99951
|
Shindo Y, Brown MG, Amodeo AA. Versatile roles for histones in early development. Curr Opin Cell Biol 2022; 75:102069. [PMID: 35279563 PMCID: PMC9064922 DOI: 10.1016/j.ceb.2022.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/30/2022] [Accepted: 02/04/2022] [Indexed: 11/28/2022]
Abstract
The nuclear environment changes dramatically over the course of early development. Histones are core chromatin components that play critical roles in regulating gene expression and nuclear architecture. Additionally, the embryos of many species, including Drosophila, Zebrafish, and Xenopus use the availability of maternally deposited histones to time critical early embryonic events including cell cycle slowing and zygotic genome activation. Here, we review recent insights into how histones control early development. We first discuss the regulation of chromatin functions through interaction of histones and transcription factors, incorporation of variant histones, and histone post-translational modifications. We also highlight emerging roles for histones as developmental regulators independent of chromatin association.
Collapse
Affiliation(s)
- Yuki Shindo
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
| | - Madeleine G Brown
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Amanda A Amodeo
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
| |
Collapse
|
99952
|
Cantrell JM, Chung CH, Chandrasekaran S. Machine learning to design antimicrobial combination therapies: promises and pitfalls. Drug Discov Today 2022; 27:1639-1651. [DOI: 10.1016/j.drudis.2022.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/20/2022] [Accepted: 04/04/2022] [Indexed: 01/13/2023]
|
99953
|
Schiano Lomoriello I, Sigismund S, Day KJ. Biophysics of endocytic vesicle formation: A focus on liquid–liquid phase separation. Curr Opin Cell Biol 2022; 75:102068. [DOI: 10.1016/j.ceb.2022.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 02/07/2023]
|
99954
|
Singh H, Kumar R, Mazumder A, Salahuddin, Mazumder R, Abdullah MM. Insights into Interactions of Human Cytochrome P450 17A1: Review. Curr Drug Metab 2022; 23:172-187. [DOI: 10.2174/1389200223666220401093833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/15/2022] [Accepted: 02/04/2022] [Indexed: 11/22/2022]
Abstract
Abstract:
Cytochrome P450s are a widespread and vast superfamily of hemeprotein monooxygenases that metabolize physiologically essential chemicals necessary for most species' survival, from protists to plants to humans. They catalyze the synthesis of steroid hormones, cholesterol, bile acids, and arachidonate metabolites and the degradation of endogenous compounds such as steroids, fatty acids, and other catabolizing compounds as an energy source and detoxifying xenobiotics such as drugs, procarcinogens, and carcinogens. The human CYP17A1 is one of the cytochrome P450 genes located at the 10q chromosome. The gene expression occurs in the adrenals and gonads, with minor amounts in the brain, placenta, and heart. This P450c17 cytochrome gene is a critical steroidogenesis regulator which performs two distinct activities: 17 alpha-hydroxylase activity (converting pregnenolone to 17-hydroxypregnenolone and progesterone to 17-hydroxyprogesterone, these precursors are further processed to provide glucocorticoids and sex hormones) and 17, 20-lyase activity (which converts 17-hydroxypregnenolone to DHEA). Dozens of mutations within CYP17A1 are found to cause 17-alpha-hydroxylase and 17, 20-lyase deficiency. This condition affects the function of certain hormone-producing glands, resulting in high blood pressure levels (hypertension), abnormal sexual development, and other deficiency diseases. This review highlights the changes in CYP17A1 associated with gene-gene interaction, drug-gene interaction, chemical-gene interaction, and its biochemical reactions; they have some insights to correlate with the fascinating functional characteristics of this human steroidogenic gene. The findings of our theoretical results will be helpful to further the design of specific inhibitors of CYP17A1.
Collapse
Affiliation(s)
- Himanshu Singh
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, India
| | - Rajnish Kumar
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, India
| | - Avijit Mazumder
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, India
| | - Salahuddin
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, India
| | - Rupa Mazumder
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, India
| | | |
Collapse
|
99955
|
Kumar N, Ghosh M, Manikandan P, Basak S, Deepa A, Singh M. Resonance assignment and secondary structure of the tandem harmonin homology domains of human RTEL1. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:159-164. [PMID: 35320499 DOI: 10.1007/s12104-022-10074-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Regulator of telomere elongation helicase 1 (RTEL1) is an Fe-S cluster containing DNA helicase that plays important roles in telomere DNA maintenance, DNA repair, and genomic stability. It is a modular protein comprising an N-terminal helicase domain, two tandem harmonin homology domains 1 & 2 (HHD1 and HHD2), and a C-terminal C4C4 type RING domain. The N-terminal helicase domain disassembles the telomere t/D-loop and unwinds the G-quadruplex via its helicase activity. The C-terminal RING domain interacts with telomere DNA binding protein TRF2 and helps RTEL1 recruitment to the telomere. The tandem HHD1 and HHD2 are characterized as a putative protein-protein interaction domain and have recently been shown to interact with a DNA repair protein SLX4. Several mutations associated with Hoyeraal-Hreidarsson syndrome and pulmonary fibrosis have been found in HHD1 and HHD2 of RTEL1. However, these domains have not been characterized for their structures. We have expressed and purified HHD1 and HHD2 of human RTEL1 for their characterization using solution NMR spectroscopy. Here, we report near complete backbone and sidechain 1H, 13C and 15N chemical shift assignments and secondary structure of the HHD1 and HHD2 domains of human RTEL1.
Collapse
Affiliation(s)
- Niranjan Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, 560012, India
| | - Meenakshi Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, 560012, India
| | | | - Sanmoyee Basak
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, 560012, India
| | - Akula Deepa
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, 560012, India
- Indian Institute of Technology, Hyderabad, 502285, India
| | - Mahavir Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, 560012, India.
| |
Collapse
|
99956
|
Zhang DG, Xu XJ, Pantopoulos K, Zhao T, Zheng H, Luo Z. HSF1-SELENOS pathway mediated dietary inorganic Se-induced lipogenesis via the up-regulation of PPARγ expression in yellow catfish. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194802. [PMID: 35248747 DOI: 10.1016/j.bbagrm.2022.194802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 02/08/2023]
Abstract
At present, studies involved in the effects of dietary Se sources on lipid metabolism were very scarce and the underlying mechanism remains unknown. Previous studies reported that dietary Se sources differentially affected selenoprotein S (SELENOS) expression and SELENOS affected lipid metabolism via the inositol-requiring enzyme 1α (IRE1α)- spliced X-box binding protein 1 (XBP1s) pathway. Thus, we used yellow catfish as an experimental model to explore whether dietary selenium sources affected the hepatic lipid metabolism, and further determined the role of SELENOS-IRE1α-XBP1s pathway in dietary selenium sources affecting hepatic lipid metabolism. Compared with the selenomethionine (S-M) group, sodium selenite (SS) group possessed higher liver triglycerides (TGs) (34.7%), lipogenic enzyme activities (57.9-70.6%), and lower antioxidant enzyme activities (23.3-35.5%), increased protein levels of heat shock transcription factor 1 (HSF1) and SELENOS (1.17-fold and 47.4%, respectively), and XBP1s- peroxisome proliferators-activated receptor γ (PPARγ) pathway. Blocking SELENOS and PPARγ by RNA interference demonstrated that the SELENOS/XBP1s/PPARγ axis was critical for S-S-induced lipid accumulation. Moreover, S-S-induced upregulation of SELENOS was via the increased DNA binding capacity of HSF1 to SELENOS promoter, which activated the XBP1s/PPARγ pathway and promoted lipogenesis and lipid accumulation. XBP1s is required for S-S-induced upregulation of PPARγ expression. Our finding elucidated the mechanism of dietary Se sources affecting the lipid metabolism in the liver of yellow catfish and demonstrated novel function of SELENOS in metabolic regulation. Our study also suggested that seleno-methionine was a better Se source than selenite against abnormal lipid deposition in the liver of yellow catfish.
Collapse
Affiliation(s)
- Dian-Guang Zhang
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agriculture University, Wuhan 430070, China
| | - Xiao-Jian Xu
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agriculture University, Wuhan 430070, China
| | - Kostas Pantopoulos
- Lady Davis Institute for Medical Research, Department of Medicine, McGill University, Montreal H3T 1E2, Quebec, Canada
| | - Tao Zhao
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agriculture University, Wuhan 430070, China
| | - Hua Zheng
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agriculture University, Wuhan 430070, China
| | - Zhi Luo
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agriculture University, Wuhan 430070, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| |
Collapse
|
99957
|
Firoz A, Talwar P. COVID-19 and Retinal Degenerative Diseases: Promising link “Kaempferol”. Curr Opin Pharmacol 2022; 64:102231. [PMID: 35544976 PMCID: PMC9080119 DOI: 10.1016/j.coph.2022.102231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/10/2022] [Accepted: 03/24/2022] [Indexed: 01/18/2023]
Abstract
Coronavirus disease (COVID-19) outbreak has caused unprecedented global disruption since 2020. Approximately 238 million people are affected worldwide where the elderly succumb to mortality. Post-COVID syndrome and its side effects have popped up with several health hazards, such as macular degeneration and vision loss. It thus necessitates better medical care and management of our dietary practices. Natural flavonoids have been included in traditional medicine and have also been used safely against COVID-19 and several other diseases. Kaempferol is an essential flavonoid that has been demonstrated to influence several vital cellular signaling pathways involved in apoptosis, angiogenesis, inflammation, and autophagy. In this review, we emphasize the plausible regulatory effects of Kaempferol on hallmarks of COVID-19 and macular degeneration.
Collapse
|
99958
|
Piccirillo S, Morgan AP, Leon AY, Smith AL, Honigberg SM. Investigating cell autonomy in microorganisms. Curr Genet 2022; 68:305-318. [PMID: 35119506 PMCID: PMC9101301 DOI: 10.1007/s00294-022-01231-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/04/2022] [Accepted: 01/18/2022] [Indexed: 11/28/2022]
Abstract
Cell-cell signaling in microorganisms is still poorly characterized. In this Methods paper, we describe a genetic procedure for detecting cell-nonautonomous genetic effects, and in particular cell-cell signaling, termed the chimeric colony assay (CCA). The CCA measures the effect of a gene on a biological response in a neighboring cell. This assay can measure cell autonomy for range of biological activities including transcript or protein accumulation, subcellular localization, and cell differentiation. To date, the CCA has been used exclusively to investigate colony patterning in the budding yeast Saccharomyces cerevisiae. To demonstrate the wider potential of the assay, we applied this assay to two other systems: the effect of Grr1 on glucose repression of GAL1 transcription in yeast and the effect of rpsL on stop-codon translational readthrough in Escherichia coli. We also describe variations of the standard CCA that address specific aspects of cell-cell signaling, and we delineate essential controls for this assay. Finally, we discuss complementary approaches to the CCA. Taken together, this Methods paper demonstrates how genetic assays can reveal and explore the roles of cell-cell signaling in microbial processes.
Collapse
Affiliation(s)
- Sarah Piccirillo
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Andrew P. Morgan
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Andy Y. Leon
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Annika L. Smith
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Saul M. Honigberg
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| |
Collapse
|
99959
|
Second MAFA Variant Causing a Phosphorylation Defect in the Transactivation Domain and Familial Insulinomatosis. Cancers (Basel) 2022; 14:cancers14071798. [PMID: 35406570 PMCID: PMC8997416 DOI: 10.3390/cancers14071798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 12/21/2022] Open
Abstract
Adult-onset familial insulinomatosis is a rare disorder with recurrent, severe hypoglycemia caused by multiple insulin-secreting pancreatic tumors. The etiology was unclear until the variant p.Ser64Phe in the transcription factor MAFA, a key coordinator of β-cell insulin secretion, was defined as the cause in two families. We here describe detailed genetic, clinical, and family analyses of two sisters with insulinomatosis, aiming to identify further disease causes. Using exome sequencing, we detected a novel, heterozygous missense variant, p.Thr57Arg, in MAFA’s highly conserved transactivation domain. The impact of the affected region is so crucial that in vitro expression studies replacing Thr57 have already been performed, demonstrating a phosphorylation defect with the impairment of transactivation activity and degradation. However, prior to our study, the link to human disease was missing. Furthermore, mild hyperglycemia was observed in six additional, heterozygote family members, indicating that not only insulinomatosis but also MODY-like symptoms co-segregate with p.Thr57Arg. The pre-described MAFA variant, p.Ser64Phe, is located in the same domain, impairs the same phosphorylation cascade, and results in the same symptoms. We confirm MAFA phosphorylation defects are important causes of a characteristic syndrome, thus complementing the pathophysiological and diagnostic disease concept. Additionally, we verify the high penetrance and autosomal dominant inheritance pattern.
