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Burclaff J. Transcriptional regulation of metabolism in the intestinal epithelium. Am J Physiol Gastrointest Liver Physiol 2023; 325:G501-G507. [PMID: 37786942 PMCID: PMC10894668 DOI: 10.1152/ajpgi.00147.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023]
Abstract
Epithelial metabolism in the intestine is increasingly known to be important for stem cell maintenance and activity while also affecting weight gain and diseases. This review compiles studies from recent years which describe major transcription factors controlling metabolic activity across the intestinal epithelium as well as transcriptional and epigenetic networks controlling the factors themselves. Recent studies show that transcriptional regulators serve as the link between signals from the microbiota and diet and epithelial metabolism. Studies have advanced this paradigm to identify druggable targets to block weight gain or disease progression in mice. As such, there is great potential that a better understanding of these regulatory networks will improve our knowledge of intestinal physiology and promote discoveries to benefit human health.
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Affiliation(s)
- Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, United States
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States
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2
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Hossain MU, Ferdous N, Reza MN, Ahammad I, Tiernan Z, Wang Y, O’Hanlon F, Wu Z, Sarker S, Mohiuddin AKM, Das KC, Keya CA, Salimullah M. Pathogen-driven gene expression patterns lead to a novel approach to the identification of common therapeutic targets. Sci Rep 2022; 12:21070. [PMID: 36473896 PMCID: PMC9726901 DOI: 10.1038/s41598-022-25102-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
Developing a common medication strategy for disease control and management could be greatly beneficial. Investigating the differences between diseased and healthy states using differentially expressed genes aids in understanding disease pathophysiology and enables the exploration of protein-drug interactions. This study aimed to find the most common genes in diarrhea-causing bacteria such as Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Escherichia coli, Shigella dysenteriae (CESS) to find new drugs. Thus, differential gene expression datasets of CESS were screened through computational algorithms and programming. Subsequently, hub and common genes were prioritized from the analysis of extensive protein-protein interactions. Binding predictions were performed to identify the common potential therapeutic targets of CESS. We identified a total of 827 dysregulated genes that are highly linked to CESS. Notably, no common gene interaction was found among all CESS bacteria, but we identified 3 common genes in both Salmonella-Escherichia and Escherichia-Campylobacter infections. Later, out of 73 protein complexes, molecular simulations confirmed 5 therapeutic candidates from the CESS. We have developed a new pipeline for identifying therapeutic targets for a common medication strategy against CESS. However, further wet-lab validation is needed to confirm their effectiveness.
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Affiliation(s)
- Mohammad Uzzal Hossain
- grid.4991.50000 0004 1936 8948Department of Pharmacology, Medical Sciences Division, University of Oxford, Oxford, OX13QT UK ,Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349 Bangladesh
| | - Nadim Ferdous
- grid.443019.b0000 0004 0479 1356Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902 Bangladesh
| | - Mahjerin Nasrin Reza
- grid.443019.b0000 0004 0479 1356Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902 Bangladesh
| | - Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349 Bangladesh
| | - Zachary Tiernan
- grid.4991.50000 0004 1936 8948Department of Pharmacology, Medical Sciences Division, University of Oxford, Oxford, OX13QT UK
| | - Yi Wang
- grid.4991.50000 0004 1936 8948Department of Pharmacology, Medical Sciences Division, University of Oxford, Oxford, OX13QT UK
| | - Fergus O’Hanlon
- grid.4991.50000 0004 1936 8948Mathematical Institute, University of Oxford, Oxford, OX2 6GG UK
| | - Zijia Wu
- grid.4991.50000 0004 1936 8948Department of Chemistry, University of Oxford, Oxford, OX2 6GG UK
