes and the clinical outcomes of OSCC patients. Materials and Methods: Immunohistochemistry analysis was performed for SPNS2 protein expression in samples from 264 cases of OSCC. Correlations of SPNS2 expression with clinicopathological variables and patient survival were analyzed. Results: Our results revealed that the cytoplasmic protein expression of SPNS2 in OSCC tissue specimens was lower than in normal tissue specimens. Negative cytoplasmic protein expression of SPNS2 was significantly correlated with T status and stage. Kaplan-Meier survival curve analysis revealed that negative cytoplasmic SPNS2 expression was predictive of poorer overall survival of OSCC patients in stage III/IV. We also determined that low SPNS2 expression was an independent prognostic factor related to overall survival among OSCC patients in stage III/IV from univariate Cox proportional hazard models. Multivariate Cox proportional hazard models revealed that cytoplasmic SPNS2 expression, T status, lymph node metastasis, and histological grade were independent prognostic factors for survival. Conclusions: Overall, this study determined that SPNS2 protein may be a useful prognostic marker for OSCC patients and potential therapeutic target for OSCC treatment.
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Affiliation(s)
- Jeng-Wei Lu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore;
| | - Yen-Shuo Tseng
- Department of Dermatology, Changhua Christian Hospital, Changhua 500, Taiwan;
| | - Yu-Sheng Lo
- Department of Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan;
| | - Yueh-Min Lin
- School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan;
- Department of Surgical Pathology, Changhua Christian Hospital, Changhua 500, Taiwan;
| | - Chung-Min Yeh
- Department of Surgical Pathology, Changhua Christian Hospital, Changhua 500, Taiwan;
- Department of Medical Technology, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli 356, Taiwan
| | - Shu-Hui Lin
- Department of Surgical Pathology, Changhua Christian Hospital, Changhua 500, Taiwan;
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung 406, Taiwan
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21
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Duan X, Tong C. Autophagy in Drosophila and Zebrafish. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1208:333-356. [PMID: 34260032 DOI: 10.1007/978-981-16-2830-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Autophagy is a highly conserved cellular process that delivers cellular contents to the lysosome for degradation. It not only serves as a bulk degradation system for various cytoplasmic components but also functions selectively to clear damaged organelles, aggregated proteins, and invading pathogens (Feng et al., Cell Res 24:24-41, 2014; Galluzzi et al., EMBO J 36:1811-36, 2017; Klionsky et al., Autophagy 12:1-222, 2016). The malfunction of autophagy leads to multiple developmental defects and diseases (Mizushima et al., Nature 451:1069-75, 2008). Drosophila and zebrafish are higher metazoan model systems with sophisticated genetic tools readily available, which make it possible to dissect the autophagic processes and to understand the physiological functions of autophagy (Lorincz et al., Cells 6:22, 2017a; Mathai et al., Cells 6:21, 2017; Zhang and Baehrecke, Trends Cell Biol 25:376-87, 2015). In this chapter, we will discuss recent progress that has been made in the autophagic field by using these animal models. We will focus on the protein machineries required for autophagosome formation and maturation as well as the physiological roles of autophagy in both Drosophila and zebrafish.
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Affiliation(s)
- Xiuying Duan
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chao Tong
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China. .,The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
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22
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Duan YN, Ge X, Jiang HW, Zhang HJ, Zhao Y, Li JL, Zhang W, Li JY. Diphyllin Improves High-Fat Diet-Induced Obesity in Mice Through Brown and Beige Adipocytes. Front Endocrinol (Lausanne) 2020; 11:592818. [PMID: 33424769 PMCID: PMC7793827 DOI: 10.3389/fendo.2020.592818] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 10/22/2020] [Indexed: 12/30/2022] Open
Abstract
Brown adipose tissue (BAT) and beige adipose tissue dissipate metabolic energy and mediate nonshivering thermogenesis, thereby boosting energy expenditure. Increasing the browning of BAT and beige adipose tissue is expected to be a promising strategy for combatting obesity. Through phenotype screening of C3H10-T1/2 mesenchymal stem cells, diphyllin was identified as a promising molecule in promoting brown adipocyte differentiation. In vitro studies revealed that diphyllin promoted C3H10-T1/2 cell and primary brown/beige preadipocyte differentiation and thermogenesis, which resulted increased energy consumption. We synthesized the compound and evaluated its effect on metabolism in vivo. Chronic experiments revealed that mice fed a high-fat diet (HFD) with 100 mg/kg diphyllin had ameliorated oral glucose tolerance and insulin sensitivity and decreased body weight and fat content ratio. Adaptive thermogenesis in HFD-fed mice under cold stimulation and whole-body energy expenditure were augmented after chronic diphyllin treatment. Diphyllin may be involved in regulating the development of brown and beige adipocytes by inhibiting V-ATPase and reducing intracellular autophagy. This study provides new clues for the discovery of anti-obesity molecules from natural products.