Collapse
|
99960
|
Li Z, Xu J, Guan H, Lai J, Yang X, Ma J. Circ_0059354 aggravates the progression of papillary thyroid carcinoma by elevating ARFGEF1 through sponging miR-766-3p. J Endocrinol Invest 2022; 45:825-836. [PMID: 34854069 DOI: 10.1007/s40618-021-01713-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 11/19/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Circular RNAs (circRNAs) have been identified as vital players in tumors, including papillary thyroid carcinoma (PTC). The purpose of this study is to explore the functions of circ_0059354 on PTC development. METHODS Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to examine the levels of circ_0059354, microRNA-766-3p (miR-766-3p) and ADP ribosylation factor guanine nucleotide exchange factor 1 (ARFGEF1). Cell Counting Kit-8 (CCK-8) assay and colony formation assay were proceeded for cell proliferation ability. Transwell assay was conducted for cell migration and invasion. Tube formation assay was employed to examine the angiogenesis ability. Flow cytometry analysis was adopted for cell apoptosis. Western blot assay was conducted for protein levels. Dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay were utilized to verify the relationships among circ_0059354, miR-766-3p and ARFGEF1. The murine xenograft model was constructed to analyze the function of circ_0059354 in vivo. RESULTS Circ_0059354 level was abnormally increased in PTC tissues and cells. Functionally, circ_0059354 silencing suppressed cell proliferation, migration, invasion and angiogenesis and facilitated apoptosis in PTC cells. Circ_0059354 was identified to sponge miR-766-3p, which directly targeted ARFGEF1. Moreover, circ_0059354 directly targeted miR-766-3p to positively regulated ARFGEF1 expression. MiR-766-3p inhibition reversed circ_0059354 knockdown-mediated effect of PTC cell malignant behaviors. Overexpression of miR-766-3p restrained the malignant behaviors of PTC cells, whereas ARFGEF1 elevation reversed the effects. Additionally, circ_0059354 deficiency blocked tumor growth in vivo. CONCLUSION Circ_0059354 served as an oncogene in PTC progression through regulating miR-766-3p/ARFGEF1 axis.
Collapse
Affiliation(s)
- Z Li
- Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xi'an, 710004, Shaanxi, China
| | - J Xu
- Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xi'an, 710004, Shaanxi, China
| | - H Guan
- Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xi'an, 710004, Shaanxi, China
| | - J Lai
- Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xi'an, 710004, Shaanxi, China
| | - X Yang
- Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xi'an, 710004, Shaanxi, China
| | - J Ma
- Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xi'an, 710004, Shaanxi, China.
| |
Collapse
|
99961
|
Wang H, Gan C, Luo X, Dong C, Zhou S, Xiong Q, Weng Q, Hu X, Du X, Zhu B. Complete chloroplast genome features of the model heavy metal hyperaccumulator Arabis paniculata Franch and its phylogenetic relationships with other Brassicaceae species. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:775-789. [PMID: 35592481 PMCID: PMC9110617 DOI: 10.1007/s12298-022-01151-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/28/2021] [Accepted: 02/17/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED Arabis paniculata Franch (Brassicaceae) has been widely used for the phytoremediation of heavy mental, owing to its hyper tolerance of extreme Pb, Zn, and Cd concentrations. However, studies on its genome or plastid genome are scarce. In the present study, we obtained the complete chloroplast (cp) genome of A. paniculata via de novo assembly through the integration of Illumina reads and PacBio subreads. The cp genome presents a typical quadripartite cycle with a length of 153,541 bp, and contains 111 unigenes, with 79 protein-coding genes, 28 tRNAs and 4 rRNAs. Codon usage analysis showed that the codons for leucine were the most frequent codons and preferentially ended with A/U. Synonymous (Ks) and non-synonymous (Ka) substitution rate analysis indicated that the unigenes, ndhF and rpoC2, related to "NADH-dehydrogenase" and "RNA polymerase" respectively, underwent the lowest purifying selection pressure. Phylogenetic analysis demonstrated that Arabis flagellosa and A. hirsuta are more similar to each other than to A. paniculata, and Arabis is the closest relative of Draba among all Brassicaceae genera. These findings provide valuable information for the optimal exploitation of this model species as a heavy-metal hyperaccumulator. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01151-1.
Collapse
Affiliation(s)
- Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Chenchen Gan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Xi Luo
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Changyu Dong
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Shijun Zhou
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Qin Xiong
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Xin Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A&F University, Lin’an Hangzhou, People’s Republic of China
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025 People’s Republic of China
| |
Collapse
|
99962
|
Cao X, Boyaci H, Chen J, Bao Y, Landick R, Campbell EA. Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile. Nature 2022; 604:541-545. [PMID: 35388215 PMCID: PMC9635844 DOI: 10.1038/s41586-022-04545-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 02/10/2022] [Indexed: 01/12/2023]
Abstract
Fidaxomicin (Fdx) is widely used to treat Clostridioides difficile (Cdiff) infections, but the molecular basis of its narrow-spectrum activity in the human gut microbiome remains unknown. Cdiff infections are a leading cause of nosocomial deaths1. Fidaxomicin, which inhibits RNA polymerase, targets Cdiff with minimal effects on gut commensals, reducing recurrence of Cdiff infection2,3. Here we present the cryo-electron microscopy structure of Cdiff RNA polymerase in complex with fidaxomicin and identify a crucial fidaxomicin-binding determinant of Cdiff RNA polymerase that is absent in most gut microbiota such as Proteobacteria and Bacteroidetes. By combining structural, biochemical, genetic and bioinformatic analyses, we establish that a single residue in Cdiff RNA polymerase is a sensitizing element for fidaxomicin narrow-spectrum activity. Our results provide a blueprint for targeted drug design against an important human pathogen.
Collapse
Affiliation(s)
- Xinyun Cao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Hande Boyaci
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, United States
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, United States
| | - Yu Bao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, United States.
| |
Collapse
|
99963
|
Zhao X, Di Q, Liu H, Quan J, Ling J, Zhao Z, Xiao Y, Wu H, Wu Z, Song W, An H, Chen W. MEF2C promotes M1 macrophage polarization and Th1 responses. Cell Mol Immunol 2022; 19:540-553. [PMID: 35194174 PMCID: PMC8975968 DOI: 10.1038/s41423-022-00841-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/25/2022] [Indexed: 12/11/2022] Open
Abstract
The polarization of macrophages to the M1 or M2 phenotype has a pivotal role in inflammation and host defense; however, the underlying molecular mechanism remains unclear. Here, we show that myocyte enhancer factor 2 C (MEF2C) is essential for regulating M1 macrophage polarization in response to infection and inflammation. Global gene expression analysis demonstrated that MEF2C deficiency in macrophages downregulated the expression of M1 phenotypic markers and upregulated the expression of M2 phenotypic markers. MEF2C significantly promoted the expression of interleukin-12 p35 subunit (Il12a) and interleukin-12 p40 subunit (Il12b). Myeloid-specific Mef2c-knockout mice showed reduced IL-12 production and impaired Th1 responses, which led to susceptibility to Listeria monocytogenes infection and protected against DSS-induced IBD in vivo. Mechanistically, we showed that MEF2C directly activated the transcription of Il12a and Il12b. These findings reveal a new function of MEF2C in macrophage polarization and Th1 responses and identify MEF2C as a potential target for therapeutic intervention in inflammatory and autoimmune diseases.
Collapse
Affiliation(s)
- Xibao Zhao
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, 518060, China
| | - Qianqian Di
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, 518060, China
| | - Han Liu
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Jiazheng Quan
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, 518060, China
| | - Jing Ling
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Zizhao Zhao
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yue Xiao
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, 518060, China
| | - Han Wu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, 518060, China
| | - Zherui Wu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, 518060, China
| | - Wengang Song
- Shandong Provincial Key Laboratory for Rheumatic Disease and Translational Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jingshi Road 16766, Jinan, Shandong, 250014, China
| | - Huazhang An
- Shandong Provincial Key Laboratory for Rheumatic Disease and Translational Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jingshi Road 16766, Jinan, Shandong, 250014, China.
| | - Weilin Chen
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, 518060, China.
| |
Collapse
|
99964
|
Yokoi K, Yamaguchi K, Umezawa M, Tsuchiya K, Aoki S. Induction of Paraptosis by Cyclometalated Iridium Complex-Peptide Hybrids and CGP37157 via a Mitochondrial Ca 2+ Overload Triggered by Membrane Fusion between Mitochondria and the Endoplasmic Reticulum. Biochemistry 2022; 61:639-655. [PMID: 35363482 PMCID: PMC9022229 DOI: 10.1021/acs.biochem.2c00061] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We previously reported that a cyclometalated iridium (Ir) complex-peptide hybrid (IPH) 4 functionalized with a cationic KKKGG peptide unit on the 2-phenylpyridine ligand induces paraptosis, a relatively newly found programmed cell death, in cancer cells (Jurkat cells) via the direct transport of calcium (Ca2+) from the endoplasmic reticulum (ER) to mitochondria. Here, we describe that CGP37157, an inhibitor of a mitochondrial sodium (Na+)/Ca2+ exchanger, induces paraptosis in Jurkat cells via intracellular pathways similar to those induced by 4. The findings allow us to suggest that the induction of paraptosis by 4 and CGP37157 is associated with membrane fusion between mitochondria and the ER, subsequent Ca2+ influx from the ER to mitochondria, and a decrease in the mitochondrial membrane potential (ΔΨm). On the contrary, celastrol, a naturally occurring triterpenoid that had been reported as a paraptosis inducer in cancer cells, negligibly induces mitochondria-ER membrane fusion. Consequently, we conclude that the paraptosis induced by 4 and CGP37157 (termed paraptosis II herein) proceeds via a signaling pathway different from that of the previously known paraptosis induced by celastrol, a process that negligibly involves membrane fusion between mitochondria and the ER (termed paraptosis I herein).
Collapse
Affiliation(s)
- Kenta Yokoi
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kohei Yamaguchi
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Masakazu Umezawa
- Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Koji Tsuchiya
- Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Shin Aoki
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.,Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.,Research Institute for Biomedical Science (RIBS), Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| |
Collapse
|
99965
|
Esfahani MS, Hamilton EG, Mehrmohamadi M, Nabet BY, Alig SK, King DA, Steen CB, Macaulay CW, Schultz A, Nesselbush MC, Soo J, Schroers-Martin JG, Chen B, Binkley MS, Stehr H, Chabon JJ, Sworder BJ, Hui ABY, Frank MJ, Moding EJ, Liu CL, Newman AM, Isbell JM, Rudin CM, Li BT, Kurtz DM, Diehn M, Alizadeh AA. Inferring gene expression from cell-free DNA fragmentation profiles. Nat Biotechnol 2022; 40:585-597. [PMID: 35361996 PMCID: PMC9337986 DOI: 10.1038/s41587-022-01222-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 01/14/2022] [Indexed: 02/07/2023]
Abstract
Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles from cell-free DNA (cfDNA), but current fragmentomic methods require high concentrations of tumor-derived DNA and provide limited resolution. Here we describe promoter fragmentation entropy as an epigenomic cfDNA feature that predicts RNA expression levels at individual genes. We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification of subtypes of lung carcinoma and diffuse large B cell lymphoma. Applying EPIC-seq to serial blood samples from patients treated with PD-(L)1 immune-checkpoint inhibitors, we show that gene expression profiles inferred by EPIC-seq are correlated with clinical response. Our results indicate that EPIC-seq could enable noninvasive, high-throughput tissue-of-origin characterization with diagnostic, prognostic and therapeutic potential.