| | - Shishir Sarker
- grid.443016.40000 0004 4684 0582Department of Microbiology, Jagannath University, Dhaka, 1100 Bangladesh
| | - A. K. M. Mohiuddin
- grid.443019.b0000 0004 0479 1356Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902 Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, Ministry of Science and Technology, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349 Bangladesh
| | - Chaman Ara Keya
- grid.443020.10000 0001 2295 3329Department of Biochemistry and Microbiology, North South University, Dhaka, 1229 Bangladesh
| | - Md. Salimullah
- Molecular Biotechnology Division, Ministry of Science and Technology, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349 Bangladesh
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Callaghan NI, Durland LJ, Ireland RG, Santerre JP, Simmons CA, Davenport Huyer L. Harnessing conserved signaling and metabolic pathways to enhance the maturation of functional engineered tissues. NPJ Regen Med 2022; 7:44. [PMID: 36057642 DOI: 10.1038/s41536-022-00246-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/05/2022] [Indexed: 11/08/2022] Open
Abstract
The development of induced-pluripotent stem cell (iPSC)-derived cell types offers promise for basic science, drug testing, disease modeling, personalized medicine, and translatable cell therapies across many tissue types. However, in practice many iPSC-derived cells have presented as immature in physiological function, and despite efforts to recapitulate adult maturity, most have yet to meet the necessary benchmarks for the intended tissues. Here, we summarize the available state of knowledge surrounding the physiological mechanisms underlying cell maturation in several key tissues. Common signaling consolidators, as well as potential synergies between critical signaling pathways are explored. Finally, current practices in physiologically relevant tissue engineering and experimental design are critically examined, with the goal of integrating greater decision paradigms and frameworks towards achieving efficient maturation strategies, which in turn may produce higher-valued iPSC-derived tissues.
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Wang Y, Yang D, Zhu R, Dai F, Yuan M, Zhang L, Zheng Y, Liu S, Yang X, Cheng Y. YY1/ITGA3 pathway may affect trophoblastic cells migration and invasion ability. J Reprod Immunol 2022; 153:103666. [DOI: 10.1016/j.jri.2022.103666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 06/19/2022] [Accepted: 07/11/2022] [Indexed: 02/06/2023]
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Madan S, Uttekar B, Chowdhary S, Rikhy R. Mitochondria Lead the Way: Mitochondrial Dynamics and Function in Cellular Movements in Development and Disease. Front Cell Dev Biol 2022; 9:781933. [PMID: 35186947 PMCID: PMC8848284 DOI: 10.3389/fcell.2021.781933] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/16/2021] [Indexed: 01/09/2023] Open
Abstract
The dynamics, distribution and activity of subcellular organelles are integral to regulating cell shape changes during various physiological processes such as epithelial cell formation, cell migration and morphogenesis. Mitochondria are famously known as the powerhouse of the cell and play an important role in buffering calcium, releasing reactive oxygen species and key metabolites for various activities in a eukaryotic cell. Mitochondrial dynamics and morphology changes regulate these functions and their regulation is, in turn, crucial for various morphogenetic processes. In this review, we evaluate recent literature which highlights the role of mitochondrial morphology and activity during cell shape changes in epithelial cell formation, cell division, cell migration and tissue morphogenesis during organism development and in disease. In general, we find that mitochondrial shape is regulated for their distribution or translocation to the sites of active cell shape dynamics or morphogenesis. Often, key metabolites released locally and molecules buffered by mitochondria play crucial roles in regulating signaling pathways that motivate changes in cell shape, mitochondrial shape and mitochondrial activity. We conclude that mechanistic analysis of interactions between mitochondrial morphology, activity, signaling pathways and cell shape changes across the various cell and animal-based model systems holds the key to deciphering the common principles for this interaction.
