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Luna-Cerralbo D, Blasco-Machín I, Adame-Pérez S, Lampaya V, Larraga A, Alejo T, Martínez-Oliván J, Broset E, Bruscolini P. A statistical-physics approach for codon usage optimisation. Comput Struct Biotechnol J 2024; 23:3050-3064. [PMID: 39188969 PMCID: PMC11345917 DOI: 10.1016/j.csbj.2024.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/25/2024] [Accepted: 07/25/2024] [Indexed: 08/28/2024] Open
Abstract
The concept of "codon optimisation" involves adjusting the coding sequence of a target protein to account for the inherent codon preferences of a host species and maximise protein expression in that species. However, there is still a lack of consensus on the most effective approach to achieve optimal results. Existing methods typically depend on heuristic combinations of different variables, leaving the user with the final choice of the sequence hit. In this study, we propose a new statistical-physics model for codon optimisation. This model, called the Nearest-Neighbour interaction (NN) model, links the probability of any given codon sequence to the "interactions" between neighbouring codons. We used the model to design codon sequences for different proteins of interest, and we compared our sequences with the predictions of some commercial tools. In order to assess the importance of the pair interactions, we additionally compared the NN model with a simpler method (Ind) that disregards interactions. It was observed that the NN method yielded similar Codon Adaptation Index (CAI) values to those obtained by other commercial algorithms, despite the fact that CAI was not explicitly considered in the algorithm. By utilising both the NN and Ind methods to optimise the reporter protein luciferase, and then analysing the translation performance in human cell lines and in a mouse model, we found that the NN approach yielded the highest protein expression in vivo. Consequently, we propose that the NN model may prove advantageous in biotechnological applications, such as heterologous protein expression or mRNA-based therapies.
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Affiliation(s)
- David Luna-Cerralbo
- Department of Theoretical Physics, Faculty of Science, University of Zaragoza, c/ Pedro Cerbuna s/n, Zaragoza, 50009, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, c/ Mariano Esquillor s/n, Zaragoza, 50018, Spain
| | - Irene Blasco-Machín
- Certest Pharma, Certest Biotec S.L, Polígono Industrial Río Gallego II, Calle J, 1, San Mateo de Gállego, 50840, Spain
| | - Susana Adame-Pérez
- Certest Pharma, Certest Biotec S.L, Polígono Industrial Río Gallego II, Calle J, 1, San Mateo de Gállego, 50840, Spain
| | - Verónica Lampaya
- Certest Pharma, Certest Biotec S.L, Polígono Industrial Río Gallego II, Calle J, 1, San Mateo de Gállego, 50840, Spain
| | - Ana Larraga
- Certest Pharma, Certest Biotec S.L, Polígono Industrial Río Gallego II, Calle J, 1, San Mateo de Gállego, 50840, Spain
| | - Teresa Alejo
- Certest Pharma, Certest Biotec S.L, Polígono Industrial Río Gallego II, Calle J, 1, San Mateo de Gállego, 50840, Spain
| | - Juan Martínez-Oliván
- Certest Pharma, Certest Biotec S.L, Polígono Industrial Río Gallego II, Calle J, 1, San Mateo de Gállego, 50840, Spain
| | - Esther Broset
- Certest Pharma, Certest Biotec S.L, Polígono Industrial Río Gallego II, Calle J, 1, San Mateo de Gállego, 50840, Spain
| | - Pierpaolo Bruscolini
- Department of Theoretical Physics, Faculty of Science, University of Zaragoza, c/ Pedro Cerbuna s/n, Zaragoza, 50009, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, c/ Mariano Esquillor s/n, Zaragoza, 50018, Spain
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Wang TT, Zhu HL, Ouyang KW, Wang H, Luo YX, Zheng XM, Ling Q, Wang KW, Zhang J, Chang W, Lu Q, Zhang YF, Yuan Z, Li H, Xiong YW, Wei T, Wang H. Environmental cadmium inhibits testicular testosterone synthesis via Parkin-dependent MFN1 degradation. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134142. [PMID: 38555669 DOI: 10.1016/j.jhazmat.2024.134142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
Low testosterone (T) levels are associated with many common diseases, such as obesity, male infertility, depression, and cardiovascular disease. It is well known that environmental cadmium (Cd) exposure can induce T decline, but the exact mechanism remains unclear. We established a murine model in which Cd exposure induced testicular T decline. Based on the model, we found Cd caused mitochondrial fusion disorder and Parkin mitochondrial translocation in mouse testes. MFN1 overexpression confirmed that MFN1-dependent mitochondrial fusion disorder mediated the Cd-induced T synthesis suppression in Leydig cells. Further data confirmed Cd induced the decrease of MFN1 protein by increasing ubiquitin degradation. Testicular specific Parkin knockdown confirmed Cd induced the ubiquitin-dependent degradation of MFN1 protein through promoting Parkin mitochondrial translocation in mouse testes. Expectedly, testicular specific Parkin knockdown also mitigated testicular T decline. Mito-TEMPO, a targeted inhibitor for mitochondrial reactive oxygen species (mtROS), alleviated Cd-caused Parkin mitochondrial translocation and mitochondrial fusion disorder. As above, Parkin mitochondrial translocation induced mitochondrial fusion disorder and the following T synthesis repression in Cd-exposed Leydig cells. Collectively, our study elucidates a novel mechanism through which Cd induces T decline and provides a new treatment strategy for patients with androgen disorders.
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Affiliation(s)
- Tian-Tian Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Hua-Long Zhu
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Kong-Wen Ouyang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Hua Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Department of Respiratory Medicine, Anhui Provincial Children's Hospital, Hefei, Anhui 230000, China
| | - Ye-Xin Luo
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Xin-Mei Zheng
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Qing Ling
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Kai-Wen Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Jin Zhang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Wei Chang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Qi Lu
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Yu-Feng Zhang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Zhi Yuan
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Hao Li
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Yong-Wei Xiong
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Tian Wei
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Hua Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China.
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3
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van den Akker GGH, Chabronova A, Housmans BAC, van der Vloet L, Surtel DAM, Cremers A, Marchand V, Motorin Y, Caron MMJ, Peffers MJ, Welting TJM. TGF-β2 Induces Ribosome Activity, Alters Ribosome Composition and Inhibits IRES-Mediated Translation in Chondrocytes. Int J Mol Sci 2024; 25:5031. [PMID: 38732249 PMCID: PMC11084827 DOI: 10.3390/ijms25095031] [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: 03/12/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
Alterations in cell fate are often attributed to (epigenetic) regulation of gene expression. An emerging paradigm focuses on specialized ribosomes within a cell. However, little evidence exists for the dynamic regulation of ribosome composition and function. Here, we stimulated a chondrocytic cell line with transforming growth factor beta (TGF-β2) and mapped changes in ribosome function, composition and ribosomal RNA (rRNA) epitranscriptomics. 35S Met/Cys incorporation was used to evaluate ribosome activity. Dual luciferase reporter assays were used to assess ribosomal modus. Ribosomal RNA expression and processing were determined by RT-qPCR, while RiboMethSeq and HydraPsiSeq were used to determine rRNA modification profiles. Label-free protein quantification of total cell lysates, isolated ribosomes and secreted proteins was done by LC-MS/MS. A three-day TGF-β2 stimulation induced total protein synthesis in SW1353 chondrocytic cells and human articular chondrocytes. Specifically, TGF-β2 induced cap-mediated protein synthesis, while IRES-mediated translation was not (P53 IRES) or little affected (CrPv IGR and HCV IRES). Three rRNA post-transcriptional modifications (PTMs) were affected by TGF-β2 stimulation (18S-Gm1447 downregulated, 18S-ψ1177 and 28S-ψ4598 upregulated). Proteomic analysis of isolated ribosomes revealed increased interaction with eIF2 and tRNA ligases and decreased association of eIF4A3 and heterogeneous nuclear ribonucleoprotein (HNRNP)s. In addition, thirteen core ribosomal proteins were more present in ribosomes from TGF-β2 stimulated cells, albeit with a modest fold change. A prolonged stimulation of chondrocytic cells with TGF-β2 induced ribosome activity and changed the mode of translation. These functional changes could be coupled to alterations in accessory proteins in the ribosomal proteome.
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Affiliation(s)
- Guus G. H. van den Akker
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Alzbeta Chabronova
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
- Department of Musculoskeletal Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Bas A. C. Housmans
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Laura van der Vloet
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Don A. M. Surtel
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Andy Cremers
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Virginie Marchand
- UAR2008 IBSLor CNRS-INSERM, Université de Lorraine, BioPole, F54000 Nancy, France; (V.M.); (Y.M.)
| | - Yuri Motorin
- UAR2008 IBSLor CNRS-INSERM, Université de Lorraine, BioPole, F54000 Nancy, France; (V.M.); (Y.M.)
- UMR7365 IMoPA, CNRS, Université de Lorraine, BioPole, F54000 Nancy, France
| | - Marjolein M. J. Caron
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Mandy J. Peffers
- Department of Musculoskeletal Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Tim J. M. Welting
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center +, 6229 HX Maastricht, The Netherlands
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Frese AN, Mariossi A, Levine MS, Wühr M. Quantitative proteome dynamics across embryogenesis in a model chordate. iScience 2024; 27:109355. [PMID: 38510129 PMCID: PMC10951915 DOI: 10.1016/j.isci.2024.109355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/11/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
The evolution of gene expression programs underlying the development of vertebrates remains poorly characterized. Here, we present a comprehensive proteome atlas of the model chordate Ciona, covering eight developmental stages and ∼7,000 translated genes, accompanied by a multi-omics analysis of co-evolution with the vertebrate Xenopus. Quantitative proteome comparisons argue against the widely held hourglass model, based solely on transcriptomic profiles, whereby peak conservation is observed during mid-developmental stages. Our analysis reveals maximal divergence at these stages, particularly gastrulation and neurulation. Together, our work provides a valuable resource for evaluating conservation and divergence of multi-omics profiles underlying the diversification of vertebrates.
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Affiliation(s)
- Alexander N. Frese
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Andrea Mariossi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael S. Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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Sinzger-D'Angelo M, Hanst M, Reinhardt F, Koeppl H. Effects of mRNA conformational switching on translational noise in gene circuits. J Chem Phys 2024; 160:134108. [PMID: 38573847 DOI: 10.1063/5.0186927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024] Open
Abstract
Intragenic translational heterogeneity describes the variation in translation at the level of transcripts for an individual gene. A factor that contributes to this source of variation is the mRNA structure. Both the composition of the thermodynamic ensemble, i.e., the stationary distribution of mRNA structures, and the switching dynamics between those play a role. The effect of the switching dynamics on intragenic translational heterogeneity remains poorly understood. We present a stochastic translation model that accounts for mRNA structure switching and is derived from a Markov model via approximate stochastic filtering. We assess the approximation on various timescales and provide a method to quantify how mRNA structure dynamics contributes to translational heterogeneity. With our approach, we allow quantitative information on mRNA switching from biophysical experiments or coarse-grain molecular dynamics simulations of mRNA structures to be included in gene regulatory chemical reaction network models without an increase in the number of species. Thereby, our model bridges a gap between mRNA structure kinetics and gene expression models, which we hope will further improve our understanding of gene regulatory networks and facilitate genetic circuit design.
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Affiliation(s)
| | - Maleen Hanst
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Felix Reinhardt
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Heinz Koeppl
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
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Damodharan S, Shireman JM, Xie E, Distler E, Kendziorski C, Dey M. Transcriptomic and Proteomic Spatial Profiling of Pediatric and Adult Diffuse Midline Glioma H3 K27-Altered, Reveals Region Specific Differences and Limited Overlap between mRNA and Protein. RESEARCH SQUARE 2024:rs.3.rs-4139314. [PMID: 38645012 PMCID: PMC11030546 DOI: 10.21203/rs.3.rs-4139314/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Diffuse midline glioma, H3 K27 -altered (DMG-Alt) are highly aggressive malignancies of the central nervous system (CNS) that primarily affect the pediatric population. Large scale spatial transcriptomic studies have implicated that tumor microenvironmental landscape plays an important role in determining the phenotypic differences in tumor presentation and clinical course, however, data connecting overall transcriptomic changes to the protein level is lacking. The NanoString GeoMx™ Digital Spatial Profiler platform was used to determine the spatial transcriptomic and proteomic landscape in a cohort of both pediatric and adult H3 K27 -altered DMG biopsy samples. Three fluorescently labeled antibodies targeting immune cells (CD45), epithelial cells (PanCK), tumor cells ( H3 K27M ) and a nucleic acid stain (SYTO-13) were used to establish regions of interest (ROI) for genomic and proteomic analysis. We found genetic alterations within the tumor which can be delineated across patient age and spatial location. We show that the H3 K27M mutation itself has a profound impact on tumor cells transcriptomics and interestingly we found limited fidelity between overall transcriptome and proteome. Our data also validate the previously described OPC like precursor signature at the proteomic level and reveal a special shift in the signature based on the local TME composition.
