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Liang M, Hody C, Yammine V, Soin R, Sun Y, Lin X, Tian X, Meurs R, Perdrau C, Delacourt N, Oumalis M, Andris F, Conrard L, Kruys V, Gueydan C. eIF4EHP promotes Ldh mRNA translation in and fruit fly adaptation to hypoxia. EMBO Rep 2023; 24:e56460. [PMID: 37144276 PMCID: PMC10328074 DOI: 10.15252/embr.202256460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/06/2023] Open
Abstract
Hypoxia induces profound modifications in the gene expression program of eukaryotic cells due to lowered ATP supply resulting from the blockade of oxidative phosphorylation. One significant consequence of oxygen deprivation is the massive repression of protein synthesis, leaving a limited set of mRNAs to be translated. Drosophila melanogaster is strongly resistant to oxygen fluctuations; however, the mechanisms allowing specific mRNA to be translated into hypoxia are still unknown. Here, we show that Ldh mRNA encoding lactate dehydrogenase is highly translated into hypoxia by a mechanism involving a CA-rich motif present in its 3' untranslated region. Furthermore, we identified the cap-binding protein eIF4EHP as a main factor involved in 3'UTR-dependent translation under hypoxia. In accordance with this observation, we show that eIF4EHP is necessary for Drosophila development under low oxygen concentrations and contributes to Drosophila mobility after hypoxic challenge. Altogether, our data bring new insight into mechanisms contributing to LDH production and Drosophila adaptation to oxygen variations.
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Affiliation(s)
- Manfei Liang
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
- Present address:
Medical Science and Technology Innovation CenterShandong First Medical UniversityJinanChina
| | - Clara Hody
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Vanessa Yammine
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Romuald Soin
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Yuqiu Sun
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Xing Lin
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Xiaoying Tian
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Romane Meurs
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Camille Perdrau
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Nadège Delacourt
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Marina Oumalis
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Fabienne Andris
- Laboratoire d'Immunobiologie, Faculté des SciencesUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Louise Conrard
- Center of Microscopy and Molecular Imaging (CMMI)Université libre de Bruxelles (ULB)GosseliesBelgium
| | - Véronique Kruys
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Cyril Gueydan
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
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Timms M, Steel R. Defining the specificity of recombinant human erythropoietin confirmation in equine samples by liquid chromatography-tandem mass spectrometry. Drug Test Anal 2021; 14:676-689. [PMID: 34898016 DOI: 10.1002/dta.3210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/17/2021] [Accepted: 11/26/2021] [Indexed: 12/14/2022]
Abstract
The proteotypic human EPO peptides YLLEAK (T4), SLTTLLR (T11), TITADTFR (T14), and VYSNFLR (T17) are often used to confirm the presence of recombinant human EPO (rhEPO) in equine samples. Each of these peptides contains one or more isomeric leucine or isoleucine amino acids, raising the possibility that a simple leucine/isoleucine substitution could lead to a false identification when compared with a rhEPO reference standard. To examine this possibility variants of these four peptides were analysed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). These studies indicate that confirmation of rhEPO in equine samples by immuno-affinity capture and LC-MS/MS analysis is true and accurate. It was also found that chromatography played a greater role in determining LC-MS/MS specificity than tandem mass spectrometry and that, in the case of more hydrophilic peptides, the accuracy of peptide identification could be enhanced by the inclusion of 13 C and 15 N labelled peptide internal standards.
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Affiliation(s)
- Mark Timms
- Biological Research Unit, Racing Analytical Services Ltd, Flemington, Victoria, Australia
| | - Rohan Steel
- Biological Research Unit, Racing Analytical Services Ltd, Flemington, Victoria, Australia
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3
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Silva J, Nina P, Romão L. Translation of ABCE1 Is Tightly Regulated by Upstream Open Reading Frames in Human Colorectal Cells. Biomedicines 2021; 9:biomedicines9080911. [PMID: 34440115 PMCID: PMC8389594 DOI: 10.3390/biomedicines9080911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022] Open
Abstract
ATP-binding cassette subfamily E member 1 (ABCE1) belongs to the ABC protein family of transporters; however, it does not behave as a drug transporter. Instead, ABCE1 actively participates in different stages of translation and is also associated with oncogenic functions. Ribosome profiling analysis in colorectal cancer cells has revealed a high ribosome occupancy in the human ABCE1 mRNA 5′-leader sequence, indicating the presence of translatable upstream open reading frames (uORFs). These cis-acting translational regulatory elements usually act as repressors of translation of the main coding sequence. In the present study, we dissect the regulatory function of the five AUG and five non-AUG uORFs identified in the human ABCE1 mRNA 5′-leader sequence. We show that the expression of the main coding sequence is tightly regulated by the ABCE1 AUG uORFs in colorectal cells. Our results are consistent with a model wherein uORF1 is efficiently translated, behaving as a barrier to downstream uORF translation. The few ribosomes that can bypass uORF1 (and/or uORF2) must probably initiate at the inhibitory uORF3 or uORF5 that efficiently repress translation of the main ORF. This inhibitory property is slightly overcome in conditions of endoplasmic reticulum stress. In addition, we observed that these potent translation-inhibitory AUG uORFs function equally in cancer and in non-tumorigenic colorectal cells, which is consistent with a lack of oncogenic function. In conclusion, we establish human ABCE1 as an additional example of uORF-mediated translational regulation and that this tight regulation contributes to control ABCE1 protein levels in different cell environments.
