1
|
Ribeiro AL, Dallagiovanna B. The Role of Long Non-Coding RNAs in Human Endoderm Differentiation. Noncoding RNA 2025; 11:29. [PMID: 40278506 PMCID: PMC12029278 DOI: 10.3390/ncrna11020029] [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: 02/26/2025] [Revised: 04/03/2025] [Accepted: 04/11/2025] [Indexed: 04/26/2025] Open
Abstract
The human genome sequencing revealed a vast complexity of transcripts, with over 80% of the genome being transcribed into non-coding RNAs. In particular, long non-coding RNAs (lncRNAs) have emerged as critical regulators of various cellular processes, including embryonic development and stem cell differentiation. Despite extensive efforts to identify and characterize lncRNAs, defining their mechanisms of action in state-specific cellular contexts remains a significant challenge. Only recently has the involvement of lncRNAs in human endoderm differentiation of pluripotent stem cells begun to be addressed, creating an opportunity to explore the mechanisms by which lncRNAs exert their functions in germ layer formation, lineage specification, and commitment. This review summarizes current findings on the roles of lncRNAs in endoderm differentiation, highlighting the functional mechanisms and regulatory aspects underlying their involvement in cell fate decisions leading to endoderm development. The key lncRNAs implicated in endoderm differentiation are discussed, along with their interaction with transcription factors and RNA-binding proteins and modulation of signaling pathways essential for endoderm development. Gaining insight into the regulatory roles of lncRNAs in endoderm differentiation enhances the understanding of developmental biology and provides a foundation for discovering novel lncRNAs involved in cell fate determination.
Collapse
Affiliation(s)
| | - Bruno Dallagiovanna
- Stem Cells Basic Biology Laboratory, Carlos Chagas Institute—FIOCRUZ/PR, Curitiba 81350-010, Brazil;
| |
Collapse
|
2
|
Saloni, Sachan M, Rahul, Verma RS, Patel GK. SOXs: Master architects of development and versatile emulators of oncogenesis. Biochim Biophys Acta Rev Cancer 2025; 1880:189295. [PMID: 40058508 DOI: 10.1016/j.bbcan.2025.189295] [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: 10/02/2024] [Revised: 02/26/2025] [Accepted: 03/03/2025] [Indexed: 03/22/2025]
Abstract
Transcription factors regulate a variety of events and maintain cellular homeostasis. Several transcription factors involved in embryonic development, has been shown to be closely associated with carcinogenesis when deregulated. Sry-like high mobility group box (SOX) proteins are potential transcription factors which are evolutionarily conserved. They regulate downstream genes to determine cell fate, via various signaling pathways and cellular processes essential for tissue and organ development. Dysregulation of SOXs has been reported to promote or suppress tumorigenesis by modulating cellular reprogramming, growth, proliferation, angiogenesis, metastasis, apoptosis, immune modulation, lineage plasticity, maintenance of the stem cell pool, therapy resistance and cancer relapse. This review provides a crucial understanding of the molecular mechanism by which SOXs play multifaceted roles in embryonic development and carcinogenesis. It also highlights their potential in advancing therapeutic strategies aimed at targeting SOXs and their downstream effectors in various malignancies.
Collapse
Affiliation(s)
- Saloni
- Cancer and Stem Cell Laboratory, Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj 211004, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj 211004, India
| | - Rahul
- Department of Surgical Gastroenterology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow 226014, India
| | - Rama Shanker Verma
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj 211004, India.
| | - Girijesh Kumar Patel
- Cancer and Stem Cell Laboratory, Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj 211004, India.
| |
Collapse
|
3
|
Ryczek N, Łyś A, Wanowska E, Kozłowska-Masłoń J, Makałowska I. Mechanism of expression regulation of head-to-head overlapping protein-coding genes INO80E and HIRIP3. Commun Biol 2025; 8:391. [PMID: 40057624 PMCID: PMC11890862 DOI: 10.1038/s42003-025-07815-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Accepted: 02/25/2025] [Indexed: 05/13/2025] Open
Abstract
Although the existence of overlapping protein-coding genes in eukaryotic genomes is known for decades, their role in regulating expression remains far from fully understood. Here, the mechanism regulating the expression of head-to-head overlapping genes, a pair of INO80E and HIRIP3 genes is presented. Based on a series of experiments, we show that the expression of these genes is strongly dependent on sense/antisense interactions. The overlapping transcripts form an RNA:RNA duplex that has a stabilizing effect on the mRNAs involved, and this stabilization may be mediated by the ELAVL1 protein. We also show that the transcription factor RARG is important for the transcription of both genes studied. In addition, we demonstrate that the overlapping isoform of INO80E forms an R-loop that may positively regulate HIRIP3 isoforms. We propose that both structures, dsRNA and R-loops, help to keep the DNA loop open to allow the transcription of the remaining variants of both genes. However, experiments suggest that RNA:RNA duplex formation plays a major role, while R-loops play only a complementary one. The absence of this dsRNA structure leads to the loss of a stable DNA opening and consequently to transcriptional interference.
Collapse
Affiliation(s)
- Natalia Ryczek
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Aneta Łyś
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Elżbieta Wanowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Joanna Kozłowska-Masłoń
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, ul. Garbary 15, 61-866, Poznań, Poland
| | - Izabela Makałowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| |
Collapse
|
4
|
Li J, Xu Y, Han Y, Yang A, Qian M, Wang B. Role of the SOX family in cancer immune evasion: Emerging player and promising therapeutic opportunities. Medicine (Baltimore) 2025; 104:e41393. [PMID: 39889187 PMCID: PMC11789896 DOI: 10.1097/md.0000000000041393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 10/12/2024] [Accepted: 11/13/2024] [Indexed: 02/02/2025] Open
Abstract
Cancer immune evasion is one of the important mechanisms for cancer development, which is essential to developing novel immunotherapeutic strategies. The SOX (SRY-related HMG-box) family of transcription factors plays a crucial role in normal physiology as well as in a variety of human diseases especially cancer. It has been shown that SOX is involved in cancer immune evasion processes. This mini-review aimed to summarize how SOX family members induce cancer immune evasion by regulating antigen presentation, shaping the tumor immunosuppressive milieu, and controlling regulatory immune checkpoint inhibitors like programmed death ligand 1. Thorough exploration of SOX family will help uncover the mechanism of cancer immune evasion, and provide new ideas and targets for the development of immunotherapy strategies.