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Affiliation(s)
- Ya-Nan Duan
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiang Ge
- School of Pharmacy, Nantong University, Nantong, China
| | - Hao-Wen Jiang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hong-Jie Zhang
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong Special Administrative Region, People’s Republic of China
| | - Yu Zhao
- School of Pharmacy, Nantong University, Nantong, China
| | - Jin-Long Li
- School of Pharmacy, Nantong University, Nantong, China
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong Special Administrative Region, People’s Republic of China
| | - Wei Zhang
- Kay Laboratory of Brain Functional Genomics, Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics, School of Life Science, East China Normal University, Shanghai, China
| | - Jing-Ya Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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23
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Khan A, Fahad TM, Akther T, Zaman T, Hasan MF, Islam Khan MR, Islam MS, Kishi S. Carbofuran accelerates the cellular senescence and declines the life span of spns1 mutant zebrafish. J Cell Mol Med 2020; 25:1048-1059. [PMID: 33277797 PMCID: PMC7812278 DOI: 10.1111/jcmm.16171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/03/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022] Open
Abstract
Carbofuran is a carbamate pesticide, widely used in agricultural practices to increase crop productivity. In mammals, carbofuran is known to cause several untoward effects, such as apoptosis in the hippocampal neuron, oxidative stress, loss of memory and chromosomal anomalies. Most of these effects are implicated with cellular senescence. Therefore, the present study aimed to determine the effect of carbofuran on cellular senescence and biological ageing. Spinster homolog 1 (Spns1) is a transmembrane transporter, regulates autolysosomal biogenesis and plays a role in cellular senescence and survival. Using senescence‐associated β‐galactosidase staining, we found that carbofuran accelerates the cellular senescence in spns1 mutant zebrafish. The yolk opaqueness, a premature ageing phenotype in zebrafish embryos, was accelerated by carbofuran treatment. In the survival study, carbofuran shortened the life span of spns1 mutant zebrafish. Autophagy is the cellular lysosomal degradation, usually up‐regulated in the senescent cells. To know the impact of carbofuran exposure on autophagy progress, we established a double‐transgenic zebrafish line, harbouring EGFP‐tagged LC3‐II and mCherry‐tagged Lamp1 on spns1 mutant background, whereas we found, carbofuran exposure synergistically accelerates autolysosome formation with insufficient lysosome‐mediated degradation. Our data collectively suggest that carbofuran exposure synergistically accelerates the cellular senescence and affects biological ageing in spns1 defective animals.
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Affiliation(s)
- Alam Khan
- Department of Pharmacy, University of Rajshahi, Rajshahi, Bangladesh.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | | | - Tanjima Akther
- Department of Pharmacy, University of Rajshahi, Rajshahi, Bangladesh
| | - Tanjeena Zaman
- Department of Fisheries, University of Rajshahi, Rajshahi, Bangladesh.,Department of Biology, University of Hail, Hail, Saudi Arabia
| | - Md Faruk Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | | | | | - Shuji Kishi
- S&J Kishi Research Corporation, Jupiter, FL, USA
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24
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Bosi E, Marselli L, De Luca C, Suleiman M, Tesi M, Ibberson M, Eizirik DL, Cnop M, Marchetti P. Integration of single-cell datasets reveals novel transcriptomic signatures of β-cells in human type 2 diabetes. NAR Genom Bioinform 2020; 2:lqaa097. [PMID: 33575641 PMCID: PMC7679065 DOI: 10.1093/nargab/lqaa097] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/26/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
Pancreatic islet β-cell failure is key to the onset and progression of type 2 diabetes (T2D). The advent of single-cell RNA sequencing (scRNA-seq) has opened the possibility to determine transcriptional signatures specifically relevant for T2D at the β-cell level. Yet, applications of this technique have been underwhelming, as three independent studies failed to show shared differentially expressed genes in T2D β-cells. We performed an integrative analysis of the available datasets from these studies to overcome confounding sources of variability and better highlight common T2D β-cell transcriptomic signatures. After removing low-quality transcriptomes, we retained 3046 single cells expressing 27 931 genes. Cells were integrated to attenuate dataset-specific biases, and clustered into cell type groups. In T2D β-cells (n = 801), we found 210 upregulated and 16 downregulated genes, identifying key pathways for T2D pathogenesis, including defective insulin secretion, SREBP signaling and oxidative stress. We also compared these results with previous data of human T2D β-cells from laser capture microdissection and diabetic rat islets, revealing shared β-cell genes. Overall, the present study encourages the pursuit of single β-cell RNA-seq analysis, preventing presently identified sources of variability, to identify transcriptomic changes associated with human T2D and underscores specific traits of dysfunctional β-cells across different models and techniques.
