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Erickson JR, Walker SE, Arenas Gomez CM, Echeverri K. Sall4 regulates downstream patterning genes during limb regeneration. Dev Biol 2024; 515:151-159. [PMID: 39067503 PMCID: PMC11325254 DOI: 10.1016/j.ydbio.2024.07.015] [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: 01/26/2024] [Revised: 07/19/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Many salamanders can completely regenerate a fully functional limb. Limb regeneration is a carefully coordinated process involving several defined stages. One key event during the regeneration process is the patterning of the blastema to inform cells of what they must differentiate into. Although it is known that many genes involved in the initial development of the limb are re-used during regeneration, the exact molecular circuitry involved in this process is not fully understood. Several large-scale transcriptional profiling studies of axolotl limb regeneration have identified many transcription factors that are up-regulated after limb amputation. Sall4 is a transcription factor that has been identified to play essential roles in maintaining cells in an undifferentiated state during development and also plays a unique role in limb development. Inactivation of Sall4 during limb bud development results in defects in anterior-posterior patterning of the limb. Sall4 has been found to be up-regulated during limb regeneration in both Xenopus and salamanders, but to date it function has been untested. We confirmed that Sall4 is up-regulated during limb regeneration in the axolotl using qRT-PCR and identified that it is present in the skin cells and also in cells within the blastema. Using CRISPR technology we microinjected gRNAs specific for Sall4 complexed with cas9 protein into the blastema to specifically knockout Sall4 in blastema cells only. This resulted in limb regenerate defects, including missing digits, fusion of digit elements, and defects in the radius and ulna. This suggests that during regeneration Sall4 may play a similar role in regulating the specification of anterior-proximal skeletal elements.
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Affiliation(s)
- J R Erickson
- Department of Genetics, Dell Biology and Development, Stell Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - S E Walker
- Marine Biological Laboratory, University of Chicago, Eugene Bell Center for Regeneration Biology and Tissue Engineering, Woods Hole, MA, USA
| | - C M Arenas Gomez
- Marine Biological Laboratory, University of Chicago, Eugene Bell Center for Regeneration Biology and Tissue Engineering, Woods Hole, MA, USA
| | - K Echeverri
- Department of Genetics, Dell Biology and Development, Stell Cell Institute, University of Minnesota, Minneapolis, MN, USA; Marine Biological Laboratory, University of Chicago, Eugene Bell Center for Regeneration Biology and Tissue Engineering, Woods Hole, MA, USA.
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2
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Ming J, Lin L, Li J, Wu L, Fang S, Huang T, Fu Y, Liu D, Zhang W, Li C, Yang Y, Huang Y, Qin Y, Kuang J, Huang X, Guo L, Zhang X, Liu J, Chen J, Zhao C, Wang B, Pei D. Cell fate decision by a morphogen-transcription factor-chromatin modifier axis. Nat Commun 2024; 15:6365. [PMID: 39075094 PMCID: PMC11286941 DOI: 10.1038/s41467-024-50144-z] [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: 09/21/2023] [Accepted: 06/28/2024] [Indexed: 07/31/2024] Open
Abstract
Cell fate decisions remain poorly understood at the molecular level. Embryogenesis provides a unique opportunity to analyze molecular details associated with cell fate decisions. Works based on model organisms have provided a conceptual framework of genes that specify cell fate control, for example, transcription factors (TFs) controlling processes from pluripotency to immunity1. How TFs specify cell fate remains poorly understood. Here we report that SALL4 relies on NuRD (nucleosome-remodeling and deacetylase complex) to interpret BMP4 signal and decide cell fate in a well-controlled in vitro system. While NuRD complex cooperates with SALL4 to convert mouse embryonic fibroblasts or MEFs to pluripotency, BMP4 diverts the same process to an alternative fate, PrE (primitive endoderm). Mechanistically, BMP4 signals the dissociation of SALL4 from NuRD physically to establish a gene regulatory network for PrE. Our results provide a conceptual framework to explore the rich landscapes of cell fate choices intrinsic to development in higher organisms involving morphogen-TF-chromatin modifier pathways.
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Affiliation(s)
- Jin Ming
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Lihui Lin
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jiajun Li
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Linlin Wu
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Shicai Fang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tao Huang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yu Fu
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Dong Liu
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Wenhui Zhang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Chen Li
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yongzheng Yang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yi Huang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yue Qin
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Junqi Kuang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China
| | - Xingnan Huang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Liman Guo
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaofei Zhang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jing Liu
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Chengchen Zhao
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
| | - Bo Wang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
- Zhejiang University of Science and Technology, School of Information and Electronic Engineering, Hangzhou, Zhejiang, China.
- Key Laboratory of Biomedical Intelligent Computing Technology of Zhejiang Province, Hangzhou, Zhejiang, China.
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China.
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Chu X, Tian W, Ning J, Xiao G, Zhou Y, Wang Z, Zhai Z, Tanzhu G, Yang J, Zhou R. Cancer stem cells: advances in knowledge and implications for cancer therapy. Signal Transduct Target Ther 2024; 9:170. [PMID: 38965243 PMCID: PMC11224386 DOI: 10.1038/s41392-024-01851-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/27/2024] [Accepted: 04/28/2024] [Indexed: 07/06/2024] Open
Abstract
Cancer stem cells (CSCs), a small subset of cells in tumors that are characterized by self-renewal and continuous proliferation, lead to tumorigenesis, metastasis, and maintain tumor heterogeneity. Cancer continues to be a significant global disease burden. In the past, surgery, radiotherapy, and chemotherapy were the main cancer treatments. The technology of cancer treatments continues to develop and advance, and the emergence of targeted therapy, and immunotherapy provides more options for patients to a certain extent. However, the limitations of efficacy and treatment resistance are still inevitable. Our review begins with a brief introduction of the historical discoveries, original hypotheses, and pathways that regulate CSCs, such as WNT/β-Catenin, hedgehog, Notch, NF-κB, JAK/STAT, TGF-β, PI3K/AKT, PPAR pathway, and their crosstalk. We focus on the role of CSCs in various therapeutic outcomes and resistance, including how the treatments affect the content of CSCs and the alteration of related molecules, CSCs-mediated therapeutic resistance, and the clinical value of targeting CSCs in patients with refractory, progressed or advanced tumors. In summary, CSCs affect therapeutic efficacy, and the treatment method of targeting CSCs is still difficult to determine. Clarifying regulatory mechanisms and targeting biomarkers of CSCs is currently the mainstream idea.
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Affiliation(s)
- Xianjing Chu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Wentao Tian
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Jiaoyang Ning
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Gang Xiao
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yunqi Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Ziqi Wang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Zhuofan Zhai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Guilong Tanzhu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Jie Yang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Rongrong Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China.
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Huang Z, Xie L, Feng H, Lan M, Xu T, Chen D, Pu L, Lu Y. DAZL regulate germline, pluripotency, and proliferation related genes in chicken PGCs and cooperate with DDX4. Theriogenology 2024; 222:22-30. [PMID: 38615433 DOI: 10.1016/j.theriogenology.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 04/16/2024]
Abstract
Primordial germ cells (PGCs) are the precursors of germ cells and play a crucial role in germline transmission. In chickens, PGCs can be cultured in vitro while maintaining their germline stem cell characteristics. The Deleted in Azoospermia-Like (DAZL) gene, which is highly expressed in PGCs, is essential for germ cell development. Here, through gene knockout experiments, we discovered that the loss of DAZL expression in chicken PGCs led to decreased proliferation and survival. By next employed techniques such as RIP-seq (RNA Binding Protein Immunoprecipitation) and Co-IP-MS/MS (Co-immunoprecipitation Mass Spectrometry), we identified genes directly regulated by DAZL or cooperating with DAZL at the transcriptomic and proteomic levels. DAZL was found to control genes related to germline development, pluripotency, and cell proliferation in PGCs. Additionally, we observed a significant overlap between RNAs and proteins that interact with both DAZL and DDX4, indicating their cooperation in the gene regulation network in chicken PGCs. Our research provides valuable insights into the function of the DAZL gene in germline cells.
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Affiliation(s)
- Zhenwen Huang
- From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Long Xie
- From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Hu Feng
- From the Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Meiyu Lan
- From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Tianpeng Xu
- From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Dongyang Chen
- From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Liping Pu
- From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Yangqing Lu
- From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China.
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5
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Kulkarni S, Alampally H, Guddattu V, Rodrigues G, Carnelio S. Expression of Fascin and SALL4 in odontogenic cysts and tumors: an immunohistochemical appraisal. F1000Res 2024; 11:1578. [PMID: 38895097 PMCID: PMC11184278 DOI: 10.12688/f1000research.126091.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2024] [Indexed: 06/21/2024] Open
Abstract
Background Various stemness markers (SOX2, OCT4, and NANOG) have been studied in odontogenic cysts and tumors. However, studies on SALL4 having similar properties of stemness has not been documented. Additionally, insight into fascin as a migratory molecule is less explored. In this study, the expression of SALL4 and fascin were evaluated in ameloblastoma, adenomatoid odontogenic tumor (AOT), odontogenic keratocyst (OKC), dentigerous cyst (DC), radicular cyst (RC), and calcifying odontogenic cyst (COC). Methods Semi-quantitative analysis of fascin and SALL4 immuno-positive cells was done in a total of 40 cases of ameloblastoma (11 plexiform, 12 follicular, 12 unicystic, and 5 desmoplastic) variants, 6 cases of AOT, 15 each of OKC, DC, RC and 5 of COC. Chi-square test was applied to evaluate the association between SALL4 and fascin expression in odontogenic cysts and tumors. Results Fascin immunopositivity was observed in peripheral ameloblast-like cells, and the expression was weak or absent in stellate reticulum-like cells. A moderate to weak immune-reactivity to SALL4 was observed in the cytoplasm of ameloblastoma, epithelial cells of dentigerous and radicular cysts, having a marked inflammatory infiltrate, which was an interesting observation. COC and AOT had negative to weak expressions. No recurrence has been reported. Conclusions Expression of fascin in ameloblastomas elucidate their role in motility and localized invasion. Its expression in less aggressive lesions like DC, COC, AOT will incite to explore the other functional properties of fascin. SALL4 expression in the cytoplasm of odontogenic cysts and tumors may represent inactive or mutant forms which requires further validation.
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Affiliation(s)
- Spoorti Kulkarni
- Oral Pathology and Microbiology, Manipal College of Dental Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Harishanker Alampally
- Oral Pathology and Microbiology, Manipal College of Dental Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Vasudev Guddattu
- Department of Data Science, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Gabriel Rodrigues
- Department of General Surgery, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Sunitha Carnelio
- Oral Pathology and Microbiology, Manipal College of Dental Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
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6
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Cardenas RP, Zyoud A, McIntyre A, Alberio R, Mongan NP, Allegrucci C. NANOG controls testicular germ cell tumour stemness through regulation of MIR9-2. Stem Cell Res Ther 2024; 15:128. [PMID: 38693576 PMCID: PMC11062916 DOI: 10.1186/s13287-024-03724-1] [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: 12/18/2023] [Accepted: 04/08/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUND Testicular germ cell tumours (TGCTs) represent a clinical challenge; they are most prevalent in young individuals and are triggered by molecular mechanisms that are not fully understood. The origin of TGCTs can be traced back to primordial germ cells that fail to mature during embryonic development. These cells express high levels of pluripotency factors, including the transcription factor NANOG which is highly expressed in TGCTs. Gain or amplification of the NANOG locus is common in advanced tumours, suggesting a key role for this master regulator of pluripotency in TGCT stemness and malignancy. METHODS In this study, we analysed the expression of microRNAs (miRNAs) that are regulated by NANOG in TGCTs via integrated bioinformatic analyses of data from The Cancer Genome Atlas and NANOG chromatin immunoprecipitation in human embryonic stem cells. Through gain-of-function experiments, MIR9-2 was further investigated as a novel tumour suppressor regulated by NANOG. After transfection with MIR9-2 mimics, TGCT cells were analysed for cell proliferation, invasion, sensitivity to cisplatin, and gene expression signatures by RNA sequencing. RESULTS For the first time, we identified 86 miRNAs regulated by NANOG in TGCTs. Among these, 37 miRNAs were differentially expressed in NANOG-high tumours, and they clustered TGCTs according to their subtypes. Binding of NANOG within 2 kb upstream of the MIR9-2 locus was associated with a negative regulation. Low expression of MIR9-2 was associated with tumour progression and MIR9-2-5p was found to play a role in the control of tumour stemness. A gain of function of MIR9-2-5p was associated with reduced proliferation, invasion, and sensitivity to cisplatin in both embryonal carcinoma and seminoma tumours. MIR9-2-5p expression in TGCT cells significantly reduced the expression of genes regulating pluripotency and cell division, consistent with its functional effect on reducing cancer stemness. CONCLUSIONS This study provides new molecular insights into the role of NANOG as a key determinant of pluripotency in TGCTs through the regulation of MIR9-2-5p, a novel epigenetic modulator of cancer stemness. Our data also highlight the potential negative feedback mediated by MIR9-2-5p on NANOG expression, which could be exploited as a therapeutic strategy for the treatment of TGCTs.
