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Rayêe D, Hwang DW, Chang WK, Karp IN, Zhao Y, Bowman T, Lachke SA, Singer RH, Eliscovich C, Cvekl A. Identification and classification of abundant RNA-binding proteins in the mouse lens and interactions of Carhsp1, Igf2bp1/ZBP1, and Ybx1 with crystallin and β-actin mRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.10.632466. [PMID: 39829794 PMCID: PMC11741318 DOI: 10.1101/2025.01.10.632466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
RNA-binding proteins (RBPs) are critical regulators of mRNAs controlling all processes such as RNA transcription, transport, localization, translation, mRNA:ncRNA interactions, and decay. Cellular differentiation is driven by tissue-specific and/or tissue-preferred expression of proteins needed for the optimal function of mature cells, tissues and organs. Lens fiber cell differentiation is marked by high levels of expression of crystallin genes encoding critical proteins for lens transparency and light refraction. Herein we performed proteomic and transcriptomic analyses of RBPs in differentiating mouse lenses to identify the most abundant RBPs and establish dynamic changes of their expression in differentiating lens. Expression analyses include highly abundant RBPs, including Carhsp1, Igf2bp1/ZBP1, Ybx1, Pabpc1, Ddx39, and Rbm38. Binding sites of Carhsp1, Ybx1, and Igf2bp1/ZBP1 were predicted in various crystallin and β-actin mRNAs. Immunoprecipitations using antibodies against Carhsp1, Igf2bp1/ZBP1, and Ybx1 confirmed their interactions with αA-, αB-, and γA-crystallin mRNAs. A combination of single molecule RNA FISH (smFISH) and immunofluorescence was used to probe in vivo interactions of these RBPs with αA-, αB-crystallin, and β-actin mRNAs in cytoplasm and nucleoplasm of cultured mouse lens epithelial cells. Together, these results open new avenues to perform comprehensive genetic, cell, and molecular biology studies of individual RBPs in the lens.
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Farberov S, Ulitsky I. Systematic analysis of the target recognition and repression by the Pumilio proteins. Nucleic Acids Res 2024; 52:13402-13418. [PMID: 39470700 PMCID: PMC11602169 DOI: 10.1093/nar/gkae929] [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: 05/03/2024] [Revised: 09/23/2024] [Accepted: 10/07/2024] [Indexed: 10/30/2024] Open
Abstract
RNA binding proteins orchestrate the post-transcriptional fate of RNA molecules, but the principles of their action remain poorly understood. Pumilio (PUM) proteins bind 3' UTRs of mRNAs and lead to mRNA decay. To comprehensively map the determinants of recognition of sequences by PUM proteins in cells and to study the binding outcomes, we developed a massively parallel RNA assay that profiled thousands of PUM-binding sites in cells undergoing various perturbations or RNA immunoprecipitation. By studying fragments from the NORAD long non-coding RNA, we find two features that antagonize repression by PUM proteins - G/C rich sequences, particularly those upstream of the PUM recognition element, and binding of FAM120A, which limits the repression elicited by PUM-binding sites. We also find that arrays of PUM sites separated by 8-12 bases offer particularly strong repression and use them to develop a particularly sensitive reporter for PUM repression. In contrast, PUM sites separated by shorter linkers, such as some of those found in NORAD, exhibit strong activity interdependence, likely mediated by competition between PUM binding and formation of strong secondary structures. Overall, our findings expand our understanding of the determinants of PUM protein activity in human cells.
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Affiliation(s)
- Svetlana Farberov
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
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3
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Imamura K, Garland W, Schmid M, Jakobsen L, Sato K, Rouvière JO, Jakobsen KP, Burlacu E, Lopez ML, Lykke-Andersen S, Andersen JS, Jensen TH. A functional connection between the Microprocessor and a variant NEXT complex. Mol Cell 2024; 84:4158-4174.e6. [PMID: 39515294 DOI: 10.1016/j.molcel.2024.10.015] [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: 06/27/2023] [Revised: 08/26/2024] [Accepted: 10/11/2024] [Indexed: 11/16/2024]
Abstract
In mammalian cells, primary miRNAs are cleaved at their hairpin structures by the Microprocessor complex, whose core is composed of DROSHA and DGCR8. Here, we show that 5' flanking regions, resulting from Microprocessor cleavage, are targeted by the RNA exosome in mouse embryonic stem cells (mESCs). This is facilitated by a physical link between DGCR8 and the nuclear exosome targeting (NEXT) component ZCCHC8. Surprisingly, however, both biochemical and mutagenesis studies demonstrate that a variant NEXT complex, containing the RNA helicase MTR4 but devoid of the RNA-binding protein RBM7, is the active entity. This Microprocessor-NEXT variant also targets stem-loop-containing RNAs expressed from other genomic regions, such as enhancers. By contrast, Microprocessor does not contribute to the turnover of less structured NEXT substrates. Our results therefore demonstrate that MTR4-ZCCHC8 can link to either RBM7 or DGCR8/DROSHA to target different RNA substrates depending on their structural context.
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Affiliation(s)
- Katsutoshi Imamura
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark; Department of Systems Medicine, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - William Garland
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Lis Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense, Denmark
| | - Kengo Sato
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Jérôme O Rouvière
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Kristoffer Pors Jakobsen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Elena Burlacu
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Marta Loureiro Lopez
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense, Denmark
| | - Søren Lykke-Andersen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark.