Collapse
Affiliation(s)
- Jinke Li
- Department of General Surgery, Longnan First People’s Hospital, Longnan, China
| | - Yawen Xu
- Department of General Surgery, Longnan First People’s Hospital, Longnan, China
| | - Yunying Han
- Department of General Surgery, Longnan First People’s Hospital, Longnan, China
| | - Aifu Yang
- Department of General Surgery, Longnan First People’s Hospital, Longnan, China
| | - Miaoshan Qian
- Department of General Surgery, Longnan First People’s Hospital, Longnan, China
| | - Bo Wang
- Department of General Surgery, Longnan First People’s Hospital, Longnan, China
| |
Collapse
|
5
|
Yaniv D, Mattson B, Talbot S, Gleber-Netto FO, Amit M. Targeting the peripheral neural-tumour microenvironment for cancer therapy. Nat Rev Drug Discov 2024; 23:780-796. [PMID: 39242781 DOI: 10.1038/s41573-024-01017-z] [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] [Accepted: 07/24/2024] [Indexed: 09/09/2024]
Abstract
As the field of cancer neuroscience expands, the strategic targeting of interactions between neurons, cancer cells and other elements in the tumour microenvironment represents a potential paradigm shift in cancer treatment, comparable to the advent of our current understanding of tumour immunology. Cancer cells actively release growth factors that stimulate tumour neo-neurogenesis, and accumulating evidence indicates that tumour neo-innervation propels tumour progression, inhibits tumour-related pro-inflammatory cytokines, promotes neovascularization, facilitates metastasis and regulates immune exhaustion and evasion. In this Review, we give an up-to-date overview of the dynamics of the tumour microenvironment with an emphasis on tumour innervation by the peripheral nervous system, as well as current preclinical and clinical evidence of the benefits of targeting the nervous system in cancer, laying a scientific foundation for further clinical trials. Combining empirical data with a biomarker-driven approach to identify and hone neuronal targets implicated in cancer and its spread can pave the way for swift clinical integration.
Collapse
Affiliation(s)
- Dan Yaniv
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brandi Mattson
- The Neurodegeneration Consortium, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sebastien Talbot
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Frederico O Gleber-Netto
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Moran Amit
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- UTHealth Houston Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
6
|
Bezamat M, Carver CE, Vieira AR. Family-based GWAS for dental class I malocclusion and clefts. BMC Oral Health 2024; 24:665. [PMID: 38849772 PMCID: PMC11162011 DOI: 10.1186/s12903-024-04444-x] [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: 03/25/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Individuals born with cleft lip and/or palate who receive corrective surgery regularly have abnormal growth in the midface region such that they exhibit premaxillary hypoplasia. However, there are also genetic contributions to craniofacial morphology in the midface region, so although these individuals appear to have Class III skeletal discrepancy, their molar relationship may be Class I. Past genome-wide association studies (GWASs) on skeletal Class II and III malocclusion suggested that multiple genetic markers contribute to these phenotypes via a multifactorial inheritance model, but research has yet to examine the genetic markers associated with dental Class I malocclusion. Thus, our goal was to conduct a family based GWAS to identify genes across the genome that are associated with Class I malocclusion, as defined by molar relations, in humans with and without clefts. METHODS Our cohort consisted of 739 individuals from 47 Filipino families originally recruited in 2006 to investigate the genetic basis of orofacial clefts. All individuals supplied blood samples for DNA extraction and genotyping, and a 5,766 single nucleotide polymorphism (SNP) custom panel was used for the analyses. We performed a transmission disequilibrium test for participants with and without clefts to identify genetic contributors potentially involved with Class I malocclusion. RESULTS In the total cohort, 13 SNPs had associations that reached the genomic control threshold (p < 0.005), while five SNPs were associated with Class I in the cohort of participants without clefts, including four associations that were identified in the total cohort. The associations for the SNPs ABCA4 rs952499, SOX1-OT rs726455, and RORA rs877228 are of particular interest, as past research found associations between these genes and various craniofacial phenotypes, including cleft lip and/or palate. CONCLUSIONS These findings support the multifactorial inheritance model for dental Class I malocclusion and suggest a common genetic basis for different aspects of craniofacial development.
Collapse
Affiliation(s)
- Mariana Bezamat
- Department of Oral and Craniofacial Sciences, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA, USA
| | - Chelsea E Carver
- Department of Oral and Craniofacial Sciences, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA, USA
| | - Alexandre R Vieira
- School of Dental Medicine, East Carolina University, Greenville, NC, 27834-4354, USA.
| |
Collapse
|
7
|
Alammari F, Al-Hujaily EM, Alshareeda A, Albarakati N, Al-Sowayan BS. Hidden regulators: the emerging roles of lncRNAs in brain development and disease. Front Neurosci 2024; 18:1392688. [PMID: 38841098 PMCID: PMC11150811 DOI: 10.3389/fnins.2024.1392688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/22/2024] [Indexed: 06/07/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as critical players in brain development and disease. These non-coding transcripts, which once considered as "transcriptional junk," are now known for their regulatory roles in gene expression. In brain development, lncRNAs participate in many processes, including neurogenesis, neuronal differentiation, and synaptogenesis. They employ their effect through a wide variety of transcriptional and post-transcriptional regulatory mechanisms through interactions with chromatin modifiers, transcription factors, and other regulatory molecules. Dysregulation of lncRNAs has been associated with certain brain diseases, including Alzheimer's disease, Parkinson's disease, cancer, and neurodevelopmental disorders. Altered expression and function of specific lncRNAs have been implicated with disrupted neuronal connectivity, impaired synaptic plasticity, and aberrant gene expression pattern, highlighting the functional importance of this subclass of brain-enriched RNAs. Moreover, lncRNAs have been identified as potential biomarkers and therapeutic targets for neurological diseases. Here, we give a comprehensive review of the existing knowledge of lncRNAs. Our aim is to provide a better understanding of the diversity of lncRNA structure and functions in brain development and disease. This holds promise for unravelling the complexity of neurodevelopmental and neurodegenerative disorders, paving the way for the development of novel biomarkers and therapeutic targets for improved diagnosis and treatment.
Collapse
Affiliation(s)
- Farah Alammari
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ensaf M. Al-Hujaily
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Alaa Alshareeda
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Saudi Biobank Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Nada Albarakati
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Jeddah, Saudi Arabia
| | - Batla S. Al-Sowayan
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| |
Collapse
|
8
|
Jiang J, Wang Y, Sun M, Luo X, Zhang Z, Wang Y, Li S, Hu D, Zhang J, Wu Z, Chen X, Zhang B, Xu X, Wang S, Xu S, Huang W, Xia L. SOX on tumors, a comfort or a constraint? Cell Death Discov 2024; 10:67. [PMID: 38331879 PMCID: PMC10853543 DOI: 10.1038/s41420-024-01834-6] [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: 11/28/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024] Open
Abstract
The sex-determining region Y (SRY)-related high-mobility group (HMG) box (SOX) family, composed of 20 transcription factors, is a conserved family with a highly homologous HMG domain. Due to their crucial role in determining cell fate, the dysregulation of SOX family members is closely associated with tumorigenesis, including tumor invasion, metastasis, proliferation, apoptosis, epithelial-mesenchymal transition, stemness and drug resistance. Despite considerable research to investigate the mechanisms and functions of the SOX family, confusion remains regarding aspects such as the role of the SOX family in tumor immune microenvironment (TIME) and contradictory impacts the SOX family exerts on tumors. This review summarizes the physiological function of the SOX family and their multiple roles in tumors, with a focus on the relationship between the SOX family and TIME, aiming to propose their potential role in cancer and promising methods for treatment.