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Zheng X, Guo C, Lv Z, Li J, Jiang H, Li S, Yu L, Zhang Z. Novel findings from arsenic‑lead combined exposure in mouse testicular TM4 Sertoli cells based on transcriptomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169611. [PMID: 38157908 DOI: 10.1016/j.scitotenv.2023.169611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/04/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Arsenic (As) and lead (Pb) exist widespread in daily life, and they are common harmful substances in the environment. As and Pb pollute the environment more often in combination than in isolation. The TM4 Sertoli cell line is one of the most common normal mouse testicular Sertoli cell lines. In vitro, we found that the type of combined action of As and Pb on TM4 Sertoli cells was additive action by using the isobologram analysis. To further investigate the combined toxicity of As and Pb, we performed mRNA and miRNA sequencing on TM4 Sertoli cells exposed to As alone (4 μM NaAsO2) and AsPb combined (4 μM NaAsO2 and 150 μM PbAc), respectively. Compared with the control group, 1391 differentially expressed genes (DEGs) and 6 differentially expressed miRNAs (DEMs) were identified in the As group. Compared with the control group, 2384 DEGs and 44 DEMs were identified in the AsPb group. Compared with the As group, 387 DEGs and 4 DEMs were identified in the AsPb group. Through data analysis, we discovered for the first time that As caused the dysfunction of cholesterol synthesis and energy metabolism, and disrupted cyclic adenosine monophosphate signaling pathway and wingless/integrated (Wnt) signaling pathway in TM4 Sertoli cells. In addition to affecting cholesterol synthesis and energy metabolism, AsPb combined exposure also up-regulated the antioxidant reaction level of TM4 Sertoli cells. Meanwhile, the Wnt signaling pathway of TM4 Sertoli cells was relatively normal when exposed to AsPb. In conclusion, at the transcription level, the combined action of AsPb is not merely additive effect, but involves synergistic and antagonistic effects. The new discovery of the joint toxic mechanism of As and Pb breaks the stereotype of the combined action and provides a good theoretical basis and research clue for future study of the combined-exposure of harmful materials.
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Affiliation(s)
- Xiaoyan Zheng
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Changming Guo
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Zhanjun Lv
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Jiayi Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Huijie Jiang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Siyu Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Lu Yu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Zhigang Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China.
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Xue M, Dong L, Zhang H, Li Y, Qiu K, Zhao Z, Gao M, Han L, Chan AKN, Li W, Leung K, Wang K, Pokharel SP, Qing Y, Liu W, Wang X, Ren L, Bi H, Yang L, Shen C, Chen Z, Melstrom L, Li H, Timchenko N, Deng X, Huang W, Rosen ST, Tian J, Xu L, Diao J, Chen CW, Chen J, Shen B, Chen H, Su R. METTL16 promotes liver cancer stem cell self-renewal via controlling ribosome biogenesis and mRNA translation. J Hematol Oncol 2024; 17:7. [PMID: 38302992 PMCID: PMC10835888 DOI: 10.1186/s13045-024-01526-9] [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: 04/19/2023] [Accepted: 01/20/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND While liver cancer stem cells (CSCs) play a crucial role in hepatocellular carcinoma (HCC) initiation, progression, recurrence, and treatment resistance, the mechanism underlying liver CSC self-renewal remains elusive. We aim to characterize the role of Methyltransferase 16 (METTL16), a recently identified RNA N6-methyladenosine (m6A) methyltransferase, in HCC development/maintenance, CSC stemness, as well as normal hepatogenesis. METHODS Liver-specific Mettl16 conditional KO (cKO) mice were generated to assess its role in HCC pathogenesis and normal hepatogenesis. Hydrodynamic tail-vein injection (HDTVi)-induced de novo hepatocarcinogenesis and xenograft models were utilized to determine the role of METTL16 in HCC initiation and progression. A limiting dilution assay was utilized to evaluate CSC frequency. Functionally essential targets were revealed via integrative analysis of multi-omics data, including RNA-seq, RNA immunoprecipitation (RIP)-seq, and ribosome profiling. RESULTS METTL16 is highly expressed in liver CSCs and its depletion dramatically decreased CSC frequency in vitro and in vivo. Mettl16 KO significantly attenuated HCC initiation and progression, yet only slightly influenced normal hepatogenesis. Mechanistic studies, including high-throughput sequencing, unveiled METTL16 as a key regulator of ribosomal RNA (rRNA) maturation and mRNA translation and identified eukaryotic translation initiation factor 3 subunit a (eIF3a) transcript as a bona-fide target of METTL16 in HCC. In addition, the functionally essential regions of METTL16 were revealed by CRISPR gene tiling scan, which will pave the way for the development of potential inhibitor(s). CONCLUSIONS Our findings highlight the crucial oncogenic role of METTL16 in promoting HCC pathogenesis and enhancing liver CSC self-renewal through augmenting mRNA translation efficiency.
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Affiliation(s)
- Meilin Xue
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lei Dong
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, 7539, USA
| | - Honghai Zhang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Yangchan Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- Department of Radiation Oncology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Kangqiang Qiu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Zhicong Zhao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Gao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Li Han
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- School of Pharmacy, China Medical University, Shenyang, 110001, Liaoning, China
| | - Anthony K N Chan
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Keith Leung
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Kitty Wang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Sheela Pangeni Pokharel
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Ying Qing
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Wei Liu
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Xueer Wang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Lili Ren
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Hongjie Bi
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Chao Shen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Zhenhua Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Laleh Melstrom
- Division of Surgical Oncology, Department of Surgery, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA
| | - Hongzhi Li
- Department of Molecular Medicine, City of Hope National Medical Center, Duarte, CA, 91016, USA
| | - Nikolai Timchenko
- Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Wendong Huang
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Graduate School of Biological Science, City of Hope, Duarte, CA, 91010, USA
| | - Steven T Rosen
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA
| | - Jingyan Tian
- State Key Laboratory of Medical Genomics, Clinical Trial Center, Shanghai Institute of Endocrine and Metabolic Diseases, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, 7539, USA
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, 91010, USA
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hao Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA.
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA.
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9
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Liu Y, Li Z, Meng Q, Ning A, Zhou S, Li S, Tao X, Wu Y, Chen Q, Tian T, Zhang L, Cui J, Mao L, Chu M. Identification of the consistently differential expressed hub mRNAs and proteins in lung adenocarcinoma and construction of the prognostic signature: a multidimensional analysis. Int J Surg 2024; 110:1052-1067. [PMID: 38016140 PMCID: PMC10871637 DOI: 10.1097/js9.0000000000000943] [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: 08/29/2023] [Accepted: 11/12/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND This study aimed to elucidate the consistency of differentially expressed hub mRNAs and proteins in lung adenocarcinoma (LUAD) across populations and to construct a comprehensive LUAD prognostic signature. METHODS The transcriptomic and proteomics data from different populations were standardized and analyzed using the same criteria to identify the consistently differential expressed mRNAs and proteins across genders and races. We then integrated prognosis-related mRNAs with clinical, pathological, and EGFR (epidermal growth factor receptor) mutation data to construct a survival model, subsequently validating it across populations. Through plasma proteomics, plasma proteins that consistently differential expressed with LUAD tissues were screened and validated, with their associations discerned by measuring expressions in tumor tissues and tumor vascular normalization. RESULTS The consistency rate of differentially expressed mRNAs and proteins was ~20-40%, with ethnic factors leading to about 40-60% consistency of differentially expressed mRNA or protein across populations. The survival model based on the identified eight hub mRNAs as well as stage, smoking status, and EGFR mutations, demonstrated good prognostic prediction capabilities in both Western and East Asian populations, with a higher number of unfavorable variables indicating poorer LUAD prognosis. Notably, GPI expression in tumor tissues was inversely correlated with vascular normalization and positively correlated with plasma GPI expression. CONCLUSION Our study underscores the significance of integrating transcriptomics and proteomics data, emphasizing the need to account for genetic diversity among ethnic groups. The developed survival model may offer a holistic perspective on LUAD progression, enhancing prognosis and therapeutic strategies.
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Affiliation(s)
- Yiran Liu
- Department of Epidemiology, School of Public Health, Nantong University
| | - Zhenyu Li
- Department of Epidemiology, School of Public Health, Nantong University
| | - Qianyao Meng
- Department of Global Health and Population, School of Public Health, Harvard University, Boston, USA
| | - Anhui Ning
- Department of Epidemiology, School of Public Health, Nantong University
| | - Shenxuan Zhou
- Department of Epidemiology, School of Public Health, Nantong University
| | - Siqi Li
- Department of Epidemiology, School of Public Health, Nantong University
| | - Xiaobo Tao
- Department of Epidemiology, School of Public Health, Nantong University
| | - Yutong Wu
- Department of Epidemiology, School of Public Health, Nantong University
| | - Qiong Chen
- Department of Epidemiology, School of Public Health, Nantong University
| | - Tian Tian
- Department of Epidemiology, School of Public Health, Nantong University
| | - Lei Zhang
- Department of Epidemiology, School of Public Health, Nantong University
| | - Jiahua Cui
- Department of Epidemiology, School of Public Health, Nantong University
| | - Liping Mao
- Department of Oncology, Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), Nantong, Jiangsu, People’s Republic of China
| | - Minjie Chu
- Department of Epidemiology, School of Public Health, Nantong University
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10
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Murao A, Jha A, Aziz M, Wang P. Transcriptomic profiling of immune cells in murine polymicrobial sepsis. Front Immunol 2024; 15:1347453. [PMID: 38343542 PMCID: PMC10853340 DOI: 10.3389/fimmu.2024.1347453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/09/2024] [Indexed: 02/15/2024] Open
Abstract
Introduction Various immune cell types play critical roles in sepsis with numerous distinct subsets exhibiting unique phenotypes even within the same cell population. Single-cell RNA sequencing (scRNA-seq) enables comprehensive transcriptome profiling and unbiased cell classification. In this study, we have unveiled the transcriptomic landscape of immune cells in sepsis through scRNA-seq analysis. Methods We induced sepsis in mice by cecal ligation and puncture. 20 h after the surgery, the spleen and peritoneal lavage were collected. Single-cell suspensions were processed using a 10× Genomics pipeline and sequenced on an Illumina platform. Count matrices were generated using the Cell Ranger pipeline, which maps reads to the mouse reference transcriptome, GRCm38/mm10. Subsequent scRNA-seq analysis was performed using the R package Seurat. Results After quality control, we subjected the entire data set to unsupervised classification. Four major clusters were identified as neutrophils, macrophages, B cells, and T cells according to their putative markers. Based on the differentially expressed genes, we identified activated pathways in sepsis for each cell type. In neutrophils, pathways related to inflammatory signaling, such as NF-κB and responses to pathogen-associated molecular patterns (PAMPs), cytokines, and hypoxia were activated. In macrophages, activated pathways were the ones related to cell aging, inflammatory signaling, and responses to PAMPs. In B cells, pathways related to endoplasmic reticulum stress were activated. In T cells, activated pathways were the ones related to inflammatory signaling, responses to PAMPs, and acute lung injury. Next, we further classified each cell type into subsets. Neutrophils consisted of four clusters. Some subsets were activated in inflammatory signaling or cell metabolism, whereas others possessed immunoregulatory or aging properties. Macrophages consisted of four clusters, namely, the ones with enhanced aging, lymphocyte activation, extracellular matrix organization, or cytokine activity. B cells consisted of four clusters, including the ones possessing the phenotype of cell maturation or aging. T cells consisted of six clusters, whose phenotypes include molecular translocation or cell activation. Conclusions Transcriptomic analysis by scRNA-seq has unveiled a comprehensive spectrum of immune cell responses and distinct subsets in the context of sepsis. These findings are poised to enhance our understanding of sepsis pathophysiology, offering avenues for targeting novel molecules, cells, and pathways to combat infectious diseases.
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Affiliation(s)
- Atsushi Murao
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Alok Jha
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Monowar Aziz
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
- Departments of Surgery and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, United States
| | - Ping Wang
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
- Departments of Surgery and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, United States
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11
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Xiao L, Fang L, Kool ET. 2'-OH as a universal handle for studying intracellular RNAs. Cell Chem Biol 2024; 31:110-124. [PMID: 37992716 PMCID: PMC10841764 DOI: 10.1016/j.chembiol.2023.10.022] [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: 07/06/2023] [Revised: 09/28/2023] [Accepted: 10/29/2023] [Indexed: 11/24/2023]
Abstract
RNA plays pivotal roles in most cellular processes, serving as both the traditional carrier of genetic information and as a key regulator of cellular functions. The advent of chemical technologies has contributed critically to the analysis of cellular RNA structures, functions, and interactions. Many of these methods and molecules involve the utilization of chemically reactive handles in RNAs, either introduced externally or inherent within the polymer itself. Among these handles, the 2'-hydroxyl (2'-OH) group has emerged as an exceptionally well-suited and general chemical moiety for the modification and profiling of RNAs in intracellular studies. In this review, we provide an overview of the recent advancements in intracellular applications of acylation at the 2'-OH group of RNA. We outline progress made in probing RNA structure and interactomes, controlling RNA function, RNA imaging, and analyzing RNA-small molecule interactions, all achieved in living cells through this simple chemical handle on the biopolymer.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA.
