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Chen B, Chen X, Hu R, Li H, Wang M, Zhou L, Chen H, Wang J, Zhang H, Zhou X, Zhang H. Alternative polyadenylation regulates the translation of metabolic and inflammation-related proteins in adipose tissue of gestational diabetes mellitus. Comput Struct Biotechnol J 2024; 23:1298-1310. [PMID: 38560280 PMCID: PMC10978812 DOI: 10.1016/j.csbj.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/25/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
In gestational diabetes mellitus (GDM), adipose tissue undergoes metabolic disturbances and chronic low-grade inflammation. Alternative polyadenylation (APA) is a post-transcriptional modification mechanism that generates mRNA with variable lengths of 3' untranslated regions (3'UTR), and it is associated with inflammation and metabolism. However, the role of APA in GDM adipose tissue has not been well characterized. In this study, we conducted transcriptomic and proteomic sequencing on subcutaneous and omental adipose tissues from both control and GDM patients. Using Dapars, a novel APA quantitative algorithm, we delineated the APA landscape of adipose tissue, revealing significant 3'UTR elongation of mRNAs in the GDM group. Omental adipose tissue exhibited a significant correlation between elongated 3'UTRs and reduced translation levels of genes related to metabolism and inflammation. Validation experiments in THP-1 derived macrophages (TDMs) demonstrated the impact of APA on translation levels by overexpressing long and short 3'UTR isoforms of a representative gene LRRC25. Additionally, LRRC25 was validated to suppress proinflammatory polarization in TDMs. Further exploration revealed two underexpressed APA trans-acting factors, CSTF3 and PPP1CB, in GDM omental adipose tissue. In conclusion, this study provides preliminary insights into the APA landscape of GDM adipose tissue. Reduced APA regulation in GDM omental adipose tissue may contribute to metabolic disorders and inflammation by downregulating gene translation levels. These findings advance our understanding of the molecular mechanisms underlying GDM-associated adipose tissue changes.
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Affiliation(s)
- Bingnan Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
- The Chongqing Key Laboratory of Translational Medicine in Major Metabolic Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xuyang Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
| | - Ruohan Hu
- Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Hongli Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
| | - Min Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
- The Chongqing Key Laboratory of Translational Medicine in Major Metabolic Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Linwei Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
| | - Hao Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
| | - Jianqi Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
| | - Hanwen Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
| | - Xiaobo Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
| | - Hua Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, China
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2
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Popper B, Bürkle M, Ciccopiedi G, Marchioretto M, Forné I, Imhof A, Straub T, Viero G, Götz M, Schieweck R. Ribosome inactivation regulates translation elongation in neurons. J Biol Chem 2024; 300:105648. [PMID: 38219816 PMCID: PMC10869266 DOI: 10.1016/j.jbc.2024.105648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/10/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024] Open
Abstract
Cellular plasticity is crucial for adapting to ever-changing stimuli. As a result, cells consistently reshape their translatome, and, consequently, their proteome. The control of translational activity has been thoroughly examined at the stage of translation initiation. However, the regulation of ribosome speed in cells is widely unknown. In this study, we utilized a timed ribosome runoff approach, along with proteomics and transmission electron microscopy, to investigate global translation kinetics in cells. We found that ribosome speeds vary among various cell types, such as astrocytes, induced pluripotent human stem cells, human neural stem cells, and human and rat neurons. Of all cell types studied, mature cortical neurons exhibit the highest rate of translation. This finding is particularly remarkable because mature cortical neurons express the eukaryotic elongation factor 2 (eEF2) at lower levels than other cell types. Neurons solve this conundrum by inactivating a fraction of their ribosomes. As a result, the increase in eEF2 levels leads to a reduction of inactive ribosomes and an enhancement of active ones. Processes that alter the demand for active ribosomes, like neuronal excitation, cause increased inactivation of redundant ribosomes in an eEF2-dependent manner. Our data suggest a novel regulatory mechanism in which neurons dynamically inactivate ribosomes to facilitate translational remodeling. These findings have important implications for developmental brain disorders characterized by, among other things, aberrant translation.
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Affiliation(s)
- Bastian Popper
- Core Facility Animal Models, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Martina Bürkle
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Giuliana Ciccopiedi
- Department for Cell Biology & Anatomy, Biomedical Center (BMC), LMU Munich, Munich, Germany; Graduate School of Systemic Neurosciences, LMU Munich, Munich, Germany
| | - Marta Marchioretto
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy
| | - Ignasi Forné
- Protein Analysis Unit, Department for Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Axel Imhof
- Protein Analysis Unit, Department for Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Tobias Straub
- Bioinformatics Core Facility, Department of Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Gabriella Viero
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy
| | - Magdalena Götz
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany; Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany; SYNERGY, Excellence Cluster of Systems Neurology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Rico Schieweck
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany; Department for Cell Biology & Anatomy, Biomedical Center (BMC), LMU Munich, Munich, Germany; Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy.
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3
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Luo J, Gong L, Yang Y, Zhang Y, Liu Q, Bai L, Fang X, Zhang B, Huang J, Liu M, Liu B, Tang Y, Wong CN, Huang J, Liu S, Li S, Ding T, Man K, Lee VHF, Li Y, Ma S, Guan XY. Enhanced mitophagy driven by ADAR1-GLI1 editing supports the self-renewal of cancer stem cells in HCC. Hepatology 2024; 79:61-78. [PMID: 36683360 DOI: 10.1097/hep.0000000000000299] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/08/2022] [Indexed: 01/24/2023]
Abstract
BACKGROUND AND AIMS Deregulation of adenosine-to-inosine editing by adenosine deaminase acting on RNA 1 (ADAR1) leads to tumor-specific transcriptome diversity with prognostic values for HCC. However, ADAR1 editase-dependent mechanisms governing liver cancer stem cell (LCSC) generation and maintenance have remained elusive. APPROACH AND RESULTS RNA-seq profiling identified ADAR1-responsive recoding editing events in HCC and showed editing frequency of GLI1 , rather than transcript abundance was clinically relevant. Functional differences in LCSC self-renewal and tumor aggressiveness between wild-type (GLI1 wt ) and edited GLI1 (GLI1 edit ) were elucidated. We showed that overediting of GLI1 induced an arginine-to-glycine (R701G) substitution, augmenting tumor-initiating potential and exhibiting a more aggressive phenotype. GLI1 R701G harbored weak affinity to SUFU, which in turn, promoted its cytoplasmic-to-nuclear translocation to support LCSC self-renewal by increased pluripotency gene expression. Moreover, editing predisposed to stabilize GLI1 by abrogating β-TrCP-GLI1 interaction. Integrative analysis of single-cell transcriptome further revealed hyperactivated mitophagy in ADAR1-enriched LCSCs. GLI1 editing promoted a metabolic switch to oxidative phosphorylation to control stress and stem-like state through PINK1-Parkin-mediated mitophagy in HCC, thereby conferring exclusive metastatic and sorafenib-resistant capacities. CONCLUSIONS Our findings demonstrate a novel role of ADAR1 as an active regulator for LCSCs properties through editing GLI1 in the highly heterogeneous HCC.
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Affiliation(s)
- Jie Luo
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lanqi Gong
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Clinical Oncology, Shenzhen Key Laboratory of recurrent metastatic cancer and personalized therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Yuma Yang
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yu Zhang
- State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qin Liu
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lu Bai
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Clinical Oncology, Shenzhen Key Laboratory of recurrent metastatic cancer and personalized therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Xiaona Fang
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Baifeng Zhang
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Clinical Oncology, Shenzhen Key Laboratory of recurrent metastatic cancer and personalized therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Jiao Huang
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ming Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Beilei Liu
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Clinical Oncology, Shenzhen Key Laboratory of recurrent metastatic cancer and personalized therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Ying Tang
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ching Ngar Wong
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jinlin Huang
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Shan Liu
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Shanshan Li
- Department of Clinical Oncology, Shenzhen Key Laboratory of recurrent metastatic cancer and personalized therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
| | - Tao Ding
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kwan Man
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Victor Ho-Fun Lee
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Clinical Oncology, Shenzhen Key Laboratory of recurrent metastatic cancer and personalized therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Yan Li
- State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Stephanie Ma
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xin-Yuan Guan
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Clinical Oncology, Shenzhen Key Laboratory of recurrent metastatic cancer and personalized therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Guangzhou, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, China
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4
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Borsa M, Obba S, Richter FC, Zhang H, Riffelmacher T, Carrelha J, Alsaleh G, Jacobsen SEW, Simon AK. Autophagy preserves hematopoietic stem cells by restraining MTORC1-mediated cellular anabolism. Autophagy 2024; 20:45-57. [PMID: 37614038 PMCID: PMC10761185 DOI: 10.1080/15548627.2023.2247310] [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: 03/23/2022] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/25/2023] Open
Abstract
Adult stem cells are long-lived and quiescent with unique metabolic requirements. Macroautophagy/autophagy is a fundamental survival mechanism that allows cells to adapt to metabolic changes by degrading and recycling intracellular components. Here we address why autophagy depletion leads to a drastic loss of the stem cell compartment. Using inducible deletion of autophagy specifically in adult hematopoietic stem cells (HSCs) and in mice chimeric for autophagy-deficient and normal HSCs, we demonstrate that the stem cell loss is cell-intrinsic. Mechanistically, autophagy-deficient HSCs showed higher expression of several amino acid transporters (AAT) when compared to autophagy-competent cells, resulting in increased amino acid (AA) uptake. This was followed by sustained MTOR (mechanistic target of rapamycin) activation, with enlarged cell size, glucose uptake and translation, which is detrimental to the quiescent HSCs. MTOR inhibition by rapamycin treatment in vivo was able to rescue autophagy-deficient HSC loss and bone marrow failure and resulted in better reconstitution after transplantation. Our results suggest that targeting MTOR may improve aged stem cell function, promote reprogramming and stem cell transplantation.List of abbreviations: 5FU: fluoracil; AA: amino acids; AKT/PKB: thymoma viral proto-oncogene 1; ATF4: activating transcription factor 4; BafA: bafilomycin A1; BM: bone marrow; EIF2: eukaryotic initiation factor 2; EIF4EBP1/4EBP1: eukaryotic translation initiation factor 4E binding protein 1; KIT/CD117/c-Kit: KIT proto-oncogene receptor tyrosine kinase; HSCs: hematopoietic stem cells; HSPCs: hematopoietic stem and progenitor cells; Kyn: kynurenine; LSK: lineage- (Lin-), LY6A/Sca-1+, KIT/c-Kit/CD117+; LY6A/Sca-1: lymphocyte antigen 6 family member A; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; MTORC2: MTOR complex 2; OPP: O-propargyl-puromycin; PI3K: phosphoinositide 3-kinase; poly(I:C): polyinosinic:polycytidylic acid; RPS6/S6: ribosomal protein S6; tam: tamoxifen; TCA: tricarboxylic acid; TFEB: transcription factor EB; PTPRC/CD45: Protein Tyrosine Phosphatase Receptor Type C, CD45 antigen.
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Affiliation(s)
- Mariana Borsa
- Kennedy Institute of Rheumatology NDORMS, University of Oxford, Oxford, UK
| | - Sandrine Obba
- Kennedy Institute of Rheumatology NDORMS, University of Oxford, Oxford, UK
| | - Felix C. Richter
- Kennedy Institute of Rheumatology NDORMS, University of Oxford, Oxford, UK
| | - Hanlin Zhang
- Kennedy Institute of Rheumatology NDORMS, University of Oxford, Oxford, UK
| | | | - Joana Carrelha
- MRC Molecular Haematology Unit, MRC WIMM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ghada Alsaleh
- Kennedy Institute of Rheumatology NDORMS, University of Oxford, Oxford, UK
| | - Sten Eirik W. Jacobsen
- MRC Molecular Haematology Unit, MRC WIMM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- H7 Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Anna Katharina Simon
- Kennedy Institute of Rheumatology NDORMS, University of Oxford, Oxford, UK
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
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5
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Hurwitz SN, Jung SK, Kobulsky DR, Fazelinia H, Spruce LA, Pérez EB, Groen N, Mesaros C, Kurre P. Neutral sphingomyelinase blockade enhances hematopoietic stem cell fitness through an integrated stress response. Blood 2023; 142:1708-1723. [PMID: 37699202 PMCID: PMC10667352 DOI: 10.1182/blood.2023022147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/14/2023] Open
Abstract
Hematopoietic stem and progenitor cell (HSPC) transplantation serves as a curative therapy for many benign and malignant hematopoietic disorders and as a platform for gene therapy. However, growing needs for ex vivo manipulation of HSPC-graft products are limited by barriers in maintaining critical self-renewal and quiescence properties. The role of sphingolipid metabolism in safeguarding these essential cellular properties has been recently recognized, but not yet widely explored. Here, we demonstrate that pharmacologic and genetic inhibition of neutral sphingomyelinase 2 (nSMase-2) leads to sustained improvements in long-term competitive transplantation efficiency after ex vivo culture. Mechanistically, nSMase-2 blockade activates a canonical integrated stress response (ISR) and promotes metabolic quiescence in human and murine HSPCs. These adaptations result in part from disruption in sphingolipid metabolism that impairs the release of nSMase-2-dependent extracellular vesicles (EVs). The aggregate findings link EV trafficking and the ISR as a regulatory dyad guarding HSPC homeostasis and long-term fitness. Translationally, transient nSMase-2 inhibition enables ex vivo graft manipulation with enhanced HSPC potency.