Collapse
Affiliation(s)
- Junqing Jiang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
| | - Yufei Wang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
| | - Mengyu Sun
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
| | - Xiangyuan Luo
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
| | - Zerui Zhang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
| | - Yijun Wang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
| | - Siwen Li
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
| | - Dian Hu
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
| | - Jiaqian Zhang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
| | - Zhangfan Wu
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
| | - Xiaoping Chen
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases; Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; Clinical Medicine Research Center for Hepatic Surgery of Hubei Province; Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, 430030, China
| | - Bixiang Zhang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases; Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; Clinical Medicine Research Center for Hepatic Surgery of Hubei Province; Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, 430030, China
| | - Xiao Xu
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Shuai Wang
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Westlake university school of medicine, Hangzhou, 310006, China
| | - Shengjun Xu
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Wenjie Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases; Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; Clinical Medicine Research Center for Hepatic Surgery of Hubei Province; Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, 430030, China.
| | - Limin Xia
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China.
| |
Collapse
|
9
|
Zeidler M, Tavares-Ferreira D, Brougher J, Price TJ, Kress M. NOCICEPTRA2.0 - A comprehensive ncRNA atlas of human native and iPSC-derived sensory neurons. iScience 2023; 26:108525. [PMID: 38162030 PMCID: PMC10755718 DOI: 10.1016/j.isci.2023.108525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/19/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
Non-coding RNAs (ncRNAs) are pivotal in gene regulation during development and disease. MicroRNAs have been extensively studied in neurogenesis. However, limited knowledge exists about the developmental signatures of other ncRNA species in sensory neuron differentiation, and human dorsal root ganglia (DRG) ncRNA expression remains undocumented. To address this gap, we generated a comprehensive atlas of small ncRNA species during iPSC-derived sensory neuron differentiation. Utilizing iPSC-derived sensory neurons and human DRG RNA sequencing, we unveiled signatures describing developmental processes. Our analysis identified ncRNAs associated with various sensory neuron stages. Striking similarities in ncRNA expression signatures between human DRG and iPSC-derived neurons support the latter as a model to bridge the translational gap between preclinical findings and human disorders. In summary, our research sheds light on the role of ncRNA species in human nociceptors, and NOCICEPTRA2.0 offers a comprehensive ncRNA database for sensory neurons that researchers can use to explore ncRNA regulators in nociceptors thoroughly.
Collapse
Affiliation(s)
- Maximilian Zeidler
- Institute of Physiology, Medical University Innsbruck, Innsbruck, Austria
- Omiqa Bioinformatics, Berlin, Germany
| | - Diana Tavares-Ferreira
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Dallas, TX, USA
| | | | - Theodore J. Price
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Dallas, TX, USA
| | - Michaela Kress
- Institute of Physiology, Medical University Innsbruck, Innsbruck, Austria
| |
Collapse
|
10
|
Stevanovic M, Kovacevic-Grujicic N, Petrovic I, Drakulic D, Milivojevic M, Mojsin M. Crosstalk between SOX Genes and Long Non-Coding RNAs in Glioblastoma. Int J Mol Sci 2023; 24:ijms24076392. [PMID: 37047365 PMCID: PMC10094781 DOI: 10.3390/ijms24076392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Glioblastoma (GBM) continues to be the most devastating primary brain malignancy. Despite significant advancements in understanding basic GBM biology and enormous efforts in developing new therapeutic approaches, the prognosis for most GBM patients remains poor with a median survival time of 15 months. Recently, the interplay between the SOX (SRY-related HMG-box) genes and lncRNAs (long non-coding RNAs) has become the focus of GBM research. Both classes of molecules have an aberrant expression in GBM and play essential roles in tumor initiation, progression, therapy resistance, and recurrence. In GBM, SOX and lncRNAs crosstalk through numerous functional axes, some of which are part of the complex transcriptional and epigenetic regulatory mechanisms. This review provides a systematic summary of current literature data on the complex interplay between SOX genes and lncRNAs and represents an effort to underscore the effects of SOX/lncRNA crosstalk on the malignant properties of GBM cells. Furthermore, we highlight the significance of this crosstalk in searching for new biomarkers and therapeutic approaches in GBM treatment.
Collapse
|
11
|
Landshammer A, Bolondi A, Kretzmer H, Much C, Buschow R, Rose A, Wu HJ, Mackowiak SD, Braendl B, Giesselmann P, Tornisiello R, Parsi KM, Huey J, Mielke T, Meierhofer D, Maehr R, Hnisz D, Michor F, Rinn JL, Meissner A. T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation. eLife 2023; 12:e83077. [PMID: 36719724 PMCID: PMC9889090 DOI: 10.7554/elife.83077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/06/2023] [Indexed: 02/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various biological processes, including embryonic development and cellular differentiation. Despite much progress over the past decade, the genome-wide annotation of lncRNAs remains incomplete and many known non-coding loci are still poorly characterized. Here, we report the discovery of a previously unannotated lncRNA that is transcribed 230 kb upstream of the SOX17 gene and located within the same topologically associating domain. We termed it T-REX17 (Transcript Regulating Endoderm and activated by soX17) and show that it is induced following SOX17 activation but its expression is more tightly restricted to early definitive endoderm. Loss of T-REX17 affects crucial functions independent of SOX17 and leads to an aberrant endodermal transcriptome, signaling pathway deregulation and epithelial to mesenchymal transition defects. Consequently, cells lacking the lncRNA cannot further differentiate into more mature endodermal cell types. Taken together, our study identified and characterized T-REX17 as a transiently expressed and essential non-coding regulator in early human endoderm differentiation.