Collapse
Affiliation(s)
- Mohammad Shahrokh Esfahani
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Emily G. Hamilton
- Program in Cancer Biology, Stanford School of Medicine, Stanford, CA, USA
| | - Mahya Mehrmohamadi
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Barzin Y. Nabet
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Stefan K. Alig
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Daniel A. King
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Chloé B. Steen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - Charles W. Macaulay
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Andre Schultz
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | | | - Joanne Soo
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Joseph G. Schroers-Martin
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Binbin Chen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Michael S. Binkley
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Jacob J. Chabon
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Brian J. Sworder
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Angela B-Y Hui
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Matthew J. Frank
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Everett J. Moding
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Chih Long Liu
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - James M. Isbell
- Thoracic Surgery Service, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY, USA
| | - Charles M. Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T. Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M. Kurtz
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
| | - Ash A. Alizadeh
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
| |
Collapse
|
99966
|
Robbe ZL, Shi W, Wasson LK, Scialdone AP, Wilczewski CM, Sheng X, Hepperla AJ, Akerberg BN, Pu WT, Cristea IM, Davis IJ, Conlon FL. CHD4 is recruited by GATA4 and NKX2-5 to repress noncardiac gene programs in the developing heart. Genes Dev 2022; 36:468-482. [PMID: 35450884 PMCID: PMC9067406 DOI: 10.1101/gad.349154.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/31/2022] [Indexed: 12/23/2022]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is one of the central chromatin remodeling complexes that mediates gene repression. NuRD is essential for numerous developmental events, including heart development. Clinical and genetic studies have provided direct evidence for the role of chromodomain helicase DNA-binding protein 4 (CHD4), the catalytic component of NuRD, in congenital heart disease (CHD), including atrial and ventricular septal defects. Furthermore, it has been demonstrated that CHD4 is essential for mammalian cardiomyocyte formation and function. A key unresolved question is how CHD4/NuRD is localized to specific cardiac target genes, as neither CHD4 nor NuRD can directly bind DNA. Here, we coupled a bioinformatics-based approach with mass spectrometry analyses to demonstrate that CHD4 interacts with the core cardiac transcription factors GATA4, NKX2-5, and TBX5 during embryonic heart development. Using transcriptomics and genome-wide occupancy data, we characterized the genomic landscape of GATA4, NKX2-5, and TBX5 repression and defined the direct cardiac gene targets of the GATA4-CHD4, NKX2-5-CHD4, and TBX5-CHD4 complexes. These data were used to identify putative cis-regulatory elements controlled by these complexes. We genetically interrogated two of these silencers in vivo: Acta1 and Myh11 We show that deletion of these silencers leads to inappropriate skeletal and smooth muscle gene misexpression, respectively, in the embryonic heart. These results delineate how CHD4/NuRD is localized to specific cardiac loci and explicates how mutations in the broadly expressed CHD4 protein lead to cardiac-specific disease states.
Collapse
Affiliation(s)
- Zachary L Robbe
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Wei Shi
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Lauren K Wasson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Angel P Scialdone
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Caralynn M Wilczewski
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Xinlei Sheng
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Austin J Hepperla
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Frank L Conlon
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| |
Collapse
|
99967
|
Exome sequencing of individuals with Huntington's disease implicates FAN1 nuclease activity in slowing CAG expansion and disease onset. Nat Neurosci 2022; 25:446-457. [PMID: 35379994 PMCID: PMC8986535 DOI: 10.1038/s41593-022-01033-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 02/11/2022] [Indexed: 12/13/2022]
Abstract
The age at onset of motor symptoms in Huntington's disease (HD) is driven by HTT CAG repeat length but modified by other genes. In this study, we used exome sequencing of 683 patients with HD with extremes of onset or phenotype relative to CAG length to identify rare variants associated with clinical effect. We discovered damaging coding variants in candidate modifier genes identified in previous genome-wide association studies associated with altered HD onset or severity. Variants in FAN1 clustered in its DNA-binding and nuclease domains and were associated predominantly with earlier-onset HD. Nuclease activities of purified variants in vitro correlated with residual age at motor onset of HD. Mutating endogenous FAN1 to a nuclease-inactive form in an induced pluripotent stem cell model of HD led to rates of CAG expansion similar to those observed with complete FAN1 knockout. Together, these data implicate FAN1 nuclease activity in slowing somatic repeat expansion and hence onset of HD.
Collapse
|
99968
|
Lazzaro BP, Tate AT. Balancing sensitivity, risk, and immunopathology in immune regulation. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100874. [PMID: 35051619 PMCID: PMC9133098 DOI: 10.1016/j.cois.2022.100874] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Activation of an immune response is energetically costly and excessive immune system activity can result in immunopathology, yet a slow or insufficient immune response carries the risk of pathogen establishment with consequent pathology arising from the infection. Mathematical theory and empirical data demonstrate that hosts balance the costs of immunity against the risk of infection by closely regulating immunological dynamics. An optimal immune system is rapidly and robustly deployed against a true infectious threat and rapidly deactivated once the threat has been controlled. Genetic variation in the sensitivity of an immune system, as well as in the activation and shutdown kinetics of host immune responses, can contribute to the evolution of pathogen virulence and host tolerance of infection. Improved understanding of the adaptive forces that operate on immune regulatory dynamics will clarify fundamental principles governing the evolution and maintenance of innate immune systems.
Collapse
Affiliation(s)
- Brian P Lazzaro
- Departments of Entomology and Ecology & Evolutionary Biology, Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, USA.
| | - Ann T Tate
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| |
Collapse
|
99969
|
Tanaka M, Fujii T, Mon H, Lee JM, Kakino K, Fukumori H, Ebihara T, Nagasato T, Hino M, Tonooka Y, Moriyama T, Fujita R, Banno Y, Kusakabe T. Silkworm FoxL21 plays important roles as a regulator of ovarian development in both oogenesis and ovariole development. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 143:103737. [PMID: 35101566 DOI: 10.1016/j.ibmb.2022.103737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
The ovary is an important organ in reproduction. In insects, especially lepidopteran insects, the oocytes and reproductive organs develop rapidly during the pupal stage. Despite their drastic morphological changes, the molecular mechanisms of ovary development are not fully understood. In this study, it is found that forkhead box transcription factor L2, member 1 (FoxL21), which is known to be involved in ovarian differentiation and maintenance in vertebrates, is required for the development of the ovary in the silkworm, Bombyx mori. FoxL21 was expressed in the ovary and ovariole during the larval and pupal stage, respectively. In silkworms in which FoxL21 was knocked out by genome editing, multiple ovarian dysfunctions, such as, abnormal egg formation, thinning of the ovariole sheaths, and defective connection of the oviductus geminus with the ovariole were observed. Finally, ovarian transplantation experiments using the knockout silkworms revealed that FoxL21 functions in the ovariole, but not in the oviductus geminus.
Collapse
Affiliation(s)
- Miyu Tanaka
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Tsuguru Fujii
- Laboratory of Creative Science for Insect Industries, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hiroaki Mon
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Jae Man Lee
- Laboratory of Creative Science for Insect Industries, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kohei Kakino
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hisayoshi Fukumori
- Graduate School of Bio Resources and Bioenvironmental Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takeru Ebihara
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takumi Nagasato
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Masato Hino
- Laboratory of Sanitary Entomology, Faculty of Agriculture, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yoshino Tonooka
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takato Moriyama
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Ryosuke Fujita
- Laboratory of Sanitary Entomology, Faculty of Agriculture, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yutaka Banno
- Graduate School of Bio Resources and Bioenvironmental Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan.
| |
Collapse
|
99970
|
Huo Y, Sawant A, Tan Y, Mahdi AH, Li T, Ma H, Bhatt V, Yan R, Coleman J, Dreyfus CF, Guo JY, Mouradian MM, White E, Xia B. Tumor suppressor PALB2 maintains redox and mitochondrial homeostasis in the brain and cooperates with ATG7/autophagy to suppress neurodegeneration. PLoS Genet 2022; 18:e1010138. [PMID: 35404932 PMCID: PMC9022806 DOI: 10.1371/journal.pgen.1010138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 04/21/2022] [Accepted: 03/09/2022] [Indexed: 01/22/2023] Open
Abstract
The PALB2 tumor suppressor plays key roles in DNA repair and has been implicated in redox homeostasis. Autophagy maintains mitochondrial quality, mitigates oxidative stress and suppresses neurodegeneration. Here we show that Palb2 deletion in the mouse brain leads to mild motor deficits and that co-deletion of Palb2 with the essential autophagy gene Atg7 accelerates and exacerbates neurodegeneration induced by ATG7 loss. Palb2 deletion leads to elevated DNA damage, oxidative stress and mitochondrial markers, especially in Purkinje cells, and co-deletion of Palb2 and Atg7 results in accelerated Purkinje cell loss. Further analyses suggest that the accelerated Purkinje cell loss and severe neurodegeneration in the double deletion mice are due to excessive oxidative stress and mitochondrial dysfunction, rather than DNA damage, and partially dependent on p53 activity. Our studies uncover a role of PALB2 in mitochondrial homeostasis and a cooperation between PALB2 and ATG7/autophagy in maintaining redox and mitochondrial homeostasis essential for neuronal survival.
Collapse
Affiliation(s)
- Yanying Huo
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Akshada Sawant
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Yongmei Tan
- Stomatological Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Amar H Mahdi
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Tao Li
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Hui Ma
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Vrushank Bhatt
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Run Yan
- Department of Neurology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
- RWJMS Institute for Neurological Therapeutics, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Jake Coleman
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Cheryl F Dreyfus
- Rutgers School of Environmental and Biological Sciences, New Brunswick, New Jersey, United States of America
| | - Jessie Yanxiang Guo
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
- Department of Chemical Biology, Rutgers Ernest Mario School of Pharmacy, Piscataway, New Jersey, United States of America
| | - M. Maral Mouradian
- Department of Neurology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
- RWJMS Institute for Neurological Therapeutics, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Eileen White
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Bing Xia
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| |
Collapse
|
99971
|
Nag N, Sasidharan S, Uversky VN, Saudagar P, Tripathi T. Phase separation of FG-nucleoporins in nuclear pore complexes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119205. [PMID: 34995711 DOI: 10.1016/j.bbamcr.2021.119205] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022]
Abstract
The nuclear envelope (NE) is a bilayer membrane that separates and physically isolates the genetic material from the cytoplasm. Nuclear pore complexes (NPCs) are cylindrical structures embedded in the NE and remain the sole channel of communication between the nucleus and the cytoplasm. The interior of NPCs contains densely packed intrinsically disordered FG-nucleoporins (FG-Nups), consequently forming a permeability barrier. This barrier facilitates the selection and specificity of the cargoes that are imported, exported, or shuttled through the NPCs. Recent studies have revealed that FG-Nups undergo the process of liquid-liquid phase separation into liquid droplets. Moreover, these liquid droplets mimic the permeability barrier observed in the interior of NPCs. This review highlights the phase separation of FG-Nups occurring inside the NPCs rooted in the NE. We discuss the phase separation of FG-Nups and compare the different aspects contributing to their phase separation. Furthermore, several diseases caused by the aberrant phase separation of the proteins are examined with respect to NEs. By understanding the fundamental process of phase separation at the nuclear membrane, the review seeks to explore the parameters influencing this phenomenon as well as its importance, ultimately paving the way for better research on the structure-function relationship of biomolecular condensates.
Collapse
Affiliation(s)
- Niharika Nag
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Santanu Sasidharan
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, United States; Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, India.
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India.
| |
Collapse
|
99972
|
Genomic evidence suggests that cutaneous neuroendocrine carcinomas can arise from squamous dysplastic precursors. Mod Pathol 2022; 35:506-514. [PMID: 34593967 PMCID: PMC8964828 DOI: 10.1038/s41379-021-00928-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/24/2021] [Accepted: 09/07/2021] [Indexed: 02/06/2023]
Abstract
Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine carcinoma without a known dysplastic precursor. In some cases, MCC is associated with SCCIS in the overlying epidermis; however, the MCC and SCCIS populations display strikingly different morphologies, and thus far a relationship between these components has not been demonstrated. To better understand the relationship between these distinct tumor cell populations, we evaluated 7 pairs of MCC-SCCIS for overlapping genomic alterations by cancer profiling panel. A subset was further characterized by transcriptional profiling and immunohistochemistry. In 6 of 7 MCC-SCCIS pairs there was highly significant mutational overlap including shared TP53 and/or RB1 mutations. In some cases, oncogenic events previously implicated in MCC (MYCL gain, MDM4 gain, HRAS mutation) were detected in both components. Although FBXW7 mutations were enriched in MCC, no gene mutation was unique to the MCC component across all cases. Transcriptome analysis identified 2736 differentially expressed genes between MCC and SCCIS. Genes upregulated in the MCC component included Polycomb repressive complex targets; downregulated transcripts included epidermal markers, and immune genes such as HLA-A. Immunohistochemical studies revealed increased expression of SOX2 in the MCC component, with diminished H3K27Me3, Rb, and HLA-A expression. In summary, MCC-SCCIS pairs demonstrate clonal relatedness. The shift to neuroendocrine phenotype is associated with loss of Rb protein expression, decrease in global H3K27Me3, and increased expression of Merkel cell genes such as SOX2. Our findings suggest an epidermal origin of MCC in this setting, and to our knowledge provide the first molecular evidence that intraepithelial squamous dysplasia may represent a direct precursor for small cell carcinoma.