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Affiliation(s)
- Emanuele Bosi
- Department of Experimental and Clinical Medicine, Pancreatic Islets Laboratory, University of Pisa, Pisa, I-56124, Italy
| | - Lorella Marselli
- Department of Experimental and Clinical Medicine, Pancreatic Islets Laboratory, University of Pisa, Pisa, I-56124, Italy
| | - Carmela De Luca
- Department of Experimental and Clinical Medicine, Pancreatic Islets Laboratory, University of Pisa, Pisa, I-56124, Italy
| | - Mara Suleiman
- Department of Experimental and Clinical Medicine, Pancreatic Islets Laboratory, University of Pisa, Pisa, I-56124, Italy
| | - Marta Tesi
- Department of Experimental and Clinical Medicine, Pancreatic Islets Laboratory, University of Pisa, Pisa, I-56124, Italy
| | - Mark Ibberson
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, University of Lausanne, Quartier Sorge, CH-1015 Lausanne, Switzerland
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, B-1070, Belgium
| | - Miriam Cnop
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, B-1070, Belgium
| | - Piero Marchetti
- Department of Experimental and Clinical Medicine, Pancreatic Islets Laboratory, University of Pisa, Pisa, I-56124, Italy
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25
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Moss JJ, Hammond CL, Lane JD. Zebrafish as a model to study autophagy and its role in skeletal development and disease. Histochem Cell Biol 2020; 154:549-564. [PMID: 32915267 PMCID: PMC7609422 DOI: 10.1007/s00418-020-01917-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2020] [Indexed: 12/13/2022]
Abstract
In the last twenty years, research using zebrafish as a model organism has increased immensely. With the many advantages that zebrafish offer such as high fecundity, optical transparency, ex vivo development, and genetic tractability, they are well suited to studying developmental processes and the effect of genetic mutations. More recently, zebrafish models have been used to study autophagy. This important protein degradation pathway is needed for cell and tissue homeostasis in a variety of contexts. Correspondingly, its dysregulation has been implicated in multiple diseases including skeletal disorders. In this review, we explore how zebrafish are being used to study autophagy in the context of skeletal development and disease, and the ways these areas are intersecting to help identify potential therapeutic targets for skeletal disorders.
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Affiliation(s)
- Joanna J Moss
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, UK.,School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences Building, University of Bristol, Bristol, UK
| | - Chrissy L Hammond
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences Building, University of Bristol, Bristol, UK.
| | - Jon D Lane
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, UK.
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26
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Meng X, Li H, Fang E, Feng J, Zhao X. Comparison of Stage 4 and Stage 4s Neuroblastoma Identifies Autophagy-Related Gene and LncRNA Signatures Associated With Prognosis. Front Oncol 2020; 10:1411. [PMID: 32974147 PMCID: PMC7466450 DOI: 10.3389/fonc.2020.01411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/03/2020] [Indexed: 01/01/2023] Open
Abstract
Background: The spontaneous regression of neuroblastoma (NB) is most prevalent and well-documented in stage 4s NB patients. However, whether autophagy plays roles in the spontaneous regression of NB is unknown. Objective: This study aimed to identify autophagy-related genes (ARGs) and autophagy-related long non-coding RNAs (lncRNAs) differentially expressed in stage 4 and stage 4s NB and to build prognostic risk signatures on the basis of the ARGs and autophagy-related lncRNAs. Methods: One RNA-sequence (RNA-Seq) dataset (TARGET NBL, n = 153) was utilized as discovery cohort, and two microarray datasets (n = 498 and n = 223) were used as validation cohorts. Differentially expressed ARGs were identified by comparing stage 4s and stage 4 NB samples. An ARG signature risk score and an autophagy-related lncRNA signature risk score were constructed. The receiver operating characteristic (ROC) curve analyses were used to evaluate the survival prediction ability of the two signatures. Gene function annotation and Gene Set Enrichment Analysis (GSEA) were performed to clarify the autophagic biological processes enriched in different risk groups. Results: Nine ARGs were integrated into the ARG signature. Patients in the high-risk group of the ARG signature had significantly poorer overall survival (OS) than patients in the low-risk group. The ROC curves analyses revealed that the ARG signature performed very well in predicting OS [5-year area under the curve (AUC) = 0.81]. Seven autophagy-related lncRNAs were integrated into the autophagy-related lncRNA signature. Patients in the high-risk group of the lncRNA signature had significantly poorer OS than patients in the low-risk group. The ROC curve analyses also revealed that the lncRNA signature performed well in predicting OS (5-year AUC = 0.77). Both the ARG signature and lncRNA signature are independent with other clinical risk factors in the multivariate Cox regression survival analyses. GSEAs revealed that autophagy-related biological processes are enriched in low-risk groups. Conclusions: Autophagy-related genes and lncRNAs are differentially expressed between stage 4 and stage 4s NB. The ARG signature and autophagy-related lncRNA signature successfully stratified NB patients into two risk groups. Autophagy-related biological processes are highly enriched in low-risk NB groups.