Collapse
Affiliation(s)
- Alexandro Landshammer
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
| | - Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Christian Much
- Department of Biochemistry, University of Colorado Boulder and BioFrontiers InstituteBoulderUnited States
| | - René Buschow
- Max Planck Institute for Molecular Genetics, Microscopy Core FacilityBerlinGermany
| | - Alina Rose
- Helmholtz Institute for Metabolic, Obesity and Vascular ResearchLeipzigGermany
| | - Hua-Jun Wu
- Department of Data Science, Dana-Farber Cancer Institute, Department of Biostatistics, Harvard T. H. Chan School of Public HealthBostonUnited States
- Center for Precision Medicine Multi-Omics Research, School of Basic Medical Sciences, Peking University Health Science Center and Peking University Cancer Hospital and InstituteBeijingChina
| | - Sebastian D Mackowiak
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Bjoern Braendl
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Pay Giesselmann
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Rosaria Tornisiello
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Krishna Mohan Parsi
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Jack Huey
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Thorsten Mielke
- Max Planck Institute for Molecular Genetics, Microscopy Core FacilityBerlinGermany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Core FacilityBerlinGermany
| | - René Maehr
- Center for Precision Medicine Multi-Omics Research, School of Basic Medical Sciences, Peking University Health Science Center and Peking University Cancer Hospital and InstituteBeijingChina
- Diabetes Center of Excellence, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Franziska Michor
- Department of Stem Cell and Regenerative Biology, Harvard UniversityCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Data Science, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard T. H. Chan School of Public HealthBostonUnited States
- The Ludwig Center at Harvard, Boston, MA 02215, USA, and Center for Cancer Evolution, Dana-Farber Cancer InstituteBostonUnited States
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder and BioFrontiers InstituteBoulderUnited States
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
- Department of Stem Cell and Regenerative Biology, Harvard UniversityCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| |
Collapse
|
12
|
Derkus B, Isik M, Eylem CC, Ergin I, Camci CB, Bilgin S, Elbuken C, Arslan YE, Akkulak M, Adali O, Kiran F, Okesola BO, Nemutlu E, Emregul E. Xenogenic Neural Stem Cell-Derived Extracellular Nanovesicles Modulate Human Mesenchymal Stem Cell Fate and Reconstruct Metabolomic Structure. Adv Biol (Weinh) 2022; 6:e2101317. [PMID: 35347890 DOI: 10.1002/adbi.202101317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/02/2022] [Indexed: 01/27/2023]
Abstract
Extracellular nanovesicles, particularly exosomes, can deliver their diverse bioactive biomolecular content, including miRNAs, proteins, and lipids, thus providing a context for investigating the capability of exosomes to induce stem cells toward lineage-specific cells and tissue regeneration. In this study, it is demonstrated that rat subventricular zone neural stem cell-derived exosomes (rSVZ-NSCExo) can control neural-lineage specification of human mesenchymal stem cells (hMSCs). Microarray analysis shows that the miRNA content of rSVZ-NSCExo is a faithful representation of rSVZ tissue. Through immunocytochemistry, gene expression, and multi-omics analyses, the capability to use rSVZ-NSCExo to induce hMSCs into a neuroglial or neural stem cell phenotype and genotype in a temporal and dose-dependent manner via multiple signaling pathways is demonstrated. The current study presents a new and innovative strategy to modulate hMSCs fate by harnessing the molecular content of exosomes, thus suggesting future opportunities for rSVZ-NSCExo in nerve tissue regeneration.
Collapse
Affiliation(s)
- Burak Derkus
- Stem Cell Research Lab, Department of ChemistryFaculty of Science, Ankara University, Ankara, 06560, Turkey.,Interdisciplinary Research Unit for Advanced Materials (INTRAM) Department of Chemistry, Faculty of Science, Ankara University, Ankara, 06560, Turkey
| | - Melis Isik
- Interdisciplinary Research Unit for Advanced Materials (INTRAM) Department of Chemistry, Faculty of Science, Ankara University, Ankara, 06560, Turkey
| | - Cemil Can Eylem
- Analytical Chemistry Division, Faculty of Pharmacy, Hacettepe University, Ankara, 06530, Turkey
| | - Irem Ergin
- Department of Surgery, Faculty of Veterinary Medicine, Ankara University, Turkey
| | - Can Berk Camci
- Interdisciplinary Research Unit for Advanced Materials (INTRAM) Department of Chemistry, Faculty of Science, Ankara University, Ankara, 06560, Turkey
| | - Sila Bilgin
- Interdisciplinary Research Unit for Advanced Materials (INTRAM) Department of Chemistry, Faculty of Science, Ankara University, Ankara, 06560, Turkey
| | - Caglar Elbuken
- UNAM-National Nanotechnology Research Center, Institute of Materials Science and Nanotechnology, Bilkent University, Ankara, 06800, Turkey.,Faculty of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Oulu, Oulu, 90014, Finland
| | - Yavuz Emre Arslan
- Regenerative Biomaterials Laboratory, Department of Bioengineering, Engineering Faculty, Canakkale Onsekiz Mart University, Canakkale, 17100, Turkey
| | - Merve Akkulak
- Department of Biological Sciences, Faculty of Science, Middle East Technical University, Ankara, 06800, Turkey
| | - Orhan Adali
- Department of Biological Sciences, Faculty of Science, Middle East Technical University, Ankara, 06800, Turkey
| | - Fadime Kiran
- Department of Biology, Faculty of Science, Ankara University, Ankara, 06560, Turkey
| | - Babatunde O Okesola
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, Faculty of Medicine, University of Liverpool, Liverpool, L7 8TX, UK
| | - Emirhan Nemutlu
- Analytical Chemistry Division, Faculty of Pharmacy, Hacettepe University, Ankara, 06530, Turkey.,Bioanalytic and Omics Laboratory, Faculty of Pharmacy, Hacettepe University, Ankara, 06530, Turkey
| | - Emel Emregul
- Interdisciplinary Research Unit for Advanced Materials (INTRAM) Department of Chemistry, Faculty of Science, Ankara University, Ankara, 06560, Turkey
| |
Collapse
|
13
|
The Emerging Roles of Long Non-Coding RNAs in Intellectual Disability and Related Neurodevelopmental Disorders. Int J Mol Sci 2022; 23:ijms23116118. [PMID: 35682796 PMCID: PMC9181295 DOI: 10.3390/ijms23116118] [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: 04/30/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 02/05/2023] Open
Abstract
In the human brain, long non-coding RNAs (lncRNAs) are widely expressed in an exquisitely temporally and spatially regulated manner, thus suggesting their contribution to normal brain development and their probable involvement in the molecular pathology of neurodevelopmental disorders (NDD). Bypassing the classic protein-centric conception of disease mechanisms, some studies have been conducted to identify and characterize the putative roles of non-coding sequences in the genetic pathogenesis and diagnosis of complex diseases. However, their involvement in NDD, and more specifically in intellectual disability (ID), is still poorly documented and only a few genomic alterations affecting the lncRNAs function and/or expression have been causally linked to the disease endophenotype. Considering that a significant fraction of patients still lacks a genetic or molecular explanation, we expect that a deeper investigation of the non-coding genome will unravel novel pathogenic mechanisms, opening new translational opportunities. Here, we present evidence of the possible involvement of many lncRNAs in the etiology of different forms of ID and NDD, grouping the candidate disease-genes in the most frequently affected cellular processes in which ID-risk genes were previously collected. We also illustrate new approaches for the identification and prioritization of NDD-risk lncRNAs, together with the current strategies to exploit them in diagnosis.