Collapse
|
99973
|
Abstract
The brain is one of the most energetically demanding tissues in the human body, and mitochondrial pathology is strongly implicated in chronic neurodegenerative diseases. In contrast to acute brain injuries in which bioenergetics and cell death play dominant roles, studies modeling familial neurodegeneration implicate a more complex and nuanced relationship involving the entire mitochondrial life cycle. Recent literature on mitochondrial mechanisms in Parkinson's disease, Alzheimer's disease, frontotemporal dementia, Huntington's disease, and amyotrophic lateral sclerosis is reviewed with an emphasis on mitochondrial quality control, transport and synaptodendritic calcium homeostasis. Potential neuroprotective interventions include targeting the mitochondrial kinase PTEN-induced kinase 1 (PINK1), which plays a role in regulating not only multiple facets of mitochondrial biology, but also neuronal morphogenesis and dendritic arborization.
Collapse
Affiliation(s)
- Charleen T Chu
- Departments of Pathology and Ophthalmology, Pittsburgh Institute for Neurodegenerative Diseases, McGowan Institute for Regenerative Medicine, Center for Protein Conformational Diseases, Center for Neuroscience at the University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| |
Collapse
|
99974
|
Cui Z, Li D, Zhao J, Chen K. Falnidamol and cisplatin combinational treatment inhibits non-small cell lung cancer (NSCLC) by targeting DUSP26-mediated signal pathways. Free Radic Biol Med 2022; 183:106-124. [PMID: 35278641 DOI: 10.1016/j.freeradbiomed.2022.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 12/12/2022]
Abstract
Non-small-cell lung cancer (NSCLC) is one of the most commonly diagnosed cancers worldwide with limited effective therapies. Cisplatin (DDP), as the first-line treatment, is always served as a mainstay of chemotherapeutic agents in combination with other drugs for NSCLC treatment. Nevertheless, DDP-based therapy is limited due to the frequent development of chemoresistance and adverse effects. Herein, it is necessary to find a more effective therapeutic approach with less toxicity. Falnidamol (FLD) is a pyrimido-pyrimidine compound and exerts anti-cancer activity. In the present study, we found that FLD could strongly promote the cytotoxicity of DDP and markedly reduce the IC50 values to restrain the proliferation of NSCLC cells. Furthermore, combination of FLD and DDP remarkably induced G2/M cell cycle arrest, DNA damage and mitochondrial apoptosis, which was largely through the induction of reactive oxygen species (ROS). Additionally, FLD/DDP in combination greatly triggered ferroptosis, along with free iron accumulation and enhanced lipid peroxidation. Epithelial to mesenchymal transition (EMT) and epidermal growth factor receptor (EGFR) phosphorylation were also considerably restrained in NSCLC cells co-treated with FLD/DDP. Mechanistically, the combinative treatment significantly reduced DUSP26 expression in NSCLC cells. More studies showed that DUSP26 was strongly up-regulated in human NSCLC samples compared with the paired normal tissues, and high DUSP26 predicted poor overall survival rate among patients. Importantly, we found that DUSP26 suppression intensively reduced the proliferation, EMT process and pEGFR expression in NSCLC cells, whereas facilitated ROS production, DNA damage and cell death; however, opposite phenotype was observed in NSCLC cells over-expressing DUSP26. More importantly, DUSP26 over-expression completely abolished the anti-cancer function of FLD/DDP in NSCLC cells. Animal studies finally confirmed that FLD/DDP in combination efficiently reduced tumor growth and lung metastasis in mice with ameliorated side effects. In conclusion, all these data illustrated that FLD and DDP combinational treatment effectively restrained NSCLC progression, and thus can be served as a promising therapeutic strategy.
Collapse
Affiliation(s)
- Zihan Cui
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Dapeng Li
- Department of Oncology, The First Hospital Affiliated to Soochow University, Suzhou, 215000, China
| | - Jun Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China.
| | - Kai Chen
- Department of Oncology, The First Hospital Affiliated to Soochow University, Suzhou, 215000, China.
| |
Collapse
|
99975
|
Sun W, Wang Y. SuperFi-Cas9: High Fidelity Meets High Activity. CRISPR J 2022; 5:171-173. [PMID: 35438514 DOI: 10.1089/crispr.2022.29146.ywa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Wei Sun
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yanli Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
99976
|
Hanisch D, Krumm A, Diehl T, Stork CM, Dejung M, Butter F, Kim E, Brenner W, Fritz G, Hofmann TG, Roos WP. Class I HDAC overexpression promotes temozolomide resistance in glioma cells by regulating RAD18 expression. Cell Death Dis 2022; 13:293. [PMID: 35365623 PMCID: PMC8975953 DOI: 10.1038/s41419-022-04751-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/05/2022] [Accepted: 03/18/2022] [Indexed: 12/22/2022]
Abstract
Overexpression of histone deacetylases (HDACs) in cancer commonly causes resistance to genotoxic-based therapies. Here, we report on the novel mechanism whereby overexpressed class I HDACs increase the resistance of glioblastoma cells to the SN1 methylating agent temozolomide (TMZ). The chemotherapeutic TMZ triggers the activation of the DNA damage response (DDR) in resistant glioma cells, leading to DNA lesion bypass and cellular survival. Mass spectrometry analysis revealed that the catalytic activity of class I HDACs stimulates the expression of the E3 ubiquitin ligase RAD18. Furthermore, the data showed that RAD18 is part of the O6-methylguanine-induced DDR as TMZ induces the formation of RAD18 foci at sites of DNA damage. Downregulation of RAD18 by HDAC inhibition prevented glioma cells from activating the DDR upon TMZ exposure. Lastly, RAD18 or O6-methylguanine-DNA methyltransferase (MGMT) overexpression abolished the sensitization effect of HDAC inhibition on TMZ-exposed glioma cells. Our study describes a mechanism whereby class I HDAC overexpression in glioma cells causes resistance to TMZ treatment. HDACs accomplish this by promoting the bypass of O6-methylguanine DNA lesions via enhancing RAD18 expression. It also provides a treatment option with HDAC inhibition to undermine this mechanism.
Collapse
Affiliation(s)
- Daniela Hanisch
- Institute of Toxicology, Medical Center of the University Mainz, Obere Zahlbacher Straße 67, 55131, Mainz, Germany
| | - Andrea Krumm
- Institute of Toxicology, Medical Center of the University Mainz, Obere Zahlbacher Straße 67, 55131, Mainz, Germany
| | - Tamara Diehl
- Institute of Toxicology, Medical Center of the University Mainz, Obere Zahlbacher Straße 67, 55131, Mainz, Germany
| | - Carla M Stork
- Institute of Toxicology, Medical Center of the University Mainz, Obere Zahlbacher Straße 67, 55131, Mainz, Germany
| | - Mario Dejung
- Institute of Molecular Biology, Ackermannweg 4, 55128, Mainz, Germany
| | - Falk Butter
- Institute of Molecular Biology, Ackermannweg 4, 55128, Mainz, Germany
| | - Ella Kim
- Laboratory for Experimental Neurooncology, Clinic for Neurosurgery, Medical Center of the University Mainz, 55131, Mainz, Germany
| | - Walburgis Brenner
- Department of Obstetrics and Gynecology, University Medical Center Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Gerhard Fritz
- Institute of Toxicology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstrasse 5, 40225, Düsseldorf, Germany
| | - Thomas G Hofmann
- Institute of Toxicology, Medical Center of the University Mainz, Obere Zahlbacher Straße 67, 55131, Mainz, Germany
| | - Wynand P Roos
- Institute of Toxicology, Medical Center of the University Mainz, Obere Zahlbacher Straße 67, 55131, Mainz, Germany.
| |
Collapse
|
99977
|
Gomes AP, Ilter D, Low V, Drapela S, Schild T, Mullarky E, Han J, Elia I, Broekaert D, Rosenzweig A, Nagiec M, Nunes JB, Schaffer BE, Mutvei AP, Asara JM, Cantley LC, Fendt SM, Blenis J. Altered propionate metabolism contributes to tumour progression and aggressiveness. Nat Metab 2022; 4:435-443. [PMID: 35361954 PMCID: PMC9050834 DOI: 10.1038/s42255-022-00553-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/15/2022] [Indexed: 12/22/2022]
Abstract
The alteration of metabolic pathways is a critical strategy for cancer cells to attain the traits necessary for metastasis in disease progression. Here, we find that dysregulation of propionate metabolism produces a pro-aggressive signature in breast and lung cancer cells, increasing their metastatic potential. This occurs through the downregulation of methylmalonyl coenzyme A epimerase (MCEE), mediated by an extracellular signal-regulated kinase 2-driven transcription factor Sp1/early growth response protein 1 transcriptional switch driven by metastatic signalling at its promoter level. The loss of MCEE results in reduced propionate-driven anaplerotic flux and intracellular and intratumoral accumulation of methylmalonic acid, a by-product of propionate metabolism that promotes cancer cell invasiveness. Altogether, we present a previously uncharacterized dysregulation of propionate metabolism as an important contributor to cancer and a valuable potential target in the therapeutic treatment of metastatic carcinomas.
Collapse
Affiliation(s)
- Ana P Gomes
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
- Department of Molecular Oncology, H. Lee Moffit Cancer Center & Research Institute, Tampa, FL, USA.
| | - Didem Ilter
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Department of Molecular Oncology, H. Lee Moffit Cancer Center & Research Institute, Tampa, FL, USA
| | - Vivien Low
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Stanislav Drapela
- Department of Molecular Oncology, H. Lee Moffit Cancer Center & Research Institute, Tampa, FL, USA
| | - Tanya Schild
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edouard Mullarky
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Julie Han
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Ilaria Elia
- Laboratory of Cellular Metabolism and Metabolic Regulation, Vlaams Instituut voor Biotechnologie Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, Katholieke Universiteit Leuven and Leuven Cancer Institute, Leuven, Belgium
| | - Dorien Broekaert
- Laboratory of Cellular Metabolism and Metabolic Regulation, Vlaams Instituut voor Biotechnologie Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, Katholieke Universiteit Leuven and Leuven Cancer Institute, Leuven, Belgium
| | - Adam Rosenzweig
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Michal Nagiec
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Joana B Nunes
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Bethany E Schaffer
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Anders P Mutvei
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - John M Asara
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, Vlaams Instituut voor Biotechnologie Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, Katholieke Universiteit Leuven and Leuven Cancer Institute, Leuven, Belgium
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
99978
|
Ding J, Shen L, Ye Y, Hu S, Ren Z, Liu T, Dai J, Li Z, Wang J, Luo Y, Zhang Q, Zhang X, Qi X, Huang J. Inflammasome Inhibition Prevents Motor Deficit and Cerebellar Degeneration Induced by Chronic Methamphetamine Administration. Front Mol Neurosci 2022; 15:861340. [PMID: 35431795 PMCID: PMC9010733 DOI: 10.3389/fnmol.2022.861340] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Methamphetamine (METH), a psychostimulant, has the potential to cause neurodegeneration by targeting the cerebrum and cerebellum. It has been suggested that the NLRP3 inflammasome may be responsible for the neurotoxicity caused by METH. However, the role of NLRP3 in METH-induced cerebellar Purkinje cell (PC) degeneration and the underlying mechanism remain elusive. This study aims to determine the consequences of NLRP3 modulation and the underlying mechanism of chronic METH-induced cerebellar PC degeneration. In METH mice models, increased NLRP3 expression, PC degeneration, myelin sheath destruction, axon degeneration, glial cell activation, and motor coordination impairment were observed. Using the NLRP3 inhibitor MCC950, we found that inhibiting NLRP3 alleviated the above-mentioned motor deficits and cerebellar pathologies. Furthermore, decreased mature IL-1β expression mediated by Caspase 1 in the cerebellum may be associated with the neuroprotective effects of NLRP3 inflammasome inhibition. Collectively, these findings suggest that mature IL-1β secretion mediated by NLRP3-ASC-Caspase 1 may be a critical step in METH-induced cerebellar degeneration and highlight the neuroprotective properties of inflammasome inhibition in cerebellar degeneration.