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Vivarelli S, Falzone L, Candido S, Bonavida B, Libra M. YY1 Silencing Induces 5-Fluorouracil-Resistance and BCL2L15 Downregulation in Colorectal Cancer Cells: Diagnostic and Prognostic Relevance. Int J Mol Sci 2021; 22:8481. [PMID: 34445183 PMCID: PMC8395225 DOI: 10.3390/ijms22168481] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer (CRC) is characterized by genetic heterogeneity and is often diagnosed at an advanced stage. Therefore, there is a need to identify novel predictive markers. Yin Yang 1 (YY1) is a transcription factor playing a dual role in cancer. The present study aimed to investigate whether YY1 expression levels influence CRC cell response to therapy and to identify the transcriptional targets involved. The diagnostic and prognostic values of YY1 and the identified factor(s) in CRC patients were also explored. Silencing of YY1 increased the resistance to 5-Fluorouracil-induced cytotoxicity in two out of four CRC cells with different genotypes. BCL2L15/Bfk pro-apoptotic factor was found selectively expressed in the responder CRC cells and downregulated upon YY1 knockdown. CRC dataset analyses corroborated a tumor-suppressive role for both YY1 and BCL2L15 whose expressions were inversely correlated with aggressiveness. CRC single-cell sequencing dataset analyses demonstrated higher co-expression levels of both YY1 and BCL2L15 within defined tumor cell clusters. Finally, elevated levels of YY1 and BCL2L15 in CRC patients were associated with larger relapse-free survival. Given their observed anti-cancer role, we propose YY1 and BCL2L15 as candidate diagnostic and prognostic CRC biomarkers.
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Affiliation(s)
- Silvia Vivarelli
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (S.V.); (S.C.)
| | - Luca Falzone
- Epidemiology and Biostatistics Unit, IRCCS Istituto Nazionale Tumori “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (S.V.); (S.C.)
- Research Centre for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy
| | - Benjamin Bonavida
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA;
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (S.V.); (S.C.)
- Research Centre for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy
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Prado NA, Brown JL, Zoller JA, Haghani A, Yao M, Bagryanova LR, Campana MG, E. Maldonado J, Raj K, Schmitt D, Robeck TR, Horvath S. Epigenetic clock and methylation studies in elephants. Aging Cell 2021; 20:e13414. [PMID: 34118182 PMCID: PMC8282242 DOI: 10.1111/acel.13414] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/15/2021] [Accepted: 05/08/2021] [Indexed: 11/30/2022] Open
Abstract
Age-associated DNA-methylation profiles have been used successfully to develop highly accurate biomarkers of age ("epigenetic clocks") in humans, mice, dogs, and other species. Here we present epigenetic clocks for African and Asian elephants. These clocks were developed using novel DNA methylation profiles of 140 elephant blood samples of known age, at loci that are highly conserved between mammalian species, using a custom Infinium array (HorvathMammalMethylChip40). We present epigenetic clocks for Asian elephants (Elephas maximus), African elephants (Loxodonta africana), and both elephant species combined. Two additional human-elephant clocks were constructed by combining human and elephant samples. Epigenome-wide association studies identified elephant age-related CpGs and their proximal genes. The products of these genes play important roles in cellular differentiation, organismal development, metabolism, and circadian rhythms. Intracellular events observed to change with age included the methylation of bivalent chromatin domains, and targets of polycomb repressive complexes. These readily available epigenetic clocks can be used for elephant conservation efforts where accurate estimates of age are needed to predict demographic trends.