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Affiliation(s)
- Joana Silva
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
- Instituto de Biossistemas e Ciências Integrativas (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Pedro Nina
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
| | - Luísa Romão
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
- Instituto de Biossistemas e Ciências Integrativas (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: ; Tel.: +351-21-750-8155
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4
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Natua S, Dhamdhere SG, Mutnuru SA, Shukla S. Interplay within tumor microenvironment orchestrates neoplastic RNA metabolism and transcriptome diversity. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1676. [PMID: 34109748 DOI: 10.1002/wrna.1676] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/03/2021] [Accepted: 05/25/2021] [Indexed: 12/11/2022]
Abstract
The heterogeneous population of cancer cells within a tumor mass interacts intricately with the multifaceted aspects of the surrounding microenvironment. The reciprocal crosstalk between cancer cells and the tumor microenvironment (TME) shapes the cancer pathophysiome in a way that renders it uniquely suited for immune tolerance, angiogenesis, metastasis, and therapy resistance. This dynamic interaction involves a dramatic reconstruction of the transcriptomic landscape of tumors by altering the synthesis, modifications, stability, and processing of gene readouts. In this review, we categorically evaluate the influence of TME components, encompassing a myriad of resident and infiltrating cells, signaling molecules, extracellular vesicles, extracellular matrix, and blood vessels, in orchestrating the cancer-specific metabolism and diversity of both mRNA and noncoding RNA, including micro RNA, long noncoding RNA, circular RNA among others. We also highlight the transcriptomic adaptations in response to the physicochemical idiosyncrasies of TME, which include tumor hypoxia, extracellular acidosis, and osmotic stress. Finally, we provide a nuanced analysis of existing and prospective therapeutics targeting TME to ameliorate cancer-associated RNA metabolism, consequently thwarting the cancer progression. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Subhashis Natua
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
| | - Shruti Ganesh Dhamdhere
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
| | - Srinivas Abhishek Mutnuru
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
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5
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Lee HC, Fu CY, Lin CY, Hu JR, Huang TY, Lo KY, Tsai HY, Sheu JC, Tsai HJ. Poly(U)-specific endoribonuclease ENDOU promotes translation of human CHOP mRNA by releasing uORF element-mediated inhibition. EMBO J 2021; 40:e104123. [PMID: 33511665 PMCID: PMC8167367 DOI: 10.15252/embj.2019104123] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 11/18/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
Upstream open reading frames (uORFs) are known to negatively affect translation of the downstream ORF. The regulatory proteins involved in relieving this inhibition are however poorly characterized. In response to cellular stress, eIF2α phosphorylation leads to an inhibition of global protein synthesis, while translation of specific factors such as CHOP is induced. We analyzed a 105‐nt inhibitory uORF in the transcript of human CHOP (huORFchop) and found that overexpression of the zebrafish or human ENDOU poly(U)‐endoribonuclease (Endouc or ENDOU‐1, respectively) increases CHOP mRNA translation also in the absence of stress. We also found that Endouc/ENDOU‐1 binds and cleaves the huORFchop transcript at position 80G‐81U, which induces CHOP translation independently of phosphorylated eIF2α. However, both ENDOU and phospho‐eIF2α are nonetheless required for maximal translation of CHOP mRNA. Increased levels of ENDOU shift a huORFchop reporter as well as endogenous CHOP transcripts from the monosome to polysome fraction, indicating an increase in translation. Furthermore, we found that the uncapped truncated huORFchop‐69‐105‐nt transcript contains an internal ribosome entry site (IRES), facilitating translation of the cleaved transcript. Therefore, we propose a model where ENDOU‐mediated transcript cleavage positively regulates CHOP translation resulting in increased CHOP protein levels upon stress. Specifically, CHOP transcript cleavage changes the configuration of huORFchop thereby releasing its inhibition and allowing the stalled ribosomes to resume translation of the downstream ORF.
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Affiliation(s)
- Hung-Chieh Lee
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
| | - Chuan-Yang Fu
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
| | - Cheng-Yung Lin
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
| | - Jia-Rung Hu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Ting-Ying Huang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Kai-Yin Lo
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hsin-Yue Tsai
- Institute of Molecular Medicine, School of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jin-Chuan Sheu
- Liver Disease Prevention and Treatment Research Foundation, Taipei, Taiwan
| | - Huai-Jen Tsai
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan.,Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan.,Department of Life Science, Fu Jen Catholic University, New Taipei, Taiwan
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6
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Xu C, Zhang J. Mammalian Alternative Translation Initiation Is Mostly Nonadaptive. Mol Biol Evol 2021; 37:2015-2028. [PMID: 32145028 DOI: 10.1093/molbev/msaa063] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Alternative translation initiation (ATLI) refers to the existence of multiple translation initiation sites per gene and is a widespread phenomenon in eukaryotes. ATLI is commonly assumed to be advantageous through creating proteome diversity or regulating protein synthesis. We here propose an alternative hypothesis that ATLI arises primarily from nonadaptive initiation errors presumably due to the limited ability of ribosomes to distinguish sequence motifs truly signaling translation initiation from similar sequences. Our hypothesis, but not the adaptive hypothesis, predicts a series of global patterns of ATLI, all of which are confirmed at the genomic scale by quantitative translation initiation sequencing in multiple human and mouse cell lines and tissues. Similarly, although many codons differing from AUG by one nucleotide can serve as start codons, our analysis suggests that using non-AUG start codons is mostly disadvantageous. These and other findings strongly suggest that ATLI predominantly results from molecular error, requiring a major revision of our understanding of the precision and regulation of translation initiation.