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12
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Grünhagel B, Borggrewe M, Hagen SH, Ziegler SM, Henseling F, Glau L, Thiele RJ, Pujantell M, Sivayoganathan V, Padoan B, Claussen JM, Düsedau A, Hennesen J, Bunders MJ, Bonn S, Tolosa E, Krebs CF, Dorn C, Altfeld M. Reduction of IFN-I responses by plasmacytoid dendritic cells in a longitudinal trans men cohort. iScience 2023; 26:108209. [PMID: 37953956 PMCID: PMC10637924 DOI: 10.1016/j.isci.2023.108209] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023] Open
Abstract
Type I interferons (IFN-I) are important mediators of antiviral immunity and autoimmune diseases. Female plasmacytoid dendritic cells (pDCs) exert an elevated capacity to produce IFN-I upon toll-like receptor 7 (TLR7) activation compared to male pDCs, and both sex hormones and X-encoded genes have been implicated in these sex-specific differences. Using longitudinal samples from a trans men cohort receiving gender-affirming hormone therapy (GAHT), the impact of testosterone injections on TLR7-mediated IFN-I production by pDCs was assessed. Single-cell RNA analyses of pDCs showed downregulation of IFN-I-related gene expression signatures but also revealed transcriptional inter-donor heterogeneity. Longitudinal quantification showed continuous reduction of IFN-I protein production by pDCs and reduced expression of IFN-I-stimulated genes in peripheral blood mononuclear cells (PBMCs). These studies in trans men demonstrate that testosterone administration reduces IFN-I production by pDCs over time and provide insights into the immune-modulatory role of testosterone in sex-specific IFN-I-mediated immune responses.
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Affiliation(s)
- Benjamin Grünhagel
- Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Malte Borggrewe
- Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
- III. Department of Medicine, University Medical Center Hamburg Eppendorf, 20251 Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg Eppendorf, 20251 Hamburg, Germany
| | - Sven Hendrik Hagen
- Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Susanne M. Ziegler
- Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Florian Henseling
- Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Laura Glau
- Institute for Immunology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Rebecca-Jo Thiele
- Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Maria Pujantell
- Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
- Institute for Immunology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Varshi Sivayoganathan
- III. Department of Medicine, University Medical Center Hamburg Eppendorf, 20251 Hamburg, Germany
- Hamburg Center for Translational Immunology, 20251 Hamburg, Germany
| | - Benedetta Padoan
- Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Janna M. Claussen
- Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Arne Düsedau
- Technology Platform Flow Cytometry/FACS, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Jana Hennesen
- Technology Platform Flow Cytometry/FACS, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Madeleine J. Bunders
- Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
- III. Department of Medicine, University Medical Center Hamburg Eppendorf, 20251 Hamburg, Germany
| | - Stefan Bonn
- Institute of Medical Systems Biology, University Medical Center Hamburg Eppendorf, 20251 Hamburg, Germany
| | - Eva Tolosa
- Institute for Immunology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Christian F. Krebs
- III. Department of Medicine, University Medical Center Hamburg Eppendorf, 20251 Hamburg, Germany
- Hamburg Center for Translational Immunology, 20251 Hamburg, Germany
| | | | - Marcus Altfeld
- Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
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13
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Zeng Z, Fu M, Hu Y, Wei Y, Wei X, Luo M. Regulation and signaling pathways in cancer stem cells: implications for targeted therapy for cancer. Mol Cancer 2023; 22:172. [PMID: 37853437 PMCID: PMC10583419 DOI: 10.1186/s12943-023-01877-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023] Open
Abstract
Cancer stem cells (CSCs), initially identified in leukemia in 1994, constitute a distinct subset of tumor cells characterized by surface markers such as CD133, CD44, and ALDH. Their behavior is regulated through a complex interplay of networks, including transcriptional, post-transcriptional, epigenetic, tumor microenvironment (TME), and epithelial-mesenchymal transition (EMT) factors. Numerous signaling pathways were found to be involved in the regulatory network of CSCs. The maintenance of CSC characteristics plays a pivotal role in driving CSC-associated tumor metastasis and conferring resistance to therapy. Consequently, CSCs have emerged as promising targets in cancer treatment. To date, researchers have developed several anticancer agents tailored to specifically target CSCs, with some of these treatment strategies currently undergoing preclinical or clinical trials. In this review, we outline the origin and biological characteristics of CSCs, explore the regulatory networks governing CSCs, discuss the signaling pathways implicated in these networks, and investigate the influential factors contributing to therapy resistance in CSCs. Finally, we offer insights into preclinical and clinical agents designed to eliminate CSCs.
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Affiliation(s)
- Zhen Zeng
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Minyang Fu
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Yuan Hu
- Department of Pediatric Nephrology Nursing, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Min Luo
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China.
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14
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Xiao L, Fang L, Kool ET. RNA Infrastructure Profiling Illuminates Transcriptome Structure in Crowded Spaces. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561413. [PMID: 37873487 PMCID: PMC10592667 DOI: 10.1101/2023.10.09.561413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
RNAs can fold into compact three-dimensional structures, and most RNAs undergo protein interactions in the cell. These compact and occluded environments can block the ability of structure-probing agents to provide useful data about the folding and modification of the underlying RNA. The development of probes that can analyze structure in crowded settings, and differentiate the proximity of interactions, can shed new light on RNA biology. To this end, here we employ 2'-OH-reactive probes that are small enough to access folded RNA structure underlying many close molecular contacts within cells, providing considerably broader coverage for intracellular RNA structural analysis. We compare reverse transcriptase stops in RNA-Seq data from probes of small and standard size to assess RNA-protein proximity and evaluate solvent-exposed tunnels adjacent to RNA. The data are analyzed first with structurally characterized complexes (human 18S and 28S RNA), and then applied transcriptome-wide to polyadenylated transcripts in HEK293 cells. In our transcriptome profile, the smallest probe acetylimidazole (AcIm) yields 80% greater structural coverage than larger conventional reagent NAIN3, providing enhanced structural information in hundreds of transcripts. We further show that acetyl probes provide superior signals for identifying m6A modification sites in transcripts, and provide information regarding methylation sites that are inaccessible to a larger standard probe. RNA infrastructure profiling (RISP) enables enhanced analysis of transcriptome structure, modification, and interactions in living cells, especially in spatially crowded settings.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | - Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA 94305, United States
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15
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Martin-Geary AC, Blakes AJM, Dawes R, Findlay SD, Lord J, Walker S, Talbot-Martin J, Wieder N, D’Souza EN, Fernandes M, Hilton S, Lahiri N, Campbell C, Jenkinson S, DeGoede CGEL, Anderson ER, Burge CB, Sanders SJ, Ellingford J, Baralle D, Banka S, Whiffin N. Systematic identification of disease-causing promoter and untranslated region variants in 8,040 undiagnosed individuals with rare disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.12.23295416. [PMID: 37745552 PMCID: PMC10516070 DOI: 10.1101/2023.09.12.23295416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Background Both promoters and untranslated regions (UTRs) have critical regulatory roles, yet variants in these regions are largely excluded from clinical genetic testing due to difficulty in interpreting pathogenicity. The extent to which these regions may harbour diagnoses for individuals with rare disease is currently unknown. Methods We present a framework for the identification and annotation of potentially deleterious proximal promoter and UTR variants in known dominant disease genes. We use this framework to annotate de novo variants (DNVs) in 8,040 undiagnosed individuals in the Genomics England 100,000 genomes project, which were subject to strict region-based filtering, clinical review, and validation studies where possible. In addition, we performed region and variant annotation-based burden testing in 7,862 unrelated probands against matched unaffected controls. Results We prioritised eleven DNVs and identified an additional variant overlapping one of the eleven. Ten of these twelve variants (82%) are in genes that are a strong match to the individual's phenotype and six had not previously been identified. Through burden testing, we did not observe a significant enrichment of potentially deleterious promoter and/or UTR variants in individuals with rare disease collectively across any of our region or variant annotations. Conclusions Overall, we demonstrate the value of screening promoters and UTRs to uncover additional diagnoses for previously undiagnosed individuals with rare disease and provide a framework for doing so without dramatically increasing interpretation burden.
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Affiliation(s)
- Alexandra C Martin-Geary
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Alexander J M Blakes
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Ruebena Dawes
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Scott D Findlay
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
| | | | | | | | - Nechama Wieder
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Elston N D’Souza
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Maria Fernandes
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Sarah Hilton
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Nayana Lahiri
- St George’s, University of London & St George’s University Hospitals NHS Foundation Trust, Institute of Molecular and Clinical Sciences, London, SW17 0QT, UK
| | - Christopher Campbell
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Sarah Jenkinson
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Christian G E L DeGoede
- Department of Paediatric Neurology, Clinical research Facility, Lancashire Teaching Hospitals NHS Trust
- Manchester Metropolitan University
| | - Emily R Anderson
- Liverpool Centre for Genomic Medicine, Liverpool Women’s Hospital, Liverpool, UK
| | | | - Stephan J Sanders
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 7TY, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- New York Genome Center, New York, NY, USA
| | - Jamie Ellingford
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Nicola Whiffin
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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16
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Duran E, Schmidt A, Welty R, Jalihal AP, Pitchiaya S, Walter NG. Utilizing functional cell-free extracts to dissect ribonucleoprotein complex biology at single-molecule resolution. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1787. [PMID: 37042458 PMCID: PMC10524090 DOI: 10.1002/wrna.1787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 03/06/2023] [Accepted: 03/21/2023] [Indexed: 04/13/2023]
Abstract
Cellular machineries that drive and regulate gene expression often rely on the coordinated assembly and interaction of a multitude of proteins and RNA together called ribonucleoprotein complexes (RNPs). As such, it is challenging to fully reconstitute these cellular machines recombinantly and gain mechanistic understanding of how they operate and are regulated within the complex environment that is the cell. One strategy for overcoming this challenge is to perform single molecule fluorescence microscopy studies within crude or recombinantly supplemented cell extracts. This strategy enables elucidation of the interaction and kinetic behavior of specific fluorescently labeled biomolecules within RNPs under conditions that approximate native cellular environments. In this review, we describe single molecule fluorescence microcopy approaches that dissect RNP-driven processes within cellular extracts, highlighting general strategies used in these methods. We further survey biological advances in the areas of pre-mRNA splicing and transcription regulation that have been facilitated through this approach. Finally, we conclude with a summary of practical considerations for the implementation of the featured approaches to facilitate their broader future implementation in dissecting the mechanisms of RNP-driven cellular processes. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Elizabeth Duran
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Andreas Schmidt
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Robb Welty
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Ameya P Jalihal
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, Department of Pathology, Department of Urology, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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17
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De Felice G, Luciano M, Boiano A, Colangelo G, Catapano P, Della Rocca B, Lapadula MV, Piegari E, Toni C, Fiorillo A. Can Brain-Derived Neurotrophic Factor Be Considered a Biomarker for Bipolar Disorder? An Analysis of the Current Evidence. Brain Sci 2023; 13:1221. [PMID: 37626577 PMCID: PMC10452328 DOI: 10.3390/brainsci13081221] [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: 07/19/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Brain-derived neurotrophic factor (BDNF) plays a key role in brain development, contributing to neuronal survival and neuroplasticity. Previous works have found that BDNF is involved in several neurological or psychiatric diseases. In this review, we aimed to collect all available data on BDNF and bipolar disorder (BD) and assess if BDNF could be considered a biomarker for BD. We searched the most relevant medical databases and included studies reporting original data on BDNF circulating levels or Val66Met polymorphism. Only articles including a direct comparison with healthy controls (HC) and patients diagnosed with BD according to international classification systems were included. Of the 2430 identified articles, 29 were included in the present review. Results of the present review show a reduction in BDNF circulating levels during acute phases of BD compared to HC, which increase after effective therapy of the disorders. The Val66Met polymorphism was related to features usually associated with worse outcomes. High heterogeneity has been observed regarding sample size, clinical differences of included patients, and data analysis approaches, reducing comparisons among studies. Although more studies are needed, BDNF seems to be a promising biomarker for BD.
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Affiliation(s)
| | - Mario Luciano
- Department of Psychiatry, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (G.D.F.); (A.B.); (G.C.); (P.C.); (B.D.R.); (M.V.L.); (E.P.); (C.T.); (A.F.)
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18
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Munro J, Gillen SL, Mitchell L, Laing S, Karim SA, Rink CJ, Waldron JA, Bushell M. Optimisation of Sample Preparation from Primary Mouse Tissue to Maintain RNA Integrity for Methods Examining Translational Control. Cancers (Basel) 2023; 15:3985. [PMID: 37568801 PMCID: PMC10417042 DOI: 10.3390/cancers15153985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
The protein output of different mRNAs can vary by two orders of magnitude; therefore, it is critical to understand the processes that control gene expression operating at the level of translation. Translatome-wide techniques, such as polysome profiling and ribosome profiling, are key methods for determining the translation rates occurring on specific mRNAs. These techniques are now widely used in cell lines; however, they are underutilised in tissues and cancer models. Ribonuclease (RNase) expression is often found to be higher in complex primary tissues in comparison to cell lines. Methods used to preserve RNA during lysis often use denaturing conditions, which need to be avoided when maintaining the interaction and position of the ribosome with the mRNA is required. Here, we detail the cell lysis conditions that produce high-quality RNA from several different tissues covering a range of endogenous RNase expression levels. We highlight the importance of RNA integrity for accurate determination of the global translation status of the cell as determined by polysome gradients and discuss key aspects to optimise for accurate assessment of the translatome from primary mouse tissue.