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Affiliation(s)
- Xinyao Meng
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Honglin Li
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Erhu Fang
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiexiong Feng
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiang Zhao
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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27
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Huo X, Qi J, Huang K, Bu S, Yao W, Chen Y, Nie J. Identification of an autophagy-related gene signature that can improve prognosis of hepatocellular carcinoma patients. BMC Cancer 2020; 20:771. [PMID: 32807131 PMCID: PMC7433127 DOI: 10.1186/s12885-020-07277-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 08/09/2020] [Indexed: 12/21/2022] Open
Abstract
Background Autophagy is a programmed cell degradation mechanism that has been associated with several physiological and pathophysiological processes, including malignancy. Improper induction of autophagy has been proposed to play a pivotal role in the progression of hepatocellular carcinoma (HCC). Methods Univariate Cox regression analysis of overall survival (OS) was performed to identify risk-associated autophagy-related genes (ARGs) in HCC data set from The Cancer Genome Atlas (TCGA). Multivariate cox regression was then performed to develop a risk prediction model for the prognosis of 370 HCC patients. The multi-target receiver operating characteristic (ROC) curve was used to determine the model’s accuracy. Besides, the relationship between drug sensitivity and ARGs expression was also examined. Results A total of 62 differentially expressed ARGs were identified in HCC patients. Univariate and multivariate regression identified five risk-associated ARGs (HDAC1, RHEB, ATIC, SPNS1 and SQSTM1) that were correlated with OS in HCC patients. Of importance, the risk-associated ARGs were independent risk factors in the multivariate risk model including clinical parameters such as malignant stage (HR = 1.433, 95% CI = 1.293–1.589, P < 0.001). In addition, the area under curve for the prognostic risk model was 0.747, which indicates the high accuracy of the model in prediction of HCC outcomes. Interestingly, the risk-associated ARGs were also correlated with drug sensitivity in HCC cell lines. Conclusion We developed a novel prognostic risk model by integrating the molecular signature and clinical parameters of HCC, which can effectively predict the outcomes of HCC patients.
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Affiliation(s)
- Xingxing Huo
- University of Science and Technology of China, Hefei, China.,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China.,Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.,Experimental Center of Clinical Research, the First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Jian Qi
- University of Science and Technology of China, Hefei, China.,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China.,Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Kaiquan Huang
- Experimental Center of Clinical Research, the First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Su Bu
- Experimental Center of Clinical Research, the First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Wei Yao
- Experimental Center of Clinical Research, the First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Ying Chen
- Experimental Center of Clinical Research, the First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Jinfu Nie
- University of Science and Technology of China, Hefei, China. .,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China. .,Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.
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28
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Yoshimoto R, Rahimi K, Hansen TB, Kjems J, Mayeda A. Biosynthesis of Circular RNA ciRS-7/CDR1as Is Mediated by Mammalian-wide Interspersed Repeats. iScience 2020; 23:101345. [PMID: 32683316 PMCID: PMC7371899 DOI: 10.1016/j.isci.2020.101345] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 04/18/2020] [Accepted: 07/02/2020] [Indexed: 01/07/2023] Open
Abstract
Circular RNAs (circRNAs) are stable non-coding RNAs with a closed circular structure. One of the best studied circRNAs is ciRS-7 (CDR1as), which acts as a regulator of the microRNA miR-7; however, its biosynthetic pathway has remained an enigma. Here we delineate the biosynthetic pathway of ciRS-7. The back-splicing events that form circRNAs are often facilitated by flanking inverted repeats of the primate-specific Alu elements. The ciRS-7 gene lacks these elements, but, instead, we identified a set of flanking inverted elements belonging to the mammalian-wide interspersed repeat (MIR) family. Splicing reporter assays in HEK293 cells demonstrated that these inverted MIRs are required to generate ciRS-7 through back-splicing, and CRISPR/Cas9-mediated deletions confirmed the requirement of the endogenous MIR elements in SH-SY5Y cells. Using bioinformatic searches, we identified several other MIR-dependent circRNAs and confirmed them experimentally. We propose that MIR-mediated RNA circularization is used to generate a subset of mammalian circRNAs. The circular RNA, ciRS-7 (CDR1as), functions as a regulator of miR-7 ciRS-7 is generated by back-splicing, not via intra-lariat splicing Back-splicing of ciRS-7 is promoted by the flanking inverted MIR elements The biosynthesis of a subset of mammalian circRNAs could be mediated by MIRs
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Affiliation(s)
- Rei Yoshimoto
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan.
| | - Karim Rahimi
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark; Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Thomas B Hansen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark; Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan.
