1
|
Wen S, Liu Y, Yang G, Chen W, Wu H, Zhu X, Wang Y. A method for miRNA diffusion association prediction using machine learning decoding of multi-level heterogeneous graph Transformer encoded representations. Sci Rep 2024; 14:20490. [PMID: 39227405 PMCID: PMC11371806 DOI: 10.1038/s41598-024-68897-4] [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: 03/13/2024] [Accepted: 07/29/2024] [Indexed: 09/05/2024] Open
Abstract
MicroRNAs (miRNAs) are a key class of endogenous non-coding RNAs that play a pivotal role in regulating diseases. Accurately predicting the intricate relationships between miRNAs and diseases carries profound implications for disease diagnosis, treatment, and prevention. However, these prediction tasks are highly challenging due to the complexity of the underlying relationships. While numerous effective prediction models exist for validating these associations, they often encounter information distortion due to limitations in efficiently retaining information during the encoding-decoding process. Inspired by Multi-layer Heterogeneous Graph Transformer and Machine Learning XGboost classifier algorithm, this study introduces a novel computational approach based on multi-layer heterogeneous encoder-machine learning decoder structure for miRNA-disease association prediction (MHXGMDA). First, we employ the multi-view similarity matrices as the input coding for MHXGMDA. Subsequently, we utilize the multi-layer heterogeneous encoder to capture the embeddings of miRNAs and diseases, aiming to capture the maximum amount of relevant features. Finally, the information from all layers is concatenated to serve as input to the machine learning classifier, ensuring maximal preservation of encoding details. We conducted a comprehensive comparison of seven different classifier models and ultimately selected the XGBoost algorithm as the decoder. This algorithm leverages miRNA embedding features and disease embedding features to decode and predict the association scores between miRNAs and diseases. We applied MHXGMDA to predict human miRNA-disease associations on two benchmark datasets. Experimental findings demonstrate that our approach surpasses several leading methods in terms of both the area under the receiver operating characteristic curve and the area under the precision-recall curve.
Collapse
Affiliation(s)
- SiJian Wen
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - YinBo Liu
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - Guang Yang
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - WenXi Chen
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - HaiTao Wu
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - XiaoLei Zhu
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China.
| | - YongMei Wang
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China.
- Anhui Provincial Engineering Laboratory for Beidou Precision Agriculture Information, Hefei, 230036, China.
| |
Collapse
|
2
|
Yang TH. DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning. J Chem Inf Model 2024; 64:3756-3766. [PMID: 38648189 PMCID: PMC11094721 DOI: 10.1021/acs.jcim.4c00458] [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: 03/15/2024] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
It is now known that RNAs play more active roles in cellular pathways beyond simply serving as transcription templates. These biological mechanisms might be mediated by higher RNA stereo conformations, triggering the need to understand RNA secondary structures first. However, experimental protocols for solving RNA structures are unavailable for large-scale investigation due to their high costs and time-consuming nature. Various computational tools were thus developed to predict the RNA secondary structures from sequences. Recently, deep networks have been investigated to help predict RNA structures directly from their sequences. However, existing deep-learning-based tools are more or less suffering from model overfitting due to their complicated problem formulation and defective model training processes, limiting their applications across sequences from different structural families. In this research, we designed a two-stage RNA structure prediction strategy called DEBFold (deep ensemble boosting and folding) based on convolution encoding/decoding and self-attention mechanisms to enhance the existing thermodynamic structure models. Moreover, the model training process followed rigorous steps to achieve an acceptable prediction generalization. On the family-wise reserved test sets and the PDB-derived test set, DEBFold achieves better structure prediction performance over traditional tools and existing deep-learning methods. In summary, we obtained a cutting-edge deep-learning-based structure prediction tool with supreme across-family generalization performance. The DEBFold tool can be accessed at https://cobis.bme.ncku.edu.tw/DEBFold/.
Collapse
Affiliation(s)
- Tzu-Hsien Yang
- Department
of Biomedical Engineering, National Cheng
Kung University, No.1, University Road, Tainan 701, Taiwan
- Medical
Device Innovation Center, National Cheng
Kung University, No.1,
University Road, Tainan 701, Taiwan
| |
Collapse
|
3
|
Gao X, Yi Y, Lv J, Li Y, Arulsamy K, Babu S, Bruno I, Zhang L, Cao Q, Chen K. Low RNA stability signifies strong expression regulatability of tumor suppressors. Nucleic Acids Res 2023; 51:11534-11548. [PMID: 37831104 PMCID: PMC10681714 DOI: 10.1093/nar/gkad838] [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: 04/25/2023] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023] Open
Abstract
RNA expression of a gene is determined by not only transcriptional regulation, but also post-transcriptional regulation of RNA decay. The precise regulation of RNA stability in the cell plays an important role in normal development. Dysregulation of RNA stability can lead to diseases such as cancer. Here we found tumor suppressor RNAs tended to decay fast in normal cell types when compared with other RNAs. Consistent with a negative effect of m6A modification on RNA stability, we observed preferential deposition of m6A on tumor suppressor RNAs. Moreover, abundant m6A and fast decay of tumor suppressor RNAs both tended to be further enhanced in prostate cancer cells relative to normal prostate epithelial cells. Further, knockdown of m6A methyltransferase METTL3 and reader YTHDF2 in prostate cancer cells both posed stronger effect on tumor suppressor RNAs than on other RNAs. These results indicated a strong post transcriptional expression regulatability mediated by abundant m6A modification on tumor suppressor RNAs.
Collapse
Affiliation(s)
- Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yang Yi
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jie Lv
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yanqiang Li
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Kulandaisamy Arulsamy
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sahana Suresh Babu
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Ivone Bruno
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Qi Cao
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
- Prostate Cancer Program, Dana-Farber Harvard cancer Center, Boston, MA 02115, USA
| |
Collapse
|
4
|
Nguyen NH, Sarangi S, McChesney EM, Sheng S, Durrant JD, Porter AW, Kleyman TR, Pitluk ZW, Brodsky JL. Genome mining yields putative disease-associated ROMK variants with distinct defects. PLoS Genet 2023; 19:e1011051. [PMID: 37956218 PMCID: PMC10695394 DOI: 10.1371/journal.pgen.1011051] [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: 08/12/2023] [Revised: 12/04/2023] [Accepted: 11/04/2023] [Indexed: 11/15/2023] Open
Abstract
Bartter syndrome is a group of rare genetic disorders that compromise kidney function by impairing electrolyte reabsorption. Left untreated, the resulting hyponatremia, hypokalemia, and dehydration can be fatal, and there is currently no cure. Bartter syndrome type II specifically arises from mutations in KCNJ1, which encodes the renal outer medullary potassium channel, ROMK. Over 40 Bartter syndrome-associated mutations in KCNJ1 have been identified, yet their molecular defects are mostly uncharacterized. Nevertheless, a subset of disease-linked mutations compromise ROMK folding in the endoplasmic reticulum (ER), which in turn results in premature degradation via the ER associated degradation (ERAD) pathway. To identify uncharacterized human variants that might similarly lead to premature degradation and thus disease, we mined three genomic databases. First, phenotypic data in the UK Biobank were analyzed using a recently developed computational platform to identify individuals carrying KCNJ1 variants with clinical features consistent with Bartter syndrome type II. In parallel, we examined genomic data in both the NIH TOPMed and ClinVar databases with the aid of Rhapsody, a verified computational algorithm that predicts mutation pathogenicity and disease severity. Subsequent phenotypic studies using a yeast screen to assess ROMK function-and analyses of ROMK biogenesis in yeast and human cells-identified four previously uncharacterized mutations. Among these, one mutation uncovered from the two parallel approaches (G228E) destabilized ROMK and targeted it for ERAD, resulting in reduced cell surface expression. Another mutation (T300R) was ERAD-resistant, but defects in channel activity were apparent based on two-electrode voltage clamp measurements in X. laevis oocytes. Together, our results outline a new computational and experimental pipeline that can be applied to identify disease-associated alleles linked to a range of other potassium channels, and further our understanding of the ROMK structure-function relationship that may aid future therapeutic strategies to advance precision medicine.
Collapse
Affiliation(s)
- Nga H. Nguyen
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Srikant Sarangi
- Paradigm4, Inc., Waltham, Massachusetts, United States of America
| | - Erin M. McChesney
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Shaohu Sheng
- Renal-Electrolyte Division, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Aidan W. Porter
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Thomas R. Kleyman
- Renal-Electrolyte Division, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Jeffrey L. Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| |
Collapse
|
5
|
Nguyen NH, Sarangi S, McChesney EM, Sheng S, Porter AW, Kleyman TR, Pitluk ZW, Brodsky JL. Genome mining yields new disease-associated ROMK variants with distinct defects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539609. [PMID: 37214976 PMCID: PMC10197530 DOI: 10.1101/2023.05.05.539609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bartter syndrome is a group of rare genetic disorders that compromise kidney function by impairing electrolyte reabsorption. Left untreated, the resulting hyponatremia, hypokalemia, and dehydration can be fatal. Although there is no cure for this disease, specific genes that lead to different Bartter syndrome subtypes have been identified. Bartter syndrome type II specifically arises from mutations in the KCNJ1 gene, which encodes the renal outer medullary potassium channel, ROMK. To date, over 40 Bartter syndrome-associated mutations in KCNJ1 have been identified. Yet, their molecular defects are mostly uncharacterized. Nevertheless, a subset of disease-linked mutations compromise ROMK folding in the endoplasmic reticulum (ER), which in turn results in premature degradation via the ER associated degradation (ERAD) pathway. To identify uncharacterized human variants that might similarly lead to premature degradation and thus disease, we mined three genomic databases. First, phenotypic data in the UK Biobank were analyzed using a recently developed computational platform to identify individuals carrying KCNJ1 variants with clinical features consistent with Bartter syndrome type II. In parallel, we examined ROMK genomic data in both the NIH TOPMed and ClinVar databases with the aid of a computational algorithm that predicts protein misfolding and disease severity. Subsequent phenotypic studies using a high throughput yeast screen to assess ROMK function-and analyses of ROMK biogenesis in yeast and human cells-identified four previously uncharacterized mutations. Among these, one mutation uncovered from the two parallel approaches (G228E) destabilized ROMK and targeted it for ERAD, resulting in reduced protein expression at the cell surface. Another ERAD-targeted ROMK mutant (L320P) was found in only one of the screens. In contrast, another mutation (T300R) was ERAD-resistant, but defects in ROMK activity were apparent after expression and two-electrode voltage clamp measurements in Xenopus oocytes. Together, our results outline a new computational and experimental pipeline that can be applied to identify disease-associated alleles linked to a range of other potassium channels, and further our understanding of the ROMK structure-function relationship that may aid future therapeutic strategies. Author Summary Bartter syndrome is a rare genetic disorder characterized by defective renal electrolyte handing, leading to debilitating symptoms and, in some patients, death in infancy. Currently, there is no cure for this disease. Bartter syndrome is divided into five types based on the causative gene. Bartter syndrome type II results from genetic variants in the gene encoding the ROMK protein, which is expressed in the kidney and assists in regulating sodium, potassium, and water homeostasis. Prior work established that some disease-associated ROMK mutants misfold and are destroyed soon after their synthesis in the endoplasmic reticulum (ER). Because a growing number of drugs have been identified that correct defective protein folding, we wished to identify an expanded cohort of similarly misshapen and unstable disease-associated ROMK variants. To this end, we developed a pipeline that employs computational analyses of human genome databases with genetic and biochemical assays. Next, we both confirmed the identity of known variants and uncovered previously uncharacterized ROMK variants associated with Bartter syndrome type II. Further analyses indicated that select mutants are targeted for ER-associated degradation, while another mutant compromises ROMK function. This work sets-the-stage for continued mining for ROMK loss of function alleles as well as other potassium channels, and positions select Bartter syndrome mutations for correction using emerging pharmaceuticals.
