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Hao P, Li Q, Zhao H. Mucin 1 expression is regulated by hsa_circ_0055054/microRNA‑122‑5p and promotes hepatocellular carcinoma development. Oncol Lett 2024; 28:404. [PMID: 38983125 PMCID: PMC11228922 DOI: 10.3892/ol.2024.14537] [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: 02/22/2024] [Accepted: 05/29/2024] [Indexed: 07/11/2024] Open
Abstract
The abnormal expression of mucin 1 (MUC1) is a major cause of poor prognosis in patients with hepatocellular carcinoma (HCC). Competitive endogenous RNA demonstrates a novel regulatory mechanism that can affect the biological behavior of tumors. In the present study, the regulatory functions of hsa_circ_0055054 as well as those of microRNA (miR/miRNA) 122-5p on MUC1 expression and its role in HCC cell proliferation, migration and invasion, were evaluated. MUC1 expression was assessed using western blotting and reverse transcription-quantitative PCR. The phenotypic functions of the HCC cell lines were evaluated following MUC1 knockdown using Cell Counting Kit-8, wound healing and Transwell assays. Bioinformatics tools were used to identify specific miRNAs and circular (circ)RNAs that interact with and can regulate MUC1. The stability of circRNAs was assessed using a Ribonuclease R assay. The binding of circRNA/miRNA/MUC1 was assessed using dual-luciferase reporter assays and cellular function tests. Finally, in vivo experiments were performed using animal models. The results demonstrated that in MHCC97L cells, MUC1 and hsa_circ_0055054 were expressed at high levels while miR-122-5p was downregulated. The proliferation, migration and invasion of MHCC97L cells were suppressed by low MUC1 expression. hsa_circ_0055054 knockdown or miR-122-5p overexpression both led to a decrease in MUC1 expression. In MHCC97L cells with a low MUC1 expression caused by hsa_circ_0055054 knockdown, miR-122-5p inhibition resulted in the increased proliferation, migration and invasion of MHCC97L cells. In combination, the results of the present study indicate that hsa_circ_0055054 knockdown in MHCC97L cells leads to an increased expression of miR-122-5p and decreased expression of MUC1, which results in the inhibition of MHCC97L cell proliferation, migration and invasion.
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Affiliation(s)
- Pengfei Hao
- Department of General Surgery, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, Shanxi 030032, P.R. China
| | - Qi Li
- Department of General Surgery, Shanxi Provincial People's Hospital, Taiyuan, Shanxi 030001, P.R. China
| | - Haoliang Zhao
- Department of General Surgery, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, Shanxi 030032, P.R. China
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2
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Zhu L, Song L, Zheng C, Wang N, Xue C, Shen Z, Huang X. Intracellular nonenzymatic in situ growth of layered nanosheet DNA architectures based on palindrome-chained dumbbell probes for miRNA imaging. Talanta 2024; 277:126333. [PMID: 38850801 DOI: 10.1016/j.talanta.2024.126333] [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: 12/30/2023] [Revised: 05/07/2024] [Accepted: 05/28/2024] [Indexed: 06/10/2024]
Abstract
MicroRNA (miRNA) represents a class of important potential biomarkers, and their intracellular imaging is extremely useful for fundamental research and early diagnosis of human cancers. Hybridization chain reaction (HCR) has been shown to be effective in detecting miRNA in living cells. However, its practical applications are still hampered by inefficient reaction kinetics and poor biological stability under complex intracellular conditions. To address these issues, we report a palindrome-mediated multiple hybridization chain reaction (P-HCR) system to better visualize intracellular miRNAs. In the presence of the target miRNA, a layered nanosheet DNA architecture (LSDA) can be assembled in situ via the palindrome-mediated multiple HCR process. We demonstrate that the biological stability of this reaction system could be significantly improved by designing the probes to dumbbell-shaped structures and the distance of hairpins was effectively decreased due to palindrome-chained effect. Consequently, miRNA can be quantitatively identified even at extremely low concentrations of 4.7 pM. The P-HCR system can effectively differentiate the expression levels of miRNA in different tumor cells and normal cells, as demonstrated in live cell tests and the results were in agreement with the PCR, which is considered the gold standard. The new (P-HCR) system has the potential to revolutionize miRNA imaging in living cells.
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Affiliation(s)
- Lingye Zhu
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China; Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Lanlan Song
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China
| | - Cheng Zheng
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China
| | - Ning Wang
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China
| | - Chang Xue
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
| | - Xiaoying Huang
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China.
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3
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Chen Y, Wang X, Na X, Zhang Y, Cai L, Song J, Yang C. DMF-DM-seq: Digital-Microfluidics Enabled Dual-Modality Sequencing of Single-Cell mRNA and microRNA with High Integration, Sensitivity, and Automation. Anal Chem 2024; 96:12916-12926. [PMID: 39038243 DOI: 10.1021/acs.analchem.4c03378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Multimodal measurement of single cells provides deep insights into the intricate relationships between individual molecular layers and the regulatory mechanisms underlying intercellular variations. Here, we reported DMF-DM-seq, a highly integrated, sensitive, and automated platform for single-cell mRNA and microRNA (miRNA) co-sequencing based on digital microfluidics. This platform first integrates the processes of single-cell isolation, lysis, component separation, and simultaneous sequencing library preparation of mRNA and miRNA within a single DMF device. Compared with the current half-cell measuring strategy, DMF-DM-seq enables complete separation of single-cell mRNA and miRNA via a magnetic field application, resulting in a higher miRNA detection ability. DMF-DM-seq revealed differential expression patterns of single cells of noncancerous breast cells and noninvasive and aggressive breast cancer cells at both mRNA and miRNA levels. The results demonstrated the anticorrelated relationship between miRNA and their mRNA targets. Further, we unravel the tumor growth and metastasis-associated biological processes enriched by miRNA-targeted genes, along with important miRNA-interaction networks involved in significant signaling pathways. We also deconstruct the miRNA regulatory mechanisms underlying different signaling pathways across different breast cell types. In summary, DMF-DM-seq offers a powerful tool for a comprehensive study of the expression heterogeneity of single-cell mRNA and miRNA, which will be widely applied in basic and clinical research.
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Affiliation(s)
- Yingwen Chen
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xuanqun Wang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xing Na
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yingkun Zhang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Linfeng Cai
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jia Song
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Chaoyong Yang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, No. 55, Zhenhai Road, Siming District, Xiamen 361003, China
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4
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Chen J, Liu K, Vadas MA, Gamble JR, McCaughan GW. The Role of the MiR-181 Family in Hepatocellular Carcinoma. Cells 2024; 13:1289. [PMID: 39120319 PMCID: PMC11311592 DOI: 10.3390/cells13151289] [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: 06/28/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the fourth-leading cause of cancer-related death worldwide. Due to the high mortality rate in HCC patients, discovering and developing novel systemic treatment options for HCC is a vital unmet medical need. Among the numerous molecular alterations in HCCs, microRNAs (miRNAs) have been increasingly recognised to play critical roles in hepatocarcinogenesis. We and others have recently revealed that members of the microRNA-181 (miR-181) family were up-regulated in some, though not all, human cirrhotic and HCC tissues-this up-regulation induced epithelial-mesenchymal transition (EMT) in hepatocytes and tumour cells, promoting HCC progression. MiR-181s play crucial roles in governing the fate and function of various cells, such as endothelial cells, immune cells, and tumour cells. Previous reviews have extensively covered these aspects in detail. This review aims to give some insights into miR-181s, their targets and roles in modulating signal transduction pathways, factors regulating miR-181 expression and function, and their roles in HCC.
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Affiliation(s)
- Jinbiao Chen
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Ken Liu
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia
| | - Mathew A. Vadas
- Vascular Biology Program, Healthy Ageing Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia; (M.A.V.); (J.R.G.)
| | - Jennifer R. Gamble
- Vascular Biology Program, Healthy Ageing Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia; (M.A.V.); (J.R.G.)
| | - Geoffrey W. McCaughan
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia
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5
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Yu S, Zhou Z, Liang Z, Ruan C, Bai L, Pi Y. Silencing lncRNA GABPB1-AS1 alleviates cerebral ischemia reperfusion injury through the miR-641/NUCKS1 axis. Am J Transl Res 2024; 16:2963-2972. [PMID: 39114718 PMCID: PMC11301495 DOI: 10.62347/eagk7098] [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: 04/07/2024] [Accepted: 06/04/2024] [Indexed: 08/10/2024]
Abstract
OBJECTIVE To investigate the possible mechanism of lncRNA GA binding protein transcription factor beta subunit 1 antisense RNA 1 (GABPB1-AS1) in cerebral ischemia/reperfusion (CI/R) injury. METHODS RT-qPCR was applied to determine GABPB1-AS1 expression in oxygen-glucose deprivation/reoxygenation (OGD/R) cells. The targeting relationships between GABPB1-AS1 and miR-641, as well as between miR-641 and nuclear casein and cyclin-dependent kinase substrate 1 (NUCKS1) were examined by dual luciferase reporter assay. The protein expression of caspase-3, Bax, Bcl-2 and NUCKS1 was examined by western blot. Cell apoptosis was measured by flow cytometry (FCM) and western blot. Cell viability was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. RESULTS GABPB1-AS1 was significantly elevated in SH-SY5Y cells under OGD/R. Downregulation of GABPB1-AS1 accelerated cell viability and suppressed cell apoptosis. GABPB1-AS1 silencing reduced ROS and MDA levels in OGD/R-treated cells. Furthermore, miR-641 inhibitor aggravated damage from OGD/R, but GABPB1-AS1 silencing notably attenuated this effect. NUCKS1 was proven to be a target gene of miR-641. CONCLUSION GABPB1-AS1 silencing alleviated CI/R injury through the miR-641/NUCKS1 axis, indicating that GABPB1-AS1 might serve as a therapeutic target for CI/R injury.
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Affiliation(s)
- Shui Yu
- Department of Neurosurgery, Dujiangyan People's Hospital Chengdu, Sichuan, China
| | - Zhangming Zhou
- Department of Neurosurgery, Dujiangyan People's Hospital Chengdu, Sichuan, China
| | - Zhang Liang
- Department of Neurosurgery, Dujiangyan People's Hospital Chengdu, Sichuan, China
| | - Chenbin Ruan
- Department of Neurosurgery, Dujiangyan People's Hospital Chengdu, Sichuan, China
| | - Lei Bai
- Department of Neurosurgery, Dujiangyan People's Hospital Chengdu, Sichuan, China
| | - Ying Pi
- Department of Neurosurgery, Dujiangyan People's Hospital Chengdu, Sichuan, China
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6
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Mok ETY, Chitty JL, Cox TR. miRNAs in pancreatic cancer progression and metastasis. Clin Exp Metastasis 2024; 41:163-186. [PMID: 38240887 PMCID: PMC11213741 DOI: 10.1007/s10585-023-10256-0] [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: 08/22/2023] [Accepted: 12/06/2023] [Indexed: 06/30/2024]
Abstract
Small non-coding RNA or microRNA (miRNA) are critical regulators of eukaryotic cells. Dysregulation of miRNA expression and function has been linked to a variety of diseases including cancer. They play a complex role in cancers, having both tumour suppressor and promoter properties. In addition, a single miRNA can be involved in regulating several mRNAs or many miRNAs can regulate a single mRNA, therefore assessing these roles is essential to a better understanding in cancer initiation and development. Pancreatic cancer is a leading cause of cancer death worldwide, in part due to the lack of diagnostic tools and limited treatment options. The most common form of pancreatic cancer, pancreatic ductal adenocarcinoma (PDAC), is characterised by major genetic mutations that drive cancer initiation and progression. The regulation or interaction of miRNAs with these cancer driving mutations suggests a strong link between the two. Understanding this link between miRNA and PDAC progression may give rise to novel treatments or diagnostic tools. This review summarises the role of miRNAs in PDAC, the downstream signalling pathways that they play a role in, how these are being used and studied as therapeutic targets as well as prognostic/diagnostic tools to improve the clinical outcome of PDAC.