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29
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A current view of molecular dissection in autophagy machinery. J Physiol Biochem 2020; 76:357-372. [DOI: 10.1007/s13105-020-00746-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023]
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30
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Huang W, Qian T, Cheng Z, Zeng T, Si C, Liu C, Deng C, Ye X, Liu Y, Cui L, Fu L. Prognostic significance of Spinster homolog gene family in acute myeloid leukemia. J Cancer 2020; 11:4581-4588. [PMID: 32489475 PMCID: PMC7255376 DOI: 10.7150/jca.44766] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/02/2020] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a clonal and heterogeneous disease characterized by proliferation of immature myeloid cells, with impaired differentiation and maturation. Spinster homolog (SPNS) is a widely distributed transmembrane transporter, which assists sphingolipids in playing their roles through the cell membrane. However, the expression and clinical implication of the SPNS family has not been investigated in AML. From the Cancer Genome Atlas database, a total of 155 AML patients with complete clinical characteristics and SPNS1-3 expression data were contained in our study. In patients who received chemotherapy only, high expressions of SPNS2 and SPNS3 had adverse effects on event-free survival (EFS) and overall survival (OS) (all P<0.05). However, in the allogeneic hematopoietic stem cell transplantation (allo-HSCT) group, we only found a significant difference in OS between the high and low SPNS3 expression groups (P=0.001), while other SPNS members showed no effect on survival. Multivariate analysis indicated that high SPNS2 expression was an independent risk factor for both EFS and OS in chemotherapy patients. The results confirmed that high expression of SPNS2 and SPNS3 were poor prognostic factors, and the effect of SPNS2 can be neutralized by allo-HSCT.
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Affiliation(s)
- Wenhui Huang
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China.,Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumor Microenvironment, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Tingting Qian
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China.,Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumor Microenvironment, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Zhiheng Cheng
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Tiansheng Zeng
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China.,Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumor Microenvironment, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Chaozeng Si
- Information Center, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Chaojun Liu
- Yinfeng Gene Technology Co., Ltd.; No.1109, Gangxing 3 Rd,New and High-tech Zone, Jinan City, Shandong Province, 250102, China
| | - Cong Deng
- Department of Clinical laboratory, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Xu Ye
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Yan Liu
- Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, 475000, China
| | - Longzhen Cui
- Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, 475000, China.,Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, 475000, China
| | - Lin Fu
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China.,Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumor Microenvironment, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, 475000, China.,Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, 475000, China
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31
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Uzor NE, McCullough LD, Tsvetkov AS. Peroxisomal Dysfunction in Neurological Diseases and Brain Aging. Front Cell Neurosci 2020; 14:44. [PMID: 32210766 PMCID: PMC7075811 DOI: 10.3389/fncel.2020.00044] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/18/2020] [Indexed: 12/17/2022] Open
Abstract
Peroxisomes exist in most cells, where they participate in lipid metabolism, as well as scavenging the reactive oxygen species (ROS) that are produced as by-products of their metabolic functions. In certain tissues such as the liver and kidneys, peroxisomes have more specific roles, such as bile acid synthesis in the liver and steroidogenesis in the adrenal glands. In the brain, peroxisomes are critically involved in creating and maintaining the lipid content of cell membranes and the myelin sheath, highlighting their importance in the central nervous system (CNS). This review summarizes the peroxisomal lifecycle, then examines the literature that establishes a link between peroxisomal dysfunction, cellular aging, and age-related disorders that affect the CNS. This review also discusses the gap of knowledge in research on peroxisomes in the CNS.
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Affiliation(s)
- Ndidi-Ese Uzor
- Department of Neurobiology and Anatomy, University of Texas McGovern Medical School, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Louise D. McCullough
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- Department of Neurology, University of Texas McGovern Medical School, Houston, TX, United States
- UTHealth Consortium on Aging, University of Texas McGovern Medical School, Houston, TX, United States
| | - Andrey S. Tsvetkov
- Department of Neurobiology and Anatomy, University of Texas McGovern Medical School, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- UTHealth Consortium on Aging, University of Texas McGovern Medical School, Houston, TX, United States
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32
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Shi X, Yan N, Niu G, Sung SHP, Liu Z, Liu J, Kwok RTK, Lam JWY, Wang WX, Sung HHY, Williams ID, Tang BZ. In vivo monitoring of tissue regeneration using a ratiometric lysosomal AIE probe. Chem Sci 2020; 11:3152-3163. [PMID: 34122820 PMCID: PMC8157324 DOI: 10.1039/c9sc06226b] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/07/2020] [Indexed: 12/11/2022] Open
Abstract
Tissue regeneration is a crucial self-renewal capability involving many complex biological processes. Although transgenic techniques and fluorescence immunohistochemical staining have promoted our understanding of tissue regeneration, simultaneous quantification and visualization of tissue regeneration processes is not easy to achieve. Herein, we developed a simple and quantitative method for the real-time and non-invasive observation of the process of tissue regeneration. The synthesized ratiometric aggregation-induced-emission (AIE) probe exhibits high selectivity and reversibility for pH responses, good ability to map lysosomal pH both in vitro and in vivo, good biocompatibility and excellent photostability. The caudal fin regeneration of a fish model (medaka larvae) was monitored by tracking the lysosomal pH change. It was found that the mean lysosomal pH is reduced during 24-48 hpa to promote the autophagic activity for cell debris degradation. Our research can quantify the changes in mean lysosomal pH and also exhibit its distribution during the caudal fin regeneration. We believe that the AIE-active lysosomal pH probe can also be potentially used for long-term tracking of various lysosome-involved biological processes, such as tracking the stress responses of tissue, tracking the inflammatory responses, and so on.
