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Tiensuu H, Haapalainen AM, Tissarinen P, Pasanen A, Hallman M, Rämet M. MicroRNA expression profile in the basal plate of human placenta associates with spontaneous preterm birth. Placenta 2024; 155:60-69. [PMID: 39137705 DOI: 10.1016/j.placenta.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 07/24/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024]
Abstract
INTRODUCTION MicroRNAs regulate post-transcriptional gene expression. Their expression has been linked to many pregnancy complications, including preterm birth. Placental microRNA levels differ between preterm and term pregnancies. Not much is known about the targets that are affected by these differences in microRNA expression. We investigated associations between microRNA expression levels in the basal plate of the placenta and their targets and the onset of preterm birth. METHODS MiRNAomes of spontaneous preterm (n = 6) and term (n = 6) placentas were characterized using RNA sequencing. MicroRNA target and enrichment analyses were performed to explore potential gene targets and pathways. Selected findings were validated using qPCR (n = 41). MicroRNA mimic transfection and luciferase reporter assays were performed to test if certain microRNAs regulate their predicted target, SLIT2, the expression of which has been shown to associate with preterm birth. RESULTS We identified 39 differentially expressed microRNAs from the preterm placentas compared to term. Many downregulated microRNAs were from the placenta-specific C14MC microRNA cluster. Target gene and pathway analyses showed that microRNAs that associate with preterm birth target transcription related factors and genes linked with protein binding and invasive pathways. Eight of the identified microRNAs putatively target SLIT2, including miR-766-3p and miR-489-3p. Luciferase reporter assay suggested that these microRNAs regulate SLIT2 expression. DISCUSSION MicroRNA expression changes are associated with spontaneous preterm birth. A group of microRNAs targeting the same gene or genes belonging to the same pathway can have a significant effect on the critical processes maintaining pregnancy and placental functions.
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Affiliation(s)
- Heli Tiensuu
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Aapistie 5A, 90220, Oulu, Finland.
| | - Antti M Haapalainen
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Aapistie 5A, 90220, Oulu, Finland
| | - Pinja Tissarinen
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Aapistie 5A, 90220, Oulu, Finland
| | - Anu Pasanen
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Aapistie 5A, 90220, Oulu, Finland
| | - Mikko Hallman
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Aapistie 5A, 90220, Oulu, Finland
| | - Mika Rämet
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Aapistie 5A, 90220, Oulu, Finland; Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520, Tampere, Finland
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Wipplinger M, Mink S, Bublitz M, Gassner C. Regulation of the Lewis Blood Group Antigen Expression: A Literature Review Supplemented with Computational Analysis. Transfus Med Hemother 2024; 51:225-236. [PMID: 39135855 PMCID: PMC11318966 DOI: 10.1159/000538863] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/11/2024] [Indexed: 08/15/2024] Open
Abstract
Background The Lewis (Le) blood group system, unlike most other blood groups, is not defined by antigens produced internally to the erythrocytes and their precursors but rather by glycan antigens adsorbed on to the erythrocyte membrane from the plasma. These oligosaccharides are synthesized by the two fucosyltransferases FUT2 and FUT3 mainly in epithelial cells of the digestive tract and transferred to the plasma. At their place of synthesis, some Lewis blood group carbohydrate antigen variants also seem to be involved in various gastrointestinal malignancies. However, relatively little is known about the transcriptional regulation of FUT2 and FUT3. Summary To address this question, we screened existing literature and additionally used in silico prediction tools to identify novel candidate regulators for FUT2 and FUT3 and combine these findings with already known data on their regulation. With this approach, we were able to describe a variety of transcription factors, RNA binding proteins and microRNAs, which increase FUT2 and FUT3 transcription and translation upon interaction. Key Messages Understanding the regulation of FUT2 and FUT3 is crucial to fully understand the blood group system Lewis (ISBT 007 LE) phenotypes, to shed light on the role of the different Lewis antigens in various pathologies, and to identify potential new diagnostic targets for these diseases.
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Affiliation(s)
- Martin Wipplinger
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Sylvia Mink
- Central Medical Laboratories, Feldkirch, Austria
- Medical-Scientific Faculty, Private University of the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Maike Bublitz
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Christoph Gassner
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
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Chang J, Liu A, Zhang J, Chu L, Hou X, Huang X, Xing Q, Bao Z. Transcriptomic analysis reveals PC4's participation in thermotolerance of scallop Argopecten irradians irradians by regulating myocardial bioelectric activity. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101295. [PMID: 39053238 DOI: 10.1016/j.cbd.2024.101295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/02/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
Rising ocean temperatures due to global warming pose a significant threat to the bay scallop aquaculture industry. Understanding the mechanisms of thermotolerance in bay scallops is crucial for developing thermotolerant breeds. Our prior research identified Arg0230340.1, part of the positive cofactor 4 (PC4) family, as a key gene associated with the thermotolerance index Arrhenius break temperature (ABT) in bay scallops. Further validation through RNA interference (RNAi) reinforced PC4's role in thermotolerance, offering a solid basis for investigating thermal response mechanisms in these scallops. In this study, we performed a comparative transcriptomic analysis on the temperature-sensitive hearts of bay scallops after siRNA-mediated RNAi targeting Arg0230340.1, to delve into the detailed molecular mechanism of PC4's participation in thermotolerance regulation. The analysis revealed that silencing Arg0230340.1 significantly reduced the expression of mitochondrial tRNA and rRNA, potentially affecting mitochondrial function and the heart's blood supply capacity. Conversely, the up-regulation of genes involved in energy metabolism, RNA polymerase II (RNAPII)-mediated basal transcription, and aminoacyl-tRNA synthesis pathways points to an intrinsic protective response, providing energy and substrates for damage repair and maintenance of essential functions under stress. GO and KEGG enrichment analyses indicated that the up-regulated genes were primarily associated with energy metabolism and spliceosome pathways, likely contributing to myocardial remodeling post-Arg0230340.1 knockdown. Down-regulated genes were enriched in ion channel pathways, particularly those for Na+, K+, and Ca2+ channels, whose dysfunction could disrupt normal myocardial bioelectric activity. The impaired cardiac performance resulting from RNAi targeting Arg0230340.1 reduced the cardiac workload in scallop hearts, thus affecting myocardial oxygen consumption and thermotolerance. We propose a hypothetical mechanism where PC4 down-regulation impairs cardiac bioelectric activity, leading to decreased thermotolerance in bay scallops, providing theoretical guidance for breeding thermotolerant scallop varieties and developing strategies for sustainable aquaculture in the face of long-term environmental changes.