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Affiliation(s)
- Ellie T Y Mok
- Matrix & Metastasis Lab, Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Jessica L Chitty
- Matrix & Metastasis Lab, Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia.
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
| | - Thomas R Cox
- Matrix & Metastasis Lab, Cancer Ecosystems Program, The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia.
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, UNSW Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
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7
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Scheuermann S, Hücker S, Engel A, Ludwig N, Lebhardt P, Langejürgen J, Kirsch S. A novel approach to generate enzyme-free single cell suspensions from archived tissues for miRNA sequencing. SLAS Technol 2024; 29:100133. [PMID: 38583803 DOI: 10.1016/j.slast.2024.100133] [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: 11/29/2023] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Obtaining high-quality omics data at the single-cell level from archived human tissue samples is crucial for gaining insights into cellular heterogeneity and pushing the field of personalized medicine forward. In this technical brief we present a comprehensive methodological framework for the efficient enzyme-free preparation of tissue-derived single cell suspensions and their conversion into single-cell miRNA sequencing libraries. The resulting data from this study have the potential to deepen our understanding of miRNA expression at the single-cell level and its relevance in the context of the examined tissues. The workflow encompasses tissue collection, RNALater immersion, storage, thawing, TissueGrinder-mediated dissociation, miRNA lysis, library preparation, sequencing, and data analysis. Quality control measures ensure reliable miRNA data, with specific attention to sample quality. The UMAP analysis reveals tissue-specific cell clustering, while miRNA diversity reflects tissue variations. The presented workflow effectively processes preserved tissues, extending opportunities for retrospective analysis and biobank utilization.
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Affiliation(s)
| | - Sarah Hücker
- Biomarkers and innovative Technology Development, Division Personalized Tumor Therapy, Fraunhofer ITEM, Regensburg, Germany
| | - Annika Engel
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Nicole Ludwig
- Human Genetics, Saarland University, University Hospital, Saarbrücken, Germany
| | | | | | - Stefan Kirsch
- Biomarkers and innovative Technology Development, Division Personalized Tumor Therapy, Fraunhofer ITEM, Regensburg, Germany.
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8
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Zhang Y, Yu L, Yang M, Han B, Luo J, Jing R. Model fusion for predicting unconventional proteins secreted by exosomes using deep learning. Proteomics 2024:e2300184. [PMID: 38643383 DOI: 10.1002/pmic.202300184] [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: 04/12/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/22/2024]
Abstract
Unconventional secretory proteins (USPs) are vital for cell-to-cell communication and are necessary for proper physiological processes. Unlike classical proteins that follow the conventional secretory pathway via the Golgi apparatus, these proteins are released using unconventional pathways. The primary modes of secretion for USPs are exosomes and ectosomes, which originate from the endoplasmic reticulum. Accurate and rapid identification of exosome-mediated secretory proteins is crucial for gaining valuable insights into the regulation of non-classical protein secretion and intercellular communication, as well as for the advancement of novel therapeutic approaches. Although computational methods based on amino acid sequence prediction exist for predicting unconventional proteins secreted by exosomes (UPSEs), they suffer from significant limitations in terms of algorithmic accuracy. In this study, we propose a novel approach to predict UPSEs by combining multiple deep learning models that incorporate both protein sequences and evolutionary information. Our approach utilizes a convolutional neural network (CNN) to extract protein sequence information, while various densely connected neural networks (DNNs) are employed to capture evolutionary conservation patterns.By combining six distinct deep learning models, we have created a superior framework that surpasses previous approaches, achieving an ACC score of 77.46% and an MCC score of 0.5406 on an independent test dataset.
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Affiliation(s)
- Yonglin Zhang
- Department of Clinical Pharmacy and Pharmacy Management, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Lezheng Yu
- School of Chemistry and Materials Science, Guizhou Education University, Guiyang, Guizhou, China
| | - Ming Yang
- Department of Clinical Pharmacy and Pharmacy Management, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Bin Han
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Jiesi Luo
- Basic Medical College, Southwest Medical University, Luzhou, Sichuan, China
| | - Runyu Jing
- School of Cyber Science and Engineering, Sichuan University, Chengdu, Sichuan, China
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9
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Zong C, Kong L, Li C, Xv H, Lv M, Chen X, Li C. Light-harvesting iridium (III) complex-sensitized NiO photocathode for photoelectrochemical bioanalysis. Mikrochim Acta 2024; 191:223. [PMID: 38556564 DOI: 10.1007/s00604-024-06321-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/20/2024] [Indexed: 04/02/2024]
Abstract
A novel iridium (III) complex bearing boron dipyrromethene (Bodipy) as the light-harvesting antenna has been synthesized and is firstly employed as photosensitizer to assemble a dye-sensitized NiO photocathode. The assembled photocathode exhibits significantly improved photoelectrochemical (PEC) performance. Integrating the prepared photocathode with hybridization chain reaction (HCR)--based signal amplification strategy, a cathodic PEC biosensor is proposed for the detection of microRNA-133a (miRNA-133a). In the presence of the target, HCR is triggered to form long duplex concatamers on the photocathode, which allows numerous manganese porphyrins (MnPP) to bind in the dsDNA groove. With the help of H2O2, MnPP with peroxidase-like activity catalyzes 4--chloro-1-naphthol (4-CN) to produce benzo--4--chlorohexadienone (4-CD) precipitate on the electrode, leading to a significant decrease of photocurrent signal. The decreased photocurrent correlates linearly with the target concentration from 0.1 fM to 1 nM with a detection limit of 66.2 aM (S/N = 3). The proposed PEC strategy exhibits delightful selectivity, reproducibility and stability.
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Affiliation(s)
- Chengxue Zong
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Linghui Kong
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Can Li
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Huijuan Xv
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Mengwei Lv
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Xiaodong Chen
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Chunxiang Li
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China.
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10
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Chen Y, Wang X, Na X, Zhang Y, Li Z, Chen X, Cai L, Song J, Xu R, Yang C. Highly Multiplexed, Efficient, and Automated Single-Cell MicroRNA Sequencing with Digital Microfluidics. SMALL METHODS 2024; 8:e2301250. [PMID: 38016072 DOI: 10.1002/smtd.202301250] [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: 09/18/2023] [Revised: 11/14/2023] [Indexed: 11/30/2023]
Abstract
Single-cell microRNA (miRNA) sequencing has allowed for comprehensively studying the abundance and complex networks of miRNAs, which provides insights beyond single-cell heterogeneity into the dynamic regulation of cellular events. Current benchtop-based technologies for single-cell miRNA sequencing are low throughput, limited reaction efficiency, tedious manual operations, and high reagent costs. Here, a highly multiplexed, efficient, integrated, and automated sample preparation platform is introduced for single-cell miRNA sequencing based on digital microfluidics (DMF), named Hiper-seq. The platform integrates major steps and automates the iterative operations of miRNA sequencing library construction by digital control of addressable droplets on the DMF chip. Based on the design of hydrophilic micro-structures and the capability of handling droplets of DMF, multiple single cells can be selectively isolated and subject to sample processing in a highly parallel way, thus increasing the throughput and efficiency for single-cell miRNA measurement. The nanoliter reaction volume of this platform enables a much higher miRNA detection ability and lower reagent cost compared to benchtop methods. It is further applied Hiper-seq to explore miRNAs involved in the ossification of mouse skeletal stem cells after bone fracture and discovered unreported miRNAs that regulate bone repairing.
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Affiliation(s)
- Yingwen Chen
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Xuanqun Wang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Xing Na
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yingkun Zhang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Zan Li
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Xiaohui Chen
- State Key Laboratory of Cellular Stress Biology, The First Affiliated Hospital of Xiamen University-ICMRS Collaborating Center for Skeletal Stem Cell, School of Medicine, Xiamen University, Xiamen, 361100, China
- Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, 361100, China
| | - Linfeng Cai
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Ren Xu
- State Key Laboratory of Cellular Stress Biology, The First Affiliated Hospital of Xiamen University-ICMRS Collaborating Center for Skeletal Stem Cell, School of Medicine, Xiamen University, Xiamen, 361100, China
- Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, 361100, China
| | - Chaoyong Yang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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11
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Hücker SM, Kirsch S. Single Cell Micro RNA Sequencing Library Preparation. Methods Mol Biol 2024; 2752:189-199. [PMID: 38194035 DOI: 10.1007/978-1-0716-3621-3_12] [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] [Indexed: 01/10/2024]
Abstract
Micro RNAs represent important post-transcriptional regulators in health and are involved in the onset of many diseases. Therefore, the further characterization of physiological miRNA functions is an important basic research question, and miRNAs even have high potential as biomarkers both for prognosis and diagnosis. In order to exploit this potential, it is mandatory to accurately quantify the miRNA expression not only in bulk but also on the single-cell level. Here, we describe a protocol, which facilitates miRNA sequencing library preparation of very low input samples, single cells, and even clinical samples such as circulating tumor cells. The protocol can be combined with different single-cell isolation methods (e.g., micromanipulation and FACS sorting). After cell lysis, sequencing adapters are ligated to the miRNAs, other ncRNA species, and adapter dimers are reduced by exonuclease digest, the miRNA library is reverse transcribed, amplified, and purified. Furthermore, quality controls are described to select only high-quality samples for sequencing.
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Affiliation(s)
- Sarah M Hücker
- Fraunhofer Institut für Toxikologie und Experimentelle Medizin, Abteilung Personalisierte Tumortherapie, Regensburg, Germany
| | - Stefan Kirsch
- Fraunhofer Institut für Toxikologie und Experimentelle Medizin, Abteilung Personalisierte Tumortherapie, Regensburg, Germany.
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12
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van den Berg NWE, Kawasaki M, Nariswari FA, Fabrizi B, Neefs J, van der Made I, Wesselink R, van Boven WJP, Driessen AHG, Jongejan A, de Groot JR. MicroRNAs in atrial fibrillation target genes in structural remodelling. Cell Tissue Res 2023; 394:497-514. [PMID: 37833432 DOI: 10.1007/s00441-023-03823-0] [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: 03/01/2022] [Accepted: 08/07/2023] [Indexed: 10/15/2023]
Abstract
We aim to elucidate how miRNAs regulate the mRNA signature of atrial fibrillation (AF), to gain mechanistic insight and identify candidate targets for future therapies. We present combined miRNA-mRNA sequencing using atrial tissues of patient without AF (n = 22), with paroxysmal AF (n = 22) and with persistent AF (n = 20). mRNA sequencing previously uncovered upregulated epithelial to mesenchymal transition, endothelial cell proliferation and extracellular matrix remodelling involving glycoproteins and proteoglycans in AF. MiRNA co-sequencing discovered miRNAs regulating the mRNA expression changes. Key downregulated miRNAs included miR-135b-5p, miR-138-5p, miR-200a-3p, miR-200b-3p and miR-31-5p and key upregulated miRNAs were miR-144-3p, miR-15b-3p, miR-182-5p miR-18b-5p, miR-4306 and miR-206. MiRNA expression levels were negatively correlated with the expression levels of a multitude of predicted target genes. Downregulated miRNAs associated with increased gene expression are involved in upregulated epithelial and endothelial cell migration and glycosaminoglycan biosynthesis. In vitro inhibition of miR-135b-5p and miR-138-5p validated an effect of miRNAs on multiple predicted targets. Altogether, the discovered miRNAs may be explored in further functional studies as potential targets for anti-fibrotic therapies in AF.
