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Ishikawa C, Mori N. Inhibitory effect of a neddylation blockade on HTLV-1-infected T cells via modulation of NF-κB, AP-1, and Akt signaling. Leuk Lymphoma 2024; 65:978-988. [PMID: 38489672 DOI: 10.1080/10428194.2024.2328219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/03/2024] [Indexed: 03/17/2024]
Abstract
Adult T-cell leukemia (ATL), caused by HTLV-1, is the most lethal hematological malignancy. NEDD8-activating enzyme (NAE) is a component of the NEDD8 conjunction pathway that regulates cullin-RING ubiquitin ligase (CRL) activity. HTLV-1-infected T cells expressed higher levels of NAE catalytic subunit UBA3 than normal peripheral blood mononuclear cells. NAE1 knockdown inhibited proliferation of HTLV-1-infected T cells. The NAE1 inhibitor MLN4924 suppressed neddylation of cullin and inhibited the CRL-mediated turnover of tumor suppressor proteins. MLN4924 inhibited proliferation of HTLV-1-infected T cells by inducing DNA damage, leading to S phase arrest and caspase-dependent apoptosis. S phase arrest was associated with CDK2 and cyclin A downregulation. MLN4924-induced apoptosis was mediated by the upregulation of pro-apoptotic and downregulation of anti-apoptotic proteins. Furthermore, MLN4924 inhibited NF-κB, AP-1, and Akt signaling pathways and activated JNK. Therefore, neddylation inhibition is an attractive strategy for ATL therapy. Our findings support the use of MLN4924 in ATL clinical trials.
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Affiliation(s)
- Chie Ishikawa
- Department of Microbiology and Oncology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
- Division of Health Sciences, Transdisciplinary Research Organization for Subtropics and Island Studies, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Naoki Mori
- Department of Microbiology and Oncology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
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2
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Boamah GA, Huang Z, Ke C, You W, Ayisi CL, Amenyogbe E, Droepenu E. Preliminary analysis of pathways and their implications during salinity stress in abalone. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101224. [PMID: 38430709 DOI: 10.1016/j.cbd.2024.101224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Transcriptome sequencing has offered immense opportunities to study non-model organisms. Abalone is an important marine mollusk that encounters harsh environmental conditions in its natural habitat and under aquaculture conditions; hence, research that increases molecular information to understand abalone physiology and stress response is noteworthy. Accordingly, the study used transcriptome sequencing of the gill tissues of abalone exposed to low salinity stress. The aim is to explore some enriched pathways during salinity stress and the crosstalk and functions of the genes involved in the candidate biological processes for future further analysis of their expression patterns. The data suggest that abalone genes such as YAP/TAZ, Myc, Nkd, and Axin (involved in the Hippo signaling pathway) and PI3K/Akt, SHC, and RTK (involved in the Ras signaling pathways) might mediate growth and development. Thus, deregulation of the Hippo and Ras pathways by salinity stress could be a possible mechanism by which unfavorable salinities influence growth in abalone. Furthermore, PEPCK, GYS, and PLC genes (mediating the Glucagon signaling pathway) might be necessary for glucose homeostasis, reproduction, and abalone meat sensory qualities; hence, a need to investigate how they might be influenced by environmental stress. Genes such as MYD88, IRAK1/4, JNK, AP-1, and TRAF6 (mediating the MAPK signaling pathway) could be useful in understanding abalone's innate immune response to environmental stresses. Finally, the aminoacyl-tRNA biosynthesis pathway hints at the mechanism by which new raw materials for protein biosynthesis are mobilized for physiological processes and how abalone might respond to this process during salinity stress. Low salinity clearly regulated genes in these pathways in a time-dependent manner, as hinted by the heat maps. In the future, qRT-PCR verification and in-depth study of the various genes and proteins discussed would provide enormous molecular information resources for the abalone biology.