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Affiliation(s)
- Jiaxi Chang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Ancheng Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Junhao Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Longfei Chu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xiujiang Hou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China.
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
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Qi Y, Zhu W, Mo K, Jiang H. CRISPR/Cas9-based genome-wide screening for metastasis ability identifies FCGR1A regulating the metastatic process of ovarian cancer by targeting LSP1. J Cancer Res Clin Oncol 2024; 150:306. [PMID: 38879666 PMCID: PMC11180010 DOI: 10.1007/s00432-024-05837-9] [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: 05/04/2024] [Accepted: 06/04/2024] [Indexed: 06/19/2024]
Abstract
BACKGROUND Metastasis is a main cause of death from ovarian cancer (OC). Identifying key markers involved in OC metastasis can aid in the effective detection of early postoperative metastasis. However, the role of FCGR1A in OC metastasis has yet to be fully established. A genome-wide CRISPR/Cas9-based screening system was used to identify regulatory factors involved in metastasis. METHODS The expression of FCGR1A and LSP1 in ovarian cancer cell lines was examined by quantitative real-time polymerase chain reaction (qRT‒PCR). The functions of FCGR1A and LSP1 in OC cell migration, invasion and proliferation were determined using wound healing, Transwell invasion and CKK-8 assays. A transcription-activated library was used to identify the potential downstream genes of FCGR1A. FCGR1A expression was detected by immunohistochemistry and the immunity risk score (IRS) scores were calculated. RESULTS FCGR1A was upregulated in OC cells compared with normal ovarian cells. Downregulation of FCGR1A inhibited metastasis, proliferation and epithelial-mesenchymal transition (EMT) progression in OC cells in vitro and intraperitoneal metastasis in vivo. Moreover, downregulation of FCGR1A was accompanied by decreased LSP1 expression. Overexpression of LSP1 partially reversed the tumor suppressive effect of FCGR1A downregulation. Higher FCGR1A expression was related to metastasis, higher grade, higher stage, and lymph node metastasis in OC. Survival analysis suggested that the group with higher FCGR1A expression had a lower tumor-free survival rate and a lower overall survival rate than did the group with low FCGR1A expression. CONCLUSIONS FCGR1A enhances OC metastasis by regulating LSP1, and FCGR1A is associated with poor prognosis, suggesting that FCGR1A is a potential predictive factor for detecting early postoperative metastasis.
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Affiliation(s)
- Yingying Qi
- Department of Gynecology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Weiyan Zhu
- Department of Obstetrics and Gynecology, The Sixth Affiliated Hospital of Guangzhou Medical University, QingYuan, China
| | - Kexin Mo
- Department of Gynecology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hui Jiang
- Department of Gynecology and Obstetrics, Guangdong Second Hospital of Traditional Chinese Medicine, Guangzhou, China.
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Liu L, Yahaya BS, Li J, Wu F. Enigmatic role of auxin response factors in plant growth and stress tolerance. FRONTIERS IN PLANT SCIENCE 2024; 15:1398818. [PMID: 38903418 PMCID: PMC11188990 DOI: 10.3389/fpls.2024.1398818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.
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Affiliation(s)
- Ling Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Baba Salifu Yahaya
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Jing Li
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
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Lu Z, Xu L, Wang X. BIT: Bayesian Identification of Transcriptional Regulators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.02.597061. [PMID: 38895220 PMCID: PMC11185535 DOI: 10.1101/2024.06.02.597061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
BIT is a novel Bayesian hierarchical model capable of predicting transcriptional regulators (TRs) from the input of user-provided epigenomic regions. TRs are critical molecules in transcriptional regulation. Many diseases and cancers are linked to the dysfunction of TRs. Knowing TRs in certain biological process can help find new biomarkers or therapeutic targets. Thus, BIT formulates a novel Bayesian hierarchical model with the Pólya-gamma data augmentation strategy. Based on collected ChIP-seq datasets, BIT can identify TRs responsible for the genome-wide binding pattern within the user-provided epigenomic regions. BIT has been validated by using a simulation study and three applications.