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Affiliation(s)
- Nicoline W E van den Berg
- Amsterdam UMC, University of Amsterdam, Heart Center; Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.
| | - Makiri Kawasaki
- Amsterdam UMC, University of Amsterdam, Heart Center; Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Fransisca A Nariswari
- Amsterdam UMC, University of Amsterdam, Heart Center; Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Benedetta Fabrizi
- Amsterdam UMC, University of Amsterdam, Heart Center; Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Jolien Neefs
- Amsterdam UMC, University of Amsterdam, Heart Center; Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Ingeborg van der Made
- Amsterdam UMC, University of Amsterdam, Heart Center; Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Robin Wesselink
- Amsterdam UMC, University of Amsterdam, Heart Center; Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Wim Jan P van Boven
- Amsterdam UMC, University of Amsterdam, Heart Center; Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Antoine H G Driessen
- Amsterdam UMC, University of Amsterdam, Heart Center; Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Amsterdam UMC, Department of Epidemiology and Data Science, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Joris R de Groot
- Amsterdam UMC, University of Amsterdam, Heart Center; Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.
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13
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Zhang X, Pan L, Zhang P, Wang L, Shen Y, Xu P, Ren Y, Huang W, Liu P, Wu Q, Li F. Single-cell analysis of the miRNA activities in tuberculous meningitis (TBM) model mice injected with the BCG vaccine. Int Immunopharmacol 2023; 124:110871. [PMID: 37708706 DOI: 10.1016/j.intimp.2023.110871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/10/2023] [Accepted: 08/27/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Our previous study revealed the transcriptome atlas of specific cell types in tuberculous meningitis (TBM) model mice injected with the BCG vaccine via scRNA sequencing. However, the activities of miRNAs in TBM at single-cell resolution remain to be explored. METHOD Cell type-specific miRNA activities were investigated by using motif enrichment analyses (miReact) on the transcriptome data of 15 cell types. The target mRNAs of miRNAs were predicted and subjected to enrichment analysis. Furthermore, miRNAs and their target mRNAs with opposite expression trends were chosen to construct functional networks. Besides, qRT-PCR and RNA scope were performed to verify the expression level of representative miRNA. RESULTS The tSNE dimensionality reduction presented 15 cell types in TBM model mice, in which microglia and endothelial cells accounted for the majority. Target mRNAs of each cell type were predicted for verification or network construction. The immune and inflammation-related miRNA-mRNA networks of macrophages and microglia, oxidative phosphorylation-related miRNA-mRNA networks of neurons, ion and protein transport-related networks of epididymal cells, and angiogenesis-related miRNA-mRNA networks of VSMCs were constructed. The miRNA activity analysis revealed that miR-21a-3p activity was increased in microglia, macrophages, neurons and epididymal cells. The result of qRT-PCR and RNA scope indicate that miR-21a-3p was significantly higher-expressed in TBM brain tissue compared with normal brain tissue. CONCLUSION In our study, an in-depth exploration of the mRNA expression and miRNA activity of macrophages, microglia, epididymal cells, neurons and vascular smooth muscle cells during TBM progression was conducted using scRNA-Seq, which provided novel insights into the immune cell engagement in TBM patients.
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Affiliation(s)
- Xiaolin Zhang
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lei Pan
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Peng Zhang
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lei Wang
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yidan Shen
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Ping Xu
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yang Ren
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Wei Huang
- Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Department of Tuberculosis, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Ping Liu
- Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Department of Tuberculosis, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Qingguo Wu
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
| | - Feng Li
- Department of Respiratory Disease and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center of Tuberculosis Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China.
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14
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Zhang J, Rima XY, Wang X, Nguyen LTH, Huntoon K, Ma Y, Palacio PL, Nguyen KT, Albert K, Duong‐Thi M, Walters N, Kwak KJ, Yoon MJ, Li H, Doon‐Ralls J, Hisey CL, Lee D, Wang Y, Ha J, Scherler K, Fallen S, Lee I, Palmer AF, Jiang W, Magaña SM, Wang K, Kim BYS, Lee LJ, Reátegui E. Engineering a tunable micropattern-array assay to sort single extracellular vesicles and particles to detect RNA and protein in situ. J Extracell Vesicles 2023; 12:e12369. [PMID: 37908159 PMCID: PMC10618633 DOI: 10.1002/jev2.12369] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 11/02/2023] Open
Abstract
The molecular heterogeneity of extracellular vesicles (EVs) and the co-isolation of physically similar particles, such as lipoproteins (LPs), confounds and limits the sensitivity of EV bulk biomarker characterization. Herein, we present a single-EV and particle (siEVP) protein and RNA assay (siEVP PRA) to simultaneously detect mRNAs, miRNAs, and proteins in subpopulations of EVs and LPs. The siEVP PRA immobilizes and sorts particles via positive immunoselection onto micropatterns and focuses biomolecular signals in situ. By detecting EVPs at a single-particle resolution, the siEVP PRA outperformed the sensitivities of bulk-analysis benchmark assays for RNA and protein. To assess the specificity of RNA detection in complex biofluids, EVs from various glioma cell lines were processed with small RNA sequencing, whereby two mRNAs and two miRNAs associated with glioblastoma multiforme (GBM) were chosen for cross-validation. Despite the presence of single-EV-LP co-isolates in serum, the siEVP PRA detected GBM-associated vesicular RNA profiles in GBM patient siEVPs. The siEVP PRA effectively examines intravesicular, intervesicular, and interparticle heterogeneity with diagnostic promise.
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Affiliation(s)
- Jingjing Zhang
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
| | - Xilal Y. Rima
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
| | - Xinyu Wang
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
| | - Luong T. H. Nguyen
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
| | - Kristin Huntoon
- Department of NeurosurgeryThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
- The Brain Tumor CenterThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Yifan Ma
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
| | - Paola Loreto Palacio
- Department of Pediatrics, Division of NeurologyNationwide Children's HospitalColumbusOhioUSA
| | - Kim Truc Nguyen
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
| | - Karunya Albert
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
| | - Minh‐Dao Duong‐Thi
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
| | - Nicole Walters
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
| | | | - Min Jin Yoon
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
| | - Hong Li
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
| | - Jacob Doon‐Ralls
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
| | - Colin L. Hisey
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
| | - Daeyong Lee
- Department of NeurosurgeryThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Yifan Wang
- Department of Radiation OncologyThe University of Texas Southwestern Medical CenterDallasTexasUSA
| | - Jonghoon Ha
- Department of Radiation OncologyThe University of Texas Southwestern Medical CenterDallasTexasUSA
| | | | | | - Inyoul Lee
- Institute for Systems BiologySeattleWashingtonUSA
| | - Andre F. Palmer
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
| | - Wen Jiang
- Department of Radiation OncologyThe University of Texas Southwestern Medical CenterDallasTexasUSA
| | - Setty M. Magaña
- Department of Pediatrics, Division of NeurologyNationwide Children's HospitalColumbusOhioUSA
| | - Kai Wang
- Institute for Systems BiologySeattleWashingtonUSA
| | - Betty Y. S. Kim
- Department of NeurosurgeryThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
- The Brain Tumor CenterThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - L. James Lee
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
- Spot Biosystems Ltd.Palo AltoCaliforniaUSA
| | - Eduardo Reátegui
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusOhioUSA
- Comprehensive Cancer CenterThe Ohio State UniversityColumbusOhioUSA
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15
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Grafanaki K, Grammatikakis I, Ghosh A, Gopalan V, Olgun G, Liu H, Kyriakopoulos GC, Skeparnias I, Georgiou S, Stathopoulos C, Hannenhalli S, Merlino G, Marie KL, Day CP. Noncoding RNA circuitry in melanoma onset, plasticity, and therapeutic response. Pharmacol Ther 2023; 248:108466. [PMID: 37301330 PMCID: PMC10527631 DOI: 10.1016/j.pharmthera.2023.108466] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/24/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
Melanoma, the cancer of the melanocyte, is the deadliest form of skin cancer with an aggressive nature, propensity to metastasize and tendency to resist therapeutic intervention. Studies have identified that the re-emergence of developmental pathways in melanoma contributes to melanoma onset, plasticity, and therapeutic response. Notably, it is well known that noncoding RNAs play a critical role in the development and stress response of tissues. In this review, we focus on the noncoding RNAs, including microRNAs, long non-coding RNAs, circular RNAs, and other small RNAs, for their functions in developmental mechanisms and plasticity, which drive onset, progression, therapeutic response and resistance in melanoma. Going forward, elucidation of noncoding RNA-mediated mechanisms may provide insights that accelerate development of novel melanoma therapies.
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Affiliation(s)
- Katerina Grafanaki
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Ioannis Grammatikakis
- Cancer Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arin Ghosh
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vishaka Gopalan
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gulden Olgun
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Huaitian Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - George C Kyriakopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Ilias Skeparnias
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Sophia Georgiou
- Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
| | | | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kerrie L Marie
- Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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16
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Walgrave H, Penning A, Tosoni G, Snoeck S, Davie K, Davis E, Wolfs L, Sierksma A, Mars M, Bu T, Thrupp N, Zhou L, Moechars D, Mancuso R, Fiers M, Howden AJ, De Strooper B, Salta E. microRNA-132 regulates gene expression programs involved in microglial homeostasis. iScience 2023; 26:106829. [PMID: 37250784 PMCID: PMC10213004 DOI: 10.1016/j.isci.2023.106829] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/13/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023] Open
Abstract
microRNA-132 (miR-132), a known neuronal regulator, is one of the most robustly downregulated microRNAs (miRNAs) in the brain of Alzheimer's disease (AD) patients. Increasing miR-132 in AD mouse brain ameliorates amyloid and Tau pathologies, and also restores adult hippocampal neurogenesis and memory deficits. However, the functional pleiotropy of miRNAs requires in-depth analysis of the effects of miR-132 supplementation before it can be moved forward for AD therapy. We employ here miR-132 loss- and gain-of-function approaches using single-cell transcriptomics, proteomics, and in silico AGO-CLIP datasets to identify molecular pathways targeted by miR-132 in mouse hippocampus. We find that miR-132 modulation significantly affects the transition of microglia from a disease-associated to a homeostatic cell state. We confirm the regulatory role of miR-132 in shifting microglial cell states using human microglial cultures derived from induced pluripotent stem cells.