Collapse
Affiliation(s)
- Jiuyang Ding
- School of Forensic Medicine, Guizhou Medical University, Guiyang, China
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
| | - Lingyi Shen
- School of Basic Medical Science, Guizhou Medical University, Guiyang, China
| | - Yuanliang Ye
- Department of Neurosurgery, Liuzhou People’s Hospital, Liuzhou, China
| | - Shanshan Hu
- Good Clinical Practice Center, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zheng Ren
- School of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Ting Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Jialin Dai
- School of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Zhu Li
- School of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jiawen Wang
- School of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Ya Luo
- School of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiaojun Zhang
- School of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Xiali Zhang
- School of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
| | - Jiang Huang
- School of Forensic Medicine, Guizhou Medical University, Guiyang, China
- *Correspondence: Jiang Huang,
| |
Collapse
|
99979
|
MEX3A promotes nasopharyngeal carcinoma progression via the miR-3163/SCIN axis by regulating NF-κB signaling pathway. Cell Death Dis 2022; 13:420. [PMID: 35490173 PMCID: PMC9056523 DOI: 10.1038/s41419-022-04871-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/14/2022] [Accepted: 04/20/2022] [Indexed: 11/08/2022]
Abstract
AbstractMex-3 RNA Binding Family Member A (MEX3A) is an RNA-binding protein that plays complex and diverse roles in the development of various malignancies. However, its role and mechanism in nasopharyngeal carcinoma (NPC) remain undefined and were therefore evaluated in this study. By analyzing Gene Expression Omnibus data and using tissue microarrays, we found that MEX3A is significantly upregulated in NPC and negatively associated with prognosis. Notably, MEX3A depletion led to decreased cell proliferation, invasion, and migration, but increased apoptosis in NPC cells in vitro, while inhibiting tumor growth in vivo. Using whole-transcript expression arrays and bioinformatic analysis, we identified scinderin (SCIN) and miR-3163 as potential downstream targets of MEX3A in NPC. The regulatory mechanisms of MEX3A, SCIN and miR-3163 were further investigated using rescue experiments. Importantly, SCIN depletion and miR-3163 inhibition reversed and rescued the oncogenic effects of MEX3A, respectively. Moreover, NF-κB signaling inhibition reversed the oncogenic effects of both SCIN and MEX3A. In summary, our results demonstrate that MEX3A may promote NPC development and progression via the miR-3163/SCIN axis by regulating NF-κB signaling, thus providing a potential target for NPC treatment.
Collapse
|
99980
|
Shan J, Wang Z, Mo Q, Long J, Fan Y, Cheng L, Zhang T, Liu X, Wang X. Ribonucleotide reductase M2 subunit silencing suppresses tumorigenesis in pancreatic cancer via inactivation of PI3K/AKT/mTOR pathway. Pancreatology 2022; 22:401-413. [PMID: 35300916 DOI: 10.1016/j.pan.2022.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/26/2022] [Accepted: 03/02/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND/OBJECTIVES Ribonucleotide Reductase M2 subunit (RRM2) is elevated in pancreatic cancer and involved in DNA synthesis and cell proliferation. But its specific mechanism including genetic differences and upstream regulatory pathways remains unclear. METHODS We analyzed RRM2 expression of 178 pancreatic cancer patients in Gene Expression Profiling Interactive Analysis (GEPIA) database. Besides, more pancreatic cancer specimens were collected and detected RRM2 expression by immunohistochemistry. RRM2 knockdown by shRNA was applied for functional and mechanism analysis in vitro. Xenograft tumor growth was significantly slower by RRM2 silencing in vivo. RESULTS It showed that high RRM2 expression had a poorer overall survival and disease free survival. RRM2 expression was higher in tumor grade 2 and 3 than grade 1. Immunohistochemistry data validated that high RRM2 expression predicted worse survival. RRM2 knockdown significantly reduced cell proliferation, inhibited colony formation and suppressed cell cycle progress. Further mechanism assay showed silencing RRM2 lead to inactivation of PI3K/AKT/mTOR pathway and inhibition of mutant p53, which induce S phase arrest and/or apoptosis. In panc-1 cells, S-phase arrest mediated by mutant p53 inhibition, p21 increase and cell cycle related proteins change. While in miapaca-2 cells, induction of apoptosis and S-phase arrest mediated by CDK1 played a coordinated role. CONCLUSION Taken together, high RRM2 expression was associated with worse prognosis. Importantly, RRM2 knockdown deactivated PI3K/AKT/mTOR pathway, resulting in cell cycle arrest and/or apoptosis. This study shed light on the molecular mechanism of RRM2 in pancreatic tumor progression and is expected to provide a new theoretical basis for pancreatic cancer treatment.
Collapse
Affiliation(s)
- Jinlan Shan
- Department of Surgery, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Department of Cancer Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhen Wang
- Department of Breast Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qiuping Mo
- Department of Breast Surgery, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
| | - Jingpei Long
- Department of Surgery, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yangfan Fan
- Department of Surgery, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lu Cheng
- Department of Pathology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tao Zhang
- Department of Breast and Thyroid Surgery, Affiliated Hospital of Shaoxing University, Shaoxing, Zhejiang, China
| | - Xiyong Liu
- Sino-America Cancer Foundation, California Cancer Institute, Temple City, CA91780, USA; Tumor Biomarker Development, California Cancer Institute, Temple City, CA,91780, USA
| | - Xiaochen Wang
- Department of Breast Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| |
Collapse
|
99981
|
Liu Z, Wang J, Zhou Y, Zhang Y, Qin A, Yu X, Zhao Z, Wu R, Guo C, Bawa G, Rochaix J, Sun X. Identification of novel regulators required for early development of vein pattern in the cotyledons by single-cell RNA-sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:7-22. [PMID: 35218590 PMCID: PMC9310732 DOI: 10.1111/tpj.15719] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/20/2022] [Indexed: 05/25/2023]
Abstract
The leaf veins of higher plants contain a highly specialized vascular system comprised of xylem and phloem cells that transport water, organic compounds and mineral nutrients. The development of the vascular system is controlled by phytohormones that interact with complex transcriptional regulatory networks. Before the emergence of true leaves, the cotyledons of young seedlings perform photosynthesis that provides energy for the sustainable growth and survival of seedlings. However, the mechanisms underlying the early development of leaf veins in cotyledons are still not fully understood, in part due to the complex cellular composition of this tissue. To better understand the development of leaf veins, we analyzed 14 117 single cells from 3-day-old cotyledons using single-cell RNA sequencing. Based on gene expression patterns, we identified 10 clusters of cells and traced their developmental trajectories. We discovered multiple new marker genes and developmental features of leaf veins. The transcription factor networks of some cell types indicated potential roles of CYCLING DOF FACTOR 5 (CDF5) and REPRESSOR OF GA (RGA) in the early development and function of the leaf veins in cotyledons. These new findings lay a foundation for understanding the early developmental dynamics of cotyledon veins. The mechanisms underlying the early development of leaf veins in cotyledons are still not fully understood. In this study, we comprehensively characterized the early differentiation and development of leaf veins in 3-day-old cotyledons based on single-cell transcriptome analysis. We identified the cell types and novel marker genes of leaf veins and characterized the novel regulators of leaf vein.
Collapse
Affiliation(s)
- Zhixin Liu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress BiologySchool of Life Sciences, Henan University85 Minglun StreetKaifeng475001China
| | - Jiajing Wang
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress BiologySchool of Life Sciences, Henan University85 Minglun StreetKaifeng475001China
| | - Yaping Zhou
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress BiologySchool of Life Sciences, Henan University85 Minglun StreetKaifeng475001China
| | - Yixin Zhang
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress BiologySchool of Life Sciences, Henan University85 Minglun StreetKaifeng475001China
| | - Aizhi Qin
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress BiologySchool of Life Sciences, Henan University85 Minglun StreetKaifeng475001China
| | - Xiaole Yu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress BiologySchool of Life Sciences, Henan University85 Minglun StreetKaifeng475001China
| | - Zihao Zhao
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress BiologySchool of Life Sciences, Henan University85 Minglun StreetKaifeng475001China
| | - Rui Wu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress BiologySchool of Life Sciences, Henan University85 Minglun StreetKaifeng475001China
| | - Chenxi Guo
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress BiologySchool of Life Sciences, Henan University85 Minglun StreetKaifeng475001China
| | - George Bawa
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress BiologySchool of Life Sciences, Henan University85 Minglun StreetKaifeng475001China
| | - Jean‐David Rochaix
- Departments of Molecular Biology and Plant BiologyUniversity of GenevaGeneva1211Switzerland
| | - Xuwu Sun
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress BiologySchool of Life Sciences, Henan University85 Minglun StreetKaifeng475001China
| |
Collapse
|
99982
|
Ma X, Li Y, Zhao B. Ribosomal protein L5 (RPL5)/ E2F transcription factor 1 (E2F1) signaling suppresses breast cancer progression via regulating endoplasmic reticulum stress and autophagy. Bioengineered 2022; 13:8076-8086. [PMID: 35293275 PMCID: PMC9161874 DOI: 10.1080/21655979.2022.2052672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 02/08/2023] Open
Abstract
Endoplasmic reticulum stress (ERS) is associated with breast cancer progression. However, the potential role of ribosomal protein L5 (RPL5) on ERS in breast cancer remains unclear. This study aimed to determine the role of RPL5/E2F transcription factor 1 (E2F1) in breast cancer. It was found that RPL5 was downregulated in breast cancer cells and tissues. Additionally, overexpression of RPL5 inhibited cell proliferation. Moreover, the levels of ERS and autophagy markers were estimated using western blotting. Overexpression of RPL5 induced ERS and suppressed autophagy. Additionally, RPL5 downregulated E2F1, which was overexpressed in breast cancer cells. However, E2F1 knockdown promoted the transcriptional activation of glucose regulated protein 78 (GRP78), suppressed ERS response, and promoted autophagy. Rescue assays indicated that the effects of RPL5 on ERS and autophagy were abolished by E2F1. Taken together, RPL5 inhibited the growth of breast cancer cells by modulating ERS and autophagy via the regulation of E2F1. These findings suggest that RPL5 has a tumor-suppressive effect in breast cancer.
Collapse
Affiliation(s)
- Xiaoping Ma
- Breast Internal Medicine Department, The 3rd Affiliated Teaching Hospital of XinJiang Medical University(Affiliated Tumor Hospital), Urumqi, China
| | - Yan Li
- Breast Internal Medicine Department, The 3rd Affiliated Teaching Hospital of XinJiang Medical University(Affiliated Tumor Hospital), Urumqi, China
| | - Bing Zhao
- Breast Internal Medicine Department, The 3rd Affiliated Teaching Hospital of XinJiang Medical University(Affiliated Tumor Hospital), Urumqi, China
| |
Collapse
|
99983
|
Xu X, Yuan L, Yang X, Zhang X, Wang L, Xie Q. Circadian clock in plants: Linking timing to fitness. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:792-811. [PMID: 35088570 DOI: 10.1111/jipb.13230] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/25/2022] [Indexed: 05/12/2023]
Abstract
Endogenous circadian clock integrates cyclic signals of environment and daily and seasonal behaviors of organisms to achieve spatiotemporal synchronization, which greatly improves genetic diversity and fitness of species. This review addresses recent studies on the plant circadian system in the field of chronobiology, covering topics on molecular mechanisms, internal and external Zeitgebers, and hierarchical regulation of physiological outputs. The architecture of the circadian clock involves the autoregulatory transcriptional feedback loops, post-translational modifications of core oscillators, and epigenetic modifications of DNA and histones. Here, light, temperature, humidity, and internal elemental nutrients are summarized to illustrate the sensitivity of the circadian clock to timing cues. In addition, the circadian clock runs cell-autonomously, driving independent circadian rhythms in various tissues. The core oscillators responds to each other with biochemical factors including calcium ions, mineral nutrients, photosynthetic products, and hormones. We describe clock components sequentially expressed during a 24-h day that regulate rhythmic growth, aging, immune response, and resistance to biotic and abiotic stresses. Notably, more data have suggested the circadian clock links chrono-culture to key agronomic traits in crops.