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Affiliation(s)
- Ryan P Cardenas
- SVMS, Faculty of Medicine and Health Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Ahmad Zyoud
- SVMS, Faculty of Medicine and Health Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Alan McIntyre
- School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
- Centre for Cancer Sciences and Nottingham Breast Cancer Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Ramiro Alberio
- School of Biosciences, Faculty of Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Nigel P Mongan
- SVMS, Faculty of Medicine and Health Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
- Centre for Cancer Sciences and Nottingham Breast Cancer Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
- Department of Pharmacology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Cinzia Allegrucci
- SVMS, Faculty of Medicine and Health Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.
- Centre for Cancer Sciences and Nottingham Breast Cancer Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK.
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Khan AQ, Hasan A, Mir SS, Rashid K, Uddin S, Steinhoff M. Exploiting transcription factors to target EMT and cancer stem cells for tumor modulation and therapy. Semin Cancer Biol 2024; 100:1-16. [PMID: 38503384 DOI: 10.1016/j.semcancer.2024.03.002] [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: 12/20/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/21/2024]
Abstract
Transcription factors (TFs) are essential in controlling gene regulatory networks that determine cellular fate during embryogenesis and tumor development. TFs are the major players in promoting cancer stemness by regulating the function of cancer stem cells (CSCs). Understanding how TFs interact with their downstream targets for determining cell fate during embryogenesis and tumor development is a critical area of research. CSCs are increasingly recognized for their significance in tumorigenesis and patient prognosis, as they play a significant role in cancer initiation, progression, metastasis, and treatment resistance. However, traditional therapies have limited effectiveness in eliminating this subset of cells, allowing CSCs to persist and potentially form secondary tumors. Recent studies have revealed that cancer cells and tumors with CSC-like features also exhibit genes related to the epithelial-to-mesenchymal transition (EMT). EMT-associated transcription factors (EMT-TFs) like TWIST and Snail/Slug can upregulate EMT-related genes and reprogram cancer cells into a stem-like phenotype. Importantly, the regulation of EMT-TFs, particularly through post-translational modifications (PTMs), plays a significant role in cancer metastasis and the acquisition of stem cell-like features. PTMs, including phosphorylation, ubiquitination, and SUMOylation, can alter the stability, localization, and activity of EMT-TFs, thereby modulating their ability to drive EMT and stemness properties in cancer cells. Although targeting EMT-TFs holds potential in tackling CSCs, current pharmacological approaches to do so directly are unavailable. Therefore, this review aims to explore the role of EMT- and CSC-TFs, their connection and impact in cellular development and cancer, emphasizing the potential of TF networks as targets for therapeutic intervention.
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Affiliation(s)
- Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar.
| | - Adria Hasan
- Molecular Cell Biology Laboratory, Integral Information and Research Centre-4 (IIRC-4), Integral University, Kursi Road, Lucknow 226026, India; Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, Lucknow 226026, India
| | - Snober S Mir
- Molecular Cell Biology Laboratory, Integral Information and Research Centre-4 (IIRC-4), Integral University, Kursi Road, Lucknow 226026, India; Department of Biosciences, Faculty of Science, Integral University, Kursi Road, Lucknow 226026, India
| | - Khalid Rashid
- Department of Urology,Feinberg School of Medicine, Northwestern University, 303 E Superior Street, Chicago, IL 60611, USA
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Department of Biosciences, Faculty of Science, Integral University, Kursi Road, Lucknow 226026, India; Laboratory Animal Research Center, Qatar University, Doha, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
| | - Martin Steinhoff
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha 3050, Qatar; Department of Medicine, Weill Cornell Medicine Qatar, Qatar Foundation-Education City, Doha 24144, Qatar; Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; College of Medicine, Qatar University, Doha 2713, Qatar
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8
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Jonz MG. Cell proliferation and regeneration in the gill : By. J Comp Physiol B 2024:10.1007/s00360-024-01548-2. [PMID: 38554225 DOI: 10.1007/s00360-024-01548-2] [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: 12/18/2023] [Revised: 02/02/2024] [Accepted: 02/29/2024] [Indexed: 04/01/2024]
Abstract
Seminal studies from the early 20th century defined the structural changes associated with development and regeneration of the gills in goldfish at the gross morphological and cellular levels using standard techniques of light and electron microscopy. More recently, investigations using cell lineage tracing, molecular biology, immunohistochemistry and single-cell RNA-sequencing have pushed the field forward and have begun to reveal the cellular and molecular processes that orchestrate cell proliferation and regeneration in the gills. The gill is a multifunctional organ that mediates an array of important physiological functions, including respiration, ion regulation and excretion of waste products. It is comprised of unique cell types, such as pavement cells, ionocytes, chemoreceptors and undifferentiated stem or progenitor cells that regulate growth and replenish cell populations. The gills develop from the embryonic endoderm and are rich in cell types derived from the neural crest. The gills have the capacity to remodel themselves in response to environmental change, such as in the case of ionocytes, chemoreceptors and the interlamellar cell mass, and can completely regenerate gill filaments and lamellae. Both processes of remodeling and regeneration invariably involve cell proliferation. Although gill regeneration has been reported in only a limited number of fish species, the process appears to have many similarities to regeneration of other organs in fish and amphibians. The present article reviews the studies that have described gill development and growth, and that demonstrate a suite of genes, transcription factors and other proteins involved in cell proliferation and regeneration in the gills.
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Affiliation(s)
- Michael G Jonz
- Department of Biology, University of Ottawa, 30 Marie Curie Pvt, Ottawa, ON, K1N 6N5, Canada.
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9
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Ling RE, Cross JW, Roy A. Aberrant stem cell and developmental programs in pediatric leukemia. Front Cell Dev Biol 2024; 12:1372899. [PMID: 38601080 PMCID: PMC11004259 DOI: 10.3389/fcell.2024.1372899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
Hematopoiesis is a finely orchestrated process, whereby hematopoietic stem cells give rise to all mature blood cells. Crucially, they maintain the ability to self-renew and/or differentiate to replenish downstream progeny. This process starts at an embryonic stage and continues throughout the human lifespan. Blood cancers such as leukemia occur when normal hematopoiesis is disrupted, leading to uncontrolled proliferation and a block in differentiation of progenitors of a particular lineage (myeloid or lymphoid). Although normal stem cell programs are crucial for tissue homeostasis, these can be co-opted in many cancers, including leukemia. Myeloid or lymphoid leukemias often display stem cell-like properties that not only allow proliferation and survival of leukemic blasts but also enable them to escape treatments currently employed to treat patients. In addition, some leukemias, especially in children, have a fetal stem cell profile, which may reflect the developmental origins of the disease. Aberrant fetal stem cell programs necessary for leukemia maintenance are particularly attractive therapeutic targets. Understanding how hijacked stem cell programs lead to aberrant gene expression in place and time, and drive the biology of leukemia, will help us develop the best treatment strategies for patients.
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Affiliation(s)
- Rebecca E. Ling
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Joe W. Cross
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Anindita Roy
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Department of Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
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10
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Dong Q, Zhang Q, Yang X, Nai S, Du X, Chen L. Glycolysis-Stimulated Esrrb Lactylation Promotes the Self-Renewal and Extraembryonic Endoderm Stem Cell Differentiation of Embryonic Stem Cells. Int J Mol Sci 2024; 25:2692. [PMID: 38473939 DOI: 10.3390/ijms25052692] [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: 01/28/2024] [Revised: 02/18/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Embryonic stem cells (ESCs) favor glycolysis over oxidative phosphorylation for energy production, and glycolytic metabolism is critical for pluripotency establishment, maintenance, and exit. However, an understanding of how glycolysis regulates the self-renewal and differentiation of ESCs remains elusive. Here, we demonstrated that protein lactylation, regulated by intracellular lactate, contributes to the self-renewal of ESCs. We further showed that Esrrb, an orphan nuclear receptor involved in pluripotency maintenance and extraembryonic endoderm stem cell (XEN) differentiation, is lactylated on K228 and K232. The lactylation of Esrrb enhances its activity in promoting ESC self-renewal in the absence of the LIF and XEN differentiation of ESCs by increasing its binding at target genes. Our studies reveal the importance of protein lactylation in the self-renewal and XEN differentiation of ESCs, and the underlying mechanism of glycolytic metabolism regulating cell fate choice.
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Affiliation(s)
- Qiman Dong
- Institute of Translational Medicine, Tianjin Union Medical Center, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Frontiers Science Center for Cell Responses, National Demonstration Center for Experimental Biology Education and College of Life Sciences, Nankai University, Tianjin 300074, China
| | - Qingye Zhang
- Institute of Translational Medicine, Tianjin Union Medical Center, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Frontiers Science Center for Cell Responses, National Demonstration Center for Experimental Biology Education and College of Life Sciences, Nankai University, Tianjin 300074, China
| | - Xiaoqiong Yang
- Institute of Translational Medicine, Tianjin Union Medical Center, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Frontiers Science Center for Cell Responses, National Demonstration Center for Experimental Biology Education and College of Life Sciences, Nankai University, Tianjin 300074, China
| | - Shanshan Nai
- Institute of Translational Medicine, Tianjin Union Medical Center, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Frontiers Science Center for Cell Responses, National Demonstration Center for Experimental Biology Education and College of Life Sciences, Nankai University, Tianjin 300074, China
| | - Xiaoling Du
- Institute of Translational Medicine, Tianjin Union Medical Center, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Frontiers Science Center for Cell Responses, National Demonstration Center for Experimental Biology Education and College of Life Sciences, Nankai University, Tianjin 300074, China
| | - Lingyi Chen
- Institute of Translational Medicine, Tianjin Union Medical Center, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Frontiers Science Center for Cell Responses, National Demonstration Center for Experimental Biology Education and College of Life Sciences, Nankai University, Tianjin 300074, China
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11
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Lospinoso Severini L, Loricchio E, Navacci S, Basili I, Alfonsi R, Bernardi F, Moretti M, Conenna M, Cucinotta A, Coni S, Petroni M, De Smaele E, Giannini G, Maroder M, Canettieri G, Mastronuzzi A, Guardavaccaro D, Ayrault O, Infante P, Bufalieri F, Di Marcotullio L. SALL4 is a CRL3 REN/KCTD11 substrate that drives Sonic Hedgehog-dependent medulloblastoma. Cell Death Differ 2024; 31:170-187. [PMID: 38062245 PMCID: PMC10850099 DOI: 10.1038/s41418-023-01246-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 11/17/2023] [Accepted: 11/23/2023] [Indexed: 02/09/2024] Open
Abstract
The Sonic Hedgehog (SHH) pathway is crucial regulator of embryonic development and stemness. Its alteration leads to medulloblastoma (MB), the most common malignant pediatric brain tumor. The SHH-MB subgroup is the best genetically characterized, however the molecular mechanisms responsible for its pathogenesis are not fully understood and therapeutic benefits are still limited. Here, we show that the pro-oncogenic stemness regulator Spalt-like transcriptional factor 4 (SALL4) is re-expressed in mouse SHH-MB models, and its high levels correlate with worse overall survival in SHH-MB patients. Proteomic analysis revealed that SALL4 interacts with REN/KCTD11 (here REN), a substrate receptor subunit of the Cullin3-RING ubiquitin ligase complex (CRL3REN) and a tumor suppressor lost in ~30% of human SHH-MBs. We demonstrate that CRL3REN induces polyubiquitylation and degradation of wild type SALL4, but not of a SALL4 mutant lacking zinc finger cluster 1 domain (ΔZFC1). Interestingly, SALL4 binds GLI1 and cooperates with HDAC1 to potentiate GLI1 deacetylation and transcriptional activity. Notably, inhibition of SALL4 suppresses SHH-MB growth both in murine and patient-derived xenograft models. Our findings identify SALL4 as a CRL3REN substrate and a promising therapeutic target in SHH-dependent cancers.