Collapse
|
6
|
Gurjar P, Karuvantevida N, Rzhepakovsky IV, Khan AA, Khandia R. A Synthetic Biology Approach for Vaccine Candidate Design against Delta Strain of SARS-CoV-2 Revealed Disruption of Favored Codon Pair as a Better Strategy over Using Rare Codons. Vaccines (Basel) 2023; 11:487. [PMID: 36851364 PMCID: PMC9967482 DOI: 10.3390/vaccines11020487] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The SARS-CoV-2 delta variant (B.1.617.2) appeared for the first time in December 2020 and later spread worldwide. Currently available vaccines are not so efficacious in curbing the viral pathogenesis of the delta strain of COVID; therefore, the development of a safe and effective vaccine is required. In the present study, we envisaged molecular patterns in the structural genes' spike, nucleoprotein, membrane, and envelope of the SARS-CoV-2 delta variant. The study was based on determining compositional features, dinucleotide odds ratio, synonymous codon usage, positive and negative codon contexts, rare codons, and insight into relatedness between the human host isoacceptor tRNA and preferred codons from the structural genes. We found specific patterns, including a significant abundance of T nucleotide over all other three nucleotides. The underrepresentation of GpA, GpG, CpC, and CpG dinucleotides and the overrepresentation of TpT, ApA, CpT, and TpG were observed. A preference towards ACT- (Thr), AAT- (Asn), TTT- (Phe), and TTG- (Leu) initiated codons and aversion towards CGG (Arg), CCG (Pro), and CAC (His) was present in the structural genes of the delta strain. The interaction between the host tRNA pool and preferred codons of the envisaged structural genes revealed that the virus preferred the codons for those suboptimal numbers of isoacceptor tRNA were present. We see this as a strategy adapted by the virus to keep the translation rate low to facilitate the correct folding of viral proteins. The information generated in the study helps design the attenuated vaccine candidate against the SARS-CoV-2 delta variant using a synthetic biology approach. Three strategies were tested: changing TpT to TpA, introducing rare codons, and disrupting favored codons. It found that disrupting favored codons is a better approach to reducing virus fitness and attenuating SARS-CoV-2 delta strain using structural genes.
Collapse
Affiliation(s)
- Pankaj Gurjar
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai P.O. Box 505055, United Arab Emirates
| | | | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah Universty, Bhopal 462026, India
| |
Collapse
|
7
|
Agarwal V, Kelley DR. The genetic and biochemical determinants of mRNA degradation rates in mammals. Genome Biol 2022; 23:245. [PMID: 36419176 PMCID: PMC9684954 DOI: 10.1186/s13059-022-02811-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/02/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Degradation rate is a fundamental aspect of mRNA metabolism, and the factors governing it remain poorly characterized. Understanding the genetic and biochemical determinants of mRNA half-life would enable more precise identification of variants that perturb gene expression through post-transcriptional gene regulatory mechanisms. RESULTS We establish a compendium of 39 human and 27 mouse transcriptome-wide mRNA decay rate datasets. A meta-analysis of these data identified a prevalence of technical noise and measurement bias, induced partially by the underlying experimental strategy. Correcting for these biases allowed us to derive more precise, consensus measurements of half-life which exhibit enhanced consistency between species. We trained substantially improved statistical models based upon genetic and biochemical features to better predict half-life and characterize the factors molding it. Our state-of-the-art model, Saluki, is a hybrid convolutional and recurrent deep neural network which relies only upon an mRNA sequence annotated with coding frame and splice sites to predict half-life (r=0.77). The key novel principle learned by Saluki is that the spatial positioning of splice sites, codons, and RNA-binding motifs within an mRNA is strongly associated with mRNA half-life. Saluki predicts the impact of RNA sequences and genetic mutations therein on mRNA stability, in agreement with functional measurements derived from massively parallel reporter assays. CONCLUSIONS Our work produces a more robust ground truth for transcriptome-wide mRNA half-lives in mammalian cells. Using these revised measurements, we trained Saluki, a model that is over 50% more accurate in predicting half-life from sequence than existing models. Saluki succinctly captures many of the known determinants of mRNA half-life and can be rapidly deployed to predict the functional consequences of arbitrary mutations in the transcriptome.
Collapse
Affiliation(s)
- Vikram Agarwal
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA.
- Present Address: mRNA Center of Excellence, Sanofi Pasteur Inc., Waltham, MA, 02451, USA.
| | - David R Kelley
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA.
| |
Collapse
|
8
|
Webster AK, Chitrakar R, Taylor SM, Baugh LR. Alternative somatic and germline gene-regulatory strategies during starvation-induced developmental arrest. Cell Rep 2022; 41:111473. [PMID: 36223742 PMCID: PMC9608353 DOI: 10.1016/j.celrep.2022.111473] [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: 06/19/2021] [Revised: 07/18/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Nutrient availability governs growth and quiescence, and many animals arrest development when starved. Using C. elegans L1 arrest as a model, we show that gene expression changes deep into starvation. Surprisingly, relative expression of germline-enriched genes increases for days. We conditionally degrade the large subunit of RNA polymerase II using the auxin-inducible degron system and analyze absolute expression levels. We find that somatic transcription is required for survival, but the germline maintains transcriptional quiescence. Thousands of genes are continuously transcribed in the soma, though their absolute abundance declines, such that relative expression of germline transcripts increases given extreme transcript stability. Aberrantly activating transcription in starved germ cells compromises reproduction, demonstrating important physiological function of transcriptional quiescence. This work reveals alternative somatic and germline gene-regulatory strategies during starvation, with the soma maintaining a robust transcriptional response to support survival and the germline maintaining transcriptional quiescence to support future reproductive success. Webster et al. show that the transcriptional response to starvation is mounted early in larval somatic cells supporting survival but that it wanes over time. In contrast, they show that the germline remains transcriptionally quiescent deep into starvation, supporting reproductive potential, while maintaining its transcriptome via transcript stability.
Collapse
Affiliation(s)
- Amy K. Webster
- Department of Biology, Duke University, Durham, NC 27708, USA,Present address: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Rojin Chitrakar
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Seth M. Taylor
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - L. Ryan Baugh
- Department of Biology, Duke University, Durham, NC 27708, USA,Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA,Lead contact,Correspondence:
| |
Collapse
|
9
|
Koide EM, Abbott EA, Helbing CC. Uncovering early thyroid hormone signalling events through temperature-mediated activation of molecular memory in the cultured bullfrog tadpole tail fin. Gen Comp Endocrinol 2022; 323-324:114047. [PMID: 35472316 DOI: 10.1016/j.ygcen.2022.114047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/10/2022] [Accepted: 04/21/2022] [Indexed: 11/04/2022]
Abstract
Thyroid hormone (TH) is a critical signalling molecule for all vertebrate organisms, playing a crucial role in postembryonic development. The best-studied mechanism of TH response is through modulating gene expression, however TH's involvement in coordinating the early steps in the TH signal transduction pathway is still poorly understood. The American bullfrog, Rana [Lithobates] catesbeiana, is a useful model to study these early responses as tadpole post-embryonic development in the form of metamorphosis of the tadpole into a frog can be experimentally induced by TH exposure. The rate of TH-induced metamorphosis can be modulated by temperature where sufficiently cold temperatures (5 °C) completely halt precocious metamorphosis. Interestingly, when premetamorphic tadpoles exposed to exogenous THs at 5 °C are shifted to permissive temperatures (24 °C), their metamorphic rate exceeds that of TH-exposed tadpoles at the permissive temperature. This suggests that a molecular memory of TH exposure is retained at 5 °C even after THs are cleared at this low temperature. However, the molecular memory machinery is poorly understood. Herein we use RNA-seq analysis to identify potential components of the molecular memory in cultured tail fin that allows for the recapitulation of the molecular memory phenomenon. Eighty-one gene transcripts were TH-responsive at 5 °C compared to matched controls indicating that the molecular memory is more complex than previously thought. Many of these transcripts encode transcription factors including thyroid hormone-induced B/Zip, thibz, and a novel krüppel-like factor family member, klfX. Actinomycin D and cycloheximide treatment had no effect on their TH induction suggesting that a change in transcription or translation is not required. Rather a change in RNA stability may be a possible mechanism contributing to the molecular memory. The ability to manipulate temperature and TH response in cultured organs provide an exciting opportunity to further elucidate the early TH signalling mechanisms during postembryonic development.
Collapse
Affiliation(s)
- E M Koide
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada
| | - E A Abbott
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada
| | - C C Helbing
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada.
| |
Collapse
|
10
|
Sex-dependent effect of aging on calcium signaling and expression of TRPM2 and CRAC channels in human neutrophils. Hum Immunol 2022; 83:645-655. [PMID: 35660323 DOI: 10.1016/j.humimm.2022.05.002] [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: 11/12/2021] [Revised: 04/26/2022] [Accepted: 05/15/2022] [Indexed: 11/22/2022]
Abstract
The vulnerability of older adults to bacterial infections has been associated with age-related changes in neutrophils. We analyzed the consequences of aging on calcium (Ca2+) mobilization and TRPM2 and CRAC channels expression in human neutrophils. The percentages of granulocytes, mature neutrophils, and neutrophil precursors were equivalent between young and older adults. However, neutrophil chemotaxis towards IL-8, C5a, or fMLP was lower in older adults of both sexes. Interestingly, a stronger Ca2+ transient followed by an identical Ca2+ influx to IL-8 was observed in older adult females. In addition, the Ca2+ response to LPS was delayed and prolonged in neutrophils of older adult males. There was no significant difference in Ca2+ response to fMLP, C5a, or store-operated Ca2+ entry in the older adults. There were also no differences in the expression of CXCR2, CD88, FPLR1, and TLR4. Interestingly, TRPM2- and ORAI1-mRNA expression was lower in neutrophils of older adults, mainly in females. Both channels were detected intracellularly in the neutrophils. TRPM2 was in late endosomes in young adults and in lysosomes in older adult neutrophils. In summary, defective neutrophil chemotaxis in aging seemed not to stem from alterations in Ca2+ signals; nevertheless, the low TRPM2 and ORAI1 expression may affect other functions.
Collapse
|
11
|
Kremer V, Stanicek L, van Ingen E, Bink DI, Hilderink S, Tijsen AJ, Wittig I, Mägdefessel L, Nossent AY, Boon RA. Long non-coding RNA MEG8 induces endothelial barrier through regulation of microRNA-370 and -494 processing. J Cell Sci 2022; 135:275515. [PMID: 35611612 PMCID: PMC9270956 DOI: 10.1242/jcs.259671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/15/2022] [Indexed: 11/20/2022] Open
Abstract
The 14q32 locus is an imprinted region in the human genome which contains multiple non-coding RNAs. We investigated the role of Maternally Expressed Gene 8 (MEG8) in endothelial function and the underlying mechanism. A 5-fold increase in MEG8 was observed with increased passage number in Human Umbilical Vein Endothelial Cells, suggesting MEG8 is induced during aging. MEG8 knockdown resulted in a 1.8-fold increase in senescence, suggesting MEG8 might be protective during aging. Endothelial barrier was impaired after MEG8 silencing. MEG8 knockdown resulted in reduced expression of miRNA-370 and -494 but not -127, -487b and -410. Overexpression of miRNA-370/-494 partially rescued MEG8-silencing-induced barrier loss. Mechanistically, MEG8 regulates expression of miRNA-370 and -494 at the mature miRNA level through interaction with RNA binding proteins Cold Inducible RNA Binding Protein (CIRBP) and Hydroxyacyl-CoA Dehydrogenase Trifunctional Multi-enzyme Complex Subunit Beta (HADHB). Precursor and mature miRNA-370/-494 were shown to interact with HADHB and CIRBP respectively. CIRBP/HADHB silencing resulted in downregulation of miRNA-370 and induction of miRNA-494. These results suggest MEG8 interacts with CIRBP and HADHB and contributes to miRNA processing at the post-transcriptional level.