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Affiliation(s)
- Stephanie N. Hurwitz
- Comprehensive Bone Marrow Failure Center, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Seul K. Jung
- Comprehensive Bone Marrow Failure Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Danielle R. Kobulsky
- Comprehensive Bone Marrow Failure Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hossein Fazelinia
- Proteomics Core Facility, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Lynn A. Spruce
- Proteomics Core Facility, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Clementina Mesaros
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA
| | - Peter Kurre
- Comprehensive Bone Marrow Failure Center, Children's Hospital of Philadelphia, Philadelphia, PA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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6
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Chen H, Zhao X, Yang W, Zhang Q, Hao R, Jiang S, Han H, Yu Z, Xing S, Feng C, Wang Q, Lu H, Li Y, Quan C, Lu Y, Zhou G. RNA N6-methyladenosine modification-based biomarkers for absorbed ionizing radiation dose estimation. Nat Commun 2023; 14:6912. [PMID: 37903783 PMCID: PMC10616291 DOI: 10.1038/s41467-023-42665-w] [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: 05/07/2023] [Accepted: 10/18/2023] [Indexed: 11/01/2023] Open
Abstract
Radiation triage and biological dosimetry are critical for the medical management of massive potentially exposed individuals following radiological accidents. Here, we performed a genome-wide screening of radiation-responding mRNAs, whose N6-methyladenosine (m6A) levels showed significant alteration after acute irradiation. The m6A levels of three genes, Ncoa4, Ate1 and Fgf22, in peripheral blood mononuclear cells (PBMCs) of mice showed excellent dose-response relationships and could serve as biomarkers of radiation exposure. Especially, the RNA m6A of Ncoa4 maintained a high level as long as 28 days after irradiation. We demonstrated its responsive specificity to radiation, conservation across the mice, monkeys and humans, and the dose-response relationship in PBMCs from cancer patients receiving radiation therapy. Finally, NOCA4 m6A-based biodosimetric models were constructed for estimating absorbed radiation doses in mice or humans. Collectively, this study demonstrated the potential feasibility of RNA m6A in radiation accidents management and clinical applications.
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Affiliation(s)
- Hongxia Chen
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xi Zhao
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Wei Yang
- Department of Radiation Oncology, the First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Qi Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- School of Medicine, University of South China, Hengyang City, Hunan Province, China
| | - Rongjiao Hao
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- School of Life Science, University of Hebei, Baoding City, Hebei Province, China
| | - Siao Jiang
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- School of Life Science, University of Hebei, Baoding City, Hebei Province, China
| | - Huihui Han
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Zuyin Yu
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Shuang Xing
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Changjiang Feng
- Department of Thoracic Surgery, the First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Qianqian Wang
- Department of Radiation Oncology, the First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Hao Lu
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yuanfeng Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Cheng Quan
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yiming Lu
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China.
- School of Life Science, University of Hebei, Baoding City, Hebei Province, China.
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China.
- School of Medicine, University of South China, Hengyang City, Hunan Province, China.
- School of Life Science, University of Hebei, Baoding City, Hebei Province, China.
- Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, Jiangsu Province, China.
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7
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Jamieson CHM, Weissman IL. Stem-Cell Aging and Pathways to Precancer Evolution. N Engl J Med 2023; 389:1310-1319. [PMID: 37792614 DOI: 10.1056/nejmra2304431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Affiliation(s)
- Catriona H M Jamieson
- From the Sanford Stem Cell Institute, Division of Regenerative Medicine, Department of Medicine, University of California at San Diego, La Jolla (C.H.M.J.), and the Institute for Stem Cell Biology and Regenerative Medicine, Stanford University Medical Center, Stanford (I.L.W.) - both in California
| | - Irving L Weissman
- From the Sanford Stem Cell Institute, Division of Regenerative Medicine, Department of Medicine, University of California at San Diego, La Jolla (C.H.M.J.), and the Institute for Stem Cell Biology and Regenerative Medicine, Stanford University Medical Center, Stanford (I.L.W.) - both in California
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8
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Hu S, Wang F, Yang J, Xu X. Elevated ADAR expression is significantly linked to shorter overall survival and immune infiltration in patients with lung adenocarcinoma. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:18063-18082. [PMID: 38052548 DOI: 10.3934/mbe.2023802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
To date, few studies have investigated whether the RNA-editing enzymes adenosine deaminases acting on RNA (ADARs) influence RNA functioning in lung adenocarcinoma (LUAD). To investigate the role of ADAR in lung cancer, we leveraged the advantages of The Cancer Genome Atlas (TCGA) database, from which we obtained transcriptome data and clinical information from 539 patients with LUAD. First, we compared ARAR expression levels in LUAD tissues with those in normal lung tissues using paired and unpaired analyses. Next, we evaluated the influence of ADARs on multiple prognostic indicators, including overall survival at 1, 3 and 5 years, as well as disease-specific survival and progression-free interval, in patients with LUAD. We also used Kaplan-Meier survival curves to estimate overall survival and Cox regression analysis to assess covariates associated with prognosis. A nomogram was constructed to validate the impact of the ADARs and clinicopathological factors on patient survival probabilities. The volcano plot and heat map revealed the differentially expressed genes associated with ADARs in LUAD. Finally, we examined ADAR expression versus immune cell infiltration in LUAD using Spearman's analysis. Using the Gene Expression Profiling Interactive Analysis (GEPIA2) database, we identified the top 100 genes most significantly correlated with ADAR expression, constructed a protein-protein interaction network and performed a Gene Ontology/Kyoto Encyclopedia of Genes and Genomes analysis on these genes. Our results demonstrate that ADARs are overexpressed in LUAD and correlated with poor patient prognosis. ADARs markedly increase the infiltration of T central memory, T helper 2 and T helper cells, while reducing the infiltration of immature dendritic, dendritic and mast cells. Most immune response markers, including T cells, tumor-associated macrophages, T cell exhaustion, mast cells, macrophages, monocytes and dendritic cells, are closely correlated with ADAR expression in LUAD.
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Affiliation(s)
- Siqi Hu
- Northern Jiangsu People's Hospital, Clinical Medical College of Yangzhou University, Yangzhou 225001, China
| | - Fang Wang
- Northern Jiangsu People's Hospital, Clinical Medical College of Yangzhou University, Yangzhou 225001, China
| | - Junjun Yang
- Northern Jiangsu People's Hospital, Clinical Medical College of Yangzhou University, Yangzhou 225001, China
| | - Xingxiang Xu
- Northern Jiangsu People's Hospital, Clinical Medical College of Yangzhou University, Yangzhou 225001, China
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9
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de Morree A, Rando TA. Regulation of adult stem cell quiescence and its functions in the maintenance of tissue integrity. Nat Rev Mol Cell Biol 2023; 24:334-354. [PMID: 36922629 PMCID: PMC10725182 DOI: 10.1038/s41580-022-00568-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2022] [Indexed: 03/18/2023]
Abstract
Adult stem cells are important for mammalian tissues, where they act as a cell reserve that supports normal tissue turnover and can mount a regenerative response following acute injuries. Quiescent stem cells are well established in certain tissues, such as skeletal muscle, brain, and bone marrow. The quiescent state is actively controlled and is essential for long-term maintenance of stem cell pools. In this Review, we discuss the importance of maintaining a functional pool of quiescent adult stem cells, including haematopoietic stem cells, skeletal muscle stem cells, neural stem cells, hair follicle stem cells, and mesenchymal stem cells such as fibro-adipogenic progenitors, to ensure tissue maintenance and repair. We discuss the molecular mechanisms that regulate the entry into, maintenance of, and exit from the quiescent state in mice. Recent studies revealed that quiescent stem cells have a discordance between RNA and protein levels, indicating the importance of post-transcriptional mechanisms, such as alternative polyadenylation, alternative splicing, and translation repression, in the control of stem cell quiescence. Understanding how these mechanisms guide stem cell function during homeostasis and regeneration has important implications for regenerative medicine.
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Affiliation(s)
- Antoine de Morree
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
| | - Thomas A Rando
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, USA.
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10
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Yang X, Liu C, Tang Q, Zhang T, Wang L, Han L, Zhang J, Pei X. Identification of LncRNAs and Functional Analysis of ceRNA Related to Fatty Acid Synthesis during Flax Seed Development. Genes (Basel) 2023; 14:genes14050967. [PMID: 37239327 DOI: 10.3390/genes14050967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/01/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Flax is a flowering plant cultivated for its oil and contains various unsaturated fatty acids. Linseed oil is known as the "deep-sea fish oil" of plants, and is beneficial to brain and blood lipids, among other positive effects. Long non-coding RNAs (lncRNAs) play an important role in plant growth and development. There are not many studies assessing how lncRNAs are related to the fatty acid synthesis of flax. The relative oil contents of the seeds of the variety Heiya NO.14 (for fiber) and the variety Macbeth (for oil) were determined at 5 day, 10 day, 20 day, and 30 day after flowering. We found that 10-20 day is an important period for ALA accumulation in the Macbeth variety. The strand-specific transcriptome data were analyzed at these four time points, and a series of lncRNAs related to flax seed development were screened. A competing endogenous RNA (ceRNA) network was constructed and the accuracy of the network was verified using qRT-PCR. MSTRG.20631.1 could act with miR156 on the same target, squamosa promoter-binding-like protein (SPL), to influence fatty acid biosynthesis through a gluconeogenesis-related pathway during flax seed development. This study provides a theoretical basis for future studies assessing the potential functions of lncRNAs during seed development.
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Affiliation(s)
- Xinsen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Caiyue Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiaoling Tang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tianbao Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Limin Wang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Lida Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianping Zhang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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11
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Chua BA, Lennan CJ, Sunshine MJ, Dreifke D, Chawla A, Bennett EJ, Signer RAJ. Hematopoietic stem cells preferentially traffic misfolded proteins to aggresomes and depend on aggrephagy to maintain protein homeostasis. Cell Stem Cell 2023; 30:460-472.e6. [PMID: 36948186 PMCID: PMC10164413 DOI: 10.1016/j.stem.2023.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 12/31/2022] [Accepted: 02/23/2023] [Indexed: 03/24/2023]
Abstract
Hematopoietic stem cells (HSCs) regenerate blood cells throughout life. To preserve their fitness, HSCs are particularly dependent on maintaining protein homeostasis (proteostasis). However, how HSCs purge misfolded proteins is unknown. Here, we show that in contrast to most cells that primarily utilize the proteasome to degrade misfolded proteins, HSCs preferentially traffic misfolded proteins to aggresomes in a Bag3-dependent manner and depend on aggrephagy, a selective form of autophagy, to maintain proteostasis in vivo. When autophagy is disabled, HSCs compensate by increasing proteasome activity, but proteostasis is ultimately disrupted as protein aggregates accumulate and HSC function is impaired. Bag3-deficiency blunts aggresome formation in HSCs, resulting in protein aggregate accumulation, myeloid-biased differentiation, and diminished self-renewal activity. Furthermore, HSC aging is associated with a severe loss of aggresomes and reduced autophagic flux. Protein degradation pathways are thus specifically configured in young adult HSCs to preserve proteostasis and fitness but become dysregulated during aging.
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Affiliation(s)
- Bernadette A Chua
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093, USA
| | - Connor J Lennan
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093, USA
| | - Mary Jean Sunshine
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093, USA
| | - Daniela Dreifke
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ashu Chawla
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Eric J Bennett
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Robert A J Signer
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093, USA.
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12
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van der Werf I, Mondala PK, Steel SK, Balaian L, Ladel L, Mason CN, Diep RH, Pham J, Cloos J, Kaspers GJL, Chan WC, Mark A, La Clair JJ, Wentworth P, Fisch KM, Crews LA, Whisenant TC, Burkart MD, Donohoe ME, Jamieson CHM. Detection and targeting of splicing deregulation in pediatric acute myeloid leukemia stem cells. Cell Rep Med 2023; 4:100962. [PMID: 36889320 PMCID: PMC10040387 DOI: 10.1016/j.xcrm.2023.100962] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/03/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023]
Abstract
Pediatric acute myeloid leukemia (pAML) is typified by high relapse rates and a relative paucity of somatic DNA mutations. Although seminal studies show that splicing factor mutations and mis-splicing fuel therapy-resistant leukemia stem cell (LSC) generation in adults, splicing deregulation has not been extensively studied in pAML. Herein, we describe single-cell proteogenomics analyses, transcriptome-wide analyses of FACS-purified hematopoietic stem and progenitor cells followed by differential splicing analyses, dual-fluorescence lentiviral splicing reporter assays, and the potential of a selective splicing modulator, Rebecsinib, in pAML. Using these methods, we discover transcriptomic splicing deregulation typified by differential exon usage. In addition, we discover downregulation of splicing regulator RBFOX2 and CD47 splice isoform upregulation. Importantly, splicing deregulation in pAML induces a therapeutic vulnerability to Rebecsinib in survival, self-renewal, and lentiviral splicing reporter assays. Taken together, the detection and targeting of splicing deregulation represent a potentially clinically tractable strategy for pAML therapy.