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Affiliation(s)
- Hannah Walgrave
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute (LBI), 3000 Leuven, Belgium
| | - Amber Penning
- Netherlands Institute for Neuroscience, 1105 BA Amsterdam, the Netherlands
| | - Giorgia Tosoni
- Netherlands Institute for Neuroscience, 1105 BA Amsterdam, the Netherlands
| | - Sarah Snoeck
- Netherlands Institute for Neuroscience, 1105 BA Amsterdam, the Netherlands
| | - Kristofer Davie
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
- VIB-KU Leuven Center for Brain & Disease Research, Bioinformatics Core Facility, 3000 Leuven, Belgium
| | - Emma Davis
- UK Dementia Research Institute at UCL, London WC1E 6BT, UK
| | - Leen Wolfs
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute (LBI), 3000 Leuven, Belgium
| | - Annerieke Sierksma
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute (LBI), 3000 Leuven, Belgium
| | - Mayte Mars
- Netherlands Institute for Neuroscience, 1105 BA Amsterdam, the Netherlands
| | - Taofeng Bu
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute (LBI), 3000 Leuven, Belgium
| | - Nicola Thrupp
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute (LBI), 3000 Leuven, Belgium
| | - Lujia Zhou
- Discovery Neuroscience, Janssen Research and Development, Division of Janssen Pharmaceutica NV, 2340 Beerse, Belgium
| | - Diederik Moechars
- Discovery Neuroscience, Janssen Research and Development, Division of Janssen Pharmaceutica NV, 2340 Beerse, Belgium
| | - Renzo Mancuso
- Microglia and Inflammation in Neurological Disorders (MIND) Lab, VIB Center for Molecular Neurology, VIB, 2610 Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Mark Fiers
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute (LBI), 3000 Leuven, Belgium
| | - Andrew J.M. Howden
- UK Dementia Research Institute, University of Dundee, Dundee DD1 4HN, UK
| | - Bart De Strooper
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute (LBI), 3000 Leuven, Belgium
- UK Dementia Research Institute at UCL, London WC1E 6BT, UK
| | - Evgenia Salta
- Netherlands Institute for Neuroscience, 1105 BA Amsterdam, the Netherlands
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17
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Sant P, Rippe K, Mallm JP. Approaches for single-cell RNA sequencing across tissues and cell types. Transcription 2023; 14:127-145. [PMID: 37062951 PMCID: PMC10807473 DOI: 10.1080/21541264.2023.2200721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/30/2023] [Indexed: 04/18/2023] Open
Abstract
Single-cell sequencing of RNA (scRNA-seq) has advanced our understanding of cellular heterogeneity and signaling in developmental biology and disease. A large number of complementary assays have been developed to profile transcriptomes of individual cells, also in combination with other readouts, such as chromatin accessibility or antibody-based analysis of protein surface markers. As scRNA-seq technologies are advancing fast, it is challenging to establish robust workflows and up-to-date protocols that are best suited to address the large range of research questions. Here, we review scRNA-seq techniques from mRNA end-counting to total RNA in relation to their specific features and outline the necessary sample preparation steps and quality control measures. Based on our experience in dealing with the continuously growing portfolio from the perspective of a central single-cell facility, we aim to provide guidance on how workflows can be best automatized and share our experience in coping with the continuous expansion of scRNA-seq techniques.
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Affiliation(s)
- Pooja Sant
- Single-cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Karsten Rippe
- Division Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Single-cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
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18
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Li J, Zhang Z, Zhuang Y, Wang F, Cai T. Small RNA transcriptome analysis using parallel single-cell small RNA sequencing. Sci Rep 2023; 13:7501. [PMID: 37160973 PMCID: PMC10170110 DOI: 10.1038/s41598-023-34390-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 04/28/2023] [Indexed: 05/11/2023] Open
Abstract
miRNA and other forms of small RNAs are known to regulate many biological processes. Single-cell small RNA sequencing can be used to profile small RNAs of individual cells; however, limitations of efficiency and scale prevent its widespread application. Here, we developed parallel single-cell small RNA sequencing (PSCSR-seq), which can overcome the limitations of existing methods and enable high-throughput small RNA expression profiling of individual cells. Analysis of PSCSR-seq data indicated that diverse cell types could be identified based on patterns of miRNA expression, and showed that miRNA content in nuclei is informative (for example, cell type marker miRNAs can be detected in isolated nuclei). PSCSR-seq is very sensitive: analysis of only 732 peripheral blood mononuclear cells (PBMCs) detected 774 miRNAs, whereas bulk small RNA analysis would require input RNA from approximately 106 cells to detect as many miRNAs. We identified 42 miRNAs as markers for PBMC subpopulations. Moreover, we analyzed the miRNA profiles of 9,533 cells from lung cancer biopsies, and by dissecting cell subpopulations, we identified potentially diagnostic and therapeutic miRNAs for lung cancers. Our study demonstrates that PSCSR-seq is highly sensitive and reproducible, thus making it an advanced tool for miRNA analysis in cancer and life science research.
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Affiliation(s)
- Jia Li
- National Institute of Biological Sciences, Beijing, China
| | - Zhirong Zhang
- National Institute of Biological Sciences, Beijing, China
- Department of Thoracic Surgery, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Yinghua Zhuang
- National Institute of Biological Sciences, Beijing, China
| | - Fengchao Wang
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Tao Cai
- National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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19
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Ho V, Baker JR, Willison KR, Barnes PJ, Donnelly LE, Klug DR. Single cell quantification of microRNA from small numbers of non-invasively sampled primary human cells. Commun Biol 2023; 6:458. [PMID: 37100999 PMCID: PMC10133449 DOI: 10.1038/s42003-023-04845-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Expression levels of microRNAs (miRNAs) in single cells are low and conventional miRNA detection methods require amplification that can be complex, time-consuming, costly and may bias results. Single cell microfluidic platforms have been developed; however, current approaches are unable to absolutely quantify single miRNA molecules expressed in single cells. Herein, we present an amplification-free sandwich hybridisation assay to detect single miRNA molecules in single cells using a microfluidic platform that optically traps and lyses individual cells. Absolute quantification of miR-21 and miR-34a molecules was achieved at a single cell level in human cell lines and validated using real-time qPCR. The sensitivity of the assay was demonstrated by quantifying single miRNA molecules in nasal epithelial cells and CD3+ T-cells, as well as nasal fluid collected non-invasively from healthy individuals. This platform requires ~50 cells or ~30 µL biofluid and can be extended for other miRNA targets therefore it could monitor miRNA levels in disease progression or clinical studies.
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Affiliation(s)
- Vanessa Ho
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Jonathan R Baker
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Keith R Willison
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
| | - Peter J Barnes
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Louise E Donnelly
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK.
| | - David R Klug
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
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20
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Natalia A, Zhang L, Sundah NR, Zhang Y, Shao H. Analytical device miniaturization for the detection of circulating biomarkers. NATURE REVIEWS BIOENGINEERING 2023; 1:1-18. [PMID: 37359772 PMCID: PMC10064972 DOI: 10.1038/s44222-023-00050-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 06/28/2023]
Abstract
Diverse (sub)cellular materials are secreted by cells into the systemic circulation at different stages of disease progression. These circulating biomarkers include whole cells, such as circulating tumour cells, subcellular extracellular vesicles and cell-free factors such as DNA, RNA and proteins. The biophysical and biomolecular state of circulating biomarkers carry a rich repertoire of molecular information that can be captured in the form of liquid biopsies for disease detection and monitoring. In this Review, we discuss miniaturized platforms that allow the minimally invasive and rapid detection and analysis of circulating biomarkers, accounting for their differences in size, concentration and molecular composition. We examine differently scaled materials and devices that can enrich, measure and analyse specific circulating biomarkers, outlining their distinct detection challenges. Finally, we highlight emerging opportunities in biomarker and device integration and provide key future milestones for their clinical translation.
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Affiliation(s)
- Auginia Natalia
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Li Zhang
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Noah R. Sundah
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
| | - Yan Zhang
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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21
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Sun G, Qi M, Kim AS, Lizhar EM, Sun OW, Al-Abdullah IH, Riggs AD. Reassessing the Abundance of miRNAs in the Human Pancreas and Rodent Cell Lines and Its Implication. Noncoding RNA 2023; 9:ncrna9020020. [PMID: 36960965 PMCID: PMC10037588 DOI: 10.3390/ncrna9020020] [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: 01/17/2023] [Revised: 02/24/2023] [Accepted: 03/13/2023] [Indexed: 03/22/2023] Open
Abstract
miRNAs are critical for pancreas development and function. However, we found that there are discrepancies regarding pancreatic miRNA abundance in published datasets. To obtain a more relevant profile that is closer to the true profile, we profiled small RNAs from human islets cells, acini, and four rodent pancreatic cell lines routinely used in diabetes and pancreatic research using a bias reduction protocol for small RNA sequencing. In contrast to the previous notion that miR-375-3p is the most abundant pancreatic miRNA, we found that miR-148a-3p and miR-7-5p were also abundant in islets. In silico studies using predicted and validated targets of these three miRNAs revealed that they may work cooperatively in endocrine and exocrine cells. Our results also suggest, compared to the most-studied miR-375, that both miR-148a-3p and miR-7-5p may play more critical roles in the human pancreas. Moreover, according to in silico-predicted targets, we found that miR-375-3p had a much broader target spectrum by targeting the coding sequence and the 5' untranslated region, rather than the conventional 3' untranslated region, suggesting additional unexplored roles of miR-375-3p beyond the pancreas. Our study provides a valuable new resource for studying miRNAs in pancreata.
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Affiliation(s)
- Guihua Sun
- Department of Diabetes Complications & Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
- Department of Neurodegenerative Diseases, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Meirigeng Qi
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Alexis S Kim
- Department of Diabetes Complications & Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Elizabeth M Lizhar
- Department of Diabetes Complications & Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Olivia W Sun
- Department of Diabetes & Cancer Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Ismail H Al-Abdullah
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Arthur D Riggs
- Department of Diabetes Complications & Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
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22
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Bilinska A, Pszczola M, Stachowiak M, Stachecka J, Garbacz F, Aksoy MO, Szczerbal I. Droplet Digital PCR Quantification of Selected Intracellular and Extracellular microRNAs Reveals Changes in Their Expression Pattern during Porcine In Vitro Adipogenesis. Genes (Basel) 2023; 14:genes14030683. [PMID: 36980955 PMCID: PMC10047974 DOI: 10.3390/genes14030683] [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: 12/15/2022] [Revised: 01/27/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Extracellular miRNAs have attracted considerable interest because of their role in intercellular communication, as well as because of their potential use as diagnostic and prognostic biomarkers for many diseases. It has been shown that miRNAs secreted by adipose tissue can contribute to the pathophysiology of obesity. Detailed knowledge of the expression of intracellular and extracellular microRNAs in adipocytes is thus urgently required. The system of in vitro differentiation of mesenchymal stem cells (MSCs) into adipocytes offers a good model for such an analysis. The aim of this study was to quantify eight intracellular and extracellular miRNAs (miR-21a, miR-26b, miR-30a, miR-92a, miR-146a, miR-148a, miR-199, and miR-383a) during porcine in vitro adipogenesis using droplet digital PCR (ddPCR), a highly sensitive method. It was found that only some miRNAs associated with the inflammatory process (miR-21a, miR-92a) were highly expressed in differentiated adipocytes and were also secreted by cells. All miRNAs associated with adipocyte differentiation were highly abundant in both the studied cells and in the cell culture medium. Those miRNAs showed a characteristic expression profile with upregulation during differentiation.
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23
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MicroRNA-148a Controls Epidermal and Hair Follicle Stem/Progenitor Cells by Modulating the Activities of ROCK1 and ELF5. J Invest Dermatol 2023; 143:480-491.e5. [PMID: 36116511 DOI: 10.1016/j.jid.2022.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/09/2022] [Accepted: 06/16/2022] [Indexed: 11/22/2022]
Abstract
Skin and hair development is regulated by complex programs of gene activation and silencing and microRNA-dependent modulation of gene expression to maintain normal skin and hair follicle development, homeostasis, and cycling. In this study, we show that miR-148a, through its gene targets, plays an important role in regulating skin homeostasis and hair follicle cycling. RNA and protein analysis of miR-148a and its gene targets were analyzed using a combination of in vitro and in vivo experiments. We show that the expression of miR-148a markedly increases during telogen (bulge and hair germ stem cell compartments). Administration of antisense miR-148a inhibitor into mouse skin during the telogen phases of the postnatal hair cycle results in accelerated anagen development and altered stem cell activity in the skin. We also show that miR-148a can regulate colony-forming abilities of hair follicle bulge stem cells as well as control keratinocyte proliferation/differentiation processes. RNA and protein analysis revealed that miR-148a may control these processes by regulating the expression of Rock1 and Elf5 in vitro and in vivo. These data provide an important foundation for further analyses of miR-148a as a crucial regulator of these genes target in the skin and hair follicles and its importance in maintaining stem/progenitor cell functions during normal tissue homeostasis and regeneration.