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Affiliation(s)
- Zeyu Lu
- Department of Statistics and Data science, Moody School of Graduate and Advanced Studies, Southern Methodist University, Dallas, TX, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xinlei Wang
- Department of Mathematics, University of Texas at Arlington, Arlington, TX 76019, USA
- Center for Data Science Research and Education, College of Science, University of Texas at Arlington, Arlington, TX 76019, USA
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Rey F, Esposito L, Maghraby E, Mauri A, Berardo C, Bonaventura E, Tonduti D, Carelli S, Cereda C. Role of epigenetics and alterations in RNA metabolism in leukodystrophies. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1854. [PMID: 38831585 DOI: 10.1002/wrna.1854] [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: 11/30/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 06/05/2024]
Abstract
Leukodystrophies are a class of rare heterogeneous disorders which affect the white matter of the brain, ultimately leading to a disruption in brain development and a damaging effect on cognitive, motor and social-communicative development. These disorders present a great clinical heterogeneity, along with a phenotypic overlap and this could be partially due to contributions from environmental stimuli. It is in this context that there is a great need to investigate what other factors may contribute to both disease insurgence and phenotypical heterogeneity, and novel evidence are raising the attention toward the study of epigenetics and transcription mechanisms that can influence the disease phenotype beyond genetics. Modulation in the epigenetics machinery including histone modifications, DNA methylation and non-coding RNAs dysregulation, could be crucial players in the development of these disorders, and moreover an aberrant RNA maturation process has been linked to leukodystrophies. Here, we provide an overview of these mechanisms hoping to supply a closer step toward the analysis of leukodystrophies not only as genetically determined but also with an added level of complexity where epigenetic dysregulation is of key relevance. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNA RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Federica Rey
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Letizia Esposito
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Erika Maghraby
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
- Department of Biology and Biotechnology "L. Spallanzani" (DBB), University of Pavia, Pavia, Italy
| | - Alessia Mauri
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Clarissa Berardo
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Eleonora Bonaventura
- Unit of Pediatric Neurology, COALA Center for Diagnosis and Treatment of Leukodystrophies, V. Buzzi Children's Hospital, Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Davide Tonduti
- Unit of Pediatric Neurology, COALA Center for Diagnosis and Treatment of Leukodystrophies, V. Buzzi Children's Hospital, Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Stephana Carelli
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
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Tjärnberg A, Beheler-Amass M, Jackson CA, Christiaen LA, Gresham D, Bonneau R. Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference. Genome Biol 2024; 25:24. [PMID: 38238840 PMCID: PMC10797903 DOI: 10.1186/s13059-023-03134-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 11/30/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Modeling of gene regulatory networks (GRNs) is limited due to a lack of direct measurements of genome-wide transcription factor activity (TFA) making it difficult to separate covariance and regulatory interactions. Inference of regulatory interactions and TFA requires aggregation of complementary evidence. Estimating TFA explicitly is problematic as it disconnects GRN inference and TFA estimation and is unable to account for, for example, contextual transcription factor-transcription factor interactions, and other higher order features. Deep-learning offers a potential solution, as it can model complex interactions and higher-order latent features, although does not provide interpretable models and latent features. RESULTS We propose a novel autoencoder-based framework, StrUcture Primed Inference of Regulation using latent Factor ACTivity (SupirFactor) for modeling, and a metric, explained relative variance (ERV), for interpretation of GRNs. We evaluate SupirFactor with ERV in a wide set of contexts. Compared to current state-of-the-art GRN inference methods, SupirFactor performs favorably. We evaluate latent feature activity as an estimate of TFA and biological function in S. cerevisiae as well as in peripheral blood mononuclear cells (PBMC). CONCLUSION Here we present a framework for structure-primed inference and interpretation of GRNs, SupirFactor, demonstrating interpretability using ERV in multiple biological and experimental settings. SupirFactor enables TFA estimation and pathway analysis using latent factor activity, demonstrated here on two large-scale single-cell datasets, modeling S. cerevisiae and PBMC. We find that the SupirFactor model facilitates biological analysis acquiring novel functional and regulatory insight.
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Affiliation(s)
- Andreas Tjärnberg
- Center for Developmental Genetics, New York University, New York, NY, 10003, USA.
- Center For Genomics and Systems Biology, NYU, New York, NY, 10008, USA.
- Department of Biology, NYU, New York, NY, 10008, USA.
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10010, USA.
- Department of Neuro-Science, University of Wisconsin-Madison - Waisman Center, Madison, USA.
| | - Maggie Beheler-Amass
- Center For Genomics and Systems Biology, NYU, New York, NY, 10008, USA
- Department of Biology, NYU, New York, NY, 10008, USA
| | - Christopher A Jackson
- Center For Genomics and Systems Biology, NYU, New York, NY, 10008, USA
- Department of Biology, NYU, New York, NY, 10008, USA
| | - Lionel A Christiaen
- Center for Developmental Genetics, New York University, New York, NY, 10003, USA
- Department of Biology, NYU, New York, NY, 10008, USA
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- Department of Heart Disease, Haukeland University Hospital, Bergen, Norway
| | - David Gresham
- Center For Genomics and Systems Biology, NYU, New York, NY, 10008, USA
- Department of Biology, NYU, New York, NY, 10008, USA
| | - Richard Bonneau
- Center For Genomics and Systems Biology, NYU, New York, NY, 10008, USA.
- Department of Biology, NYU, New York, NY, 10008, USA.
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY, 10010, USA.
- Courant Institute of Mathematical Sciences, Computer Science Department, New York University, New York, NY, 10003, USA.
- Center For Data Science, NYU, New York, NY, 10008, USA.
- Prescient Design, a Genentech accelerator, New York, NY, 10010, USA.
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O'Brien MJ, Gurdziel K, Ansari A. Global Run-On sequencing to measure nascent transcription in Saccharomyces cerevisiae. Methods 2023; 217:18-26. [PMID: 37356780 PMCID: PMC10529987 DOI: 10.1016/j.ymeth.2023.06.009] [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: 01/27/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023] Open
Abstract
Global Run-On sequencing is a reliable and widely used approach for monitoring nascent transcription on a genomewide scale. The assay has been successfully used for studying global transcription in humans, plants, worms, flies, and fission yeast. Here we describe a GRO-seq protocol for studying transcription in budding yeast, Saccharomyces cerevisiae. Briefly, the technique involves permeabilization of actively growing yeast cells, allowing transcription to proceed in permeabilized cells in the presence of brominated UTP, affinity purification of bromo-UMP incorporated nascent transcripts followed by cDNA library construction, deep sequencing, and mapping against the reference genome. The approach maps the position of transcriptionally active RNA polymerase on a genomewide basis. In addition to identifying the complete set of transcriptionally active genes in a cell under a given set of conditions, the method can be used to determine elongation rate, termination defect and promoter directionality at the genomewide level. The approach is especially useful in identifying short-lived unstable transcripts that are rapidly degraded even before they leave the nucleus.
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Affiliation(s)
- Michael J O'Brien
- Department of Biological Science, Wayne State University, Detroit, MI 48202, USA
| | | | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI 48202, USA.
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Marques-Ramos A, Cervantes R. Expression of mTOR in normal and pathological conditions. Mol Cancer 2023; 22:112. [PMID: 37454139 PMCID: PMC10349476 DOI: 10.1186/s12943-023-01820-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/08/2023] [Indexed: 07/18/2023] Open
Abstract
The mechanistic/mammalian target of rapamycin (mTOR), a protein discovered in 1991, integrates a complex pathway with a key role in maintaining cellular homeostasis. By comprising two functionally distinct complexes, mTOR complex 1 (mTORC1) and mTORC2, it is a central cellular hub that integrates intra- and extracellular signals of energy, nutrient, and hormone availability, modulating the molecular responses to acquire a homeostatic state through the regulation of anabolic and catabolic processes. Accordingly, dysregulation of mTOR pathway has been implicated in a variety of human diseases. While major advances have been made regarding the regulators and effectors of mTOR signaling pathway, insights into the regulation of mTOR gene expression are beginning to emerge. Here, we present the current available data regarding the mTOR expression regulation at the level of transcription, translation and mRNA stability and systematize the current knowledge about the fluctuations of mTOR expression observed in several diseases, both cancerous and non-cancerous. In addition, we discuss whether mTOR expression changes can be used as a biomarker for diagnosis, disease progression, prognosis and/or response to therapeutics. We believe that our study will contribute for the implementation of new disease biomarkers based on mTOR as it gives an exhaustive perspective about the regulation of mTOR gene expression in both normal and pathological conditions.