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Affiliation(s)
- Grace Afumwaa Boamah
- Department of Water Resources and Aquaculture Management, University of Environment and Sustainable Development, PMB, Somanya, Ghana.
| | - Zekun Huang
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, PR China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, PR China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, PR China
| | - Christian Larbi Ayisi
- Department of Water Resources and Aquaculture Management, University of Environment and Sustainable Development, PMB, Somanya, Ghana
| | - Eric Amenyogbe
- Department of Water Resources and Aquaculture Management, University of Environment and Sustainable Development, PMB, Somanya, Ghana
| | - Eric Droepenu
- Department of Water Resources and Aquaculture Management, University of Environment and Sustainable Development, PMB, Somanya, Ghana
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3
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Sherwood M, Zhou Y, Sui Y, Wang Y, Skipp P, Kaid C, Gray J, Okamoto K, Ewing RM. Integrated re-analysis of transcriptomic and proteomic datasets reveals potential mechanisms for Zika viral-based oncolytic therapy in neuroblastoma. F1000Res 2024; 12:719. [PMID: 38903860 PMCID: PMC11187533 DOI: 10.12688/f1000research.132627.3] [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: 05/17/2024] [Indexed: 06/22/2024] Open
Abstract
Background Paediatric neuroblastoma and brain tumours account for a third of all childhood cancer-related mortality. High-risk neuroblastoma is highly aggressive and survival is poor despite intensive multi-modal therapies with significant toxicity. Novel therapies are desperately needed. The Zika virus (ZIKV) can access the nervous system and there is growing interest in employing ZIKV as a potential therapy against paediatric nervous system tumours, including neuroblastoma. Methods Here, we perform extensive data mining, integration and re-analysis of ZIKV infection datasets to highlight molecular mechanisms that may govern the oncolytic response in neuroblastoma cells. We collate infection data of multiple neuroblastoma cell lines by different ZIKV strains from a body of published literature to inform the susceptibility of neuroblastoma to the ZIKV oncolytic response. Integrating published transcriptomics, interaction proteomics, dependency factor and compound datasets we propose the involvement of multiple host systems during ZIKV infection. Results Through data mining of published literature, we observed most paediatric neuroblastoma cell lines to be highly susceptible to ZIKV infection and propose the PRVABC59 ZIKV strain to be the most promising candidate for neuroblastoma oncolytic virotherapy. ZIKV induces TNF signalling, lipid metabolism, the Unfolded Protein Response (UPR), and downregulates cell cycle and DNA replication processes. ZIKV infection is dependent on sterol regulatory element binding protein (SREBP)-regulated lipid metabolism and three protein complexes; V-ATPase, ER Membrane Protein Complex (EMC) and mammalian translocon. We propose ZIKV non-structural protein 4B (NS4B) as a likely mediator of ZIKVs interaction with IRE1-mediated UPR, lipid metabolism and mammalian translocon. Conclusions Our work provides a significant understanding of ZIKV infection in neuroblastoma cells, which will facilitate the progression of ZIKV-based oncolytic virotherapy through pre-clinical research and clinical trials.
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Affiliation(s)
- Matt Sherwood
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Yilu Zhou
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Yi Sui
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Yihua Wang
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Paul Skipp
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Carolini Kaid
- Human Genome and Stem-Cell Center (HUG-CELL), Biosciences Institute, Universidade de Sao Paulo, São Paulo, State of São Paulo, Brazil
| | - Juliet Gray
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, England, UK
| | - Keith Okamoto
- Human Genome and Stem-Cell Center (HUG-CELL), Biosciences Institute, Universidade de Sao Paulo, São Paulo, State of São Paulo, Brazil
| | - Rob M. Ewing
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
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Iida K, Okada M. Identifying Key Regulatory Genes in Drug Resistance Acquisition: Modeling Pseudotime Trajectories of Breast Cancer Single-Cell Transcriptome. Cancers (Basel) 2024; 16:1884. [PMID: 38791962 PMCID: PMC11119661 DOI: 10.3390/cancers16101884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/11/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) technology has provided significant insights into cancer drug resistance at the single-cell level. However, understanding dynamic cell transitions at the molecular systems level remains limited, requiring a systems biology approach. We present an approach that combines mathematical modeling with a pseudotime analysis using time-series scRNA-seq data obtained from the breast cancer cell line MCF-7 treated with tamoxifen. Our single-cell analysis identified five distinct subpopulations, including tamoxifen-sensitive and -resistant groups. Using a single-gene mathematical model, we discovered approximately 560-680 genes out of 6000 exhibiting multistable expression states in each subpopulation, including key estrogen-receptor-positive breast cancer cell survival genes, such as RPS6KB1. A bifurcation analysis elucidated their regulatory mechanisms, and we mapped these genes into a molecular network associated with cell survival and metastasis-related pathways. Our modeling approach comprehensively identifies key regulatory genes for drug resistance acquisition, enhancing our understanding of potential drug targets in breast cancer.