Collapse
Affiliation(s)
- Veerle Kremer
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands.,Amsterdam UMC location University of Amsterdam, Department of Medical Chemistry, Meibergdreef 9, Amsterdam, the Netherlands
| | - Laura Stanicek
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands.,German Center for Cardiovascular research (DZHK), partner site Munich Heart Alliance, Germany
| | - Eva van Ingen
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, the Netherlands
| | - Diewertje I Bink
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands
| | - Sarah Hilderink
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands
| | - Anke J Tijsen
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands.,Amsterdam UMC location University of Amsterdam, Department of Experimental Cardiology, Meibergdreef 9, Amsterdam, the Netherlands
| | - Ilka Wittig
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany.,German Centre for Cardiovascular Research DZHK, Partner site Frankfurt Rhein/Main, Frankfurt am Main, Germany
| | - Lars Mägdefessel
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University of Munich, Germany.,Department of Medicine, Molecular Vascular Medicine Unit, Karolinska Institute, Stockholm, Sweden.,German Center for Cardiovascular research (DZHK), partner site Munich Heart Alliance, Germany
| | - Anne Yaël Nossent
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, the Netherlands.,Departments of Laboratory Medicine and Internal Medicine II, Medical University of Vienna, Austria
| | - Reinier A Boon
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands.,Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany.,German Centre for Cardiovascular Research DZHK, Partner site Frankfurt Rhein/Main, Frankfurt am Main, Germany
| |
Collapse
|
12
|
Rana A, Gupta N, Thakur A. Post-transcriptional and translational control of the morphology and virulence in human fungal pathogens. Mol Aspects Med 2021; 81:101017. [PMID: 34497025 DOI: 10.1016/j.mam.2021.101017] [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: 02/11/2021] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022]
Abstract
Host-pathogen interactions at the molecular level are the key to fungal pathogenesis. Fungal pathogens utilize several mechanisms such as adhesion, invasion, phenotype switching and metabolic adaptations, to survive in the host environment and respond. Post-transcriptional and translational regulations have emerged as key regulatory mechanisms ensuring the virulence and survival of fungal pathogens. Through these regulations, fungal pathogens effectively alter their protein pool, respond to various stress, and undergo morphogenesis, leading to efficient and comprehensive changes in fungal physiology. The regulation of virulence through post-transcriptional and translational regulatory mechanisms is mediated through mRNA elements (cis factors) or effector molecules (trans factors). The untranslated regions upstream and downstream of the mRNA, as well as various RNA-binding proteins involved in translation initiation or circularization of the mRNA, play pivotal roles in the regulation of morphology and virulence by influencing protein synthesis, protein isoforms, and mRNA stability. Therefore, post-transcriptional and translational mechanisms regulating the morphology, virulence and drug-resistance processes in fungal pathogens can be the target for new therapeutics. With improved "omics" technologies, these regulatory mechanisms are increasingly coming to the forefront of basic biology and drug discovery. This review aims to discuss various modes of post-transcriptional and translation regulations, and how these mechanisms exert influence in the virulence and morphogenesis of fungal pathogens.
Collapse
Affiliation(s)
- Aishwarya Rana
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Nidhi Gupta
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Anil Thakur
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India.
| |
Collapse
|
13
|
Zhang J, Zhang Y, Gao J, Wang M, Li X, Cui Z, Fu G. Long Noncoding RNA Tug1 Promotes Angiotensin II-Induced Renal Fibrosis by Binding to Mineralocorticoid Receptor and Negatively Regulating MicroR-29b-3p. Hypertension 2021; 78:693-705. [PMID: 34333990 DOI: 10.1161/hypertensionaha.120.16395] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Juhong Zhang
- Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University, Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Hangzhou, China (J.Z., J.G., M.W., X.L., G.F.)
| | - Yuqing Zhang
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China (Y.Z.)
| | - Jing Gao
- Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University, Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Hangzhou, China (J.Z., J.G., M.W., X.L., G.F.)
| | - Meihui Wang
- Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University, Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Hangzhou, China (J.Z., J.G., M.W., X.L., G.F.)
| | - Xiaoting Li
- Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University, Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Hangzhou, China (J.Z., J.G., M.W., X.L., G.F.)
| | - Zhaoqiang Cui
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China (Z.C.)
| | - Guosheng Fu
- Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University, Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Hangzhou, China (J.Z., J.G., M.W., X.L., G.F.)
| |
Collapse
|
14
|
Derksen A, Shih HY, Forget D, Darbelli L, Tran LT, Poitras C, Guerrero K, Tharun S, Alkuraya FS, Kurdi WI, Nguyen CTE, Laberge AM, Si Y, Gauthier MS, Bonkowsky JL, Coulombe B, Bernard G. Variants in LSM7 impair LSM complexes assembly, neurodevelopment in zebrafish and may be associated with an ultra-rare neurological disease. HGG ADVANCES 2021; 2:100034. [PMID: 35047835 PMCID: PMC8756503 DOI: 10.1016/j.xhgg.2021.100034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 11/15/2022] Open
Abstract
Leukodystrophies, genetic neurodevelopmental and/or neurodegenerative disorders of cerebral white matter, result from impaired myelin homeostasis and metabolism. Numerous genes have been implicated in these heterogeneous disorders; however, many individuals remain without a molecular diagnosis. Using whole-exome sequencing, biallelic variants in LSM7 were uncovered in two unrelated individuals, one with a leukodystrophy and the other who died in utero. LSM7 is part of the two principle LSM protein complexes in eukaryotes, namely LSM1-7 and LSM2-8. Here, we investigate the molecular and functional outcomes of these LSM7 biallelic variants in vitro and in vivo. Affinity purification-mass spectrometry of the LSM7 variants showed defects in the assembly of both LSM complexes. Lsm7 knockdown in zebrafish led to central nervous system defects, including impaired oligodendrocyte development and motor behavior. Our findings demonstrate that variants in LSM7 cause misassembly of the LSM complexes, impair neurodevelopment of the zebrafish, and may be implicated in human disease. The identification of more affected individuals is needed before the molecular mechanisms of mRNA decay and splicing regulation are added to the categories of biological dysfunctions implicated in leukodystrophies, neurodevelopmental and/or neurodegenerative diseases.
Collapse
|
15
|
Specificity of RNA Folding and Its Association with Evolutionarily Adaptive mRNA Secondary Structures. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:882-900. [PMID: 33607297 PMCID: PMC9403030 DOI: 10.1016/j.gpb.2019.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 08/03/2019] [Accepted: 11/08/2019] [Indexed: 11/23/2022]
Abstract
The secondary structure is a fundamental feature of both noncoding and messenger RNAs. However, our understanding of the secondary structure of mRNA, especially that of the coding regions, remains elusive, likely due to translation and the lack of RNA-binding proteins that sustain the consensus structure, such as those that bind to noncoding RNA. Indeed, mRNA has recently been found to adopt diverse alternative structures, the overall functional significance of which remains untested. We hereby approached this problem by estimating the folding specificity, i.e., the probability that a fragment of RNA folds back to the same partner once refolded. We showed that the folding specificity of mRNA is lower than that of noncoding RNA and exhibits moderate evolutionary conservation. Notably, we found that specific rather than alternative folding is likely evolutionarily adaptive since specific folding is frequently associated with functionally important genes or sites within a gene. Additional analysis in combination with ribosome density suggests the ability to modulate ribosome movement as one potential functional advantage provided by specific folding. Our findings revealed a novel facet of the RNA structurome with important functional and evolutionary implications and indicated a potential method for distinguishing the mRNA secondary structures maintained by natural selection from molecular noise.
Collapse
|
16
|
Basu S, Mallik S, Hait S, Kundu S. Genome-scale molecular principles of mRNA half-life regulation in yeast. FEBS J 2020; 288:3428-3447. [PMID: 33319437 DOI: 10.1111/febs.15670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 11/07/2020] [Accepted: 12/11/2020] [Indexed: 12/22/2022]
Abstract
Precise control of protein and messenger RNA (mRNA) degradation is essential for cellular metabolism and homeostasis. Controlled and specific degradation of both molecular species necessitates their engagements with the respective degradation machineries; this engagement involves a disordered/unstructured segment of the substrate traversing the degradation tunnel of the machinery and accessing the catalytic sites. However, while molecular factors influencing protein degradation have been extensively explored on a genome scale, and in multiple organisms, such a comprehensive understanding remains missing for mRNAs. Here, we analyzed multiple genome-scale experimental yeast mRNA half-life data in light of experimentally derived mRNA secondary structures and protein binding data, along with high-resolution X-ray crystallographic structures of the RNase machines. Results unraveled a consistent genome-scale trend that mRNAs comprising longer terminal and/or internal unstructured segments have significantly shorter half-lives; the lengths of the 5'-terminal, 3'-terminal, and internal unstructured segments that affect mRNA half-life are compatible with molecular structures of the 5' exo-, 3' exo-, and endoribonuclease machineries. Sequestration into ribonucleoprotein complexes elongates mRNA half-life, presumably by burying ribonuclease engagement sites under oligomeric interfaces. After gene duplication, differences in terminal unstructured lengths, proportions of internal unstructured segments, and oligomerization modes result in significantly altered half-lives of paralogous mRNAs. Side-by-side comparison of molecular principles underlying controlled protein and mRNA degradation in yeast unravels their remarkable mechanistic similarities and suggests how the intrinsic structural features of the two molecular species, at two different levels of the central dogma, regulate their half-lives on genome scale.
Collapse
Affiliation(s)
- Sudipto Basu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, Kolkata, India
| | - Saurav Mallik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Suman Hait
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, Kolkata, India
| |
Collapse
|
17
|
Xin W, Zhang M, Yu Y, Li S, Ma C, Zhang J, Jiang Y, Li Y, Zheng X, Zhang L, Zhao X, Pei X, Zhu D. BCAT1 binds the RNA-binding protein ZNF423 to activate autophagy via the IRE1-XBP-1-RIDD axis in hypoxic PASMCs. Cell Death Dis 2020; 11:764. [PMID: 32938905 PMCID: PMC7494854 DOI: 10.1038/s41419-020-02930-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 12/24/2022]
Abstract
Abnormal functional changes in pulmonary artery smooth muscle cells are the main causes of many lung diseases. Among, autophagy plays a crucial role. However, the specific molecular regulatory mechanism of autophagy in PASMCs remains unclear. Here, we first demonstrate that BCAT1 played a key role in the autophagy of hypoxic PASMCs and hypoxic model rats. BCAT1-induced activation and accumulation of the autophagy signaling proteins BECN1 and Atg5 by the endoplasmic reticulum (ER) stress pathway. Interestingly, we discovered that BCAT1 bound IRE1 on the ER to activate expression of its downstream pathway XBP-1-RIDD axis to activate autophagy. More importantly, we identified an RNA-binding protein, zinc finger protein 423, which promoted autophagy by binding adenylate/uridylate (AU)-rich elements in the BCAT1 mRNA 3′-untranslated region. Overall, our results identify BCAT1 as a potential therapeutic target for the clinical treatment of lung diseases and reveal a novel posttranscriptional regulatory mechanism and signaling pathway in hypoxia-induced PASMC autophagy.