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Affiliation(s)
- Xiujuan Shi
- HKUST-Shenzhen Research Institute No. 9 Yuexing 1st RD, South Area, Hi-tech Park, Nanshan Shenzhen 518057 China
- Department of Chemical and Biological Engineering, Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Neng Yan
- Department of Ocean Science, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Guangle Niu
- HKUST-Shenzhen Research Institute No. 9 Yuexing 1st RD, South Area, Hi-tech Park, Nanshan Shenzhen 518057 China
- Department of Chemical and Biological Engineering, Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Simon H P Sung
- Department of Chemical and Biological Engineering, Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Zhiyang Liu
- Department of Chemical and Biological Engineering, Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Junkai Liu
- Department of Chemical and Biological Engineering, Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Ryan T K Kwok
- HKUST-Shenzhen Research Institute No. 9 Yuexing 1st RD, South Area, Hi-tech Park, Nanshan Shenzhen 518057 China
- Department of Chemical and Biological Engineering, Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Jacky W Y Lam
- Department of Chemical and Biological Engineering, Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Wen-Xiong Wang
- HKUST-Shenzhen Research Institute No. 9 Yuexing 1st RD, South Area, Hi-tech Park, Nanshan Shenzhen 518057 China
- School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong Kowloon Hong Kong China
| | - Herman H-Y Sung
- Department of Chemical and Biological Engineering, Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Ian D Williams
- Department of Chemical and Biological Engineering, Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
| | - Ben Zhong Tang
- HKUST-Shenzhen Research Institute No. 9 Yuexing 1st RD, South Area, Hi-tech Park, Nanshan Shenzhen 518057 China
- Department of Chemical and Biological Engineering, Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong China
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institute Hong Kong China
- Centre for Aggregation-Induced Emission, SCUT-HKUST Joint Research Laboratory, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology Guangzhou 510640 China
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33
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Lizák B, Szarka A, Kim Y, Choi KS, Németh CE, Marcolongo P, Benedetti A, Bánhegyi G, Margittai É. Glucose Transport and Transporters in the Endomembranes. Int J Mol Sci 2019; 20:ijms20235898. [PMID: 31771288 PMCID: PMC6929180 DOI: 10.3390/ijms20235898] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/16/2019] [Accepted: 11/21/2019] [Indexed: 12/18/2022] Open
Abstract
Glucose is a basic nutrient in most of the creatures; its transport through biological membranes is an absolute requirement of life. This role is fulfilled by glucose transporters, mediating the transport of glucose by facilitated diffusion or by secondary active transport. GLUT (glucose transporter) or SLC2A (Solute carrier 2A) families represent the main glucose transporters in mammalian cells, originally described as plasma membrane transporters. Glucose transport through intracellular membranes has not been elucidated yet; however, glucose is formed in the lumen of various organelles. The glucose-6-phosphatase system catalyzing the last common step of gluconeogenesis and glycogenolysis generates glucose within the lumen of the endoplasmic reticulum. Posttranslational processing of the oligosaccharide moiety of glycoproteins also results in intraluminal glucose formation in the endoplasmic reticulum (ER) and Golgi. Autophagic degradation of polysaccharides, glycoproteins, and glycolipids leads to glucose accumulation in lysosomes. Despite the obvious necessity, the mechanism of glucose transport and the molecular nature of mediating proteins in the endomembranes have been hardly elucidated for the last few years. However, recent studies revealed the intracellular localization and functional features of some glucose transporters; the aim of the present paper was to summarize the collected knowledge.
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Affiliation(s)
- Beáta Lizák
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 1094 Budapest, Hungary; (B.L.); (C.E.N.); (G.B.)
| | - András Szarka
- Laboratory of Biochemistry and Molecular Biology, Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, 1111 Budapest, Hungary;
| | - Yejin Kim
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary; (Y.K.); (K.-s.C.)
| | - Kyu-sung Choi
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary; (Y.K.); (K.-s.C.)
| | - Csilla E. Németh
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 1094 Budapest, Hungary; (B.L.); (C.E.N.); (G.B.)
| | - Paola Marcolongo
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (P.M.); (A.B.)
| | - Angelo Benedetti
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (P.M.); (A.B.)
| | - Gábor Bánhegyi
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 1094 Budapest, Hungary; (B.L.); (C.E.N.); (G.B.)
| | - Éva Margittai
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary; (Y.K.); (K.-s.C.)