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Affiliation(s)
- Keita Iida
- Institute for Protein Research, Osaka University, Suita 565-0871, Osaka, Japan;
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Váchová L, Plocek V, Maršíková J, Rešetárová S, Hatáková L, Palková Z. Differential stability of Gcn4p controls its cell-specific activity in differentiated yeast colonies. mBio 2024; 15:e0068924. [PMID: 38624209 PMCID: PMC11077963 DOI: 10.1128/mbio.00689-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
Gcn4p belongs to conserved AP-1 transcription factors involved in many cellular processes, including cell proliferation, stress response, and nutrient availability in yeast and mammals. AP-1 activities are regulated at different levels, such as translational activation or protein degradation, which increases the variability of regulation under different conditions. Gcn4p activity in unstructured yeast liquid cultures increases upon amino acid deficiency and is rapidly eliminated upon amino acid excess. Gcn2p kinase is the major described regulator of Gcn4p that enables GCN4 mRNA translation via the uORFs mechanism. Here, we show that Gcn4p is specifically active in U cells in the upper regions and inactive in L cells in the lower regions of differentiated colonies. Using in situ microscopy in combination with analysis of mutants and strains with GFP at different positions in the translational regulatory region of Gcn4p, we show that cell-specific Gcn4p activity is independent of Gcn2p or other translational or transcriptional regulation. Genetically, biochemically, and microscopically, we identified cell-specific proteasomal degradation as a key mechanism that diversifies Gcn4p function between U and L cells. The identified regulation leading to active Gcn4p in U cells with amino acids and efficient degradation in starved L cells differs from known regulations of Gcn4p in yeast but shows similarities to the activity of AP-1 ATF4 in mammals during insulin signaling. These findings may open new avenues for understanding the parallel activities of Gcn4p/ATF4 and reveal a novel biological role for cell type-specific regulation of proteasome-dependent degradation.IMPORTANCEIn nature, microbes usually live in spatially structured communities and differentiate into precisely localized, functionally specialized cells. The coordinated interplay of cells and their response to environmental changes, such as starvation, followed by metabolic adaptation, is critical for the survival of the entire community. Transcription factor Gcn4p is responsible for yeast adaptation under amino acid starvation in liquid cultures, and its activity is regulated mainly at the level of translation involving Gcn2p kinase. Whether Gcn4p functions in structured communities was unknown. We show that translational regulation of Gcn4p plays no role in the development of colony subpopulations; the main regulation occurs at the level of stabilization of the Gcn4p molecule in the cells of one subpopulation and its proteasomal degradation in the other. This regulation ensures specific spatiotemporal activity of Gcn4p in the colony. Our work highlights differences in regulatory networks in unorganized populations and organized structures of yeast, which in many respects resemble multicellular organisms.