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Affiliation(s)
- June Munro
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Sarah L. Gillen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Louise Mitchell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Sarah Laing
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
| | - Saadia A. Karim
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Curtis J. Rink
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
| | - Joseph A. Waldron
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
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19
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Chen J, Vishweshwaraiah YL, Mailman RB, Tabdanov ED, Dokholyan NV. A noncommutative combinatorial protein logic circuit controls cell orientation in nanoenvironments. SCIENCE ADVANCES 2023; 9:eadg1062. [PMID: 37235645 PMCID: PMC10219599 DOI: 10.1126/sciadv.adg1062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
Single-protein-based devices that integrate signal sensing with logical operations to generate functional outputs offer exceptional promise for monitoring and modulating biological systems. Engineering such intelligent nanoscale computing agents is challenging, as it requires the integration of sensor domains into a functional protein via intricate allosteric networks. We incorporate a rapamycin-sensitive sensor (uniRapR) and a blue light-responsive LOV2 domain into human Src kinase, creating a protein device that functions as a noncommutative combinatorial logic circuit. In our design, rapamycin activates Src kinase, causing protein localization to focal adhesions, whereas blue light exerts the reverse effect that inactivates Src translocation. Focal adhesion maturation induced by Src activation reduces cell migration dynamics and shifts cell orientation to align along collagen nanolane fibers. Using this protein device, we reversibly control cell orientation by applying the appropriate input signals, a framework that may be useful in tissue engineering and regenerative medicine.
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Affiliation(s)
- Jiaxing Chen
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
| | | | - Richard B. Mailman
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
| | - Erdem D. Tabdanov
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
| | - Nikolay V. Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
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20
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Kessel JC, Weiskirchen R, Schröder SK. Expression Analysis of Lipocalin 2 (LCN2) in Reproductive and Non-Reproductive Tissues of Esr1-Deficient Mice. Int J Mol Sci 2023; 24:ijms24119280. [PMID: 37298232 DOI: 10.3390/ijms24119280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Estrogen receptor alpha (ERα) is widely expressed in reproductive organs, but also in non-reproductive tissues of females and males. There is evidence that lipocalin 2 (LCN2), which has diverse immunological and metabolic functions, is regulated by ERα in adipose tissue. However, in many other tissues, the impact of ERα on LCN2 expression has not been studied yet. Therefore, we used an Esr1-deficient mouse strain and analyzed LCN2 expression in reproductive (ovary, testes) and non-reproductive tissues (kidney, spleen, liver, lung) of both sexes. Tissues collected from adult wild-type (WT) and Esr1-deficient animals were analyzed by immunohistochemistry, Western blot analysis, and RT-qPCR for Lcn2 expression. In non-reproductive tissues, only minor genotype- or sex-specific differences in LCN2 expression were detected. In contrast, significant differences in LCN2 expression were observed in reproductive tissues. Particularly, there was a strong increase in LCN2 in Esr1-deficient ovaries when compared to WTs. In summary, we found an inverse correlation between the presence of ERα and the expression of LCN2 in testes and ovaries. Our results provide an important basis to better understand LCN2 regulation in the context of hormones and in health and disease.
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Affiliation(s)
- Jan C Kessel
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany
| | - Sarah K Schröder
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany
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21
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Xu H, Lin S, Zhou Z, Li D, Zhang X, Yu M, Zhao R, Wang Y, Qian J, Li X, Li B, Wei C, Chen K, Yoshimura T, Wang JM, Huang J. New genetic and epigenetic insights into the chemokine system: the latest discoveries aiding progression toward precision medicine. Cell Mol Immunol 2023:10.1038/s41423-023-01032-x. [PMID: 37198402 DOI: 10.1038/s41423-023-01032-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
Over the past thirty years, the importance of chemokines and their seven-transmembrane G protein-coupled receptors (GPCRs) has been increasingly recognized. Chemokine interactions with receptors trigger signaling pathway activity to form a network fundamental to diverse immune processes, including host homeostasis and responses to disease. Genetic and nongenetic regulation of both the expression and structure of chemokines and receptors conveys chemokine functional heterogeneity. Imbalances and defects in the system contribute to the pathogenesis of a variety of diseases, including cancer, immune and inflammatory diseases, and metabolic and neurological disorders, which render the system a focus of studies aiming to discover therapies and important biomarkers. The integrated view of chemokine biology underpinning divergence and plasticity has provided insights into immune dysfunction in disease states, including, among others, coronavirus disease 2019 (COVID-19). In this review, by reporting the latest advances in chemokine biology and results from analyses of a plethora of sequencing-based datasets, we outline recent advances in the understanding of the genetic variations and nongenetic heterogeneity of chemokines and receptors and provide an updated view of their contribution to the pathophysiological network, focusing on chemokine-mediated inflammation and cancer. Clarification of the molecular basis of dynamic chemokine-receptor interactions will help advance the understanding of chemokine biology to achieve precision medicine application in the clinic.
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Affiliation(s)
- Hanli Xu
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Shuye Lin
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, 101149, Beijing, China
| | - Ziyun Zhou
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Duoduo Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Xiting Zhang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Muhan Yu
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Ruoyi Zhao
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Yiheng Wang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Junru Qian
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Xinyi Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Bohan Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Chuhan Wei
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Keqiang Chen
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Teizo Yoshimura
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Ji Ming Wang
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Jiaqiang Huang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China.
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, 101149, Beijing, China.
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA.
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22
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Quercetin and Its Fermented Extract as a Potential Inhibitor of Bisphenol A-Exposed HT-29 Colon Cancer Cells’ Viability. Int J Mol Sci 2023; 24:ijms24065604. [PMID: 36982678 PMCID: PMC10052295 DOI: 10.3390/ijms24065604] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Bisphenol A (BPA) promotes colon cancer by altering the physiological functions of hormones. Quercetin (Q) can regulate signaling pathways through hormone receptors, inhibiting cancer cells. The antiproliferative effects of Q and its fermented extract (FEQ, obtained by Q gastrointestinal digestion and in vitro colonic fermentation) were analyzed in HT-29 cells exposed to BPA. Polyphenols were quantified in FEQ by HPLC and their antioxidant capacity by DPPH and ORAC. Q and 3,4-dihydroxyphenylacetic acid (DOPAC) were quantified in FEQ. Q and FEQ exhibited antioxidant capacity. Cell viability with Q+BPA and FEQ+BPA was 60% and 50%, respectively; less than 20% of dead cells were associated with the necrosis process (LDH). Treatments with Q and Q+BPA induced cell cycle arrest in the G0/G1 phase, and FEQ and FEQ+BPA in the S phase. Compared with other treatments, Q positively modulated ESR2 and GPR30 genes. Using a gene microarray of the p53 pathway, Q, Q+BPA, FEQ and FEQ+BPA positively modulated genes involved in apoptosis and cell cycle arrest; bisphenol inhibited the expression of pro-apoptotic and cell cycle repressor genes. In silico analyses demonstrated the binding affinity of Q > BPA > DOPAC molecules for ERα and ERβ. Further studies are needed to understand the role of disruptors in colon cancer.
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23
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Feng X, Li X, Feng J, Xia J. Intracranial hemorrhage management in the multi-omics era. Heliyon 2023; 9:e14749. [PMID: 37101482 PMCID: PMC10123201 DOI: 10.1016/j.heliyon.2023.e14749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Intracranial hemorrhage (ICH) is a devastating disorder. Neuroprotective strategies that prevent tissue injury and improve functional outcomes have been identified in multiple animal models of ICH. However, these potential interventions in clinical trials produced generally disappointing results. With progress in omics, studies of omics data, including genomics, transcriptomics, epigenetics, proteomics, metabolomics, and the gut microbiome, may help promote precision medicine. In this review, we focused on introducing the applications of all omics in ICH and shed light on all of the considerable advantages to systematically analyze the necessity and importance of multiple omics technology in ICH.
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Affiliation(s)
- Xianjing Feng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xi Li
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jie Feng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jian Xia
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- Clinical Research Center for Cerebrovascular Disease of Hunan Province, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Corresponding author. Department of Neurology, Xiangya Hospital, Central South University, No.87, Xiangya Road, Changsha, 410008, China
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24
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Kochavi A, Lovecchio D, Faller WJ, Agami R. Proteome diversification by mRNA translation in cancer. Mol Cell 2023; 83:469-480. [PMID: 36521491 DOI: 10.1016/j.molcel.2022.11.014] [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: 09/19/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022]
Abstract
mRNA translation is a highly conserved and tightly controlled mechanism for protein synthesis and is well known to be altered by oncogenes to promote cancer development. This distorted mRNA translation is accompanied by the vulnerability of cancer to inhibitors of key mRNA translation components. Novel studies also suggest that these alternations could be utilized for immunotherapy. Ribosome heterogeneity and alternative responses to nutrient shortages, which aid cancer growth and spread, are proposed to elicit aberrant protein production but may also result in previously unidentified therapeutic targets, such as the presentation of cancer-specific peptides at the surface of cancer cells (neoepitopes). This review will assess the driving forces in tRNA and ribosome function that underlie proteome diversification due to alterations in mRNA translation in cancer cells.
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Affiliation(s)
- Adva Kochavi
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - Domenica Lovecchio
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - William James Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands; Erasmus MC, Rotterdam University, Rotterdam, the Netherlands.
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25
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Single-molecule visualization of mRNA circularization during translation. Exp Mol Med 2023; 55:283-289. [PMID: 36720916 PMCID: PMC9981743 DOI: 10.1038/s12276-023-00933-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/04/2022] [Accepted: 12/04/2022] [Indexed: 02/02/2023] Open
Abstract
Translation is mediated by precisely orchestrated sequential interactions among translation initiation components, mRNA, and ribosomes. Biochemical, structural, and genetic techniques have revealed the fundamental mechanism that determines what occurs and when, where and in what order. Most mRNAs are circularized via the eIF4E-eIF4G-PABP interaction, which stabilizes mRNAs and enhances translation by recycling ribosomes. However, studies using single-molecule fluorescence imaging have allowed for the visualization of complex data that opposes the traditional "functional circularization" theory. Here, we briefly introduce single-molecule techniques applied to studies on mRNA circularization and describe the results of in vitro and live-cell imaging. Finally, we discuss relevant insights and questions gained from single-molecule research related to translation.
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26
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Deviatkin AA, Simonov RA, Trutneva KA, Maznina AA, Soroka AB, Kogan AA, Feoktistova SG, Khavina EM, Mityaeva ON, Volchkov PY. Cap-Independent Circular mRNA Translation Efficiency. Vaccines (Basel) 2023; 11:vaccines11020238. [PMID: 36851116 PMCID: PMC9967249 DOI: 10.3390/vaccines11020238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Recently, the mRNA platform has become the method of choice in vaccine development to find new ways to fight infectious diseases. However, this approach has shortcomings, namely that mRNA vaccines require special storage conditions, which makes them less accessible. This instability is due to the fact that the five-prime and three-prime ends of the mRNA are a substrate for the ubiquitous exoribonucleases. To address the problem, circular mRNAs have been proposed for transgene delivery as they lack these ends. Notably, circular RNAs do not have a capped five-prime end, which makes it impossible to initiate translation canonically. In this review, we summarize the current knowledge on cap-independent translation initiation methods and discuss which approaches might be most effective in developing vaccines and other biotechnological products based on circular mRNAs.