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Affiliation(s)
- A Marques-Ramos
- H&TRC-Health & Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal.
| | - R Cervantes
- H&TRC-Health & Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
- Public Health Research Centre, NOVA National School of Public Health, Universidade Nova de Lisboa, Lisbon, Portugal
- Comprehensive Health Research Center (CHRC), Lisbon, Portugal
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Ranjitkar S, Shiri M, Sun J, Tian X. Intergenic transcription in in vivo developed bovine oocytes and pre-implantation embryos. RESEARCH SQUARE 2023:rs.3.rs-2934322. [PMID: 37293046 PMCID: PMC10246250 DOI: 10.21203/rs.3.rs-2934322/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background Intergenic transcription, either failure to terminate at the transcription end site (TES), or transcription initiation at other intergenic regions, is present in cultured cells and enhanced in the presence of stressors such as viral infection. Transcription termination failure has not been characterized in natural biological samples such as pre-implantation embryos which express more than 10,000 genes and undergo drastic changes in DNA methylation. Results Using Automatic Readthrough Transcription Detection (ARTDeco) and data of in vivo developed bovine oocytes and embryos, we found abundant intergenic transcripts that we termed as read-outs (transcribed from 5 to 15 kb after TES) and read-ins (transcribed 1 kb up-stream of reference genes, extending up to 15 kb up-stream). Read-throughs (continued transcription from TES of expressed reference genes, 4-15 kb in length), however, were much fewer. For example, the numbers of read-outs and read-ins ranged from 3,084 to 6,565 or 33.36-66.67% of expressed reference genes at different stages of embryo development. The less copious read-throughs were at an average of 10% and significantly correlated with reference gene expression (P < 0.05). Interestingly, intergenic transcription did not seem to be random because many intergenic transcripts (1,504 read-outs, 1,045 read-ins, and 1,021 read-throughs) were associated with common reference genes across all stages of pre-implantation development. Their expression also seemed to be regulated by developmental stages because many were differentially expressed (log2 fold change ≥ 2, P < 0.05). Additionally, while gradual but un-patterned decreases in DNA methylation densities 10 kb both up- and down-stream of the intergenic transcribed regions were observed, the correlation between intergenic transcription and DNA methylation was insignificant. Finally, transcription factor binding motifs and polyadenylation signals were found in 27.2% and 12.15% of intergenic transcripts, respectively, suggesting considerable novel transcription initiation and RNA processing. Conclusion In summary, in vivo developed oocytes and pre-implantation embryos express large numbers of intergenic transcripts, which are not related to the overall DNA methylation profiles either up- or down-stream.
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Casamassimi A, Ciccodicola A, Rienzo M. Transcriptional Regulation and Its Misregulation in Human Diseases. Int J Mol Sci 2023; 24:ijms24108640. [PMID: 37239985 DOI: 10.3390/ijms24108640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Transcriptional regulation is a critical biological process that allows the cell or an organism to respond to a variety of intra- and extracellular signals, to define cell identity during development, to maintain it throughout its lifetime, and to coordinate cellular activity [...].
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Affiliation(s)
- Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 80138 Naples, Italy
| | - Alfredo Ciccodicola
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", CNR, Via P. Castellino 111, 80131 Naples, Italy
- Department of Science and Technology, University of Naples "Parthenope", 80143 Naples, Italy
| | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
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Zhang G, Xu X, Zhu L, Li S, Chen R, Lv N, Li Z, Wang J, Li Q, Zhou W, Yang P, Liu J. A Novel Molecular Classification Method for Glioblastoma Based on Tumor Cell Differentiation Trajectories. Stem Cells Int 2023; 2023:2826815. [PMID: 37964983 PMCID: PMC10643041 DOI: 10.1155/2023/2826815] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/29/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2023] Open
Abstract
The latest 2021 WHO classification redefines glioblastoma (GBM) as the hierarchical reporting standard by eliminating glioblastoma, IDH-mutant and only retaining the tumor entity of "glioblastoma, IDH-wild type." Knowing that subclassification of tumors based on molecular features is supposed to facilitate the therapeutic choice and increase the response rate in cancer patients, it is necessary to carry out molecular classification of the newly defined GBM. Although differentiation trajectory inference based on single-cell sequencing (scRNA-seq) data holds great promise for identifying cell heterogeneity, it has not been used in the study of GBM molecular classification. Single-cell transcriptome sequencing data from 10 GBM samples were used to identify molecular classification based on differentiation trajectories. The expressions of identified features were validated by public bulk RNA-sequencing data. Clinical feasibility of the classification system was examined in tissue samples by immunohistochemical (IHC) staining and immunofluorescence, and their clinical significance was investigated in public cohorts and clinical samples with complete clinical follow-up information. By analyzing scRNA-seq data of 10 GBM samples, four differentiation trajectories from the glioblastoma stem cell-like (GSCL) cluster were identified, based on which malignant cells were classified into five characteristic subclusters. Each cluster exhibited different potential drug sensitivities, pathways, functions, and transcriptional modules. The classification model was further examined in TCGA and CGGA datasets. According to the different abundance of five characteristic cell clusters, the patients were classified into five groups which we named Ac-G, Class-G, Neo-G, Opc-G, and Undiff-G groups. It was found that the Undiff-G group exhibited the worst overall survival (OS) in both TCGA and CGGA cohorts. In addition, the classification model was verified by IHC staining in 137 GBM samples to further clarify the difference in OS between the five groups. Furthermore, the novel biomarkers of glioblastoma stem cells (GSCs) were also described. In summary, we identified five classifications of GBM and found that they exhibited distinct drug sensitivities and different prognoses, suggesting that the new grouping system may be able to provide important prognostic information and have certain guiding significance for the treatment of GBM, and identified the GSCL cluster in GBM tissues and described its characteristic program, which may help develop new potential therapeutic targets for GSCs in GBM.