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Affiliation(s)
- Inge van der Werf
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA; Department of Hematology, Amsterdam University Medical Center, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Phoebe K Mondala
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA
| | - S Kathleen Steel
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA
| | - Larisa Balaian
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA
| | - Luisa Ladel
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA
| | - Cayla N Mason
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA
| | - Raymond H Diep
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jessica Pham
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jacqueline Cloos
- Department of Hematology, Amsterdam University Medical Center, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Gertjan J L Kaspers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Emma Children's Hospital Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Pediatric Oncology, Amsterdam, the Netherlands
| | - Warren C Chan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92037, USA
| | - Adam Mark
- Center for Computational Biology and Bioinformatics (CCBB), University of California, San Diego, La Jolla, CA 92037, USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92037, USA
| | - Peggy Wentworth
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics (CCBB), University of California, San Diego, La Jolla, CA 92037, USA
| | - Leslie A Crews
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA
| | - Thomas C Whisenant
- Center for Computational Biology and Bioinformatics (CCBB), University of California, San Diego, La Jolla, CA 92037, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92037, USA
| | - Mary E Donohoe
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA
| | - Catriona H M Jamieson
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Institute, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA.
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13
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Zhang C, Yi X, Hou M, Li Q, Li X, Lu L, Qi E, Wu M, Qi L, Jian H, Qi Z, Lv Y, Kong X, Bi M, Feng S, Zhou H. The landscape of m 1A modification and its posttranscriptional regulatory functions in primary neurons. eLife 2023; 12:85324. [PMID: 36880874 PMCID: PMC9991057 DOI: 10.7554/elife.85324] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Cerebral ischaemia‒reperfusion injury (IRI), during which neurons undergo oxygen-glucose deprivation/reoxygenation (OGD/R), is a notable pathological process in many neurological diseases. N1-methyladenosine (m1A) is an RNA modification that can affect gene expression and RNA stability. The m1A landscape and potential functions of m1A modification in neurons remain poorly understood. We explored RNA (mRNA, lncRNA, and circRNA) m1A modification in normal and OGD/R-treated mouse neurons and the effect of m1A on diverse RNAs. We investigated the m1A landscape in primary neurons, identified m1A-modified RNAs, and found that OGD/R increased the number of m1A RNAs. m1A modification might also affect the regulatory mechanisms of noncoding RNAs, e.g., lncRNA-RNA binding proteins (RBPs) interactions and circRNA translation. We showed that m1A modification mediates the circRNA/lncRNA‒miRNA-mRNA competing endogenous RNA (ceRNA) mechanism and that 3' untranslated region (3'UTR) modification of mRNAs can hinder miRNA-mRNA binding. Three modification patterns were identified, and genes with different patterns had intrinsic mechanisms with potential m1A-regulatory specificity. Systematic analysis of the m1A landscape in normal and OGD/R neurons lays a critical foundation for understanding RNA modification and provides new perspectives and a theoretical basis for treating and developing drugs for OGD/R pathology-related diseases.
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Affiliation(s)
- Chi Zhang
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Xianfu Yi
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical UniversityTianjinChina
| | - Mengfan Hou
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal CordTianjinChina
| | - Qingyang Li
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Xueying Li
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Lu Lu
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal CordTianjinChina
| | - Enlin Qi
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Mingxin Wu
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal CordTianjinChina
| | - Lin Qi
- Department of Orthopedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South UniversityChangshaChina
| | - Huan Jian
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal CordTianjinChina
| | - Zhangyang Qi
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Yigang Lv
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal CordTianjinChina
| | - Xiaohong Kong
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Mingjun Bi
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
| | - Shiqing Feng
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal CordTianjinChina
| | - Hengxing Zhou
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong UniversityJinanChina
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal CordTianjinChina
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14
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Simultaneous activation of Tor and suppression of ribosome biogenesis by TRIM-NHL proteins promotes terminal differentiation. Cell Rep 2023; 42:112181. [PMID: 36870055 DOI: 10.1016/j.celrep.2023.112181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
Tissue development and homeostasis depend on the balance between growth and terminal differentiation, but the mechanisms coordinating these processes remain elusive. Accumulating evidence indicates that ribosome biogenesis (RiBi) and protein synthesis, two cellular processes sustaining growth, are tightly regulated and yet can be uncoupled during stem cell differentiation. Using the Drosophila adult female germline stem cell and larval neuroblast systems, we show that Mei-P26 and Brat, two Drosophila TRIM-NHL paralogs, are responsible for uncoupling RiBi and protein synthesis during differentiation. In differentiating cells, Mei-P26 and Brat activate the target of rapamycin (Tor) kinase to promote translation, while concomitantly repressing RiBi. Depletion of Mei-P26 or Brat results in defective terminal differentiation, which can be rescued by ectopic activation of Tor together with suppression of RiBi. Our results indicate that uncoupling RiBi and translation activities by TRIM-NHL activity creates the conditions required for terminal differentiation.
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15
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Su J, Jiao T, Liu X, Zhu L, Ma B, Ma F, Li M. Calcyclin-binding protein-promoted degradation of MdFRUCTOKINASE2 regulates sugar homeostasis in apple. PLANT PHYSIOLOGY 2023; 191:1052-1065. [PMID: 36461944 PMCID: PMC9922394 DOI: 10.1093/plphys/kiac549] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Fructokinase (FRK) activates fructose through phosphorylation, which sends the activated fructose into primary metabolism and regulates fructose signaling capabilities in plants. The apple (Malus × domestica) FRK gene MdFRK2 shows especially high affinity to fructose, and its overexpression decreases fructose levels in the leaves of young plants. However, in the current study of mature plants, fruits of transgenic apple trees overexpressing MdFRK2 accumulated a higher level of fructose than wild-type (WT) fruits (at both young and mature stages). Transgenic apple trees with high mRNA MdFRK2 expression showed no significant differences in MdFRK2 protein abundance or FRK enzyme activity compared to WT in mature leaves, young fruits, and mature fruits. Immunoprecipitation-mass spectrometry analysis identified an skp1, cullin, F-box (SCF) E3 ubiquitin ligase, calcyclin-binding protein (CacyBP), that interacted with MdFRK2. RNA-sequencing analysis provided evidence for ubiquitin-mediated post-transcriptional regulation of MdFRK2 protein for the maintenance of fructose homeostasis in mature leaves and fruits. Further analyses suggested an MdCacyBP-MdFRK2 regulatory module, in which MdCacyBP interacts with and ubiquitinates MdFRK2 to facilitate its degradation by the 26S proteasome, thus decreasing the FRK enzyme activity to elevate fructose concentration in transgenic apple trees. This result uncovered an important mechanism underlying plant fructose homeostasis in different organs through regulating the MdFRK2 protein level via ubiquitination and degradation. Our study provides usable data for the future improvement of apple flavor and expands our understanding of the molecular mechanisms underlying plant fructose content and signaling regulation.
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Affiliation(s)
- Jing Su
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Shaanxi Key Laboratory of Apple, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Tiantian Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Shaanxi Key Laboratory of Apple, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xi Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Shaanxi Key Laboratory of Apple, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lingcheng Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Shaanxi Key Laboratory of Apple, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Baiquan Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Shaanxi Key Laboratory of Apple, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Shaanxi Key Laboratory of Apple, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Shaanxi Key Laboratory of Apple, Northwest A&F University, Yangling 712100, Shaanxi, China
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16
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Zhou F, Aroua N, Liu Y, Rohde C, Cheng J, Wirth AK, Fijalkowska D, Göllner S, Lotze M, Yun H, Yu X, Pabst C, Sauer T, Oellerich T, Serve H, Röllig C, Bornhäuser M, Thiede C, Baldus C, Frye M, Raffel S, Krijgsveld J, Jeremias I, Beckmann R, Trumpp A, Müller-Tidow C. A Dynamic rRNA Ribomethylome Drives Stemness in Acute Myeloid Leukemia. Cancer Discov 2023; 13:332-347. [PMID: 36259929 PMCID: PMC9900322 DOI: 10.1158/2159-8290.cd-22-0210] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 09/12/2022] [Accepted: 10/14/2022] [Indexed: 02/07/2023]
Abstract
The development and regulation of malignant self-renewal remain unresolved issues. Here, we provide biochemical, genetic, and functional evidence that dynamics in ribosomal RNA (rRNA) 2'-O-methylation regulate leukemia stem cell (LSC) activity in vivo. A comprehensive analysis of the rRNA 2'-O-methylation landscape of 94 patients with acute myeloid leukemia (AML) revealed dynamic 2'-O-methylation specifically at exterior sites of ribosomes. The rRNA 2'-O-methylation pattern is closely associated with AML development stage and LSC gene expression signature. Forced expression of the 2'-O-methyltransferase fibrillarin (FBL) induced an AML stem cell phenotype and enabled engraftment of non-LSC leukemia cells in NSG mice. Enhanced 2'-O-methylation redirected the ribosome translation program toward amino acid transporter mRNAs enriched in optimal codons and subsequently increased intracellular amino acid levels. Methylation at the single site 18S-guanosine 1447 was instrumental for LSC activity. Collectively, our work demonstrates that dynamic 2'-O-methylation at specific sites on rRNAs shifts translational preferences and controls AML LSC self-renewal. SIGNIFICANCE We establish the complete rRNA 2'-O-methylation landscape in human AML. Plasticity of rRNA 2'-O-methylation shifts protein translation toward an LSC phenotype. This dynamic process constitutes a novel concept of how cancers reprogram cell fate and function. This article is highlighted in the In This Issue feature, p. 247.
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Affiliation(s)
- Fengbiao Zhou
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit EMBL-UKHD, Heidelberg, Germany
- Corresponding Authors: Carsten Müller-Tidow, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-2215-68000; E-mail: ; Fengbiao Zhou, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-221-563-7487; E-mail: ; and Andreas Trumpp, Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. Phone: 4906-2214-23901; E-mail:
| | - Nesrine Aroua
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Yi Liu
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit EMBL-UKHD, Heidelberg, Germany
| | - Christian Rohde
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit EMBL-UKHD, Heidelberg, Germany
| | - Jingdong Cheng
- Gene Center, Department of Biochemistry, University of Munich, Munich, Germany
| | - Anna-Katharina Wirth
- Research Unit Apoptosis in Hematopoietic Stem Cells (AHS), Helmholtz Center Munich, German Center for Environmental Health, Munich, Germany
| | - Daria Fijalkowska
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Göllner
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Michelle Lotze
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Haiyang Yun
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Xiaobing Yu
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Caroline Pabst
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Tim Sauer
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt Am Main, Germany
| | - Hubert Serve
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt Am Main, Germany
| | - Christoph Röllig
- Medical Department 1, University Hospital Dresden, Dresden, Germany
| | | | - Christian Thiede
- Medical Department 1, University Hospital Dresden, Dresden, Germany
| | - Claudia Baldus
- Department of Medicine II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Michaela Frye
- Division of Mechanisms Regulating Gene Expression, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simon Raffel
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells (AHS), Helmholtz Center Munich, German Center for Environmental Health, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center, Department of Biochemistry, University of Munich, Munich, Germany
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- National Center for Tumor Diseases, NCT Heidelberg, Heidelberg, Germany
- Corresponding Authors: Carsten Müller-Tidow, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-2215-68000; E-mail: ; Fengbiao Zhou, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-221-563-7487; E-mail: ; and Andreas Trumpp, Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. Phone: 4906-2214-23901; E-mail:
| | - Carsten Müller-Tidow
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit EMBL-UKHD, Heidelberg, Germany
- National Center for Tumor Diseases, NCT Heidelberg, Heidelberg, Germany
- Corresponding Authors: Carsten Müller-Tidow, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-2215-68000; E-mail: ; Fengbiao Zhou, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-221-563-7487; E-mail: ; and Andreas Trumpp, Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. Phone: 4906-2214-23901; E-mail:
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Dong G, Xu X, Li Y, Ouyang W, Zhao W, Gu Y, Li J, Liu T, Zeng X, Zou H, Wang S, Chen Y, Liu S, Sun H, Liu C. Stemness-related genes revealed by single-cell profiling of naïve and stimulated human CD34 + cells from CB and mPB. Clin Transl Med 2023; 13:e1175. [PMID: 36683248 PMCID: PMC9868212 DOI: 10.1002/ctm2.1175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/28/2022] [Accepted: 01/03/2023] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Hematopoietic stem cells (HSCs) from different sources show varied repopulating capacity, and HSCs lose their stemness after long-time ex vivo culture. A deep understanding of these phenomena may provide helpful insights for HSCs. METHODS Here, we applied single-cell RNA-seq (scRNA-seq) to analyse the naïve and stimulated human CD34+ cells from cord blood (CB) and mobilised peripheral blood (mPB). RESULTS We collected over 16 000 high-quality single-cell data to construct a comprehensive inference map and characterised the HSCs under a quiescent state on the hierarchy top. Then, we compared HSCs in CB with those in mPB and HSCs of naïve samples to those of cultured samples, and identified stemness-related genes (SRGs) associated with cell source (CS-SRGs) and culture time (CT-SRGs), respectively. Interestingly, CS-SRGs and CT-SRGs share genes enriched in the signalling pathways such as mRNA catabolic process, translational initiation, ribonucleoprotein complex biogenesis and cotranslational protein targeting to membrane, suggesting dynamic protein translation and processing may be a common requirement for stemness maintenance. Meanwhile, CT-SRGs are enriched in pathways involved in glucocorticoid and corticosteroid response that affect HSCs homing and engraftment. In contrast, CS-SRGs specifically contain genes related to purine and ATP metabolic process, which is crucial for HSC homeostasis in the stress settings. Particularly, when CT-SRGs are used as reference genes for the construction of the development trajectory of CD34+ cells, lymphoid and myeloid lineages are clearly separated after HSCs/MPPs. Finally, we presented an application through a small-scale drug screening using Connectivity Map (CMap) against CT-SRGs. A small molecule, cucurbitacin I, was found to efficiently expand HSCs ex vivo while maintaining its stemness. CONCLUSIONS Our findings provide new perspectives for understanding HSCs, and the strategy to identify candidate molecules through SRGs may be applicable to study other stem cells.