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Affiliation(s)
- Libuše Váchová
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, Prague, Czech Republic
| | - Vítězslav Plocek
- Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
| | - Jana Maršíková
- Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
| | - Stanislava Rešetárová
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, Prague, Czech Republic
| | | | - Zdena Palková
- Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
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Stachon T, Latta L, Fries FN, Seitz B, Szentmáry N. Secondary Data Analysis of Inflammation-Related mRNAs in Conjunctival Impression Cytology Samples of Aniridia Patients. Cornea 2024; 43:627-634. [PMID: 38147570 DOI: 10.1097/ico.0000000000003454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/14/2023] [Indexed: 12/28/2023]
Abstract
PURPOSE Aniridia is a rare corneal disease that is often associated with aniridia-associated keratopathy (AAK). In AAK, the conjunctival tissue crosses the limbal border, forming a corneal pannus that extends into the corneal center. With increasing AAK severity, corneal pannus formation, vascularization, and ocular surface inflammation increase. The purpose of this study was to investigate inflammation-related mRNA expression in conjunctival epithelial cells in AAK and its relationship with AAK severity. METHODS Using impression cytology, bulbar conjunctival cells were sampled from 20 subjects with congenital aniridia and 20 age-matched and sex-matched healthy control subjects. RNA was extracted, and mRNA analyses were performed using microarray, which was evaluated for inflammatory markers. RESULTS In the analyzed aniridia subjects, 70 deregulated mRNAs encoding proinflammatory or antiinflammatory cytokines or factors associated with chronic inflammation, including increased IL-1, IL-8, and MIP3A/CCL20 mRNA. The most downregulated mRNA was TIMP3, and the most upregulated mRNA was Protein c-Fos.Of the 70 mRNAs, 14 inflammation-related genes were altered only in the mild AAK forms, whereas only 2 mRNAs were altered only in the severe AAK forms (TLR4 and PPARG). CONCLUSIONS The expression of numerous proinflammatory and antiinflammatory cytokines is deregulated at the ocular surface of aniridia subjects with mild AAK. Thus, early antiinflammatory treatment may prevent or slow down corneal scarring and pannus formation in aniridia subjects.
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Affiliation(s)
- Tanja Stachon
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Homburg, Saarland, Germany; and
| | - Lorenz Latta
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Homburg, Saarland, Germany; and
| | - Fabian N Fries
- Department of Ophthalmology, Saarland University Medical Center, Homburg, Saarland, Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center, Homburg, Saarland, Germany
| | - Nóra Szentmáry
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Homburg, Saarland, Germany; and
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Li Z, Li X, Feng B, Zhao J, Liu K, Xie F, Xie J. The application of a self-designed microfluidic lung chip in the assessment of different inhalable aerosols. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:2111-2119. [PMID: 38516815 DOI: 10.1039/d4ay00017j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Microfluidic-based assessment platforms have recently attracted considerable attention and have been widely used for evaluating in vitro toxic effects. In the present study, we developed an original real-time aerosol exposure system, which focused on a self-designed microfluidic chip, in order to evaluate the toxicological effects following exposure to inhalable aerosols. The three-layer structured microfluidic chip enables real-time aerosol exposure at the gas-liquid interface. The comprehensive detection of toxic effect biomarkers based on this assessment platform encompasses transcriptomics, in situ fluorescence detection, and the identification of extracellular secretagogues. Correspondingly, the effects of selected inhalable aerosols such as cigarette smoke (CS), heated tobacco product smoke (HS), and electronic cigarette smoke (ES) on gene expression profiles, cell viability, intracellular biomarkers (reactive oxygen species and nitric oxide), apoptosis (caspase-3/7 activity), and extracellular biomarkers (IL-8, IL-1β, TNF-α, and malondialdehyde) in the BEAS-2B cells present on the chip were investigated. Following exposure to aerosols derived from CS, HS, and ES, the transcriptome analysis revealed differential expression in these cells. In addition, the overlapping DEGs from the different treatment groups were found to be primarily associated with stimuli and inflammatory responses. Correspondingly, each of the three categories of selected inhalable aerosols was confirmed to induce significant changes in biomarkers that were associated with toxic effects. These results suggest that the original real-time aerosol exposure system centered around a self-designed chip can be applied to the toxic effect evaluation of inhalable aerosol exposure.