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Affiliation(s)
- Andrei A. Deviatkin
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Endocrinology Research Centre, 117036 Moscow, Russia
| | - Ruslan A. Simonov
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Kseniya A. Trutneva
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Endocrinology Research Centre, 117036 Moscow, Russia
| | - Anna A. Maznina
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Endocrinology Research Centre, 117036 Moscow, Russia
| | - Anastasiia B. Soroka
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
| | - Anna A. Kogan
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
| | - Sofya G. Feoktistova
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Endocrinology Research Centre, 117036 Moscow, Russia
| | - Elena M. Khavina
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Faculty of Biology, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Olga N. Mityaeva
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Endocrinology Research Centre, 117036 Moscow, Russia
| | - Pavel Y. Volchkov
- Life Sciences Research Center, Moscow Institute of Physics and Technology, National Research University, 141700 Dolgoprudniy, Russia
- Endocrinology Research Centre, 117036 Moscow, Russia
- Correspondence:
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27
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Shen M, Goforth JB, Eisenstein RS. Iron-dependent post transcriptional control of mitochondrial aconitase expression. Metallomics 2023; 15:mfac099. [PMID: 36702557 PMCID: PMC9902864 DOI: 10.1093/mtomcs/mfac099] [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: 10/28/2022] [Accepted: 12/23/2022] [Indexed: 01/28/2023]
Abstract
Iron regulatory proteins (IRPs) control the translation of animal cell mRNAs encoding proteins with diverse roles. This includes the iron storage protein ferritin and the tricarboxylic cycle (TCA) enzyme mitochondrial aconitase (ACO2) through iron-dependent binding of IRP to the iron responsive element (IRE) in the 5' untranslated region (UTR). To further elucidate the mechanisms allowing IRPs to control translation of 5' IRE-containing mRNA differentially, we focused on Aco2 mRNA, which is weakly controlled versus the ferritins. Rat liver contains two classes of Aco2 mRNAs, with and without an IRE, due to alterations in the transcription start site. Structural analysis showed that the Aco2 IRE adopts the canonical IRE structure but lacks the dynamic internal loop/bulge five base pairs 5' of the CAGUG(U/C) terminal loop in the ferritin IREs. Unlike ferritin mRNAs, the Aco2 IRE lacks an extensive base-paired flanking region. Using a full-length Aco2 mRNA expression construct, iron controlled ACO2 expression in an IRE-dependent and IRE-independent manner, the latter of which was eliminated with the ACO23C3S mutant that cannot bind the FeS cluster. Iron regulation of ACO23C3S encoded by the full-length mRNA was completely IRE-dependent. Replacement of the Aco23C3S 5' UTR with the Fth1 IRE with base-paired flanking sequences substantially improved iron responsiveness, as did fusing of the Fth1 base-paired flanking sequences to the native IRE in the Aco3C3S construct. Our studies further define the mechanisms underlying the IRP-dependent translational regulatory hierarchy and reveal that Aco2 mRNA species lacking the IRE contribute to the expression of this TCA cycle enzyme.
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Affiliation(s)
- Macy Shen
- Department of Nutritional Sciences, University of Wisconsin-Madison, 1415 Linden Drive, Madison, WI 53706, USA
- Department of Chemistry and Biochemistry, California State University-Fullerton, Fullerton, CA 92834-6866, USA
| | - Jeremy B Goforth
- Department of Nutritional Sciences, University of Wisconsin-Madison, 1415 Linden Drive, Madison, WI 53706, USA
- Science Department, Lodi Middle School, 945 S. Ham Lane, Lodi, CA 95242, USA
| | - Richard S Eisenstein
- Department of Nutritional Sciences, University of Wisconsin-Madison, 1415 Linden Drive, Madison, WI 53706, USA
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28
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Gandin V, English BP, Freeman M, Leroux LP, Preibisch S, Walpita D, Jaramillo M, Singer RH. Cap-dependent translation initiation monitored in living cells. Nat Commun 2022; 13:6558. [PMID: 36323665 PMCID: PMC9630388 DOI: 10.1038/s41467-022-34052-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 10/06/2022] [Indexed: 11/19/2022] Open
Abstract
mRNA translation is tightly regulated to preserve cellular homeostasis. Despite extensive biochemical, genetic, and structural studies, a detailed understanding of mRNA translation regulation is lacking. Imaging methodologies able to resolve the binding dynamics of translation factors at single-cell and single-mRNA resolution were necessary to fully elucidate regulation of this paramount process. Here live-cell spectroscopy and single-particle tracking were combined to interrogate the binding dynamics of endogenous initiation factors to the 5'cap. The diffusion of initiation factors (IFs) changed markedly upon their association with mRNA. Quantifying their diffusion characteristics revealed the sequence of IFs assembly and disassembly in cell lines and the clustering of translation in neurons. This approach revealed translation regulation at high spatial and temporal resolution that can be applied to the formation of any endogenous complex that results in a measurable shift in diffusion.
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Affiliation(s)
- Valentina Gandin
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA
| | - Brian P. English
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA
| | - Melanie Freeman
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA
| | - Louis-Philippe Leroux
- grid.418084.10000 0000 9582 2314Institut National de la Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie (CAFSB), Laval, QC Canada
| | - Stephan Preibisch
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA
| | - Deepika Walpita
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA
| | - Maritza Jaramillo
- grid.418084.10000 0000 9582 2314Institut National de la Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie (CAFSB), Laval, QC Canada
| | - Robert H. Singer
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA
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29
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Champagne J, Mordente K, Nagel R, Agami R. Slippy-Sloppy translation: a tale of programmed and induced-ribosomal frameshifting. Trends Genet 2022; 38:1123-1133. [PMID: 35641342 DOI: 10.1016/j.tig.2022.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 01/24/2023]
Abstract
Programmed ribosomal frameshifting (PRF) is a key mechanism that viruses use to generate essential proteins for replication, and as a means of regulating gene expression. PRF generally involves recoding signals or frameshift stimulators to elevate the occurrence of frameshifting at shift-prone 'slippery' sequences. Given its essential role in viral replication, targeting PRF was envisioned as an attractive tool to block viral infection. However, in contrast to controlled-PRF mechanisms, recent studies have shown that ribosomes of many human cancer cell types are prone to frameshifting upon amino acid shortage; thus, these cells are deemed to be sloppy. The resulting products of a sloppy frameshift at the 'hungry' codons are aberrant proteins the degradation and display of which at the cell surface can trigger T cell activation. In this review, we address recent discoveries in ribosomal frameshifting and their functional consequences for the proteome in human cancer cells.
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Affiliation(s)
- Julien Champagne
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Kelly Mordente
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Remco Nagel
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands; Erasmus MC, Rotterdam University, Rotterdam, The Netherlands.
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Ruiz-Conca M, Gardela J, Olvera-Maneu S, López-Béjar M, Álvarez-Rodríguez M. NR3C1 and glucocorticoid-regulatory genes mRNA and protein expression in the endometrium and ampulla during the bovine estrous cycle. Res Vet Sci 2022; 152:510-523. [PMID: 36174371 DOI: 10.1016/j.rvsc.2022.09.018] [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: 03/01/2022] [Revised: 09/08/2022] [Accepted: 09/18/2022] [Indexed: 10/14/2022]
Abstract
The bovine reproductive tract exhibits changes during the estrous cycle modulated by the interplay of steroid hormones. Glucocorticoids can be detrimental when stress-induced but are relevant at baseline levels for appropriate reproductive function. Here, an analysis of quantitative real-time PCR was performed to study the bovine glucocorticoid-related baseline gene transcription in endometrial and ampullar tissue samples derived from three time points of the estrous cycle, stage I (Days 1-4), stage III (Days 11-17) and stage IV (Days 18-20). Our results revealed expression differences during stages, as expression observed in the ampulla was higher during the post-ovulatory phase (stage I), including the glucocorticoid receptor NR3C1, and some of its regulators, involved in glucocorticoid availability (HSD11B1 and HSD11B2) and transcriptional actions (FKBP4 and FKBP5). In contrast, in the endometrium, higher expression of the steroid receptors was observed during the late luteal phase (stage III), including ESR1, ESR2, PGRMC1 and PGRMC2, and HSD11B1 expression decreased, while HSD11B2 increased. Moreover, at protein level, FKBP4 was higher expressed during the late luteal phase, and NR3C1 during the pre-ovulatory phase (stage IV). These results suggest that tight regulation of the glucocorticoid activity is promoted in the ampulla, when reproductive events are taking place, including oocyte maturation. Moreover, most expression changes in the endometrium were observed during the late luteal phase, and may be related to the embryonic maternal recognition. In conclusion, the glucocorticoid regulation changes across the estrous cycle and may be playing a role on the reproductive events occurring in the bovine ampulla and endometrium.
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Affiliation(s)
- Mateo Ruiz-Conca
- Division of Children's and Women Health (BKH), Department of Biomedical and Clinical Sciences (BKV), Obstetrics and Gynecology, Linköping University, 58185 Linköping, Sweden; Department of Animal Health and Anatomy, Faculty of Veterinary Medicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Jaume Gardela
- Division of Children's and Women Health (BKH), Department of Biomedical and Clinical Sciences (BKV), Obstetrics and Gynecology, Linköping University, 58185 Linköping, Sweden; Department of Animal Health and Anatomy, Faculty of Veterinary Medicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Sergi Olvera-Maneu
- Department of Animal Health and Anatomy, Faculty of Veterinary Medicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Manel López-Béjar
- Department of Animal Health and Anatomy, Faculty of Veterinary Medicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Manuel Álvarez-Rodríguez
- Division of Children's and Women Health (BKH), Department of Biomedical and Clinical Sciences (BKV), Obstetrics and Gynecology, Linköping University, 58185 Linköping, Sweden; Department of Animal Health and Anatomy, Faculty of Veterinary Medicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Muñoz-Ayala A, Chimal-Vega B, García-González V. Translation initiation and its relationship with metabolic mechanisms in cancer development, progression and chemoresistance. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:111-141. [PMID: 36088073 DOI: 10.1016/bs.apcsb.2022.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Pathways that regulate protein homeostasis (proteostasis) in cells range from mRNA processing to protein degradation; perturbations in regulatory mechanisms of these pathways can lead to oncogenic cellular processes. Protein synthesis modulation failures are common phenomena in cancer cells, wherein specific conditions that promote the translation of protein factors promoting carcinogenesis are present. These specific conditions may be favored by metabolic lipid alterations like those found in metabolic syndrome and obesity. Protein translation modifications have been described in obesity, favoring the translation of protein targets that benefit lipid accumulation; a determining factor is the activity of the cap-binding eukaryotic translation initiation factor 4E (eIF4E), a crosstalk in protein translation and lipogenesis. Besides, alterations of protein translation initiation steps are critical participants for the development of both pathogenic conditions, cancer, and obesity. This chapter is focused on the regulation of recognition and processing of carcinogenic-mRNA and the connections among lipid metabolism and cell signaling pathways that promote oncogenesis, tumoral microenvironment generation and potentially the development of chemoresistance. We performed an in-depth analysis of events, such as those occurring in obesity and dyslipidemias, that may influence protein translation, driving the recognition of certain mRNAs and favoring cancer development and chemoresistance.
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Affiliation(s)
- Andrea Muñoz-Ayala
- Departamento de Bioquímica, Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali, México; Laboratorio Multidisciplinario de Estudios Metabólicos y Cáncer, Universidad Autónoma de Baja California, Mexicali, México
| | - Brenda Chimal-Vega
- Departamento de Bioquímica, Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali, México; Laboratorio Multidisciplinario de Estudios Metabólicos y Cáncer, Universidad Autónoma de Baja California, Mexicali, México
| | - Victor García-González
- Departamento de Bioquímica, Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali, México; Laboratorio Multidisciplinario de Estudios Metabólicos y Cáncer, Universidad Autónoma de Baja California, Mexicali, México.
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Tang YL, Li GS, Li DM, Tang D, Huang JZ, Feng H, He RQ, Huang ZG, Dang YW, Kong JL, Gan TQ, Zhou HF, Zeng JJ, Chen G. The clinical significance of integrin subunit alpha V in cancers: from small cell lung carcinoma to pan-cancer. BMC Pulm Med 2022; 22:300. [PMID: 35927660 PMCID: PMC9354352 DOI: 10.1186/s12890-022-02095-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Little is known about the relationship between integrin subunit alpha V (ITGAV) and cancers, including small cell lung cancer (SCLC). METHODS Using large sample size from multiple sources, the clinical roles of ITGAV expression in SCLC were explored using differential expression analysis, receiver operating characteristic curves, Kaplan-Meier curves, etc. RESULTS: Decreased mRNA (SMD = - 1.05) and increased protein levels of ITGAV were detected in SCLC (n = 865). Transcription factors-ZEB2, IK2F1, and EGR2-may regulate ITGAV expression in SCLC, as they had ChIP-Seq (chromatin immunoprecipitation followed by sequencing) peaks upstream of the transcription start site of ITGAV. ITGAV expression made it feasible to distinguish SCLC from non-SCLC (AUC = 0.88, sensitivity = 0.78, specificity = 0.84), and represented a risk role in the prognosis of SCLC (p < 0.05). ITGAV may play a role in cancers by influencing several immunity-related signaling pathways and immune cells. Further, the extensive pan-cancer analysis verified the differential expression of ITGAV and its clinical significance in multiple cancers. CONCLUSION ITGAV served as a potential marker for prognosis and identification of cancers including SCLC.
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Affiliation(s)
- Yu-Lu Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Guo-Sheng Li
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Dong-Ming Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Deng Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jie-Zhuang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hao Feng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Rong-Quan He
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jin-Liang Kong
- Ward of Pulmonary and Critical Care Medicine, Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Ting-Qing Gan
- Department of Medical Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hua-Fu Zhou
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jing-Jing Zeng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China.