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Affiliation(s)
- Guoyi Dong
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
- China National GeneBankBGI‐ShenzhenShenzhen518120China
- BGI‐ShenzhenShenzhen518083China
| | - Xiaojing Xu
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
- China National GeneBankBGI‐ShenzhenShenzhen518120China
- BGI‐ShenzhenShenzhen518083China
| | - Yue Li
- Department of Hematology and OncologyShenzhen Children's HospitalShenzhenChina
| | - Wenjie Ouyang
- China National GeneBankBGI‐ShenzhenShenzhen518120China
- BGI‐ShenzhenShenzhen518083China
| | - Weihua Zhao
- Shenzhen Second People's HospitalFirst Affiliated Hospital of Shenzhen UniversityShenzhenChina
| | - Ying Gu
- China National GeneBankBGI‐ShenzhenShenzhen518120China
- BGI‐ShenzhenShenzhen518083China
| | - Jie Li
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
- China National GeneBankBGI‐ShenzhenShenzhen518120China
- BGI‐ShenzhenShenzhen518083China
| | - Tianbin Liu
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
- China National GeneBankBGI‐ShenzhenShenzhen518120China
- BGI‐ShenzhenShenzhen518083China
| | - Xinru Zeng
- China National GeneBankBGI‐ShenzhenShenzhen518120China
| | - Huilin Zou
- China National GeneBankBGI‐ShenzhenShenzhen518120China
| | - Shuguang Wang
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Yue Chen
- China National GeneBankBGI‐ShenzhenShenzhen518120China
- BGI‐ShenzhenShenzhen518083China
| | - Sixi Liu
- Department of Hematology and OncologyShenzhen Children's HospitalShenzhenChina
| | - Hai‐Xi Sun
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
- China National GeneBankBGI‐ShenzhenShenzhen518120China
- BGI‐BeijingBeijing102601China
| | - Chao Liu
- China National GeneBankBGI‐ShenzhenShenzhen518120China
- BGI‐ShenzhenShenzhen518083China
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18
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Yang Y, Meng WJ, Wang ZQ. MicroRNAs (miRNAs): Novel potential therapeutic targets in colorectal cancer. Front Oncol 2022; 12:1054846. [PMID: 36591525 PMCID: PMC9794577 DOI: 10.3389/fonc.2022.1054846] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Colorectal cancer (CRC) is the most common malignant tumor and one of the most lethal malignant tumors in the world. Despite treatment with a combination of surgery, radiotherapy, and/or systemic treatment, including chemotherapy and targeted therapy, the prognosis of patients with advanced CRC remains poor. Therefore, there is an urgent need to explore novel therapeutic strategies and targets for the treatment of CRC. MicroRNAs (miRNAs/miRs) are a class of short noncoding RNAs (approximately 22 nucleotides) involved in posttranscriptional gene expression regulation. The dysregulation of its expression is recognized as a key regulator related to the development, progression and metastasis of CRC. In recent years, a number of miRNAs have been identified as regulators of drug resistance in CRC, and some have gained attention as potential targets to overcome the drug resistance of CRC. In this review, we introduce the miRNAs and the diverse mechanisms of miRNAs in CRC and summarize the potential targeted therapies of CRC based on the miRNAs.
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19
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Li D, Yang J, Malik V, Huang Y, Huang X, Zhou H, Wang J. An RNAi screen of RNA helicases identifies eIF4A3 as a regulator of embryonic stem cell identity. Nucleic Acids Res 2022; 50:12462-12479. [PMID: 36416264 PMCID: PMC9757061 DOI: 10.1093/nar/gkac1084] [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: 01/31/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
RNA helicases are involved in multiple steps of RNA metabolism to direct their roles in gene expression, yet their functions in pluripotency control remain largely unexplored. Starting from an RNA interference (RNAi) screen of RNA helicases, we identified that eIF4A3, a DEAD-box (Ddx) helicase component of the exon junction complex (EJC), is essential for the maintenance of embryonic stem cells (ESCs). Mechanistically, we show that eIF4A3 post-transcriptionally controls the pluripotency-related cell cycle regulators and that its depletion causes the loss of pluripotency via cell cycle dysregulation. Specifically, eIF4A3 is required for the efficient nuclear export of Ccnb1 mRNA, which encodes Cyclin B1, a key component of the pluripotency-promoting pathway during the cell cycle progression of ESCs. Our results reveal a previously unappreciated role for eIF4A3 and its associated EJC in maintaining stem cell pluripotency through post-transcriptional control of the cell cycle.
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Affiliation(s)
- Dan Li
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Cell, Developmental and Regenerative Biology; The Black Family Stem Cell Institute; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jihong Yang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vikas Malik
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yuting Huang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xin Huang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hongwei Zhou
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
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20
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Fakhraldeen SA, Berry SM, Beebe DJ, Alexander CM. Enhanced Ribonucleoprotein Immunoprecipitation (RIP) Technique for the Identification of mRNA Species in Ribonucleoprotein Complexes. Bio Protoc 2022; 12:e4526. [PMID: 36313200 PMCID: PMC9548516 DOI: 10.21769/bioprotoc.4526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 12/29/2022] Open
Abstract
RNA binding proteins (RBPs) are critical regulators of cellular phenotypes, and dysregulated RBP expression is implicated in various diseases including cancer. A single RBP can bind to and regulate the expression of many RNA molecules via a variety of mechanisms, including translational suppression, prevention of RNA degradation, and alteration in subcellular localization. To elucidate the role of a specific RBP within a given cellular context, it is essential to first identify the group of RNA molecules to which it binds. This has traditionally been achieved using cross-linking-based assays in which cells are first exposed to agents that cross-link RBPs to nucleic acids and then lysed to extract and purify the RBP-nucleic acid complexes. The nucleic acids within the mixture are then released and analyzed via conventional means (e.g., microarray analysis, qRT-PCR, RNA sequencing, or Northern blot). While cross-linking-based ribonucleoprotein immunoprecipitation (RIP) has proven its utility within some contexts, it is technically challenging, inefficient, and suboptimal given the amount of time and resources (e.g., cells and antibodies) required. Additionally, these types of studies often require the use of over-expressed versions of proteins, which can introduce artifacts. Here, we describe a streamlined version of RIP that utilizes exclusion-based purification technologies. This approach requires significantly less starting material and resources compared to traditional RIP approaches, takes less time, which is tantamount given the labile nature of RNA, and can be used with endogenously expressed proteins. The method described here can be used to study RNA-protein interactions in a variety of cellular contexts. Graphical abstract.
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Affiliation(s)
- Saja A. Fakhraldeen
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
,
*For correspondence:
| | - Scott M. Berry
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David J. Beebe
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Caroline M. Alexander
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
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21
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Chow PM, Dong JR, Chang YW, Kuo KL, Lin WC, Liu SH, Huang KH. The UCHL5 Inhibitor b-AP15 Overcomes Cisplatin Resistance via Suppression of Cancer Stemness in Urothelial Carcinoma. MOLECULAR THERAPY - ONCOLYTICS 2022; 26:387-398. [PMID: 36090476 PMCID: PMC9421311 DOI: 10.1016/j.omto.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022]
Abstract
Urothelial carcinoma (UC) comprises the majority of bladder cancers. Standard platinum-based chemotherapy has a response rate of approximately 50%, but drug resistance develops after short-term treatment. Deubiquitinating (DUB) enzyme inhibitors increase protein polyubiquitination and endoplasmic reticulum (ER) stress, which might further suppress cancer stemness and overcome cisplatin resistance. Therefore, we investigated the cytotoxic effect and potential mechanisms of b-AP15 on urothelial carcinoma. Our results revealed that b-AP15 induced ER stress and apoptosis in BFTC905, T24, T24/R (cisplatin-resistant), and RT4 urothelial carcinoma cell lines. Inhibition of the MYC signaling pathway and cancer stemness by b-AP15 was confirmed by RNA sequencing, RT-PCR, immunoblotting, and sphere-forming assays. In the mouse xenograft model, the combination of b-AP15 and cisplatin showed superior therapeutic effects compared with either monotherapy.
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Affiliation(s)
- Po-Ming Chow
- Department of Urology, National Taiwan University Hospital, Taipei 100, Taiwan
- Department of Urology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Jun-Ren Dong
- Department of Urology, National Taiwan University Hospital, Taipei 100, Taiwan
- Department of Urology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Yu-Wei Chang
- Department of Urology, National Taiwan University Hospital, Taipei 100, Taiwan
- Department of Urology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Kuan-Lin Kuo
- Department of Urology, National Taiwan University Hospital, Taipei 100, Taiwan
- Department of Urology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Wei-Chou Lin
- Department of Pathology, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Shing-Hwa Liu
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 404, Taiwan
- Department of Pediatrics, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Kuo-How Huang
- Department of Urology, National Taiwan University Hospital, Taipei 100, Taiwan
- Department of Urology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Corresponding author Kuo-How Huang, MD, PhD, Department of Urology, National Taiwan University Hospital and College of Medicine, National Taiwan University, No. 7, Zhongshan S. Rd., Zhongzheng Dist., Taipei 100, Taiwan.
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22
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Li C, Wu B, Li Y, Chen J, Ye Z, Tian X, Wang J, Xu X, Pan S, Zheng Y, Cai X, Jiang L, Zhao M. Amino acid catabolism regulates hematopoietic stem cell proteostasis via a GCN2-eIF2α axis. Cell Stem Cell 2022; 29:1119-1134.e7. [PMID: 35803229 DOI: 10.1016/j.stem.2022.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/28/2022] [Accepted: 06/08/2022] [Indexed: 12/20/2022]
Abstract
Hematopoietic stem cells (HSCs) adapt their metabolism to maintenance and proliferation; however, the mechanism remains incompletely understood. Here, we demonstrated that homeostatic HSCs exhibited high amino acid (AA) catabolism to reduce cellular AA levels, which activated the GCN2-eIF2α axis, a protein synthesis inhibitory checkpoint to restrain protein synthesis for maintenance. Furthermore, upon proliferation conditions, HSCs enhanced mitochondrial oxidative phosphorylation (OXPHOS) for higher energy production but decreased AA catabolism to accumulate cellular AAs, which inactivated the GCN2-eIF2α axis to increase protein synthesis and coupled with proteotoxic stress. Importantly, GCN2 deletion impaired HSC function in repopulation and regeneration. Mechanistically, GCN2 maintained proteostasis and inhibited Src-mediated AKT activation to repress mitochondrial OXPHOS in HSCs. Moreover, the glycolytic metabolite, NAD+ precursor nicotinamide riboside (NR), accelerated AA catabolism to activate GCN2 and sustain the long-term function of HSCs. Overall, our study uncovered direct links between metabolic alterations and translation control in HSCs during homeostasis and proliferation.
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Affiliation(s)
- Changzheng Li
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510000, China; Key Laboratory of Stem Cells and Tissue Engineering (Ministry of Education), Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Binghuo Wu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510000, China; Key Laboratory of Stem Cells and Tissue Engineering (Ministry of Education), Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Yishan Li
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510000, China; Key Laboratory of Stem Cells and Tissue Engineering (Ministry of Education), Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Jie Chen
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Zhitao Ye
- Key Laboratory of Stem Cells and Tissue Engineering (Ministry of Education), Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Xiaobin Tian
- Key Laboratory of Stem Cells and Tissue Engineering (Ministry of Education), Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Jin Wang
- Key Laboratory of Stem Cells and Tissue Engineering (Ministry of Education), Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Xi Xu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Shuai Pan
- Key Laboratory of Stem Cells and Tissue Engineering (Ministry of Education), Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Yucan Zheng
- Key Laboratory of Stem Cells and Tissue Engineering (Ministry of Education), Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Xiongwei Cai
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University, Chongqing 404100, China
| | - Linjia Jiang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Meng Zhao
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510000, China; Key Laboratory of Stem Cells and Tissue Engineering (Ministry of Education), Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510000, China.