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Affiliation(s)
- Chuan Xu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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7
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Torma G, Tombácz D, Csabai Z, Moldován N, Mészáros I, Zádori Z, Boldogkői Z. Combined Short and Long-Read Sequencing Reveals a Complex Transcriptomic Architecture of African Swine Fever Virus. Viruses 2021; 13:v13040579. [PMID: 33808073 PMCID: PMC8103240 DOI: 10.3390/v13040579] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/17/2021] [Accepted: 03/28/2021] [Indexed: 11/16/2022] Open
Abstract
African swine fever virus (ASFV) is a large DNA virus belonging to the Asfarviridae family. Despite its agricultural importance, little is known about the fundamental molecular mechanisms of this pathogen. Short-read sequencing (SRS) can produce a huge amount of high-precision sequencing reads for transcriptomic profiling, but it is inefficient for comprehensively annotating transcriptomes. Long-read sequencing (LRS) can overcome some of SRS's limitations, but it also has drawbacks, such as low-coverage and high error rate. The limitations of the two approaches can be surmounted by the combined use of these techniques. In this study, we used Illumina SRS and Oxford Nanopore Technologies LRS platforms with multiple library preparation methods (amplified and direct cDNA sequencings and native RNA sequencing) for constructing the ASFV transcriptomic atlas. This work identified many novel transcripts and transcript isoforms and annotated the precise termini of previously described RNAs. This study identified a novel species of ASFV transcripts, the replication origin-associated RNAs. Additionally, we discovered several nested genes embedded into larger canonical genes. In contrast to the current view that the ASFV transcripts are monocistronic, we detected a significant extent of polycistronism. A multifaceted meshwork of transcriptional overlaps was also discovered.
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Affiliation(s)
- Gábor Torma
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
| | - Norbert Moldován
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
| | - István Mészáros
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, H-1143 Budapest, Hungary; (I.M.); (Z.Z.)
| | - Zoltán Zádori
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, H-1143 Budapest, Hungary; (I.M.); (Z.Z.)
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
- Correspondence:
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8
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Lee LJ, Papadopoli D, Jewer M, Del Rincon S, Topisirovic I, Lawrence MG, Postovit LM. Cancer Plasticity: The Role of mRNA Translation. Trends Cancer 2020; 7:134-145. [PMID: 33067172 PMCID: PMC8023421 DOI: 10.1016/j.trecan.2020.09.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/08/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022]
Abstract
Tumor progression is associated with dedifferentiated histopathologies concomitant with cancer cell survival within a changing, and often hostile, tumor microenvironment. These processes are enabled by cellular plasticity, whereby intracellular cues and extracellular signals are integrated to enable rapid shifts in cancer cell phenotypes. Cancer cell plasticity, at least in part, fuels tumor heterogeneity and facilitates metastasis and drug resistance. Protein synthesis is frequently dysregulated in cancer, and emerging data suggest that translational reprograming collaborates with epigenetic and metabolic programs to effectuate phenotypic plasticity of neoplasia. Herein, we discuss the potential role of mRNA translation in cancer cell plasticity, highlight emerging histopathological correlates, and deliberate on how this is related to efforts to improve understanding of the complex tumor ecology.
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Affiliation(s)
- Laura J Lee
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - David Papadopoli
- Lady Davis Institute, Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Michael Jewer
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Sonia Del Rincon
- Lady Davis Institute, Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Ivan Topisirovic
- Lady Davis Institute, Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, McGill University, Montreal, QC, Canada.
| | - Mitchell G Lawrence
- Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Lynne-Marie Postovit
- Department of Oncology, University of Alberta, Edmonton, AB, Canada; Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.
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9
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Dumortier L, Bricout VA. Obstructive sleep apnea syndrome in adults with down syndrome: Causes and consequences. Is it a "chicken and egg" question? Neurosci Biobehav Rev 2020; 108:124-138. [DOI: 10.1016/j.neubiorev.2019.10.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/11/2019] [Accepted: 10/26/2019] [Indexed: 12/31/2022]
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10
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Abstract
Cells respond to hypoxia by shifting cellular processes from general housekeeping functions to activating specialized hypoxia-response pathways. Oxygen plays an important role in generating ATP to maintain a productive rate of protein synthesis in normoxia. In hypoxia, the rate of the canonical protein synthesis pathway is significantly slowed and impaired due to limited ATP availability, necessitating an alternative mechanism to mediate protein synthesis and facilitate adaptation. Hypoxia adaptation is largely mediated by hypoxia-inducible factors (HIFs). While HIFs are well known for their transcriptional functions, they also play imperative roles in translation to mediate hypoxic protein synthesis. Such adaptations to hypoxia are often hyperactive in solid tumors, contributing to the expression of cancer hallmarks, including treatment resistance. The current literature on protein synthesis in hypoxia is reviewed here, inclusive of hypoxia-specific mRNA selection to translation termination. Current HIF targeting therapies are also discussed as are the opportunities involved with targeting hypoxia specific protein synthesis pathways.