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24
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Kong S, Li R, Tian Y, Zhang Y, Lu Y, Ou Q, Gao P, Li K, Zhang Y. Single-cell omics: A new direction for functional genetic research in human diseases and animal models. Front Genet 2023; 13:1100016. [PMID: 36685871 PMCID: PMC9846559 DOI: 10.3389/fgene.2022.1100016] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Over the past decade, with the development of high-throughput single-cell sequencing technology, single-cell omics has been emerged as a powerful tool to understand the molecular basis of cellular mechanisms and refine our knowledge of diverse cell states. They can reveal the heterogeneity at different genetic layers and elucidate their associations by multiple omics analysis, providing a more comprehensive genetic map of biological regulatory networks. In the post-GWAS era, the molecular biological mechanisms influencing human diseases will be further elucidated by single-cell omics. This review mainly summarizes the development and trend of single-cell omics. This involves single-cell omics technologies, single-cell multi-omics technologies, multiple omics data integration methods, applications in various human organs and diseases, classic laboratory cell lines, and animal disease models. The review will reveal some perspectives for elucidating human diseases and constructing animal models.
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Affiliation(s)
- Siyuan Kong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Rongrong Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yunhan Tian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Yaqiu Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuhui Lu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiaoer Ou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peiwen Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Life Science and Engineering, Foshan University, Foshan, China
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25
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Schmitz U. Overview of Computational and Experimental Methods to Identify Tissue-Specific MicroRNA Targets. Methods Mol Biol 2023; 2630:155-177. [PMID: 36689183 DOI: 10.1007/978-1-0716-2982-6_12] [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] [Indexed: 01/24/2023]
Abstract
As ubiquitous posttranscriptional regulators of gene expression, microRNAs (miRNAs) play key roles in cell physiology and function across taxa. In the last two decades, we have gained a good understanding about miRNA biogenesis pathways, modes of action, and consequences of miRNA-mediated gene regulation. More recently, research has focused on exploring causes for miRNA dysregulation, miRNA-mediated crosstalk between genes and signaling pathways, and the role of miRNAs in disease.This chapter discusses methods for the identification of miRNA-target interactions and causes for tissue-specific miRNA-target regulation. Computational approaches for predicting miRNA target sites and assessing tissue-specific target regulation are discussed. Moreover, there is an emphasis on features that affect miRNA target recognition and how high-throughput sequencing protocols can help in assessing miRNA-mediated gene regulation on a genome-wide scale. In addition, this chapter introduces some experimental approaches for the validation of miRNA targets as well as web-based resources sharing predicted and validated miRNA-target interactions.
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Affiliation(s)
- Ulf Schmitz
- Department of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Douglas, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia.
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26
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Yang Q, Wu L, Meng J, Ma L, Zuo E, Sun Y. EpiCas-DL: Predicting sgRNA activity for CRISPR-mediated epigenome editing by deep learning. Comput Struct Biotechnol J 2022; 21:202-211. [PMID: 36582444 PMCID: PMC9763632 DOI: 10.1016/j.csbj.2022.11.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022] Open
Abstract
CRISPR-mediated epigenome editing enables gene expression regulation without changing the underlying DNA sequence, and thus has vast potential for basic research and gene therapy. Effective selection of a single guide RNA (sgRNA) with high on-target efficiency and specificity would facilitate the application of epigenome editing tools. Here we performed an extensive analysis of CRISPR-mediated epigenome editing tools on thousands of experimentally examined on-target sites and established EpiCas-DL, a deep learning framework to optimize sgRNA design for gene silencing or activation. EpiCas-DL achieves high accuracy in sgRNA activity prediction for targeted gene silencing or activation and outperforms other available in silico methods. In addition, EpiCas-DL also identifies both epigenetic and sequence features that affect sgRNA efficacy in gene silencing and activation, facilitating the application of epigenome editing for research and therapy. EpiCas-DL is available at http://www.sunlab.fun:3838/EpiCas-DL.
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Affiliation(s)
- Qianqian Yang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Leilei Wu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Juan Meng
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Lei Ma
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Erwei Zuo
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yidi Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
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27
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Liu W, Shomron N. Analysis of MicroRNA Regulation and Gene Expression Variability in Single Cell Data. J Pers Med 2022; 12:jpm12101750. [PMID: 36294889 PMCID: PMC9605646 DOI: 10.3390/jpm12101750] [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: 08/12/2022] [Revised: 09/29/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
MicroRNAs (miRNAs) regulate gene expression by binding to mRNAs, and thus reduce target gene expression levels and expression variability, also known as 'noise'. Single-cell RNA sequencing (scRNA-seq) technology has been used to study miRNA and mRNA expression in single cells. To evaluate scRNA-seq as a tool for investigating miRNA regulation, we analyzed datasets with both mRNA and miRNA expression in single-cell format. We found that miRNAs slightly reduce the expression noise of target genes; however, this effect is easily masked by strong technical noise from scRNA-seq. We suggest improvements aimed at reducing technical noise, which can be implemented in experimental design and computational analysis prior to running scRNA-seq. Our study provides useful guidelines for experiments that evaluate the effect of miRNAs on mRNA expression from scRNA-seq.
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Affiliation(s)
- Wendao Liu
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6329302, Israel
- Correspondence: ; Tel.: +972-3-640-7387
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28
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Hou H, Chan C, Yuki KE, Sokolowski D, Roy A, Qu R, Uusküla-Reimand L, Faykoo-Martinez M, Hudson M, Corre C, Goldenberg A, Zhang Z, Palmert MR, Wilson MD. Postnatal developmental trajectory of sex-biased gene expression in the mouse pituitary gland. Biol Sex Differ 2022; 13:57. [PMID: 36221127 PMCID: PMC9552479 DOI: 10.1186/s13293-022-00467-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The pituitary gland regulates essential physiological processes such as growth, pubertal onset, stress response, metabolism, reproduction, and lactation. While sex biases in these functions and hormone production have been described, the underlying identity, temporal deployment, and cell-type specificity of sex-biased pituitary gene regulatory networks are not fully understood. METHODS To capture sex differences in pituitary gene regulation dynamics during postnatal development, we performed 3' untranslated region sequencing and small RNA sequencing to ascertain gene and microRNA expression, respectively, across five postnatal ages (postnatal days 12, 22, 27, 32, 37) that span the pubertal transition in female and male C57BL/6J mouse pituitaries (n = 5-6 biological replicates for each sex at each age). RESULTS We observed over 900 instances of sex-biased gene expression and 17 sex-biased microRNAs, with the majority of sex differences occurring with puberty. Using miRNA-gene target interaction databases, we identified 18 sex-biased genes that were putative targets of 5 sex-biased microRNAs. In addition, by combining our bulk RNA-seq with publicly available male and female mouse pituitary single-nuclei RNA-seq data, we obtained evidence that cell-type proportion sex differences exist prior to puberty and persist post-puberty for three major hormone-producing cell types: somatotropes, lactotropes, and gonadotropes. Finally, we identified sex-biased genes in these three pituitary cell types after accounting for cell-type proportion differences between sexes. CONCLUSION Our study reveals the identity and postnatal developmental trajectory of sex-biased gene expression in the mouse pituitary. This work also highlights the importance of considering sex biases in cell-type composition when understanding sex differences in the processes regulated by the pituitary gland.
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Affiliation(s)
- Huayun Hou
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Cadia Chan
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada
| | - Kyoko E Yuki
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Dustin Sokolowski
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Anna Roy
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Rihao Qu
- Interdepartmental Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.,Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | | | - Mariela Faykoo-Martinez
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Matt Hudson
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Christina Corre
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.,Division of Endocrinology, The Hospital for Sick Children, Toronto, ON, Canada.,Departments of Pediatrics and Physiology, University of Toronto, Toronto, ON, Canada
| | - Anna Goldenberg
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Mark R Palmert
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada. .,Division of Endocrinology, The Hospital for Sick Children, Toronto, ON, Canada. .,Institute of Medical Science, University of Toronto, Toronto, ON, Canada. .,Departments of Pediatrics and Physiology, University of Toronto, Toronto, ON, Canada.
| | - Michael D Wilson
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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29
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Hayder H, Shan Y, Chen Y, O’Brien JA, Peng C. Role of microRNAs in trophoblast invasion and spiral artery remodeling: Implications for preeclampsia. Front Cell Dev Biol 2022; 10:995462. [PMID: 36263015 PMCID: PMC9575991 DOI: 10.3389/fcell.2022.995462] [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: 07/15/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
It is now well-established that microRNAs (miRNAs) are important regulators of gene expression. The role of miRNAs in placental development and trophoblast function is constantly expanding. Trophoblast invasion and their ability to remodel uterine spiral arteries are essential for proper placental development and successful pregnancy outcome. Many miRNAs are reported to be dysregulated in pregnancy complications, especially preeclampsia and they exert various regulatory effects on trophoblasts. In this review, we provide a brief overview of miRNA biogenesis and their mechanism of action, as well as of trophoblasts differentiation, invasion and spiral artery remodeling. We then discuss the role of miRNAs in trophoblasts invasion and spiral artery remodeling, focusing on miRNAs that have been thoroughly investigated, especially using multiple model systems. We also discuss the potential role of miRNAs in the pathogenesis of preeclampsia.
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Affiliation(s)
- Heyam Hayder
- Department of Biology, York University, Toronto, ON, Canada
| | - Yanan Shan
- Department of Biology, York University, Toronto, ON, Canada
| | - Yan Chen
- Department of Biology, York University, Toronto, ON, Canada
| | | | - Chun Peng
- Department of Biology, York University, Toronto, ON, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, ON, Canada
- *Correspondence: Chun Peng,
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30
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Olgun G, Gopalan V, Hannenhalli S. miRSCAPE - inferring miRNA expression from scRNA-seq data. iScience 2022; 25:104962. [PMID: 36060076 PMCID: PMC9437856 DOI: 10.1016/j.isci.2022.104962] [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: 03/02/2022] [Revised: 05/09/2022] [Accepted: 08/12/2022] [Indexed: 11/27/2022] Open
Abstract
Our understanding of miRNA activity at cellular resolution is thwarted by the inability of standard scRNA-seq protocols to capture miRNAs. We introduce a novel tool, miRSCAPE, to infer miRNA expression in a sample from its RNA-seq profile. We establish miRSCAPE's accuracy in 10 tumor and normal cohorts demonstrating its superiority over alternatives. miRSCAPE accurately infers cell type-specific miRNA activities (predicted versus observed fold-difference correlation ∼0.81) in two independent scRNA-seq datasets. We apply miRSCAPE to infer miRNA activities in scRNA clusters in pancreatic and lung adenocarcinomas, as well as in 56 cell types in the human cell landscape (HCL). In pancreatic and breast cancer scRNA-seq data, miRSCAPE recapitulates miRNAs associated with stemness and epithelial-mesenchymal transition (EMT) cell states, respectively. Overall, miRSCAPE recapitulates and refines miRNA biology at cellular resolution. miRSCAPE is freely available and is easily applicable to scRNA-seq data to infer miRNA activities at cellular resolution.