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23
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Involvement of Cancer Stem Cells in Chemoresistant Relapse of Epithelial Ovarian Cancer Identified by Transcriptome Analysis. JOURNAL OF ONCOLOGY 2022; 2022:6406122. [PMID: 35401749 PMCID: PMC8991408 DOI: 10.1155/2022/6406122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/03/2022] [Accepted: 03/10/2022] [Indexed: 11/26/2022]
Abstract
Epithelial ovarian cancer (EOC) is the most lethal gynecological malignancy. Despite the initial resection and chemotherapeutic treatment, relapse is common, which leads to poor survival rates in patients. A primary cause of recurrence is the persistence of ovarian cancer stem cells (OCSCs) with high tumorigenicity and chemoresistance. To achieve a better therapeutic response in EOC relapse, the mechanisms underlying acquired chemoresistance associated with relapse-initiating OCSCs need to be studied. Transcriptomes of both chemosensitive primary and chemoresistant relapse EOC samples were obtained from ICGC OV-AU dataset for differential expression analysis. The upregulated genes were further studied using KEGG and GO analysis. Significantly increased expression of eighteen CSC-related genes was found in chemoresistant relapse EOC groups. Upregulation of the expression in four hub genes including WNT3A, SMAD3, KLF4, and PAX6 was verified in chemoresistant relapse samples via immunohistochemistry staining, which confirmed the existence and enrichment of OCSCs in chemoresistant relapse EOC. KEGG and GO enrichment analysis in microarray expression datasets of isolated OCSCs indicated that quiescent state, increased ability of drug efflux, and enhanced response to DNA damage may have caused the chemoresistance in relapse EOC patients. These findings demonstrated a correlation between OCSCs and acquired chemoresistance and illustrated potential underlying mechanisms of OCSC-initiated relapse in EOC patients. Meanwhile, the differentially expressed genes in OCSCs may serve as novel preventive or therapeutic targets against EOC recurrence in the future.
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24
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Quiroga M, Rodríguez-Alonso A, Alfonsín G, Rodríguez JJE, Breijo SM, Chantada V, Figueroa A. Protein Degradation by E3 Ubiquitin Ligases in Cancer Stem Cells. Cancers (Basel) 2022; 14:cancers14040990. [PMID: 35205738 PMCID: PMC8870109 DOI: 10.3390/cancers14040990] [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: 12/30/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary The aim of this review was to discuss the fundamental role of E3 ubiquitin ligases in controlling cancer stem cells. It will be surmised that protein degradation controlled by the E3 ubiquitin ligases plays a fundamental role in the self-renewal, maintenance and differentiation of cancer stem cells, highlighting its potential as an effective therapeutic target for anticancer drug development. Abstract Cancer stem cells are a small subpopulation within the tumor with high capacity for self-renewal, differentiation and reconstitution of tumor heterogeneity. Cancer stem cells are major contributors of tumor initiation, metastasis and therapy resistance in cancer. Emerging evidence indicates that ubiquitination-mediated post-translational modification plays a fundamental role in the maintenance of cancer stem cell characteristics. In this review, we will discuss how protein degradation controlled by the E3 ubiquitin ligases plays a fundamental role in the self-renewal, maintenance and differentiation of cancer stem cells, highlighting the possibility to develop novel therapeutic strategies against E3 ubiquitin ligases targeting CSCs to fight cancer.
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25
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Kretov DA. Role of Y-Box Binding Proteins in Ontogenesis. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S71-S74. [PMID: 35501987 DOI: 10.1134/s0006297922140061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 06/14/2023]
Abstract
Y-box binding proteins (YB proteins) are multifunctional DNA/RNA-binding proteins capable of regulating gene expression at multiple levels. At present, the most studied function of these proteins is the regulation of protein synthesis. Special attention in this review has been paid to the role of YB proteins in the control of mRNA translation and stability at the earliest stages of organism formation, from fertilization to gastrulation. Furthermore, the functions of YB proteins in the formation of germ cells, in which they accumulate in large amounts, are summarized. The review then discusses the contribution of YB proteins to the regulation of gene expression during the differentiation of various types of somatic cells. Finally, future directions in the study of YB proteins and their role in ontogenesis are considered.
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Affiliation(s)
- Dmitry A Kretov
- Department of Biochemistry, School of Medicine, Boston University, Boston, USA, 02218.
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26
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Du Y, Han M, Cao K, Li Q, Pang J, Dou L, Liu S, Shi Z, Yan F, Feng S. Gold Nanorods Exhibit Intrinsic Therapeutic Activity via Controlling N6-Methyladenosine-Based Epitranscriptomics in Acute Myeloid Leukemia. ACS NANO 2021; 15:17689-17704. [PMID: 34694795 DOI: 10.1021/acsnano.1c05547] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Reprograming the N6-methyladenosine (m6A) landscape is a promising therapeutic strategy against recalcitrant leukemia. In this study, we synthesized gold nanorods (GNRs) of different aspect ratios using a binary surfactant mixture of hexadecyltrimethylammonium bromide and sodium oleate. Following surface functionalization with chitosan and a 12-mer peptide, GNRa-CSP12 measuring 130 × 21 nm2 was selectively taken up by leukemia cells via targeted endocytosis. Low doses of GNRa-CSP12 inhibited the growth of leukemia cells by disrupting the redox balance and inducing ferroptosis. Mechanistically, GNRa-CSP12 abrogated endogenous Fe2+-dependent m6A demethylase activity, which led to global m6A hypomethylation and post-transcriptional regulation of downstream genes that are involved in glycolysis, hypoxia, and immune checkpoint pathways. In addition, combination treatment with GNRa-CSP12 and tyrosine kinases inhibitors (TKIs) synergistically obviated the m6A-mediated TKI resistance phenotype. Finally, GNRa-CSP12 as a potential immunotherapeutic agent could enhance immunotherapy outcome in leukemia. Our preclinical findings provide the proof-of-concept for targeting m6A-methylation-based epitranscriptomics using nanoparticle as an "epigenetic drug" for cancer therapy.
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Affiliation(s)
- Yangyang Du
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), International Research Center for Chemistry-Medicine Joint Innovation, College of Chemistry, Jilin University, Changchun 130012, China
| | - Mingda Han
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), International Research Center for Chemistry-Medicine Joint Innovation, College of Chemistry, Jilin University, Changchun 130012, China
| | - Kunxia Cao
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), International Research Center for Chemistry-Medicine Joint Innovation, College of Chemistry, Jilin University, Changchun 130012, China
| | - Qing Li
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), International Research Center for Chemistry-Medicine Joint Innovation, College of Chemistry, Jilin University, Changchun 130012, China
| | - Jiuxia Pang
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, Minnesota 55912, United States
| | - Liping Dou
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, 100853 Beijing, China
| | - Shujun Liu
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, Minnesota 55912, United States
| | - Zhan Shi
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), International Research Center for Chemistry-Medicine Joint Innovation, College of Chemistry, Jilin University, Changchun 130012, China
| | - Fei Yan
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), International Research Center for Chemistry-Medicine Joint Innovation, College of Chemistry, Jilin University, Changchun 130012, China
| | - Shouhua Feng
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), International Research Center for Chemistry-Medicine Joint Innovation, College of Chemistry, Jilin University, Changchun 130012, China
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27
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Duk MA, Gursky VV, Samsonova MG, Surkova SY. Application of Domain- and Genotype-Specific Models to Infer Post-Transcriptional Regulation of Segmentation Gene Expression in Drosophila. Life (Basel) 2021; 11:life11111232. [PMID: 34833107 PMCID: PMC8618293 DOI: 10.3390/life11111232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/05/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
Unlike transcriptional regulation, the post-transcriptional mechanisms underlying zygotic segmentation gene expression in early Drosophila embryo have been insufficiently investigated. Condition-specific post-transcriptional regulation plays an important role in the development of many organisms. Our recent study revealed the domain- and genotype-specific differences between mRNA and the protein expression of Drosophila hb, gt, and eve genes in cleavage cycle 14A. Here, we use this dataset and the dynamic mathematical model to recapitulate protein expression from the corresponding mRNA patterns. The condition-specific nonuniformity in parameter values is further interpreted in terms of possible post-transcriptional modifications. For hb expression in wild-type embryos, our results predict the position-specific differences in protein production. The protein synthesis rate parameter is significantly higher in hb anterior domain compared to the posterior domain. The parameter sets describing Gt protein dynamics in wild-type embryos and Kr mutants are genotype-specific. The spatial discrepancy between gt mRNA and protein posterior expression in Kr mutants is well reproduced by the whole axis model, thus rejecting the involvement of post-transcriptional mechanisms. Our models fail to describe the full dynamics of eve expression, presumably due to its complex shape and the variable time delays between mRNA and protein patterns, which likely require a more complex model. Overall, our modeling approach enables the prediction of regulatory scenarios underlying the condition-specific differences between mRNA and protein expression in early embryo.
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Affiliation(s)
- Maria A. Duk
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia; (M.A.D.); (M.G.S.)
- Theoretical Department, Ioffe Institute, 194021 St. Petersburg, Russia;
| | - Vitaly V. Gursky
- Theoretical Department, Ioffe Institute, 194021 St. Petersburg, Russia;
| | - Maria G. Samsonova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia; (M.A.D.); (M.G.S.)
| | - Svetlana Yu. Surkova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia; (M.A.D.); (M.G.S.)
- Correspondence:
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28
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Windmöller BA, Höving AL, Knabbe C, Greiner JFW. Inter- and Intrapopulational Heterogeneity of Characteristic Markers in Adult Human Neural Crest-derived Stem Cells. Stem Cell Rev Rep 2021; 18:1510-1520. [PMID: 34748196 PMCID: PMC9033708 DOI: 10.1007/s12015-021-10277-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 11/24/2022]
Abstract
Adult human neural crest-derived stem cells (NCSCs) are found in a variety of adult tissues and show an extraordinary broad developmental potential. Despite their great differentiation capacity, increasing evidence suggest a remaining niche-dependent variability between different NCSC-populations regarding their differentiation behavior and expression signatures. In the present study, we extended the view on heterogeneity of NCSCs by identifying heterogeneous expression levels and protein amounts of characteristic markers even between NCSCs from the same niche of origin. In particular, populations of neural crest-derived inferior turbinate stem cells (ITSCs) isolated from different individuals showed significant variations in characteristic NCSC marker proteins Nestin, S100 and Slug in a donor-dependent manner. Notably, increased nuclear protein amounts of Slug were accompanied by a significantly elevated level of nuclear NF-κB-p65 protein, suggesting an NF-κB-dependent regulation of NCSC-makers. In addition to this interpopulational genetic heterogeneity of ITSC-populations from different donors, single ITSCs also revealed a strong heterogeneity regarding the protein amounts of Nestin, S100, Slug and NF-κB-p65 even within the same clonal culture. Our present findings therefor strongly suggest ITSC-heterogeneity to be at least partly based on an interpopulational genetic heterogeneity dependent on the donor accompanied by a stochastic intrapopulational heterogeneity between single cells. We propose this stochastic intrapopulational heterogeneity to occur in addition to the already described genetic variability between clonal NCSC-cultures and the niche-dependent plasticity of NCSCs. Our observations offer a novel perspective on NCSC-heterogeneity, which may build the basis to understand heterogeneous NCSC-behavior.
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Affiliation(s)
- Beatrice A Windmöller
- Department of Cell Biology, University of Bielefeld, Bielefeld, Germany.,Forschungsverbund BioMedizin Bielefeld FBMB e.V, Bielefeld, Germany.,Department of Cellular Neurophysiology, Faculty of Medicine, University of Bielefeld, Bielefeld, Germany
| | - Anna L Höving
- Department of Cell Biology, University of Bielefeld, Bielefeld, Germany.,Institute for Laboratory and Transfusion Medicine, Heart and Diabetes Centre NRW, Ruhr-University Bochum, 32545, Bad Oeynhausen, Germany
| | - Cornelius Knabbe
- Forschungsverbund BioMedizin Bielefeld FBMB e.V, Bielefeld, Germany.,Institute for Laboratory and Transfusion Medicine, Heart and Diabetes Centre NRW, Ruhr-University Bochum, 32545, Bad Oeynhausen, Germany
| | - Johannes F W Greiner
- Department of Cell Biology, University of Bielefeld, Bielefeld, Germany. .,Forschungsverbund BioMedizin Bielefeld FBMB e.V, Bielefeld, Germany.
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29
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Mirzaei R, Gordon A, Zemp FJ, Kumar M, Sarkar S, Luchman HA, Bellail AC, Hao C, Mahoney DJ, Dunn JF, Bose P, Yong VW. PD-1 independent of PD-L1 ligation promotes glioblastoma growth through the NFκB pathway. SCIENCE ADVANCES 2021; 7:eabh2148. [PMID: 34739319 PMCID: PMC8570610 DOI: 10.1126/sciadv.abh2148] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Brain tumor–initiating cells (BTICs) drive glioblastoma growth through not fully understood mechanisms. Here, we found that about 8% of cells within the human glioblastoma microenvironment coexpress programmed cell death 1 (PD-1) and BTIC marker. Gain- or loss-of-function studies revealed that tumor-intrinsic PD-1 promoted proliferation and self-renewal of BTICs. Phosphorylation of tyrosines within the cytoplasmic tail of PD-1 recruited Src homology 2–containing phosphatase 2 and activated the nuclear factor kB in BTICs. Notably, the tumor-intrinsic promoting effects of PD-1 did not require programmed cell death ligand 1(PD-L1) ligation; thus, the therapeutic antibodies inhibiting PD-1/PD-L1 interaction could not overcome the growth advantage of PD-1 in BTICs. Last, BTIC-intrinsic PD-1 accelerated intracranial tumor growth, and this occurred in mice lacking T and B cells. These findings point to a critical role for PD-1 in BTICs and uncover a nonimmune resistance mechanism of patients with glioblastoma to PD-1– or PD-L1–blocking therapies.