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Affiliation(s)
- Guanghao Zhang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Xiaolong Xu
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Luojiang Zhu
- Neurosurgery Department, 922th Hospital of Joint Logistics Support Force, PLA, China
| | - Sisi Li
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Rundong Chen
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Nan Lv
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Zifu Li
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Jing Wang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Qiang Li
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Wang Zhou
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Pengfei Yang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Jianmin Liu
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
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14
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Abramov T, Suwansa-ard S, da Silva PM, Wang T, Dove M, O’Connor W, Parker L, Russell FD, Lovejoy DA, Cummins SF, Elizur A. A novel role for Teneurin C-terminal Associated Peptide (TCAP) in the regulation of cardiac activity in the Sydney rock oyster, Saccostrea glomerata. Front Endocrinol (Lausanne) 2023; 14:1020368. [PMID: 36814576 PMCID: PMC9939839 DOI: 10.3389/fendo.2023.1020368] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/23/2023] [Indexed: 02/08/2023] Open
Abstract
Teneurin C-terminal associated peptide (TCAP) is an ancient bioactive peptide that is highly conserved in metazoans. TCAP administration reduces cellular and behavioural stress in vertebrate and urochordate models, yet despite numerous studies in higher animals, there is limited knowledge of its role in invertebrates. In particular, there are no studies on TCAP's effects on the heart of any metazoan, which is a critical organ in the stress response. We used the Sydney rock oyster (SRO) as an invertebrate model to investigate a potential role for sroTCAP in regulating cardiac activity, including during stress. sroTCAP is localized to the neural innervation network of the SRO heart, and suggested binding with various heart proteins related to metabolism and stress, including SOD, GAPDH and metabotropic glutamate receptor. Intramuscular injection of sroTCAP (10 pmol) significantly altered the expression of heart genes that are known to regulate remodelling processes under different conditions, and modulated several gene families responsible for stress mitigation. sroTCAP (1 and 10 pmol) was shown to cause transient bradycardia (heart rate was reduced by up to 63% and for up to 40 min post-administration), indicative of an unstressed state. In summary, this study has established a role for a TCAP in the regulation of cardiac activity through modulation of physiological and molecular components associated with energy conservation, stress and adaptation. This represents a novel function for TCAP and may have implications for higher-order metazoans.
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Affiliation(s)
- Tomer Abramov
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Saowaros Suwansa-ard
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Patricia Mirella da Silva
- Invertebrate Immunology and Pathology Laboratory, Department of Molecular Biology, Federal University of Paraíba, João Pessoa, Brazil
| | - Tianfang Wang
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Michael Dove
- New South Wales (NSW) Department of Primary Industries, Port Stephens Fisheries Institute Taylors Beach, Port Stephens NSW, Australia
| | - Wayne O’Connor
- New South Wales (NSW) Department of Primary Industries, Port Stephens Fisheries Institute Taylors Beach, Port Stephens NSW, Australia
| | - Laura Parker
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Kensington, NSW, Australia
| | - Fraser D. Russell
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
- School of Health and Behavioural Sciences, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - David A. Lovejoy
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Scott F. Cummins
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Abigail Elizur
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia
- *Correspondence: Abigail Elizur,
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B. Soro A, Shokri S, Nicolau-Lapeña I, Ekhlas D, Burgess CM, Whyte P, Bolton DJ, Bourke P, Tiwari BK. Current challenges in the application of the UV-LED technology for food decontamination. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Tolibia SEM, Pacheco AD, Balbuena SYG, Rocha J, López Y López VE. Engineering of global transcription factors in Bacillus, a genetic tool for increasing product yields: a bioprocess overview. World J Microbiol Biotechnol 2022; 39:12. [PMID: 36372802 DOI: 10.1007/s11274-022-03460-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/06/2022] [Indexed: 11/15/2022]
Abstract
Transcriptional factors are well studied in bacteria for their global interactions and the effects they produce at the phenotypic level. Particularly, Bacillus subtilis has been widely employed as a model Gram-positive microorganism used to characterize these network interactions. Bacillus species are currently used as efficient commercial microbial platforms to produce diverse metabolites such as extracellular enzymes, antibiotics, surfactants, industrial chemicals, heterologous proteins, among others. However, the pleiotropic effects caused by the genetic modification of specific genes that codify for global regulators (transcription factors) have not been implicated commonly from a bioprocess point of view. Recently, these strategies have attracted the attention in Bacillus species because they can have an application to increase production efficiency of certain commercial interest metabolites. In this review, we update the recent advances that involve this trend in the use of genetic engineering (mutations, deletion, or overexpression) performed to global regulators such as Spo0A, CcpA, CodY and AbrB, which can provide an advantage for the development or improvement of bioprocesses that involve Bacillus species as production platforms. Genetic networks, regulation pathways and their relationship to the development of growth stages are also discussed to correlate the interactions that occur between these regulators, which are important to consider for application in the improvement of commercial-interest metabolites. Reported yields from these products currently produced mostly under laboratory conditions and, in a lesser extent at bioreactor level, are also discussed to give valuable perspectives about their potential use and developmental level directed to process optimization at large-scale.
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Affiliation(s)
- Shirlley Elizabeth Martínez Tolibia
- Centro de Investigación en Biotecnología Aplicada del Instituto Politécnico Nacional, Carretera Estatal Santa Inés Tecuexcomac-Tepetitla, Km 1.5, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, Mexico
| | - Adrián Díaz Pacheco
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Tlaxcala del Instituto Politécnico Nacional, CP 90000, Guillermo Valle, Tlaxcala, Mexico
| | - Sulem Yali Granados Balbuena
- Centro de Investigación en Biotecnología Aplicada del Instituto Politécnico Nacional, Carretera Estatal Santa Inés Tecuexcomac-Tepetitla, Km 1.5, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, Mexico
| | - Jorge Rocha
- CONACyT - Unidad Regional Hidalgo, Centro de Investigación en Alimentación y Desarrollo, A.C. Blvd. Santa Catarina, SN, C.P. 42163, San Agustín Tlaxiaca, Hidalgo, Mexico
| | - Víctor Eric López Y López
- Centro de Investigación en Biotecnología Aplicada del Instituto Politécnico Nacional, Carretera Estatal Santa Inés Tecuexcomac-Tepetitla, Km 1.5, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, Mexico.