Collapse
|
14
|
Morys J, Borkowska P, Zielinska A, Kowalski J. Study of the influence of NGF-β gene overexpression in human mesenchymal stem cells on the expression level of SOX1 and neural pathway genes. Mol Biol Rep 2022; 49:4435-4441. [PMID: 35348963 DOI: 10.1007/s11033-022-07283-7] [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: 01/14/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Nerve growth factor (NGF) is a protein exhibiting an influence on the neural development and also, its' impact on the stem cells remains a great potential treatment strategy. The influence of its overexpression on the neural pathway differentiation on Wharton's Jelly derived MSC (WJ-MSC) has not been studied so far, but considering the fact that these cells are relatively easy to obtain, using them may indicate an innovative change in stem cell therapies. The aim of this study was to evaluate the effect of NGF overexpression in human mesenchymal stem cells (MSC) on SOX1 and genes related to the neural pathway. METHODS AND RESULTS The lentiviral transduction was performed in order to obtain the NGF overexpression, as well as RT-PCR to evaluate the expression level SOX1, SOX2, NES, NGF under influence of overexpressed NGF protein in WJ-MSC. During the study we have observed a decrease in SOX1 expression as the marker of neural stem cells. Other than that an increase of SOX2, NES and NGF was noticed, as they all are markers of early-neural as well as already differentiated neural cells. The results show a great potential of using those examined genes' expression as a form of a new stem cell therapy. CONCLUSIONS The achieved overexpression of NGF in this study, led the modified MSC onto the neural pathway as well as caused a decrease of SOX1 expression and an increase of expression of genes related to neural differentiated cells.
Collapse
Affiliation(s)
- Julia Morys
- Department of Medical Genetics, Medical University of Silesia, Jednosci 8 street, 41-200, Sosnowiec, Poland.
| | - Paulina Borkowska
- Department of Medical Genetics, Medical University of Silesia, Jednosci 8 street, 41-200, Sosnowiec, Poland
| | - Aleksandra Zielinska
- Department of Medical Genetics, Medical University of Silesia, Jednosci 8 street, 41-200, Sosnowiec, Poland
| | - Jan Kowalski
- Department of Medical Genetics, Medical University of Silesia, Jednosci 8 street, 41-200, Sosnowiec, Poland
| |
Collapse
|
15
|
Xi J, Xu Y, Guo Z, Li J, Wu Y, Sun Q, Wang Y, Chen M, Zhu S, Bian S, Kang J. LncRNA SOX1-OT V1 acts as a decoy of HDAC10 to promote SOX1-dependent hESC neuronal differentiation. EMBO Rep 2022; 23:e53015. [PMID: 34927789 PMCID: PMC8811645 DOI: 10.15252/embr.202153015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 02/05/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are abundantly expressed in the nervous system, but their regulatory roles in neuronal differentiation are poorly understood. Using a human embryonic stem cell (hESC)-based 2D neural differentiation approach and a 3D cerebral organoid system, we show that SOX1-OT variant 1 (SOX1-OT V1), a SOX1 overlapping noncoding RNA, plays essential roles in both dorsal cortical neuron differentiation and ventral GABAergic neuron differentiation by facilitating SOX1 expression. SOX1-OT V1 physically interacts with HDAC10 through its 5' region, acts as a decoy to block HDAC10 binding to the SOX1 promoter, and thus maintains histone acetylation levels at the SOX1 promoter. SOX1 in turn activates ASCL1 expression and promotes neuronal differentiation. Taken together, we identify a SOX1-OT V1/HDAC10-SOX1-ASCL1 axis, which promotes neurogenesis, highlighting a role for lncRNAs in hESC neuronal differentiation.
Collapse
Affiliation(s)
- Jiajie Xi
- Clinical and Translational Research Center of Shanghai First Maternity and Infant HospitalShanghai Key Laboratory of Maternal Fetal MedicineShanghai Key Laboratory of Signaling and Disease ResearchFrontier Science Center for Stem Cell ResearchNational Stem Cell Translational Resource CenterSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Yanxin Xu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant HospitalShanghai Key Laboratory of Maternal Fetal MedicineShanghai Key Laboratory of Signaling and Disease ResearchFrontier Science Center for Stem Cell ResearchNational Stem Cell Translational Resource CenterSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Zhenming Guo
- Institute for Regenerative MedicineShanghai East HospitalSchool of Life Sciences and TechnologyFrontier Science Center for Stem Cell ResearchTongji UniversityShanghaiChina
| | - Jianguo Li
- Clinical and Translational Research Center of Shanghai First Maternity and Infant HospitalShanghai Key Laboratory of Maternal Fetal MedicineShanghai Key Laboratory of Signaling and Disease ResearchFrontier Science Center for Stem Cell ResearchNational Stem Cell Translational Resource CenterSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Yukang Wu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant HospitalShanghai Key Laboratory of Maternal Fetal MedicineShanghai Key Laboratory of Signaling and Disease ResearchFrontier Science Center for Stem Cell ResearchNational Stem Cell Translational Resource CenterSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Qiaoyi Sun
- Clinical and Translational Research Center of Shanghai First Maternity and Infant HospitalShanghai Key Laboratory of Maternal Fetal MedicineShanghai Key Laboratory of Signaling and Disease ResearchFrontier Science Center for Stem Cell ResearchNational Stem Cell Translational Resource CenterSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Yuxi Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant HospitalShanghai Key Laboratory of Maternal Fetal MedicineShanghai Key Laboratory of Signaling and Disease ResearchFrontier Science Center for Stem Cell ResearchNational Stem Cell Translational Resource CenterSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Mengxia Chen
- Institute for Regenerative MedicineShanghai East HospitalSchool of Life Sciences and TechnologyFrontier Science Center for Stem Cell ResearchTongji UniversityShanghaiChina
| | - Songcheng Zhu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant HospitalShanghai Key Laboratory of Maternal Fetal MedicineShanghai Key Laboratory of Signaling and Disease ResearchFrontier Science Center for Stem Cell ResearchNational Stem Cell Translational Resource CenterSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Shan Bian
- Institute for Regenerative MedicineShanghai East HospitalSchool of Life Sciences and TechnologyFrontier Science Center for Stem Cell ResearchTongji UniversityShanghaiChina
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant HospitalShanghai Key Laboratory of Maternal Fetal MedicineShanghai Key Laboratory of Signaling and Disease ResearchFrontier Science Center for Stem Cell ResearchNational Stem Cell Translational Resource CenterSchool of Life Sciences and TechnologyTongji UniversityShanghaiChina
| |
Collapse
|
16
|
Long non-coding RNAs in lung cancer: implications for lineage plasticity-mediated TKI resistance. Cell Mol Life Sci 2020; 78:1983-2000. [PMID: 33170304 PMCID: PMC7965852 DOI: 10.1007/s00018-020-03691-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/15/2020] [Accepted: 10/23/2020] [Indexed: 02/06/2023]
Abstract
The efficacy of targeted therapy in non-small-cell lung cancer (NSCLC) has been impeded by various mechanisms of resistance. Besides the mutations in targeted oncogenes, reversible lineage plasticity has recently considered to play a role in the development of tyrosine kinase inhibitors (TKI) resistance in NSCLC. Lineage plasticity enables cells to transfer from one committed developmental pathway to another, and has been a trigger of tumor adaptation to adverse microenvironment conditions including exposure to various therapies. More importantly, besides somatic mutation, lineage plasticity has also been proposed as another source of intratumoural heterogeneity. Lineage plasticity can drive NSCLC cells to a new cell identity which no longer depends on the drug-targeted pathway. Histological transformation and epithelial–mesenchymal transition are two well-known pathways of lineage plasticity-mediated TKI resistance in NSCLC. In the last decade, increased re-biopsy practice upon disease recurrence has increased the recognition of lineage plasticity induced resistance in NSCLC and has improved our understanding of the underlying biology. Long non-coding RNAs (lncRNAs), the dark matter of the genome, are capable of regulating variant malignant processes of NSCLC like the invisible hands. Recent evidence suggests that lncRNAs are involved in TKI resistance in NSCLC, particularly in lineage plasticity-mediated resistance. In this review, we summarize the mechanisms of lncRNAs in regulating lineage plasticity and TKI resistance in NSCLC. We also discuss how understanding these themes can alter therapeutic strategies, including combination therapy approaches to overcome TKI resistance.