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Affiliation(s)
- Natalia A. Prado
- Center for Species SurvivalSmithsonian Conservation Biology InstituteFront RoyalVAUSA
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDCUSA
| | - Janine L. Brown
- Center for Species SurvivalSmithsonian Conservation Biology InstituteFront RoyalVAUSA
| | - Joseph A. Zoller
- Department of BiostatisticsFielding School of Public HealthUniversity of CaliforniaLos AngelesCAUSA
| | - Amin Haghani
- Department of Human GeneticsDavid Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Mingjia Yao
- Department of BiostatisticsFielding School of Public HealthUniversity of CaliforniaLos AngelesCAUSA
| | - Lora R. Bagryanova
- Department of EpidemiologyFielding School of Public HealthUniversity of CaliforniaLos Angeles, Los AngelesCAUSA
| | - Michael G. Campana
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDCUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDCUSA
| | - Ken Raj
- Radiation Effects DepartmentCentre for Radiation, Chemical and Environmental HazardsPublic Health EnglandDidcotUK
| | - Dennis Schmitt
- College of AgricultureMissouri State UniversitySpringfieldMOUSA
| | | | - Steve Horvath
- Department of BiostatisticsFielding School of Public HealthUniversity of CaliforniaLos AngelesCAUSA
- Department of Human GeneticsDavid Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
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Abstract
Accumulating evidence strongly indicates that the presence of cancer stem cells (CSCs) leads to the emergence of worse clinical scenarios, such as chemo- and radiotherapy resistance, metastasis, and cancer recurrence. CSCs are a highly tumorigenic population characterized by self-renewal capacity and differentiation potential. Thus, CSCs establish a hierarchical intratumor organization that enables tumor adaptation to evade the immune response and resist anticancer therapy. YY1 functions as a transcription factor, RNA-binding protein, and 3D chromatin regulator. Thus, YY1 has multiple effects and regulates several molecular processes. Emerging evidence indicates that the development of lethal YY1-mediated cancer phenotypes is associated with the presence of or enrichment in cancer stem-like cells. Therefore, it is necessary to investigate whether and to what extent YY1 regulates the CSC phenotype. Since CSCs mirror the phenotypic behavior of stem cells, we initially describe the roles played by YY1 in embryonic and adult stem cells. Next, we scrutinize evidence supporting the contributions of YY1 in CSCs from a number of various cancer types. Finally, we identify new areas for further investigation into the YY1-CSCs axis, including the participation of YY1 in the CSC niche.
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Jin G, Tang Q, Ma J, Liu X, Zhou B, Sun Y, Pang X, Guo Z, Xie R, Liu T, Wang B, Cao H. Maternal Emulsifier P80 Intake Induces Gut Dysbiosis in Offspring and Increases Their Susceptibility to Colitis in Adulthood. mSystems 2021; 6:e01337-20. [PMID: 33727402 DOI: 10.1128/mSystems.01337-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Early life events can lead to multiple diseases in adulthood. Previous studies suggested that polysorbate 80 (P80) as a widely used emulsifier in pharmaceutical formulations and food industries could impair the intestinal barrier. However, whether maternal P80 (MP80) exposure could affect the long-term health of offspring remains unknown. In this study, we found that maternal P80 intake could retard intestinal development, disrupt the intestinal barrier, and cause low-grade intestinal inflammation in 3-week-old offspring. 16S rRNA sequencing and correlation analysis revealed that Mucispirillum, Clostridium XI, and Parabacteroides, which positively correlated with intestinal proliferation and differentiation, were decreased in the maternal P80 group. Interestingly, the increase in some harmful bacteria, including Proteobacteria, Helicobacteraceae, Campylobacterales, and Desulfovibrionales, persisted from the weaning period to adulthood (3 to 8 weeks). Furthermore, a fecal microbiota transplantation assay showed that the mice gavaged with feces from 3-week-old offspring of the MP80 group presented more severe intestinal inflammation and barrier disruption than the mice that received feces from the offspring of the control group. Finally, maternal P80 intake remarkably aggravated the structural disorder of intestinal crypt, increased proinflammatory factors, and exacerbated dextran sulfate sodium (DSS)-induced colitis in adulthood. Conclusively, maternal P80 intake could induce gut dysbiosis and promote colitis susceptibility in adulthood. This study provides new insights into the prevention of inflammatory bowel disease (IBD). IMPORTANCE The main findings of this research showed that maternal P80 intake could disrupt the intestinal barrier, induce gut dysbiosis, and promote colitis susceptibility in adulthood. This study will enhance understanding of the prevention of IBD.