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Affiliation(s)
- Zezhi Li
- Beijing Technology and Business University, Beijing 100048, PR China
- Key Laboratory of Tobacco Chemistry, Zhengzhou Tobacco Research Institute of CNTC, No. 2 Fengyang Street, Zhengzhou 450001, PR China.
| | - Xiang Li
- Key Laboratory of Tobacco Chemistry, Zhengzhou Tobacco Research Institute of CNTC, No. 2 Fengyang Street, Zhengzhou 450001, PR China.
- Beijing Life Science Academy, Beijing 102209, PR China
| | - Boyang Feng
- Key Laboratory of Tobacco Chemistry, Zhengzhou Tobacco Research Institute of CNTC, No. 2 Fengyang Street, Zhengzhou 450001, PR China.
| | - Junwei Zhao
- Key Laboratory of Tobacco Chemistry, Zhengzhou Tobacco Research Institute of CNTC, No. 2 Fengyang Street, Zhengzhou 450001, PR China.
- Beijing Life Science Academy, Beijing 102209, PR China
| | - Kejian Liu
- Key Laboratory of Tobacco Chemistry, Zhengzhou Tobacco Research Institute of CNTC, No. 2 Fengyang Street, Zhengzhou 450001, PR China.
| | - Fuwei Xie
- Key Laboratory of Tobacco Chemistry, Zhengzhou Tobacco Research Institute of CNTC, No. 2 Fengyang Street, Zhengzhou 450001, PR China.
| | - Jianping Xie
- Key Laboratory of Tobacco Chemistry, Zhengzhou Tobacco Research Institute of CNTC, No. 2 Fengyang Street, Zhengzhou 450001, PR China.
- Beijing Life Science Academy, Beijing 102209, PR China
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Sawant N, Watanabe A, Ueda H, Okano H, Morita M. Incomplete accumulation of perilesional reactive astrocytes exacerbates wound healing after closed-head injury by increasing inflammation and BBB disruption. Exp Neurol 2024; 374:114700. [PMID: 38272160 DOI: 10.1016/j.expneurol.2024.114700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 01/27/2024]
Abstract
Wound healing after closed-head injury is a significant medical issue. However, conventional models of focal traumatic brain injury, such as fluid percussion injury and controlled cortical impact, employ mechanical impacts on the exposed cerebral cortex after craniotomy. These animal models are inappropriate for studying gliosis, as craniotomy itself induces gliosis. To address this, we developed a closed-head injury model and named "photo injury", which employs intense light illumination through a thinned-skull cranial window. Our prior work demonstrated that the gliosis of focal cerebral lesion after the photo injury does not encompass artificial gliosis and comprises two distinct reactive astrocyte subpopulations. The reactive astrocytes accumulated in the perilesional recovery area actively proliferate and express Nestin, a neural stem cell marker, while those in distal regions do not exhibit these traits. The present study investigated the role of perilesional reactive astrocytes (PRAs) in wound healing using the ablation of reactive astrocytes by the conditional knockout of Stat3. The extensive and non-selective ablation of reactive astrocytes in Nestin-Cre:Stat3f/f mice resulted in an exacerbation of injury, marked by increased inflammation and BBB disruption. On the other hand, GFAP-CreERT2:Stat3f/f mice exhibited the partial and selective ablation of the PRAs, while their exacerbation of injury was at the same extent as in Nestin-Cre:Stat3f/f mice. The comparison of these two mouse strains indicates that the PRAs are an essential astrocyte component for wound healing after closed-head injury, and their anti-inflammatory and regenerative functions are significantly affected even by incomplete accumulation. In addition, the reporter gene expression in the PRAs by GFAP-CreERT2 indicated a substantial elimination of these cells and an absence of differentiation into other cell types, despite Nestin expression, after wound healing. Thus, the accumulation and subsequent elimination of PRA are proposed as promising diagnostic and therapeutic avenues to bolster wound healing after closed-head injury.
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Affiliation(s)
- Nitin Sawant
- Biomolecular Organization, Department of Biology, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Airi Watanabe
- Biomolecular Organization, Department of Biology, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Haruna Ueda
- Biomolecular Organization, Department of Biology, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Mitsuhiro Morita
- Biomolecular Organization, Department of Biology, Kobe University, Kobe, Hyogo 657-8501, Japan; Application Division, Center of Optical Scattering Image Science, Kobe University, Kobe, Hyogo 657-8501, Japan.