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Affiliation(s)
| | - Elena Loricchio
- Department of Molecular Medicine, University of Rome La Sapienza, 00161, Rome, Italy
| | - Shirin Navacci
- Department of Molecular Medicine, University of Rome La Sapienza, 00161, Rome, Italy
| | - Irene Basili
- Department of Molecular Medicine, University of Rome La Sapienza, 00161, Rome, Italy
- Institut Curie, PSL Research University, CNRS UMR, INSERM, 91401, Orsay, France
| | - Romina Alfonsi
- Centro Nazionale per il Controllo e la Valutazione dei Farmaci, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Flavia Bernardi
- Institut Curie, PSL Research University, CNRS UMR, INSERM, 91401, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR, INSERM U, 91401, Orsay, France
| | - Marta Moretti
- Department of Experimental Medicine, University of Rome La Sapienza, 00161, Rome, Italy
| | - Marilisa Conenna
- Department of Molecular Medicine, University of Rome La Sapienza, 00161, Rome, Italy
| | - Antonino Cucinotta
- Department of Molecular Medicine, University of Rome La Sapienza, 00161, Rome, Italy
| | - Sonia Coni
- Department of Molecular Medicine, University of Rome La Sapienza, 00161, Rome, Italy
| | - Marialaura Petroni
- Department of Molecular Medicine, University of Rome La Sapienza, 00161, Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, University of Rome La Sapienza, 00161, Rome, Italy
| | - Enrico De Smaele
- Department of Experimental Medicine, University of Rome La Sapienza, 00161, Rome, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, University of Rome La Sapienza, 00161, Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, University of Rome La Sapienza, 00161, Rome, Italy
| | - Marella Maroder
- Department of Molecular Medicine, University of Rome La Sapienza, 00161, Rome, Italy
| | - Gianluca Canettieri
- Department of Molecular Medicine, University of Rome La Sapienza, 00161, Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, University of Rome La Sapienza, 00161, Rome, Italy
| | - Angela Mastronuzzi
- Department of Pediatric Haematology and Oncology, and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, 00165, Rome, Italy
| | | | - Olivier Ayrault
- Institut Curie, PSL Research University, CNRS UMR, INSERM, 91401, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR, INSERM U, 91401, Orsay, France
| | - Paola Infante
- Department of Molecular Medicine, University of Rome La Sapienza, 00161, Rome, Italy
| | - Francesca Bufalieri
- Department of Molecular Medicine, University of Rome La Sapienza, 00161, Rome, Italy.
| | - Lucia Di Marcotullio
- Department of Molecular Medicine, University of Rome La Sapienza, 00161, Rome, Italy.
- Istituto Pasteur-Fondazione Cenci Bolognetti, University of Rome La Sapienza, 00161, Rome, Italy.
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12
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Melchionna R, Trono P, Di Carlo A, Di Modugno F, Nisticò P. Transcription factors in fibroblast plasticity and CAF heterogeneity. J Exp Clin Cancer Res 2023; 42:347. [PMID: 38124183 PMCID: PMC10731891 DOI: 10.1186/s13046-023-02934-4] [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: 11/14/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
In recent years, research focused on the multifaceted landscape and functions of cancer-associated fibroblasts (CAFs) aimed to reveal their heterogeneity and identify commonalities across diverse tumors for more effective therapeutic targeting of pro-tumoral stromal microenvironment. However, a unified functional categorization of CAF subsets remains elusive, posing challenges for the development of targeted CAF therapies in clinical settings.The CAF phenotype arises from a complex interplay of signals within the tumor microenvironment, where transcription factors serve as central mediators of various cellular pathways. Recent advances in single-cell RNA sequencing technology have emphasized the role of transcription factors in the conversion of normal fibroblasts to distinct CAF subtypes across various cancer types.This review provides a comprehensive overview of the specific roles of transcription factor networks in shaping CAF heterogeneity, plasticity, and functionality. Beginning with their influence on fibroblast homeostasis and reprogramming during wound healing and fibrosis, it delves into the emerging insights into transcription factor regulatory networks. Understanding these mechanisms not only enables a more precise characterization of CAF subsets but also sheds light on the early regulatory processes governing CAF heterogeneity and functionality. Ultimately, this knowledge may unveil novel therapeutic targets for cancer treatment, addressing the existing challenges of stromal-targeted therapies.
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Affiliation(s)
- Roberta Melchionna
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy.
| | - Paola Trono
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Rome, Italy
| | - Anna Di Carlo
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Francesca Di Modugno
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Paola Nisticò
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
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13
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Kawakami H, Chen KQ, Zhang R, Pappas MP, Bailey A, Reisz JA, Corcoran D, Nishinakamura R, D'Alessandro A, Kawakami Y. Sall4 restricts glycolytic metabolism in limb buds through transcriptional regulation of glycolytic enzyme genes. Dev Biol 2023; 501:28-38. [PMID: 37301463 PMCID: PMC10330914 DOI: 10.1016/j.ydbio.2023.06.004] [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: 01/16/2023] [Revised: 04/09/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
Recent studies illustrate the importance of regulation of cellular metabolism, especially glycolysis and pathways branching from glycolysis, during vertebrate embryo development. For example, glycolysis generates cellular energy ATP. Glucose carbons are also directed to the pentose phosphate pathway, which is needed to sustain anabolic processes in the rapidly growing embryos. However, our understanding of the exact status of glycolytic metabolism as well as genes that regulate glycolytic metabolism are still incomplete. Sall4 is a zinc finger transcription factor that is highly expressed in undifferentiated cells in developing mouse embryos, such as blastocysts and the post-implantation epiblast. TCre; Sall4 conditional knockout mouse embryos exhibit various defects in the posterior part of the body, including hindlimbs. Using transcriptomics approaches, we found that many genes encoding glycolytic enzymes are upregulated in the posterior trunk, including the hindlimb-forming region, of Sall4 conditional knockout mouse embryos. In situ hybridization and qRT-PCR also confirmed upregulation of expression of several glycolytic genes in hindlimb buds. A fraction of those genes are bound by SALL4 at the promoters, gene bodies or distantly-located regions, suggesting that Sall4 directly regulates expression of several glycolytic enzyme genes in hindlimb buds. To further gain insight into the metabolic status associated with the observed changes at the transcriptional level, we performed a comprehensive analysis of metabolite levels in limb buds in wild type and Sall4 conditional knockout embryos by high-resolution mass spectrometry. We found that the levels of metabolic intermediates of glycolysis are lower, but glycolytic end-products pyruvate and lactate did not exhibit differences in Sall4 conditional knockout hindlimb buds. The increased expression of glycolytic genes would have caused accelerated glycolytic flow, resulting in low levels of intermediates. This condition may have prevented intermediates from being re-directed to other pathways, such as the pentose phosphate pathway. Indeed, the change in glycolytic metabolite levels is associated with reduced levels of ATP and metabolites of the pentose phosphate pathway. To further test whether glycolysis regulates limb patterning downstream of Sall4, we conditionally inactivated Hk2, which encodes a rate-limiting enzyme gene in glycolysis and is regulated by Sall4. The TCre; Hk2 conditional knockout hindlimb exhibited a short femur, and a lack of tibia and anterior digits in hindlimbs, which are defects similarly found in the TCre; Sall4 conditional knockout. The similarity of skeletal defects in Sall4 mutants and Hk2 mutants suggests that regulation of glycolysis plays a role in hindlimb patterning. These data suggest that Sall4 restricts glycolysis in limb buds and contributes to patterning and regulation of glucose carbon flow during development of limb buds.
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Affiliation(s)
- Hiroko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN, USA
| | - Katherine Q Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ruizhi Zhang
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Matthew P Pappas
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Abigail Bailey
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN, USA.
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14
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de Albuquerque Dias R, Balbinot KM, da Silva Kataoka MS, de Melo Alves Júnior S, de Jesus Viana Pinheiro J. Expression of stem cell markers SALL4, LIN28A, and KLF4 in ameloblastoma. Diagn Pathol 2023; 18:92. [PMID: 37559082 PMCID: PMC10413759 DOI: 10.1186/s13000-023-01379-9] [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: 07/14/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Ameloblastoma (AME) is a benign odontogenic tumour of epithelial origin characterised by slow but aggressive growth, infiltration, and recurrence; it is capable of reaching large dimensions and invading adjacent structures. Stem cell research has proven to be significant in the sphere of tumour biology through these cells' possible involvement in the aetiopathogenesis of this tumour. METHODS Immunohistochemistry was performed on AME, dentigerous cyst (DC), and dental follicle (DF) samples, and indirect immunofluorescence was performed on the AME-hTERT cell line to determine the expression of SALL4, LIN28A, and KLF4. RESULTS Expression of proteins related to cellular pluripotency was higher in AME cells than in DC and DF cells. The analysis revealed that the proteins in question were mainly expressed in the parenchyma of AME tissue samples and were detected in the nuclei of AME-hTERT cells. CONCLUSIONS Stem cells may be related to the origin and progression of AME.
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Affiliation(s)
- Rafaela de Albuquerque Dias
- Laboratory of Pathological Anatomy and Immunohistochemistry, Federal University of Pará, Belém, Pará, Brazil.
| | - Karolyny Martins Balbinot
- Laboratory of Pathological Anatomy and Immunohistochemistry, Federal University of Pará, Belém, Pará, Brazil
| | | | - Sérgio de Melo Alves Júnior
- Laboratory of Pathological Anatomy and Immunohistochemistry, Federal University of Pará, Belém, Pará, Brazil
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15
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Yang X, Yang L. Current understanding of the genomic abnormities in premature ovarian failure: chance for early diagnosis and management. Front Med (Lausanne) 2023; 10:1194865. [PMID: 37332766 PMCID: PMC10274511 DOI: 10.3389/fmed.2023.1194865] [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: 03/27/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023] Open
Abstract
Premature ovarian failure (POF) is an insidious cause of female infertility and a devastating condition for women. POF also has a strong familial and heterogeneous genetic background. Management of POF is complicated by the variable etiology and presentation, which are generally characterized by abnormal hormone levels, gene instability and ovarian dysgenesis. To date, abnormal regulation associated with POF has been found in a small number of genes, including autosomal and sex chromosomal genes in folliculogenesis, granulosa cells, and oocytes. Due to the complex genomic contributions, ascertaining the exact causative mechanisms has been challenging in POF, and many pathogenic genomic characteristics have yet to be elucidated. However, emerging research has provided new insights into genomic variation in POF as well as novel etiological factors, pathogenic mechanisms and therapeutic intervention approaches. Meanwhile, scattered studies of transcriptional regulation revealed that ovarian cell function also depends on specific biomarker gene expression, which can influence protein activities, thus causing POF. In this review, we summarized the latest research and issues related to the genomic basis for POF and focused on insights gained from their biological effects and pathogenic mechanisms in POF. The present integrated studies of genomic variants, gene expression and related protein abnormalities were structured to establish the role of etiological genes associated with POF. In addition, we describe the design of some ongoing clinical trials that may suggest safe, feasible and effective approaches to improve the diagnosis and therapy of POF, such as Filgrastim, goserelin, resveratrol, natural plant antitoxin, Kuntai capsule et al. Understanding the candidate genomic characteristics in POF is beneficial for the early diagnosis of POF and provides appropriate methods for prevention and drug treatment. Additional efforts to clarify the POF genetic background are necessary and are beneficial for researchers and clinicians regarding genetic counseling and clinical practice. Taken together, recent genomic explorations have shown great potential to elucidate POF management in women and are stepping from the bench to the bedside.