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Xiong X, Lv DH, Liu YH, Song MH, Zou LJ, Xiao DF, Yin YL. Effect of glucose, soya oil and glutamine on protein expression and mammalian target of rapamycin complex 1 pathway of jejunal crypt enterocytes in weaned piglets. Br J Nutr 2020; 123:481-8. [PMID: 31623699 DOI: 10.1017/S0007114519002629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The present study was conducted to evaluate the effects of glucose, soya oil or glutamine on jejunal morphology, protein metabolism and protein expression of the mammalian target of rapamycin complex 1 (mTORC1) signalling pathway in jejunal villus or crypt compartment of piglets. Forty-two 21 d-weaned piglets were randomly allotted to one of the three isoenergetic diets formulated with glucose, soya oil or glutamine for 28 d. On day 14 or 28, the proteins in crypt enterocytes were analysed with isobaric tags for relative and absolute quantification and proteins involved in mTORC1 signalling pathway in villus or crypt compartment cells were determined by Western blotting. Our results showed no significant differences (P > 0·05) in jejunal morphology among the three treatments on day 14 or 28. The differentially expressed proteins mainly took part in a few network pathways, including antimicrobial or inflammatory response, cell death and survival, digestive system development and function and carbohydrate metabolism. On day 14 or 28, there were higher protein expression of eukaryotic initiation factor-4E binding protein-1 in jejunal crypt compartment of piglets supplemented with glucose or glutamine compared with soya oil. On day 28, higher protein expression of phosphor-mTOR in crypt compartment was observed in piglets supplemented with glucose compared with the soya oil. In conclusion, the isoenergetic glucose, soya oil or glutamine did not affect the jejunal morphology of piglets; however, they had different effects on the protein metabolism in crypt compartment. Compared with soya oil, glucose or glutamine may be better energy supplies for enterocytes in jejunal crypt compartment.
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Meliala ITS, Hosea R, Kasim V, Wu S. The biological implications of Yin Yang 1 in the hallmarks of cancer. Theranostics 2020; 10:4183-4200. [PMID: 32226547 PMCID: PMC7086370 DOI: 10.7150/thno.43481] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 02/09/2020] [Indexed: 12/24/2022] Open
Abstract
Tumorigenesis is a multistep process characterized by the acquisition of genetic and epigenetic alterations. During the course of malignancy development, tumor cells acquire several features that allow them to survive and adapt to the stress-related conditions of the tumor microenvironment. These properties, which are known as hallmarks of cancer, include uncontrolled cell proliferation, metabolic reprogramming, tumor angiogenesis, metastasis, and immune system evasion. Zinc-finger protein Yin Yang 1 (YY1) regulates numerous genes involved in cell death, cell cycle, cellular metabolism, and inflammatory response. YY1 is highly expressed in many cancers, whereby it is associated with cell proliferation, survival, and metabolic reprogramming. Furthermore, recent studies also have demonstrated the important role of YY1-related non-coding RNAs in acquiring cancer-specific characteristics. Therefore, these YY1-related non-coding RNAs are also crucial for YY1-mediated tumorigenesis. Herein, we summarize recent progress with respect to YY1 and its biological implications in the context of hallmarks of cancer.
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12
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Okkelman IA, Neto N, Papkovsky DB, Monaghan MG, Dmitriev RI. A deeper understanding of intestinal organoid metabolism revealed by combining fluorescence lifetime imaging microscopy (FLIM) and extracellular flux analyses. Redox Biol 2020; 30:101420. [PMID: 31935648 PMCID: PMC6957829 DOI: 10.1016/j.redox.2019.101420] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/13/2019] [Accepted: 12/29/2019] [Indexed: 12/21/2022] Open
Abstract
Stem cells and the niche in which they reside feature a complex microenvironment with tightly regulated homeostasis, cell-cell interactions and dynamic regulation of metabolism. A significant number of organoid models has been described over the last decade, yet few methodologies can enable single cell level resolution analysis of the stem cell niche metabolic demands, in real-time and without perturbing integrity. Here, we studied the redox metabolism of Lgr5-GFP intestinal organoids by two emerging microscopy approaches based on luminescence lifetime measurement - fluorescence-based FLIM for NAD(P)H, and phosphorescence-based PLIM for real-time oxygenation. We found that exposure of stem (Lgr5-GFP) and differentiated (no GFP) cells to high and low glucose concentrations resulted in measurable shifts in oxygenation and redox status. NAD(P)H-FLIM and O2-PLIM both indicated that at high 'basal' glucose conditions, Lgr5-GFP cells had lower activity of oxidative phosphorylation when compared with cells lacking Lgr5. However, when exposed to low (0.5 mM) glucose, stem cells utilized oxidative metabolism more dynamically than non-stem cells. The high heterogeneity of complex 3D architecture and energy production pathways of Lgr5-GFP organoids were also confirmed by the extracellular flux (XF) analysis. Our data reveals that combined analysis of NAD(P)H-FLIM and organoid oxygenation by PLIM represents promising approach for studying stem cell niche metabolism in a live readout.