- Correspondence: ; Tel.: +36-459-1500 (ext. 60311); Fax: +36-1-2662615
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34
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Nakano Y. Stories of spinster with various faces: from courtship rejection to tumor metastasis rejection. J Neurogenet 2019; 33:90-95. [PMID: 30939968 DOI: 10.1080/01677063.2019.1586897] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Drosophila spinster (spin) mutant was isolated as a mutant that showed abnormal morphology and function in the nervous system. The spin defect induces neural degeneration similar to human lysosomal storage diseases. Various studies have shown that Spin proteins are localized in lysosomes and participate in the late stages of the autophagic process. Vertebrates have three spinster orthologs, Spns1, Spns2, and Spns3. A defect in Spns1 caused a short lifespan with aberrant lysosomal function in zebrafish. Spns2 was originally isolated as the gene responsible for abnormal heart development and was identified as a sphingosine 1-phosphate transporter in zebrafish. An endothelial cell-specific defect in Spns2 resulted in impaired egress of lymphocytes and the prevention of tumor metastasis in mice. Herein, I reviewed the history of spin/Spns research and discussed the conserved and newly diverged spin/Spns function and possible implications for human diseases.
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Affiliation(s)
- Yoshiro Nakano
- a Department of Genetics , Hyogo College of Medicine , Nishinomiya , Japan
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35
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Biological function of SPNS2: From zebrafish to human. Mol Immunol 2018; 103:55-62. [DOI: 10.1016/j.molimm.2018.08.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/20/2018] [Accepted: 08/23/2018] [Indexed: 01/01/2023]
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36
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Lopez A, Fleming A, Rubinsztein DC. Seeing is believing: methods to monitor vertebrate autophagy in vivo. Open Biol 2018; 8:rsob.180106. [PMID: 30355753 PMCID: PMC6223212 DOI: 10.1098/rsob.180106] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/25/2018] [Indexed: 02/06/2023] Open
Abstract
Autophagy is an intracellular clearance pathway that delivers cytoplasmic contents to the lysosome for degradation. It plays a critical role in maintaining protein homeostasis and providing nutrients under conditions where the cell is starved. It also helps to remove damaged organelles and misfolded or aggregated proteins. Thus, it is not surprising that defects in this pathway are associated with a variety of pathological conditions, such as neurodegeneration, cancer and infection. Pharmacological upregulation of autophagy is considered a promising therapeutic strategy for the treatment of neurodegenerative and infectious diseases. Studies in knockout mice have demonstrated that autophagy is essential for nervous system function, and data from invertebrate and vertebrate models suggest that the efficiency of autophagic processes generally declines with age. However, much of our understanding of the intracellular regulation of autophagy comes from in vitro studies, and there is a paucity of knowledge about how this process is regulated within different tissues and during the processes of ageing and disease. Here, we review the available tools to probe these questions in vivo within vertebrate model systems. We discuss how these tools have been used to date and consider future avenues of research.
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Affiliation(s)
- Ana Lopez
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Angeleen Fleming
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - David C Rubinsztein
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK .,UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
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37
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Hammoudi PM, Maco B, Dogga SK, Frénal K, Soldati-Favre D. Toxoplasma gondiiTFP1 is an essential transporter family protein critical for microneme maturation and exocytosis. Mol Microbiol 2018; 109:225-244. [DOI: 10.1111/mmi.13981] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Pierre-Mehdi Hammoudi
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine; University of Geneva, 1 Rue Michel-Servet; Geneva 1206 Switzerland
| | - Bohumil Maco
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine; University of Geneva, 1 Rue Michel-Servet; Geneva 1206 Switzerland
| | - Sunil Kumar Dogga
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine; University of Geneva, 1 Rue Michel-Servet; Geneva 1206 Switzerland
| | - Karine Frénal
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine; University of Geneva, 1 Rue Michel-Servet; Geneva 1206 Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine; University of Geneva, 1 Rue Michel-Servet; Geneva 1206 Switzerland
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38
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Yanagisawa H, Ishii T, Endo K, Kawakami E, Nagao K, Miyashita T, Akiyama K, Watabe K, Komatsu M, Yamamoto D, Eto Y. L-leucine and SPNS1 coordinately ameliorate dysfunction of autophagy in mouse and human Niemann-Pick type C disease. Sci Rep 2017; 7:15944. [PMID: 29162837 PMCID: PMC5698481 DOI: 10.1038/s41598-017-15305-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 10/24/2017] [Indexed: 12/25/2022] Open
Abstract
Lysosomal storage disorders are characterized by progressive accumulation of undigested macromolecules within the cell due to lysosomal dysfunction. 573C10 is a Schwann cell line derived from a mouse model of Niemann-Pick type C disease-1, NPC (−/−). Under serum-starved conditions, NPC (−/−) cells manifested impaired autophagy accompanied by an increase in the amount of p62 and lysosome enlargement. Addition of L-leucine to serum-starved NPC (−/−) cells ameliorated the enlargement of lysosomes and the p62 accumulation. Similar autophagy defects were observed in NPC (−/−) cells even without serum starvation upon the knockdown of Spinster-like 1 (SPNS1), a putative transporter protein thought to function in lysosomal recycling. Conversely, SPNS1 overexpression impeded the enlargement of lysosomes, p62 accumulation and mislocalization of the phosphorylated form of the mechanistic Target of rapamycin in NPC (−/−) cells. In addition, we found a reduction in endogenous SPNS1 expression in fibroblasts derived from NPC-1 patients compared with normal fibroblasts. We propose that SPNS1-dependent L-leucine export across the lysosomal membrane is a key step for triggering autophagy, and that this mechanism is impaired in NPC-1.