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Yadav A, Verhaegen S, Filis P, Domanska D, Lyle R, Sundaram AYM, Leithaug M, Østby GC, Aleksandersen M, Berntsen HF, Zimmer KE, Fowler PA, Paulsen RE, Ropstad E. Exposure to a human relevant mixture of persistent organic pollutants or to perfluorooctane sulfonic acid alone dysregulates the developing cerebellum of chicken embryo. ENVIRONMENT INTERNATIONAL 2022; 166:107379. [PMID: 35792514 DOI: 10.1016/j.envint.2022.107379] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/07/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Prenatal exposure to persistent organic pollutants (POPs) is associated with neurodevelopmental disorders. In the present study, we explored whether a human-relevant POP mixture affects the development of chicken embryo cerebellum. We used a defined mixture of 29 POPs, with chemical composition and concentrations based on blood levels in the Scandinavian population. We also evaluated exposure to a prominent compound in the mixture, perfluorooctane sulfonic acid (PFOS), alone. Embryos (n = 7-9 per exposure group) were exposed by injection directly into the allantois at embryonic day 13 (E13). Cerebella were isolated at E17 and subjected to morphological, RNA-seq and shot-gun proteomics analyses. There was a reduction in thickness of the molecular layer of cerebellar cortex in both exposure scenarios. Exposure to the POP mixture significantly affected expression of 65 of 13,800 transcripts, and 43 of 2,568 proteins, when compared to solvent control. PFOS alone affected expression of 80 of 13,859 transcripts, and 69 of 2,555 proteins. Twenty-five genes and 15 proteins were common for both exposure groups. These findings point to alterations in molecular events linked to retinoid X receptor (RXR) signalling, neuronal cell proliferation and migration, cellular stress responses including unfolded protein response, lipid metabolism, and myelination. Exposure to the POP mixture increased methionine oxidation, whereas PFOS decreased oxidation. Several of the altered genes and proteins are involved in a wide variety of neurological disorders. We conclude that POP exposure can interfere with fundamental aspects of neurodevelopment, altering molecular pathways that are associated with adverse neurocognitive and behavioural outcomes.
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Affiliation(s)
- Ajay Yadav
- Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway; Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, NO-0316 Oslo, Norway.
| | - Steven Verhaegen
- Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway.
| | - Panagiotis Filis
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK.
| | - Diana Domanska
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Pathology, Oslo University Hospital-Rikshospitalet, Oslo, Norway.
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway; Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.
| | - Arvind Y M Sundaram
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
| | - Magnus Leithaug
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
| | - Gunn Charlotte Østby
- Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway.
| | - Mona Aleksandersen
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway.
| | - Hanne Friis Berntsen
- Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway; National Institute of Occupational Health, P.O. Box 5330 Majorstuen, NO-0304, Oslo, Norway.
| | - Karin Elisabeth Zimmer
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway.
| | - Paul A Fowler
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK.
| | - Ragnhild Elisabeth Paulsen
- Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, NO-0316 Oslo, Norway.
| | - Erik Ropstad
- Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway.
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Çetin B, O’Leary SE. mRNA- and factor-driven dynamic variability controls eIF4F-cap recognition for translation initiation. Nucleic Acids Res 2022; 50:8240-8261. [PMID: 35871304 PMCID: PMC9371892 DOI: 10.1093/nar/gkac631] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/29/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022] Open
Abstract
mRNA 5′ cap recognition by eIF4F is a key element of eukaryotic translational control. Kinetic differences in eIF4F–mRNA interactions have long been proposed to mediate translation-efficiency differences between mRNAs, and recent transcriptome-wide studies have revealed significant heterogeneity in eIF4F engagement with differentially-translated mRNAs. However, detailed kinetic information exists only for eIF4F interactions with short model RNAs. We developed and applied single-molecule fluorescence approaches to directly observe real-time Saccharomyces cerevisiae eIF4F subunit interactions with full-length polyadenylated mRNAs. We found that eIF4E–mRNA association rates linearly anticorrelate with mRNA length. eIF4G–mRNA interaction accelerates eIF4E–mRNA association in proportion to mRNA length, as does an eIF4F-independent activity of eIF4A, though cap-proximal secondary structure still plays an important role in defining the final association rates. eIF4F–mRNA interactions remained dominated by effects of eIF4G, but were modulated to different extents for different mRNAs by the presence of eIF4A and ATP. We also found that eIF4A-catalyzed ATP hydrolysis ejects eIF4E, and likely eIF4E•eIF4G from the mRNA after initial eIF4F•mRNA complex formation, suggesting a mechanism to prepare the mRNA 5′ end for ribosome recruitment. Our results support a role for mRNA-specific, factor-driven eIF4F association rates in kinetically controlling translation.
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Affiliation(s)
- Burak Çetin
- Graduate Program in Cell, Molecular, and Developmental Biology, University of California Riverside , Riverside, CA 92521, USA
| | - Seán E O’Leary
- Graduate Program in Cell, Molecular, and Developmental Biology, University of California Riverside , Riverside, CA 92521, USA
- Department of Biochemistry, University of California Riverside , Riverside, CA 92521, USA
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35
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Segura I, Egea J. Editorial: Molecular and Cellular Crosstalk on Neuronal Functionality and Regulation, From Development to Pathology. Front Mol Neurosci 2022; 15:966423. [PMID: 35845614 PMCID: PMC9280617 DOI: 10.3389/fnmol.2022.966423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Inmaculada Segura
- Max Planck Institute for Biological Intelligence (in Foundation), Planegg, Germany
- Department of Cellular Physiology, Biomedical Center Munich, Ludwig Maximilian University, Planegg, Germany
- *Correspondence: Inmaculada Segura
| | - Joaquim Egea
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
- Biomedical Research Institute of Lleida (IRBLLEIDA), Lleida, Spain
- Serra Húnter Programme, Generalitat de Catalunya, Barcelona, Spain
- Joaquim Egea
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Liu Z, Gao Z, Li B, Li J, Ou Y, Yu X, Zhang Z, Liu S, Fu X, Jin H, Wu J, Sun S, Sun S, Wu Q. Lipid-associated macrophages in the tumor-adipose microenvironment facilitate breast cancer progression. Oncoimmunology 2022; 11:2085432. [PMID: 35712121 PMCID: PMC9196645 DOI: 10.1080/2162402x.2022.2085432] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The tumor-adipose microenvironment (TAME) is a universal microecosystem, that is characterized by the dysfunction of lipid metabolism, such as excessive free fatty acids (FFAs). Macrophages are the most abundant immune cell type within TAME, although their diversity in the TAME is not clear. We first reveal that infiltration of M2-like macrophages in the TAME is associated with poor survival in breast cancer. To explore lipid-associated alterations in the TAME, we also detected the levels of FFAs transporters including fatty acid binding proteins (FABPs) and fatty acid transport protein 1 (FATP1). The results indicated that expression of fatty acid transporters in the TAME is tightly linked to the function of macrophages and predicts survival in breast cancer. To explore the impact of FFAs transporters on the function of macrophages, we performed single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics. Consequently, we identified a special subpopulation of macrophages defined as lipid-associated macrophages (LAMs), highly expressed macrophage markers (CD163, SPP1 and C1QC), genes involved in lipid metabolism (FABP3, FABP4, FABP5, LPL and LIPA) and some lipid receptors (LGALS3 and TREM2). Functionally, LAMs were characterized by a canonical functional signature of M2-like macrophages, lipid accumulation and enhancing phagocytosis, and they were mostly distributed in tumor-adipose junctional regions. Finally, the allograft cancer mouse models confirmed that LAMs depletion in the TAME synergizes the antitumorigenic effects of anti-PD1 therapy. In summary, we defined a novel subtype of macrophages in the TAME, that has unique features and clinical outcomes.
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Affiliation(s)
- Zhou Liu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Zhijie Gao
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Bei Li
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Juanjuan Li
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Yangyang Ou
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Xin Yu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Zun Zhang
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Siqin Liu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Xiaoyu Fu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Hongzhong Jin
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Juan Wu
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Si Sun
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Shengrong Sun
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Qi Wu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, Tongji University, Shanghai, P. R. China
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Sun Y, Kinsela AS, Waite TD. Elucidation of alveolar macrophage cell response to coal dusts: Role of ferroptosis in pathogenesis of coal workers' pneumoconiosis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153727. [PMID: 35149061 DOI: 10.1016/j.scitotenv.2022.153727] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/26/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Causal factors underlying coal workers' pneumoconiosis (CWP) have been variously attributed to the presence of carbon, crystalline silica and reduced iron (Fe) minerals, especially pyrite and Fe/Si-amorphous compounds. The aim of this research was to assess the role of iron in CWP and, more specifically, the cytotoxicity of coal dusts with different elemental composition towards alveolar macrophages (AMs). Survival rate of AMs, alteration in the production of pro-inflammatory cytokine TNF-α, MDA (the lipid peroxidation product) and intracellular GSH were assessed using commercial assay kits. The quantitative interaction between iron and GSH was investigated by developing a numerical model. The presence of various reduced Fe minerals (viz. pyrite and siderite) in coal dusts exhibited a consistently acute adverse impact on the viability of AMs and enhanced the production of TNF-α. The presence of the clinically available Fe chelator deferiprone (DFP) and the cytosolic antioxidant glutathione (GSH) significantly increased the viability of AMs exposed to Fe bearing coal dusts, suggesting coal dusts containing reduced Fe minerals were likely contributors to the initial stages of AM cytotoxicity via a ferroptosis related pathway. Chemical kinetic modeling indicated that these results may be attributed to an enhanced consumption of GSH as a result of Fe redox cycling. FeIIGSH and GS• produced from the interaction between ferric Fe and GSH facilitated the production of O2•- which further oxidized GSH via a direct reaction between GSH and GS• or GSO•. These results suggest that coal dusts containing reduced Fe minerals and Fe compounds may elevate acute inflammation levels in AMs, indicating that crystalline silica may not be the only hazard of concern in mining environments.
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Affiliation(s)
- Yingying Sun
- School of Civil and Environmental Engineering, Water Research Centre, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Andrew S Kinsela
- School of Civil and Environmental Engineering, Water Research Centre, The University of New South Wales, Sydney, NSW 2052, Australia
| | - T David Waite
- School of Civil and Environmental Engineering, Water Research Centre, The University of New South Wales, Sydney, NSW 2052, Australia.
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Wong GYM, Diakos C, Hugh TJ, Molloy MP. Proteomic Profiling and Biomarker Discovery in Colorectal Liver Metastases. Int J Mol Sci 2022; 23:ijms23116091. [PMID: 35682769 PMCID: PMC9181741 DOI: 10.3390/ijms23116091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 12/14/2022] Open
Abstract
Colorectal liver metastases (CRLM) are the leading cause of death among patients with metastatic colorectal cancer (CRC). As part of multimodal therapy, liver resection is the mainstay of curative-intent treatment for select patients with CRLM. However, effective treatment of CRLM remains challenging as recurrence occurs in most patients after liver resection. Proposed clinicopathologic factors for predicting recurrence are inconsistent and lose prognostic significance over time. The rapid development of next-generation sequencing technologies and decreasing DNA sequencing costs have accelerated the genomic profiling of various cancers. The characterisation of genomic alterations in CRC has significantly improved our understanding of its carcinogenesis. However, the functional context at the protein level has not been established for most of this genomic information. Furthermore, genomic alterations do not always result in predicted changes in the corresponding proteins and cancer phenotype, while post-transcriptional and post-translational regulation may alter synthesised protein levels, affecting phenotypes. More recent advancements in mass spectrometry-based technology enable accurate protein quantitation and comprehensive proteomic profiling of cancers. Several studies have explored proteomic biomarkers for predicting CRLM after oncologic resection of primary CRC and recurrence after curative-intent resection of CRLM. The current review aims to rationalise the proteomic complexity of CRC and explore the potential applications of proteomic biomarkers in CRLM.
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Affiliation(s)
- Geoffrey Yuet Mun Wong
- Department of Upper Gastrointestinal Surgery, Royal North Shore Hospital, Sydney, NSW 2065, Australia;
- Northern Clinical School, The University of Sydney, Sydney, NSW 2065, Australia;
- Correspondence:
| | - Connie Diakos
- Northern Clinical School, The University of Sydney, Sydney, NSW 2065, Australia;
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Thomas J. Hugh
- Department of Upper Gastrointestinal Surgery, Royal North Shore Hospital, Sydney, NSW 2065, Australia;
- Northern Clinical School, The University of Sydney, Sydney, NSW 2065, Australia;
| | - Mark P. Molloy
- Bowel Cancer and Biomarker Research Laboratory, Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia;
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Li M, He M, Xu F, Guan Y, Tian J, Wan Z, Zhou H, Gao M, Chong T. Abnormal expression and the significant prognostic value of aquaporins in clear cell renal cell carcinoma. PLoS One 2022; 17:e0264553. [PMID: 35245343 PMCID: PMC8896691 DOI: 10.1371/journal.pone.0264553] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/12/2022] [Indexed: 12/11/2022] Open
Abstract
Aquaporins (AQPs) are a kind of transmembrane proteins that exist in various organs of the human body. AQPs play an important role in regulating water transport, lipid metabolism and glycolysis of cells. Clear cell renal cell carcinoma (ccRCC) is a common malignant tumor of the kidney, and the prognosis is worse than other types of renal cell cancer (RCC). The impact of AQPs on the prognosis of ccRCC and the potential relationship between AQPs and the occurrence and development of ccRCC are demanded to be investigated. In this study, we first explored the expression pattern of AQPs by using Oncomine, UALCAN, and HPA databases. Secondly, we constructed protein-protein interaction (PPI) network and performed function enrichment analysis through STRING, GeneMANIA, and Metascape. Then a comprehensive analysis of the genetic mutant frequency of AQPs in ccRCC was carried out using the cBioPortal database. In addition, we also analyzed the main enriched biological functions of AQPs and the correlation with seven main immune cells. Finally, we confirmed the prognostic value of AQPs throughGEPIA and Cox regression analysis. We found that the mRNA expression levels of AQP0/8/9/10 were up-regulated in patients with ccRCC, while those of AQP1/2/3/4/5/6/7/11 showed the opposite. Among them, the expression differences of AQP1/2/3/4/5/6/7/8/9/11 were statistically significant. The differences in protein expression levels of AQP1/2/3/4/5/6 in ccRCC and normal renal tissues were consistent with the change trends of mRNA. The biological functions of AQPs were mainly concentrated in water transport, homeostasis maintenance, glycerol transport, and intracellular movement of sugar transporters. The high mRNA expression levels of AQP0/8/9 were significantly correlated with worse overall survival (OS), while those of AQP1/4/7 were correlated with better OS. AQP0/1/4/9 were prognostic-related factors, and AQP1/9 were independent prognostic factors. In general, this research has investigated the values of AQPs in ccRCC, which could become new survival markers for ccRCC targeted therapy.