Collapse
|
17
|
Pan L, McClain L, Shaw P, Donnellan N, Chu T, Finegold D, Peters D. Non-invasive epigenomic molecular phenotyping of the human brain via liquid biopsy of cerebrospinal fluid and next generation sequencing. Eur J Neurosci 2020; 52:4536-4545. [PMID: 33020990 DOI: 10.1111/ejn.14997] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 01/15/2023]
Abstract
Our goal was to undertake a genome-wide epigenomic liquid biopsy of cerebrospinal fluid (CSF) for the comprehensive analysis of cell-free DNA (cfDNA) methylation signatures in the human central nervous system (CNS). Solution-phase hybridization and massively parallel sequencing of bisulfite converted human DNA was employed to compare methylation signatures of cfDNA obtained from CSF with plasma. Recovery of cfDNA from CSF was relatively low (68-840 pg/mL) compared to plasma (2720-8390 pg/mL) and cfDNA fragments from CSF were approximately 20 bp shorter than their plasma-derived counterparts. Distributions of CpG methylation signatures were significantly altered between CSF and plasma, both globally and at the level of functional elements including exons, introns, CpG islands, and shores. Sliding window analysis was used to identify differentially methylated regions. We found numerous gene/locus-specific differences in CpG methylation between cfDNA from CSF and plasma. These loci were more frequently hypomethylated in CSF compared to plasma. Differentially methylated CpGs in CSF were identified in genes related to branching of neurites and neuronal development. Using the GTEx RNA expression database, we found clear association between tissue-specific gene expression in the CNS and cfDNA methylation patterns in CSF. Ingenuity pathway analysis of differentially methylated regions identified an enrichment of functional pathways related to neurobiology. In conclusion, we present a genome-wide analysis of DNA methylation in human CSF. Our methods and the resulting data demonstrate the potential of epigenomic liquid biopsy of the human CNS for molecular phenotyping of brain-derived DNA methylation signatures.
Collapse
Affiliation(s)
- Lisa Pan
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, USA.,Department of Psychiatry, University of Pittsburgh, Pittsburgh, USA
| | - Lora McClain
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, USA
| | | | - Nicole Donnellan
- Magee-Womens Research Institute, Pittsburgh, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, USA
| | - Tianjiao Chu
- Magee-Womens Research Institute, Pittsburgh, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, USA
| | - David Finegold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, USA
| | - David Peters
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, USA.,Department of Psychiatry, University of Pittsburgh, Pittsburgh, USA.,Magee-Womens Research Institute, Pittsburgh, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, USA
| |
Collapse
|
18
|
Jung E, Alfonso J, Monyer H, Wick W, Winkler F. Neuronal signatures in cancer. Int J Cancer 2020; 147:3281-3291. [PMID: 32510582 DOI: 10.1002/ijc.33138] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/26/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022]
Abstract
Despite advances in the treatment of solid tumors, the prognosis of patients with many cancers remains poor, particularly of those with primary and metastatic brain tumors. In the last years, "Cancer Neuroscience" emerged as novel field of research at the crossroads of oncology and classical neuroscience. In primary brain tumors, including glioblastoma (GB), communicating networks that render tumor cells resistant against cytotoxic therapies were identified. To build these networks, GB cells extend neurite-like protrusions called tumor microtubes (TMs). Synapses on TMs allow tumor cells to retrieve neuronal input that fosters growth. Single cell sequencing further revealed that primary brain tumors recapitulate many steps of neurodevelopment. Interestingly, neuronal characteristics, including the ability to extend neurite-like protrusions, neuronal gene expression signatures and interactions with neurons, have now been found not only in brain and neuroendocrine tumors but also in some cancers of epithelial origin. In this review, we will provide an overview about neurite-like protrusions as well as neurodevelopmental origins, hierarchies and gene expression signatures in cancer. We will also discuss how "Cancer Neuroscience" might provide a framework for the development of novel therapies.
Collapse
Affiliation(s)
- Erik Jung
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julieta Alfonso
- Department of Clinical Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hannah Monyer
- Department of Clinical Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Clinical Neurobiology, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Wolfgang Wick
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Winkler
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
19
|
Zhao Y, Liu H, Zhang Q, Zhang Y. The functions of long non-coding RNAs in neural stem cell proliferation and differentiation. Cell Biosci 2020; 10:74. [PMID: 32514332 PMCID: PMC7260844 DOI: 10.1186/s13578-020-00435-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/23/2020] [Indexed: 02/06/2023] Open
Abstract
The capacities for neural stem cells (NSCs) self-renewal with differentiation are need to be precisely regulated for ensuring brain development and homeostasis. Recently, increasing number of studies have highlighted that long non-coding RNAs (lncRNAs) are associated with NSC fate determination during brain development stages. LncRNAs are a class of non-coding RNAs more than 200 nucleotides without protein-coding potential and function as novel critical regulators in multiple biological processes. However, the correlation between lncRNAs and NSC fate decision still need to be explored in-depth. In this review, we will summarize the roles and molecular mechanisms of lncRNAs focusing on NSCs self-renewal, neurogenesis and gliogenesis over the course of neural development, still more, dysregulation of lncRNAs in all stage of neural development have closely relationship with development disorders or glioma. In brief, lncRNAs may be explored as effective modulators in NSCs related neural development and novel biomarkers for diagnosis and prognosis of neurological disorders in the future.