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Affiliation(s)
- Xu Yang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lin Yang
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
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16
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Markman S, Zada M, David E, Giladi A, Amit I, Zelzer E. A single-cell census of mouse limb development identifies complex spatiotemporal dynamics of skeleton formation. Dev Cell 2023; 58:565-581.e4. [PMID: 36931270 DOI: 10.1016/j.devcel.2023.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 10/20/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023]
Abstract
Limb development has long served as a model system for coordinated spatial patterning of progenitor cells. Here, we identify a population of naive limb progenitors and show that they differentiate progressively to form the skeleton in a complex, non-consecutive, three-dimensional pattern. Single-cell RNA sequencing of the developing mouse forelimb identified three progenitor states: naive, proximal, and autopodial, as well as Msx1 as a marker for the naive progenitors. In vivo lineage tracing confirmed this role and localized the naive progenitors to the outer margin of the limb, along the anterior-posterior axis. Sequential pulse-chase experiments showed that the progressive transition of Msx1+ naive progenitors into proximal and autopodial progenitors coincides with their differentiation to Sox9+ chondroprogenitors, which occurs along all the forming skeletal segments. Indeed, tracking the spatiotemporal sequence of differentiation showed that the skeleton forms progressively in a complex pattern. These findings suggest an alternative model for limb skeleton development.
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Affiliation(s)
- Svetlana Markman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mor Zada
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Elazar Zelzer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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17
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The transcription factor ELF5 is essential for early preimplantation development. Mol Biol Rep 2023; 50:2119-2125. [PMID: 36542237 DOI: 10.1007/s11033-022-08217-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND During early embryonic development, the cell adhesion molecule E-cadherin encoded by the Cdh1 gene plays a vital role in providing proper cell-cell adhesion, ensuring an undifferentiated state critical for maintaining the pluripotency for the development of the preimplantation embryo. The transcriptional regulation of Cdh1 gained attention recently but is not yet fully understood. In a previous study, our team established a correlation between Elf3 and Cdh1 expression and showed its importance in the regulation of MET. METHODS AND RESULTS Here, the regulation of Cdh1 by Ets transcription factors in early embryogenesis was investigated. A loss-of-function approach was used to study the effect of Elf5 loss on Cdh1 gene expression by small interfering RNAs in fertilized oocytes. Changes in gene expression were measured by qPCR analysis, and developing embryos were visualized by microscopy. Loss of Elf5 arrested the embryos at the 2-cell stage, accompanied by a significant downregulation of Cdh1 expression. CONCLUSION The findings presented here illustrate the role of ELF5 in preimplantation development and in regulating the expression of Cdh1. The maintenance of the ELF5 and Cdh1 regulatory node proved essential for the proper development of the early mouse embryos, which is in agreement with the critical role of Elf5 and Cdh1 genes in regulating the early events during embryogenesis.
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18
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Kaewlert W, Sakonsinsiri C, Lert-itthiporn W, Ungarreevittaya P, Pairojkul C, Pinlaor S, Murata M, Thanan R. Overexpression of Insulin Receptor Substrate 1 (IRS1) Relates to Poor Prognosis and Promotes Proliferation, Stemness, Migration, and Oxidative Stress Resistance in Cholangiocarcinoma. Int J Mol Sci 2023; 24:ijms24032428. [PMID: 36768755 PMCID: PMC9916965 DOI: 10.3390/ijms24032428] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/13/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
Cholangiocarcinoma (CCA) is one of the oxidative stress-driven carcinogenesis through chronic inflammation. Insulin receptor substrate 1 (IRS1), an adaptor protein of insulin signaling pathways, is associated with the progression of many inflammation-related cancers. This study hypothesized that oxidative stress regulates IRS1 expression and that up-regulation of IRS1 induces CCA progression. The localizations of IRS1 and an oxidative stress marker (8-oxodG) were detected in CCA tissues using immunohistochemistry (IHC). The presence of IRS1 in CCA tissues was confirmed using immortal cholangiocyte cells (MMNK1), a long-term oxidative-stress-induced cell line (ox-MMNK1-L), and five CCA cell lines as cell culture models. IRS1 was overexpressed in tumor cells and this was associated with a shorter patient survival time and an increase in 8-oxodG. IRS1 expression was higher in ox-MMNK1-L cells than in MMNK1 cells. Knockdown of IRS1 by siRNA in two CCA cell lines led to inhibition of proliferation, cell cycle progression, migration, invasion, stemness, and oxidative stress resistance properties. Moreover, a transcriptomics study demonstrated that suppressing IRS1 in the KKU-213B CCA cell line reduced the expression levels of several genes and pathways involved in the cellular functions. The findings indicate that IRS1 is a key molecule in the connection between oxidative stress and CCA progression. Therefore, IRS1 and its related genes can be used as prognostic markers and therapeutic targets for CCA therapy.
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Affiliation(s)
- Waleeporn Kaewlert
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chadamas Sakonsinsiri
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Worachart Lert-itthiporn
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Piti Ungarreevittaya
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chawalit Pairojkul
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Somchai Pinlaor
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Mariko Murata
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Mie 514-8507, Japan
| | - Raynoo Thanan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Correspondence: ; Tel.: +66-43-363-265
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19
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Vienot A, Monnien F, Truntzer C, Mougey V, Bouard A, Pallandre JR, Molimard C, Loyon R, Asgarov K, Averous G, Ghiringhelli F, Bibeau F, Peixoto P, Borg C. SALL4-related gene signature defines a specific stromal subset of pancreatic ductal adenocarcinoma with poor prognostic features. Mol Oncol 2023. [PMID: 36587397 DOI: 10.1002/1878-0261.13370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/20/2022] [Accepted: 12/30/2022] [Indexed: 01/02/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is marked by molecular heterogeneity and poor prognosis. Among the stemness-related transcription factors, Spalt-like Transcription Factor 4 (SALL4) is correlated with unfavorable outcomes; however, its roles in PDAC remain unclear. SALL4high expression defines a PDAC subpopulation characterized by a shortened patient survival. Although SALL4 expression was mostly evaluated in tumor cells, our findings identify this embryonic transcription factor as a new biomarker in PDAC-derived stroma. Gene expression analysis reveals that the SALL4high PDAC subset is enriched in cancer stem cell properties and stromal enrichment pathways; notably, an interaction with cancer-associated fibroblasts (CAF) activated by TGF-β. A particular oncogenic network was unraveled where Netrin-1 and TGF-β1 collaborate to induce SALL4 expression in CAF and drive their cancer-stemness-promoting functions. A 7-gene stromal signature related to SALL4high PDAC samples was highlighted and validated by immunochemistry for prognosis and clinical application. This SALL4-related stroma discriminated pancreatic preinvasive from invasive lesions and was enriched in short-term survivors. Our results show that SALL4 transcriptional activity controls a molecular network defined by a specific stromal signature that characterizes PDAC invasiveness and worse clinical outcomes.
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Affiliation(s)
- Angélique Vienot
- INSERM, EFS BFC, UMR1098, RIGHT, University of Bourgogne Franche-Comté, Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,Department of Medical Oncology, University Hospital of Besançon, France.,Clinical Investigational Center, CIC-1431, Besançon, France.,ITAC Platform, University of Bourgogne Franche-Comté, Besançon, France
| | - Franck Monnien
- INSERM, EFS BFC, UMR1098, RIGHT, University of Bourgogne Franche-Comté, Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,Department of Pathology, University Hospital of Besançon, France
| | - Caroline Truntzer
- Platform of Transfer in Cancer Biology, Georges François Leclerc Cancer Center, Center-Unicancer, Dijon, France.,UMR INSERM 1231, Dijon, France
| | - Virginie Mougey
- INSERM, EFS BFC, UMR1098, RIGHT, University of Bourgogne Franche-Comté, Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,ITAC Platform, University of Bourgogne Franche-Comté, Besançon, France
| | - Adeline Bouard
- INSERM, EFS BFC, UMR1098, RIGHT, University of Bourgogne Franche-Comté, Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,ITAC Platform, University of Bourgogne Franche-Comté, Besançon, France
| | - Jean-René Pallandre
- INSERM, EFS BFC, UMR1098, RIGHT, University of Bourgogne Franche-Comté, Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Chloé Molimard
- Department of Pathology, University Hospital of Besançon, France
| | - Romain Loyon
- INSERM, EFS BFC, UMR1098, RIGHT, University of Bourgogne Franche-Comté, Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Kamal Asgarov
- INSERM, EFS BFC, UMR1098, RIGHT, University of Bourgogne Franche-Comté, Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,ITAC Platform, University of Bourgogne Franche-Comté, Besançon, France
| | - Gerlinde Averous
- Department of Pathology, University Hospital of Strasbourg, France
| | - François Ghiringhelli
- Platform of Transfer in Cancer Biology, Georges François Leclerc Cancer Center, Center-Unicancer, Dijon, France.,UMR INSERM 1231, Dijon, France
| | - Frédéric Bibeau
- Department of Pathology, University Hospital of Besançon, France
| | - Paul Peixoto
- INSERM, EFS BFC, UMR1098, RIGHT, University of Bourgogne Franche-Comté, Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,EPIgenetics and GENe EXPression Technical Platform (EPIGENExp), University of Bourgogne Franche-Comté, Besançon, France
| | - Christophe Borg
- INSERM, EFS BFC, UMR1098, RIGHT, University of Bourgogne Franche-Comté, Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,Department of Medical Oncology, University Hospital of Besançon, France.,Clinical Investigational Center, CIC-1431, Besançon, France.,ITAC Platform, University of Bourgogne Franche-Comté, Besançon, France
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20
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Wnt signaling and the regulation of pluripotency. Curr Top Dev Biol 2023; 153:95-119. [PMID: 36967203 DOI: 10.1016/bs.ctdb.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The role of Wnt signaling in stem cells has been mired in seemingly contradictory findings. On one hand, Wnt has been heralded as a self-renewal factor. On the other hand, Wnt's association with differentiation and lineage commitment is indisputable. This apparent contradiction is particularly evident in pluripotent stem cells, where Wnt promotes self-renewal as well as differentiation. To resolve this discrepancy one must delve into fundamental principles of pluripotency and gain an appreciation for the concept of pluripotency states, which exist in a continuum with intermediate metastable states, some of which have been stabilized in vitro. Wnt signaling is a critical regulator of transitions between pluripotent states. Here, we will discuss Wnt's roles in maintaining pluripotency, promoting differentiation, as well as stimulating reprogramming of somatic cells to an induced pluripotent state.
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21
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Wang M, Lou E, Xue Z. The role of bile acid in intestinal metaplasia. Front Physiol 2023; 14:1115250. [PMID: 36891144 PMCID: PMC9986488 DOI: 10.3389/fphys.2023.1115250] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
A precancerous lesion of gastric cancer (GC), intestinal metaplasia (IM) is a pathological transformation of non-intestinal epithelium into an intestinal-like mucosa. It greatly raises the risk of developing the intestinal type of GC, which is frequently observed in the stomach and esophagus. It is understood that esophageal adenocarcinoma's precursor lesion, chronic gastroesophageal reflux disease (GERD), is what causes Barrett's esophagus (BE), an acquired condition. Recently, Bile acids (BAs), which are one of the compositions of gastric and duodenal contents, have been confirmed that it led to the occurrence and development of BE and gastric intestinal metaplasia (GIM). The objective of the current review is to discuss the mechanism of IM induced by bile acids. This review serves as a foundation for further research aimed at improving the way BE and GIM are currently managed.
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Affiliation(s)
- Menglei Wang
- Department of Digestive Diseases, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China
| | - Enzhe Lou
- Department of Digestive Diseases, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China
| | - Zengfu Xue
- Department of Digestive Diseases, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China
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22
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Comparison of POU5F1 gene expression and protein localization in two differentiated and undifferentiated spermatogonial stem cells. Biol Futur 2022; 73:503-512. [PMID: 36583847 DOI: 10.1007/s42977-022-00149-w] [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: 08/02/2022] [Accepted: 12/17/2022] [Indexed: 12/31/2022]
Abstract
The POU domain, class 5, transcription factor 1 (POU5F1), plays a vital role in creating pluripotency and maintaining self-renewal of the spermatogonial stem cells (SSCs). In this experimental research, the gene and protein expression of POU5F1 in two populations of differentiated and undifferentiated spermatogonia were examined, by immunohistochemistry (IMH), immunocytochemistry (ICC) and Fluidigm real-time RT-PCR. Our study was extended with online databases and the creation of PPI networks. The results indicated that the POU5F1 protein was localized in the basal compartment of seminiferous tubules. Under in vitro conditions, isolated SSC colonies were ICC-positive for the POU5F1, but the protein expression level of POU5F1 in the undifferentiated populations was higher than that in differentiated. A significant POU5F1 mRNA expression was seen in passage 4 compared to passage 0 for both populations. POU5F1 has a significantly higher mRNA expression in undifferentiated SSCs than that in differentiated SSCs, also in mESCs than in SSC-like cells. Bioinformatic analysis on POU5F1 shows its impressive connection with other genes involved in spermatogonia differentiation. These results support the advanced investigations of spermatogonia differentiation, both in vitro and in vivo. A better understanding of the POU5F1 gene and its function during differentiation will give the scientific community an open perspective for the development of direct differentiation of SSC to other male germline cells which is very important in infertility treatment.