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Affiliation(s)
- Mingrui Li
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Minxin He
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Fangshi Xu
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Yibing Guan
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Juanhua Tian
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Ziyan Wan
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Haibin Zhou
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Mei Gao
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Tie Chong
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
- * E-mail:
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Lin S, Xu H, Pang M, Zhou X, Pan Y, Zhang L, Guan X, Wang X, Lin B, Tian R, Chen K, Zhang X, Yang Z, Ji F, Huang Y, Wei W, Gong W, Ren J, Wang JM, Guo M, Huang J. CpG Site-Specific Methylation-Modulated Divergent Expression of PRSS3 Transcript Variants Facilitates Nongenetic Intratumor Heterogeneity in Human Hepatocellular Carcinoma. Front Oncol 2022; 12:831268. [PMID: 35480112 PMCID: PMC9035874 DOI: 10.3389/fonc.2022.831268] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/16/2022] [Indexed: 01/18/2023] Open
Abstract
BackgroundHepatocellular carcinoma (HCC) is one of the most lethal human tumors with extensive intratumor heterogeneity (ITH). Serine protease 3 (PRSS3) is an indispensable member of the trypsin family and has been implicated in the pathogenesis of several malignancies, including HCC. However, the paradoxical effects of PRSS3 on carcinogenesis due to an unclear molecular basis impede the utilization of its biomarker potential. We hereby explored the contribution of PRSS3 transcripts to tumor functional heterogeneity by systematically dissecting the expression of four known splice variants of PRSS3 (PRSS3-SVs, V1~V4) and their functional relevance to HCC.MethodsThe expression and DNA methylation of PRSS3 transcripts and their associated clinical relevance in HCC were analyzed using several publicly available datasets and validated using qPCR-based assays. Functional experiments were performed in gain- and loss-of-function cell models, in which PRSS3 transcript constructs were separately transfected after deleting PRSS3 expression by CRISPR/Cas9 editing.ResultsPRSS3 was aberrantly differentially expressed toward bipolarity from very low (PRSS3Low) to very high (PRSS3High) expression across HCC cell lines and tissues. This was attributable to the disruption of PRSS3-SVs, in which PRSS3-V2 and/or PRSS3-V1 were dominant transcripts leading to PRSS3 expression, whereas PRSS3-V3 and -V4 were rarely or minimally expressed. The expression of PRSS3-V2 or -V1 was inversely associated with site-specific CpG methylation at the PRSS3 promoter region that distinguished HCC cells and tissues phenotypically between hypermethylated low-expression (mPRSS3-SVLow) and hypomethylated high-expression (umPRSS3-SVHigh) groups. PRSS3-SVs displayed distinct functions from oncogenic PRSS3-V2 to tumor-suppressive PRSS3-V1, -V3 or PRSS3-V4 in HCC cells. Clinically, aberrant expression of PRSS3-SVs was translated into divergent relevance in patients with HCC, in which significant epigenetic downregulation of PRSS3-V2 was seen in early HCC and was associated with favorable patient outcome.ConclusionsThese results provide the first evidence for the transcriptional and functional characterization of PRSS3 transcripts in HCC. Aberrant expression of divergent PRSS3-SVs disrupted by site-specific CpG methylation may integrate the effects of oncogenic PRSS3-V2 and tumor-suppressive PRSS3-V1, resulting in the molecular diversity and functional plasticity of PRSS3 in HCC. Dysregulated expression of PRSS3-V2 by site-specific CpG methylation may have potential diagnostic value for patients with early HCC.
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Affiliation(s)
- Shuye Lin
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Hanli Xu
- College of Life Sciences & Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Mengdi Pang
- College of Life Sciences & Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Xiaomeng Zhou
- College of Life Sciences & Bioengineering, Beijing Jiaotong University, Beijing, China
- Department of Gastroenterology and Hepatology, Chinese People’s Liberation Army of China (PLA) General Hospital, Beijing, China
| | - Yuanming Pan
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Lishu Zhang
- College of Life Sciences & Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Xin Guan
- College of Life Sciences & Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Xiaoyue Wang
- College of Life Sciences & Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Bonan Lin
- College of Life Sciences & Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Rongmeng Tian
- College of Life Sciences & Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Keqiang Chen
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Xiaochen Zhang
- College of Life Sciences & Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Zijiang Yang
- College of Life Sciences & Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Fengmin Ji
- College of Life Sciences & Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Yingying Huang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wu Wei
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wanghua Gong
- Basic Research Program, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - Jianke Ren
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ji Ming Wang
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, Chinese People’s Liberation Army of China (PLA) General Hospital, Beijing, China
- *Correspondence: Jiaqiang Huang, ; Mingzhou Guo,
| | - Jiaqiang Huang
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
- College of Life Sciences & Bioengineering, Beijing Jiaotong University, Beijing, China
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
- *Correspondence: Jiaqiang Huang, ; Mingzhou Guo,
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Kim DW, Hong H, Kim JK. Systematic inference identifies a major source of heterogeneity in cell signaling dynamics: The rate-limiting step number. SCIENCE ADVANCES 2022; 8:eabl4598. [PMID: 35302852 PMCID: PMC8932658 DOI: 10.1126/sciadv.abl4598] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Identifying the sources of cell-to-cell variability in signaling dynamics is essential to understand drug response variability and develop effective therapeutics. However, it is challenging because not all signaling intermediate reactions can be experimentally measured simultaneously. This can be overcome by replacing them with a single random time delay, but the resulting process is non-Markovian, making it difficult to infer cell-to-cell heterogeneity in reaction rates and time delays. To address this, we developed an efficient and scalable moment-based Bayesian inference method (MBI) with a user-friendly computational package that infers cell-to-cell heterogeneity in the non-Markovian signaling process. We applied MBI to single-cell expression profiles from promoters responding to antibiotics and discovered a major source of cell-to-cell variability in antibiotic stress response: the number of rate-limiting steps in signaling cascades. This knowledge can help identify effective therapies that destroy all pathogenic or cancer cells, and the approach can be applied to precision medicine.
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Affiliation(s)
- Dae Wook Kim
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Hyukpyo Hong
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Jae Kyoung Kim
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Institute for Basic Science, Daejeon 34126, Republic of Korea
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Tsoi H, You CP, Leung MH, Man EPS, Khoo US. Targeting Ribosome Biogenesis to Combat Tamoxifen Resistance in ER+ve Breast Cancer. Cancers (Basel) 2022; 14:1251. [PMID: 35267559 PMCID: PMC8909264 DOI: 10.3390/cancers14051251] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/24/2022] [Accepted: 02/27/2022] [Indexed: 02/07/2023] Open
Abstract
Breast cancer is a heterogeneous disease. Around 70% of breast cancers are estrogen receptor-positive (ER+ve), with tamoxifen being most commonly used as an adjuvant treatment to prevent recurrence and metastasis. However, half of the patients will eventually develop tamoxifen resistance. The overexpression of c-MYC can drive the development of ER+ve breast cancer and confer tamoxifen resistance through multiple pathways. One key mechanism is to enhance ribosome biogenesis, synthesising mature ribosomes. The over-production of ribosomes sustains the demand for proteins necessary to maintain a high cell proliferation rate and combat apoptosis induced by therapeutic agents. c-MYC overexpression can induce the expression of eIF4E that favours the translation of structured mRNA to produce oncogenic factors that promote cell proliferation and confer tamoxifen resistance. Either non-phosphorylated or phosphorylated eIF4E can mediate such an effect. Since ribosomes play an essential role in c-MYC-mediated cancer development, suppressing ribosome biogenesis may help reduce aggressiveness and reverse tamoxifen resistance in breast cancer. CX-5461, CX-3543 and haemanthamine have been shown to repress ribosome biogenesis. Using these chemicals might help reverse tamoxifen resistance in ER+ve breast cancer, provided that c-MYC-mediated ribosome biogenesis is the crucial factor for tamoxifen resistance. To employ these ribosome biogenesis inhibitors to combat tamoxifen resistance in the future, identification of predictive markers will be necessary.
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Affiliation(s)
| | | | | | | | - Ui-Soon Khoo
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (H.T.); (C.-P.Y.); (M.-H.L.); (E.P.S.M.)
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Bono BS, Koziel Ly NK, Miller PA, Williams-Ikhenoba J, Dumiaty Y, Chee MJ. Spatial distribution of beta-klotho mRNA in the mouse hypothalamus, hippocampal region, subiculum, and amygdala. J Comp Neurol 2022; 530:1634-1657. [PMID: 35143049 DOI: 10.1002/cne.25306] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 01/05/2022] [Accepted: 01/20/2022] [Indexed: 11/10/2022]
Abstract
Beta-klotho (KLB) is a co-receptor required for endocrine fibroblast growth factor (FGF) 15/19 and FGF21 signaling in the brain. Klb is prominent within the hypothalamus, which is consistent with its metabolic functions, but diverse roles for Klb are now emerging. Central Klb expression is low but discrete and may govern FGF-targeted sites. However, given its low expression, it is unclear if Klb mRNA is more widespread. We performed in situ hybridization to label Klb mRNA to generate spatial maps capturing the distribution and level of Klb within the mouse hypothalamus, hippocampal region, subiculum, and amygdala. Semi-quantitative analysis revealed that Klb-labeled cells may express low, medium, or high levels of Klb mRNA. Hypothalamic Klb hybridization was heterogeneous and varied rostrocaudally within the same region. Most Klb-labeled cells were found in the lateral hypothalamic zone, but the periventricular hypothalamic region, including the suprachiasmatic nucleus, contained the greatest proportion of cells expressing medium or high Klb levels. We also found heterogeneous Klb hybridization in the amygdala and subiculum, where Klb was especially distinct within the central amygdalar nucleus and ventral subiculum, respectively. By contrast, Klb-labeled cells in the hippocampal region only expressed low levels of Klb and were typically found in the pyramidal layer of Ammon's horn or dentate gyrus. The Klb-labeled regions identified in this study are consistent with reported roles of Klb in metabolism, taste preference, and neuroprotection. However, additional identified sites, including within the hypothalamus and amygdala, may suggest novel roles for FGF15/19 or FGF21 signaling. The central expression of beta-klotho (Klb) is essential for the physiological actions of endocrine fibroblast growth factors. Klb mRNA was widely expressed throughout the hypothalamus, hippocampus, and amygdala. However, the level of Klb expression varied between cells and contributed to a distinctive pattern of distribution within each brain structure. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Bianca S Bono
- Department of Neuroscience, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Nikita K Koziel Ly
- Department of Neuroscience, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Persephone A Miller
- Department of Neuroscience, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | | | - Yasmina Dumiaty
- Department of Neuroscience, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Melissa J Chee
- Department of Neuroscience, Carleton University, Ottawa, ON, K1S 5B6, Canada
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Tureckova J, Kamenicka M, Kolenicova D, Filipi T, Hermanova Z, Kriska J, Meszarosova L, Pukajova B, Valihrach L, Androvic P, Zucha D, Chmelova M, Vargova L, Anderova M. Compromised Astrocyte Swelling/Volume Regulation in the Hippocampus of the Triple Transgenic Mouse Model of Alzheimer’s Disease. Front Aging Neurosci 2022; 13:783120. [PMID: 35153718 PMCID: PMC8829436 DOI: 10.3389/fnagi.2021.783120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, we aimed to disclose the impact of amyloid-β toxicity and tau pathology on astrocyte swelling, their volume recovery and extracellular space (ECS) diffusion parameters, namely volume fraction (α) and tortuosity (λ), in a triple transgenic mouse model of Alzheimer’s disease (3xTg-AD). Astrocyte volume changes, which reflect astrocyte ability to take up ions/neurotransmitters, were quantified during and after exposure to hypo-osmotic stress, or hyperkalemia in acute hippocampal slices, and were correlated with alterations in ECS diffusion parameters. Astrocyte volume and ECS diffusion parameters were monitored during physiological aging (controls) and during AD progression in 3-, 9-, 12- and 18-month-old mice. In the hippocampus of controls α gradually declined with age, while it remained unaffected in 3xTg-AD mice during the entire time course. Moreover, age-related increases in λ occurred much earlier in 3xTg-AD animals than in controls. In 3xTg-AD mice changes in α induced by hypo-osmotic stress or hyperkalemia were comparable to those observed in controls, however, AD progression affected α recovery following exposure to both. Compared to controls, a smaller astrocyte swelling was detected in 3xTg-AD mice only during hyperkalemia. Since we observed a large variance in astrocyte swelling/volume regulation, we divided them into high- (HRA) and low-responding astrocytes (LRA). In response to hyperkalemia, the incidence of LRA was higher in 3xTg-AD mice than in controls, which may also reflect compromised K+ and neurotransmitter uptake. Furthermore, we performed single-cell RT-qPCR to identify possible age-related alterations in astrocytic gene expression profiles. Already in 3-month-old 3xTg-AD mice, we detected a downregulation of genes affecting the ion/neurotransmitter uptake and cell volume regulation, namely genes of glutamate transporters, α2β2 subunit of Na+/K+-ATPase, connexin 30 or Kir4.1 channel. In conclusion, the aged hippocampus of 3xTg-AD mice displays an enlarged ECS volume fraction and an increased number of obstacles, which emerge earlier than in physiological aging. Both these changes may strongly affect intercellular communication and influence astrocyte ionic/neurotransmitter uptake, which becomes impaired during aging and this phenomenon is manifested earlier in 3xTg-AD mice. The increased incidence of astrocytes with limited ability to take up ions/neurotransmitters may further add to a cytotoxic environment.