Collapse
Affiliation(s)
- Yanfang Zhao
- Institute of Biomedical Research, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, School for Life Science, Shandong University of Technology, Zibo, China
| | - Hongliang Liu
- Institute of Biomedical Research, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, School for Life Science, Shandong University of Technology, Zibo, China
| | - Qili Zhang
- Institute of Biomedical Research, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, School for Life Science, Shandong University of Technology, Zibo, China
| | - Yuan Zhang
- Institute for Translational Medicine, Qingdao University, Qingdao, China
| |
Collapse
|
20
|
Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. EMBO J 2020; 39:e103777. [PMID: 32090359 PMCID: PMC7073466 DOI: 10.15252/embj.2019103777] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
Research on non-coding RNA (ncRNA) is a rapidly expanding field. Providing an official gene symbol and name to ncRNA genes brings order to otherwise potential chaos as it allows unambiguous communication about each gene. The HUGO Gene Nomenclature Committee (HGNC, www.genenames.org) is the only group with the authority to approve symbols for human genes. The HGNC works with specialist advisors for different classes of ncRNA to ensure that ncRNA nomenclature is accurate and informative, where possible. Here, we review each major class of ncRNA that is currently annotated in the human genome and describe how each class is assigned a standardised nomenclature.
Collapse
Affiliation(s)
- Ruth L Seal
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Dawn O'Reilly
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew J Pierce
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, Santa Fe, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Sandra L Wolin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| |
Collapse
|
21
|
Liang Z, Xu J, Gu C. Novel role of the SRY-related high-mobility-group box D gene in cancer. Semin Cancer Biol 2019; 67:83-90. [PMID: 31356865 DOI: 10.1016/j.semcancer.2019.07.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/28/2019] [Accepted: 07/16/2019] [Indexed: 12/18/2022]
Abstract
The SRY-related high-mobility-group box (Sox) gene family encodes a set of transcription factors and is defined by the presence of highly conserved domains. The Sox gene can be divided into 10 groups (A-J). The SoxD subpopulation consists of Sox5, Sox6, Sox13 and Sox23, which are involved in the transcriptional regulation of developmental processes, including embryonic development, nerve growth and cartilage formation. Recently, the SoxD gene family was recognized as important transcriptional regulators associated with many types of cancer. In addition, Sox5 and Sox6 are representatives of the D subfamily, and there are many related studies; however, there are few reports on Sox13 and Sox23. In this review, we first introduce the structures of the SoxD genes. Next, we summarize the latest research progress on SoxD in various types of cancer. Finally, we discuss the potential direction of future SoxD research. In general, the information reviewed here may contribute to future experimental design and increase the potential of SoxD as a cancer treatment target.
Collapse
Affiliation(s)
- Zhenxing Liang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East, Zhengzhou 450052, China.
| | - Jing Xu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East, Zhengzhou 450052, China
| | - Chunhu Gu
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, 127 Changle West Road, Xi'an 710032, China.
| |
Collapse
|
22
|
Kumar P, Mistri TK. Transcription factors in SOX family: Potent regulators for cancer initiation and development in the human body. Semin Cancer Biol 2019; 67:105-113. [PMID: 31288067 DOI: 10.1016/j.semcancer.2019.06.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 06/17/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022]
Abstract
Transcription factors (TFs) have a key role in controlling the gene regulatory network that sustains explicit cell states in humans. However, an uncontrolled regulation of these genes potentially results in a wide range of diseases, including cancer. Genes of the SOX family are indeed crucial as deregulation of SOX family TFs can potentially lead to changes in cell fate as well as irregular cell growth. SOX TFs are a conserved group of transcriptional regulators that mediate DNA binding through a highly conserved high-mobility group (HMG) domain. Accumulating evidence demonstrates that cell fate and differentiation in major developmental processes are controlled by SOX TFs. Besides; numerous reports indicate that both up- and down-regulation of SOX TFs may induce cancer progression. In this review, we discuss the involvement of key TFs of SOX family in human cancers.
Collapse
Affiliation(s)
- Prasann Kumar
- The Division of Research and Development, Lovely Professional University, Jalandhar, Punjab, 144411, India; The Department of Agronomy, Lovely Professional University, Jalandhar, Punjab, 144411, India
| | - Tapan Kumar Mistri
- The Division of Research and Development, Lovely Professional University, Jalandhar, Punjab, 144411, India; The Department of Chemistry, Lovely Professional University, Jalandhar, Punjab, 144411, India.
| |
Collapse
|
23
|
The role of SOX family members in solid tumours and metastasis. Semin Cancer Biol 2019; 67:122-153. [PMID: 30914279 DOI: 10.1016/j.semcancer.2019.03.004] [Citation(s) in RCA: 260] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/07/2019] [Accepted: 03/21/2019] [Indexed: 02/07/2023]
Abstract
Cancer is a heavy burden for humans across the world with high morbidity and mortality. Transcription factors including sex determining region Y (SRY)-related high-mobility group (HMG) box (SOX) proteins are thought to be involved in the regulation of specific biological processes. The deregulation of gene expression programs can lead to cancer development. Here, we review the role of the SOX family in breast cancer, prostate cancer, renal cell carcinoma, thyroid cancer, brain tumours, gastrointestinal and lung tumours as well as the entailing therapeutic implications. The SOX family consists of more than 20 members that mediate DNA binding by the HMG domain and have regulatory functions in development, cell-fate decision, and differentiation. SOX2, SOX4, SOX5, SOX8, SOX9, and SOX18 are up-regulated in different cancer types and have been found to be associated with poor prognosis, while the up-regulation of SOX11 and SOX30 appears to be favourable for the outcome in other cancer types. SOX2, SOX4, SOX5 and other SOX members are involved in tumorigenesis, e.g. SOX2 is markedly up-regulated in chemotherapy resistant cells. The SoxF family (SOX7, SOX17, SOX18) plays an important role in angio- and lymphangiogenesis, with SOX18 seemingly being an attractive target for anti-angiogenic therapy and the treatment of metastatic disease in cancer. In summary, SOX transcription factors play an important role in cancer progression, including tumorigenesis, changes in the tumour microenvironment, and metastasis. Certain SOX proteins are potential molecular markers for cancer prognosis and putative potential therapeutic targets, but further investigations are required to understand their physiological functions.
Collapse
|
24
|
Regulation of Neuroregeneration by Long Noncoding RNAs. Mol Cell 2018; 72:553-567.e5. [PMID: 30401432 DOI: 10.1016/j.molcel.2018.09.021] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/27/2018] [Accepted: 09/14/2018] [Indexed: 12/24/2022]
Abstract
In mammals, neurons in the peripheral nervous system (PNS) have regenerative capacity following injury, but it is generally absent in the CNS. This difference is attributed, at least in part, to the intrinsic ability of PNS neurons to activate a unique regenerative transcriptional program following injury. Here, we profiled gene expression following sciatic nerve crush in mice and identified long noncoding RNAs (lncRNAs) that act in the regenerating neurons and which are typically not expressed in other contexts. We show that two of these lncRNAs regulate the extent of neuronal outgrowth. We then focus on one of these, Silc1, and show that it regulates neuroregeneration in cultured cells and in vivo, through cis-acting activation of the transcription factor Sox11.