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23
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Wang L, Tan X, Chen L, Xu S, Huang W, Chen N, Wu Y, Wang C, Zhou D, Li M. Sall4 Guides p53-Mediated Enhancer Interference upon DNA Damage in Mouse Embryonic Stem Cells. Stem Cells 2022; 40:1008-1019. [PMID: 35977539 DOI: 10.1093/stmcls/sxac058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022]
Abstract
p53 plays a pivotal role in maintaining the genomic stability of mouse embryonic stem cells (mESCs) through transcriptionally activating and repressing target genes. However, how p53 recognizes its repressed targets remains largely unknown. Herein, we demonstrate that Sall4 negatively regulates DNA damage induced apoptosis (DIA) of mESCs through mediating p53 recruitment to enhancers of ESC-associated genes repressed by p53 from promoters of p53-activated genes. Upon DNA damage, Sall4 is transcriptionally repressed by p53 and plays an anti-apoptotic role without altering p53 activation. Moreover, Sall4 is identified as a novel p53-interacting partner. Consistently, Sall4 exerts its anti-apoptotic function in a p53-dependent manner. Intriguingly, Sall4 depletion not only promotes the transcriptional activation of several p53-regulated pro-apoptotic genes but also compromises p53-mediated repression of ESC master transcription factors in response to DNA damage. Mechanistically, Sall4 balances p53-binding affinity between p53-activated and -repressed genes through tethering p53 to ESC enhancers. In light of our study, Sall4 may contribute to tumorigenesis by antagonizing p53-mediated apoptosis.
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Affiliation(s)
- Lei Wang
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Xiaojun Tan
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Lu Chen
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Sisi Xu
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Weiping Huang
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Nan Chen
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Yizhou Wu
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Chunyan Wang
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Daqiang Zhou
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Mangmang Li
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
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24
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Lakpour N, Ghods R, Sadeghi MR, Ranjbar MM, Abolhasani M, Kiani J, Saliminejad K, Balay-Goli L, Bayat AA, Souri F, Madjd Z. Production and characterization of a new specific monoclonal antibody against A-isoform of SALL4: A novel emerging testicular cancer marker. Andrologia 2022; 54:e14608. [PMID: 36229227 DOI: 10.1111/and.14608] [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: 07/02/2022] [Accepted: 09/13/2022] [Indexed: 11/28/2022] Open
Abstract
SALL4 transcription factor plays an important role to maintain the pluripotent and self-renewal of embryonic stem cells. It contributes to the growth of many cancers and embryonic development. With the exception of spermatogonia, SALL4 expression is silenced in most adult tissues after birth; nevertheless, it is re-expressed in a subset of different solid malignancies. SALL4 is a new, precise biomarker for testicular germ cell cancers that was just introduced. The whole isoform of SALL4 is called SALL4-A. Regarding the lack of antibody against human SALL4 isoforms, the pattern of expression, the role of each isoform remain unknown. Furthermore, in isoform specific evaluations, we aimed, for the first time, to produce and characterize mAb against human SALL4-A. Immunization of mice were performed with a selected 33-mer synthetic peptide of SALL4-A conjugated with KLH. Hybridoma cells were screened by ELISA for positive reactivity with SALL4-A peptide. From the ascites fluid of mice that had been injected with hybridoma cells, anti-SALL4-A mAbs were isolated using a protein G column. Reactivity of the mAbs was evaluated using the peptide and SALL4-A recombinant protein by ELISA and IHC on testicular cancer tissue as positive control, and normal kidney, stomach and prostate tissues as negative control. The produced mAb could well detect SALL4-A in testicular cancer tissues using IHC, while the reactivity was negative in normal kidney, stomach and prostate tissues. Using ELISA, the mAb affinity for the peptide and SALL4-A recombinant protein was assessed, and it was shown to be reasonably high. The mAb detected SALL4-A in nucleus and cytoplasm of several cancer cells and spermatogonia in testicular cancer tissue. In addition, it could recognize SALL4-A recombinant protein. Our produced monoclonal antibody against isoform-A of human SALL4 can specifically recognize SALL4-A using either IHC or ELISA. We hope that this mAb could help researchers in isoform-specific study of human SALL4.
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Affiliation(s)
- Niknam Lakpour
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.,Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Roya Ghods
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.,Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Sadeghi
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | | | - Maryam Abolhasani
- Department of Pathology, Faculty of Medicine, Iran University of Medical Sciences, (IUMS), Tehran, Iran
| | - Jafar Kiani
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.,Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Kioomars Saliminejad
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Leila Balay-Goli
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Ali Ahmad Bayat
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Fahimeh Souri
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Zahra Madjd
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.,Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.,Department of Pathology, Faculty of Medicine, Iran University of Medical Sciences, (IUMS), Tehran, Iran
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25
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Patel I, Parchem RJ. Regulation of Oct4 in stem cells and neural crest cells. Birth Defects Res 2022; 114:983-1002. [PMID: 35365980 PMCID: PMC9525453 DOI: 10.1002/bdr2.2007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/25/2022] [Accepted: 03/14/2022] [Indexed: 12/30/2022]
Abstract
During embryonic development, cells gradually restrict their developmental potential as they exit pluripotency and differentiate into various cell types. The POU transcription factor Oct4 (encoded by Pou5f1) lies at the center of the pluripotency machinery that regulates stemness and differentiation in stem cells, and is required for reprogramming of somatic cells into induced pluripotent stem cells (iPSCs). Several studies have revealed that Oct4 and other stemness genes are also expressed in multipotent cell populations such as neural crest cells (NCCs), and are required to expand the NCC developmental potential. Transcriptional regulation of Oct4 has been studied extensively in stem cells during early embryonic development and reprogramming, but not in NCCs. Here, we review how Oct4 is regulated in pluripotent stem cells, and address some of the gaps in knowledge about regulation of the pluripotency network in NCCs.
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Affiliation(s)
- Ivanshi Patel
- Department of Molecular and Cellular BiologyBaylor College of MedicineHoustonTexasUSA,Stem Cells and Regenerative Medicine Center, Center for Cell and Gene TherapyBaylor College of MedicineHoustonTexasUSA,Dan L Duncan Comprehensive Cancer CenterBaylor College of MedicineHoustonTexasUSA
| | - Ronald J. Parchem
- Department of Molecular and Cellular BiologyBaylor College of MedicineHoustonTexasUSA,Stem Cells and Regenerative Medicine Center, Center for Cell and Gene TherapyBaylor College of MedicineHoustonTexasUSA,Dan L Duncan Comprehensive Cancer CenterBaylor College of MedicineHoustonTexasUSA
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26
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Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells. CELL GENOMICS 2022; 2:100177. [PMID: 36381608 PMCID: PMC9648144 DOI: 10.1016/j.xgen.2022.100177] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human chromosomes are pervasively transcribed, but systematic understanding of coding and lncRNA genome function in cell differentiation is lacking. Using CRISPR interference (CRISPRi) in human induced pluripotent stem cells, we performed dual genome-wide screens - assessing 18,905 protein-coding and 10,678 lncRNA loci - and identified 419 coding and 201 lncRNA genes that regulate neural induction. Integrative analyses revealed distinct properties of coding and lncRNA genome function, including a 10-fold enrichment of lncRNA genes for roles in differentiation compared to proliferation. Further, we applied Perturb-seq to obtain granular insights into neural induction phenotypes. While most coding hits stalled or aborted differentiation, lncRNA hits were enriched for the genesis of diverse cellular states, including those outside the neural lineage. In addition to providing a rich resource (danlimlab.shinyapps.io/dualgenomewide) for understanding coding and lncRNA gene function in development, these results indicate that the lncRNA genome regulates lineage commitment in a manner fundamentally distinct from coding genes.
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27
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Chen F, Li C. Inferring structural and dynamical properties of gene networks from data with deep learning. NAR Genom Bioinform 2022; 4:lqac068. [PMID: 36110897 PMCID: PMC9469930 DOI: 10.1093/nargab/lqac068] [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: 04/18/2022] [Revised: 07/22/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
The reconstruction of gene regulatory networks (GRNs) from data is vital in systems biology. Although different approaches have been proposed to infer causality from data, some challenges remain, such as how to accurately infer the direction and type of interactions, how to deal with complex network involving multiple feedbacks, as well as how to infer causality between variables from real-world data, especially single cell data. Here, we tackle these problems by deep neural networks (DNNs). The underlying regulatory network for different systems (gene regulations, ecology, diseases, development) can be successfully reconstructed from trained DNN models. We show that DNN is superior to existing approaches including Boolean network, Random Forest and partial cross mapping for network inference. Further, by interrogating the ensemble DNN model trained from single cell data from dynamical system perspective, we are able to unravel complex cell fate dynamics during preimplantation development. We also propose a data-driven approach to quantify the energy landscape for gene regulatory systems, by combining DNN with the partial self-consistent mean field approximation (PSCA) approach. We anticipate the proposed method can be applied to other fields to decipher the underlying dynamical mechanisms of systems from data.
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Affiliation(s)
- Feng Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai 200433, China
| | - Chunhe Li
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai 200433, China
- School of Mathematical Sciences, Fudan University, Shanghai 200433, China
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28
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Forghanifard MM, Salehi S. Co-overexpression of self-renewal markers SALL4 and HIWI is correlated with depth of tumor invasion and metastasis in colorectal cancer. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00333-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
SALL4 and HIWI are involved in the maintenance of self-renewal capacity of stem cells. Several scrutinizes have demonstrated that SALL4 and HIWI play a key role in cancer development. However, the correlation between these genes regarding different clinicopathological features of patients with colorectal cancer (CRC) is still unclear.
Methods
The expression of SALL4 and HIWI in different clinicopathological features of 46 CRC patients was analyzed using relative comparative real-time PCR.
Results
mRNA expression levels of SALL4 and HIWI genes were significantly correlated with each other in CRC (P = 0.013, Pearson correlation = 0.364). HIWI expression was notably increased in tumors with overexpression of SALL4 in comparison with other samples. This correlation was significant in non-metastatic CRCs compared to the metastatic tumors and in invaded tumors to the serosa (T3/T4) in comparison with non-invaded tumors (T1/T2).
Conclusions
Based on the significant association of SALL4 and HIWI in different indices of CRC poor prognosis, it may be concluded that simultaneous expression of these genes is notably contributed to the growth and development of the disease, and therefore, their co-overexpression may be considered for prognosis of aggressive CRCs.