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Lobo V, Nowak I, Fernandez C, Correa Muler AI, Westholm J, Huang HC, Fabrik I, Huynh HT, Shcherbinina E, Poyraz M, Härtlova A, Benhalevy D, Angeletti D, Sarshad AA. Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference. Nucleic Acids Res 2024; 52:9917-9935. [PMID: 38994560 PMCID: PMC11381323 DOI: 10.1093/nar/gkae589] [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: 06/06/2023] [Revised: 05/31/2024] [Accepted: 06/25/2024] [Indexed: 07/13/2024] Open
Abstract
In mammals, RNA interference (RNAi) was historically studied as a cytoplasmic event; however, in the last decade, a growing number of reports convincingly show the nuclear localization of the Argonaute (AGO) proteins. Nevertheless, the extent of nuclear RNAi and its implication in biological mechanisms remain to be elucidated. We found that reduced Lamin A levels significantly induce nuclear influx of AGO2 in SHSY5Y neuroblastoma and A375 melanoma cancer cell lines, which normally have no nuclear AGO2. Lamin A KO manifested a more pronounced effect in SHSY5Y cells compared to A375 cells, evident by changes in cell morphology, increased cell proliferation, and oncogenic miRNA expression. Moreover, AGO fPAR-CLIP in Lamin A KO SHSY5Y cells revealed significantly reduced RNAi activity. Further exploration of the nuclear AGO interactome by mass spectrometry identified FAM120A, an RNA-binding protein and known interactor of AGO2. Subsequent FAM120A fPAR-CLIP, revealed that FAM120A co-binds AGO targets and that this competition reduces the RNAi activity. Therefore, loss of Lamin A triggers nuclear AGO2 translocation, FAM120A mediated RNAi impairment, and upregulation of oncogenic miRNAs, facilitating cancer cell proliferation.
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Affiliation(s)
- Vivian Lobo
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Iwona Nowak
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Carola Fernandez
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Ana Iris Correa Muler
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Jakub O Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, SE-17121 Solna, Sweden
| | - Hsiang-Chi Huang
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Ivo Fabrik
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - Hang T Huynh
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Evgeniia Shcherbinina
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Melis Poyraz
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Anetta Härtlova
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Daniel Benhalevy
- Lab of Cellular RNA Biology, The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Davide Angeletti
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- SciLifeLab, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Aishe A Sarshad
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
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Tian K, Xu W, Chen M, Deng F. miR-155 promotes Th17 differentiation by targeting FOXP3 to aggravate inflammation in MRSA pneumonia. Cytokine 2024; 180:156662. [PMID: 38824863 DOI: 10.1016/j.cyto.2024.156662] [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: 02/06/2024] [Revised: 05/04/2024] [Accepted: 05/21/2024] [Indexed: 06/04/2024]
Abstract
BACKGROUND Previous researches have clarified that miR-155 is increased in methicillin-resistant Staphylococcus aureus (MRSA) pneumonia, and modulates Th9 differentiation. Like Th9 cells, Th17 cells were also a subset of CD4+ T cells and involved in MRSA pneumonia progression. This work aimed to investigate the role and mechanism of miR-155 in Th17 differentiation. METHODS Bronchoalveolar lavage fluid (BALF) was collected from children with MRSA pneumonia and bronchial foreign bodies. MRSA-infected murine model was established followed by collecting BALF and lung tissues. qRT-PCR, ELISA and flow cytometry were performed to examine the mRNA expression and concentration of IL-17 and the number of Th17 cells in above samples. HE and ELISA were used to evaluate inflammatory responses in lung. Furthermore, CD4+ T cells were isolated from BALF of children for in vitro experiments. After treatments with miR-155 mimic/inhibitor, the roles of miR-155 in Th17/IL-17 regulation were determined. The downstream of miR-155 was explored by qRT-PCR, western blotting, dual luciferase reporter analysis and RIP assay. RESULTS The levels of IL-17 and the proportion of Th17 cells were increased in children with MRSA pneumonia. A similar pattern was observed in MRSA-infected mice. On the contrary, IL-17 neutralization abolished the activation of Th17/IL-17 induced by MRSA infection. Furthermore, IL-17 blockade diminished the inflammation caused by MRSA. In vitro experiments demonstrated miR-155 positively regulated IL-17 expression and Th17 differentiation. Mechanistically, FOXP3 was a direct target of miR-155. miR-155 inhibited FOXP3 level via binding between FOXP3 and Argonaute 2 (AGO2), the key component of RNA-induced silencing complex (RISC). FOXP3 overexpression reversed elevated IL-17 levels and Th17 differentiation induced by miR-155. CONCLUSIONS miR-155 facilitates Th17 differentiation by reducing FOXP3 through interaction of AGO2 and FOXP3 to promote the pathogenesis of MRSA pneumonia. IL-17 blockade weakens the inflammation due to MRSA, which provides a nonantibiotic treatment strategy for MRSA pneumonia.
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Affiliation(s)
- Keyin Tian
- Children's Medical Center of Anhui Medical University, Department of Pediatric nephrology, Hefei 230051, Anhui, China; The Fifth Clinical College of Anhui Medical University, Hefei 230051, Anhui, China; Anhui Provincial Children's Hospital, Department of Pediatric emergency, Hefei 230051, Anhui, China
| | - Weihua Xu
- Anhui Provincial Children's Hospital, Department of Pediatric emergency, Hefei 230051, Anhui, China
| | - Mingxiao Chen
- Anhui Provincial Children's Hospital, Department of Pediatric emergency, Hefei 230051, Anhui, China
| | - Fang Deng
- Children's Medical Center of Anhui Medical University, Department of Pediatric nephrology, Hefei 230051, Anhui, China; The Fifth Clinical College of Anhui Medical University, Hefei 230051, Anhui, China; Anhui Provincial Children's Hospital, Department of Pediatric nephrology, Hefei 230051, Anhui, China.
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Sandoval R, Dilsavor CN, Grishanina NR, Patel V, Zamudio JR. Mammalian RNAi represses pericentromeric lncRNAs to maintain genome stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593425. [PMID: 38765997 PMCID: PMC11100815 DOI: 10.1101/2024.05.09.593425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Mammalian pericentromeric tandem repeats produce long noncoding RNAs (lncRNAs) that are dysregulated in cancer and linked to genomic instability. Identifying the basic molecular characteristics of these lncRNAs and their regulation is important to understanding their biological function. Here, we determine that the Argonaute (Ago) proteins of the RNA interference (RNAi) pathway directly and uniformly repress bidirectional pericentromeric lncRNAs in a Dicer-dependent manner in mouse embryonic and adult stem cells. Ago-dependent and Dicer-dependent autoregulatory small RNAs were identified within pericentromeric lncRNA degradation intermediates. We develop an RNase H cleavage assay to determine the relative proportions and lengths of the pericentromeric lncRNA targets. We find that 5'-phosphate and non-polyadenylated bidirectional pericentromeric lncRNAs are expressed at similar proportions. These lncRNAs can span up to 9 repeats, with transcription from the reverse strand template yielding the longer products. Using pericentromeric repeat RNA reporters, we determine that Ago represses pericentromeric lncRNAs after S phase transcription. Upon loss of Ago, pericentromeric lncRNA dysregulation results in delayed cell cycle progression, a defective mitotic spindle assembly checkpoint (SAC) and genomic instability. These results show that an evolutionarily conserved Ago activity at pericentromeres contributes to mammalian genome stability.