Collapse
Affiliation(s)
- Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xin Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiao Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| |
Collapse
|
99984
|
Lee U, Cho EY, Jho EH. Regulation of Hippo signaling by metabolic pathways in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119201. [PMID: 35026349 DOI: 10.1016/j.bbamcr.2021.119201] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/12/2021] [Accepted: 12/18/2021] [Indexed: 12/12/2022]
Abstract
Hippo signaling is known to maintain balance between cell proliferation and apoptosis via tight regulation of factors, such as metabolic cues, cell-cell contact, and mechanical cues. Cells directly recognize glucose, lipids, and other metabolic cues and integrate multiple signaling pathways, including Hippo signaling, to adjust their proliferation and apoptosis depending on nutrient conditions. Therefore, the dysregulation of the Hippo signaling pathway can promote tumor initiation and progression. Alteration in metabolic cues is considered a major factor affecting the risk of cancer formation and progression. It has recently been shown that the dysregulation of the Hippo signaling pathway, through diverse routes activated by metabolic cues, can lead to cancer with a poor prognosis. In addition, unique crosstalk between metabolic pathways and Hippo signaling pathways can inhibit the effect of anticancer drugs and promote drug resistance. In this review, we describe an integrated perspective of the relationship between the Hippo signaling pathway and metabolic signals in the context of cancer. We also characterize the mechanisms involved in changes in metabolism that are linked to the Hippo signaling pathway in the cancer microenvironment and propose several novel targets for anticancer drug treatment.
Collapse
Affiliation(s)
- Ukjin Lee
- Department of Life Science, University of Seoul, 02504 Seoul, Republic of Korea
| | - Eun-Young Cho
- Department of Life Science, University of Seoul, 02504 Seoul, Republic of Korea
| | - Eek-Hoon Jho
- Department of Life Science, University of Seoul, 02504 Seoul, Republic of Korea.
| |
Collapse
|
99985
|
Wen SY, Qadir J, Yang BB. Circular RNA translation: novel protein isoforms and clinical significance. Trends Mol Med 2022; 28:405-420. [DOI: 10.1016/j.molmed.2022.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 02/07/2023]
|
99986
|
miRNA-Mediated Low Expression of EPHX3 Is Associated with Poor Prognosis and Tumor Immune Infiltration in Head and Neck Squamous Cell Carcinomas. JOURNAL OF ONCOLOGY 2022; 2022:7633720. [PMID: 35401746 PMCID: PMC8993555 DOI: 10.1155/2022/7633720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/10/2022] [Accepted: 03/20/2022] [Indexed: 11/17/2022]
Abstract
The aim of this study was to explore the regulatory role of epoxide hydrolase 3 (EPHX3) in head and neck squamous cell carcinoma (HNSCC) and to analyze its bioinformatic function, as well as, to screen and predict the miRNAs that can regulate EPHX3 expression in HNSCC. We examined the expression profile and prognostic potential of EPHX3 in TCGA and GTEX databases and performed functional enrichment analysis of EPHX3 using string database. Subsequently, we analyzed the regulatory role of miRNAs on EPHX3, including expression analysis, correlation analysis, and survival analysis. In addition, we also used TIMER to investigate the relationship among EPHX3 expression level, immune checkpoints, and immune infiltration in HNSCC. The results of data analysis after TGCA showed that EPHX3 is a key regulator of tumorigenesis in 13 cancers and can be used as a marker of poor prognosis in HNSCC patients. Bioinformatics analysis revealed that miR-4713-3p is a key miRNA of EPHX3 in HNSCC. Together, our findings indicate that EPHX3 exerts its anticancer effects by suppressing tumor immune checkpoint expression and immune cell infiltration. Overall, our data uncovered miRNA-mediated EPHX3 downregulation as a contributor to poor HNSCC prognosis and reduced tumor immune infiltration.
Collapse
|
99987
|
Tong J, Tan X, Song X, Gao M, Risnik D, Hao S, Ermine K, Wang P, Li H, Huang Y, Yu J, Zhang L. CDK4/6 Inhibition Suppresses p73 Phosphorylation and Activates DR5 to Potentiate Chemotherapy and Immune Checkpoint Blockade. Cancer Res 2022; 82:1340-1352. [PMID: 35149588 PMCID: PMC8983601 DOI: 10.1158/0008-5472.can-21-3062] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/12/2022] [Accepted: 02/08/2022] [Indexed: 11/16/2022]
Abstract
Targeting cyclin-dependent kinases 4 and 6 (CDK4/6) is a successful therapeutic approach against breast and other solid tumors. Inhibition of CDK4/6 halts cell cycle progression and promotes antitumor immunity. However, the mechanisms underlying the antitumor activity of CDK4/6 inhibitors are not fully understood. We found that CDK4/6 bind and phosphorylate the p53 family member p73 at threonine 86, which sequesters p73 in the cytoplasm. Inhibition of CDK4/6 led to dephosphorylation and nuclear translocation of p73, which transcriptionally activated death receptor 5 (DR5), a cytokine receptor and key component of the extrinsic apoptotic pathway. p73-mediated induction of DR5 by CDK4/6 inhibitors promoted immunogenic cell death of cancer cells. Deletion of DR5 in cancer cells in vitro and in vivo abrogated the potentiating effects of CDK4/6 inhibitors on immune cytokine TRAIL, 5-fluorouracil chemotherapy, and anti-PD-1 immunotherapy. Together, these results reveal a previously unrecognized consequence of CDK4/6 inhibition, which may be critical for potentiating the killing and immunogenic effects on cancer cells. SIGNIFICANCE This work demonstrates how inhibition of CDK4/6 sensitizes cancer cells to chemotherapy and immune checkpoint blockade and may provide a new molecular marker for improving CDK4/6-targeted cancer therapies. See related commentary by Frank, p. 1170.
Collapse
Affiliation(s)
- Jingshan Tong
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Xiao Tan
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Xiangping Song
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Man Gao
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213. USA
| | - Denise Risnik
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Suisui Hao
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Kaylee Ermine
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Peng Wang
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Hua Li
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Yi Huang
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jian Yu
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213. USA
| | - Lin Zhang
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| |
Collapse
|
99988
|
Zhang Y, Dho SE, Othman K, Simpson CD, Lapierre J, Bondoc A, McGlade CJ. Numb exon 9 inclusion regulates Integrinβ5 surface expression and promotes breast cancer metastasis. Oncogene 2022; 41:2079-2094. [PMID: 35181737 DOI: 10.1038/s41388-022-02225-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/14/2022] [Accepted: 02/01/2022] [Indexed: 01/07/2023]
Abstract
The endocytic adaptor protein Numb acts as a tumor suppressor through downregulation of oncogenic pathways in multiple cancer types. The identification of splicing alterations giving rise to changes in Numb protein isoform expression indicate that Numb also has tumor promoting activity, though the underlying mechanisms are unknown. Here we report that NUMB exon 9 inclusion, which results in production of a protein isoform with an additional 49 amino acids, is a feature of multiple cancer types including all subtypes of breast cancer and correlates with worse progression-free survival. Specific deletion of exon 9-included Numb isoforms (Exon9in) from breast cancer cells reduced cell growth and prevents spontaneous lung metastasis in a mouse model. Quantitative proteome profiling showed that loss of Exon9in causes downregulation of membrane receptors and adhesion molecules, as well as proteins involved in extracellular matrix organization and the epithelial-mesenchymal transition (EMT) state. In addition, exon 9 deletion caused remodeling of the endocytic network, decreased ITGβ5 surface localization, cell spreading on vitronectin and downstream signaling to ERK and SRC. Together these observations suggest that Exon9in isoform expression disrupts the endocytic trafficking functions of Numb, resulting in increased surface expression of ITGβ5 as well as other plasma membrane proteins to promote cell adhesion, EMT, and tumor metastasis.
Collapse
Affiliation(s)
- Yangjing Zhang
- Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
| | - Sascha E Dho
- The Arthur and Sonia Labatt Brain Tumour Research Centre, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
- Program in Cell Biology, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
| | - Kamal Othman
- Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
| | - Craig D Simpson
- SPARC BioCentre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
| | - Jessica Lapierre
- The Arthur and Sonia Labatt Brain Tumour Research Centre, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
- Program in Cell Biology, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
| | - Andrew Bondoc
- The Arthur and Sonia Labatt Brain Tumour Research Centre, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
- Program in Cell Biology, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
| | - C Jane McGlade
- Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, ON, M5G 2M9, Canada.
- The Arthur and Sonia Labatt Brain Tumour Research Centre, 555 University Avenue, Toronto, ON, M5G 1X8, Canada.
- Program in Cell Biology, 555 University Avenue, Toronto, ON, M5G 1X8, Canada.
| |
Collapse
|
99989
|
Ferreira FS, Dos Santos TM, Ramires Junior OV, Silveira JS, Schmitz F, Wyse ATS. Quinolinic Acid Impairs Redox Homeostasis, Bioenergetic, and Cell Signaling in Rat Striatum Slices: Prevention by Coenzyme Q 10. Neurotox Res 2022; 40:473-484. [PMID: 35239160 DOI: 10.1007/s12640-022-00484-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 12/19/2022]
Abstract
Quinolinic acid (QUIN) is an important agonist of NMDA receptors that are found at high levels in cases of brain injury and neuroinflammation. Therefore, it is necessary to investigate neuroprotection strategies capable of neutralizing the effects of the QUIN on the brain. Coenzyme Q10 (CoQ10) is a provitamin that has an important antioxidant and anti-inflammatory action. This work aims to evaluate the possible neuroprotective effect of CoQ10 against the toxicity caused by QUIN. Striatal slices from 30-day-old Wistar rats were preincubated with CoQ10 25-100 μM for 15 min; then, QUIN 100 μM was added to the incubation medium for 30 min. A dose-response curve was used to select the CoQ10 concentration to be used in the study. Results showed that QUIN caused changes in the production of ROS, nitrite levels, activities of antioxidant enzymes, glutathione content, and damage to proteins and lipids. CoQ10 was able to prevent the effects caused by QUIN, totally or partially, except for damage to proteins. QUIN also altered the activities of electron transport chain complexes and ATP levels, and CoQ10 prevented totally and partially these effects, respectively. CoQ10 prevented the increase in acetylcholinesterase activity, but not the decrease in the activity of Na+,K+-ATPase caused by QUIN. We also observed that QUIN caused changes in the total ERK and phospho-Akt content, and these effects were partially prevented by CoQ10. These findings suggest that CoQ10 may be a promising therapeutic alternative for neuroprotection against QUIN neurotoxicity.
Collapse
Affiliation(s)
- Fernanda Silva Ferreira
- Programa de Pós-Graduação Em Ciências Biológicas: Bioquímica, ICBS, UFRGS, Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
- Laboratório de Neuroproteção E Doenças Neurometabólicas, Departamento de Bioquímica, ICBS, UFRGS, Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
| | - Tiago Marcon Dos Santos
- Programa de Pós-Graduação Em Ciências Biológicas: Bioquímica, ICBS, UFRGS, Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
- Laboratório de Neuroproteção E Doenças Neurometabólicas, Departamento de Bioquímica, ICBS, UFRGS, Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
| | - Osmar Vieira Ramires Junior
- Programa de Pós-Graduação Em Ciências Biológicas: Bioquímica, ICBS, UFRGS, Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
- Laboratório de Neuroproteção E Doenças Neurometabólicas, Departamento de Bioquímica, ICBS, UFRGS, Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
| | - Josiane Silva Silveira
- Programa de Pós-Graduação Em Ciências Biológicas: Bioquímica, ICBS, UFRGS, Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
- Laboratório de Neuroproteção E Doenças Neurometabólicas, Departamento de Bioquímica, ICBS, UFRGS, Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
| | - Felipe Schmitz
- Laboratório de Neuroproteção E Doenças Neurometabólicas, Departamento de Bioquímica, ICBS, UFRGS, Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
| | - Angela T S Wyse
- Programa de Pós-Graduação Em Ciências Biológicas: Bioquímica, ICBS, UFRGS, Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil.
- Laboratório de Neuroproteção E Doenças Neurometabólicas, Departamento de Bioquímica, ICBS, UFRGS, Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil.