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Affiliation(s)
- Nancy T Chee
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL, 33136, USA
| | - Ines Lohse
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL, 33136, USA
| | - Shaun P Brothers
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL, 33136, USA.
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11
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Khitun A, Ness TJ, Slavoff SA. Small open reading frames and cellular stress responses. Mol Omics 2019; 15:108-116. [PMID: 30810554 DOI: 10.1039/c8mo00283e] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Small open reading frames (smORFs) encoding polypeptides of less than 100 amino acids in eukaryotes (50 amino acids in prokaryotes) were historically excluded from genome annotation. However, recent advances in genomics, ribosome footprinting, and proteomics have revealed thousands of translated smORFs in genomes spanning evolutionary space. These smORFs can encode functional polypeptides, or act as cis-translational regulators. Herein we review evidence that some smORF-encoded polypeptides (SEPs) participate in stress responses in both prokaryotes and eukaryotes, and that some upstream ORFs (uORFs) regulate stress-responsive translation of downstream cistrons in eukaryotic cells. These studies provide insight into a regulated subclass of smORFs and suggest that at least some SEPs may participate in maintenance of cellular homeostasis under stress.
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Affiliation(s)
- Alexandra Khitun
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. and Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Travis J Ness
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. and Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Sarah A Slavoff
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. and Department of Chemistry, Yale University, New Haven, CT 06520, USA and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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12
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Zmajkovic J, Lundberg P, Nienhold R, Torgersen ML, Sundan A, Waage A, Skoda RC. A Gain-of-Function Mutation in EPO in Familial Erythrocytosis. N Engl J Med 2018. [PMID: 29514032 DOI: 10.1056/nejmoa1709064] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Familial erythrocytosis with elevated erythropoietin levels is frequently caused by mutations in genes that regulate oxygen-dependent transcription of the gene encoding erythropoietin ( EPO). We identified a mutation in EPO that cosegregated with disease with a logarithm of the odds (LOD) score of 3.3 in a family with autosomal dominant erythrocytosis. This mutation, a single-nucleotide deletion (c.32delG), introduces a frameshift in exon 2 that interrupts translation of the main EPO messenger RNA (mRNA) transcript but initiates excess production of erythropoietin from what is normally a noncoding EPO mRNA transcribed from an alternative promoter located in intron 1. (Funded by the Gebert Rüf Foundation and others.).
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Affiliation(s)
- Jakub Zmajkovic
- From the Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel (J.Z., P.L., R.N., R.C.S.), and Diagnostic Hematology, University Hospital Basel (P.L.), Basel, Switzerland; and the Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (M.L.T., A.S., A.W.), and the Department of Hematology, St. Olavs Hospital (A.W.) - both in Trondheim, Norway
| | - Pontus Lundberg
- From the Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel (J.Z., P.L., R.N., R.C.S.), and Diagnostic Hematology, University Hospital Basel (P.L.), Basel, Switzerland; and the Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (M.L.T., A.S., A.W.), and the Department of Hematology, St. Olavs Hospital (A.W.) - both in Trondheim, Norway
| | - Ronny Nienhold
- From the Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel (J.Z., P.L., R.N., R.C.S.), and Diagnostic Hematology, University Hospital Basel (P.L.), Basel, Switzerland; and the Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (M.L.T., A.S., A.W.), and the Department of Hematology, St. Olavs Hospital (A.W.) - both in Trondheim, Norway
| | - Maria L Torgersen
- From the Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel (J.Z., P.L., R.N., R.C.S.), and Diagnostic Hematology, University Hospital Basel (P.L.), Basel, Switzerland; and the Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (M.L.T., A.S., A.W.), and the Department of Hematology, St. Olavs Hospital (A.W.) - both in Trondheim, Norway
| | - Anders Sundan
- From the Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel (J.Z., P.L., R.N., R.C.S.), and Diagnostic Hematology, University Hospital Basel (P.L.), Basel, Switzerland; and the Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (M.L.T., A.S., A.W.), and the Department of Hematology, St. Olavs Hospital (A.W.) - both in Trondheim, Norway
| | - Anders Waage
- From the Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel (J.Z., P.L., R.N., R.C.S.), and Diagnostic Hematology, University Hospital Basel (P.L.), Basel, Switzerland; and the Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (M.L.T., A.S., A.W.), and the Department of Hematology, St. Olavs Hospital (A.W.) - both in Trondheim, Norway
| | - Radek C Skoda
- From the Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel (J.Z., P.L., R.N., R.C.S.), and Diagnostic Hematology, University Hospital Basel (P.L.), Basel, Switzerland; and the Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (M.L.T., A.S., A.W.), and the Department of Hematology, St. Olavs Hospital (A.W.) - both in Trondheim, Norway
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13
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Kiss DL, Baez W, Huebner K, Bundschuh R, Schoenberg DR. Impact of FHIT loss on the translation of cancer-associated mRNAs. Mol Cancer 2017; 16:179. [PMID: 29282095 PMCID: PMC5745650 DOI: 10.1186/s12943-017-0749-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/10/2017] [Indexed: 11/30/2022] Open
Abstract
Background FHIT is a genome caretaker/tumor suppressor that is silenced in >50% of cancers. Although it was identified more than 20 years ago, questions remain as to how FHIT loss contributes to cancer, and conversely, how FHIT acts to maintain genome integrity and suppress malignancy. Fhit belongs to the histidine triad family of enzymes that catalyze the degradation of nucleoside 5′,5′-triphosphates, including the m7GpppN ‘caps’ that are generated when mRNAs undergo 3′-5′ decay. This raised the possibility that Fhit loss might affect changes in the translation of cancer-associated mRNAs, possibly as a consequence of increased intracellular concentrations of these molecules. Results Ribosome profiling identified several hundred mRNAs for which coding region ribosome occupancy changed as a function of Fhit expression. While many of these changes could be explained by changes in mRNA steady-state, a subset of these showed changes in translation efficiency as a function of Fhit expression. The onset of malignancy has been linked to changes in 5’-UTR ribosome occupancy and this analysis also identified ribosome binding to 5′-untranslated regions (UTRs) of a number of cancer-associated mRNAs. 5’-UTR ribosome occupancy of these mRNAs differed between Fhit-negative and Fhit-positive cells, and in some cases these differences correlated with differences in coding region ribosome occupancy. Conclusions In summary, these findings show Fhit expression impacts the translation of a number of cancer associated genes, and they support the hypothesis that Fhit’s genome protective/tumor suppressor function is associated with post-transcriptional changes in expression of genes whose dysregulation contributes to malignancy. Electronic supplementary material The online version of this article (10.1186/s12943-017-0749-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel L Kiss
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA.,Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA.,Biomarker Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - William Baez
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Kay Huebner
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH, 43210, USA.,Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, 43210, USA.,Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Daniel R Schoenberg
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA. .,Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA. .,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA.