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Uekita T, Yagi R, Ichimura T, Sakai R. C9orf10/Ossa regulates the bone metastasis of established lung adenocarcinoma cell subline H322L-BO4 in a mouse model. Genes Cells 2024; 29:290-300. [PMID: 38339971 PMCID: PMC11447824 DOI: 10.1111/gtc.13103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
Abstract
Lung cancer frequently metastasizes to the bones. An in vivo model is urgently required to identify potential therapeutic targets for the prevention and treatment of lung cancer with bone metastasis. We established a lung adenocarcinoma cell subline (H322L-BO4) that specifically showed metastasis to the leg bones and adrenal glands. This was achieved by repeated isolation of metastatic cells from the leg bones of mice. The cells were intracardially injected into nude mice. Survival was prolonged for mice that received H322L-BO4 cells versus original cells (H322L). H322L-BO4 cells did not exhibit obvious changes in general in vitro properties associated with the metastatic potential (e.g., cell growth, migration, and invasion) compared with H322L cells. However, the phosphorylation of chromosome 9 open reading frame 10/oxidative stress-associated Src activator (C9orf10/Ossa) was increased in H322L-BO4 cells. This result confirmed the increased anchorage independence through C9orf10/Ossa-mediated activation of Src family tyrosine kinase. Reduction of C9orf10/Ossa by shRNA reduced cells' metastasis to the leg bone and prolonged survival in mice. These findings indicate that H322L-BO4 cells can be used to evaluate the effect of candidate therapeutic targets against bone metastatic lung cancer cells. Moreover, C9orf10/Ossa may be a useful target for treatment of lung cancer with bone metastasis.
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Affiliation(s)
- Takamasa Uekita
- Department of Applied ChemistryNational Defense AcademyYokosukaJapan
| | - Reiko Yagi
- Division of Metastasis and Invasion SignalingNational Cancer Center Research InstituteTokyoJapan
| | - Tohru Ichimura
- Department of Applied ChemistryNational Defense AcademyYokosukaJapan
| | - Ryuichi Sakai
- Department of BiochemistryKitasato University School of MedicineKanagawaJapan
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Larivera S, Neumeier J, Meister G. Post-transcriptional gene silencing in a dynamic RNP world. Biol Chem 2023; 404:1051-1067. [PMID: 37739934 DOI: 10.1515/hsz-2023-0203] [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: 05/05/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
MicroRNA (miRNA)-guided gene silencing is a key regulatory process in various organisms and linked to many human diseases. MiRNAs are processed from precursor molecules and associate with Argonaute proteins to repress the expression of complementary target mRNAs. Excellent work by numerous labs has contributed to a detailed understanding of the mechanisms of miRNA function. However, miRNA effects have mostly been analyzed and viewed as isolated events and their natural environment as part of complex RNA-protein particles (RNPs) is often neglected. RNA binding proteins (RBPs) regulate key enzymes of the miRNA processing machinery and furthermore RBPs or readers of RNA modifications may modulate miRNA activity on mRNAs. Such proteins may function similarly to miRNAs and add their own contributions to the overall expression level of a particular gene. Therefore, post-transcriptional gene regulation might be more the sum of individual regulatory events and should be viewed as part of a dynamic and complex RNP world.
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Affiliation(s)
- Simone Larivera
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Julia Neumeier
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
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Robinson K, Mosley TJ, Rivera-González KS, Jabbarpour CR, Curtis SW, Adeyemo WL, Beaty TH, Butali A, Buxó CJ, Cutler DJ, Epstein MP, Gowans LJ, Hecht JT, Murray JC, Shaw GM, Uribe LM, Weinberg SM, Brand H, Marazita ML, Lipinski RJ, Leslie EJ. Trio-based GWAS identifies novel associations and subtype-specific risk factors for cleft palate. HGG ADVANCES 2023; 4:100234. [PMID: 37719664 PMCID: PMC10502411 DOI: 10.1016/j.xhgg.2023.100234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023] Open
Abstract
Cleft palate (CP) is one of the most common craniofacial birth defects; however, there are relatively few established genetic risk factors associated with its occurrence despite high heritability. Historically, CP has been studied as a single phenotype, although it manifests across a spectrum of defects involving the hard and/or soft palate. We performed a genome-wide association study using transmission disequilibrium tests of 435 case-parent trios to evaluate broad risks for any cleft palate (ACP) (n = 435), and subtype-specific risks for any cleft soft palate (CSP), (n = 259) and any cleft hard palate (CHP) (n = 125). We identified a single genome-wide significant locus at 9q33.3 (lead SNP rs7035976, p = 4.24 × 10-8) associated with CHP. One gene at this locus, angiopoietin-like 2 (ANGPTL2), plays a role in osteoblast differentiation. It is expressed both in craniofacial tissue of human embryos and developing mouse palatal shelves. We found 19 additional loci reaching suggestive significance (p < 5 × 10-6), of which only one overlapped between groups (chromosome 17q24.2, ACP and CSP). Odds ratios for the 20 loci were most similar across all 3 groups for SNPs associated with the ACP group, but more distinct when comparing SNPs associated with either subtype. We also found nominal evidence of replication (p < 0.05) for 22 SNPs previously associated with orofacial clefts. Our study to evaluate CP risks in the context of its subtypes and we provide newly reported associations affecting the broad risk for CP as well as evidence of subtype-specific risks.