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29
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Andersson E, Sjö M, Kaji K, Olariu V. CELLoGeNe - An energy landscape framework for logical networks controlling cell decisions. iScience 2022; 25:104743. [PMID: 35942105 PMCID: PMC9356104 DOI: 10.1016/j.isci.2022.104743] [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: 04/04/2022] [Revised: 06/01/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
Experimental and computational efforts are constantly made to elucidate mechanisms controlling cell fate decisions during development and reprogramming. One powerful computational method is to consider cell commitment and reprogramming as movements in an energy landscape. Here, we develop Computation of Energy Landscapes of Logical Gene Networks (CELLoGeNe), which maps Boolean implementation of gene regulatory networks (GRNs) into energy landscapes. CELLoGeNe removes inadvertent symmetries in the energy landscapes normally arising from standard Boolean operators. Furthermore, CELLoGeNe provides tools to visualize and stochastically analyze the shapes of multi-dimensional energy landscapes corresponding to epigenetic landscapes for development and reprogramming. We demonstrate CELLoGeNe on two GRNs governing different aspects of induced pluripotent stem cells, identifying experimentally validated attractors and revealing potential reprogramming roadblocks. CELLoGeNe is a general framework that can be applied to various biological systems offering a broad picture of intracellular dynamics otherwise inaccessible with existing methods. CELLoGeNe – Computation of Energy Landscapes of Logical Gene Networks Cell states as landscape attractors Maintenance and acquisition of cell pluripotency applications Single cell stochastic landscape navigation and visualization tool
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30
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HDACs and the epigenetic plasticity of cancer cells: Target the complexity. Pharmacol Ther 2022; 238:108190. [PMID: 35430294 DOI: 10.1016/j.pharmthera.2022.108190] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 12/11/2022]
Abstract
Cancer cells must adapt to the hostile conditions of the microenvironment in terms of nutrition, space, and immune system attack. Mutations of DNA are the drivers of the tumorigenic process, but mutations must be able to hijack cellular functions to sustain the spread of mutant genomes. Transcriptional control is a key function in this context and is controlled by the rearrangement of the epigenome. Unlike genomic mutations, the epigenome of cancer cells can in principle be reversed. The discovery of the first epigenetic drugs triggered a contaminating enthusiasm. Unfortunately, the complexity of the epigenetic machinery has frustrated this enthusiasm. To develop efficient patient-oriented epigenetic therapies, we need to better understand the nature of this complexity. In this review, we will discuss recent advances in understanding the contribution of HDACs to the maintenance of the transformed state and the rational for their selective targeting.
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31
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Olechnowicz A, Oleksiewicz U, Machnik M. KRAB-ZFPs and cancer stem cells identity. Genes Dis 2022. [PMID: 37492743 PMCID: PMC10363567 DOI: 10.1016/j.gendis.2022.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Studies on carcinogenesis continue to provide new information about different disease-related processes. Among others, much research has focused on the involvement of cancer stem cells (CSCs) in tumor initiation and progression. Studying the similarities and differences between CSCs and physiological stem cells (SCs) allows for a better understanding of cancer biology. Recently, it was shown that stem cell identity is partially governed by the Krϋppel-associated box domain zinc finger proteins (KRAB-ZFPs), the biggest family of transcription regulators. Several KRAB-ZFP factors exert a known effect in tumor cells, acting as tumor suppressor genes (TSGs) or oncogenes, yet their role in CSCs is still poorly characterized. Here, we review recent studies regarding the influence of KRAB-ZFPs and their cofactor protein TRIM28 on CSCs phenotype, stemness features, migration and invasion potential, metastasis, and expression of parental markers.
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32
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Sun B, Xu L, Bi W, Ou WB. SALL4 Oncogenic Function in Cancers: Mechanisms and Therapeutic Relevance. Int J Mol Sci 2022; 23:ijms23042053. [PMID: 35216168 PMCID: PMC8876671 DOI: 10.3390/ijms23042053] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 02/06/2023] Open
Abstract
SALL4, a member of the SALL family, is an embryonic stem cell regulator involved in self-renewal and pluripotency. Recently, SALL4 overexpression was found in malignant cancers, including lung cancer, hepatocellular carcinoma, breast cancer, gastric cancer, colorectal cancer, osteosarcoma, acute myeloid leukemia, ovarian cancer, and glioma. This review updates recent advances of our knowledge of the biology of SALL4 with a focus on its mechanisms and regulatory functions in tumors and human hematopoiesis. SALL4 overexpression promotes proliferation, development, invasion, and migration in cancers through activation of the Wnt/β-catenin, PI3K/AKT, and Notch signaling pathways; expression of mitochondrial oxidative phosphorylation genes; and inhibition of the expression of the Bcl-2 family, caspase-related proteins, and death receptors. Additionally, SALL4 regulates tumor progression correlated with the immune microenvironment involved in the TNF family and gene expression through epigenetic mechanisms, consequently affecting hematopoiesis. Therefore, SALL4 plays a critical oncogenic role in gene transcription and tumor growth. However, there are still some scientific hypotheses to be tested regarding whether SALL4 is a therapeutic target, such as different tumor microenvironments and drug resistance. Thus, an in-depth understanding and study of the functions and mechanisms of SALL4 in cancer may help develop novel strategies for cancer therapy.
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Affiliation(s)
| | | | | | - Wen-Bin Ou
- Correspondence: ; Tel./Fax: +86-571-8684-3303
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Williams RM, Lukoseviciute M, Sauka-Spengler T, Bronner ME. Single-cell atlas of early chick development reveals gradual segregation of neural crest lineage from the neural plate border during neurulation. eLife 2022; 11:74464. [PMID: 35088714 PMCID: PMC8798042 DOI: 10.7554/elife.74464] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/01/2021] [Indexed: 12/16/2022] Open
Abstract
The epiblast of vertebrate embryos is comprised of neural and non-neural ectoderm, with the border territory at their intersection harboring neural crest and cranial placode progenitors. Here, we a generate single-cell atlas of the developing chick epiblast from late gastrulation through early neurulation stages to define transcriptional changes in the emerging ‘neural plate border’ as well as other regions of the epiblast. Focusing on the border territory, the results reveal gradual establishment of heterogeneous neural plate border signatures, including novel genes that we validate by fluorescent in situ hybridization. Developmental trajectory analysis infers that segregation of neural plate border lineages only commences at early neurulation, rather than at gastrulation as previously predicted. We find that cells expressing the prospective neural crest marker Pax7 contribute to multiple lineages, and a subset of premigratory neural crest cells shares a transcriptional signature with their border precursors. Together, our results suggest that cells at the neural plate border remain heterogeneous until early neurulation, at which time progenitors become progressively allocated toward defined neural crest and placode lineages. The data also can be mined to reveal changes throughout the developing epiblast.
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Affiliation(s)
- Ruth M Williams
- California Institute of Technology, Division of Biology and Biological engineering, Pasadena, United States.,University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, United Kingdom
| | - Martyna Lukoseviciute
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, United Kingdom
| | - Tatjana Sauka-Spengler
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, United Kingdom
| | - Marianne E Bronner
- California Institute of Technology, Division of Biology and Biological engineering, Pasadena, United States
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Wang Y, Zheng X, Cheng R, Han J, Ma X, Xu W, Gao L, Lei A, Liu J, Quan F, Zhang Y, Liu X. Asymmetric expression of maternal mRNA governs first cell-fate decision. FASEB J 2021; 35:e22006. [PMID: 34694646 DOI: 10.1096/fj.202101196r] [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: 07/27/2021] [Revised: 09/23/2021] [Accepted: 10/06/2021] [Indexed: 11/11/2022]
Abstract
The goal of preimplantation development is to establish the fates of the embryonic and extra-embryonic cells. However, when and how cell fates are determined during early mammalian embryonic development remains unclear. We report that the high mobility group (HMG) protein family member HMGA1 was distributed differentially in mouse two-cell blastomeres. Knockdown of Hmga1 expression in one of the two cells reduced the number of cells contributing to the inner cell mass (ICM), suggesting that differential distribution of HMGA1 in the blastomeres in two-cell mouse embryos affected the selection of embryonic cell lineages. Mechanistically, HMGA1 promotes the expression of the ICM-specific gene Sox2. The results of this study show that mouse embryos demonstrate heterogeneity as early as the two-cell stage, and that these differences are related to cell-fate differentiation in early mouse embryos.
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Affiliation(s)
- Yingmei Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Xiaoman Zheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Rui Cheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Jing Han
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Xing Ma
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Wenjun Xu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Lu Gao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Anmin Lei
- College of Veterinary Medicine, Shaanxi Stem Cell Engineering and Technology Center, Northwest A&F University, Yangling, PR China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Fusheng Quan
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Xu Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
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Vigueras-Villaseñor RM, Ramírez Cuevas Z, Chávez-Saldaña M, Landero-Huerta DA, Cuevas Alpuche JO, Arceo Olaiz RA, Rojas-Castañeda JC. Disorders in the function of Sertoli cells and arrest in the differentiation of gonocytes in patients with cryptochidism and microlithiasis. J Pediatr Surg 2021; 56:1886-1893. [PMID: 33461744 DOI: 10.1016/j.jpedsurg.2020.12.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023]
Abstract
PURPOSE This study aimed to correlate the presence of microlithiasis (ML) in cryptorchidism (CO) patients with the functionality of Sertoli cells and the arrest of gonocyte differentiation. METHODS Testicular biopsies were obtained from 21 inguinal CO pediatric patients and were classified in two groups as follows: patients with ML and those without ML. In both groups, the number of Sertoli cells/seminiferous cords and their functionality were determined, considering the concentrations of inhibin B. In addition, the area and the histological alterations of seminiferous epithelium were evaluated. The arrest of gonocyte differentiation was determined by immunoreactivity to SALL4, AP2ɣ, PLAP and POU5F1. RESULTS We found a statistical correlation between the presence of ML with the alterations in the functionality of Sertoli cells without reflecting in the differentiation of the gonocytes. CONCLUSION The study of this population suggests that the association between CO and ML shows a malfunction of the Sertoli cells without necessarily causing arrest in the differentiation of gonocytes in these patients.
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Affiliation(s)
| | - Zayra Ramírez Cuevas
- Laboratorio de Biología de la Reproducción, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Margarita Chávez-Saldaña
- Laboratorio de Biología de la Reproducción, Instituto Nacional de Pediatría, Mexico City, Mexico
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Kwon J, Liu YV, Gao C, Bassal MA, Jones AI, Yang J, Chen Z, Li Y, Yang H, Chen L, Di Ruscio A, Tay Y, Chai L, Tenen DG. Pseudogene-mediated DNA demethylation leads to oncogene activation. SCIENCE ADVANCES 2021; 7:eabg1695. [PMID: 34597139 PMCID: PMC10938534 DOI: 10.1126/sciadv.abg1695] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
Pseudogenes, noncoding homologs of protein-coding genes, once considered nonfunctional evolutionary relics, have recently been linked to patient prognoses and cancer subtypes. Despite this potential clinical importance, only a handful of >12,000 pseudogenes in humans have been characterized in cancers to date. Here, we describe a previously unrecognized role for pseudogenes as potent epigenetic regulators that can demethylate and activate oncogenes. We focused on SALL4, a known oncogene in hepatocellular carcinoma (HCC) with eight pseudogenes. Using a locus-specific demethylating technology, we identified the critical CpG region for SALL4 expression. We demonstrated that SALL4 pseudogene 5 hypomethylates this region through interaction with DNMT1, resulting in SALL4 up-regulation. Intriguingly, pseudogene 5 is significantly up-regulated in a hepatitis B virus model before SALL4 induction, and both are increased in patients with HBV-HCC. Our results suggest that pseudogene-mediated demethylation represents a novel mechanism of oncogene activation in cancer.
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Affiliation(s)
- Junsu Kwon
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Yanjing V. Liu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Chong Gao
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Mahmoud A. Bassal
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Adrianna I. Jones
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Junyu Yang
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Zhiyuan Chen
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ying Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Annalisa Di Ruscio
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Translational Medicine, University of Eastern Piedmont, Novara 28100, Italy
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Li Chai
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Daniel G. Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115 USA
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
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Ouban A. Expression of SALL4 stemness marker in laryngeal squamous cell carcinomas (LSCCs) and its clinical significance. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1972349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Abderrahman Ouban
- Department of Pathology, Alfaisal University College of Medicine, Riyadh, Kingdom of Saudi Arabia
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38
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Diener J, Baggiolini A, Pernebrink M, Dalcher D, Lerra L, Cheng PF, Varum S, Häusel J, Stierli S, Treier M, Studer L, Basler K, Levesque MP, Dummer R, Santoro R, Cantù C, Sommer L. Epigenetic control of melanoma cell invasiveness by the stem cell factor SALL4. Nat Commun 2021; 12:5056. [PMID: 34417458 PMCID: PMC8379183 DOI: 10.1038/s41467-021-25326-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/03/2021] [Indexed: 02/06/2023] Open
Abstract
Melanoma cells rely on developmental programs during tumor initiation and progression. Here we show that the embryonic stem cell (ESC) factor Sall4 is re-expressed in the Tyr::NrasQ61K; Cdkn2a-/- melanoma model and that its expression is necessary for primary melanoma formation. Surprisingly, while Sall4 loss prevents tumor formation, it promotes micrometastases to distant organs in this melanoma-prone mouse model. Transcriptional profiling and in vitro assays using human melanoma cells demonstrate that SALL4 loss induces a phenotype switch and the acquisition of an invasive phenotype. We show that SALL4 negatively regulates invasiveness through interaction with the histone deacetylase (HDAC) 2 and direct co-binding to a set of invasiveness genes. Consequently, SALL4 knock down, as well as HDAC inhibition, promote the expression of an invasive signature, while inhibition of histone acetylation partially reverts the invasiveness program induced by SALL4 loss. Thus, SALL4 appears to regulate phenotype switching in melanoma through an HDAC2-mediated mechanism.