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Ge D, Luo T, Sun Y, Liu M, Lyu Y, Yin W, Li R, Zhang Y, Yue H, Liu N. Natural diterpenoid EKO activates deubiqutinase ATXN3 to preserve vascular endothelial integrity and alleviate diabetic retinopathy through c-fos/focal adhesion axis. Int J Biol Macromol 2024; 260:129341. [PMID: 38218272 DOI: 10.1016/j.ijbiomac.2024.129341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/26/2023] [Accepted: 01/07/2024] [Indexed: 01/15/2024]
Abstract
Diabetic retinopathy (DR) is one of the most prevalent severe diabetic microvascular complications caused by hyperglycemia. Deciphering the underlying mechanism of vascular injury and finding ways to alleviate hyperglycemia induced microvascular complications is of great necessity. In this study, we identified that a compound ent-9α-hydroxy-15-oxo-16-kauren-19-oic acid (EKO), the diterpenoid isolated and purified from Pteris semipinnata L., exhibited good protective roles against vascular endothelial injury associated with diabetic retinopathy in vitro and in vivo. To further uncover the underlying mechanism, we used unbiased transcriptome sequencing analysis and showed substantial impairment in the focal adhesion pathway upon high glucose and IL-1β stimulation. EKO could effectively improve endothelial focal adhesion pathway by enhancing the expression of two focal adhesion proteins Vinculin and ITGA11. We found that c-fos protein was involved in regulating the expression of Vinculin and ITGA11, a transcription factor component that was downregulated by high glucose and IL-1β stimulation and recovered by EKO. Mechanically, EKO facilitated the binding of deubiquitylation enzyme ATXN3 to c-fos protein and promoted its deubiquitylation, thereby elevating its protein level to enhance the expression of Vinculin and ITGA11. Besides, EKO effectively suppressed ROS production and restored mitochondrial function. In vivo studies, we confirmed EKO could alleviate some of the indicators of diabetic mice. In addition, protein levels of ATXN3 and focal adhesion Vinculin molecule were also verified in vivo. Collectively, our findings addressed the endothelial protective role of natural diterpenoid EKO, with emphasize of mechanism on ATXN3/c-fos/focal adhesion signaling pathway as well as oxygen stress suppression, implicating its therapeutic potential in alleviating vascular endothelium injury and diabetic retinopathy.
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Affiliation(s)
- Di Ge
- School of Biological Science and Technology, University of Jinan, Jinan 250024, China
| | - Tingting Luo
- School of Biological Science and Technology, University of Jinan, Jinan 250024, China
| | - Yajie Sun
- School of Biological Science and Technology, University of Jinan, Jinan 250024, China
| | - Mengjia Liu
- School of Biological Science and Technology, University of Jinan, Jinan 250024, China
| | - Yuzhu Lyu
- School of Biological Science and Technology, University of Jinan, Jinan 250024, China
| | - Wenying Yin
- School of Biological Science and Technology, University of Jinan, Jinan 250024, China
| | - Rongxian Li
- School of Biological Science and Technology, University of Jinan, Jinan 250024, China
| | - Yongqi Zhang
- School of Biological Science and Technology, University of Jinan, Jinan 250024, China
| | - Hongwei Yue
- Department of Emergency Medicine, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital, Shandong University, Jinan, China.
| | - Na Liu
- School of Biological Science and Technology, University of Jinan, Jinan 250024, China.