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Affiliation(s)
- Kelsey Robinson
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Trenell J. Mosley
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Kenneth S. Rivera-González
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Christopher R. Jabbarpour
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sarah W. Curtis
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Wasiu Lanre Adeyemo
- Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos, Lagos 101017, Nigeria
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Azeez Butali
- Department of Oral Biology, Radiology, and Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Carmen J. Buxó
- School of Dental Medicine, University of Puerto Rico, San Juan, PR 00925, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | | | - Lord J.J. Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School University of Texas Health at Houston, Houston, TX 77030, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Lina Moreno Uribe
- Department of Orthodontics & The Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA 52242, USA
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Robert J. Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
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10
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Robinson K, Mosley TJ, Rivera-González KS, Jabbarpour CR, Curtis SW, Adeyemo WL, Beaty TH, Butali A, Buxó CJ, Cutler DJ, Epstein MP, Gowans LJ, Hecht JT, Murray JC, Shaw GM, Uribe LM, Weinberg SM, Brand H, Marazita ML, Lipinski RJ, Leslie EJ. Trio-based GWAS identifies novel associations and subtype-specific risk factors for cleft palate. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.01.23286642. [PMID: 37066311 PMCID: PMC10104215 DOI: 10.1101/2023.03.01.23286642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Orofacial clefts (OFCs) are the most common craniofacial birth defects and are often categorized into two etiologically distinct groups: cleft lip with or without cleft palate (CL/P) and isolated cleft palate (CP). CP is highly heritable, but there are still relatively few established genetic risk factors associated with its occurrence compared to CL/P. Historically, CP has been studied as a single phenotype despite manifesting across a spectrum of defects involving the hard and/or soft palate. We performed GWAS using transmission disequilibrium tests using 435 case-parent trios to evaluate broad risks for any cleft palate (ACP, n=435), as well as subtype-specific risks for any cleft soft palate (CSP, n=259) and any cleft hard palate (CHP, n=125). We identified a single genome-wide significant locus at 9q33.3 (lead SNP rs7035976, p=4.24×10 -8 ) associated with CHP. One gene at this locus, angiopoietin-like 2 ( ANGPTL2 ), plays a role in osteoblast differentiation. It is expressed in craniofacial tissue of human embryos, as well as in the developing mouse palatal shelves. We found 19 additional loci reaching suggestive significance (p<5×10 -6 ), of which only one overlapped between groups (chromosome 17q24.2, ACP and CSP). Odds ratios (ORs) for each of the 20 loci were most similar across all three groups for SNPs associated with the ACP group, but more distinct when comparing SNPs associated with either the CSP or CHP groups. We also found nominal evidence of replication (p<0.05) for 22 SNPs previously associated with cleft palate (including CL/P). Interestingly, most SNPs associated with CL/P cases were found to convey the opposite effect in those replicated in our dataset for CP only. Ours is the first study to evaluate CP risks in the context of its subtypes and we provide newly reported associations affecting the broad risk for CP as well as evidence of subtype-specific risks.
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Affiliation(s)
| | - Trenell J Mosley
- Department of Human Genetics, Emory University, Atlanta, GA
- Current address: Chief Officer for Scientific Workforce Diversity Office, National Institutes of Health, Bethesda, MD
| | - Kenneth S Rivera-González
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI
| | - Christopher R Jabbarpour
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI
| | - Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA
| | - Wasiu Lanre Adeyemo
- Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD
| | - Azeez Butali
- Department of Oral Biology, Radiology, and Medicine, University of Iowa, Iowa City, IA
| | - Carmen J Buxó
- School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA
| | | | - Lord Jj Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jacqueline T Hecht
- Department of Pediatrics, McGovern Medical School University of Texas Health at Houston, Houston, TX
| | | | - Gary M Shaw
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Lina Moreno Uribe
- Department of Orthodontics & The Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Robert J Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI
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11
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Komatsu S, Kitai H, Suzuki HI. Network Regulation of microRNA Biogenesis and Target Interaction. Cells 2023; 12:306. [PMID: 36672241 PMCID: PMC9856966 DOI: 10.3390/cells12020306] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/15/2023] Open
Abstract
MicroRNAs (miRNAs) are versatile, post-transcriptional regulators of gene expression. Canonical miRNAs are generated through the two-step DROSHA- and DICER-mediated processing of primary miRNA (pri-miRNA) transcripts with optimal or suboptimal features for DROSHA and DICER cleavage and loading into Argonaute (AGO) proteins, whereas multiple hairpin-structured RNAs are encoded in the genome and could be a source of non-canonical miRNAs. Recent advances in miRNA biogenesis research have revealed details of the structural basis of miRNA processing and cluster assistance mechanisms that facilitate the processing of suboptimal hairpins encoded together with optimal hairpins in polycistronic pri-miRNAs. In addition, a deeper investigation of miRNA-target interaction has provided insights into the complexity of target recognition with distinct outcomes, including target-mediated miRNA degradation (TDMD) and cooperation in target regulation by multiple miRNAs. Therefore, the coordinated or network regulation of both miRNA biogenesis and miRNA-target interaction is prevalent in miRNA biology. Alongside recent advances in the mechanistic investigation of miRNA functions, this review summarizes recent findings regarding the ordered regulation of miRNA biogenesis and miRNA-target interaction.
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Affiliation(s)
- Shintaro Komatsu
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Hiroki Kitai
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Institute for Glyco-Core Research (iGCORE), Nagoya University, Nagoya 464-8601, Japan
- Center for One Medicine Innovative Translational Research, Gifu University Institute for Advanced Study, Gifu 501-1193, Japan
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12
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AGO-RBP crosstalk on target mRNAs: Implications in miRNA-guided gene silencing and cancer. Transl Oncol 2022; 21:101434. [PMID: 35477066 PMCID: PMC9136600 DOI: 10.1016/j.tranon.2022.101434] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs) and RNA-binding proteins (RBPs) are important regulators of mRNA translation and stability in eukaryotes. While miRNAs can only bind their target mRNAs in association with Argonaute proteins (AGOs), RBPs directly bind their targets either as single entities or in complex with other RBPs to control mRNA metabolism. miRNA binding in 3' untranslated regions (3' UTRs) of mRNAs facilitates an intricate network of interactions between miRNA-AGO and RBPs, thus determining the fate of overlapping targets. Here, we review the current knowledge on the interplay between miRNA-AGO and multiple RBPs in different cellular contexts, the rules underlying their synergism and antagonism on target mRNAs, as well as highlight the implications of these regulatory modules in cancer initiation and progression.