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Affiliation(s)
- Jana Tureckova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
- *Correspondence: Jana Tureckova,
| | - Monika Kamenicka
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
- Second Faculty of Medicine, Charles University, Prague, Czechia
| | - Denisa Kolenicova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
- Second Faculty of Medicine, Charles University, Prague, Czechia
| | - Tereza Filipi
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
- Second Faculty of Medicine, Charles University, Prague, Czechia
| | - Zuzana Hermanova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
- Second Faculty of Medicine, Charles University, Prague, Czechia
| | - Jan Kriska
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
| | - Lenka Meszarosova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
| | - Barbora Pukajova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czechia
| | - Peter Androvic
- Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czechia
| | - Daniel Zucha
- Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czechia
- Faculty of Chemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Martina Chmelova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
- Second Faculty of Medicine, Charles University, Prague, Czechia
| | - Lydia Vargova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
- Second Faculty of Medicine, Charles University, Prague, Czechia
| | - Miroslava Anderova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
- Second Faculty of Medicine, Charles University, Prague, Czechia
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Herbert CJ, Labarre-Mariotte S, Cornu D, Sophie C, Panozzo C, Michel T, Dujardin G, Bonnefoy N. Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria. Nucleic Acids Res 2021; 49:11145-11166. [PMID: 34634819 PMCID: PMC8565316 DOI: 10.1093/nar/gkab789] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/24/2021] [Accepted: 10/05/2021] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial mRNAs encode key subunits of the oxidative phosphorylation complexes that produce energy for the cell. In Saccharomyces cerevisiae, mitochondrial translation is under the control of translational activators, specific to each mRNA. In Schizosaccharomyces pombe, which more closely resembles the human system by its mitochondrial DNA structure and physiology, most translational activators appear to be either lacking, or recruited for post-translational functions. By combining bioinformatics, genetic and biochemical approaches we identified two interacting factors, Cbp7 and Cbp8, controlling Cytb production in S. pombe. We show that their absence affects cytb mRNA stability and impairs the detection of the Cytb protein. We further identified two classes of Cbp7/Cbp8 partners and showed that they modulated Cytb or Cox1 synthesis. First, two isoforms of bS1m, a protein of the small mitoribosomal subunit, that appear mutually exclusive and confer translational specificity. Second, a complex of four proteins dedicated to Cox1 synthesis, which includes an RNA helicase that interacts with the mitochondrial ribosome. Our results suggest that S. pombe contains, in addition to complexes of translational activators, a heterogeneous population of mitochondrial ribosomes that could specifically modulate translation depending on the mRNA translated, in order to optimally balance the production of different respiratory complex subunits.
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Affiliation(s)
- Christopher J Herbert
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Sylvie Labarre-Mariotte
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - David Cornu
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Cyrielle Sophie
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Cristina Panozzo
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Thomas Michel
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Geneviève Dujardin
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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Translational regulation in pathogenic and beneficial plant-microbe interactions. Biochem J 2021; 478:2775-2788. [PMID: 34297042 DOI: 10.1042/bcj20210066] [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: 05/12/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/17/2022]
Abstract
Plants are surrounded by a vast diversity of microorganisms. Limiting pathogenic microorganisms is crucial for plant survival. On the other hand, the interaction of plants with beneficial microorganisms promotes their growth or allows them to overcome nutrient deficiencies. Balancing the number and nature of these interactions is crucial for plant growth and development, and thus, for crop productivity in agriculture. Plants use sophisticated mechanisms to recognize pathogenic and beneficial microorganisms and genetic programs related to immunity or symbiosis. Although most research has focused on characterizing changes in the transcriptome during plant-microbe interactions, the application of techniques such as Translating Ribosome Affinity Purification (TRAP) and Ribosome profiling allowed examining the dynamic association of RNAs to the translational machinery, highlighting the importance of the translational level of control of gene expression in both pathogenic and beneficial interactions. These studies revealed that the transcriptional and the translational responses are not always correlated, and that translational control operates at cell-specific level. In addition, translational control is governed by cis-elements present in the 5'mRNA leader of regulated mRNAs, e.g. upstream open reading frames (uORFs) and sequence-specific motifs. In this review, we summarize and discuss the recent advances made in the field of translational control during pathogenic and beneficial plant-microbe interactions.
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Mantri S, Wu SM, Goodyer WR. Molecular Profiling of the Cardiac Conduction System: the Dawn of a New Era. Curr Cardiol Rep 2021; 23:103. [PMID: 34196831 DOI: 10.1007/s11886-021-01536-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/17/2021] [Indexed: 11/28/2022]
Abstract
PURPOSE OF REVIEW Recent technological advances have led to an increased ability to define the gene expression profile of the cardiac conduction system (CCS). Here, we review the most salient studies to emerge in recent years and discuss existing gaps in our knowledge as well as future areas of investigation. RECENT FINDINGS Molecular profiling of the CCS spans several decades. However, the advent of high-throughput sequencing strategies has allowed for the discovery of unique transcriptional programs of the many diverse CCS cell types. The CCS, a diverse structure with significant inter- and intra-component cellular heterogeneity, is essential to the normal function of the heart. Progress in transcriptomic profiling has improved the resolution and depth of characterization of these unique and clinically relevant CCS cell types. Future studies leveraging this big data will play a crucial role in improving our understanding of CCS development and function as well as translating these findings into tangible translational tools for the improved detection, prevention, and treatment of cardiac arrhythmias.
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Affiliation(s)
- Sruthi Mantri
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sean M Wu
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Division of Pediatric Cardiology, Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA.,Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - William R Goodyer
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Division of Pediatric Cardiology, Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA. .,Division of Pediatric Cardiology, Electrophysiology, Department of Pediatrics, Lucile Packard Children's Hospital, Stanford University School of Medicine, Room G1105 Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, 94305, USA.
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48
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Saravanaperumal SA, Pallotti S, Pediconi D, Renieri C, La Terza A. Exon-1 skipping and intron-1 retaining by alternative splicing of the c-KIT gene encodes a novel splice variant in the skin of Merino sheep (Ovis aries). Mol Biol Rep 2021; 48:4987-4994. [PMID: 34148208 DOI: 10.1007/s11033-021-06486-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/08/2021] [Indexed: 12/01/2022]
Abstract
c-KIT, a type III receptor protein tyrosine kinase, plays an essential role in melanocyte development, migration, and survival. Mutations within the c-KIT gene are previously shown to cause the white coat color phenotypes in pigs, mice, goats, and humans. However, up so far, the splicing isoform(s), genomic architecture of c-KIT have not been characterized well in merino sheep. Reverse transcriptase (RT)-PCR analysis with molecular prediction identified two basic splice variants: Transcript Variant-1, 2 for 12 bp insertion coding sequences (CDS) corresponding to the four amino acids 'GNSK', respectively. Using 5' RACE, here we report for the first time a novel c-KIT 'Transcript Variant-3' from the skin of merino sheep by comparative genome analyses at exon(1)-intron(1)-exon(2) boundaries. In contrast, a single product of 795 bp was characterized by 3' RACE. We also demonstrated that the c-KIT gene expression at the transcript level is not mediated via an intron-9 splicing event. Overall, beyond what was observed in other mammals, our data provide novel insights into the molecular structure of the c-KIT gene in sheep.
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Affiliation(s)
- Siva Arumugam Saravanaperumal
- Department of Physiology and Biomedical Engineering, Mayo Clinic, 200 First Street SW Guggenheim 10-21C, Rochester, MN, 55905, USA.
| | - Stefano Pallotti
- School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy.
| | - Dario Pediconi
- School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Carlo Renieri
- School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Antonietta La Terza
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy.
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49
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Gabriel CH, Del Olmo M, Zehtabian A, Jäger M, Reischl S, van Dijk H, Ulbricht C, Rakhymzhan A, Korte T, Koller B, Grudziecki A, Maier B, Herrmann A, Niesner R, Zemojtel T, Ewers H, Granada AE, Herzel H, Kramer A. Live-cell imaging of circadian clock protein dynamics in CRISPR-generated knock-in cells. Nat Commun 2021; 12:3796. [PMID: 34145278 PMCID: PMC8213786 DOI: 10.1038/s41467-021-24086-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
The cell biology of circadian clocks is still in its infancy. Here, we describe an efficient strategy for generating knock-in reporter cell lines using CRISPR technology that is particularly useful for genes expressed transiently or at low levels, such as those coding for circadian clock proteins. We generated single and double knock-in cells with endogenously expressed PER2 and CRY1 fused to fluorescent proteins allowing us to simultaneously monitor the dynamics of CRY1 and PER2 proteins in live single cells. Both proteins are highly rhythmic in the nucleus of human cells with PER2 showing a much higher amplitude than CRY1. Surprisingly, CRY1 protein is nuclear at all circadian times indicating the absence of circadian gating of nuclear import. Furthermore, in the nucleus of individual cells CRY1 abundance rhythms are phase-delayed (~5 hours), and CRY1 levels are much higher (>5 times) compared to PER2 questioning the current model of the circadian oscillator.
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Affiliation(s)
- Christian H Gabriel
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Marta Del Olmo
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Amin Zehtabian
- Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Marten Jäger
- Berlin Institute of Health (BIH) Core Genomics Facility, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Silke Reischl
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Hannah van Dijk
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Carolin Ulbricht
- Immune Dynamics, Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Asylkhan Rakhymzhan
- Biophysical Analytics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Thomas Korte
- Molecular Biophysics, Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Barbara Koller
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Astrid Grudziecki
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Bert Maier
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Andreas Herrmann
- Molecular Biophysics, Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Raluca Niesner
- Biophysical Analytics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
- Dynamic and Functional in vivo Imaging, Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Tomasz Zemojtel
- Berlin Institute of Health (BIH) Core Genomics Facility, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Helge Ewers
- Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Adrián E Granada
- Charité Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Achim Kramer
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
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50
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Ho JJD, Man JHS, Schatz JH, Marsden PA. Translational remodeling by RNA-binding proteins and noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1647. [PMID: 33694288 DOI: 10.1002/wrna.1647] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Responsible for generating the proteome that controls phenotype, translation is the ultimate convergence point for myriad upstream signals that influence gene expression. System-wide adaptive translational reprogramming has recently emerged as a pillar of cellular adaptation. As classic regulators of mRNA stability and translation efficiency, foundational studies established the concept of collaboration and competition between RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) on individual mRNAs. Fresh conceptual innovations now highlight stress-activated, evolutionarily conserved RBP networks and ncRNAs that increase the translation efficiency of populations of transcripts encoding proteins that participate in a common cellular process. The discovery of post-transcriptional functions for long noncoding RNAs (lncRNAs) was particularly intriguing given their cell-type-specificity and historical definition as nuclear-functioning epigenetic regulators. The convergence of RBPs, lncRNAs, and microRNAs on functionally related mRNAs to enable adaptive protein synthesis is a newer biological paradigm that highlights their role as "translatome (protein output) remodelers" and reinvigorates the paradigm of "RNA operons." Together, these concepts modernize our understanding of cellular stress adaptation and strategies for therapeutic development. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- J J David Ho
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Jeffrey H S Man
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Respirology, University Health Network, Latner Thoracic Research Laboratories, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Philip A Marsden
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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