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14
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Balázs Z, Tombácz D, Szűcs A, Csabai Z, Megyeri K, Petrov AN, Snyder M, Boldogkői Z. Long-Read Sequencing of Human Cytomegalovirus Transcriptome Reveals RNA Isoforms Carrying Distinct Coding Potentials. Sci Rep 2017; 7:15989. [PMID: 29167532 PMCID: PMC5700075 DOI: 10.1038/s41598-017-16262-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/07/2017] [Indexed: 12/22/2022] Open
Abstract
The human cytomegalovirus (HCMV) is a ubiquitous, human pathogenic herpesvirus. The complete viral genome is transcriptionally active during infection; however, a large part of its transcriptome has yet to be annotated. In this work, we applied the amplified isoform sequencing technique from Pacific Biosciences to characterize the lytic transcriptome of HCMV strain Towne varS. We developed a pipeline for transcript annotation using long-read sequencing data. We identified 248 transcriptional start sites, 116 transcriptional termination sites and 80 splicing events. Using this information, we have annotated 291 previously undescribed or only partially annotated transcript isoforms, including eight novel antisense transcripts and their isoforms, as well as a novel transcript (RS2) in the short repeat region, partially antisense to RS1. Similarly to other organisms, we discovered a high transcriptional diversity in HCMV, with many transcripts only slightly differing from one another. Comparing our transcriptome profiling results to an earlier ribosome footprint analysis, we have concluded that the majority of the transcripts contain multiple translationally active ORFs, and also that most isoforms contain unique combinations of ORFs. Based on these results, we propose that one important function of this transcriptional diversity may be to provide a regulatory mechanism at the level of translation.
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Affiliation(s)
- Zsolt Balázs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, 6720, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, 6720, Hungary.,Department of Genetics, School of Medicine, Stanford University, Stanford, California, 94305, USA
| | - Attila Szűcs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, 6720, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, 6720, Hungary
| | - Klára Megyeri
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, Szeged, 6720, Hungary
| | - Alexey N Petrov
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, California, 94305, USA.,Department of Biological Sciences, College of Sciences and Mathematics, Auburn University, Auburn, Alabama, 36849, USA
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, Stanford, California, 94305, USA
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, 6720, Hungary.
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15
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Marques-Ramos A, Candeias MM, Menezes J, Lacerda R, Willcocks M, Teixeira A, Locker N, Romão L. Cap-independent translation ensures mTOR expression and function upon protein synthesis inhibition. RNA (NEW YORK, N.Y.) 2017; 23:1712-1728. [PMID: 28821580 PMCID: PMC5648038 DOI: 10.1261/rna.063040.117] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 08/15/2017] [Indexed: 06/07/2023]
Abstract
The mechanistic/mammalian target of rapamycin (mTOR) is a conserved serine/threonine kinase that integrates cellular signals from the nutrient and energy status to act, namely, on the protein synthesis machinery. While major advances have emerged regarding the regulators and effects of the mTOR signaling pathway, little is known about the regulation of mTOR gene expression. Here, we show that the human mTOR transcript can be translated in a cap-independent manner, and that its 5' untranslated region (UTR) is a highly folded RNA scaffold capable of binding directly to the 40S ribosomal subunit. We further demonstrate that mTOR is able to bypass the cap requirement for translation both in normal and hypoxic conditions. Moreover, our data reveal that the cap-independent translation of mTOR is necessary for its ability to induce cell-cycle progression into S phase. These results suggest a novel regulatory mechanism for mTOR gene expression that integrates the global protein synthesis changes induced by translational inhibitory conditions.