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Affiliation(s)
- Hiroko Yanagisawa
- Advanced Clinical Research Center, Institute for Neurological Disorders, Kawasaki, Japan.
| | - Tomohiro Ishii
- Division of Pharmacology, Faculty of Pharmacy, Keio University, Tokyo, Japan
| | - Kentaro Endo
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Emiko Kawakami
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kazuaki Nagao
- Department of Molecular Genetics, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan
| | - Toshiyuki Miyashita
- Department of Molecular Genetics, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan
| | - Keiko Akiyama
- Advanced Clinical Research Center, Institute for Neurological Disorders, Kawasaki, Japan
| | - Kazuhiko Watabe
- Department of Medical Technology, Faculty of Health Sciences, Kyorin University, Tokyo, Japan
| | - Masaaki Komatsu
- Department of Biochemistry, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Daisuke Yamamoto
- Division of Neurogenetics, Graduate School of Life Science, Tohoku University, Sendai, Japan
| | - Yoshikatsu Eto
- Advanced Clinical Research Center, Institute for Neurological Disorders, Kawasaki, Japan.
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39
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Mathai BJ, Meijer AH, Simonsen A. Studying Autophagy in Zebrafish. Cells 2017; 6:E21. [PMID: 28698482 PMCID: PMC5617967 DOI: 10.3390/cells6030021] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/01/2017] [Accepted: 07/03/2017] [Indexed: 12/26/2022] Open
Abstract
Autophagy is an evolutionarily conserved catabolic process which allows lysosomal degradation of complex cytoplasmic components into basic biomolecules that are recycled for further cellular use. Autophagy is critical for cellular homeostasis and for degradation of misfolded proteins and damaged organelles as well as intracellular pathogens. The role of autophagy in protection against age-related diseases and a plethora of other diseases is now coming to light; assisted by several divergent eukaryotic model systems ranging from yeast to mice. We here give an overview of different methods used to analyse autophagy in zebrafish-a relatively new model for studying autophagy-and briefly discuss what has been done so far and possible future directions.
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Affiliation(s)
- Benan John Mathai
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Sognsvannsveien 9, 0317 Oslo, Norway.
| | - Annemarie H Meijer
- Institute of Biology Leiden, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Sognsvannsveien 9, 0317 Oslo, Norway.
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40
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Cui J, Chew SJL, Shi Y, Gong Z, Shen HM. CRISPR system for genome engineering: the application for autophagy study. BMB Rep 2017; 50:247-256. [PMID: 28288698 PMCID: PMC5458674 DOI: 10.5483/bmbrep.2017.50.5.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Indexed: 11/20/2022] Open
Abstract
CRISPR/Cas9 is the latest tool introduced in the field of genome engineering and is so far the best genome-editing tool as compared to its precedents such as, meganucleases, zinc finger nucleases (ZFNs) and transcription activator-like effectors (TALENs). The simple design and assembly of the CRISPR/Cas9 system makes genome editing easy to perform as it uses small guide RNAs that correspond to their DNA targets for high efficiency editing. This has helped open the doors for multiplexible genome targeting in many species that were intractable using old genetic perturbation techniques. Currently, The CRISPR system is revolutionizing the way biological researches are conducted and paves a bright future not only in research but also in medicine and biotechnology. In this review, we evaluated the history, types and structure, the mechanism of action of CRISPR/Cas System. In particular, we focused on the application of this powerful tool in autophagy research. [BMB Reports 2017; 50(5): 247-256].
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Affiliation(s)
- Jianzhou Cui
- Department of Physiology, Yong Loo Lin School of Medicine, National University of
Singapore
| | - Shirley Jia Li Chew
- Department of Physiology, Yong Loo Lin School of Medicine, National University of
Singapore
| | - Yin Shi
- Department of Physiology, Yong Loo Lin School of Medicine, National University of
Singapore
| | - Zhiyuan Gong
- Department of Biological Sciences, National University of
Singapore
| | - Han-Ming Shen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of
Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore,
Singapore
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