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13
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Verma M, Michalec L, Sripada A, McKay J, Sirohi K, Verma D, Sheth D, Martin R, Dyjack N, Seibold MA, Knapp JR, Tu TH, O'Connor BP, Gorska MM, Alam R. The molecular and epigenetic mechanisms of innate lymphoid cell (ILC) memory and its relevance for asthma. J Exp Med 2021; 218:212204. [PMID: 34076685 PMCID: PMC8176441 DOI: 10.1084/jem.20201354] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/11/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
Repetitive exposure of Rag1−/− mice to the Alternaria allergen extract generated a form of memory that elicited an asthma-like response upon a subthreshold recall challenge 3–15 wk later. This memory was associated with lung ICOS+ST2+ ILC2s. Genetic, pharmacologic, and antibody-mediated inhibition and adoptive transfer established an essential role for ILC2s in memory-driven asthma. ATAC-seq demonstrated a distinct epigenetic landscape of memory ILC2s and identified Bach2 and AP1 (JunD and Fosl2) motifs as major drivers of altered gene accessibility. scRNA-seq, gene knockout, and signaling studies suggest that repetitive allergenic stress induces a gene repression program involving Nr4a2, Zeb1, Bach2, and JunD and a preparedness program involving Fhl2, FosB, Stat6, Srebf2, and MPP7 in memory ILC2s. A mutually regulated balance between these two programs establishes and maintains memory. The preparedness program (e.g., Fhl2) can be activated with a subthreshold cognate stimulation, which down-regulates repressors and activates effector pathways to elicit the memory-driven phenotype.
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Affiliation(s)
- Mukesh Verma
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO
| | - Lidia Michalec
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO
| | - Anand Sripada
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO
| | - Jerome McKay
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO
| | - Kapil Sirohi
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO
| | - Divya Verma
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO
| | - Dipa Sheth
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO
| | - Richard Martin
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO.,Department of Pediatrics, National Jewish Health, Denver, CO
| | - Nathan Dyjack
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO
| | - Max A Seibold
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO.,Department of Pediatrics, National Jewish Health, Denver, CO
| | - Jennifer R Knapp
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO
| | - Ting-Hui Tu
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO
| | - Brian P O'Connor
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO
| | - Magdalena M Gorska
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO.,School of Medicine, University of Colorado Denver, Denver, CO
| | - Rafeul Alam
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO.,School of Medicine, University of Colorado Denver, Denver, CO
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14
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Embarc-Buh A, Francisco-Velilla R, Martinez-Salas E. RNA-Binding Proteins at the Host-Pathogen Interface Targeting Viral Regulatory Elements. Viruses 2021; 13:952. [PMID: 34064059 PMCID: PMC8224014 DOI: 10.3390/v13060952] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
Viral RNAs contain the information needed to synthesize their own proteins, to replicate, and to spread to susceptible cells. However, due to their reduced coding capacity RNA viruses rely on host cells to complete their multiplication cycle. This is largely achieved by the concerted action of regulatory structural elements on viral RNAs and a subset of host proteins, whose dedicated function across all stages of the infection steps is critical to complete the viral cycle. Importantly, not only the RNA sequence but also the RNA architecture imposed by the presence of specific structural domains mediates the interaction with host RNA-binding proteins (RBPs), ultimately affecting virus multiplication and spreading. In marked difference with other biological systems, the genome of positive strand RNA viruses is also the mRNA. Here we focus on distinct types of positive strand RNA viruses that differ in the regulatory elements used to promote translation of the viral RNA, as well as in the mechanisms used to evade the series of events connected to antiviral response, including translation shutoff induced in infected cells, assembly of stress granules, and trafficking stress.
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Affiliation(s)
| | | | - Encarnacion Martinez-Salas
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, 28049 Madrid, Spain; (A.E.-B.); (R.F.-V.)
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15
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Ma X, Li Y, Song Y, Xu G. Long Noncoding RNA CCDC26 Promotes Thyroid Cancer Malignant Progression via miR-422a/EZH2/Sirt6 Axis. Onco Targets Ther 2021; 14:3083-3094. [PMID: 34007185 PMCID: PMC8124016 DOI: 10.2147/ott.s282011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 04/07/2021] [Indexed: 12/21/2022] Open
Abstract
Purpose Long noncoding RNAs are crucial regulators in thyroid cancer progression. However, the role of lncRNA CCDC26 in thyroid cancer remains unclear. Here, we aimed to explore the effect of CCDC26 on thyroid cancer progression and the underlying mechanism. Materials and Methods A total of 50 clinical thyroid cancer samples were studied in patients' samples, cultured cells, and nude mice before and after treatment using quantitative reverse transcription-PCR, CCK-8 assays, BrdU incorporation assays, Transwell assays, cell apoptosis analysis, luciferase reporter gene assay, RNA immunoprecipitation, Western blot analysis, and tumorigenicity analysis. Results CCDC26 expression was elevated in patients' thyroid cancer tissues and thyroid cancer cell lines. CCDC26 depletion remarkably reduced proliferation, invasion, and migration but induced apoptosis of thyroid cancer cells. Mechanically, miR-422a mimic remarkably reduced the luciferase activity of CCDC26 transfected cells but failed to affect cells transfected with CCDC26 containing the mutated miR-422a-binding site. RNA immunoprecipitation (RIP) assays showed that CCDC26 and miR-422a preferentially interacted with Ago2, but not IgG, in the micro-ribonucleoprotein complexes (miRNPs). CCDC26 depletion enhanced miR-422a expression and MiR-422a inhibitor reversed CCDC26 knockdown-induced inhibition of thyroid cancer progression in vitro. CCDC26 upregulated EZH2 and Sirt6 expression by sponging miR-422a in thyroid cancer cells. Tumorigenicity analysis in nude mice revealed that CCDC26 contributed to thyroid tumor growth via miR-422a/EZH2/Sirt6 axis in vivo. Conclusion CCDC26 promotes thyroid cancer malignant progression via miR-422a/EZH2/Sirt6 axis. This finding provides new insights into the mechanism by which CCDC26 promotes malignant thyroid cancer development, advances our understanding of lncRNAs' association with thyroid cancer, and indicates that CCDC26 and miR-422a may serve as potential targets for thyroid cancer.