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Affiliation(s)
- Ana Marques-Ramos
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Marco M Candeias
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Juliane Menezes
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Rafaela Lacerda
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Margaret Willcocks
- Microbial and Cellular Sciences Department, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7TE, United Kingdom
| | - Alexandre Teixeira
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal
| | - Nicolas Locker
- Microbial and Cellular Sciences Department, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7TE, United Kingdom
| | - Luísa Romão
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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16
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Jiang Z, Yang J, Dai A, Wang Y, Li W, Xie Z. Ribosome profiling reveals translational regulation of mammalian cells in response to hypoxic stress. BMC Genomics 2017; 18:638. [PMID: 28826393 PMCID: PMC5563900 DOI: 10.1186/s12864-017-3996-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 08/01/2017] [Indexed: 12/30/2022] Open
Abstract
Background Retinal pigment epithelium (RPE) cells transfer oxygen and nutrients from choroid to the neural retina. Reduced oxygen to RPE perturbs development and functions of blood vessels in retina. Previous efforts of genome-wide studies have been largely focused on transcriptional changes of cells in response to hypoxia. Recently developed ribosome profiling provides an opportunity to study genome-wide translational changes. To gain systemic insights into the transcriptional and translational regulation of cellular in response to hypoxic stress, we used simultaneous RNA sequencing and ribosome profiling on an RPE cells line, ARPE-19, under hypoxia condition. Results Both HIF-1α and EPAS1 (HIF-2α) proteins were stabilized in ARPE-19 under hypoxic stress treatment at 1 h, 2 h and 4 h. Analysis of simultaneous RNA sequencing and ribosome profiling data showed genome-wide gene expression changes at both transcriptional and translational levels. Comparative analysis of ribosome profiling and RNA-seq data revealed that hypoxia induced changes of more genes at the translational than the transcriptional levels. Ribosomes densities at 5′ untranslated region (UTR) significantly increased under hypoxic stress. Interestingly, the increase in ribosome densities at 5′ UTR is positively correlated with the presence of upstream open reading frames (uORFs) in the 5′ UTR of mRNAs. Conclusion Our results characterized translational profiles of mRNAs for a RPE cell line in response to hypoxia. In particular, uORFs play important roles in the regulation of translation efficiency by affecting ribosomes loading onto mRNAs. This study provides the first attempt to understand translational response of mammalian cells under hypoxic condition. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3996-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhiwen Jiang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jiaqi Yang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Aimei Dai
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yuming Wang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wei Li
- Retinal Neurobiology Section, National Eye Institute, Bethesda, MD, USA
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.
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17
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Erythropoietin levels in patients with sleep apnea: a meta-analysis. Eur Arch Otorhinolaryngol 2017; 274:2505-2512. [PMID: 28280920 PMCID: PMC5420001 DOI: 10.1007/s00405-017-4483-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/24/2017] [Indexed: 02/08/2023]
Abstract
Currently available data regarding the blood levels of erythropoietin (EPO) in sleep apnea (SA) patients are contradictory. The aim of the present meta-analysis was to evaluate the EPO levels in SA patients via quantitative analysis. A systematic search of Pubmed, Embase, and Web of Science were performed. EPO levels in SA group and control group were extracted from each eligible study. Weight mean difference (WMD) or Standard mean difference (SMD) with 95% confidence interval (CI) was calculated by using fixed-effects or random effect model analysis according to the degree of heterogeneity between studies. A total of 9 studies involving 407 participants were enrolled. The results indicated that EPO levels in SA group were significantly higher than that in control group (SMD 0.61, 95% CI 0.11–1.11, p = 0.016). Significantly higher EPO levels were found in patients with body mass index <30 kg/m2, and cardiovascular complications in the subsequent subgroup analysis (both p < 0.05). High blood EPO levels were found in SA patients in the present meta-analysis.
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18
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Tsai CC, Wu KM, Chiang TY, Huang CY, Chou CH, Li SJ, Chiang YC. Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes. BMC Genomics 2016; 17:212. [PMID: 26960548 PMCID: PMC4784368 DOI: 10.1186/s12864-016-2508-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 02/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gastrodia elata Blume (Orchidaceae) is an important Chinese medicine with several functional components. In the life cycle of G. elata, the orchid develops a symbiotic relationship with two compatible mycorrhizal fungi Mycena spp. and Armillaria mellea during seed germination to form vegetative propagation corm and vegetative growth to develop tubers, respectively. Gastrodin (p-hydroxymethylphenol-beta-D-glucoside) is the most important functional component in G. elata, and gastrodin significantly increases from vegetative propagation corms to tubers. To address the gene regulation mechanism in gastrodin biosynthesis in G. elata, a comparative analysis of de novo transcriptome sequencing among the vegetative propagation corms and tubers of G. elata and A. mellea was conducted using deep sequencing. RESULTS Transcriptome comparison between the vegetative propagation corms and juvenile tubers of G. elata revealed 703 differentially expressed unigenes, of which 298 and 405 unigenes were, respectively up-regulated (fold-change ≥ 2, q-value < 0.05, the trimmed mean of M-values (TMM)-normalized fragments per kilobase of transcript per Million mapped reads (FPKM) > 10) and down-regulated (fold-change ≤ 0.5, q-value <0.05, TMM-normalized FPKM > 10) in juvenile tubers. After Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, 112 up-regulated unigenes with KEGG Ortholog identifiers (KOids) or enzyme commission (EC) numbers were assigned to 159 isogroups involved in seventy-eight different pathways, and 132 down-regulated unigenes with KOids or EC numbers were assigned to 168 isogroups, involved in eighty different pathways. The analysis of the isogroup genes from all pathways revealed that the two unigenes TRINITY_DN54282_c0_g1 (putative monooxygenases) and TRINITY_DN50323_c0_g1 (putative glycosyltransferases) might participate in hydroxylation and glucosylation in the gastrodin biosynthetic pathway. CONCLUSIONS The gene expression of the two unique unigenes encoding monooxygenase and glycosyltransferase significantly increases from vegetative propagation corms to tubers, and the molecular basis of gastrodin biosynthesis in the tubers of G. elata is proposed.