Collapse
Affiliation(s)
- Wei Xin
- College of Pharmacy, Harbin Medical University, Harbin, 150081, P.R. China.,Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, P.R. China
| | - Min Zhang
- College of Pharmacy, Harbin Medical University, Harbin, 150081, P.R. China.,Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, P.R. China.,Division of Cardiology and Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. China
| | - Yang Yu
- College of Pharmacy, Harbin Medical University, Harbin, 150081, P.R. China.,Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, P.R. China
| | - Songlin Li
- College of Pharmacy, Harbin University of Commerce, Harbin, 150076, P.R. China
| | - Cui Ma
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, P.R. China.,College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, 163319, P.R. China
| | - Junting Zhang
- College of Pharmacy, Harbin Medical University, Harbin, 150081, P.R. China.,Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, P.R. China
| | - Yuan Jiang
- College of Pharmacy, Harbin Medical University, Harbin, 150081, P.R. China.,Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, P.R. China
| | - Yiying Li
- College of Pharmacy, Harbin Medical University, Harbin, 150081, P.R. China.,Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, P.R. China
| | - Xiaodong Zheng
- Department of Genetic and Cell Biology, Harbin Medical University (Daqing), Daqing, 163319, P.R. China
| | - Lixin Zhang
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, P.R. China.,College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, 163319, P.R. China
| | - Xijuan Zhao
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, P.R. China.,College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, 163319, P.R. China
| | - Xuzhong Pei
- College of Pharmacy, Harbin Medical University, Harbin, 150081, P.R. China.,Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, P.R. China
| | - Daling Zhu
- College of Pharmacy, Harbin Medical University, Harbin, 150081, P.R. China. .,Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, P.R. China. .,State Province Key Laboratories of Biomedicine-Pharmaceutics of China, Daqing, 163319, P.R. China. .,Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, Harbin, 150081, P.R. China.
| |
Collapse
|
18
|
Rodriguez W, Macveigh-Fierro D, Miles J, Muller M. Fated for decay: RNA elements targeted by viral endonucleases. Semin Cell Dev Biol 2020; 111:119-125. [PMID: 32522410 PMCID: PMC7276228 DOI: 10.1016/j.semcdb.2020.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/28/2020] [Accepted: 05/13/2020] [Indexed: 11/22/2022]
Abstract
For over a decade, studies of messenger RNA regulation have revealed an unprecedented level of connectivity between the RNA pool and global gene expression. These connections are underpinned by a vast array of RNA elements that coordinate RNA-protein and RNA-RNA interactions, each directing mRNA fate from transcription to translation. Consequently, viruses have evolved an arsenal of strategies to target these RNA features and ultimately take control of the pathways they influence, and these strategies contribute to the global shutdown of the host gene expression machinery known as “Host Shutoff”. This takeover of the host cell is mechanistically orchestrated by a number of non-homologous virally encoded endoribonucleases. Recent large-scale screens estimate that over 70 % of the host transcriptome is decimated by the expression of these viral nucleases. While this takeover strategy seems extraordinarily well conserved, each viral endonuclease has evolved to target distinct mRNA elements. Herein, we will explore each of these RNA structures/sequence features that render messenger RNA susceptible or resistant to viral endonuclease cleavage. By further understanding these targeting and escape mechanisms we will continue to unravel untold depths of cellular RNA regulation that further underscores the integral relationship between RNA fate and the fate of the cell.
Collapse
Affiliation(s)
- William Rodriguez
- Microbiology Department, University of Massachusetts, Amherst, MA, United States
| | | | - Jacob Miles
- Microbiology Department, University of Massachusetts, Amherst, MA, United States
| | - Mandy Muller
- Microbiology Department, University of Massachusetts, Amherst, MA, United States.
| |
Collapse
|
19
|
Yemanyi F, Vranka J, Raghunathan V. Generating cell-derived matrices from human trabecular meshwork cell cultures for mechanistic studies. Methods Cell Biol 2020; 156:271-307. [PMID: 32222223 DOI: 10.1016/bs.mcb.2019.10.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ocular hypertension has been attributed to increased resistance to aqueous outflow often as a result of changes in trabecular meshwork (TM) extracellular matrix (ECM) using in vivo animal models (for example, by genetic manipulation) and ex vivo anterior segment perfusion organ cultures. These are, however, complex and difficult in dissecting molecular mechanisms and interactions. In vitro approaches to mimic the underlying substrate exist by manipulating either ECM topography, mechanics, or chemistry. These models best investigate the role of individual ECM protein(s) and/or substrate property, and thus do not recapitulate the multifactorial extracellular microenvironment; hence, mitigating its physiological relevance for mechanistic studies. Cell-derived matrices (CDMs), however, are capable of presenting a 3D-microenvironment rich in topography, chemistry, and whose mechanics can be tuned to better represent the network of native ECM constituents in vivo. Critically, the composition of CDMs may also be fine-tuned by addition of small molecules or relevant bioactive factors to mimic homeostasis or pathology. Here, we first provide a streamlined protocol for generating CDMs from TM cell cultures from normal or glaucomatous donor tissues. Second, we document how TM cells can be pharmacologically manipulated to obtain glucocorticoid-induced CDMs and how generated pristine CDMs can be manipulated with reagents like genipin. Finally, we summarize how CDMs may be used in mechanistic studies and discuss their probable application in future TM regenerative studies.
Collapse
Affiliation(s)
- Felix Yemanyi
- Department of Basic Sciences, University of Houston, Houston, TX, United States
| | - Janice Vranka
- Casey Eye Institute, Oregon Health and Science University, Portland, OR, United States
| | - VijayKrishna Raghunathan
- Department of Basic Sciences, University of Houston, Houston, TX, United States; The Ocular Surface Institute, College of Optometry, University of Houston, Houston, TX, United States; Department of Biomedical Engineering, Cullen College of Engineering, University of Houston, Houston, TX, United States.
| |
Collapse
|
20
|
Gossypol but not cottonseed extracts or lipopolysaccharides stimulates HuR gene expression in mouse cells. J Funct Foods 2019. [DOI: 10.1016/j.jff.2019.05.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
|
21
|
Exposure to Pb and Cd alters MCT4/CD147 expression and MCT4/CD147-dependent lactate transport in mice Sertoli cells cultured in vitro. Toxicol In Vitro 2019; 56:30-40. [PMID: 30615929 DOI: 10.1016/j.tiv.2019.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 10/28/2018] [Accepted: 01/03/2019] [Indexed: 12/22/2022]
Abstract
Sertoli cells (SCs) provide lactate as an energy substrate to develop germ cells during spermatogenesis. Lead (Pb) and cadmium (Cd) can induce SC toxicity. However, the mechanisms remain unclear. This study aimed to investigate the molecular mechanisms by which Pb and Cd alter lactate transport and production by SCs. Mouse SC line (15P-1 cells) were cultured in the absence and presence of lead acetate (PbAc, 1, 10, 20 and 30 μM) or cadmium chloride (CdCl2, 0.5, 5, 10 and 15 μM) for 24 h. The results showed that PbAc exposure significantly decreased lactate dehydrogenase (LDH) activity and mRNA level, intracellular and extracellular lactate, and MCT4 and CD147 protein levels but increased MCT4 and CD147 mRNA levels. However, PbAc did not alter the glucose uptake, glucose transporters 1 (GLUT1) and 3 (GLUT3) mRNA expression of SCs. Thus, PbAc mainly decreased lactate production by inhibiting LDH activity. In CdCl2-treated SCs, intracellular lactate content increased but extracellular lactate content decreased significantly, P < .05. The glucose uptake, LDH activity, and mRNA expression of GLUT1, GLUT3 and LDH, all significantly increased. But the mRNA and protein levels of MCT4 and CD147 significantly decreased. Moreover, the fluorescence intensity of co-localizations of the MCT4-CD147 complex dose-dependently decreased in the cell membrane. Thus, CdCl2 may reduce lactate export by suppressing MCT4 and CD147 expression. These results suggest that PbAc and CdCl2 disrupt lactate production and transport in mouse SCs by disturbing glycolysis or inhibiting MCT4-CD147 transporter expression and co-localizations.
Collapse
|
22
|
Ryu HG, Kim S, Lee S, Lee E, Kim HJ, Kim DY, Kim KT. HNRNP Q suppresses polyglutamine huntingtin aggregation by post-transcriptional regulation of vaccinia-related kinase 2. J Neurochem 2019; 149:413-426. [PMID: 30488434 DOI: 10.1111/jnc.14638] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 12/22/2022]
Abstract
Misfolded proteins with abnormal polyglutamine (polyQ) expansion cause neurodegenerative disorders, including Huntington's disease. Recently, it was found that polyQ aggregates accumulate as a result of vaccinia-related kinase 2 (VRK2)-mediated degradation of TCP-1 ring complex (TRiC)/chaperonin-containing TCP-1 (CCT), which has an essential role in the prevention of polyQ protein aggregation and cytotoxicity. The levels of VRK2 are known to be much higher in actively proliferating cells but are maintained at a low level in the brain via an unknown mechanism. Here, we found that basal levels of neuronal cell-specific VRK2 mRNA are maintained by post-transcriptional, rather than transcriptional, regulation. Moreover, heterogeneous nuclear ribonucleoprotein Q (HNRNP Q) specifically binds to the 3'untranslated region of VRK2 mRNA in neuronal cells to reduce the mRNA stability. As a result, we found a dramatic decrease in CCT4 protein levels in response to a reduction in HNRNP Q levels, which was followed by an increase in polyQ aggregation in human neuroblastoma cells and mouse cortical neurons. Taken together, these results provide new insights into how neuronal HNRNP Q decreases VRK2 mRNA stability and contributes to the prevention of Huntington's disease, while also identifying new prognostic markers of HD.
Collapse
Affiliation(s)
- Hye Guk Ryu
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| | - Sangjune Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea.,Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Baltimore, Maryland, USA.,Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Saebom Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea.,Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Baltimore, Maryland, USA.,Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eunju Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Korea.,Advanced Bio Convergence Center, Pohang Technopark, Pohang, Korea
| | - Hyo-Jin Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Korea.,SL BIGEN, Seongnam, Korea
| | - Do-Yeon Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea.,Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu, Korea.,Brain Science & Engineering Institute, Kyungpook National University, Daegu, Korea
| | - Kyong-Tai Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| |
Collapse
|
23
|
Herman AB, Vrakas CN, Ray M, Kelemen SE, Sweredoski MJ, Moradian A, Haines DS, Autieri MV. FXR1 Is an IL-19-Responsive RNA-Binding Protein that Destabilizes Pro-inflammatory Transcripts in Vascular Smooth Muscle Cells. Cell Rep 2018; 24:1176-1189. [PMID: 30067974 PMCID: PMC11004729 DOI: 10.1016/j.celrep.2018.07.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/18/2018] [Accepted: 07/01/2018] [Indexed: 12/22/2022] Open
Abstract
This work identifies the fragile-X-related protein (FXR1) as a reciprocal regulator of HuR target transcripts in vascular smooth muscle cells (VSMCs). FXR1 was identified as an HuR-interacting protein by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The HuR-FXR1 interaction is abrogated in RNase-treated extracts, indicating that their association is tethered by mRNAs. FXR1 expression is induced in diseased but not normal arteries. siRNA knockdown of FXR1 increases the abundance and stability of inflammatory mRNAs, while overexpression of FXR1 reduces their abundance and stability. Conditioned media from FXR1 siRNA-treated VSMCs enhance activation of naive VSMCs. RNA EMSA and RIP demonstrate that FXR1 interacts with an ARE and an element in the 3' UTR of TNFα. FXR1 expression is increased in VSMCs challenged with the anti-inflammatory cytokine IL-19, and FXR1 is required for IL-19 reduction of HuR. This suggests that FXR1 is an anti-inflammation responsive, HuR counter-regulatory protein that reduces abundance of pro-inflammatory transcripts.