- Departamento de Bioquímica, ICBS, Universidade Federal Do Rio Grande Do Sul, Rua Ramiro Barcelos, 2600-Anexo, CEP, Porto Alegre, RS, 90035-003, Brazil.
| |
Collapse
|
99990
|
Breuss MW, Yang X, Schlachetzki JCM, Antaki D, Lana AJ, Xu X, Chung C, Chai G, Stanley V, Song Q, Newmeyer TF, Nguyen A, O'Brien S, Hoeksema MA, Cao B, Nott A, McEvoy-Venneri J, Pasillas MP, Barton ST, Copeland BR, Nahas S, Van Der Kraan L, Ding Y, Glass CK, Gleeson JG. Somatic mosaicism reveals clonal distributions of neocortical development. Nature 2022; 604:689-696. [PMID: 35444276 PMCID: PMC9436791 DOI: 10.1038/s41586-022-04602-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/25/2022] [Indexed: 11/09/2022]
Abstract
The structure of the human neocortex underlies species-specific traits and reflects intricate developmental programs. Here we sought to reconstruct processes that occur during early development by sampling adult human tissues. We analysed neocortical clones in a post-mortem human brain through a comprehensive assessment of brain somatic mosaicism, acting as neutral lineage recorders1,2. We combined the sampling of 25 distinct anatomic locations with deep whole-genome sequencing in a neurotypical deceased individual and confirmed results with 5 samples collected from each of three additional donors. We identified 259 bona fide mosaic variants from the index case, then deconvolved distinct geographical, cell-type and clade organizations across the brain and other organs. We found that clones derived after the accumulation of 90-200 progenitors in the cerebral cortex tended to respect the midline axis, well before the anterior-posterior or ventral-dorsal axes, representing a secondary hierarchy following the overall patterning of forebrain and hindbrain domains. Clones across neocortically derived cells were consistent with a dual origin from both dorsal and ventral cellular populations, similar to rodents, whereas the microglia lineage appeared distinct from other resident brain cells. Our data provide a comprehensive analysis of brain somatic mosaicism across the neocortex and demonstrate cellular origins and progenitor distribution patterns within the human brain.
Collapse
Affiliation(s)
- Martin W Breuss
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Danny Antaki
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Addison J Lana
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xin Xu
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Changuk Chung
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Guoliang Chai
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Qiong Song
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Traci F Newmeyer
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - An Nguyen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sydney O'Brien
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marten A Hoeksema
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Beibei Cao
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Alexi Nott
- Department of Brain Sciences, Imperial College London, White City Campus, London, UK
- UK Dementia Research Institute, Imperial College London, White City Campus, London, UK
| | - Jennifer McEvoy-Venneri
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Martina P Pasillas
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Scott T Barton
- Division of Medical Education, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Brett R Copeland
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
| |
Collapse
|
99991
|
Desai HS, Yan T, Yu F, Sun AW, Villanueva M, Nesvizhskii AI, Backus KM. SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State-Dependent Redox-Sensitive Cysteines. Mol Cell Proteomics 2022; 21:100218. [PMID: 35219905 PMCID: PMC9010637 DOI: 10.1016/j.mcpro.2022.100218] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 02/07/2023] Open
Abstract
Proteinaceous cysteine residues act as privileged sensors of oxidative stress. As reactive oxygen and nitrogen species have been implicated in numerous pathophysiological processes, deciphering which cysteines are sensitive to oxidative modification and the specific nature of these modifications is essential to understanding protein and cellular function in health and disease. While established mass spectrometry-based proteomic platforms have improved our understanding of the redox proteome, the widespread adoption of these methods is often hindered by complex sample preparation workflows, prohibitive cost of isotopic labeling reagents, and requirements for custom data analysis workflows. Here, we present the SP3-Rox redox proteomics method that combines tailored low cost isotopically labeled capture reagents with SP3 sample cleanup to achieve high throughput and high coverage proteome-wide identification of redox-sensitive cysteines. By implementing a customized workflow in the free FragPipe computational pipeline, we achieve accurate MS1-based quantitation, including for peptides containing multiple cysteine residues. Application of the SP3-Rox method to cellular proteomes identified cysteines sensitive to the oxidative stressor GSNO and cysteine oxidation state changes that occur during T cell activation. High-coverage Cys oxidation state quantification using custom isotopic probes. FragPipe-IonQuant accurately quantifies Cys labeling comparably to Skyline. PTMProphet enables site-of-labeling localization for multi-Cys–containing peptides. SP3-Rox identifies changes in Cys oxidation during T cell activation.
Collapse
Affiliation(s)
- Heta S Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California, USA; Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Tianyang Yan
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, California, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexander W Sun
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California, USA; Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA; Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Keriann M Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, California, USA; Molecular Biology Institute, UCLA, Los Angeles, California, USA; DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, California, USA.
| |
Collapse
|
99992
|
Chandra B, Michmerhuizen NL, Shirnekhi HK, Tripathi S, Pioso BJ, Baggett DW, Mitrea DM, Iacobucci I, White MR, Chen J, Park CG, Wu H, Pounds S, Medyukhina A, Khairy K, Gao Q, Qu C, Abdelhamed S, Gorman SD, Bawa S, Maslanka C, Kinger S, Dogra P, Ferrolino MC, Di Giacomo D, Mecucci C, Klco JM, Mullighan CG, Kriwacki RW. Phase Separation Mediates NUP98 Fusion Oncoprotein Leukemic Transformation. Cancer Discov 2022; 12:1152-1169. [PMID: 34903620 PMCID: PMC8983581 DOI: 10.1158/2159-8290.cd-21-0674] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 11/08/2021] [Accepted: 12/09/2021] [Indexed: 01/07/2023]
Abstract
NUP98 fusion oncoproteins (FO) are drivers in pediatric leukemias and many transform hematopoietic cells. Most NUP98 FOs harbor an intrinsically disordered region from NUP98 that is prone to liquid-liquid phase separation (LLPS) in vitro. A predominant class of NUP98 FOs, including NUP98-HOXA9 (NHA9), retains a DNA-binding homeodomain, whereas others harbor other types of DNA- or chromatin-binding domains. NUP98 FOs have long been known to form puncta, but long-standing questions are how nuclear puncta form and how they drive leukemogenesis. Here we studied NHA9 condensates and show that homotypic interactions and different types of heterotypic interactions are required to form nuclear puncta, which are associated with aberrant transcriptional activity and transformation of hematopoietic stem and progenitor cells. We also show that three additional leukemia-associated NUP98 FOs (NUP98-PRRX1, NUP98-KDM5A, and NUP98-LNP1) form nuclear puncta and transform hematopoietic cells. These findings indicate that LLPS is critical for leukemogenesis by NUP98 FOs. SIGNIFICANCE We show that homotypic and heterotypic mechanisms of LLPS control NUP98-HOXA9 puncta formation, modulating transcriptional activity and transforming hematopoietic cells. Importantly, these mechanisms are generalizable to other NUP98 FOs that share similar domain structures. These findings address long-standing questions on how nuclear puncta form and their link to leukemogenesis. This article is highlighted in the In This Issue feature, p. 873.
Collapse
Affiliation(s)
- Bappaditya Chandra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Hazheen K. Shirnekhi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Swarnendu Tripathi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Brittany J. Pioso
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - David W. Baggett
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Diana M. Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael R. White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jingjing Chen
- Integrated Biomedical Sciences Program, the University of Tennessee Health Science Center, Memphis, Tennessee
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Anna Medyukhina
- Center for Bioimage Informatics, St. Jude Children's Research Hospital Memphis, Tennessee
| | - Khaled Khairy
- Center for Bioimage Informatics, St. Jude Children's Research Hospital Memphis, Tennessee
| | - Qingsong Gao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Scott D. Gorman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Simranjot Bawa
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Carolyn Maslanka
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Rhodes College, Memphis, Tennessee
| | - Swati Kinger
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Rhodes College, Memphis, Tennessee
| | - Priyanka Dogra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mylene C. Ferrolino
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Danika Di Giacomo
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Cristina Mecucci
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Corresponding Authors: Richard W. Kriwacki, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105. Phone: 901-595-3290; Fax: 901-595-3032; E-mail: ; and Charles G. Mullighan,
| | - Richard W. Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, Tennessee
- Corresponding Authors: Richard W. Kriwacki, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105. Phone: 901-595-3290; Fax: 901-595-3032; E-mail: ; and Charles G. Mullighan,
| |
Collapse
|
99993
|
Multi-omics research in sarcopenia: Current progress and future prospects. Ageing Res Rev 2022; 76:101576. [PMID: 35104630 DOI: 10.1016/j.arr.2022.101576] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 12/13/2021] [Accepted: 01/26/2022] [Indexed: 12/17/2022]
Abstract
Sarcopenia is a systemic disease with progressive and generalized skeletal muscle dysfunction defined by age-related low muscle mass, high content of muscle slow fibers, and low muscle function. Muscle phenotypes and sarcopenia risk are heritable; however, the genetic architecture and molecular mechanisms underlying sarcopenia remain largely unclear. In recent years, significant progress has been made in determining susceptibility loci using genome-wide association studies. In addition, recent advances in omics techniques, including genomics, epigenomics, transcriptomics, proteomics, and metabolomics, offer new opportunities to identify novel targets to help us understand the pathophysiology of sarcopenia. However, each individual technology cannot capture the entire view of the biological complexity of this disorder, while integrative multi-omics analyses may be able to reveal new insights. Here, we review the latest findings of multi-omics studies for sarcopenia and provide an in-depth summary of our current understanding of sarcopenia pathogenesis. Leveraging multi-omics data could give us a holistic understanding of sarcopenia etiology that may lead to new clinical applications. This review offers guidance and recommendations for fundamental research, innovative perspectives, and preventative and therapeutic interventions for sarcopenia.
Collapse
|
99994
|
Johnson C, Burkhart DL, Haigis KM. Classification of KRAS-Activating Mutations and the Implications for Therapeutic Intervention. Cancer Discov 2022; 12:913-923. [PMID: 35373279 PMCID: PMC8988514 DOI: 10.1158/2159-8290.cd-22-0035] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/02/2022] [Accepted: 02/02/2022] [Indexed: 12/12/2022]
Abstract
Members of the family of RAS proto-oncogenes, discovered just over 40 years ago, were among the first cancer-initiating genes to be discovered. Of the three RAS family members, KRAS is the most frequently mutated in human cancers. Despite intensive biological and biochemical study of RAS proteins over the past four decades, we are only now starting to devise therapeutic strategies to target their oncogenic properties. Here, we highlight the distinct biochemical properties of common and rare KRAS alleles, enabling their classification into functional subtypes. We also discuss the implications of this functional classification for potential therapeutic avenues targeting mutant subtypes. SIGNIFICANCE Efforts in the recent past to inhibit KRAS oncogenicity have focused on kinases that function in downstream signal transduction cascades, although preclinical successes have not translated to patients with KRAS-mutant cancer. Recently, clinically effective covalent inhibitors of KRASG12C have been developed, establishing two principles that form a foundation for future efforts. First, KRAS is druggable. Second, each mutant form of KRAS is likely to have properties that make it uniquely druggable.
Collapse
Affiliation(s)
- Christian Johnson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Deborah L Burkhart
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kevin M Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
99995
|
Najafi S, Tan SC, Aghamiri S, Raee P, Ebrahimi Z, Jahromi ZK, Rahmati Y, Sadri Nahand J, Piroozmand A, Jajarmi V, Mirzaei H. Therapeutic potentials of CRISPR-Cas genome editing technology in human viral infections. Biomed Pharmacother 2022; 148:112743. [PMID: 35228065 PMCID: PMC8872819 DOI: 10.1016/j.biopha.2022.112743] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 11/25/2022] Open
Abstract
Viral infections are a common cause of morbidity worldwide. The emergence of Coronavirus Disease 2019 (COVID-19) has led to more attention to viral infections and finding novel therapeutics. The CRISPR-Cas9 system has been recently proposed as a potential therapeutic tool for the treatment of viral diseases. Here, we review the research progress in the use of CRISPR-Cas technology for treating viral infections, as well as the strategies for improving the delivery of this gene-editing tool in vivo. Key challenges that hinder the widespread clinical application of CRISPR-Cas9 technology are also discussed, and several possible directions for future research are proposed.