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Rampioni Vinciguerra GL, Capece M, Scafetta G, Rentsch S, Vecchione A, Lovat F, Croce CM. Role of Fra-2 in cancer. Cell Death Differ 2024; 31:136-149. [PMID: 38104183 PMCID: PMC10850073 DOI: 10.1038/s41418-023-01248-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023] Open
Abstract
Fos-related antigen-2 (Fra-2) is the most recently discovered member of the Fos family and, by dimerizing with Jun proteins, forms the activator protein 1 (AP-1) transcription factor. By inducing or repressing the transcription of several target genes, Fra-2 is critically involved in the modulation of cell response to a variety of extracellular stimuli, stressors and intracellular changes. In physiological conditions, Fra-2 has been found to be ubiquitously expressed in human cells, regulating differentiation and homeostasis of bone, muscle, nervous, lymphoid and other tissues. While other AP-1 members, like Jun and Fos, are well characterized, studies of Fra-2 functions in cancer are still at an early stage. Due to the lack of a trans-activating domain, which is present in other Fos proteins, it has been suggested that Fra-2 might inhibit cell transformation, eventually exerting an anti-tumor effect. In human malignancies, however, Fra-2 activity is enhanced (or induced) by dysregulation of microRNAs, oncogenes and extracellular signaling, suggesting a multifaceted role. Therefore, Fra-2 can promote or prevent transformation, proliferation, migration, epithelial-mesenchymal transition, drug resistance and metastasis formation in a tumor- and context-dependent manner. Intriguingly, recent data reports that Fra-2 is also expressed in cancer associated cells, contributing to the intricate crosstalk between neoplastic and non-neoplastic cells, that leads to the evolution and remodeling of the tumor microenvironment. In this review we summarize three decades of research on Fra-2, focusing on its oncogenic and anti-oncogenic effects in tumor progression and dissemination.
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Affiliation(s)
- Gian Luca Rampioni Vinciguerra
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Psychology, Sant'Andrea Hospital, University of Rome "Sapienza", Rome, 00189, Italy
| | - Marina Capece
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Giorgia Scafetta
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Psychology, Sant'Andrea Hospital, University of Rome "Sapienza", Rome, 00189, Italy
| | - Sydney Rentsch
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Andrea Vecchione
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Psychology, Sant'Andrea Hospital, University of Rome "Sapienza", Rome, 00189, Italy
| | - Francesca Lovat
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Carlo M Croce
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
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Majerciak V, Alvarado-Hernandez B, Ma Y, Duduskar S, Lobanov A, Cam M, Zheng ZM. KSHV promotes oncogenic FOS to inhibit nuclease AEN and transactivate RGS2 for AKT phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.27.577582. [PMID: 38410462 PMCID: PMC10896338 DOI: 10.1101/2024.01.27.577582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 is a lytic RNA-binding protein. We applied BCBL-1 cells in lytic KSHV infection and performed UV cross-linking immunoprecipitation (CLIP) followed by RNA-seq of the CLIPed RNA fragments (CLIP-seq). We identified ORF57-bound transcripts from 544 host protein-coding genes. By comparing with the RNA-seq profiles from BCBL-1 cells with latent and lytic KSHV infection and from HEK293T cells with and without ORF57 expression, we identified FOS and CITED2 RNAs being two common ORF57-specific RNA targets. FOS dimerizes with JUN as a transcription factor AP-1 involved in cell proliferation, differentiation, and transformation. Knockout of the ORF57 gene from the KSHV genome led BAC16-iSLK cells incapable of FOS expression in KSHV lytic infection. The dysfunctional KSHV genome in FOS expression could be rescued by Lenti-ORF57 virus infection. ORF57 protein does not regulate FOS translation but binds to the 13-nt RNA motif near the FOS RNA 5' end and prolongs FOS mRNA half-life 7.7 times longer than it is in the absence of ORF57. This binding of ORF57 to FOS RNA is competitive to the binding of a host nuclease AEN (also referred to as ISG20L1). KSHV infection inhibits the expression of AEN, but not exosomal RNA helicase MTR4. FOS expression mediated by ORF57 inhibits AEN transcription, but transactivates RGS2, a regulator of G-protein coupled receptors. FOS binds a conserved AP-1 site in the RGS2 promoter and enhances RGS2 expression to phosphorylate AKT. Altogether, we have discovered that KSHV ORF57 specifically binds and stabilizes FOS RNA to increase FOS expression, thereby disturbing host gene expression and inducing pathogenesis during KSHV lytic infection.