Collapse
Affiliation(s)
- Allison B Herman
- Department of Physiology, Independence Blue Cross Cardiovascular Research Center, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Christine N Vrakas
- Department of Physiology, Independence Blue Cross Cardiovascular Research Center, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Mitali Ray
- Department of Physiology, Independence Blue Cross Cardiovascular Research Center, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Sheri E Kelemen
- Department of Physiology, Independence Blue Cross Cardiovascular Research Center, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Annie Moradian
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dale S Haines
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University Philadelphia, PA 19140, USA
| | - Michael V Autieri
- Department of Physiology, Independence Blue Cross Cardiovascular Research Center, Temple University School of Medicine, Philadelphia, PA 19140, USA.
| |
Collapse
|
24
|
Raghunathan VK, Benoit J, Kasetti R, Zode G, Salemi M, Phinney BS, Keller KE, Staverosky JA, Murphy CJ, Acott T, Vranka J. Glaucomatous cell derived matrices differentially modulate non-glaucomatous trabecular meshwork cellular behavior. Acta Biomater 2018. [PMID: 29524673 DOI: 10.1016/j.actbio.2018.02.037] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ocular hypertension is a causal risk-factor to developing glaucoma. This is associated with stiffening of the trabecular meshwork (TM), the primary site of resistance to aqueous-humor-outflow. The mechanisms underlying this stiffening or how pathologic extracellular matrix (ECM) affects cell function are poorly understood. It is recognized that mechanotransduction systems allow cells to sense and translate the intrinsic biophysical properties of ECM into intracellular signals to control gene transcription, protein expression, and cell behavior. Using an anterior segment perfusion model, we document that there are significantly more low flow regions that are much stiffer, and fewer high flow regions that are less stiff in glaucomatous TM (GTM) when compared to non-glaucomatous TMs (NTM). GTM tissue also has fewer cells overall when compared with NTM tissue. In order to study the role of pathologic ECM in glaucoma disease progression, we conducted studies using cell derived matrices (CDM). First, we characterized the mechanics, composition and organization of fibronectin in ECM deposited by GTM and NTM cells treated with glucocorticosteroids. Then, we determined that these GTM-derived ECM are able to induce stiffening of normal NTM cells, and alter their gene/protein expression to resemble that of a glaucomatous phenotype. Further, we demonstrate that GTM-derived ECM causes endoplasmic reticular stress in NTM. They also became resistant to being reorganized by these NTM cells. These phenomena were exacerbated by ECMs obtained from steroid treated glaucoma model groups. Collectively, our data demonstrates that CDMs represent a novel tool for the study of bidirectional interactions between TM cells and their immediate microenvironment. STATEMENT OF SIGNIFICANCE Extracellular matrix (ECM) changes are prevalent in a number of diseases. The precise mechanisms by which changes in the ECM contribute to disease progression is unclear, primarily due to absence of appropriate models. Here, using glaucoma as a disease model, we document changes in cell derived matrix (CDM) and tissue mechanics that contribute to the pathology. Subsequently, we determine the effect that ECMs from diseased and healthy individuals have on healthy cell behaviors. Data emanating from this study demonstrate that CDMs are a potent tool for the study of cell-ECM interactions.
Collapse
|
25
|
Yin J, Li R, Liu W, Chen Y, Zhang X, Li X, He X, Duan C. Neuroprotective Effect of Protein Phosphatase 2A/Tristetraprolin Following Subarachnoid Hemorrhage in Rats. Front Neurosci 2018; 12:96. [PMID: 29535596 PMCID: PMC5835096 DOI: 10.3389/fnins.2018.00096] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/06/2018] [Indexed: 11/25/2022] Open
Abstract
Early brain injury (EBI) following subarachnoid hemorrhage (SAH) can lead to inflammation and neuronal dysfunction. There is a need for effective strategies to mitigate these effects and improve the outcome of patients who experience SAH. The mRNA-destabilizing protein tristetraprolin (TTP) is an anti-inflammatory factor that induces the decay of cytokine transcripts and has been implicated in diseases such as glioma. However, the mechanism of action of TTP in EBI after SAH is unclear. The present study investigated the effects of TTP regulation via phosphorylation in a rat model of SAH by protein phosphatase (PP)2A, which is a pleiotropic enzyme complex with multiple substrate phospho-proteins. We hypothesized that inhibitory phosphorylation of TTP by PP2A would reduce neuroinflammation and apoptosis. To evaluate the function of each factor, the PP2A agonist FTY720, short interfering (si)RNAs targeting TTP and PP2A were administered to rats by intracerebroventricular injection 24 h before SAH. Rats were evaluated with SAH grade, neurological score, brain water content and by western blotting, and terminal deoxynucleotidyltransferase dUTP nick-end labeling. We found that endogenous PP2A and TTP levels were increased after SAH. FTY720 induced PP2A activation would lead to dephosphorylation and activation of TTP and decreased production of tumor necrosis factor (TNF)-α, interleukin (IL)-6, and IL-8. SiRNA-mediated TTP knockdown abolished anti-inflammatory effects of FTY720 treatment, indicating that PP2A was associated with TTP activation in vivo. Decreased TNF-α, IL-6, and IL-8 levels were associated with improvement of neurological function, reduction of brain edema, suppression of caspase-3, and up-regulation of B cell lymphoma-2. These results demonstrated that PP2A activation could enhance the anti-inflammatory and anti-apoptotic effects of TTP, by which it might shed light on the development of an effective therapeutic strategy against EBI following SAH.
Collapse
Affiliation(s)
- Jian Yin
- The National Key Clinic Specialty, The Neurosurgery Institute of Guangdong Province, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Departments of Neurosurgery, Hanghzou Red Cross Hospital, Hangzhou, China
| | - Ran Li
- The National Key Clinic Specialty, The Neurosurgery Institute of Guangdong Province, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Wenchao Liu
- The National Key Clinic Specialty, The Neurosurgery Institute of Guangdong Province, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yunchang Chen
- The National Key Clinic Specialty, The Neurosurgery Institute of Guangdong Province, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xin Zhang
- The National Key Clinic Specialty, The Neurosurgery Institute of Guangdong Province, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xifeng Li
- The National Key Clinic Specialty, The Neurosurgery Institute of Guangdong Province, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xuying He
- The National Key Clinic Specialty, The Neurosurgery Institute of Guangdong Province, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Chuanzhi Duan
- The National Key Clinic Specialty, The Neurosurgery Institute of Guangdong Province, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| |
Collapse
|
26
|
Inflammation-regulated mRNA stability and the progression of vascular inflammatory diseases. Clin Sci (Lond) 2017; 131:2687-2699. [PMID: 29109302 DOI: 10.1042/cs20171373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/22/2022]
Abstract
Cardiovascular disease remains a major medical and socioeconomic burden in developed and developing societies, and will increase with an aging and increasingly sedentary society. Vascular disease and atherosclerotic vascular syndromes are essentially inflammatory disorders, and transcriptional and post-transcriptional processes play essential roles in the ability of resident vascular and inflammatory cells to adapt to environmental stimuli. The regulation of mRNA translocation, stability, and translation are key processes of post-transcriptional regulation that permit these cells to rapidly respond to inflammatory stimuli. For the most part, these processes are controlled by elements in the 3'-UTR of labile, proinflammatory transcripts. Since proinflammatory transcripts almost exclusively contain AU-rich elements (AREs), this represents a tightly regulated and specific mechanism for initiation and maintenance of the proinflammatory phenotype. RNA-binding proteins (RBPs) recognize cis elements in 3'-UTR, and regulate each of these processes, but there is little literature exploring the concept that RBPs themselves can be directly regulated by inflammatory stimuli. Conceptually, inflammation-responsive RBPs represent an attractive target of rational therapies to combat vascular inflammatory syndromes. Herein we briefly describe the cellular and molecular etiology of atherosclerosis, and summarize our current understanding of RBPs and their specific roles in regulation of inflammatory mRNA stability. We also detail RBPs as targets of current anti-inflammatory modalities and how this may translate into better treatment for vascular inflammatory diseases.
Collapse
|
27
|
Dong D, Zhong W, Sun Q, Zhang W, Sun X, Zhou Z. Oxidative products from alcohol metabolism differentially modulate pro-inflammatory cytokine expression in Kupffer cells and hepatocytes. Cytokine 2016; 85:109-19. [PMID: 27314544 DOI: 10.1016/j.cyto.2016.06.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 12/20/2022]
Abstract
Pro-inflammatory cytokines play a vital role in the pathogenesis of alcoholic steatohepatitis. The present study was to determine the role of alcohol-induced oxidative stress in modulating cytokine production. A rat model of alcohol consumption was used to determine alcohol-induced hepatic cytokine expression. Chronic alcohol exposure caused lipid accumulation, oxidative stress, and inflammation in the livers of Wistar rats. The role of oxidative stress in regulating cell type-specific cytokine production was further dissected in vitro. Lipopolysaccharide (LPS) dose-dependently upregulated TNF-α, MIP-1α, MCP-1, and CINC-1 in Kupffer cells-SV40, whereas TNF-α dose-dependently induced CINC-1, IP-10, and MIP-2 expression in H4IIEC3 hepatoma cells. An additive effect on cytokine production was observed in both Kupffer cells-SV40 and hepatocytes when combined hydrogen peroxide with LPS or TNF-α, respectively, which was associated with NF-κB activation and histone H3 hyper-acetylation. Unexpectedly, an inhibitory effect of 4-hydroxynonenal on cytokine production was revealed in LPS-treated Kupffer cells-SV40. Mechanistic study showed that 4-hydroxynonenal significantly enhanced mRNA degradation of TNF-α, MCP-1, and MIP-1α, and decreased the protein levels of MCP-1 in LPS-stimulated Kupffer cells-SV40 through reducing the phosphorylation of mRNA binding proteins. This study suggests that Kupffer cells and hepatocytes express distinct pro-inflammatory cytokines/chemokines in response to alcohol intoxication, and oxidative products (4-hydroxynonenal) differentially modulate pro-inflammatory cytokine/chemokine production via NF-κB signaling, histone acetylation, and mRNA stability.
Collapse
Affiliation(s)
- Daoyin Dong
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, USA
| | - Wei Zhong
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, USA
| | - Qian Sun
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, USA; Department of Nutrition, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Wenliang Zhang
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, USA
| | - Xinguo Sun
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, USA
| | - Zhanxiang Zhou
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, USA; Department of Nutrition, University of North Carolina at Greensboro, Greensboro, NC, USA.
| |
Collapse
|
28
|
Rougemaille M, Libri D. Control of cryptic transcription in eukaryotes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 702:122-31. [PMID: 21713682 DOI: 10.1007/978-1-4419-7841-7_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Over the last few years, the development of large-scale technologies has radically modified our conception of genome-wide transcriptional control by unveiling an unexpected high complexity of the eukaryotic transcriptome. In organisms ranging from yeast to human, a considerable number of novel small RNA species have been discovered in regions that were previously thought to be incompatible with high levels of transcription. Intriguingly, these transcripts, which are rapidly targeted for degradation by the exosome, appear to be devoid of any coding potential and may be the consequence of unwanted transcription events. However, the notion that an important fraction of these RNAs represent by-products of regulatory transcription is progressively emerging. In this chapter, we discuss the recent advances made in our understanding of the shape of the eukaryotic transcriptome. We also focus on the molecular mechanisms that cells exploit to prevent cryptic transcripts from interfering with the expression of protein-coding genes. Finally, we summarize data obtained in different systems suggesting that such RNAs may play a critical role in the regulation of gene expression as well as the evolution of genomes.