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Gong Y, Srinivasan SS, Zhang R, Kessenbrock K, Zhang J. scEpiLock: A Weakly Supervised Learning Framework for cis-Regulatory Element Localization and Variant Impact Quantification for Single-Cell Epigenetic Data. Biomolecules 2022; 12:874. [PMID: 35883430 PMCID: PMC9312957 DOI: 10.3390/biom12070874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/16/2022] [Accepted: 06/16/2022] [Indexed: 02/04/2023] Open
Abstract
Recent advances in single-cell transposase-accessible chromatin using a sequencing assay (scATAC-seq) allow cellular heterogeneity dissection and regulatory landscape reconstruction with an unprecedented resolution. However, compared to bulk-sequencing, its ultra-high missingness remarkably reduces usable reads in each cell type, resulting in broader, fuzzier peak boundary definitions and limiting our ability to pinpoint functional regions and interpret variant impacts precisely. We propose a weakly supervised learning method, scEpiLock, to directly identify core functional regions from coarse peak labels and quantify variant impacts in a cell-type-specific manner. First, scEpiLock uses a multi-label classifier to predict chromatin accessibility via a deep convolutional neural network. Then, its weakly supervised object detection module further refines the peak boundary definition using gradient-weighted class activation mapping (Grad-CAM). Finally, scEpiLock provides cell-type-specific variant impacts within a given peak region. We applied scEpiLock to various scATAC-seq datasets and found that it achieves an area under receiver operating characteristic curve (AUC) of ~0.9 and an area under precision recall (AUPR) above 0.7. Besides, scEpiLock's object detection condenses coarse peaks to only ⅓ of their original size while still reporting higher conservation scores. In addition, we applied scEpiLock on brain scATAC-seq data and reported several genome-wide association studies (GWAS) variants disrupting regulatory elements around known risk genes for Alzheimer's disease, demonstrating its potential to provide cell-type-specific biological insights in disease studies.
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Affiliation(s)
- Yanwen Gong
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA;
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
| | | | - Ruiyi Zhang
- Department of Computer Science, University of California, Irvine, CA 92697, USA; (S.S.S.); (R.Z.)
| | - Kai Kessenbrock
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA;
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA 92697, USA; (S.S.S.); (R.Z.)
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Zhang L, Zhang J, Nie Q. DIRECT-NET: An efficient method to discover cis-regulatory elements and construct regulatory networks from single-cell multiomics data. SCIENCE ADVANCES 2022; 8:eabl7393. [PMID: 35648859 PMCID: PMC9159696 DOI: 10.1126/sciadv.abl7393] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The emergence of single-cell multiomics data provides unprecedented opportunities to scrutinize the transcriptional regulatory mechanisms controlling cell identity. However, how to use those datasets to dissect the cis-regulatory element (CRE)–to–gene relationships at a single-cell level remains a major challenge. Here, we present DIRECT-NET, a machine-learning method based on gradient boosting, to identify genome-wide CREs and their relationship to target genes, either from parallel single-cell gene expression and chromatin accessibility data or from single-cell chromatin accessibility data alone. By extensively evaluating and characterizing DIRECT-NET’s predicted CREs using independent functional genomics data, we find that DIRECT-NET substantially improves the accuracy of inferring CRE-to-gene relationships in comparison to existing methods. DIRECT-NET is also capable of revealing cell subpopulation–specific and dynamic regulatory linkages. Overall, DIRECT-NET provides an efficient tool for predicting transcriptional regulation codes from single-cell multiomics data.
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Affiliation(s)
- Lihua Zhang
- School of Computer Science, Wuhan University, Wuhan 430072, China
- Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, Irvine, CA 92697, USA
- Corresponding author. (J.Z.); (Q.N.)
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
- Corresponding author. (J.Z.); (Q.N.)
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Bottom-Up Approach to the Discovery of Clinically Relevant Biomarker Genes: The Case of Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14112654. [PMID: 35681633 PMCID: PMC9179423 DOI: 10.3390/cancers14112654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/26/2022] [Accepted: 05/26/2022] [Indexed: 12/07/2022] Open
Abstract
Traditional approaches to genome-wide marker discovery often follow a common top-down strategy, where a large scale ‘omics’ investigation is followed by the analysis of functional pathways involved, to narrow down the list of identified putative biomarkers, and to deconvolute gene expression networks, or to obtain an insight into genetic alterations observed in cancer. We set out to investigate whether a reverse approach would allow full or partial reconstruction of the transcriptional programs and biological pathways specific to a given cancer and whether the full or substantially expanded list of putative markers could thus be identified by starting with the partial knowledge of a few disease-specific markers. To this end, we used 10 well-documented differentially expressed markers of colorectal cancer (CRC), analyzed their transcription factor networks and biological pathways, and predicted the existence of 193 new putative markers. Incredibly, the use of a validation marker set of 10 other completely different known CRC markers and the same procedure resulted in a very similar set of 143 predicted markers. Of these, 138 were identical to those found using the training set, confirming our main hypothesis that a much-expanded set of disease markers can be predicted by starting with just a small subset of validated markers. Further to this, we validated the expression of 42 out of 138 top-ranked predicted markers experimentally using qPCR in surgically removed CRC tissues. We showed that 41 out of 42 mRNAs tested have significantly altered levels of mRNA expression in surgically excised CRC tissues. Of the markers tested, 36 have been reported to be associated with aspects of CRC in the past, whilst only limited published evidence exists for another three genes (BCL2, PDGFRB and TSC2), and no published evidence directly linking genes to CRC was found for CCNA1, SHC1 and TGFB3. Whilst we used CRC to test and validate our marker discovery strategy, the reported procedures apply more generally to cancer marker discovery.