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Affiliation(s)
- Reza Mirzaei
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Ashley Gordon
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Franz J. Zemp
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Mehul Kumar
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology, University of Calgary, Calgary, Alberta, Canada
| | - Susobhan Sarkar
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - H. Artee Luchman
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Anita C. Bellail
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chunhai Hao
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Douglas J. Mahoney
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Jeff F. Dunn
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Radiology, University of Calgary, Calgary, Alberta, Canada
| | - Pinaki Bose
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology, University of Calgary, Calgary, Alberta, Canada
- Department of Surgery, University of Calgary, Calgary, Alberta, Canada
| | - V. Wee Yong
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology, University of Calgary, Calgary, Alberta, Canada
- Corresponding author.
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30
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The Balance between Differentiation and Terminal Differentiation Maintains Oral Epithelial Homeostasis. Cancers (Basel) 2021; 13:cancers13205123. [PMID: 34680271 PMCID: PMC8534139 DOI: 10.3390/cancers13205123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Oral cancer affecting the oral cavity represents the most common cancer of the head and neck region. Oral cancer develops in a multistep process in which normal cells gradually accumulate genetic and epigenetic modifications to evolve into a malignant disease. Mortality for oral cancer patients is high and morbidity has a significant long-term impact on the health and wellbeing of affected individuals, typically resulting in facial disfigurement and a loss of the ability to speak, chew, taste, and swallow. The limited scope to which current treatments are able to control oral cancer underlines the need for novel therapeutic strategies. This review highlights the molecular differences between oral cell proliferation, differentiation and terminal differentiation, defines terminal differentiation as an important tumour suppressive mechanism and establishes a rationale for clinical investigation of differentiation-paired therapies that may improve outcomes in oral cancer. Abstract The oral epithelium is one of the fastest repairing and continuously renewing tissues. Stem cell activation within the basal layer of the oral epithelium fuels the rapid proliferation of multipotent progenitors. Stem cells first undergo asymmetric cell division that requires tightly controlled and orchestrated differentiation networks to maintain the pool of stem cells while producing progenitors fated for differentiation. Rapidly expanding progenitors subsequently commit to advanced differentiation programs towards terminal differentiation, a process that regulates the structural integrity and homeostasis of the oral epithelium. Therefore, the balance between differentiation and terminal differentiation of stem cells and their progeny ensures progenitors commitment to terminal differentiation and prevents epithelial transformation and oral squamous cell carcinoma (OSCC). A recent comprehensive molecular characterization of OSCC revealed that a disruption of terminal differentiation factors is indeed a common OSCC event and is superior to oncogenic activation. Here, we discuss the role of differentiation and terminal differentiation in maintaining oral epithelial homeostasis and define terminal differentiation as a critical tumour suppressive mechanism. We further highlight factors with crucial terminal differentiation functions and detail the underlying consequences of their loss. Switching on terminal differentiation in differentiated progenitors is likely to represent an extremely promising novel avenue that may improve therapeutic interventions against OSCC.
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31
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Lv Z, Shi D. Molecule-based osteoarthritis diagnosis comes of age. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1112. [PMID: 34430553 PMCID: PMC8350692 DOI: 10.21037/atm-21-1745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/24/2021] [Indexed: 01/03/2023]
Affiliation(s)
- Zhongyang Lv
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,Laboratory for Bone and Joint Disease, Model Animal Research Center (MARC), Nanjing University, Nanjing, China
| | - Dongquan Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,Laboratory for Bone and Joint Disease, Model Animal Research Center (MARC), Nanjing University, Nanjing, China
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32
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Byres LP, Mufteev M, Yuki KE, Wei W, Piekna A, Wilson MD, Rodrigues DC, Ellis J. Identification of TIA1 mRNA targets during human neuronal development. Mol Biol Rep 2021; 48:6349-6361. [PMID: 34410578 PMCID: PMC8437838 DOI: 10.1007/s11033-021-06634-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/05/2021] [Indexed: 12/11/2022]
Abstract
Background Neuronal development is a tightly controlled process involving multi-layered regulatory mechanisms. While transcriptional pathways regulating neurodevelopment are well characterized, post-transcriptional programs are still poorly understood. TIA1 is an RNA-binding protein that can regulate splicing, stability, or translation of target mRNAs, and has been shown to play critical roles in stress response and neurodevelopment. However, the identity of mRNAs regulated by TIA1 during neurodevelopment under unstressed conditions is still unknown. Methods and Results To identify the mRNAs targeted by TIA1 during the first stages of human neurodevelopment, we performed RNA immunoprecipitation-sequencing (RIP-seq) on human embryonic stem cells (hESCs) and derived neural progenitor cells (NPCs), and cortical neurons under unstressed conditions. While there was no change in TIA1 protein levels, the number of TIA1 targeted mRNAs decreased from pluripotent cells to neurons. We identified 2400, 845, and 330 TIA1 mRNA targets in hESCs, NPC, and neurons, respectively. The vast majority of mRNA targets in hESC were genes associated with neurodevelopment and included autism spectrum disorder-risk genes that were not bound in neurons. Additionally, we found that most TIA1 mRNA targets have reduced ribosomal engagement levels. Conclusion Our results reveal TIA1 mRNA targets in hESCs and during human neurodevelopment, indicate that translation repression is a key process targeted by TIA1 binding and implicate TIA1 function in neuronal differentiation. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-021-06634-0.
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Affiliation(s)
- Loryn P Byres
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Marat Mufteev
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Kyoko E Yuki
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Wei Wei
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Alina Piekna
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Deivid C Rodrigues
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
| | - James Ellis
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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33
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Kruta M, Sunshine MJ, Chua BA, Fu Y, Chawla A, Dillingham CH, Hidalgo San Jose L, De Jong B, Zhou FJ, Signer RAJ. Hsf1 promotes hematopoietic stem cell fitness and proteostasis in response to ex vivo culture stress and aging. Cell Stem Cell 2021; 28:1950-1965.e6. [PMID: 34388375 DOI: 10.1016/j.stem.2021.07.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 05/18/2021] [Accepted: 07/21/2021] [Indexed: 12/20/2022]
Abstract
Maintaining proteostasis is key to resisting stress and promoting healthy aging. Proteostasis is necessary to preserve stem cell function, but little is known about the mechanisms that regulate proteostasis during stress in stem cells, and whether disruptions of proteostasis contribute to stem cell aging is largely unexplored. We determined that ex-vivo-cultured mouse and human hematopoietic stem cells (HSCs) rapidly increase protein synthesis. This challenge to HSC proteostasis was associated with nuclear accumulation of Hsf1, and deletion of Hsf1 impaired HSC maintenance ex vivo. Strikingly, supplementing cultures with small molecules that enhance Hsf1 activation partially suppressed protein synthesis, rebalanced proteostasis, and supported retention of HSC serial reconstituting activity. Although Hsf1 was dispensable for young adult HSCs in vivo, Hsf1 deficiency increased protein synthesis and impaired the reconstituting activity of middle-aged HSCs. Hsf1 thus promotes proteostasis and the regenerative activity of HSCs in response to culture stress and aging.
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Affiliation(s)
- Miriama Kruta
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mary Jean Sunshine
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bernadette A Chua
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yunpeng Fu
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ashu Chawla
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Christopher H Dillingham
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA; La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Lorena Hidalgo San Jose
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bijou De Jong
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fanny J Zhou
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert A J Signer
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
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34
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Rosner A, Armengaud J, Ballarin L, Barnay-Verdier S, Cima F, Coelho AV, Domart-Coulon I, Drobne D, Genevière AM, Jemec Kokalj A, Kotlarska E, Lyons DM, Mass T, Paz G, Pazdro K, Perić L, Ramšak A, Rakers S, Rinkevich B, Spagnuolo A, Sugni M, Cambier S. Stem cells of aquatic invertebrates as an advanced tool for assessing ecotoxicological impacts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:144565. [PMID: 33736145 DOI: 10.1016/j.scitotenv.2020.144565] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 06/12/2023]
Abstract
Environmental stressors are assessed through methods that quantify their impacts on a wide range of metrics including species density, growth rates, reproduction, behaviour and physiology, as on host-pathogen interactions and immunocompetence. Environmental stress may induce additional sublethal effects, like mutations and epigenetic signatures affecting offspring via germline mediated transgenerational inheritance, shaping phenotypic plasticity, increasing disease susceptibility, tissue pathologies, changes in social behaviour and biological invasions. The growing diversity of pollutants released into aquatic environments requires the development of a reliable, standardised and 3R (replacement, reduction and refinement of animals in research) compliant in vitro toolbox. The tools have to be in line with REACH regulation 1907/2006/EC, aiming to improve strategies for potential ecotoxicological risks assessment and monitoring of chemicals threatening human health and aquatic environments. Aquatic invertebrates' adult stem cells (ASCs) are numerous and can be pluripotent, as illustrated by high regeneration ability documented in many of these taxa. This is of further importance as in many aquatic invertebrate taxa, ASCs are able to differentiate into germ cells. Here we propose that ASCs from key aquatic invertebrates may be harnessed for applicable and standardised new tests in ecotoxicology. As part of this approach, a battery of modern techniques and endpoints are proposed to be tested for their ability to correctly identify environmental stresses posed by emerging contaminants in aquatic environments. Consequently, we briefly describe the current status of the available toxicity testing and biota-based monitoring strategies in aquatic environmental ecotoxicology and highlight some of the associated open issues such as replicability, consistency and reliability in the outcomes, for understanding and assessing the impacts of various chemicals on organisms and on the entire aquatic environment. Following this, we describe the benefits of aquatic invertebrate ASC-based tools for better addressing ecotoxicological questions, along with the current obstacles and possible overhaul approaches.
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Affiliation(s)
- Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 8030, Tel Shikmona, Haifa 3108001, Israel.
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols-sur-Cèze, France.
| | - Loriano Ballarin
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35121 Padova, Italy.
| | - Stéphanie Barnay-Verdier
- Sorbonne Université; CNRS, INSERM, Université Côte d'Azur, Institute for Research on Cancer and Aging Nice, F-06107 Nice, France.
| | - Francesca Cima
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35121 Padova, Italy.
| | - Ana Varela Coelho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
| | - Isabelle Domart-Coulon
- Muséum National d'Histoire Naturelle, CNRS, Microorganism Communication and Adaptation Molecules MCAM, Paris F-75005, France.
| | - Damjana Drobne
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Večna pot 111,D, 1000 Ljubljana, Slovenia.
| | - Anne-Marie Genevière
- Sorbonne Université, CNRS, Integrative Biology of Marine Organisms, BIOM, F-6650 Banyuls-sur-mer, France.
| | - Anita Jemec Kokalj
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Večna pot 111,D, 1000 Ljubljana, Slovenia.
| | - Ewa Kotlarska
- Institute of Oceanology of the Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland.
| | - Daniel Mark Lyons
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, HR-52210 Rovinj, Croatia.
| | - Tali Mass
- Marine Biology Department, Leon H. Charney School of Marine Sciences, 199 Aba Khoushy Ave, University of Haifa, 3498838, Israel.
| | - Guy Paz
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 8030, Tel Shikmona, Haifa 3108001, Israel.
| | - Ksenia Pazdro
- Institute of Oceanology of the Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Lorena Perić
- Rudjer Boskovic Institute, Laboratory for Aquaculture and Pathology of Aquaculture Organisms, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
| | - Andreja Ramšak
- National Institute of Biology, Marine Biology Station, Fornače 41, 6330 Piran, Slovenia.
| | | | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 8030, Tel Shikmona, Haifa 3108001, Israel.
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria 2, 20133 Milano, Italy.
| | - Sébastien Cambier
- Luxembourg Institute of Science and Technology, 5, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
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Lung T, Sakem B, Hemmerle A, Nydegger M, Risch M, Risch L, Nydegger U. Autoimmune diseases - New insights into a troublesome field. J Transl Autoimmun 2021; 4:100108. [PMID: 34179743 PMCID: PMC8188057 DOI: 10.1016/j.jtauto.2021.100108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 11/25/2022] Open
Abstract
Recent updates in the diagnosis and management of chronic inflammatory conditions can be brought together to better understand autoimmune diseases (ADs). With organ-specific or organ-limited and systemic ADs, physicians often are faced with a dilemma when making a diagnosis and may feel a kind of embarrassment when a more distinct nosological entity cannot be found. ADs often overlap with other diseases and good diagnostic procedures for ADs only become evidence-based when refined histopathologic, immunopathologic, and general laboratory analyses are available. Immunofluorescence analyses, Western blotting, CUT & RUN technology allow localization of the site of autoantibody-reactivity on the relevant DNA sequence. The Polymerase chain reaction technology and CRISPR-Cas9, the new gene editor using pools of synthetic non-coding RNAs in screening experiments, are expected to lead to advances in the diagnosis of ADs. The current use of mRNA as a vaccine against COVID-19 has increased confidence in the use of mRNA or long non-coding RNAs in the treatment strategy for ADs. The integration of new knowledge about innate immunity, the complement system, vaccinology, and senescence into the care of patients with ADs expands the therapeutic arsenal of disease-modifying drugs and allows for the repurposing of anti-cytokine monoclonal/biosimilar antibodies, originally designed for chronic inflammatory diseases, for ADs. This review article brings together some of the most relevant ideas; a case report included in this review highlights the difficulty of distinguishing between ADs, chronic inflammation, and/or granular disease.