Collapse
Affiliation(s)
- Sajad Najafi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shing Cheng Tan
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Shahin Aghamiri
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pourya Raee
- Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Ebrahimi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Kargar Jahromi
- Central Research Laboratory, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Yazdan Rahmati
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahmad Piroozmand
- Autoimmune Diseases Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Vahid Jajarmi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Correspondence to: Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19395-4818, Iran
| | - Hamed Mirzaei
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran,Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran,Corresponding author at: Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| |
Collapse
|
99996
|
Cojocari D, Smith BN, Purkal JJ, Arrate MP, Huska JD, Xiao Y, Gorska A, Hogdal LJ, Ramsey HE, Boghaert ER, Phillips DC, Savona MR. Pevonedistat and azacitidine upregulate NOXA (PMAIP1) to increase sensitivity to venetoclax in preclinical models of acute myeloid leukemia. Haematologica 2022; 107:825-835. [PMID: 33853293 PMCID: PMC8968901 DOI: 10.3324/haematol.2020.272609] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 04/07/2021] [Indexed: 11/09/2022] Open
Abstract
Dysregulation of apoptotic machinery is one mechanism by which acute myeloid leukemia (AML) acquires a clonal survival advantage. B-cell lymphoma protein-2 (BCL2) overexpression is a common feature in hematologic malignancies. The selective BCL2 inhibitor, venetoclax (VEN) is used in combination with azacitidine (AZA), a DNAmethyltransferase inhibitor (DNMTi), to treat patients with AML. Despite promising response rates to VEN/AZA, resistance to the agent is common. One identified mechanism of resistance is the upregulation of myeloid cell leukemia-1 protein (MCL1). Pevonedistat (PEV), a novel agent that inhibits NEDD8-activating enzyme, and AZA both upregulate NOXA (PMAIP1), a BCL2 family protein that competes with effector molecules at the BH3 binding site of MCL1. We demonstrate that PEV/AZA combination induces NOXA to a greater degree than either PEV or AZA alone, which enhances VEN-mediated apoptosis. Herein, using AML cell lines and primary AML patient samples ex vivo, including in cells with genetic alterations linked to treatment resistance, we demonstrate robust activity of the PEV/VEN/AZA triplet. These findings were corroborated in preclinical systemic engrafted models of AML. Collectively, these results provide rational for combining PEV/VEN/AZA as a novel therapeutic approach in overcoming AML resistance in current therapies.
Collapse
Affiliation(s)
| | - Brianna N Smith
- Department of Pediatrics; Medicine; Program in Cancer Biology, Vanderbilt University School of Medicine
| | | | | | | | - Yu Xiao
- Oncology Discovery, AbbVie, Inc
| | | | - Leah J Hogdal
- Precision Medicine, AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL 60064
| | - Haley E Ramsey
- Medicine; Program in Cancer Biology, Vanderbilt University School of Medicine
| | | | | | - Michael R Savona
- Medicine; Program in Cancer Biology, Vanderbilt University School of Medicine; Vanderbilt-Ingram Cancer Center; Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN 37232.
| |
Collapse
|
99997
|
Song H, Zhang J, Liu B, Xu J, Cai B, Yang H, Straube J, Yu X, Ma T. Biological roles of RNA m 5C modification and its implications in Cancer immunotherapy. Biomark Res 2022; 10:15. [PMID: 35365216 PMCID: PMC8973801 DOI: 10.1186/s40364-022-00362-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/03/2022] [Indexed: 01/08/2023] Open
Abstract
Epigenetics including DNA and RNA modifications have always been the hotspot field of life sciences in the post-genome era. Since the first mapping of N6-methyladenosine (m6A) and the discovery of its widespread presence in mRNA, there are at least 160-170 RNA modifications have been discovered. These methylations occur in different RNA types, and their distribution is species-specific. 5-methylcytosine (m5C) has been found in mRNA, rRNA and tRNA of representative organisms from all kinds of species. As reversible epigenetic modifications, m5C modifications of RNA affect the fate of the modified RNA molecules and play important roles in various biological processes including RNA stability control, protein synthesis, and transcriptional regulation. Furthermore, accumulative evidence also implicates the role of RNA m5C in tumorigenesis. Here, we review the latest progresses in the biological roles of m5C modifications and how it is regulated by corresponding "writers", "readers" and "erasers" proteins, as well as the potential molecular mechanism in tumorigenesis and cancer immunotherapy.
Collapse
Affiliation(s)
- Hang Song
- Department of Biochemistry and Molecular Biology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China
- Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Jianye Zhang
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China.
| | - Bin Liu
- Department of Cellular and Molecular Biology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Jing Xu
- Department of Biochemistry and Molecular Biology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Biao Cai
- Department of Biochemistry and Molecular Biology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China
- Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Hai Yang
- Division of Surgical Research, Department of Surgery, University Medical Center Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, 91054, Erlangen, Germany
| | - Julia Straube
- Division of Molecular and Experimental Surgery, Department of Surgery, University Medical Center Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, 91054, Erlangen, Germany
| | - Xiyong Yu
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China.
| | - Teng Ma
- Department of Cellular and Molecular Biology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China.
| |
Collapse
|
99998
|
Lu J, Chen J, Liu C, Zeng Y, Sun Q, Li J, Shen Z, Chen S, Zhang R. Identification of antibiotic resistance and virulence-encoding factors in Klebsiella pneumoniae by Raman spectroscopy and deep learning. Microb Biotechnol 2022; 15:1270-1280. [PMID: 34843635 PMCID: PMC8966003 DOI: 10.1111/1751-7915.13960] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
Klebsiella pneumoniae has become the number one bacterial pathogen that causes high mortality in clinical settings worldwide. Clinical K. pneumoniae strains with carbapenem resistance and/or hypervirulent phenotypes cause higher mortality comparing with classical K. pneumoniae strains. Rapid differentiation of clinical K. pneumoniae with high resistance/hypervirulence from classical K. pneumoniae would allow us to develop rational and timely treatment plans. In this study, we developed a convolution neural network (CNN) as a prediction method using Raman spectra raw data for rapid identification of ARGs, hypervirulence-encoding factors and resistance phenotypes from K. pneumoniae strains. A total of 71 K. pneumoniae strains were included in this study. The minimum inhibitory concentrations (MICs) of 15 commonly used antimicrobial agents on K. pneumoniae strains were determined. Seven thousand four hundred fifty-five spectra were obtained using the InVia Reflex confocal Raman microscope and used for deep learning-based and machine learning (ML) algorithms analyses. The quality of predictors was estimated in an independent data set. The results of antibiotic resistance and virulence-encoding factors identification showed that the CNN model not only simplified the classification system for Raman spectroscopy but also provided significantly higher accuracy to identify K. pneumoniae with high resistance and virulence when compared with the support vector machine (SVM) and logistic regression (LR) models. By back-testing the Raman-CNN platform on 71 K. pneumoniae strains, we found that Raman spectroscopy allows for highly accurate and rationally designed treatment plans against bacterial infections within hours. More importantly, this method could reduce healthcare costs and antibiotics misuse, limiting the development of antimicrobial resistance and improving patient outcomes.
Collapse
Affiliation(s)
- Jiayue Lu
- Department of Clinical LaboratorySecond Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Jifan Chen
- Department of UltrasoundSecond Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Congcong Liu
- Department of Clinical LaboratorySecond Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Yu Zeng
- Department of Clinical LaboratorySecond Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Qiaoling Sun
- Department of Clinical LaboratorySecond Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Jiaping Li
- Department of Clinical LaboratorySecond Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Zhangqi Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Veterinary MedicineChina Agricultural UniversityBeijingChina
| | - Sheng Chen
- Department of Infectious Diseases and Public HealthJockey Club College of Veterinary Medicine and Life SciencesCity University of Hong KongHong KongChina
| | - Rong Zhang
- Department of Clinical LaboratorySecond Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| |
Collapse
|
99999
|
Hammonds EF, Harwig MC, Paintsil EA, Tillison EA, Hill RB, Morrison EA. Histone H3 and H4 tails play an important role in nucleosome phase separation. Biophys Chem 2022; 283:106767. [PMID: 35158124 PMCID: PMC8963862 DOI: 10.1016/j.bpc.2022.106767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 11/28/2022]
Abstract
Chromatin organization and its dynamic regulation are crucial in governing the temporal and spatial accessibility of DNA for proper gene expression. Disordered chains of nucleosomes comprise the basis of eukaryotic chromatin, forming higher-level organization across a range of length scales. Models of chromatin organization involving phase separation driven by chromatin-associating proteins have been proposed. More recently, evidence has emerged that nucleosome arrays can phase separate in the absence of other protein factors, yet questions remain regarding the molecular basis of chromatin phase separation that governs this dynamic nuclear organization. Here, we break chromatin down into its most basic subunit, the nucleosome core particle, and investigate phase separation using turbidity assays in conjunction with differential interference contrast microscopy. We show that, at physiologically-relevant concentrations, this fundamental subunit of chromatin undergoes phase separation. Individually removing the H3 and H4 tails abrogates phase separation under the same conditions. Taking a reductionist approach to investigate H3 and H4 tail peptide interactions in-trans with DNA and nucleosome core particles supports the direct involvement of these tails in chromatin phase separation. These results provide insight into fundamental mechanisms underlying phase separation of chromatin, which starts at the level of the nucleosome core particle, and support that long-range inter-nucleosomal interactions are sufficient to drive phase separation at nuclear concentrations. Additionally, our data have implications for understanding crosstalk between histone tails and provide a lens through which to interpret the effect of histone post-translational modifications and sequence variants. STATEMENT OF SIGNIFICANCE: Emerging models propose that chromatin organization is based in phase separation, however, mechanisms that drive this dynamic nuclear organization are only beginning to be understood. Previous focus has been on phase separation driven by chromatin-associating proteins, but this has recently shifted to recognize a direct role of chromatin in phase separation. Here, we take a fundamental approach in understanding chromatin phase separation and present new findings that the basic subunit of chromatin, the nucleosome core particle, undergoes phase separation under physiological concentrations of nucleosome and monovalent salt. Furthermore, the histone H3 and H4 tails are involved in phase separation in a manner independent of histone-associating proteins. These data suggest that H3 and H4 tail epigenetic factors may modulate chromatin phase separation.
Collapse
Affiliation(s)
- Erin F Hammonds
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States of America
| | - Megan Cleland Harwig
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States of America
| | - Emeleeta A Paintsil
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States of America
| | - Emma A Tillison
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States of America; Medical Scientist Training Program, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States of America
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States of America
| | - Emma A Morrison
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States of America.
| |
Collapse
|
100000
|
Wang G, Zhao Y, Zhou Y, Jiang L, Liang L, Kong F, Yan Y, Wang X, Wang Y, Wen X, Zeng X, Tian G, Deng G, Shi J, Liu L, Chen H, Li C. PIAS1-mediated SUMOylation of influenza A virus PB2 restricts viral replication and virulence. PLoS Pathog 2022; 18:e1010446. [PMID: 35377920 PMCID: PMC9009768 DOI: 10.1371/journal.ppat.1010446] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 04/14/2022] [Accepted: 03/14/2022] [Indexed: 11/28/2022] Open
Abstract
Host defense systems employ posttranslational modifications to protect against invading pathogens. Here, we found that protein inhibitor of activated STAT 1 (PIAS1) interacts with the nucleoprotein (NP), polymerase basic protein 1 (PB1), and polymerase basic protein 2 (PB2) of influenza A virus (IAV). Lentiviral-mediated stable overexpression of PIAS1 dramatically suppressed the replication of IAV, whereas siRNA knockdown or CRISPR/Cas9 knockout of PIAS1 expression significantly increased virus growth. The expression of PIAS1 was significantly induced upon IAV infection in both cell culture and mice, and PIAS1 was involved in the overall increase in cellular SUMOylation induced by IAV infection. We found that PIAS1 inhibited the activity of the viral RNP complex, whereas the C351S or W372A mutant of PIAS1, which lacks the SUMO E3 ligase activity, lost the ability to suppress the activity of the viral RNP complex. Notably, the SUMO E3 ligase activity of PIAS1 catalyzed robust SUMOylation of PB2, but had no role in PB1 SUMOylation and a minimal role in NP SUMOylation. Moreover, PIAS1-mediated SUMOylation remarkably reduced the stability of IAV PB2. When tested in vivo, we found that the downregulation of Pias1 expression in mice enhanced the growth and virulence of IAV. Together, our findings define PIAS1 as a restriction factor for the replication and pathogenesis of IAV.
Collapse
Affiliation(s)
- Guangwen Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Yuhui Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Yuan Zhou
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Li Jiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Libin Liang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Fandi Kong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Ya Yan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Xuyuan Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Yihan Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Xia Wen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Xianying Zeng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Guobin Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Guohua Deng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Jianzhong Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Liling Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| | - Chengjun Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, The People’s Republic of China
| |
Collapse
|