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Affiliation(s)
- Gulden Olgun
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vishaka Gopalan
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sridhar Hannenhalli
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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31
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Zhang Z, Ma X, Zhu J, Yan R, Miao P. Roll-to-Roll DNA Nanomachine for Ultrasensitive Electrochemical Determination of miRNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11130-11135. [PMID: 36045009 DOI: 10.1021/acs.langmuir.2c02102] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) are a family of endogenous noncoding RNAs with the functions of gene regulation, which serve as promising markers for a range of diseases such as diabetic foot ulcers, cancers, etc. In this work, we engineered a roll-to-roll DNA nanomachine for highly sensitive electrochemical detection of miRNA. A dumbbell-structured DNA probe could be transitioned to be wheel-structured conformation upon target recognition, which rolls around track strands on the surface of gold nanoparticles (AuNPs) in the presence of nicking endonuclease. The resulting single strands on AuNPs are activated for the second round of rolling at the DNA-modified electrode interface, leading to the variation of electrochemical responses. The roll-to-roll amplification behavior allows a wide detection range with a limit of detection as low as 10 aM. The practicability is also demonstrated by the application in human serum samples with satisfactory results. It is expected that the proposed electrochemical method offers a new paradigm to develop miRNA assays based on DNA nanotechnology.
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Affiliation(s)
- Zhenming Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P.R. China
- Department of Orthopedic Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Xin Ma
- Department of Orthopedic Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Jinwen Zhu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P.R. China
| | - Ruhong Yan
- Department of Clinical Laboratory, Suzhou Science & Technology Town Hospital, Nanjing Medical University, Suzhou 215153, P.R. China
| | - Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P.R. China
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32
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Jiang S, Hu Y, Zhou Y, Tang G, Cui W, Wang X, Chen B, Hu Z, Xu B. miRNAs as Biomarkers and Possible Therapeutic Strategies in Synovial Sarcoma. Front Pharmacol 2022; 13:881007. [PMID: 36003502 PMCID: PMC9394702 DOI: 10.3389/fphar.2022.881007] [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: 02/22/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Synovial sarcoma (SS) is an epithelial-differentiated malignant stromal tumor that has the highest incidence in young people and can occur almost anywhere in the body. Many noncoding RNAs are involved in the occurrence, development, or pathogenesis of SS. In particular, the role of MicroRNAs (miRNAs) in SS is receiving increasing attention. MiRNA is a noncoding RNA abundant in cells and extracellular serums. Increasing evidence suggests that miRNA has played a significant role in the incidence and development of tumors in recent years, including sarcomas. Previous studies show that various sarcomas have their unique miRNA expression patterns and that various miRNA expression profiles can illustrate the classes of miRNAs that may elicit cancer-relevant activities in specific sarcoma subtypes. Furthermore, SS has been reported to have the most number of differentially expressed miRNAs, which indicated that miRNA is linked to SS. In fact, according to many publications, miRNAs have been shown to have a role in the development and appearance of SS in recent years, according to many publications. Since many studies showing that various miRNAs have a role in the development and appearance of SS in recent years have not been systematically summarized, we summarize the recent studies on the relationship between miRNA and SS in this review. For example, miR-494 promotes the development of SS via modulating cytokine gene expression. The role of miR-494-3p as a tumor suppressor is most likely linked to the CXCR4 (C-X-C chemokine receptor 4) regulator, although the exact mechanism is unknown. Our review aims to reveal in detail the potential biological value and clinical significance of miRNAs for SS and the potential clinical value brought by the association between SS and miRNAs.
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Affiliation(s)
- Shaowei Jiang
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ying Hu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- School of Pharmacy, Anhui Medical University, Hefei, China
| | - Yi Zhou
- The First Clinical Medical College of Anhui Medical University, Hefei, China
| | - Guozheng Tang
- The First Clinical Medical College of Anhui Medical University, Hefei, China
- Department of Orthopedics, Lu’an People’s Hospital, Lu’an, China
| | - Wenxu Cui
- The First Clinical Medical College of Anhui Medical University, Hefei, China
| | - Xinyi Wang
- The First Clinical Medical College of Anhui Medical University, Hefei, China
| | - Bangjie Chen
- The First Clinical Medical College of Anhui Medical University, Hefei, China
| | - Zuhong Hu
- The First Clinical Medical College of Anhui Medical University, Hefei, China
| | - Bing Xu
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- *Correspondence: Bing Xu,
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33
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Shahidi M, Abazari O, Dayati P, Bakhshi A, Zavarreza J, Modarresi MH, Haghiralsadat F, Rahmanian M, Naghib SM, Tofighi D. Multicomponent siRNA/miRNA-loaded modified mesoporous silica nanoparticles targeted bladder cancer for a highly effective combination therapy. Front Bioeng Biotechnol 2022; 10:949704. [PMID: 35992340 PMCID: PMC9388766 DOI: 10.3389/fbioe.2022.949704] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 07/04/2022] [Indexed: 01/03/2023] Open
Abstract
Bladder cancer is one of the concerning urological malignant diseases in the world, which has a clinical need for effective targeted therapy. The development of nanotechnology-based gene delivery to bladder tumor sites is an effective strategy for targeted cancer therapy with low/no toxicity. With this view, in the present work, the mesoporous silica nanoparticles (MSNs) modified with c(RGDfK)-PLGA-PEG [c(RGDfK)-MSN NPs] were constructed for co-delivery of miR-34a and siPD-L1 within bladder cancer cells and tissues. Our findings showed that miR-34a is downregulated while PD-L1 is up-regulated in cell lines and animal studies. This nano-carrier is biocompatible in the serum environment and effectively protects miR-34a and siPD-L1 against serum degradation. However, we showed that c(RGDfK)-MSN NPs could simultaneously downregulate PD-L1 expression and up-regulate miR-34a in the T24 cells and T24 mice model and enhance anti-tumor effects both in vivo and in vitro. In conclusion, these findings presented new suggestions for improving targeted therapeutic strategies with specified molecular objectives for bladder cancer treatment.
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Affiliation(s)
- Maryamsadat Shahidi
- Department of Clinical Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Omid Abazari
- Department of Clinical Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Parisa Dayati
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Bakhshi
- Department of Clinical Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Javad Zavarreza
- Department of Clinical Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | | | - Fateme Haghiralsadat
- Department of Advanced Medical Sciences and Technologies, School of Paramedicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mehdi Rahmanian
- Biomaterials and Tissue Engineering Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Seyed Morteza Naghib
- Nanotechnology Department, School of Advanced Technologies, Iran University of Science and Technology (IUST), Tehran, Iran
| | - Davood Tofighi
- Department of Psychology, Epidemiology, and Research Design Support (BERD), Clinical and Translational Science Center, University of NM, Albuquerque, NM, United States
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34
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Benevento M, Hökfelt T, Harkany T. Ontogenetic rules for the molecular diversification of hypothalamic neurons. Nat Rev Neurosci 2022; 23:611-627. [PMID: 35906427 DOI: 10.1038/s41583-022-00615-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2022] [Indexed: 11/09/2022]
Abstract
The hypothalamus is an evolutionarily conserved endocrine interface that, among other roles, links central homeostatic control to adaptive bodily responses by releasing hormones and neuropeptides from its many neuronal subtypes. In its preoptic, anterior, tuberal and mammillary subdivisions, a kaleidoscope of magnocellular and parvocellular neuroendocrine command neurons, local-circuit neurons, and neurons that project to extrahypothalamic areas are intermingled in partially overlapping patches of nuclei. Molecular fingerprinting has produced data of unprecedented mass and depth to distinguish and even to predict the synaptic and endocrine competences, connectivity and stimulus selectivity of many neuronal modalities. These new insights support eminent studies from the past century but challenge others on the molecular rules that shape the developmental segregation of hypothalamic neuronal subtypes and their use of morphogenic cues for terminal differentiation. Here, we integrate single-cell RNA sequencing studies with those of mouse genetics and endocrinology to describe key stages of hypothalamus development, including local neurogenesis, the direct terminal differentiation of glutamatergic neurons, transition cascades for GABAergic and GABAergic cell-derived dopamine cells, waves of local neuronal migration, and sequential enrichment in neuropeptides and hormones. We particularly emphasize how transcription factors determine neuronal identity and, consequently, circuit architecture, and whether their deviations triggered by environmental factors and hormones provoke neuroendocrine illnesses.
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Affiliation(s)
- Marco Benevento
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Tomas Hökfelt
- Department of Neuroscience, Biomedicum 7D, Karolinska Institutet, Solna, Sweden
| | - Tibor Harkany
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria. .,Department of Neuroscience, Biomedicum 7D, Karolinska Institutet, Solna, Sweden.
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35
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Aass KR, Nedal TMV, Tryggestad SS, Haukås E, Slørdahl TS, Waage A, Standal T, Mjelle R. Paired miRNA- and messenger RNA-sequencing identifies novel miRNA-mRNA interactions in multiple myeloma. Sci Rep 2022; 12:12147. [PMID: 35840794 PMCID: PMC9287335 DOI: 10.1038/s41598-022-16448-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/11/2022] [Indexed: 01/15/2023] Open
Abstract
Multiple myeloma (MM) is an incurable cancer of terminally differentiated plasma cells that proliferate in the bone marrow. miRNAs are promising biomarkers for risk stratification in MM and several miRNAs are shown to have a function in disease pathogenesis. However, to date, surprisingly few miRNA-mRNA interactions have been described for and functionally validated in MM. In this study, we performed miRNA-seq and mRNA-seq on CD138 + cells isolated from bone marrow aspirates of 86 MM patients to identify novel interactions between sRNAs and mRNAs. We detected 9.8% significantly correlated miRNA-mRNA pairs of which 5.17% were positively correlated and 4.65% were negatively correlated. We found that miRNA-mRNA pairs that were predicted by in silico target-prediction algorithms were more negatively correlated than non-target pairs, indicating functional miRNA targeting and that correlation between miRNAs and mRNAs from patients can be used to identify miRNA-targets. mRNAs for negatively correlated miRNA-mRNA target pairs were associated with gene ontology terms such as autophagy, protein degradation and endoplasmic stress response, reflecting important processes in MM. Targets for two specific miRNAs, miR-125b-5p and miR-365b-3p, were functionally validated in MM cell line transfection experiments followed by RNA-sequencing and qPCR. In summary, we identified functional miRNA-mRNA target pairs by correlating miRNA and mRNA data from primary MM cells. We identified several target pairs that are of potential interest for further studies. The data presented here may serve as a hypothesis-generating knowledge base for other researchers in the miRNA/MM field. We also provide an interactive web application that can be used to exploit the miRNA-target interactions as well as clinical parameters associated to these target-pairs.