Collapse
Affiliation(s)
- Mathieu Rougemaille
- LEA Laboratory of Nuclear RNA Metabolism, Centre de Génétique Moléculaire, CNRS-UPR2167, Gif-sur-Yvette, France,
| | | |
Collapse
|
29
|
Joe Y, Kim SK, Chen Y, Yang JW, Lee JH, Cho GJ, Park JW, Chung HT. Tristetraprolin mediates anti-inflammatory effects of carbon monoxide on lipopolysaccharide-induced acute lung injury. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:2867-74. [PMID: 26348577 DOI: 10.1016/j.ajpath.2015.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 07/24/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022]
Abstract
Low-dose inhaled carbon monoxide is reported to suppress inflammatory responses and exhibit a therapeutic effect in models of lipopolysaccharide (LPS)-induced acute lung injury (ALI). However, the precise mechanism by which carbon monoxide confers protection against ALI is not clear. Tristetraprolin (TTP; official name ZFP36) exerts anti-inflammatory effects by enhancing decay of proinflammatory cytokine mRNAs. With the use of TTP knockout mice, we demonstrate here that the protection by carbon monoxide against LPS-induced ALI is mediated by TTP. Inhalation of carbon monoxide substantially increased the pulmonary expression of TTP. carbon monoxide markedly enhanced the decay of mRNA-encoding inflammatory cytokines, blocked the expression of inflammatory cytokines, and decreased tissue damage in LPS-treated lung tissue. Moreover, knockout of TTP abrogated the anti-inflammatory and tissue-protective effects of carbon monoxide in LPS-induced ALI. These results suggest that carbon monoxide-induced TTP mediates the protective effect of carbon monoxide against LPS-induced ALI by enhancing the decay of mRNA encoding proinflammatory cytokines.
Collapse
Affiliation(s)
- Yeonsoo Joe
- Department of Biological Sciences, University of Ulsan, Ulsan, Republic of Korea
| | - Seul-Ki Kim
- Department of Biological Sciences, University of Ulsan, Ulsan, Republic of Korea
| | - Yingqing Chen
- Department of Biological Sciences, University of Ulsan, Ulsan, Republic of Korea
| | - Jung Wook Yang
- Department of Pathology, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Jeong-Hee Lee
- Department of Pathology, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Gyeong Jae Cho
- Department of Anatomy, School of Medicine and Institute of Health Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Jeong Woo Park
- Department of Biological Sciences, University of Ulsan, Ulsan, Republic of Korea.
| | - Hun Taeg Chung
- Department of Biological Sciences, University of Ulsan, Ulsan, Republic of Korea.
| |
Collapse
|
30
|
Bernardino RL, Martins AD, Jesus TT, Sá R, Sousa M, Alves MG, Oliveira PF. Estrogenic regulation of bicarbonate transporters from SLC4 family in rat Sertoli cells. Mol Cell Biochem 2015; 408:47-54. [DOI: 10.1007/s11010-015-2481-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/13/2015] [Indexed: 11/30/2022]
|
31
|
Vinther AML, Skovgaard K, Heegaard PMH, Andersen PH. Dynamic expression of leukocyte innate immune genes in whole blood from horses with lipopolysaccharide-induced acute systemic inflammation. BMC Vet Res 2015; 11:134. [PMID: 26076814 PMCID: PMC4467047 DOI: 10.1186/s12917-015-0450-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 06/02/2015] [Indexed: 01/05/2023] Open
Abstract
Background In horses, insights into the innate immune processes in acute systemic inflammation are limited even though these processes may be highly important for future diagnostic and therapeutic advances in high-mortality disease conditions as the systemic inflammatory response syndrome (SIRS) and sepsis. Therefore, the aim of this study was to investigate the expression of 31 selected blood leukocyte immune genes in an equine model of acute systemic inflammation to identify significantly regulated genes and to describe their expression dynamics during a 24-h experimental period. Systemic inflammation was induced in 6 adult horses by the intravenous injection of 1 μg lipopolysaccharide (LPS) per kg btw. Sixteen blood samples were collected for each horse at predetermined intervals and analyzed by reverse transcription quantitative real-time PCR. Post-induction expression levels for each gene were compared with baseline levels. Results Systemic inflammation was confirmed by the presence of clinical and hematological changes which were consistent with SIRS. The clinical response to LPS was transient and brief as all horses except one showed unaltered general demeanor after 24 h. Twenty-two leukocyte genes were significantly regulated at at least one time point during the experimental period. By close inspection of the temporal responses the dynamic changes in mRNA abundance revealed a very rapid onset of both pro- and anti-inflammatory mediators and a substantial variation in both expression magnitudes and duration of changes between genes. A majority of the 22 significantly regulated genes peaked within the first 8 h after induction, and an on-going, albeit tightly controlled, regulation was seen after 24 h despite approximate clinical recovery. Conclusions This first broad study of gene expressions in blood leukocytes during equine acute LPS-induced systemic inflammation thoroughly characterized a highly regulated and dynamic innate immune response. These results provide new insights into the molecular mechanisms of equine systemic inflammation. Electronic supplementary material The online version of this article (doi:10.1186/s12917-015-0450-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Anne Mette L Vinther
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Taastrup, Denmark.
| | - Kerstin Skovgaard
- Innate Immunology Group, Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark.
| | - Peter M H Heegaard
- Innate Immunology Group, Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark.
| | - Pia H Andersen
- Department of Clinical Sciences, Faculty of Veterinary and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| |
Collapse
|
32
|
Quercetin Decreases Claudin-2 Expression Mediated by Up-Regulation of microRNA miR-16 in Lung Adenocarcinoma A549 Cells. Nutrients 2015; 7:4578-92. [PMID: 26061016 PMCID: PMC4488803 DOI: 10.3390/nu7064578] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/26/2015] [Accepted: 06/01/2015] [Indexed: 12/27/2022] Open
Abstract
Claudin-2 is highly expressed in human lung adenocarcinoma tissues and cells. Knockdown of claudin-2 decreases cell proliferation and migration. Claudin-2 may be a novel target for lung adenocarcinoma. However, there are no physiologically active substances of foods which decrease claudin-2 expression. We here found that quercetin, a flavonoid present in fruits and vegetables, time- and concentration-dependently decreases claudin-2 expression in lung adenocarcinoma A549 cells. In the present study, we examined what regulatory mechanism is involved in the decrease in claudin-2 expression by quercetin. Claudin-2 expression was decreased by LY-294002, a phosphatidylinositol 3-kinase (PI3-K) inhibitor, and U0126, a MEK inhibitor. These drugs inhibited the phosphorylation of Akt and ERK1/2, which are downstream targets of PI3-K and MEK, respectively. In contrast, quercetin did not inhibit the phosphorylation. Both LY-294002 and U0126 inhibited promoter activity of claudin-2, but quercetin did not. The stability of claudin-2 mRNA was decreased by quercetin. Quercetin increased the expression of microRNA miR-16. An inhibitor of miR-16 rescued quercetin-induced decrease in the claudin-2 expression. These results suggest that quercetin decreases claudin-2 expression mediated by up-regulation of miR-16 expression and instability of claudin-2 mRNA in lung adenocarcinoma cells.
Collapse
|
33
|
Posttranscriptional adaptations of the vascular endothelium to hypoxia. Curr Opin Hematol 2015; 22:243-51. [PMID: 25767954 DOI: 10.1097/moh.0000000000000139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE OF REVIEW Remarkable new advances have been made in the field of posttranscriptional gene regulation over recent years. These include the revelation of noncoding RNAs, such as microRNAs, antisense transcripts and their interactions with RNA-binding proteins (RBPs) in the context of both health and disease settings, such as hypoxia. In particular, these discoveries bear much relevance to the field of vascular biology, which historically has focused upon transcriptional processes. Thus, the contributions of these posttranscriptional gene regulatory mechanisms to vascular and endothelial biology represent a newer concept that warrants discussion. RECENT FINDINGS Recent studies have revealed two emerging themes that are critical to endothelial/vascular biology and function. First is the functional integration between the microRNA pathway and the cellular hypoxic response, which, in addition to specific microRNAs, involves key components of the microRNA biogenesis machinery. A key concept here is the regulation of a master transcriptional programme through posttranscriptional mechanisms. The second major theme involves the dynamic interactions between RBPs, microRNAs and antisense RNAs. The condition-dependent collaborations and competitions between these different classes of posttranscriptional regulators reveal a critical layer of control for gene expression. SUMMARY Taken together, these findings bear significant diagnostic and therapeutic implications for vascular disease.
Collapse
|
34
|
León-Novelo LG, McIntyre LM, Fear JM, Graze RM. A flexible Bayesian method for detecting allelic imbalance in RNA-seq data. BMC Genomics 2014; 15:920. [PMID: 25339465 PMCID: PMC4230747 DOI: 10.1186/1471-2164-15-920] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 10/09/2014] [Indexed: 01/01/2023] Open
Abstract
Background One method of identifying cis regulatory differences is to analyze allele-specific expression (ASE) and identify cases of allelic imbalance (AI). RNA-seq is the most common way to measure ASE and a binomial test is often applied to determine statistical significance of AI. This implicitly assumes that there is no bias in estimation of AI. However, bias has been found to result from multiple factors including: genome ambiguity, reference quality, the mapping algorithm, and biases in the sequencing process. Two alternative approaches have been developed to handle bias: adjusting for bias using a statistical model and filtering regions of the genome suspected of harboring bias. Existing statistical models which account for bias rely on information from DNA controls, which can be cost prohibitive for large intraspecific studies. In contrast, data filtering is inexpensive and straightforward, but necessarily involves sacrificing a portion of the data. Results Here we propose a flexible Bayesian model for analysis of AI, which accounts for bias and can be implemented without DNA controls. In lieu of DNA controls, this Poisson-Gamma (PG) model uses an estimate of bias from simulations. The proposed model always has a lower type I error rate compared to the binomial test. Consistent with prior studies, bias dramatically affects the type I error rate. All of the tested models are sensitive to misspecification of bias. The closer the estimate of bias is to the true underlying bias, the lower the type I error rate. Correct estimates of bias result in a level alpha test. Conclusions To improve the assessment of AI, some forms of systematic error (e.g., map bias) can be identified using simulation. The resulting estimates of bias can be used to correct for bias in the PG model, without data filtering. Other sources of bias (e.g., unidentified variant calls) can be easily captured by DNA controls, but are missed by common filtering approaches. Consequently, as variant identification improves, the need for DNA controls will be reduced. Filtering does not significantly improve performance and is not recommended, as information is sacrificed without a measurable gain. The PG model developed here performs well when bias is known, or slightly misspecified. The model is flexible and can accommodate differences in experimental design and bias estimation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-920) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | - Rita M Graze
- Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, 36849 Auburn, AL, USA.
| |
Collapse
|
35
|
Expression of STEAP1 and STEAP1B in prostate cell lines, and the putative regulation of STEAP1 by post-transcriptional and post-translational mechanisms. Genes Cancer 2014; 5:142-51. [PMID: 25053991 PMCID: PMC4091532 DOI: 10.18632/genesandcancer.13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 06/10/2014] [Indexed: 12/26/2022] Open
Abstract
STEAP1 gene is overexpressed in several kinds of tumors, particularly in prostate cancer. Besides STEAP1, there is another related gene, STEAP1B, which may encode two different transcripts. Although several studies have been pointing STEAP1 as a putative immunotherapeutic target and biomarker, the mechanisms underlying its regulation are not fully understood. In silico analysis allowed us to show that STEAP1 and STEAP1B share high homology, but with slight differences at structural level. Experiments with prostate cells showed that STEAP1B2 is overexpressed in cancer cells. Regarding STEAP1 regulation, it is demonstrated that the stability of mRNA and protein is higher in LNCaP than in PNT1A cells. Of note, serum triggered opposite effects in LNCaP and PNT1A in relation to STEAP1 stability, e.g., increasing it in PNT1A and decreasing in LNCaP. These results suggest that STEAP1 may be regulated by post-transcriptional and post-translational modifications (PTM), which may differ between non-neoplastic and neoplastic cells. These PTM are supported through in silico analysis, where several modifications such as N-glycosylation, N-Glycation, Phosphorylation and O-linked β-N-acetylglucosamine, may occur in STEAP1 protein. In conclusion, these data indicate that STEAP1B2 is overexpressed in neoplastic cells, and PTM may be involved in regulation of STEAP1 expression in prostate cells.