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Affiliation(s)
- Johanna Diener
- University of Zürich, Institute of Anatomy, Zürich, Switzerland
| | - Arianna Baggiolini
- University of Zürich, Institute of Anatomy, Zürich, Switzerland
- Developmental Biology, The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mattias Pernebrink
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology; Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Damian Dalcher
- University of Zürich, Department of Molecular Mechanisms of Disease, Zürich, Switzerland
| | - Luigi Lerra
- University of Zürich, Department of Molecular Mechanisms of Disease, Zürich, Switzerland
| | - Phil F Cheng
- University Hospital of Zürich, Department of Dermatology, Zürich, Switzerland
| | - Sandra Varum
- University of Zürich, Institute of Anatomy, Zürich, Switzerland
| | - Jessica Häusel
- University of Zürich, Institute of Anatomy, Zürich, Switzerland
| | - Salome Stierli
- University of Zürich, Institute of Anatomy, Zürich, Switzerland
| | - Mathias Treier
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lorenz Studer
- Developmental Biology, The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Konrad Basler
- University of Zürich, Institute of Molecular Life Sciences, Zürich, Switzerland
| | - Mitchell P Levesque
- University Hospital of Zürich, Department of Dermatology, Zürich, Switzerland
| | - Reinhard Dummer
- University Hospital of Zürich, Department of Dermatology, Zürich, Switzerland
| | - Raffaella Santoro
- University of Zürich, Department of Molecular Mechanisms of Disease, Zürich, Switzerland
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology; Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
- University of Zürich, Institute of Molecular Life Sciences, Zürich, Switzerland
| | - Lukas Sommer
- University of Zürich, Institute of Anatomy, Zürich, Switzerland.
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ALDH1 and SALL4 Expression in Cell Block Samples from Patients with Lung Adenocarcinoma and Malignant Pleural Effusion. Diagnostics (Basel) 2021; 11:diagnostics11081463. [PMID: 34441397 PMCID: PMC8394086 DOI: 10.3390/diagnostics11081463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/25/2021] [Accepted: 08/09/2021] [Indexed: 12/14/2022] Open
Abstract
Malignant pleural effusion (MPE) can accompany advanced lung adenocarcinoma. Recent studies suggest that MPE could contain a heterogeneous subpopulation of cells with stem-like properties, such as tumorigenicity and self-renewal, indicating that they could be the source of metastasis. Although previous studies analyzed the correlation between cancer stem cell (CSC) marker expression and clinical outcomes using lung cancer tissues, investigations regarding the association of MPE with CSC marker expression are limited. We performed immunohistochemistry to examine the expression of aldehyde dehydrogenase 1 (ALDH1) and Sal-like 4 (SALL4) in 46 cell block samples of MPE from patients with lung adenocarcinoma. ALDH1-positive and SALL4-positive cancer cells in MPE were detected in 30 (65.2%) and 21 samples (45.7%), respectively. Cluster formation was detected in 26 samples (56.5%). The number of clusters was significantly higher in ALDH1-positive/SALL4-negative samples. SALL4 expression was inversely correlated with the cluster ratio (r = −0.356) and positively associated with the Ki-67 index (r = 0.326), suggesting that MPE cells with high SALL4 expression comprised the proliferative subpopulation. In conclusion, we demonstrated that MPE contains an ALDH1-positive/SALL4-negative subpopulation exhibiting cluster formation and a SALL4-positive proliferative subpopulation.
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40
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Saddozai UAK, Wang F, Akbar MU, Zhang L, An Y, Zhu W, Xie L, Li Y, Ji X, Guo X. Identification of Clinical Relevant Molecular Subtypes of Pheochromocytoma. Front Endocrinol (Lausanne) 2021; 12:605797. [PMID: 34234737 PMCID: PMC8256389 DOI: 10.3389/fendo.2021.605797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 05/10/2021] [Indexed: 12/30/2022] Open
Abstract
Pheochromocytoma (PCC) is a rare neuroendocrine tumor of the adrenal gland with a high rate of mortality if diagnosed at a late stage. Common symptoms of pheochromocytoma include headache, anxiety, palpitation, and diaphoresis. Different treatments are under observation for PCC but there is still no effective treatment option. Recently, the gene expression profiling of various tumors has provided new subtype-specific options for targeted therapies. In this study, using data sets from TCGA and the GSE19422 cohorts, we identified two distinct PCC subtypes with distinct gene expression patterns. Genes enriched in Subtype I PCCs were involved in the dopaminergic synapse, nicotine addiction, and long-term depression pathways, while genes enriched in subtype II PCCs were involved in protein digestion and absorption, vascular smooth muscle contraction, and ECM receptor interaction pathways. We further identified subtype specific genes such as ALK, IGF1R, RET, and RSPO2 for subtype I and EGFR, ESR1, and SMO for subtype II, the overexpression of which led to cell invasion and tumorigenesis. These genes identified in the present research may serve as potential subtype-specific therapeutic targets to understand the underlying mechanisms of tumorigenesis. Our findings may further guide towards the development of targeted therapies and potential molecular biomarkers against PCC.
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Affiliation(s)
- Umair Ali Khan Saddozai
- Department of Preventive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Fengling Wang
- Department of Preventive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Muhammad Usman Akbar
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Lu Zhang
- Department of Preventive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Yang An
- Department of Preventive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Wan Zhu
- Department of Anesthesia, Stanford University, Stanford, CA, United States
| | - Longxiang Xie
- Department of Preventive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Yongqiang Li
- Department of Preventive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Xinying Ji
- Department of Preventive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Xiangqian Guo
- Department of Preventive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, Henan University, Kaifeng, China
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Islam Z, Ali AM, Naik A, Eldaw M, Decock J, Kolatkar PR. Transcription Factors: The Fulcrum Between Cell Development and Carcinogenesis. Front Oncol 2021; 11:681377. [PMID: 34195082 PMCID: PMC8236851 DOI: 10.3389/fonc.2021.681377] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/26/2021] [Indexed: 12/15/2022] Open
Abstract
Higher eukaryotic development is a complex and tightly regulated process, whereby transcription factors (TFs) play a key role in controlling the gene regulatory networks. Dysregulation of these regulatory networks has also been associated with carcinogenesis. Transcription factors are key enablers of cancer stemness, which support the maintenance and function of cancer stem cells that are believed to act as seeds for cancer initiation, progression and metastasis, and treatment resistance. One key area of research is to understand how these factors interact and collaborate to define cellular fate during embryogenesis as well as during tumor development. This review focuses on understanding the role of TFs in cell development and cancer. The molecular mechanisms of cell fate decision are of key importance in efforts towards developing better protocols for directed differentiation of cells in research and medicine. We also discuss the dysregulation of TFs and their role in cancer progression and metastasis, exploring TF networks as direct or indirect targets for therapeutic intervention, as well as specific TFs' potential as biomarkers for predicting and monitoring treatment responses.
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Affiliation(s)
- Zeyaul Islam
- Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Ameena Mohamed Ali
- Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Adviti Naik
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Mohamed Eldaw
- Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Julie Decock
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Prasanna R. Kolatkar
- Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
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Biological importance of OCT transcription factors in reprogramming and development. Exp Mol Med 2021; 53:1018-1028. [PMID: 34117345 PMCID: PMC8257633 DOI: 10.1038/s12276-021-00637-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
Ectopic expression of Oct4, Sox2, Klf4 and c-Myc can reprogram somatic cells into induced pluripotent stem cells (iPSCs). Attempts to identify genes or chemicals that can functionally replace each of these four reprogramming factors have revealed that exogenous Oct4 is not necessary for reprogramming under certain conditions or in the presence of alternative factors that can regulate endogenous Oct4 expression. For example, polycistronic expression of Sox2, Klf4 and c-Myc can elicit reprogramming by activating endogenous Oct4 expression indirectly. Experiments in which the reprogramming competence of all other Oct family members tested and also in different species have led to the decisive conclusion that Oct proteins display different reprogramming competences and species-dependent reprogramming activity despite their profound sequence conservation. We discuss the roles of the structural components of Oct proteins in reprogramming and how donor cell epigenomes endow Oct proteins with different reprogramming competences. Cells can be reprogrammed into induced pluripotent stem cells (iPSCs), embryonic-like stem cells that can turn into any cell type and have extensive potential medical uses, without adding the transcription factor OCT4. Although other nearly identical OCT family members had been tried, only OCT4 could induce reprogramming and was previously thought to be indispensable. However, it now appears that the reprogramming can be induced by multiple pathways, as detailed in a review by Hans Schöler, Max Planck Institute for Biomolecular Medicine, Münster, and Johnny Kim, Max Planck Institute for Heart and Lung Research, Bad Nauheim, in Germany. They report that any factors that trigger cells to activate endogeous OCT4 can produce iPSCs without exogeously admistration of OCT4. The mechanisms for producing iPSCs can differ between species. These results illuminate the complex mechanisms of reprogramming.
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Xie D, Tong M, Xia B, Feng G, Wang L, Li A, Luo G, Wan H, Zhang Z, Zhang H, Yang YG, Zhou Q, Wang M, Wang XJ. Long noncoding RNA lnc-NAP sponges mmu-miR-139-5p to modulate Nanog functions in mouse ESCs and embryos. RNA Biol 2021; 18:875-887. [PMID: 32991228 PMCID: PMC8081037 DOI: 10.1080/15476286.2020.1827591] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/30/2020] [Accepted: 09/20/2020] [Indexed: 12/30/2022] Open
Abstract
The pluripotency of embryonic stem cells (ESCs) is controlled by a multilayer regulatory network, of which the key factors include core pluripotency genes Oct4, Sox2 and Nanog, and multiple microRNAs (miRNAs). Recently, long noncoding RNAs (lncRNAs) have been discovered as a class of new regulators for ESCs, and some lncRNAs could function as competing endogenous RNAs (ceRNAs) to regulate mRNAs by competitively binding to miRNAs. Here, we identify mmu-miR-139-5p as a new regulator for Nanog by targeting Nanog 3' untranslated region (UTR) to repress Nanog expression in mouse ESCs and embryos. Such regulation could be released by an ESC-specifically expressed ceRNA named lnc-NAP. The expression of lnc-NAP is activated by OCT4, SOX2, as well as NANOG through promoter binding. Downregulation of lnc-NAP reduces Nanog abundance, which leads to decreased pluripotency of mouse ESCs and embryonic lethality. These results reveal lnc-NAP as a new regulator for Nanog in mouse ESCs, and uncover a feed-forward regulatory loop of Nanog through the participation of lnc-NAP.