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Affiliation(s)
- Kristin Roseth Aass
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Gastrosenteret, Prinsesse Kristinas gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway
| | - Tonje Marie Vikene Nedal
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Gastrosenteret, Prinsesse Kristinas gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway
| | - Synne Stokke Tryggestad
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Gastrosenteret, Prinsesse Kristinas gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway
| | - Einar Haukås
- grid.412835.90000 0004 0627 2891Department of Hematology, Stavanger University Hospital, 4011 Stavanger, Norway
| | - Tobias S. Slørdahl
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway ,grid.52522.320000 0004 0627 3560Department of Hematology, St. Olavs University Hospital, 7030 Trondheim, Norway
| | - Anders Waage
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway ,grid.52522.320000 0004 0627 3560Department of Hematology, St. Olavs University Hospital, 7030 Trondheim, Norway
| | - Therese Standal
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Gastrosenteret, Prinsesse Kristinas gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway ,grid.52522.320000 0004 0627 3560Department of Hematology, St. Olavs University Hospital, 7030 Trondheim, Norway
| | - Robin Mjelle
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Bioinformatics Core Facility - BioCore, Norwegian University of Science and Technology NTNU, 7491 Trondheim, Norway
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36
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Soutschek M, Germade T, Germain PL, Schratt G. enrichMiR predicts functionally relevant microRNAs based on target collections. Nucleic Acids Res 2022; 50:W280-W289. [PMID: 35609985 PMCID: PMC9252831 DOI: 10.1093/nar/gkac395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/25/2022] [Accepted: 05/05/2022] [Indexed: 11/12/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are among the main post-transcriptional regulators of gene expression. A number of data collections and prediction tools have gathered putative or confirmed targets of these regulators. It is often useful, for discovery and validation, to harness such collections to perform target enrichment analysis in given transcriptional signatures or gene-sets in order to predict involved miRNAs. While several methods have been proposed to this end, a flexible and user-friendly interface for such analyses using various approaches and collections is lacking. enrichMiR (https://ethz-ins.org/enrichMiR/) addresses this gap by enabling users to perform a series of enrichment tests, based on several target collections, to rank miRNAs according to their likely involvement in the control of a given transcriptional signature or gene-set. enrichMiR results can furthermore be visualised through interactive and publication-ready plots. To guide the choice of the appropriate analysis method, we benchmarked various tests across a panel of experiments involving the perturbation of known miRNAs. Finally, we showcase enrichMiR functionalities in a pair of use cases.
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Affiliation(s)
- Michael Soutschek
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland
| | - Tomás Germade
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich, Switzerland
| | - Pierre-Luc Germain
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich, Switzerland.,Lab of Statistical Bioinformatics, DMLS, University of Zürich, Switzerland.,Swiss Institute of Bioinformatics, Switzerland
| | - Gerhard Schratt
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland
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37
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Du M, Espinosa-Diez C, Liu M, Ahmed IA, Mahan S, Wei J, Handen AL, Chan SY, Gomez D. miRNA/mRNA co-profiling identifies the miR-200 family as a central regulator of SMC quiescence. iScience 2022; 25:104169. [PMID: 35465051 PMCID: PMC9018390 DOI: 10.1016/j.isci.2022.104169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/01/2022] [Accepted: 03/24/2022] [Indexed: 12/14/2022] Open
Abstract
miRNAs are versatile regulators of smooth muscle cell (SMC) fate and behavior in vascular development and disease. Targeted loss-of-function studies have established the relevance of specific miRNAs in controlling SMC differentiation or mediating phenotypic modulation. Our goal was to characterize SMC miRNAome and its contribution to transcriptome changes during phenotypic modulation. Small RNA sequencing revealed that dedifferentiation led to the differential expression of over 50 miRNAs in cultured SMC. miRNA/mRNA comparison predicted that over a third of SMC transcript expression was regulated by differentially expressed miRNAs. Our screen identified the miR-200 cluster as highly downregulated during dedifferentiation. miR-200 maintains SMC quiescence and represses proliferation, migration, and neointima formation, in part by targeting Quaking, a central SMC phenotypic switching mediator. Our study unraveled the substantial contribution of miRNAs in regulating the SMC transcriptome and identified the miR-200 cluster as a pro-quiescence mechanism and a potential inhibitor of vascular restenosis.
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Affiliation(s)
- Mingyuan Du
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Department of Vascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Cristina Espinosa-Diez
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Mingjun Liu
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Ibrahim Adeola Ahmed
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Sidney Mahan
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jianxin Wei
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Adam L Handen
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Stephen Y Chan
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Delphine Gomez
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
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38
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Zhao C, Cheng Q, Xie W, Xu J, Xu S, Wang Y, Feng W. Methods for predicting single-cell miRNA in breast cancer. Genomics 2022; 114:110353. [PMID: 35364269 DOI: 10.1016/j.ygeno.2022.110353] [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: 07/07/2021] [Revised: 02/13/2022] [Accepted: 03/26/2022] [Indexed: 01/14/2023]
Abstract
It has been demonstrated that miRNAs are involved in many biological processes including cell proliferation and differentiation, apoptosis, and stress responses. Although single-cell RNA sequencing technology is prevailing nowadays, it still remains challenging in quantifying miRNA at the single-cell level. Herein, we present the computational methods to infer the single-cell miRNA expression level using its target gene abundances. Firstly, we developed an enrichment-based approach in estimating miRNA expression considering miRNA-mRNA regulation information and miRNA-mRNA correlation signal captured from existing TCGA datasets. Further efforts were made to infer the miRNA expression with machine learning models. The methods were applied to compare the accuracy and robustness with the simulated single-cell data. Finally, we applied the method in single-cell RNA-seq triple negative breast cancer (TNBC) patients to further discover miRNA marker at the single-cell level for the malignant cells. Our tool is available online at: https://github.com/ChengkuiZhao/Single-cell-miRNA-prediction.
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Affiliation(s)
- Chengkui Zhao
- Institute of Intelligent System and Bioinformatics, College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin 150001, China
| | - Qi Cheng
- Institute of Intelligent System and Bioinformatics, College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin 150001, China
| | - Weixin Xie
- Institute of Intelligent System and Bioinformatics, College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin 150001, China
| | - Jiayu Xu
- Institute of Intelligent System and Bioinformatics, College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin 150001, China
| | - Siwen Xu
- Institute of Intelligent System and Bioinformatics, College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin 150001, China
| | - Ying Wang
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 510080 Guangzhou, China
| | - Weixing Feng
- Institute of Intelligent System and Bioinformatics, College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin 150001, China.
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39
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Cancer: More than a geneticist’s Pandora’s box. J Biosci 2022. [DOI: 10.1007/s12038-022-00254-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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40
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Single-molecule imaging of microRNA-mediated gene silencing in cells. Nat Commun 2022; 13:1435. [PMID: 35301300 PMCID: PMC8931058 DOI: 10.1038/s41467-022-29046-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/16/2022] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs, which regulate the expression of thousands of genes; miRNAs silence gene expression from complementary mRNAs through translational repression and mRNA decay. For decades, the function of miRNAs has been studied primarily by ensemble methods, where a bulk collection of molecules is measured outside cells. Thus, the behavior of individual molecules during miRNA-mediated gene silencing, as well as their spatiotemporal regulation inside cells, remains mostly unknown. Here we report single-molecule methods to visualize each step of miRNA-mediated gene silencing in situ inside cells. Simultaneous visualization of single mRNAs, translation, and miRNA-binding revealed that miRNAs preferentially bind to translated mRNAs rather than untranslated mRNAs. Spatiotemporal analysis based on our methods uncovered that miRNAs bind to mRNAs immediately after nuclear export. Subsequently, miRNAs induced translational repression and mRNA decay within 30 and 60 min, respectively, after the binding to mRNAs. This methodology provides a framework for studying miRNA function at the single-molecule level with spatiotemporal information inside cells.
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41
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Krovi SH, Loh L, Spengler A, Brunetti T, Gapin L. Current insights in mouse iNKT and MAIT cell development using single cell transcriptomics data. Semin Immunol 2022; 60:101658. [PMID: 36182863 DOI: 10.1016/j.smim.2022.101658] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/17/2022] [Accepted: 09/21/2022] [Indexed: 01/15/2023]
Abstract
Innate T (Tinn) cells are a collection of T cells with important regulatory functions that have a crucial role in immunity towards tumors, bacteria, viruses, and in cell-mediated autoimmunity. In mice, the two main αβ Tinn cell subsets include the invariant NKT (iNKT) cells that recognize glycolipid antigens presented by non-polymorphic CD1d molecules and the mucosal associated invariant T (MAIT) cells that recognize vitamin B metabolites presented by the non-polymorphic MR1 molecules. Due to their ability to promptly secrete large quantities of cytokines either after T cell antigen receptor (TCR) activation or upon exposure to tissue- and antigen-presenting cell-derived cytokines, Tinn cells are thought to act as a bridge between the innate and adaptive immune systems and have the ability to shape the overall immune response. Their swift response reflects the early acquisition of helper effector programs during their development in the thymus, independently of pathogen exposure and prior to taking up residence in peripheral tissues. Several studies recently profiled, in an unbiased manner, the transcriptomes of mouse thymic iNKT and MAIT cells at the single cell level. Based on these data, we re-examine in this review how Tinn cells develop in the mouse thymus and undergo effector differentiation.
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Affiliation(s)
| | - Liyen Loh
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | | | - Tonya Brunetti
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Laurent Gapin
- University of Colorado Anschutz Medical Campus, Aurora, USA.
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42
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Li D, Niu G, Landén NX. Beyond the Code: Noncoding RNAs in Skin Wound Healing. Cold Spring Harb Perspect Biol 2022; 14:a041230. [PMID: 35197246 PMCID: PMC9438779 DOI: 10.1101/cshperspect.a041230] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
An increasing number of noncoding RNAs (ncRNAs) have been found to regulate gene expression and protein functions, playing important roles in diverse biological processes and diseases. Their crucial functions have been reported in almost every cell type and all stages of skin wound healing. Evidence of their pathogenetic roles in common wound complications, such as chronic nonhealing wounds and excessive scarring, is also accumulating. Given their unique expression and functional properties, ncRNAs are promising therapeutic and diagnostic entities. In this review, we discuss current knowledge about the functional roles of noncoding elements, such as microRNAs, long ncRNAs, and circular RNAs, in skin wound healing, focusing on in vivo evidence from studies of human wound samples and animal wound models. Finally, we provide a perspective on the outlook of ncRNA-based therapeutics in wound care.
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Affiliation(s)
- Dongqing Li
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Guanglin Niu
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Ning Xu Landén
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176 Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institute, 17177 Stockholm, Sweden
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A comparative analysis of single cell small RNA sequencing data reveals heterogeneous isomiR expression and regulation. Sci Rep 2022; 12:2834. [PMID: 35181712 PMCID: PMC8857176 DOI: 10.1038/s41598-022-06876-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 01/31/2022] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding small RNAs which play a critical role in the regulation of gene expression in cells. It is known that miRNAs are often expressed as multiple isoforms, called isomiRs, which may have alternative regulatory functions. Despite the recent development of several single cell small RNA sequencing protocols, these methods have not been leveraged to investigate isomiR expression and regulation to better understand their role on a single cell level. Here we integrate sequencing data from three independent studies and find substantial differences in isomiR composition that suggest that cell autonomous mechanisms may drive isomiR processing. We also find evidence of altered regulatory functions of different classes of isomiRs, when compared to their respective wild-type miRNA, which supports a biological role for many of the isomiRs that are expressed.
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Cuperus JT. Single-cell genomics in plants: current state, future directions, and hurdles to overcome. PLANT PHYSIOLOGY 2022; 188:749-755. [PMID: 34662424 PMCID: PMC8825463 DOI: 10.1093/plphys/kiab478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/21/2021] [Indexed: 05/26/2023]
Abstract
Single-cell genomics has the potential to revolutionize the study of plant development and tissue-specific responses to environmental stimuli by revealing heretofore unknown players and gene regulatory processes. Here, I focus on the current state of single-cell genomics in plants, emerging technologies and applications, in addition to outlining possible future directions for experiments. I describe approaches to enable cheaper and larger experiments and technologies to measure multiple types of molecules to better model and understand cell types and their different states and trajectories throughout development. Lastly, I discuss the inherent limitations of single-cell studies and the technological hurdles that need to be overcome to widely apply single-cell genomics in crops to generate the greatest possible knowledge gain.