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Affiliation(s)
- Xiao Ma
- Key Laboratory of Carcinogenesis and Translational Research, Department of Head and Neck, Peking University Cancer Hospital and Institute, Beijing, 100142, People's Republic of China
| | - Yanyan Li
- Department of Cardiology, Air Force Medical Center, Beijing, 100036, People's Republic of China
| | - Yuntao Song
- Key Laboratory of Carcinogenesis and Translational Research, Department of Head and Neck, Peking University Cancer Hospital and Institute, Beijing, 100142, People's Republic of China
| | - Guohui Xu
- Key Laboratory of Carcinogenesis and Translational Research, Department of Head and Neck, Peking University Cancer Hospital and Institute, Beijing, 100142, People's Republic of China
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16
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Kakumani PK, Guitart T, Houle F, Harvey LM, Goyer B, Germain L, Gebauer F, Simard MJ. CSDE1 attenuates microRNA-mediated silencing of PMEPA1 in melanoma. Oncogene 2021; 40:3231-3244. [PMID: 33833398 DOI: 10.1038/s41388-021-01767-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 03/10/2021] [Accepted: 03/23/2021] [Indexed: 02/08/2023]
Abstract
MicroRNAs and RNA-binding proteins (RBPs) primarily target the 3' UTR of mRNAs to control their translation and stability. However, their co-regulatory effects on specific mRNAs in physiology and disease are yet to be fully explored. CSDE1 is an RBP that promotes metastasis in melanoma and mechanisms underlying its oncogenic activities need to be completely defined. Here we report that CSDE1 interacts with specific miRNA-induced silencing complexes (miRISC) in melanoma. We find an association of CSDE1 with AGO2, the essential component of miRISC, which is facilitated by target mRNAs and depends on the first cold shock domain of CSDE1. Both CSDE1 and AGO2 bind to 3' UTR of PMEPA1. CSDE1 counters AGO2 binding, leading to an increase of PMEPA1 expression. We also identify a miRNA, miR-129-5p, that represses PMEPA1 expression in melanoma. Collectively, our results show that PMEPA1 promotes tumorigenic traits and that CSDE1 along with miR-129-5p/AGO2 miRISC act antagonistically to fine-tune PMEPA1 expression toward the progression of melanoma.
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Affiliation(s)
- Pavan Kumar Kakumani
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec, QC, Canada.
- Université Laval Cancer Research Centre, Québec, QC, Canada.
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francois Houle
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec, QC, Canada
- Université Laval Cancer Research Centre, Québec, QC, Canada
| | - Louis-Mathieu Harvey
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec, QC, Canada
- Université Laval Cancer Research Centre, Québec, QC, Canada
| | - Benjamin Goyer
- Centre de recherche du CHU de Québec-Université Laval (Axe Médecine Régénératrice) and Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Québec, QC, Canada
- Département de chirurgie, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Lucie Germain
- Centre de recherche du CHU de Québec-Université Laval (Axe Médecine Régénératrice) and Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Québec, QC, Canada
- Département de chirurgie, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Martin J Simard
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec, QC, Canada.
- Université Laval Cancer Research Centre, Québec, QC, Canada.
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17
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Knoener R, Evans E, Becker JT, Scalf M, Benner B, Sherer NM, Smith LM. Identification of host proteins differentially associated with HIV-1 RNA splice variants. eLife 2021; 10:e62470. [PMID: 33629952 PMCID: PMC7906601 DOI: 10.7554/elife.62470] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
HIV-1 generates unspliced (US), partially spliced (PS), and completely spliced (CS) classes of RNAs, each playing distinct roles in viral replication. Elucidating their host protein 'interactomes' is crucial to understanding virus-host interplay. Here, we present HyPR-MSSV for isolation of US, PS, and CS transcripts from a single population of infected CD4+ T-cells and mass spectrometric identification of their in vivo protein interactomes. Analysis revealed 212 proteins differentially associated with the unique RNA classes, including preferential association of regulators of RNA stability with US and PS transcripts and, unexpectedly, mitochondria-linked proteins with US transcripts. Remarkably, >80 of these factors screened by siRNA knockdown impacted HIV-1 gene expression. Fluorescence microscopy confirmed several to co-localize with HIV-1 US RNA and exhibit changes in abundance and/or localization over the course of infection. This study validates HyPR-MSSV for discovery of viral splice variant protein interactomes and provides an unprecedented resource of factors and pathways likely important to HIV-1 replication.
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Affiliation(s)
- Rachel Knoener
- Department of Chemistry, University of WisconsinMadisonUnited States
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Edward Evans
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Jordan T Becker
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Mark Scalf
- Department of Chemistry, University of WisconsinMadisonUnited States
| | - Bayleigh Benner
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Nathan M Sherer
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of WisconsinMadisonUnited States
| | - Lloyd M Smith
- Department of Chemistry, University of WisconsinMadisonUnited States
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18
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Park CY, Zhou J, Wong AK, Chen KM, Theesfeld CL, Darnell RB, Troyanskaya OG. Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk. Nat Genet 2021; 53:166-173. [PMID: 33462483 PMCID: PMC7886016 DOI: 10.1038/s41588-020-00761-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 12/08/2020] [Indexed: 01/29/2023]
Abstract
Despite the strong genetic basis of psychiatric disorders, the underlying molecular mechanisms are largely unmapped. RNA-binding proteins (RBPs) are responsible for most post-transcriptional regulation, from splicing to translation to localization. RBPs thus act as key gatekeepers of cellular homeostasis, especially in the brain. However, quantifying the pathogenic contribution of noncoding variants impacting RBP target sites is challenging. Here, we leverage a deep learning approach that can accurately predict the RBP target site dysregulation effects of mutations and discover that RBP dysregulation is a principal contributor to psychiatric disorder risk. RBP dysregulation explains a substantial amount of heritability not captured by large-scale molecular quantitative trait loci studies and has a stronger impact than common coding region variants. We share the genome-wide profiles of RBP dysregulation, which we use to identify DDHD2 as a candidate schizophrenia risk gene. This resource provides a new analytical framework to connect the full range of RNA regulation to complex disease.