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Affiliation(s)
- Irina A Okkelman
- Laboratory of Biophysics and Bioanalysis, ABCRF, University College Cork, Cavanagh Pharmacy Building, College Road, Cork, T12 K8AF, Ireland
| | - Nuno Neto
- Department of Mechanical and Manufacturing Engineering, Trinity College Dublin, Ireland; Trinity Centre for Biomedical Engineering, Trinity College Dublin, Ireland
| | - Dmitri B Papkovsky
- Laboratory of Biophysics and Bioanalysis, ABCRF, University College Cork, Cavanagh Pharmacy Building, College Road, Cork, T12 K8AF, Ireland
| | - Michael G Monaghan
- Department of Mechanical and Manufacturing Engineering, Trinity College Dublin, Ireland; Trinity Centre for Biomedical Engineering, Trinity College Dublin, Ireland; Advanced Materials and BioEngineering Research (AMBER) Centre at Trinity College Dublin and Royal College of Surgeons in Ireland, Dublin, Ireland.
| | - Ruslan I Dmitriev
- Laboratory of Biophysics and Bioanalysis, ABCRF, University College Cork, Cavanagh Pharmacy Building, College Road, Cork, T12 K8AF, Ireland; Institute for Regenerative Medicine, I.M. Sechenov First Moscow State University, Moscow, Russian Federation.
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Zurkirchen L, Varum S, Giger S, Klug A, Häusel J, Bossart R, Zemke M, Cantù C, Atak ZK, Zamboni N, Basler K, Sommer L. Yin Yang 1 sustains biosynthetic demands during brain development in a stage-specific manner. Nat Commun 2019; 10:2192. [PMID: 31097699 PMCID: PMC6522535 DOI: 10.1038/s41467-019-09823-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 03/26/2019] [Indexed: 12/12/2022] Open
Abstract
The transcription factor Yin Yang 1 (YY1) plays an important role in human disease. It is often overexpressed in cancers and mutations can lead to a congenital haploinsufficiency syndrome characterized by craniofacial dysmorphisms and neurological dysfunctions, consistent with a role in brain development. Here, we show that Yy1 controls murine cerebral cortex development in a stage-dependent manner. By regulating a wide range of metabolic pathways and protein translation, Yy1 maintains proliferation and survival of neural progenitor cells (NPCs) at early stages of brain development. Despite its constitutive expression, however, the dependence on Yy1 declines over the course of corticogenesis. This is associated with decreasing importance of processes controlled by Yy1 during development, as reflected by diminished protein synthesis rates at later developmental stages. Thus, our study unravels a novel role for Yy1 as a stage-dependent regulator of brain development and shows that biosynthetic demands of NPCs dynamically change throughout development. The transcription factor Yin Yang 1 (YY1) plays an important role in human disease, yet little is known about its role in brain development. This study shows that YY1 controls cerebral cortex development by maintaining proliferation and survival of neural progenitor cells via transcriptional regulation of genes involved in metabolism and protein translation.