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Affiliation(s)
- Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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Herrera V, Hsu SCJ, Naveen VY, Liu WF, Haun JB. Multiplexed Detection of Secreted Cytokines at near-Molecular Resolution Elucidates Macrophage Polarization Heterogeneity. Anal Chem 2022; 94:658-668. [PMID: 34936345 DOI: 10.1021/acs.analchem.1c02222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Monitoring the secretion of proteins from single cells can provide important insights into how cells respond to their microenvironment. This is particularly true for immune cells, which can exhibit a large degree of response heterogeneity. Microfabricated well arrays provide a powerful and versatile method to assess the secretion of cytokines, chemokines, and growth factors from single cells, but detection sensitivity has been limited to high levels on the order of 10,000 per cell. Recently, we reported a quantum dot-based immunoassay that lowered the detection limit for the cytokine TNF-α to concentrations to nearly the single-cell level. Here, we adapted this detection method to three additional targets while maintaining high detection sensitivity. Specifically, we detected MCP-1, TGF-β, IL-10, and TNF-α using quantum dots with different emission spectra, each of which displayed a detection threshold in the range of 1-10 fM or ∼1-2 molecules per well. We then quantified secretion of all four proteins from single macrophage cells that were stimulated toward a pro-inflammatory state with lipopolysaccharide (LPS) or toward a pro-healing state with both LPS and interleukin 4 (IL-4). We found that MCP-1 and TGF-β were predominantly secreted at high levels only (>10,000 molecules/cell), while a substantial number of cells secreted IL-10 and TNF-α at lower levels that could only be detected using our method. Subsequent principal component and cluster analysis revealed that secretion profiles could be classified as either exclusively pro-inflammatory, including MCP-1 and/or TNF-α, or more subtle responses displaying both pro-healing and pro-inflammatory characters. Our results highlight the heterogeneous and nondiscrete nature of macrophage phenotypes following in vitro stimulation of a cell line. Future work will focus on expanding the multiplexing capacity by extending emission spectra bandwidth and/or spatially barcoding capture antibodies, as well as evaluating the enhanced detection sensitivity capabilities with normal and diseased immune cell populations in vitro and in vivo.
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Affiliation(s)
- Vanessa Herrera
- Department of Biomedical Engineering, University of California Irvine, Irvine, California 92697, United States
| | - Ssu-Chieh Joseph Hsu
- Department of Biomedical Engineering, University of California Irvine, Irvine, California 92697, United States
| | - Veena Y Naveen
- Department of Biomedical Engineering, University of California Irvine, Irvine, California 92697, United States
| | - Wendy F Liu
- Department of Biomedical Engineering, University of California Irvine, Irvine, California 92697, United States
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, California 92697, United States
- Department of Materials Science and Engineering, University of California Irvine, Irvine, California 92697, United States
- Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California Irvine, Irvine, California 92697, United States
| | - Jered B Haun
- Department of Biomedical Engineering, University of California Irvine, Irvine, California 92697, United States
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, California 92697, United States
- Department of Materials Science and Engineering, University of California Irvine, Irvine, California 92697, United States
- Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, California 92697, United States
- Center for Advanced Design and Manufacturing of Integrated Microfluidics, University of California Irvine, Irvine, California 92697, United States
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Ej M, Em M, N D, Ho M. A Peptide/MicroRNA-31 nanomedicine within an electrospun biomaterial designed to regenerate wounds in vivo. Acta Biomater 2022; 138:285-300. [PMID: 34800718 DOI: 10.1016/j.actbio.2021.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 12/20/2022]
Abstract
microRNA-31 (miR-31) has been identified to be downregulated in pathologies associated with delayed wound repair. Thus, it was proposed that the delivery of a plasmid encoding miR-31 (pmiR-31) to the skin could hold potential in promoting wound healing. Effective delivery of pmiR-31 was potentiated by encapsulation with the CHAT peptide to form nanocomplexes, this improved cellular entry and elicited a potent increase in miR-31 expression in vitro in both skin human keratinocyte cell line (HaCaT) and human microvascular endothelial cell line (HMEC-1). Transfection efficiencies with CHAT/pEFGP-N1 were significant at 15.2 ± 8.1% in HMEC-1 cells and >40% in HaCaT cells. In this study, the CHAT/pmiR-31 nanocomplexes at a N:P ratio of 10 had an average particle size of 74.2 nm with a cationic zeta potential of 9.7 mV. Delivery of CHAT/pmiR-31 to HaCaT and HMEC-1 cells resulted in significant improvements in cell migration capacity and increased angiogenesis. In vivo studies were conducted in C57BL/6 J mice were CHAT/pmiR-31 was delivered via electrospun PVA nanofibres, demonstrating a significant increase in epidermal (increase of ∼38.2 µm) and stratum corneum (increase of 8.2 µm) layers compared to controls. Furthermore, treatment in vivo with CHAT/pmiR-31 increased angiogenesis in wounds compared to controls, with a significant increase in vessel diameter by ∼20.4 µm compared against a commercial dressing control (Durafiber™). Together, these data demonstrate that the delivery of CHAT/pmiR-31 nanocomplexes from electrospun PVA nanofibres represent an innovative therapy for wound repair, eliciting a positive therapeutic response across both stromal and epithelial tissue compartments of the skin. STATEMENT OF SIGNIFICANCE: This study advances research regarding the development of our unique electrospun nanofibre patch to deliver genetic nanoparticles into wounds in vivo to promote healing. The genetic nanoparticles are comprised of: (a) plasmid micro-RNA31 that has been shown to be downregulated in pathologies with delayed wound repair and (b) a 15 amino acid linear peptide termed CHAT. The CHAT facilitates complexation of miR-31 and cellular uptake. Herein, we report for the first time on the use of CHAT to deliver a therapeutic cargo pmiR-31 for wound healing applications from a nanofibre patch. Application of the nanofibre patch resulted in the controlled delivery of the CHAT/pmiR-31 nanoparticles with a significant increase in both epidermal and stratum corneum layers compared to untreated and commercial controls.
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Affiliation(s)
- Mulholland Ej
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom; Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom.
| | - McErlean Em
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
| | - Dunne N
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom; School of Mechanical and Manufacturing Engineering, Dublin City University, Dublin 9, Ireland; Centre for Medical Engineering Research, School of Mechanical and Manufacturing Engineering, Dublin City University, Dublin 9, Ireland; Department of Mechanical and Manufacturing Engineering, School of Engineering, Trinity College Dublin, Dublin 2, Ireland; Advanced Manufacturing Research Centre (I-Form), School of Mechanical and Manufacturing Engineering, Dublin City University, Glasnevin, Dublin 9, Ireland; Advanced Materials and Bioengineering Research Centre (AMBER), Royal College of Surgeons in Ireland and Trinity College Dublin, Dublin, Ireland; Advanced Processing Technology Research Centre, Dublin City University, Dublin 9, Ireland; Trinity Centre for Biomedical Engineering, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - McCarthy Ho
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom; School of Chemical Sciences, Dublin City University, Dublin 9, Ireland.
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47
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Kaller M, Hünten S, Siemens H, Hermeking H. Analysis of the p53/microRNA Network in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1385:187-228. [DOI: 10.1007/978-3-031-08356-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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48
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Wu G, Li Y. Distinct characteristics of correlation analysis at the single-cell and the population level. Stat Appl Genet Mol Biol 2022; 21:sagmb-2022-0015. [PMID: 35918809 DOI: 10.1515/sagmb-2022-0015] [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: 03/27/2022] [Accepted: 06/13/2022] [Indexed: 11/15/2022]
Abstract
Correlation analysis is widely used in biological studies to infer molecular relationships within biological networks. Recently, single-cell analysis has drawn tremendous interests, for its ability to obtain high-resolution molecular phenotypes. It turns out that there is little overlap of co-expressed genes identified in single-cell level investigations with that of population level investigations. However, the nature of the relationship of correlations between single-cell and population levels remains unclear. In this manuscript, we aimed to unveil the origin of the differences between the correlation coefficients at the single-cell level and that at the population level, and bridge the gap between them. Through developing formulations to link correlations at the single-cell and the population level, we illustrated that aggregated correlations could be stronger, weaker or equal to the corresponding individual correlations, depending on the variations and the correlations within the population. When the correlation within the population is weaker than the individual correlation, the aggregated correlation is stronger than the corresponding individual correlation. Besides, our data indicated that aggregated correlation is more likely to be stronger than the corresponding individual correlation, and it was rare to find gene-pairs exclusively strongly correlated at the single-cell level. Through a bottom-up approach to model interactions between molecules in a signaling cascade or a multi-regulator-controlled gene expression, we surprisingly found that the existence of interaction between two components could not be excluded simply based on their low correlation coefficients, suggesting a reconsideration of connectivity within biological networks which was derived solely from correlation analysis. We also investigated the impact of technical random measurement errors on the correlation coefficients for the single-cell level and the population level. The results indicate that the aggregated correlation is relatively robust and less affected. Because of the heterogeneity among single cells, correlation coefficients calculated based on data of the single-cell level might be different from that of the population level. Depending on the specific question we are asking, proper sampling and normalization procedure should be done before we draw any conclusions.
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Affiliation(s)
- Guoyu Wu
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yuchao Li
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- MegaLab, MegaRobo Technologies Co., Ltd, Beijing, China
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Isakova A, Neff N, Quake SR. Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states. Proc Natl Acad Sci U S A 2021; 118:e2113568118. [PMID: 34911763 PMCID: PMC8713755 DOI: 10.1073/pnas.2113568118] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2021] [Indexed: 12/22/2022] Open
Abstract
The ability to interrogate total RNA content of single cells would enable better mapping of the transcriptional logic behind emerging cell types and states. However, current single-cell RNA-sequencing (RNA-seq) methods are unable to simultaneously monitor all forms of RNA transcripts at the single-cell level, and thus deliver only a partial snapshot of the cellular RNAome. Here we describe Smart-seq-total, a method capable of assaying a broad spectrum of coding and noncoding RNA from a single cell. Smart-seq-total does not require splitting the RNA content of a cell and allows the incorporation of unique molecular identifiers into short and long RNA molecules for absolute quantification. It outperforms current poly(A)-independent total RNA-seq protocols by capturing transcripts of a broad size range, thus enabling simultaneous analysis of protein-coding, long-noncoding, microRNA, and other noncoding RNA transcripts from single cells. We used Smart-seq-total to analyze the total RNAome of human primary fibroblasts, HEK293T, and MCF7 cells, as well as that of induced murine embryonic stem cells differentiated into embryoid bodies. By analyzing the coexpression patterns of both noncoding RNA and mRNA from the same cell, we were able to discover new roles of noncoding RNA throughout essential processes, such as cell cycle and lineage commitment during embryonic development. Moreover, we show that independent classes of short-noncoding RNA can be used to determine cell-type identity.
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Affiliation(s)
- Alina Isakova
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA 94305;
- Chan Zuckerberg Biohub, San Francisco, CA 94158
- Department of Applied Physics, Stanford University, Stanford, CA 94305
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50
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Wohl SG. View on microRNAs as a potential tool to fight blindness: focus on Müller glia and gliosis. Neural Regen Res 2021; 17:1501-1502. [PMID: 34916433 PMCID: PMC8771108 DOI: 10.4103/1673-5374.330610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Stefanie Gabriele Wohl
- The State University of New York, College of Optometry, Department of Biological and Vision Sciences, New York, NY, USA
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