Collapse
|
36
|
Edri S, Tuller T. Quantifying the effect of ribosomal density on mRNA stability. PLoS One 2014; 9:e102308. [PMID: 25020060 PMCID: PMC4096589 DOI: 10.1371/journal.pone.0102308] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 06/17/2014] [Indexed: 11/18/2022] Open
Abstract
Gene expression is a fundamental cellular process by which proteins are eventually synthesized based on the information coded in the genes. This process includes four major steps: transcription of the DNA segment corresponding to a gene to mRNA molecules, the degradation of the mRNA molecules, the translation of mRNA molecules to proteins by the ribosome and the degradation of the proteins. We present an innovative quantitative study of the interaction between the gene translation stage and the mRNA degradation stage using large scale genomic data of S. cerevisiae, which include measurements of mRNA levels, mRNA half-lives, ribosomal densities and protein abundances, for thousands of genes. The reported results support the conjecture that transcripts with higher ribosomal density, which is related to the translation stage, tend to have elevated half-lives, and we suggest a novel quantitative estimation of the strength of this relation. Specifically, we show that on average, an increase of 78% in ribosomal density yields an increase of 25% in mRNA half-life, and that this relation between ribosomal density and mRNA half-life is not function specific. In addition, our analyses demonstrate that ribosomal density along the entire ORF, and not in specific locations, has a significant effect on the transcript half-life. Finally, we show that the reported relation cannot be explained by different expression levels among genes. A plausible explanation for the reported results is that ribosomes tend to protect the mRNA molecules from the exosome complexes degrading them; however, additional non-mutually exclusive possible explanations for the reported relation and experiments for their verifications are discussed in the paper.
Collapse
Affiliation(s)
- Shlomit Edri
- The Department of Biomedical Engineering, Tel-Aviv University, Tel-Aviv, Israel
| | - Tamir Tuller
- The Department of Biomedical Engineering, Tel-Aviv University, Tel-Aviv, Israel
| |
Collapse
|
37
|
Goodarzi H, Zhang S, Buss CG, Fish L, Tavazoie S, Tavazoie SF. Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins. Nature 2014; 513:256-60. [PMID: 25043050 DOI: 10.1038/nature13466] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 05/12/2014] [Indexed: 01/30/2023]
Abstract
Aberrant regulation of RNA stability has an important role in many disease states. Deregulated post-transcriptional modulation, such as that governed by microRNAs targeting linear sequence elements in messenger RNAs, has been implicated in the progression of many cancer types. A defining feature of RNA is its ability to fold into structures. However, the roles of structural mRNA elements in cancer progression remain unexplored. Here we performed an unbiased search for post-transcriptional modulators of mRNA stability in breast cancer by conducting whole-genome transcript stability measurements in poorly and highly metastatic isogenic human breast cancer lines. Using a computational framework that searches RNA sequence and structure space, we discovered a family of GC-rich structural cis-regulatory RNA elements, termed sRSEs for structural RNA stability elements, which are significantly overrepresented in transcripts displaying reduced stability in highly metastatic cells. By integrating computational and biochemical approaches, we identified TARBP2, a double-stranded RNA-binding protein implicated in microRNA processing, as the trans factor that binds the sRSE family and similar structural elements--collectively termed TARBP2-binding structural elements (TBSEs)--in transcripts. TARBP2 is overexpressed in metastatic cells and metastatic human breast tumours and destabilizes transcripts containing TBSEs. Endogenous TARBP2 promotes metastatic cell invasion and colonization by destabilizing amyloid precursor protein (APP) and ZNF395 transcripts, two genes previously associated with Alzheimer's and Huntington's disease, respectively. We reveal these genes to be novel metastasis suppressor genes in breast cancer. The cleavage product of APP, extracellular amyloid-α peptide, directly suppresses invasion while ZNF395 transcriptionally represses a pro-metastatic gene expression program. The expression levels of TARBP2, APP and ZNF395 in human breast carcinomas support their experimentally uncovered roles in metastasis. Our findings establish a non-canonical and direct role for TARBP2 in mammalian gene expression regulation and reveal that regulated RNA destabilization through protein-mediated binding of mRNA structural elements can govern cancer progression.
Collapse
Affiliation(s)
- Hani Goodarzi
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Steven Zhang
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Colin G Buss
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Lisa Fish
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Saeed Tavazoie
- Department of Biochemistry and Molecular Biophysics, and Department of Systems Biology, Columbia University, New York, New York 10032, USA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| |
Collapse
|
38
|
Kim T, Do MHT, Lawson MA. Translational control of gene expression in the gonadotrope. Mol Cell Endocrinol 2014; 385:78-87. [PMID: 24035865 PMCID: PMC4009948 DOI: 10.1016/j.mce.2013.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/30/2013] [Accepted: 09/03/2013] [Indexed: 12/15/2022]
Abstract
The study of gene expression in gonadotropes has largely focused on the variety of mechanisms regulating transcription of the gonadotropin genes and ancillary factors that contribute to the overall phenotype and function of these cells in reproduction. However, there are aspects of the response to GNRH signaling that are not readily explained by changes at the level of transcription. As our understanding of regulation at the level of mRNA translation has increased, it has become evident that GNRH receptor signaling engages multiple aspects of translational regulation. This includes activation of cap-dependent translation initiation, translational pausing caused by the unfolded protein response and RNA binding protein interaction. Gonadotropin mRNAs and the mRNAs of other factors that control the transcriptional and signaling responses to GNRH have been identified as targets of regulation at the level of translation. In this review we examine the impact of translational control of the expression of gonadotropin genes and other genes relevant to GNRH-mediated control of gonadotrope function.
Collapse
Affiliation(s)
- Taeshin Kim
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA 92093, United States
| | - Minh-Ha T Do
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA 92093, United States
| | - Mark A Lawson
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA 92093, United States.
| |
Collapse
|
39
|
Uddin MJ, Joe Y, Zheng M, Blackshear PJ, Ryter SW, Park JW, Chung HT. A functional link between heme oxygenase-1 and tristetraprolin in the anti-inflammatory effects of nicotine. Free Radic Biol Med 2013; 65:1331-9. [PMID: 24095726 PMCID: PMC4798239 DOI: 10.1016/j.freeradbiomed.2013.09.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/27/2013] [Accepted: 09/27/2013] [Indexed: 10/26/2022]
Abstract
Nicotine stimulates the cholinergic anti-inflammatory pathway and prevents excessive inflammation by inhibiting the release of inflammatory cytokines from macrophages. We have previously reported that heme oxygenase-1 (HO-1) and tristetraprolin (TTP) are induced by nicotine and mediate the anti-inflammatory function of nicotine in macrophages. However, it was not clear whether the two molecules are functionally linked. In this study, we sought to determine whether HO-1 associates with TTP to mediate the anti-inflammatory effects of nicotine. Inhibition of HO-1 activity or HO-1 expression attenuated the effects of nicotine on STAT3 activation, TTP induction, and TNF-α production in LPS-treated macrophages. Induction of HO-1 expression increased the level of TTP in the absence of nicotine. In an LPS-induced endotoxemia model, HO-1 deficiency blocked the effects of nicotine on the STAT3 phosphorylation, TTP induction, and LPS-induced TNF-α production in the liver. Downregulation of STAT3 by siRNA attenuated the effect of nicotine on TTP expression and TNF-α production but did not affect the nicotine-mediated induction of HO-1. In TTP knockout mice, nicotine treatment enhanced HO-1 expression and STAT3 activation but failed to inhibit LPS-induced TNF-α production. Our results suggest that HO-1 and TTP are functionally linked in mediating the anti-inflammatory effects of nicotine; HO-1 is necessary for the induction of TTP by nicotine. This novel nicotine-HO-1-TTP signaling pathway provides new possibilities for the treatment of inflammatory diseases.
Collapse
Affiliation(s)
- Md. Jamal Uddin
- School of Biological Sciences, University of Ulsan, Ulsan 680-749, Korea
| | - Yeonsoo Joe
- School of Biological Sciences, University of Ulsan, Ulsan 680-749, Korea
| | - Min Zheng
- School of Biological Sciences, University of Ulsan, Ulsan 680-749, Korea
- Department of Thoracic and Cardiovascular Surgery, Affiliated Hospital of YanBian University
| | - Perry J. Blackshear
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Stefan W. Ryter
- Department of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jeong Woo Park
- School of Biological Sciences, University of Ulsan, Ulsan 680-749, Korea
| | - Hun Taeg Chung
- School of Biological Sciences, University of Ulsan, Ulsan 680-749, Korea
| |
Collapse
|
40
|
Bernardino RL, Martins AD, Socorro S, Alves MG, Oliveira PF. Effect of Prediabetes on Membrane Bicarbonate Transporters in Testis and Epididymis. J Membr Biol 2013; 246:877-83. [DOI: 10.1007/s00232-013-9601-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 09/24/2013] [Indexed: 11/29/2022]
|
41
|
Kidane YH, Lawrence C, Murali TM. Computational approaches for discovery of common immunomodulators in fungal infections: towards broad-spectrum immunotherapeutic interventions. BMC Microbiol 2013; 13:224. [PMID: 24099000 PMCID: PMC3853472 DOI: 10.1186/1471-2180-13-224] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 09/17/2013] [Indexed: 01/16/2023] Open
Abstract
Background Fungi are the second most abundant type of human pathogens. Invasive fungal pathogens are leading causes of life-threatening infections in clinical settings. Toxicity to the host and drug-resistance are two major deleterious issues associated with existing antifungal agents. Increasing a host’s tolerance and/or immunity to fungal pathogens has potential to alleviate these problems. A host’s tolerance may be improved by modulating the immune system such that it responds more rapidly and robustly in all facets, ranging from the recognition of pathogens to their clearance from the host. An understanding of biological processes and genes that are perturbed during attempted fungal exposure, colonization, and/or invasion will help guide the identification of endogenous immunomodulators and/or small molecules that activate host-immune responses such as specialized adjuvants. Results In this study, we present computational techniques and approaches using publicly available transcriptional data sets, to predict immunomodulators that may act against multiple fungal pathogens. Our study analyzed data sets derived from host cells exposed to five fungal pathogens, namely, Alternaria alternata, Aspergillus fumigatus, Candida albicans, Pneumocystis jirovecii, and Stachybotrys chartarum. We observed statistically significant associations between host responses to A. fumigatus and C. albicans. Our analysis identified biological processes that were consistently perturbed by these two pathogens. These processes contained both immune response-inducing genes such as MALT1, SERPINE1, ICAM1, and IL8, and immune response-repressing genes such as DUSP8, DUSP6, and SPRED2. We hypothesize that these genes belong to a pool of common immunomodulators that can potentially be activated or suppressed (agonized or antagonized) in order to render the host more tolerant to infections caused by A. fumigatus and C. albicans. Conclusions Our computational approaches and methodologies described here can now be applied to newly generated or expanded data sets for further elucidation of additional drug targets. Moreover, identified immunomodulators may be used to generate experimentally testable hypotheses that could help in the discovery of broad-spectrum immunotherapeutic interventions. All of our results are available at the following supplementary website: http://bioinformatics.cs.vt.edu/~murali/supplements/2013-kidane-bmc
Collapse
Affiliation(s)
- Yared H Kidane
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA.