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Affiliation(s)
- Luis Zurkirchen
- Institute of Anatomy, University of Zurich, 8057, Zurich, Switzerland
| | - Sandra Varum
- Institute of Anatomy, University of Zurich, 8057, Zurich, Switzerland
| | - Sonja Giger
- Institute of Anatomy, University of Zurich, 8057, Zurich, Switzerland
| | - Annika Klug
- Institute of Anatomy, University of Zurich, 8057, Zurich, Switzerland
| | - Jessica Häusel
- Institute of Anatomy, University of Zurich, 8057, Zurich, Switzerland
| | - Raphaël Bossart
- Institute of Anatomy, University of Zurich, 8057, Zurich, Switzerland
| | - Martina Zemke
- Institute of Anatomy, University of Zurich, 8057, Zurich, Switzerland
| | - Claudio Cantù
- Institute of Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland.,Wallenberg Centre for Molecular Medicine (WCMM), Department of Clinical and Experimental Medicine (IKE), Linköping University, Linköping, 58183, Sweden
| | - Zeynep Kalender Atak
- Laboratory of Computational Biology, KU Leuven Center for Human Genetics, Leuven, 3000, Belgium
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland
| | - Lukas Sommer
- Institute of Anatomy, University of Zurich, 8057, Zurich, Switzerland.
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Hays E, Bonavida B. YY1 regulates cancer cell immune resistance by modulating PD-L1 expression. Drug Resist Updat 2019; 43:10-28. [PMID: 31005030 DOI: 10.1016/j.drup.2019.04.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 02/08/2023]
Abstract
Recent advances in the treatment of various cancers have resulted in the adaptation of several novel immunotherapeutic strategies. Notably, the recent intervention through immune checkpoint inhibitors has resulted in significant clinical responses and prolongation of survival in patients with several therapy-resistant cancers (melanoma, lung, bladder, etc.). This intervention was mediated by various antibodies directed against inhibitory receptors expressed on cytotoxic T-cells or against corresponding ligands expressed on tumor cells and other cells in the tumor microenvironment (TME). However, the clinical responses were only observed in a subset of the treated patients; it was not clear why the remaining patients did not respond to checkpoint inhibitor therapies. One hypothesis stated that the levels of PD-L1 expression correlated with poor clinical responses to cell-mediated anti-tumor immunotherapy. Hence, exploring the underlying mechanisms that regulate PD-L1 expression on tumor cells is one approach to target such mechanisms to reduce PD-L1 expression and, therefore, sensitize the resistant tumor cells to respond to PD-1/PD-L1 antibody treatments. Various investigations revealed that the overexpression of the transcription factor Yin Yang 1 (YY1) in most cancers is involved in the regulation of tumor cells' resistance to cell-mediated immunotherapies. We, therefore, hypothesized that the role of YY1 in cancer immune resistance may be correlated with PD-L1 overexpression on cancer cells. This hypothesis was investigated and analysis of the reported literature revealed that several signaling crosstalk pathways exist between the regulations of both YY1 and PD-L1 expressions. Such pathways include p53, miR34a, STAT3, NF-kB, PI3K/AKT/mTOR, c-Myc, and COX-2. Noteworthy, many clinical and pre-clinical drugs have been utilized to target these above pathways in various cancers independent of their roles in the regulation of PD-L1 expression. Therefore, the direct inhibition of YY1 and/or the use of the above targeted drugs in combination with checkpoint inhibitors should result in enhancing the cell-mediated anti-tumor cell response and also reverse the resistance observed with the use of checkpoint inhibitors alone.
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Affiliation(s)
- Emily Hays
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, United States
| | - Benjamin Bonavida
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, United States.