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MESH Headings
- 3' Untranslated Regions/genetics
- Animals
- Cell Differentiation/genetics
- Embryo, Mammalian/cytology
- Embryo, Mammalian/embryology
- Embryo, Mammalian/metabolism
- Embryonic Stem Cells/cytology
- Embryonic Stem Cells/metabolism
- Gene Expression Regulation, Developmental
- Mice, Inbred C57BL
- Mice, Inbred DBA
- Mice, Inbred NOD
- Mice, SCID
- MicroRNAs/genetics
- Nanog Homeobox Protein/genetics
- Nanog Homeobox Protein/metabolism
- Octamer Transcription Factor-3/genetics
- Octamer Transcription Factor-3/metabolism
- Promoter Regions, Genetic/genetics
- Protein Binding
- RNA, Long Noncoding/genetics
- RNA-Seq/methods
- Reverse Transcriptase Polymerase Chain Reaction/methods
- SOXB1 Transcription Factors/genetics
- SOXB1 Transcription Factors/metabolism
- Mice
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Affiliation(s)
- Dongfang Xie
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Man Tong
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Baolong Xia
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Leyun Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ang Li
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Guanzheng Luo
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Haifeng Wan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zeyu Zhang
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Hao Zhang
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yun-Gui Yang
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meng Wang
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xiu-Jie Wang
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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44
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Kim SH, Choi KH, Lee M, Lee DK, Lee CK. Porcine OCT4 Reporter System Can Monitor Species-Specific Pluripotency During Somatic Cell Reprogramming. Cell Reprogram 2021; 23:168-179. [PMID: 34037424 DOI: 10.1089/cell.2021.0001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This study examined the activity and function of pig OCT4 enhancer in porcine reprogramming cells. Dual fluorescent protein reporter systems controlled by the upstream regulatory region of OCT4, which is one of the master regulators for pluripotency, are widely used in studies of the mechanism of pluripotency. We analyzed how this reporter system functions in fibroblast growth factor (FGF)- or leukemia inhibitory factor (LIF)-dependent reprogrammed porcine pluripotent stem cells using the previously established porcine-specific reporter system. Porcine embryonic fibroblasts were coinfected with the pOCT4-ΔPE-eGFP (distal enhancer [DE]-green fluorescent protein [GFP]) and pOCT4-ΔDE-DsRed2 (proximal enhancer [PE]-red fluorescent protein [RFP]) vectors, and GFP and RFP expression were verified during a DOX-dependent reprogramming process. We demonstrated that the porcine OCT4 DE and PE were activated in different expression patterns simultaneously as changes in the expression of pluripotent marker genes during the establishment of porcine-induced pluripotent stem cells (iPSCs). Porcine OCT4 upstream region-derived dual fluorescent protein reporter systems confirmed that porcine iPSCs are in primed state after reprogramming in FGF2- or LIF-containing media. This work demonstrates the applicability of porcine OCT4 upstream region-derived dual fluorescence reporter system, which may be applied to investigations of species-specific pluripotency in porcine-origin cells. These reporter systems may be useful tools for studies of porcine-specific pluripotency, early embryo development, and embryonic stem cells.
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Affiliation(s)
- Seung-Hun Kim
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Korea
| | - Kwang-Hwan Choi
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Korea
| | - Mingyun Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Korea
| | - Dong-Kyung Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Korea
| | - Chang-Kyu Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Korea.,Designed Animal & Transplantation Research Institute, Institute of Green Bio Science and Technology, Seoul National University, Gangwon-do, Korea
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45
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He R, Dantas A, Riabowol K. Histone Acetyltransferases and Stem Cell Identity. Cancers (Basel) 2021; 13:2407. [PMID: 34067525 PMCID: PMC8156521 DOI: 10.3390/cancers13102407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 12/13/2022] Open
Abstract
Acetylation of histones is a key epigenetic modification involved in transcriptional regulation. The addition of acetyl groups to histone tails generally reduces histone-DNA interactions in the nucleosome leading to increased accessibility for transcription factors and core transcriptional machinery to bind their target sequences. There are approximately 30 histone acetyltransferases and their corresponding complexes, each of which affect the expression of a subset of genes. Because cell identity is determined by gene expression profile, it is unsurprising that the HATs responsible for inducing expression of these genes play a crucial role in determining cell fate. Here, we explore the role of HATs in the maintenance and differentiation of various stem cell types. Several HAT complexes have been characterized to play an important role in activating genes that allow stem cells to self-renew. Knockdown or loss of their activity leads to reduced expression and or differentiation while particular HATs drive differentiation towards specific cell fates. In this study we review functions of the HAT complexes active in pluripotent stem cells, hematopoietic stem cells, muscle satellite cells, mesenchymal stem cells, neural stem cells, and cancer stem cells.
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Affiliation(s)
- Ruicen He
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (R.H.); (A.D.)
- Department of Molecular Genetics, Temerty School of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Arthur Dantas
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (R.H.); (A.D.)
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Karl Riabowol
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (R.H.); (A.D.)
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
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46
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Interaction between LINC-ROR and Stemness State in Gastric Cancer Cells with Helicobacter pylori Infection. IRANIAN BIOMEDICAL JOURNAL 2021. [PMID: 33745265 PMCID: PMC8183384 DOI: 10.52547/ibj.25.3.157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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47
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Fan T, Huang Y. Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis. Sci Rep 2021; 11:7896. [PMID: 33846424 PMCID: PMC8042068 DOI: 10.1038/s41598-021-86919-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
This study was conducted to investigate epigenetic landscape across multiple species and identify transcription factors (TFs) and their roles in controlling cell fate decision events during early embryogenesis. We made a comprehensively joint-research of chromatin accessibility of five species during embryogenesis by integration of ATAC-seq and RNA-seq datasets. Regulatory roles of candidate early embryonic TFs were investigated. Widespread accessible chromatin in early embryos overlapped with putative cis-regulatory sequences. Sets of cell-fate-determining TFs were identified. YOX1, a key cell cycle regulator, were found to homologous to clusters of TFs that are involved in neuron and epidermal cell-fate determination. Our research provides an intriguing insight into evolution of cell-fate decision during early embryogenesis among organisms.
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Affiliation(s)
- Tongqiang Fan
- grid.443483.c0000 0000 9152 7385State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 People’s Republic of China
| | - Youjun Huang
- grid.443483.c0000 0000 9152 7385State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 People’s Republic of China
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48
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Garikipati VNS, Arakelyan A, Blakely EA, Chang PY, Truongcao MM, Cimini M, Malaredy V, Bajpai A, Addya S, Bisserier M, Brojakowska A, Eskandari A, Khlgatian MK, Hadri L, Fish KM, Kishore R, Goukassian DA. Long-Term Effects of Very Low Dose Particle Radiation on Gene Expression in the Heart: Degenerative Disease Risks. Cells 2021; 10:cells10020387. [PMID: 33668521 PMCID: PMC7917872 DOI: 10.3390/cells10020387] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/27/2021] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
Compared to low doses of gamma irradiation (γ-IR), high-charge-and-energy (HZE) particle IR may have different biological response thresholds in cardiac tissue at lower doses, and these effects may be IR type and dose dependent. Three- to four-month-old female CB6F1/Hsd mice were exposed once to one of four different doses of the following types of radiation: γ-IR 137Cs (40-160 cGy, 0.662 MeV), 14Si-IR (4-32 cGy, 260 MeV/n), or 22Ti-IR (3-26 cGy, 1 GeV/n). At 16 months post-exposure, animals were sacrificed and hearts were harvested and archived as part of the NASA Space Radiation Tissue Sharing Forum. These heart tissue samples were used in our study for RNA isolation and microarray hybridization. Functional annotation of twofold up/down differentially expressed genes (DEGs) and bioinformatics analyses revealed the following: (i) there were no clear lower IR thresholds for HZE- or γ-IR; (ii) there were 12 common DEGs across all 3 IR types; (iii) these 12 overlapping genes predicted various degrees of cardiovascular, pulmonary, and metabolic diseases, cancer, and aging; and (iv) these 12 genes revealed an exclusive non-linear DEG pattern in 14Si- and 22Ti-IR-exposed hearts, whereas two-thirds of γ-IR-exposed hearts revealed a linear pattern of DEGs. Thus, our study may provide experimental evidence of excess relative risk (ERR) quantification of low/very low doses of full-body space-type IR-associated degenerative disease development.
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Affiliation(s)
- Venkata Naga Srikanth Garikipati
- Department of Emergency Medicine, Dorothy M Davis Heart and Lung Research Institute, Wexner Medical School, The Ohio State University, Columbus, OH 43210, USA;
| | - Arsen Arakelyan
- Bioinformatics Group, The Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia;
- PathVerse, Yerevan 0014, Armenia
| | | | | | - May M. Truongcao
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (M.M.T.); (M.C.); (V.M.); (A.B.); (R.K.)
| | - Maria Cimini
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (M.M.T.); (M.C.); (V.M.); (A.B.); (R.K.)
| | - Vandana Malaredy
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (M.M.T.); (M.C.); (V.M.); (A.B.); (R.K.)
| | - Anamika Bajpai
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (M.M.T.); (M.C.); (V.M.); (A.B.); (R.K.)
| | - Sankar Addya
- Kimmel Cancer Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Malik Bisserier
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.B.); (A.B.); (A.E.); (M.K.K.); (L.H.); (K.M.F.)
| | - Agnieszka Brojakowska
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.B.); (A.B.); (A.E.); (M.K.K.); (L.H.); (K.M.F.)
| | - Abrisham Eskandari
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.B.); (A.B.); (A.E.); (M.K.K.); (L.H.); (K.M.F.)
| | - Mary K. Khlgatian
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.B.); (A.B.); (A.E.); (M.K.K.); (L.H.); (K.M.F.)
| | - Lahouaria Hadri
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.B.); (A.B.); (A.E.); (M.K.K.); (L.H.); (K.M.F.)
| | - Kenneth M. Fish
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.B.); (A.B.); (A.E.); (M.K.K.); (L.H.); (K.M.F.)
| | - Raj Kishore
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (M.M.T.); (M.C.); (V.M.); (A.B.); (R.K.)
| | - David. A. Goukassian
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.B.); (A.B.); (A.E.); (M.K.K.); (L.H.); (K.M.F.)
- Correspondence: ; Tel.: +1-212-824-8917
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49
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Markers of Stem Cells. Stem Cells 2021. [DOI: 10.1007/978-981-16-1638-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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50
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Kong NR, Bassal MA, Tan HK, Kurland JV, Yong KJ, Young JJ, Yang Y, Li F, Lee JD, Liu Y, Wu CS, Stein A, Luo HR, Silberstein LE, Bulyk ML, Tenen DG, Chai L. Zinc Finger Protein SALL4 Functions through an AT-Rich Motif to Regulate Gene Expression. Cell Rep 2021; 34:108574. [PMID: 33406418 PMCID: PMC8197658 DOI: 10.1016/j.celrep.2020.108574] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/29/2020] [Accepted: 12/08/2020] [Indexed: 11/19/2022] Open
Abstract
The zinc finger transcription factor SALL4 is highly expressed in embryonic stem cells, downregulated in most adult tissues, but reactivated in many aggressive cancers. This unique expression pattern makes SALL4 an attractive therapeutic target. However, whether SALL4 binds DNA directly to regulate gene expression is unclear, and many of its targets in cancer cells remain elusive. Here, through an unbiased screen of protein binding microarray (PBM) and cleavage under targets and release using nuclease (CUT&RUN) experiments, we identify and validate the DNA binding domain of SALL4 and its consensus binding sequence. Combined with RNA sequencing (RNA-seq) analyses after SALL4 knockdown, we discover hundreds of new SALL4 target genes that it directly regulates in aggressive liver cancer cells, including genes encoding a family of histone 3 lysine 9-specific demethylases (KDMs). Taken together, these results elucidate the mechanism of SALL4 DNA binding and reveal pathways and molecules to target in SALL4-dependent tumors. In this paper, Kong et al. elucidate the DNA binding mechanisms of the transcription factor SALL4 and an epigenetic pathway that it regulates. Due to its important role in driving aggressive cancers, better understanding of SALL4 function will lead to strategies to target this protein in cancer.
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Affiliation(s)
- Nikki R Kong
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Mahmoud A Bassal
- Harvard Stem Cell Institute, Boston, MA 02115, USA; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Hong Kee Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117599, Singapore
| | - Jesse V Kurland
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Kol Jia Yong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Biochemistry, Yoon Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - John J Young
- Department of Biology, Simmons University, Boston, MA 02115, USA
| | - Yang Yang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jonathan D Lee
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Yue Liu
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Chan-Shuo Wu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Alicia Stein
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hongbo R Luo
- Joint Program in Transfusion Medicine, Department of Laboratory Medicne, Children's Hospital Boston, Boston, MA 02115, USA
| | - Leslie E Silberstein
- Joint Program in Transfusion Medicine, Department of Laboratory Medicne, Children's Hospital Boston, Boston, MA 02115, USA
| | - Martha L Bulyk
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Daniel G Tenen
- Harvard Stem Cell Institute, Boston, MA 02115, USA; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.
| | - Li Chai
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA.
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