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20
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Kemppainen M, Pardo A. Nucleus-directed fluorescent reporter system for promoter studies in the ectomycorrhizal fungus Laccaria bicolor. J Microbiol Methods 2021; 190:106341. [PMID: 34610385 DOI: 10.1016/j.mimet.2021.106341] [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: 08/09/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022]
Abstract
Currently ectomycorrhizal research suffers from a lack of molecular tools specifically adapted to study gene expression in fungal symbionts. Considering that, we designed pReNuK, a cloning vector for transcriptional promoter studies in the ectomycorrhizal basidiomycete Laccaria bicolor. The pReNuK vector offers the use of a nuclear localizing and chromatin incorporating histone H2B-mCherry fluorescent reporter protein and it is specifically optimized for efficient transgene expression in Laccaria. Moreover, pReNuK is designed to work in concert with Agrobacterium-mediated transformation under hygromycin B resistance selection. The functionality of the pReNuK reporter system was tested with the constitutive Laccaria glyceraldehyde 3-phosphate dehydrogenase gene promoter and further validated with the nitrogen source regulated nitrate reductase gene promoter. The expression of the nucleus-directed H2B-mCherry reporter is highly stable in time. Moreover, the transformation of Laccaria with pReNuK and the expression of the reporter do not have negative effects on the growth of the fungus. The pReNuK offers a novel tool for studying in vivo gene expression regulation in Laccaria, the leading fungal model for ectomycorrhizal research.
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Affiliation(s)
- Minna Kemppainen
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, National University of Quilmes and CONICET, Bernal, Province of Buenos Aires, Argentina.
| | - Alejandro Pardo
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, National University of Quilmes and CONICET, Bernal, Province of Buenos Aires, Argentina
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Liu B, Shi H, Qiu W, Wu X, Li L, Wu W. A two-microRNA signature predicts the progression of male thyroid cancer. Open Life Sci 2021; 16:981-991. [PMID: 34595349 PMCID: PMC8439266 DOI: 10.1515/biol-2021-0099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/17/2021] [Accepted: 07/27/2021] [Indexed: 12/24/2022] Open
Abstract
In various cancers, microRNAs (miRNAs) are abnormally expressed, including thyroid cancer (TC). In recent years, the incidence of TC has increased annually around the world. Compared with female patients, male TC patients are more likely to have a postoperative recurrence and lymph node metastasis, and hence need second treatments. However, the molecular biological processes underlying this phenomenon are not understood. Therefore, we collected data on miRNA expression and clinical information of male TC patients from The Cancer Genome Atlas (TCGA) database. Differentially expressed miRNAs were identified between male TC tissues and matched normal tissues. The Kaplan–Meier method, univariate and multivariate Cox regressions, and receiver operating characteristic curve analyses were performed to assess the association between miRNAs and the disease-free survival of male TC patients. Gene Ontology (GO) and the Kyoto Encyclopaedia of Gene and Genome (KEGG) enrichment analyses were then used to explore the function of miRNA target genes. Furthermore, we evaluated the ability of the miRNA biomarker to predict survival in female TC patients. As a result, a total of 118 differentially expressed miRNAs were identified, including 25 upregulated and 93 downregulated miRNAs. Among them, miR-451a and miR-16-1-3p were confirmed to be independent prognostic factors for the disease-free survival rate. The target genes of miR-451a and miR-16-1-3p were identified, and functional analysis showed that these genes were enriched in 25 Go and KEGG accessions, including cell signal transduction, motor adhesion, phagocytosis, regulation of transcription, cell proliferation, angiogenesis, etc. Neither miR-451a and miR-16-1-3p, nor a prediction model based on both miRNAs effectively predicted survival in female TC patients. In conclusion, both miR-451a and miR-16-1-3p may play important roles in the processes of male TC. The two-miRNA signature involving miR-1258 and miR-193a may serve as a novel prognostic biomarker for male TC patients.
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Affiliation(s)
- Bingyang Liu
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, People's Republic of China
| | - Haihong Shi
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, People's Republic of China
| | - Weigang Qiu
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, People's Republic of China
| | - Xinquan Wu
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, People's Republic of China
| | - Liqiong Li
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, People's Republic of China
| | - Wenyi Wu
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, People's Republic of China
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22
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Kui L, Kong Q, Yang X, Pan Y, Xu Z, Wang S, Chen J, Wei K, Zhou X, Yang X, Wu T, Mastan A, Liu Y, Miao J. High-Throughput In Vitro Gene Expression Profile to Screen of Natural Herbals for Breast Cancer Treatment. Front Oncol 2021; 11:684351. [PMID: 34490085 PMCID: PMC8418118 DOI: 10.3389/fonc.2021.684351] [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: 03/23/2021] [Accepted: 07/23/2021] [Indexed: 11/13/2022] Open
Abstract
Breast cancer has surpassed lung cancer as the most commonly diagnosed cancer in women worldwide. Some therapeutic drugs and approaches could cause side effects and weaken the immune system. The combination of conventional therapies and traditional Chinese medicine (TCM) significantly improves treatment efficacy in breast cancer. However, the chemical composition and underlying anti-tumor mechanisms of TCM still need to be investigated. The primary aim of this study is to provide unique insights to screen the natural components for breast cancer therapy using high-throughput transcriptome analysis. Differentially expressed genes were identified based on two conditions: single samples and groups were classified according to their pharmaceutical effect. Subsequently, the sample treated with E. cochinchinensis Lour. generated the most significant DEGs set, including 1,459 DEGs, 805 upregulated and 654 downregulated. Similarly, group 3 treatment contained the most DEGs (414 DEGs, 311 upregulated and 103 downregulated). KEGG pathway analyses showed five significant pathways associated with the inflammatory and metastasis processes in cancer, which include the TNF, IL−17, NF-kappa B, MAPK signaling pathways, and transcriptional misregulation in cancer. Samples were classified into 13 groups based on their pharmaceutical effects. The results of the KEGG pathway analyses remained consistent with signal samples; group 3 presents a high significance. A total of 21 genes were significantly regulated in these five pathways, interestingly, IL6, TNFAIP3, and BRIC3 were enriched on at least two pathways, seven genes (FOSL1, S100A9, CXCL12, ID2, PRS6KA3, AREG, and DUSP6) have been reported as the target biomarkers and even the diagnostic tools in cancer therapy. In addition, weighted correlation network analysis (WGCNA) was used to identify 18 modules. Among them, blue and thistle2 were the most relevant modules. A total of 26 hub genes in blue and thistle2 modules were identified as the hub genes. In conclusion, we screened out three new TCM (R. communis L., E. cochinchinensis Lour., and B. fruticosa) that have the potential to develop natural drugs for breast cancer therapy, and obtained the therapeutic targets.