Collapse
|
25
|
Abdalla BA, Li Z, Ouyang H, Jebessa E, Sun T, Yu JA, Cai B, Chen B, Nie Q, Zhang X. A Novel Dnmt3a1 Transcript Inhibits Adipogenesis. Front Physiol 2018; 9:1270. [PMID: 30333755 PMCID: PMC6176318 DOI: 10.3389/fphys.2018.01270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 08/21/2018] [Indexed: 12/17/2022] Open
Abstract
DNA (cytosine-5)-methyltransferase 3a (Dnmt3a) is an enzyme that catalyzes the transfer of methyl groups to specific CpG forms in DNA. In mammals, two variant transcripts of Dnmt3a have been successfully identified. To the best of our knowledge, no Dnmt3a transcripts in an avian have been successfully identified. This study was performed to detect different transcripts of Dnmt3a in chickens and to examine whether a novel Dnmt3a transcript named Dnmt3a1 may regulate adipogenesis. In addition to cloning, sequencing, transcript detection, and expression studies, a novel Dnmt3a1 transcript overexpression and knockdown were conducted to explore the potential role of Dnmt3a1 in preadipocyte proliferation and the early stage of adipocyte differentiation. In chicken abdominal fat tissue, we detected a novel Dnmt3a1 transcript that differs from Dnmt3a by lacking 23 amino acids at the exon-1/exon-2 border. Dnmt3a1 mRNA was ubiquitously expressed in a variety of tissues or cells and highly expressed in chicken adipose tissue/cells. The expression of Dnmt3a1 was regulated under different physiological conditions including aging, fasting, and high-fat diet. In addition, overexpression of Dnmt3a1 significantly decreased preadipocyte proliferation and induced cell-cycle arrest while its inhibition increased cell proliferation and S-phase cells. Furthermore, the overexpression of Dnmt3a1 significantly upregulated the mRNA level of cell-cycle-related genes, such as CDKN1A, CDKN1B, CCNB3, CCND2, CCNG2, CDKN2B, and CDK9, or the protein level of CDKN1A, CDKN1B, and CCNG2. Conversely, the knockdown of Dnmt3a1 by siRNA had the opposite effects. Moreover, during early adipocyte differentiation, the overexpression of Dnmt3a1 significantly decreased the mRNA and the protein levels of PPAR-γ, C/EBP-α, ADIPOR1, and STAT3, and the mRNA levels of FAS, LEPR, LPL, PRKAB2, and ATGL. In contrast, their expression was significantly increased after the knockdown of Dnmt3a1. Taken together, we identified a novel transcript of Dnmt3a, and it played a potential role in adipogenesis.
Collapse
Affiliation(s)
- Bahareldin A Abdalla
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Zhenhui Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Hongjia Ouyang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Endashaw Jebessa
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Tianhao Sun
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Jia-Ao Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Bolin Cai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Biao Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| |
Collapse
|
26
|
Harrison R, Lugo Leija HA, Strohbuecker S, Crutchley J, Marsh S, Denning C, El Haj A, Sottile V. Development and validation of broad-spectrum magnetic particle labelling processes for cell therapy manufacturing. Stem Cell Res Ther 2018; 9:248. [PMID: 30257709 PMCID: PMC6158868 DOI: 10.1186/s13287-018-0968-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/26/2018] [Accepted: 08/02/2018] [Indexed: 12/20/2022] Open
Abstract
Background Stem cells are increasingly seen as a solution for many health challenges for an ageing population. However, their potential benefits in the clinic are currently curtailed by technical challenges such as high cell dose requirements and point of care delivery, which pose sourcing and logistics challenges. Cell manufacturing solutions are currently in development to address the supply issue, and ancillary technologies such as nanoparticle-based labelling are being developed to improve stem cell delivery and enable post-treatment follow-up. Methods The application of magnetic particle (MP) labelling to potentially scalable cell manufacturing processes was investigated in a range of therapeutically relevant cells, including mesenchymal stromal cells (MSC), cardiomyocytes (CMC) and neural progenitor cells (ReN). The efficiency and the biological effect of particle labelling were analysed using fluorescent imaging and cellular assays. Results Flow cytometry and fluorescent microscopy confirmed efficient labelling of monolayer cultures. Viability was shown to be retained post labelling for all three cell types. MSC and CMC demonstrated higher tolerance to MP doses up to 100× the standard concentration. This approach was also successful for MP labelling of suspension cultures, demonstrating efficient MP uptake within 3 h, while cell viability was unaffected by this suspension labelling process. Furthermore, a procedure to enable the storing of MP-labelled cell populations to facilitate cold chain transport to the site of clinical use was investigated. When MP-labelled cells were stored in hypothermic conditions using HypoThermosol solution for 24 h, cell viability and differentiation potential were retained post storage for ReN, MSC and beating CMC. Conclusions Our results show that a generic MP labelling strategy was successfully developed for a range of clinically relevant cell populations, in both monolayer and suspension cultures. MP-labelled cell populations were able to undergo transient low-temperature storage whilst maintaining functional capacity in vitro. These results suggest that this MP labelling approach can be integrated into cell manufacturing and cold chain transport processes required for future cell therapy approaches. Electronic supplementary material The online version of this article (10.1186/s13287-018-0968-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Richard Harrison
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Medicine, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Hilda Anaid Lugo Leija
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Medicine, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Stephanie Strohbuecker
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Medicine, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - James Crutchley
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Medicine, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Sarah Marsh
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Medicine, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Chris Denning
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Medicine, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alicia El Haj
- Institute for Science and Technology in Medicine-Keele University, Stoke-on-Trent, ST4 7QB, UK
| | - Virginie Sottile
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Medicine, The University of Nottingham, Nottingham, NG7 2RD, UK.
| |
Collapse
|
27
|
Wu H, Yao R, Yu S, Chen H, Cai J, Peng S, Pang X, Sun X, Zhang Y, Zhang J. Transcriptome analysis identifies the potential roles of long non‐coding RNAs during parainfluenza virus infection. FEBS Lett 2018; 592:2444-2457. [DOI: 10.1002/1873-3468.13166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Haoming Wu
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Ran‐Ran Yao
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Shuang‐Shuang Yu
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Hong‐Yan Chen
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Juan Cai
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Shu‐Jie Peng
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Xue‐Wen Pang
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Xiu‐Yuan Sun
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Yu Zhang
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| | - Jun Zhang
- Department of Immunology School of Basic Medical Sciences Key Laboratory of Medical Immunology Ministry of Health (Peking University) Peking University Health Science Center Beijing China
| |
Collapse
|