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Affiliation(s)
- Chi-Chu Tsai
- Crop Improvement Division, Kaohsiung District Agricultural Improvement Station, Pingtung, 900, Taiwan.
- Graduate Institute of Biotechnology, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan.
| | - Keh-Ming Wu
- Welgene Biotech. Co., Ltd., Taipei, 115, Taiwan.
| | - Tzen-Yuh Chiang
- Department of Life Science, Cheng-Kung University, Tainan, 701, Taiwan.
| | - Chun-Yen Huang
- Crop Improvement Division, Kaohsiung District Agricultural Improvement Station, Pingtung, 900, Taiwan.
| | - Chang-Hung Chou
- Research Center for Biodiversity, China Medical University, Taichung, 404, Taiwan.
| | - Shu-Ju Li
- Crop Improvement Division, Kaohsiung District Agricultural Improvement Station, Pingtung, 900, Taiwan.
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.
- Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
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19
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Pierre CC, Longo J, Bassey-Archibong BI, Hallett RM, Milosavljevic S, Beatty L, Hassell JA, Daniel JM. Methylation-dependent regulation of hypoxia inducible factor-1 alpha gene expression by the transcription factor Kaiso. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1432-41. [PMID: 26514431 DOI: 10.1016/j.bbagrm.2015.10.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 10/01/2015] [Accepted: 10/23/2015] [Indexed: 01/19/2023]
Abstract
Low oxygen tension (hypoxia) is a common characteristic of solid tumors and strongly correlates with poor prognosis and resistance to treatment. In response to hypoxia, cells initiate a cascade of transcriptional events regulated by the hypoxia inducible factor-1 (HIF-1) heterodimer. Since the oxygen-sensitive HIF-1α subunit is stabilized during hypoxia, it functions as the regulatory subunit of the protein. To date, while the mechanisms governing HIF-1α protein stabilization and function have been well studied, those governing HIF1A gene expression are not fully understood. However, recent studies have suggested that methylation of a HIF-1 binding site in the HIF1A promoter prevents its autoregulation. Here we report that the POZ-ZF transcription factor Kaiso modulates HIF1A gene expression by binding to the methylated HIF1A promoter in a region proximal to the autoregulatory HIF-1 binding site. Interestingly, Kaiso's regulation of HIF1A occurs primarily during hypoxia, which is consistent with the finding that Kaiso protein levels peak after 4 h of hypoxic incubation and return to normoxic levels after 24 h. Our data thus support a role for Kaiso in fine-tuning HIF1A gene expression after extended periods of hypoxia.
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Affiliation(s)
- Christina C Pierre
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Joseph Longo
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | | | - Robin M Hallett
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | | | - Laura Beatty
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - John A Hassell
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Juliet M Daniel
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada.
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20
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Putlyaeva LV, Schwartz AM, Korneev KV, Covic M, Uroshlev LA, Makeev VY, Dmitriev SE, Kuprash DV. Upstream open reading frames regulate translation of the long isoform of SLAMF1 mRNA that encodes costimulatory receptor CD150. BIOCHEMISTRY (MOSCOW) 2015; 79:1405-11. [PMID: 25716736 DOI: 10.1134/s0006297914120165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
More than 40% of human genes contain upstream open reading frames (uORF) in their 5'-untranslated regions (5'-UTRs) and at the same time express at least one truncated mRNA isoform containing no uORF. We studied translational regulation by four uORFs found in the 5'-UTR of full-length mRNA for SLAMF1, the gene encoding CD150 membrane protein. CD150 is a member of the CD2 superfamily, a costimulatory lymphocyte receptor, a receptor for measles virus, and a microbial sensor on macrophages. The SLAMF1 gene produces at least two mRNA isoforms that differ in their 5'-UTRs. In the long isoform of the SLAMF1 mRNA that harbors four uORFs in the 5'-UTR, the stop codon of uORF4 overlaps with the AUG codon of the main ORF forming a potential termination-reinitiation site UGAUG, while uORF2 and uORF3 start codons flank a sequence identical to Motif 1 from the TURBS regulatory element. TURBS was shown to be required for a coupled termination-reinitiation event during translation of polycistronic RNAs of some viruses. In a model cell system, reporter mRNA based on the 5'-UTR of SLAMF1 short isoform, which lacks any uORF, is translated 5-6 times more efficiently than the mRNA with 5'-UTR from the long isoform. Nucleotide substitutions disrupting start codons in either uORF2-4 result in significant increase in translation efficiency, while substitution of two nucleotides in TURBS Motif 1 leads to a 2-fold decrease in activity. These data suggest that TURBS-like elements can serve for translation control of certain cellular mRNAs containing uORFs.