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Affiliation(s)
- Christopher Y. Park
- Flatiron Institute, Simons Foundation, New York, New York, United States of America,()Corresponding authors: Olga G. Troyanskaya, , Christopher Y. Park,
| | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, New York, United States of America
| | - Aaron K. Wong
- Flatiron Institute, Simons Foundation, New York, New York, United States of America
| | - Kathleen M. Chen
- Flatiron Institute, Simons Foundation, New York, New York, United States of America
| | - Chandra L. Theesfeld
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Robert B. Darnell
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA.,Howard Hughes Medical Institute
| | - Olga G. Troyanskaya
- Flatiron Institute, Simons Foundation, New York, New York, United States of America,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America,Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America,()Corresponding authors: Olga G. Troyanskaya, , Christopher Y. Park,
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19
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Davies JP, Almasy KM, McDonald EF, Plate L. Comparative Multiplexed Interactomics of SARS-CoV-2 and Homologous Coronavirus Nonstructural Proteins Identifies Unique and Shared Host-Cell Dependencies. ACS Infect Dis 2020; 6:3174-3189. [PMID: 33263384 PMCID: PMC7724760 DOI: 10.1021/acsinfecdis.0c00500] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Indexed: 12/15/2022]
Abstract
Human coronaviruses (hCoVs) have become a threat to global health and society, as evident from the SARS outbreak in 2002 caused by SARS-CoV-1 and the most recent COVID-19 pandemic caused by SARS-CoV-2. Despite a high sequence similarity between SARS-CoV-1 and -2, each strain has a distinctive virulence. A better understanding of the basic molecular mechanisms mediating changes in virulence is needed. Here, we profile the virus-host protein-protein interactions of two hCoV nonstructural proteins (nsps) that are critical for virus replication. We use tandem mass tag-multiplexed quantitative proteomics to sensitively compare and contrast the interactomes of nsp2 and nsp4 from three betacoronavirus strains: SARS-CoV-1, SARS-CoV-2, and hCoV-OC43-an endemic strain associated with the common cold. This approach enables the identification of both unique and shared host cell protein binding partners and the ability to further compare the enrichment of common interactions across homologues from related strains. We identify common nsp2 interactors involved in endoplasmic reticulum (ER) Ca2+ signaling and mitochondria biogenesis. We also identify nsp4 interactors unique to each strain, such as E3 ubiquitin ligase complexes for SARS-CoV-1 and ER homeostasis factors for SARS-CoV-2. Common nsp4 interactors include N-linked glycosylation machinery, unfolded protein response associated proteins, and antiviral innate immune signaling factors. Both nsp2 and nsp4 interactors are strongly enriched in proteins localized at mitochondria-associated ER membranes suggesting a new functional role for modulating host processes, such as calcium homeostasis, at these organelle contact sites. Our results shed light on the role these hCoV proteins play in the infection cycle, as well as host factors that may mediate the divergent pathogenesis of OC43 from SARS strains. Our mass spectrometry workflow enables rapid and robust comparisons of multiple bait proteins, which can be applied to additional viral proteins. Furthermore, the identified common interactions may present new targets for exploration by host-directed antiviral therapeutics.
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Affiliation(s)
- Jonathan P. Davies
- Department of Biological Sciences, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
| | - Katherine M. Almasy
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
| | - Eli F. McDonald
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
| | - Lars Plate
- Department of Biological Sciences, Immunology and Inflammation, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
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20
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Turcotte MA, Garant JM, Cossette-Roberge H, Perreault JP. Guanine Nucleotide-Binding Protein-Like 1 (GNL1) binds RNA G-quadruplex structures in genes associated with Parkinson's disease. RNA Biol 2020; 18:1339-1353. [PMID: 33305682 PMCID: PMC8354592 DOI: 10.1080/15476286.2020.1847866] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RNAs are highly regulated at the post-transcriptional level in neurodegenerative diseases and just a few mutations can significantly affect the fate of neuronal cells. To date, the impact of G-quadruplex (G4) regulation in neurodegenerative diseases like Parkinson’s disease (PD) has not been analysed. In this study, in silico potential G4s located in deregulated genes related to the nervous system were initially identified and were found to be significantly enriched. Several G4 sequences found in the 5ʹ untranslated regions (5ʹUTR) of mRNAs associated with Parkinson’s disease were demonstrated to in fact fold in vitro by biochemical assays. Subcloning of the full-length 5ʹUTRs of these candidates upstream of a luciferase reporter system led to the demonstration that the G4s of both Parkin RBR E3 Ubiquitin Protein Ligase (PRKN) and Vacuolar Protein Sorting-Associated Protein 35 (VPS35) significantly repressed the translation of both genes in SH-SY5Y cells. Subsequently, a strategy of using label-free RNA affinity purification assays with either of these two G4 sequences as bait isolated the Guanine Nucleotide-Binding Protein-Like 1 (GNL1). The latter was shown to have a higher affinity for the G4 sequences than for their mutated version. This study sheds light on new RNA G-quadruplexes located in genes dysregulated in Parkinson disease and a new G4-binding protein, GNL1.