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Abstract
The intestinal epithelium is a multicellular interface in close proximity to a dense microbial milieu that is completely renewed every 3-5 days. Pluripotent stem cells reside at the crypt, giving rise to transient amplifying cells that go through continuous steps of proliferation, differentiation and finally anoikis (a form of programmed cell death) while migrating upwards to the villus tip. During these cellular transitions, intestinal epithelial cells (IECs) possess distinct metabolic identities reflected by changes in mitochondrial activity. Mitochondrial function emerges as a key player in cell fate decisions and in coordinating cellular metabolism, immunity, stress responses and apoptosis. Mediators of mitochondrial signalling include molecules such as ATP and reactive oxygen species and interrelate with pathways such as the mitochondrial unfolded protein response (MT-UPR) and AMP kinase signalling, in turn affecting cell cycle progression and stemness. Alterations in mitochondrial function and MT-UPR activation are integral aspects of pathologies, including IBD and cancer. Mitochondrial signalling and concomitant changes in metabolism contribute to intestinal homeostasis and regulate IEC dedifferentiation-differentiation programmes in the context of diseases, suggesting that mitochondrial function as a cellular checkpoint critically contributes to disease outcome. This Review highlights mitochondrial function and MT-UPR signalling in epithelial cell stemness, differentiation and lineage commitment and illustrates mitochondrial function in intestinal diseases.
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Srivillibhuthur M, Warder BN, Toke NH, Shah PP, Feng Q, Gao N, Bonder EM, Verzi MP. TFAM is required for maturation of the fetal and adult intestinal epithelium. Dev Biol 2018; 439:92-101. [PMID: 29684311 PMCID: PMC5978755 DOI: 10.1016/j.ydbio.2018.04.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 04/18/2018] [Accepted: 04/18/2018] [Indexed: 12/14/2022]
Abstract
During development, the embryo transitions from a metabolism favoring glycolysis to a metabolism favoring mitochondrial respiration. How metabolic shifts regulate developmental processes, or how developmental processes regulate metabolic shifts, remains unclear. To test the requirement of mitochondrial function in developing endoderm-derived tissues, we genetically inactivated the mitochondrial transcription factor, Tfam, using the Shh-Cre driver. Tfam mutants did not survive postnatally, exhibiting defects in lung development. In the developing intestine, TFAM-loss was tolerated until late fetal development, during which the process of villus elongation was compromised. While progenitor cell populations appeared unperturbed, markers of enterocyte maturation were diminished and villi were blunted. Loss of TFAM was also tested in the adult intestinal epithelium, where enterocyte maturation was similarly dependent upon the mitochondrial transcription factor. While progenitor cells in the transit amplifying zone of the adult intestine remained proliferative, intestinal stem cell renewal was dependent upon TFAM, as indicated by molecular profiling and intestinal organoid formation assays. Taken together, these studies point to critical roles for the mitochondrial regulator TFAM for multiple aspects of intestinal development and maturation, and highlight the importance of mitochondrial regulators in tissue development and homeostasis.
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Affiliation(s)
- Manasa Srivillibhuthur
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA; Lewis Katz School of Medicine at Temple University, 3500 N Broad Street, Philadelphia, PA 19140, USA
| | - Bailey N Warder
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Natalie H Toke
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Pooja P Shah
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Qiang Feng
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Edward M Bonder
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Michael P Verzi
- Rutgers University, Department of Genetics, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA; Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA.
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17
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Chin AM, Hill DR, Aurora M, Spence JR. Morphogenesis and maturation of the embryonic and postnatal intestine. Semin Cell Dev Biol 2017; 66:81-93. [PMID: 28161556 DOI: 10.1016/j.semcdb.2017.01.011] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 12/12/2022]
Abstract
The intestine is a vital organ responsible for nutrient absorption, bile and waste excretion, and a major site of host immunity. In order to keep up with daily demands, the intestine has evolved a mechanism to expand the absorptive surface area by undergoing a morphogenetic process to generate finger-like units called villi. These villi house specialized cell types critical for both absorbing nutrients from food, and for protecting the host from commensal and pathogenic microbes present in the adult gut. In this review, we will discuss mechanisms that coordinate intestinal development, growth, and maturation of the small intestine, starting from the formation of the early gut tube, through villus morphogenesis and into early postnatal life when the intestine must adapt to the acquisition of nutrients through food intake, and to interactions with microbes.
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Affiliation(s)
- Alana M Chin
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - David R Hill
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Megan Aurora
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, United States; Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI, United States.
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