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Affiliation(s)
- L V Putlyaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
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21
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Timms M, Steel R, Vine J. Identification of recombinant human EPO variants in greyhound plasma and urine by ELISA, LC-MS/MS and western blotting: a comparative study. Drug Test Anal 2015; 8:164-76. [DOI: 10.1002/dta.1835] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 03/19/2015] [Accepted: 06/07/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Mark Timms
- Biological Research Unit; Racing Analytical Services Ltd; 400 Epsom Road Flemington Victoria 3031 Australia
| | - Rohan Steel
- Biological Research Unit; Racing Analytical Services Ltd; 400 Epsom Road Flemington Victoria 3031 Australia
| | - John Vine
- Biological Research Unit; Racing Analytical Services Ltd; 400 Epsom Road Flemington Victoria 3031 Australia
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Expression of human Hemojuvelin (HJV) is tightly regulated by two upstream open reading frames in HJV mRNA that respond to iron overload in hepatic cells. Mol Cell Biol 2015; 35:1376-89. [PMID: 25666510 DOI: 10.1128/mcb.01462-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The gene encoding human hemojuvelin (HJV) is one of the genes that, when mutated, can cause juvenile hemochromatosis, an early-onset inherited disorder associated with iron overload. The 5' untranslated region of the human HJV mRNA has two upstream open reading frames (uORFs), with 28 and 19 codons formed by two upstream AUGs (uAUGs) sharing the same in-frame stop codon. Here we show that these uORFs decrease the translational efficiency of the downstream main ORF in HeLa and HepG2 cells. Indeed, ribosomal access to the main AUG is conditioned by the strong uAUG context, which results in the first uORF being translated most frequently. The reach of the main ORF is then achieved by ribosomes that resume scanning after uORF translation. Furthermore, the amino acid sequences of the uORF-encoded peptides also reinforce the translational repression of the main ORF. Interestingly, when iron levels increase, translational repression is relieved specifically in hepatic cells. The upregulation of protein levels occurs along with phosphorylation of the eukaryotic initiation factor 2α. Nevertheless, our results support a model in which the increasing recognition of the main AUG is mediated by a tissue-specific factor that promotes uORF bypass. These results support a tight HJV translational regulation involved in iron homeostasis.
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Moreira L, Beirão JM, Beirão I, Pinho e Costa P. Oligomeric TTR V30M aggregates compromise cell viability, erythropoietin gene expression and promoter activity in the human hepatoma cell line Hep3B. Amyloid 2015; 22:93-9. [PMID: 26088020 DOI: 10.3109/13506129.2015.1007497] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Familial amyloidotic polyneuropathy, ATTRV30M (p. TTRV50M) amyloidosis, is a neurodegenerative disease characterized by systemic extracellular amyloid deposition of a mutant transthyretin, TTR V30M. Anemia, with low erythropoietin (EPO) levels and spared kidney function, affects about 25% of symptomatic patients, suggesting a blockage of EPO-producing cells. Early non-fibrillar TTR aggregates are highly cytotoxic, inducing oxidative stress, the expression of apoptosis-related molecules and secretion of pro-inflammatory cytokines, factors capable of inhibiting EPO production. Low EPO levels in these patients are not related to renal amyloid deposition or the presence of circulating TTR V30M. However, the role of early non-fibrillar TTR aggregates remains unexplored. We used the EPO producing Hep3B human hepatoma cell line to study the effect of TTR oligomeric aggregates on EPO expression. Hep3B cells were incubated with soluble and oligomeric TTR V30M, and cell proliferation as well as caspase 3/7 activation was evaluated. Relative quantification of EPO mRNA transcripts was performed by real-time PCR. Significant reductions in cell viability (13 ± 7.3%) and activation of caspases 3/7 were seen after 24 h in the presence of oligomeric TTR V30M. Also, EPO expression was significantly reduced (50 ± 2.8%), in normoxic conditions. A reporter assay was constructed with a PCR fragment of the EPO promoter linked to the luciferase gene to evaluate the role of transcription factors targeting the promoter. A significant reduction of EPO promoter activity (53 ± 6.5%) was observed in transfected cells exposed to TTR oligomers. Our results show that oligomeric TTR V30M reduces EPO expression, at least in part through inhibition of promoter activity.
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Affiliation(s)
- Luciana Moreira
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge , INSA I.P., Porto , Portugal
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Glucose, insulin, and oxygen interplay in placental hypervascularisation in diabetes mellitus. BIOMED RESEARCH INTERNATIONAL 2014; 2014:145846. [PMID: 25258707 PMCID: PMC4167234 DOI: 10.1155/2014/145846] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/06/2014] [Indexed: 02/07/2023]
Abstract
The placental vasculature rapidly expands during the course of pregnancy in order to sustain the growing needs of the fetus. Angiogenesis and vascular growth are stimulated and regulated by a variety of growth factors expressed in the placenta or present in the fetal circulation. Like in tumors, hypoxia is a major regulator of angiogenesis because of its ability to stimulate expression of various proangiogenic factors. Chronic fetal hypoxia is often found in pregnancies complicated by maternal diabetes as a result of fetal hyperglycaemia and hyperinsulinemia. Both are associated with altered levels of hormones, growth factors, and proinflammatory cytokines, which may act in a proangiogenic manner and, hence, affect placental angiogenesis and vascular development. Indeed, the placenta in diabetes is characterized by hypervascularisation, demonstrating high placental plasticity in response to diabetic metabolic derangements. This review describes the major regulators of placental angiogenesis and how the diabetic environment in utero alters their expression. In the light of hypervascularized diabetic placenta, the focus was placed on proangiogenic factors.
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