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Affiliation(s)
- Marc-Antoine Turcotte
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Michel Garant
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Hélène Cossette-Roberge
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Pierre Perreault
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
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21
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Song K, Jiang Y, Zhao Y, Xie Y, Zhou J, Yu W, Wang Q. Members of the miR-30 family inhibit the epithelial-to-mesenchymal transition of non-small-cell lung cancer cells by suppressing XB130 expression levels. Oncol Lett 2020; 20:68. [PMID: 32863901 PMCID: PMC7436119 DOI: 10.3892/ol.2020.11929] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 06/23/2020] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRs) are associated with cancer metastasis. Aberrant expression levels of members of the miR-30 family have been observed in non-small-cell lung cancer (NSCLC). However, the effects of miR-30 family members on the epithelial-to-mesenchymal transition (EMT) of NSCLC cells and the underlying molecular mechanisms have not yet been fully elucidated. The present study investigated the effects of miR-30 family members on EMT, migration and invasion of NSCLC cells and found that overexpression of these miRs inhibited EMT via decreasing the expression levels of N-cadherin, β-catenin and SNAI1, along with weakened migration and invasion abilities. Then, XB130 was identified as a downstream target of the miR-30 family members. XB130-knockdown also inhibited EMT of NSCLC cells, whereas ectopic overexpression of XB130 partly rescued the suppressive effects of miR-30c and miR-30d on EMT. In conclusion, miR-30 family members inhibited EMT of NSCLC cells, partially via suppressing XB130 expression levels.
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Affiliation(s)
- Kewei Song
- College of Sport and Health and Key Laboratory of Endemic and Ethnic Diseases of The Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Yinhui Jiang
- College of Sport and Health and Key Laboratory of Endemic and Ethnic Diseases of The Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China.,Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Yan Zhao
- College of Sport and Health and Key Laboratory of Endemic and Ethnic Diseases of The Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China.,Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Yuan Xie
- College of Sport and Health and Key Laboratory of Endemic and Ethnic Diseases of The Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China.,Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Jianjiang Zhou
- College of Sport and Health and Key Laboratory of Endemic and Ethnic Diseases of The Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China.,Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Wenfeng Yu
- College of Sport and Health and Key Laboratory of Endemic and Ethnic Diseases of The Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China.,Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Qinrong Wang
- College of Sport and Health and Key Laboratory of Endemic and Ethnic Diseases of The Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China.,Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
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22
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Davies JP, Almasy KM, McDonald EF, Plate L. Comparative multiplexed interactomics of SARS-CoV-2 and homologous coronavirus non-structural proteins identifies unique and shared host-cell dependencies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.07.13.201517. [PMID: 32699849 PMCID: PMC7373130 DOI: 10.1101/2020.07.13.201517] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Human coronaviruses (hCoV) have become a threat to global health and society, as evident from the SARS outbreak in 2002 caused by SARS-CoV-1 and the most recent COVID-19 pandemic caused by SARS-CoV-2. Despite high sequence similarity between SARS-CoV-1 and -2, each strain has distinctive virulence. A better understanding of the basic molecular mechanisms mediating changes in virulence is needed. Here, we profile the virus-host protein-protein interactions of two hCoV non-structural proteins (nsps) that are critical for virus replication. We use tandem mass tag-multiplexed quantitative proteomics to sensitively compare and contrast the interactomes of nsp2 and nsp4 from three betacoronavirus strains: SARS-CoV-1, SARS-CoV-2, and hCoV-OC43 - an endemic strain associated with the common cold. This approach enables the identification of both unique and shared host cell protein binding partners and the ability to further compare the enrichment of common interactions across homologs from related strains. We identify common nsp2 interactors involved in endoplasmic reticulum (ER) Ca 2+ signaling and mitochondria biogenesis. We also identifiy nsp4 interactors unique to each strain, such as E3 ubiquitin ligase complexes for SARS-CoV-1 and ER homeostasis factors for SARS-CoV-2. Common nsp4 interactors include N -linked glycosylation machinery, unfolded protein response (UPR) associated proteins, and anti-viral innate immune signaling factors. Both nsp2 and nsp4 interactors are strongly enriched in proteins localized at mitochondrial-associated ER membranes suggesting a new functional role for modulating host processes, such as calcium homeostasis, at these organelle contact sites. Our results shed light on the role these hCoV proteins play in the infection cycle, as well as host factors that may mediate the divergent pathogenesis of OC43 from SARS strains. Our mass spectrometry workflow enables rapid and robust comparisons of multiple bait proteins, which can be applied to additional viral proteins. Furthermore, the identified common interactions may present new targets for exploration by host-directed anti-viral therapeutics.
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Affiliation(s)
- Jonathan P. Davies
- Department of Biological Sciences, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
| | - Katherine M. Almasy
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
| | - Eli F. McDonald
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
| | - Lars Plate
- Department of Biological Sciences, Immunology and Inflammation, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
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23
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Kakumani PK, Harvey LM, Houle F, Guitart T, Gebauer F, Simard MJ. CSDE1 controls gene expression through the miRNA-mediated decay machinery. Life Sci Alliance 2020; 3:e201900632. [PMID: 32161113 PMCID: PMC7067469 DOI: 10.26508/lsa.201900632] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 12/15/2022] Open
Abstract
In animals, miRNAs are the most prevalent small non-coding RNA molecules controlling posttranscriptional gene regulation. The Argonaute proteins (AGO) mediate miRNA-guided gene silencing by recruiting multiple factors involved in translational repression, deadenylation, and decapping. Here, we report that CSDE1, an RNA-binding protein linked to stem cell maintenance and metastasis in cancer, interacts with AGO2 within miRNA-induced silencing complex and mediates gene silencing through its N-terminal domains. We show that CSDE1 interacts with LSM14A, a constituent of P-body assembly and further associates to the DCP1-DCP2 decapping complex, suggesting that CSDE1 could promote the decay of miRNA-induced silencing complex-targeted mRNAs. Together, our findings uncover a hitherto unknown mechanism used by CSDE1 in the control of gene expression mediated by the miRNA pathway.
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Affiliation(s)
- Pavan Kumar Kakumani
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada
- Laval University Cancer Research Centre, Québec City, Canada
| | - Louis-Mathieu Harvey
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada
- Laval University Cancer Research Centre, Québec City, Canada
| | - François Houle
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada
- Laval University Cancer Research Centre, Québec City, Canada
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin J Simard
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada
- Laval University Cancer Research Centre, Québec City, Canada
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