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Affiliation(s)
- Ling Kui
- Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China.,Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States.,School of Pharmacy, Jiangsu University, Zhenjiang, China
| | - Qinghua Kong
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xiaonan Yang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Medicinal Botanical Garden, Nanning, China.,Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Yunbing Pan
- Nowbio Biotechnology Company, Kunming, China
| | - Zetan Xu
- Nowbio Biotechnology Company, Kunming, China
| | | | - Jian Chen
- International Genome Center, Jiangsu University, Zhenjiang, China
| | - Kunhua Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Medicinal Botanical Garden, Nanning, China.,Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Xiaolei Zhou
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Medicinal Botanical Garden, Nanning, China.,Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Xingzhi Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Tingqin Wu
- Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Anthati Mastan
- Research Center, Microbial Technology Laboratory, Council of Scientific & Industrial Research (CSIR)-Central Institute of Medicinal and Aromatic Plants, Bangalore, India
| | - Yao Liu
- Baoji High-tech Hospital , Baoji, China
| | - Jianhua Miao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Medicinal Botanical Garden, Nanning, China.,School of Pharmacy, Guangxi Medical University, Nanning, China
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Cancer and pH Dynamics: Transcriptional Regulation, Proteostasis, and the Need for New Molecular Tools. Cancers (Basel) 2020; 12:cancers12102760. [PMID: 32992762 PMCID: PMC7601256 DOI: 10.3390/cancers12102760] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022] Open
Abstract
An emerging hallmark of cancer cells is dysregulated pH dynamics. Recent work has suggested that dysregulated intracellular pH (pHi) dynamics enable diverse cancer cellular behaviors at the population level, including cell proliferation, cell migration and metastasis, evasion of apoptosis, and metabolic adaptation. However, the molecular mechanisms driving pH-dependent cancer-associated cell behaviors are largely unknown. In this review article, we explore recent literature suggesting pHi dynamics may play a causative role in regulating or reinforcing tumorigenic transcriptional and proteostatic changes at the molecular level, and discuss outcomes on tumorigenesis and tumor heterogeneity. Most of the data we discuss are population-level analyses; lack of single-cell data is driven by a lack of tools to experimentally change pHi with spatiotemporal control. Data is also sparse on how pHi dynamics play out in complex in vivo microenvironments. To address this need, at the end of this review, we cover recent advances for live-cell pHi measurement at single-cell resolution. We also discuss the essential role for tool development in revealing mechanisms by which pHi dynamics drive tumor initiation, progression, and metastasis.
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Expression of Genes Related to Carrageenan Synthesis during Carposporogenesis of the Red Seaweed Grateloupia imbricata. Mar Drugs 2020; 18:md18090432. [PMID: 32824959 PMCID: PMC7551501 DOI: 10.3390/md18090432] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/18/2022] Open
Abstract
Carrageenan, the foremost constituent of extracellular matrix of some rhodophyta, is a galactan backbone with a different number of sulphate groups attached. Variations of degree of sulphation are associated with different types of carrageenans, which vary according to seaweed life cycles, and have consequences for the exploitation of this raw material. In this work, we used three well-recognised stages of development thalli and two stages of cystocarp maturation to analyse genes that encode addition and elimination of sulphate groups to cell-wall galactan of the red seaweed Grateloupia imbricata. Expressions of carbohydrate sulfotransferase and galactose-6 sulfurylase and genes encoding stress proteins such as cytochrome P450 and WD40, were examined. Results showed that transcript expression of carbohydrate sulfotransferase occurs at all stage of thalli development. Meanwhile galactose-6 sulfurylase expressions displayed different roles, which could be related to a temporal regulation of cystocarp maturation. Cytochrome P450 and WD40 are related to the disclosure and maturation of cystocarps of G. imbricata. Our conclusion is that differential expression of genes encoding proteins involved in the sulphation and desulphation of galactan backbone is associated with alterations in thalli development and cystocarp maturation in the red seaweed Grateloupia imbricata. Exploitation of industry-valued carrageenan will depend on insight into gene mechanisms of red seaweeds.
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25
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Fry M. Ontologically simple theories do not indicate the true nature of complex biological systems: three test cases. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2020; 42:17. [PMID: 32346811 DOI: 10.1007/s40656-020-00310-5] [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: 02/10/2020] [Accepted: 04/13/2020] [Indexed: 06/11/2023]
Abstract
A longstanding philosophical premise perceives simplicity as a desirable attribute of scientific theories. One of several raised justifications for this notion is that simple theories are more likely to indicate the true makeup of natural systems. Qualitatively parsimonious hypotheses and theories keep to a minimum the number of different postulated entities within a system. Formulation of such ontologically simple working hypotheses proved to be useful in the experimental probing of narrowly defined bio systems. It is less certain, however, whether qualitatively parsimonious theories are effective indicators of the true nature of complex biological systems. This paper assesses the success of ontologically simple theories in envisaging the makeup of three complex systems in bacteriology, immunology, and molecular biology. Evidence shows that parsimonious theories completely misconstrued the actual ontologically complex constitutions of the three examined systems. Since evolution and selective pressures typically produce ontologically intricate rather than simple bio systems, qualitatively parsimonious theories are mostly inapt indicators of the true nature of complex biological systems.
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Affiliation(s)
- Michael Fry
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, POB 9649, 31096, Bat Galim, Haifa, Israel.
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Izzi V, Koivunen J, Rappu P, Heino J, Pihlajaniemi T. Integration of Matrisome Omics: Towards System Biology of the Tumor Matrisome. EXTRACELLULAR MATRIX OMICS 2020. [DOI: 10.1007/978-3-030-58330-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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