| | | | | |
Collapse
|
42
|
Ho JJD, Marsden PA. Competition and collaboration between RNA-binding proteins and microRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:69-86. [PMID: 24124109 DOI: 10.1002/wrna.1197] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/21/2013] [Accepted: 08/27/2013] [Indexed: 01/08/2023]
Abstract
Posttranscriptional regulation of mRNA species represents a major regulatory checkpoint in the control of gene expression. Historically, RNA-binding proteins (RBPs) have been regarded as the primary regulators of mRNA stability and translation. More recently, however, microRNAs have emerged as a class of potent and pervasive posttranscriptional rheostats that similarly affect mRNA stability and translation. The observation that both microRNAs and RBPs regulate mRNA stability and translation has initiated a newer area of research that involves the examination of dynamic interactions between these two important classes of posttranscriptional regulators, the myriad of factors that influence these biological interactions, and ultimately, their effects on target mRNAs. Specifically, microRNAs and RBPs can act synergistically to effect mRNA destabilization and translational inhibition. They can also engage in competition with each other and exert opposing effects on target mRNAs. To date, several key studies have provided critical details regarding the mechanisms and principles of interaction between these molecules. Additionally, these findings raise important questions regarding the regulation of these interactions, including the roles of posttranslational modification, subcellular localization, target inhibition versus activation, and changes in expression levels of these regulatory factors, especially under stimulus- and cell-specific conditions. Indeed, further experimentation is warranted to address these key issues that pertain to the collaboration and competition between microRNAs and RBPs. Significantly, the elucidation of these important details bears critical implications for disease management, especially for those diseases in which these cellular factors are dysregulated.
Collapse
Affiliation(s)
- J J David Ho
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Medicine, Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
| | | |
Collapse
|
43
|
Martins AD, Alves MG, Simões VL, Dias TR, Rato L, Moreira PI, Socorro S, Cavaco JE, Oliveira PF. Control of Sertoli cell metabolism by sex steroid hormones is mediated through modulation in glycolysis-related transporters and enzymes. Cell Tissue Res 2013; 354:861-8. [DOI: 10.1007/s00441-013-1722-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 08/16/2013] [Indexed: 11/29/2022]
|
44
|
Casper I, Nowag S, Koch K, Hubrich T, Bollmann F, Henke J, Schmitz K, Kleinert H, Pautz A. Post-transcriptional regulation of the human inducible nitric oxide synthase (iNOS) expression by the cytosolic poly(A)-binding protein (PABP). Nitric Oxide 2013; 33:6-17. [DOI: 10.1016/j.niox.2013.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 12/21/2022]
|
45
|
Exposure to 2,4-dichlorophenoxyacetic acid alters glucose metabolism in immature rat Sertoli cells. Reprod Toxicol 2013; 38:81-8. [DOI: 10.1016/j.reprotox.2013.03.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 02/12/2013] [Accepted: 03/16/2013] [Indexed: 11/22/2022]
|
46
|
Sharma S, Verma S, Vasudevan M, Samanta S, Thakur JK, Kulshreshtha R. The interplay of HuR and miR-3134 in regulation of AU rich transcriptome. RNA Biol 2013; 10:1283-90. [PMID: 23823647 DOI: 10.4161/rna.25482] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs and AU Rich element (ARE)-mediated degradation of transcripts are thought to be two independent means of gene regulation at the post-transcriptional level. However, since their site of action is the same (3'UTR of mRNA), there exists a high probability that specific miRNAs may bind to AREs and, thus, interact with ARE-binding proteins (ARE-BPs) to regulate transcript levels. In this study, we have characterized AREs as potential targets of hsa-miR-3134. An analysis of the global gene expression profile of breast cancer cell line MCF7 overexpressing miR-3134 revealed the presence of at least one AUUUA element in the 3'-UTRs of 63% of miR-3134 regulated protein coding genes. Quantitative RT-PCR or 3'UTR luciferase assays show that miR-3134 mediates an up to 4-8-fold increase in the levels of ARE bearing transcripts-SOX9, VEGFA, and EGFR, while mutated miR-3134 shows a decreased effect. The miR-3134-mediated increase in transcript levels was unaffected by treatment with transcription inhibitor (actinomycin D), indicating that miR-3134 enhances transcript stability. To investigate a possible interplay between miR-3134 and a prototype ARE-BP, HuR, we compared their overexpression transcriptome profiles. Interestingly, up to 80% of miR-3134-regulated genes were also regulated by HuR. Overexpression studies of HuR alone or in combination with miR-3134 shows that wt miR-3134 but not a mutated miR-3134 promotes stabilization of HuR-regulated transcripts SOX9, VEGFA, and EGFR as confirmed by qRT-PCR or RNA-immunoprecipitation experiments. Overall, this report suggests that collaboration between ARE-binding microRNAs and ARE-binding proteins could be a general mechanism of 3'-UTR mediated regulation of gene expression in human cells.
Collapse
Affiliation(s)
- Shivani Sharma
- Department of Biochemical Engineering and Biotechnology; Indian Institute of Technology; Delhi, India
| | | | | | | | | | | |
Collapse
|
47
|
Gomes IM, Santos CR, Socorro S, Maia CJ. Six transmembrane epithelial antigen of the prostate 1 is down-regulated by sex hormones in prostate cells. Prostate 2013; 73:605-13. [PMID: 23060075 DOI: 10.1002/pros.22601] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 09/10/2012] [Indexed: 11/07/2022]
Abstract
BACKGROUND STEAP1 is over-expressed in several types of tumors, especially prostate cancer, where it is localized in the plasma membrane of epithelial cells, at cell-cell junctions. Its role in prostate carcinogenesis and its regulation in prostate cells remain unknown. Therefore, we propose to study the effect of sex hormones in the regulation of STEAP1 expression in prostate cells in vitro and in vivo. METHODS LNCaP prostate cells were incubated with fetal bovine serum (FBS), charcoal-stripped FBS (CS-FBS), 5α-dihydrotestosterone (DHT), and 17β-estradiol (E2 ) for different periods of stimulation. In addition, adult male Wistar rats were castrated and treated with DHT and E2 . The levels of STEAP1 in response to treatments were analyzed by real-time PCR, Western blot, and immunohistochemistry. RESULTS The treatment of LNCaP cells with DHT or E2 induces a down-regulation of STEAP1 expression, while incubation with CS-FBS has the opposite effect. Experiments using inhibitors of androgen and estrogen receptor (AR and ER) showed that down-regulation of STEAP1 is AR-dependent, but ER-independent. However, the mediation of six transmembrane epithelial antigen of the prostate 1 (STEAP1) expression by AR seems to be dependent of de novo protein synthesis. In vivo studies showed that castrated rats express higher levels of STEAP1 protein when compared to intact rats, an effect reversed by DHT or E2 replacement. CONCLUSIONS STEAP1 is down-regulated by DHT and E2 in LNCaP cells and in rat prostate.
Collapse
Affiliation(s)
- Inês M Gomes
- CICS-UBI-Health Sciences Research Center, University of Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | | | | | | |
Collapse
|
48
|
Bollmann F, Fechir K, Nowag S, Koch K, Art J, Kleinert H, Pautz A. Human inducible nitric oxide synthase (iNOS) expression depends on chromosome region maintenance 1 (CRM1)- and eukaryotic translation initiation factor 4E (elF4E)-mediated nucleocytoplasmic mRNA transport. Nitric Oxide 2013; 30:49-59. [PMID: 23471078 DOI: 10.1016/j.niox.2013.02.083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/15/2013] [Accepted: 02/25/2013] [Indexed: 12/31/2022]
Abstract
Human inducible nitric oxide synthase (iNOS) is regulated on the expressional level mostly by post-transcriptional mechanisms modulating the mRNA stability. Another important step in the control of eukaryotic gene expression is the nucleocytoplasmic mRNA transport. Most cellular mRNAs are exported via the TAP/Nxt complex of proteins. However, some mRNAs are transported by a different mechanism involving the nuclear export receptor CRM1. Treatment of DLD-1 cells with the CRM1 inhibitor leptomycin B (LMB) or anti-CRM1 siRNAs reduced cytokine-induced iNOS expression. We could demonstrate that the iNOS mRNA is exported from the nucleus in a CRM1-dependent manner. Since CRM1 itself does not possess any RNA binding affinity, an adapter protein is needed to mediate CRM1-dependent mRNA export. Western blot experiments showed that the eukaryotic translation initiation factor eIF4E is retained in the nucleus after LMB treatment. Blockade of eIF4E by ribavirin or overexpression of the promyelocytic leukemia protein (PML) decreased iNOS expression due to reduced iNOS mRNA export from the nucleus. Transfection experiments provide evidence that the 3'-untranslated region of the iNOS mRNA is involved in eIF4E-mediated iNOS mRNA transport. In summary, CRM1 and eIF4E seem to play an important role in the nucleocytoplasmic export of human iNOS mRNA.
Collapse
Affiliation(s)
- Franziska Bollmann
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University Mainz, D 55101 Mainz, Germany
| | | | | | | | | | | | | |
Collapse
|
49
|
Exon array analysis of alternative splicing of genes in SOD1G93A transgenic mice. Appl Biochem Biotechnol 2013; 170:301-19. [PMID: 23508861 DOI: 10.1007/s12010-013-0155-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 02/18/2013] [Indexed: 01/15/2023]
Abstract
Alternative splicing is a common strategy for creating functional diversities of proteins. While conventional identification of splice variants generally targets individual genes in amyotrophic lateral sclerosis, we present a novel exon-centric array that allows genome-wide identification of splice variants and concurrently provides analysis of gene expression. Compare 1 was asymptomatic SOD1G93A transgenic mice with nontransgenic littermates; compare 2 was symptomatic with asymptomatic transgenic mice. RT-PCR was performed to validate. Pathway and GO analysis were performed on abnormal genes. These findings could guide us to demonstrated the potential influence of mutant human CuZn-SOD1 and of splicing regulation in pathological processes.
Collapse
|
50
|
Sokhi UK, Das SK, Dasgupta S, Emdad L, Shiang R, DeSalle R, Sarkar D, Fisher PB. Human polynucleotide phosphorylase (hPNPaseold-35): should I eat you or not--that is the question? Adv Cancer Res 2013; 119:161-90. [PMID: 23870512 DOI: 10.1016/b978-0-12-407190-2.00005-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
RNA degradation plays a fundamental role in maintaining cellular homeostasis whether it occurs as a surveillance mechanism eliminating aberrant mRNAs or during RNA processing to generate mature transcripts. 3'-5' exoribonucleases are essential mediators of RNA decay pathways, and one such evolutionarily conserved enzyme is polynucleotide phosphorylase (PNPase). The human homologue of this fascinating enzymatic protein (hPNPaseold-35) was cloned a decade ago in the context of terminal differentiation and senescence through a novel "overlapping pathway screening" approach. Since then, significant insights have been garnered about this exoribonuclease and its repertoire of expanding functions. The objective of this review is to provide an up-to-date perspective of the recent discoveries made relating to hPNPaseold-35 and the impact they continue to have on our comprehension of its expanding and diverse array of functions.
Collapse
|