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Affiliation(s)
- Thomas Lung
- Center for Laboratory Medicine Dr Risch, Vaduz, Liechtenstein
| | - Benjamin Sakem
- Center for Laboratory Medicine Dr Risch, Vaduz, Liechtenstein
| | | | - Michèle Nydegger
- Institute of Anesthesiology and Intensive Care Medicine, Triemli City Hospital, Zurich, Switzerland
| | - Martin Risch
- Center for Laboratory Medicine Dr Risch, Vaduz, Liechtenstein
- Central Laboratory, Kantonsspital Graubünden, Chur, Switzerland
| | - Lorenz Risch
- Center for Laboratory Medicine Dr Risch, Vaduz, Liechtenstein
- University of Berne, Berne, Switzerland
| | - Urs Nydegger
- Center for Laboratory Medicine Dr Risch, Vaduz, Liechtenstein
- University of Berne, Berne, Switzerland
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Endoplasmic reticulum stress regulates the intestinal stem cell state through CtBP2. Sci Rep 2021; 11:9892. [PMID: 33972635 PMCID: PMC8111031 DOI: 10.1038/s41598-021-89326-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
Enforcing differentiation of cancer stem cells is considered as a potential strategy to sensitize colorectal cancer cells to irradiation and chemotherapy. Activation of the unfolded protein response, due to endoplasmic reticulum (ER) stress, causes rapid stem cell differentiation in normal intestinal and colon cancer cells. We previously found that stem cell differentiation was mediated by a Protein kinase R-like ER kinase (PERK) dependent arrest of mRNA translation, resulting in rapid protein depletion of WNT-dependent transcription factor c-MYC. We hypothesize that ER stress dependent stem cell differentiation may rely on the depletion of additional transcriptional regulators with a short protein half-life that are rapidly depleted due to a PERK-dependent translational pause. Using a novel screening method, we identify novel transcription factors that regulate the intestinal stem cell fate upon ER stress. ER stress was induced in LS174T cells with thapsigargin or subtilase cytotoxin (SubAB) and immediate alterations in nuclear transcription factor activity were assessed by the CatTFRE assay in which transcription factors present in nuclear lysate are bound to plasmid DNA, co-extracted and quantified using mass-spectrometry. The role of altered activity of transcription factor CtBP2 was further examined by modification of its expression levels using CAG-rtTA3-CtBP2 overexpression in small intestinal organoids, shCtBP2 knockdown in LS174T cells, and familial adenomatous polyposis patient-derived organoids. CtBP2 overexpression organoids were challenged by ER stress and ionizing irradiation. We identified a unique set of transcription factors with altered activation upon ER stress. Gene ontology analysis showed that transcription factors with diminished binding were involved in cellular differentiation processes. ER stress decreased CtBP2 protein expression in mouse small intestine. ER stress induced loss of CtBP2 expression which was rescued by inhibition of PERK signaling. CtBP2 was overexpressed in mouse and human colorectal adenomas. Inducible CtBP2 overexpression in organoids conferred higher clonogenic potential, resilience to irradiation-induced damage and a partial rescue of ER stress-induced loss of stemness. Using an unbiased proteomics approach, we identified a unique set of transcription factors for which DNA-binding activity is lost directly upon ER stress. We continued investigating the function of co-regulator CtBP2, and show that CtBP2 mediates ER stress-induced loss of stemness which supports the intestinal stem cell state in homeostatic stem cells and colorectal cancer cells.
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Maeda R, Kami D, Shikuma A, Suzuki Y, Taya T, Matoba S, Gojo S. RNA decay in processing bodies is indispensable for adipogenesis. Cell Death Dis 2021; 12:285. [PMID: 33731683 PMCID: PMC7969960 DOI: 10.1038/s41419-021-03537-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 12/19/2022]
Abstract
The RNA decay pathway plays key regulatory roles in cell identities and differentiation processes. Although adipogenesis is transcriptionally and epigenetically regulated and has been thoroughly investigated, how RNA metabolism that contributes to the stability of phenotype-shaping transcriptomes participates in differentiation remains elusive. In this study, we investigated Ddx6, an essential component of processing bodies (PBs) that executes RNA decay and translational repression in the cytoplasm and participates in the cellular transition of reprogramming. Upon adipogenic induction, Ddx6 dynamically accumulated to form PBs with a binding partner, 4E-T, at the early phase prior to emergence of intracellular lipid droplets. In contrast, preadipocytes with Ddx6 knockout (KO) or 4E-T knockdown (KD) failed to generate PBs, resulting in significant suppression of adipogenesis. Transcription factors related to preadipocytes and negative regulators of adipogenesis that were not expressed under adipogenic stimulation were maintained in Ddx6-KO and 4E-T-KD preadipocytes under adipogenic induction. Elimination of Dlk1, a major negative regulator of adipogenesis, in 3T3L1 Ddx6-KO cells did not restore adipogenic differentiation capacity to any extent. Similar to murine cells, human primary mesenchymal stem cells, which can differentiate into adipocytes upon stimulation with adipogenic cocktails, required DDX6 to maturate into adipocytes. Therefore, RNA decay of the entire parental transcriptome, rather than removal of a strong negative regulator, could be indispensable for adipogenesis.
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Affiliation(s)
- Ryotaro Maeda
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Daisuke Kami
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Akira Shikuma
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yosuke Suzuki
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Toshihiko Taya
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoshi Gojo
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan.
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38
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Rosu A, El Hachem N, Rapino F, Rouault-Pierre K, Jorssen J, Somja J, Ramery E, Thiry M, Nguyen L, Jacquemyn M, Daelemans D, Adams CM, Bonnet D, Chariot A, Close P, Bureau F, Desmet CJ. Loss of tRNA-modifying enzyme Elp3 activates a p53-dependent antitumor checkpoint in hematopoiesis. J Exp Med 2021; 218:e20200662. [PMID: 33507234 PMCID: PMC7849823 DOI: 10.1084/jem.20200662] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 10/23/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
The hematopoietic system is highly sensitive to perturbations in the translational machinery, of which an emerging level of regulation lies in the epitranscriptomic modification of transfer RNAs (tRNAs). Here, we interrogate the role of tRNA anticodon modifications in hematopoiesis by using mouse models of conditional inactivation of Elp3, the catalytic subunit of Elongator that modifies wobble uridine in specific tRNAs. Loss of Elp3 causes bone marrow failure by inducing death in committing progenitors and compromises the grafting activity of hematopoietic stem cells. Mechanistically, Elp3 deficiency activates a p53-dependent checkpoint in what resembles a misguided amino acid deprivation response that is accompanied by Atf4 overactivation and increased protein synthesis. While deletion of p53 rescues hematopoiesis, loss of Elp3 prompts the development of p53-mutated leukemia/lymphoma, and inactivation of p53 and Elongator cooperatively promotes tumorigenesis. Specific tRNA-modifying enzymes thus condition differentiation and antitumor fate decisions in hematopoietic stem cells and progenitors.
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Affiliation(s)
- Adeline Rosu
- Laboratory of Molecular and Cellular Immunology, GIGA-Stem Cells, GIGA-Research, Liege University, Liège, Belgium
| | - Najla El Hachem
- Laboratory of Cancer Signaling, GIGA-Stem Cells, GIGA-Research, Liege University, Liège, Belgium
| | - Francesca Rapino
- Laboratory of Cancer Signaling, GIGA-Stem Cells, GIGA-Research, Liege University, Liège, Belgium
| | - Kevin Rouault-Pierre
- Haematopoietic Stem Cell Laboratory, Francis Crick Institute, Queen Mary University of London, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Joseph Jorssen
- Laboratory of Molecular and Cellular Immunology, GIGA-Stem Cells, GIGA-Research, Liege University, Liège, Belgium
| | - Joan Somja
- Laboratory of Pathological Anatomy and Cytology, Centre Hospitalier Universitaire, GIGA-Stem Cells and GIGA-Neurosciences, Liege University, Liège, Belgium
| | - Eve Ramery
- Department of Functional Sciences, Faculty of Veterinary Medicine, Liege University, Liège, Belgium
| | - Marc Thiry
- Laboratory of Cellular and Tissular Biology, GIGA-Stem Cells and GIGA-Neurosciences, Liege University, Liège, Belgium
| | - Laurent Nguyen
- Laboratory of MolecularRegulation of Neurogenesis, GIGA-Stem Cells and GIGA-Neurosciences, Liege University, Liège, Belgium
| | - Maarten Jacquemyn
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Christopher M. Adams
- Departments of Internal Medicine and Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA
| | - Dominique Bonnet
- Haematopoietic Stem Cell Laboratory, Francis Crick Institute, Queen Mary University of London, London, UK
| | - Alain Chariot
- Laboratory of Medical Chemistry, GIGA-Stem Cells, Liege University, Liège, Belgium
- Walloon Excellence in Life Sciences and Biotechnology, Wavres, Belgium
| | - Pierre Close
- Laboratory of Cancer Signaling, GIGA-Stem Cells, GIGA-Research, Liege University, Liège, Belgium
- Walloon Excellence in Life Sciences and Biotechnology, Wavres, Belgium
| | - Fabrice Bureau
- Laboratory of Molecular and Cellular Immunology, GIGA-Stem Cells, GIGA-Research, Liege University, Liège, Belgium
- Walloon Excellence in Life Sciences and Biotechnology, Wavres, Belgium
| | - Christophe J. Desmet
- Laboratory of Molecular and Cellular Immunology, GIGA-Stem Cells, GIGA-Research, Liege University, Liège, Belgium
- Walloon Excellence in Life Sciences and Biotechnology, Wavres, Belgium
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Jiang Q, Isquith J, Ladel L, Mark A, Holm F, Mason C, He Y, Mondala P, Oliver I, Pham J, Ma W, Reynoso E, Ali S, Morris IJ, Diep R, Nasamran C, Xu G, Sasik R, Rosenthal SB, Birmingham A, Coso S, Pineda G, Crews L, Donohoe ME, Venter JC, Whisenant T, Mesa RA, Alexandrov LB, Fisch KM, Jamieson C. Inflammation-driven deaminase deregulation fuels human pre-leukemia stem cell evolution. Cell Rep 2021; 34:108670. [PMID: 33503434 PMCID: PMC8477897 DOI: 10.1016/j.celrep.2020.108670] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 12/03/2020] [Accepted: 12/29/2020] [Indexed: 12/11/2022] Open
Abstract
Inflammation-dependent base deaminases promote therapeutic resistance in many malignancies. However, their roles in human pre-leukemia stem cell (pre-LSC) evolution to acute myeloid leukemia stem cells (LSCs) had not been elucidated. Comparative whole-genome and whole-transcriptome sequencing analyses of FACS-purified pre-LSCs from myeloproliferative neoplasm (MPN) patients reveal APOBEC3C upregulation, an increased C-to-T mutational burden, and hematopoietic stem and progenitor cell (HSPC) proliferation during progression, which can be recapitulated by lentiviral APOBEC3C overexpression. In pre-LSCs, inflammatory splice isoform overexpression coincides with APOBEC3C upregulation and ADAR1p150-induced A-to-I RNA hyper-editing. Pre-LSC evolution to LSCs is marked by STAT3 editing, STAT3β isoform switching, elevated phospho-STAT3, and increased ADAR1p150 expression, which can be prevented by JAK2/STAT3 inhibition with ruxolitinib or fedratinib or lentiviral ADAR1 shRNA knockdown. Conversely, lentiviral ADAR1p150 expression enhances pre-LSC replating and STAT3 splice isoform switching. Thus, pre-LSC evolution to LSCs is fueled by primate-specific APOBEC3C-induced pre-LSC proliferation and ADAR1-mediated splicing deregulation.
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Affiliation(s)
- Qingfei Jiang
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Jane Isquith
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Luisa Ladel
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Adam Mark
- Center for Computational Biology & Bioinformatics (CCBB), Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0681, USA
| | - Frida Holm
- Karolinska Institutet, Stockholm, Sweden
| | - Cayla Mason
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Yudou He
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Phoebe Mondala
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Isabelle Oliver
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Jessica Pham
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Wenxue Ma
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Eduardo Reynoso
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Shawn Ali
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Isabella Jamieson Morris
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Raymond Diep
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Chanond Nasamran
- Center for Computational Biology & Bioinformatics (CCBB), Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0681, USA
| | - Guorong Xu
- Center for Computational Biology & Bioinformatics (CCBB), Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0681, USA
| | - Roman Sasik
- Center for Computational Biology & Bioinformatics (CCBB), Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0681, USA
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics (CCBB), Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0681, USA
| | - Amanda Birmingham
- Center for Computational Biology & Bioinformatics (CCBB), Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0681, USA
| | - Sanja Coso
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Gabriel Pineda
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Leslie Crews
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Mary E Donohoe
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | | | - Thomas Whisenant
- Center for Computational Biology & Bioinformatics (CCBB), Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0681, USA
| | - Ruben A Mesa
- Mays Cancer Center at UT Health San Antonio MD Anderson, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Kathleen M Fisch
- Center for Computational Biology & Bioinformatics (CCBB), Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0681, USA.
| | - Catriona Jamieson
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA.
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40
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Magee JA, Signer RAJ. Developmental Stage-Specific Changes in Protein Synthesis Differentially Sensitize Hematopoietic Stem Cells and Erythroid Progenitors to Impaired Ribosome Biogenesis. Stem Cell Reports 2021; 16:20-28. [PMID: 33440178 PMCID: PMC7815942 DOI: 10.1016/j.stemcr.2020.11.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/16/2022] Open
Abstract
Adult hematopoietic stem cell (HSC) self-renewal requires precise control of protein synthesis, but fetal and adult HSCs have distinct self-renewal mechanisms and lineage outputs. This raises the question of whether protein synthesis rates change with age. Here, we show that protein synthesis rates decline during HSC ontogeny, yet erythroid protein synthesis rates increase. A ribosomal mutation that impairs ribosome biogenesis (Rpl24Bst/+) disrupts both fetal and adult HSC self-renewal. However, the Rpl24Bst/+ mutation selectively impairs fetal erythropoiesis at differentiation stages that exhibit fetal-specific attenuation of protein synthesis. Developmental changes in protein synthesis thus differentially sensitize hematopoietic stem and progenitor cells to impaired ribosome biogenesis. Fetal HSCs synthesize much more protein per hour than young adult HSCs in vivo Fetal erythroid progenitors synthesize less protein than adult erythroid progenitors Differences in protein synthesis distinguish fetal and adult erythroid differentiation Rpl24Bst/+ impairs fetal and adult HSCs, but only impairs fetal erythroid progenitors
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Affiliation(s)
- Jeffrey A Magee
- Division of Hematology and Oncology, Department of Pediatrics, and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert A J Signer
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0652, USA.
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41
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Fraga de Andrade I, Mehta C, Bresnick EH. Post-transcriptional control of cellular differentiation by the RNA exosome complex. Nucleic Acids Res 2020; 48:11913-11928. [PMID: 33119769 PMCID: PMC7708067 DOI: 10.1093/nar/gkaa883] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/21/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Given the complexity of intracellular RNA ensembles and vast phenotypic remodeling intrinsic to cellular differentiation, it is instructive to consider the role of RNA regulatory machinery in controlling differentiation. Dynamic post-transcriptional regulation of protein-coding and non-coding transcripts is vital for establishing and maintaining proteomes that enable or oppose differentiation. By contrast to extensively studied transcriptional mechanisms governing differentiation, many questions remain unanswered regarding the involvement of post-transcriptional mechanisms. Through its catalytic activity to selectively process or degrade RNAs, the RNA exosome complex dictates the levels of RNAs comprising multiple RNA classes, thereby regulating chromatin structure, gene expression and differentiation. Although the RNA exosome would be expected to control diverse biological processes, studies to elucidate its biological functions and how it integrates into, or functions in parallel with, cell type-specific transcriptional mechanisms are in their infancy. Mechanistic analyses have demonstrated that the RNA exosome confers expression of a differentiation regulatory receptor tyrosine kinase, downregulates the telomerase RNA component TERC, confers genomic stability and promotes DNA repair, which have considerable physiological and pathological implications. In this review, we address how a broadly operational RNA regulatory complex interfaces with cell type-specific machinery to control cellular differentiation.
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Affiliation(s)
- Isabela Fraga de Andrade
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| | - Charu Mehta
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| | - Emery H Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
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42
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Fischl H, McManus D, Oldenkamp R, Schermelleh L, Mellor J, Jagannath A, Furger A. Cold-induced chromatin compaction and nuclear retention of clock mRNAs resets the circadian rhythm. EMBO J 2020; 39:e105604. [PMID: 33034091 PMCID: PMC7667876 DOI: 10.15252/embj.2020105604] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 12/22/2022] Open
Abstract
Cooling patients to sub‐physiological temperatures is an integral part of modern medicine. We show that cold exposure induces temperature‐specific changes to the higher‐order chromatin and gene expression profiles of human cells. These changes are particularly dramatic at 18°C, a temperature synonymous with that experienced by patients undergoing controlled deep hypothermia during surgery. Cells exposed to 18°C exhibit largely nuclear‐restricted transcriptome changes. These include the nuclear accumulation of mRNAs encoding components of the negative limbs of the core circadian clock, most notably REV‐ERBα. This response is accompanied by compaction of higher‐order chromatin and hindrance of mRNPs from engaging nuclear pores. Rewarming reverses chromatin compaction and releases the transcripts into the cytoplasm, triggering a pulse of negative limb gene proteins that reset the circadian clock. We show that cold‐induced upregulation of REV‐ERBα is sufficient to trigger this reset. Our findings uncover principles of the cellular cold response that must be considered for current and future applications involving therapeutic deep hypothermia.
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Affiliation(s)
- Harry Fischl
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - David McManus
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Roel Oldenkamp
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Jane Mellor
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Aarti Jagannath
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - André Furger
- Department of Biochemistry, University of Oxford, Oxford, UK
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43
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Sciarrillo R, Wojtuszkiewicz A, Assaraf YG, Jansen G, Kaspers GJL, Giovannetti E, Cloos J. The role of alternative splicing in cancer: From oncogenesis to drug resistance. Drug Resist Updat 2020; 53:100728. [PMID: 33070093 DOI: 10.1016/j.drup.2020.100728] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 12/15/2022]
Abstract
Alternative splicing is a tightly regulated process whereby non-coding sequences of pre-mRNA are removed and protein-coding segments are assembled in diverse combinations, ultimately giving rise to proteins with distinct or even opposing functions. In the past decade, whole genome/transcriptome sequencing studies revealed the high complexity of splicing regulation, which occurs co-transcriptionally and is influenced by chromatin status and mRNA modifications. Consequently, splicing profiles of both healthy and malignant cells display high diversity and alternative splicing was shown to be widely deregulated in multiple cancer types. In particular, mutations in pre-mRNA regulatory sequences, splicing regulators and chromatin modifiers, as well as differential expression of splicing factors are important contributors to cancer pathogenesis. It has become clear that these aberrations contribute to many facets of cancer, including oncogenic transformation, cancer progression, response to anticancer drug treatment as well as resistance to therapy. In this respect, alternative splicing was shown to perturb the expression a broad spectrum of relevant genes involved in drug uptake/metabolism (i.e. SLC29A1, dCK, FPGS, and TP), activation of nuclear receptor pathways (i.e. GR, AR), regulation of apoptosis (i.e. MCL1, BCL-X, and FAS) and modulation of response to immunotherapy (CD19). Furthermore, aberrant splicing constitutes an important source of novel cancer biomarkers and the spliceosome machinery represents an attractive target for a novel and rapidly expanding class of therapeutic agents. Small molecule inhibitors targeting SF3B1 or splice factor kinases were highly cytotoxic against a wide range of cancer models, including drug-resistant cells. Importantly, these effects are enhanced in specific cancer subsets, such as splicing factor-mutated and c-MYC-driven tumors. Furthermore, pre-clinical studies report synergistic effects of spliceosome modulators in combination with conventional antitumor agents. These strategies based on the use of low dose splicing modulators could shift the therapeutic window towards decreased toxicity in healthy tissues. Here we provide an extensive overview of the latest findings in the field of regulation of splicing in cancer, including molecular mechanisms by which cancer cells harness alternative splicing to drive oncogenesis and evade anticancer drug treatment as well as splicing-based vulnerabilities that can provide novel treatment opportunities. Furthermore, we discuss current challenges arising from genome-wide detection and prediction methods of aberrant splicing, as well as unravelling functional relevance of the plethora of cancer-related splicing alterations.
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Affiliation(s)
- Rocco Sciarrillo
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Department of Pediatric Oncology, Emma's Children's Hospital, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Anna Wojtuszkiewicz
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Gerrit Jansen
- Amsterdam Immunology and Rheumatology Center, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Gertjan J L Kaspers
- Department of Pediatric Oncology, Emma's Children's Hospital, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Fondazione Pisana per la Scienza, Pisa, Italy
| | - Jacqueline Cloos
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands.
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Schüler SC, Gebert N, Ori A. Stem cell aging: The upcoming era of proteins and metabolites. Mech Ageing Dev 2020; 190:111288. [DOI: 10.1016/j.mad.2020.111288] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/04/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023]
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Xu Y, Ye S, Zhang N, Zheng S, Liu H, Zhou K, Wang L, Cao Y, Sun P, Wang T. The FTO/miR-181b-3p/ARL5B signaling pathway regulates cell migration and invasion in breast cancer. Cancer Commun (Lond) 2020; 40:484-500. [PMID: 32805088 PMCID: PMC7571404 DOI: 10.1002/cac2.12075] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 04/22/2020] [Accepted: 06/27/2020] [Indexed: 12/20/2022] Open
Abstract
Background N6‐methyladenosine (m6A) RNA modification has been demonstrated to be a significant regulatory process in the progression of various tumors, including breast cancer. Fat mass and obesity‐associated (FTO) enzyme, initially known as the obesity‐related protein, is the first identified m6A demethylase. However, the relationship between FTO and breast cancer remains controversial. In this study, we aimed to elucidate the role and clinical significance of FTO in breast cancer and to explore the underlying mechanism. Methods We first investigated the expression of FTO in breast cancer cell lines and tissues by quantitative reverse transcription‐PCR (qRT‐PCR), Western blotting, and immunohistochemistry. Wound healing assay and Transwell assay were performed to determine the migration and invasion abilities of SKBR3 and MDA‐MB453 cells with either knockdown or overexpression of FTO. RNA sequencing (RNA‐seq) was conducted to decipher the downstream targets of FTO. qRT‐PCR, luciferase reporter assay, and Western blotting were employed to confirm the existence of the FTO/miR‐181b‐3p/ARL5B axis. The biological function of ADP ribosylation factor like GTPase 5B (ARL5B) in breast cancer cells was evaluated by wound healing assay and Transwell invasion assay. Results High FTO expression was observed in human epidermal growth factor receptor 2 (HER2)‐positive breast cancer, predicting advanced progression (tumor size [P < 0.001], nuclear grade [P = 0.001], peritumoral lymphovascular invasion [P < 0.001), lymph node metastasis [P = 0.002], and TNM stage [P = 0.001]) and poor prognosis. Moreover, FTO promoted cell invasion and migration in vitro. Mechanistically, RNA‐seq and further confirmation studies suggested that FTO up‐regulated ARL5B by inhibiting miR‐181b‐3p. We further verified that ARL5B also displayed carcinogenic activity in breast cancer cells. Conclusion Our work demonstrated the carcinogenic activity of FTO in promoting the invasion and migration of breast cancer cells via the FTO/miR‐181b‐3p/ARL5B signaling pathway.
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Affiliation(s)
- Yuanyuan Xu
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Shuang Ye
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Nan Zhang
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Shuhui Zheng
- Research Center for Translational Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Huatao Liu
- Department of Clinical Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Kewen Zhou
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Ling Wang
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Yue Cao
- Department of Basic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Peng Sun
- Department of Pathology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Tinghuai Wang
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
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Abstract
PURPOSE OF REVIEW Protein homeostasis (proteostasis) is maintained by an integrated network of physiological mechanisms and stress response pathways that regulate the content and quality of the proteome. Maintenance of cellular proteostasis is key to ensuring normal development, resistance to environmental stress, coping with infection, and promoting healthy aging and lifespan. Recent studies have revealed that several proteostasis mechanisms can function in a cell-type-specific manner within hematopoietic stem cells (HSCs). Here, we review recent studies demonstrating that the proteostasis network functions uniquely in HSCs to promote their maintenance and regenerative function. RECENT FINDINGS The proteostasis network is regulated differently in HSCs as compared with restricted hematopoietic progenitors. Disruptions in proteostasis are particularly detrimental to HSC maintenance and function. These findings suggest that multiple aspects of cellular physiology are uniquely regulated in HSCs to maintain proteostasis, and that precise control of proteostasis is particularly important to support life-long HSC maintenance and regenerative function. SUMMARY The proteostasis network is uniquely configured within HSCs to promote their longevity and hematopoietic function. Future work uncovering cell-type-specific differences in proteostasis network configuration, integration, and function will be essential for understanding how HSCs function during homeostasis, in response to stress, and in disease.
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Affiliation(s)
- Bernadette A Chua
- Department of Medicine, Division of Regenerative Medicine, Moores Cancer Center, University of California San Diego, La Jolla, California, USA
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