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Affiliation(s)
- Vladimir Majerciak
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, MD, 21702, USA
| | - Beatriz Alvarado-Hernandez
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, MD, 21702, USA
| | - Yanping Ma
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, MD, 21702, USA
| | - Shivalee Duduskar
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, MD, 21702, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, NCI/NIH, Bethesda, MD, 20892, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, NCI/NIH, Bethesda, MD, 20892, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI/NIH, Frederick, MD, 21702, USA
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12
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Natali EN, Horst A, Meier P, Greiff V, Nuvolone M, Babrak LM, Fink K, Miho E. The dengue-specific immune response and antibody identification with machine learning. NPJ Vaccines 2024; 9:16. [PMID: 38245547 PMCID: PMC10799860 DOI: 10.1038/s41541-023-00788-7] [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: 12/01/2022] [Accepted: 12/07/2023] [Indexed: 01/22/2024] Open
Abstract
Dengue virus poses a serious threat to global health and there is no specific therapeutic for it. Broadly neutralizing antibodies recognizing all serotypes may be an effective treatment. High-throughput adaptive immune receptor repertoire sequencing (AIRR-seq) and bioinformatic analysis enable in-depth understanding of the B-cell immune response. Here, we investigate the dengue antibody response with these technologies and apply machine learning to identify rare and underrepresented broadly neutralizing antibody sequences. Dengue immunization elicited the following signatures on the antibody repertoire: (i) an increase of CDR3 and germline gene diversity; (ii) a change in the antibody repertoire architecture by eliciting power-law network distributions and CDR3 enrichment in polar amino acids; (iii) an increase in the expression of JNK/Fos transcription factors and ribosomal proteins. Furthermore, we demonstrate the applicability of computational methods and machine learning to AIRR-seq datasets for neutralizing antibody candidate sequence identification. Antibody expression and functional assays have validated the obtained results.
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Affiliation(s)
- Eriberto Noel Natali
- FHNW University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Muttenz, Switzerland
| | - Alexander Horst
- FHNW University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Muttenz, Switzerland
| | - Patrick Meier
- FHNW University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Muttenz, Switzerland
| | - Victor Greiff
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Lmar Marie Babrak
- FHNW University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Muttenz, Switzerland
| | | | - Enkelejda Miho
- FHNW University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Muttenz, Switzerland.
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- aiNET GmbH, Basel, Switzerland.
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13
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Shimizu M, Yokote T, Hatooka J, Kinoshita Y, Imagawa A, Yasuda E. Reduced CC Chemokine Receptor 4 Expression in Tumor Cells after Lenalidomide Treatment for Adult T-Cell Leukemia/Lymphoma: A Case Report. Case Rep Oncol 2024; 17:602-607. [PMID: 39015631 PMCID: PMC11250255 DOI: 10.1159/000539122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 04/23/2024] [Indexed: 07/18/2024] Open
Abstract
Introduction CC chemokine receptor 4 (CCR4), which is involved in leukocyte migration, is expressed in most tumor cells in patients with adult T-cell leukemia/lymphoma (ATLL). Case Presentation Here we report the case of a 78-year-old man diagnosed with lymphoma-type ATLL expressing CCR4. The patient was administered two cycles of lenalidomide but died because of sepsis 5 months after the initial diagnosis. Autopsy revealed ATLL cells at several sites. Immunohistochemical analysis revealed that these ATLL cells had reduced CCR4 expression. Conclusion The present case suggests that treatment should be carefully determined in ATLL with reference to a history of lenalidomide use and CCR4 expression.
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Affiliation(s)
- Masatomo Shimizu
- Department of Internal Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Taiji Yokote
- Department of Internal Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Jun Hatooka
- Department of Internal Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Yuuki Kinoshita
- Department of Internal Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Akihisa Imagawa
- Department of Internal Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Emi Yasuda
- Department of Pathology, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
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14
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Ghosh I, Dey Ghosh R, Mukhopadhyay S. Identification of genes associated with gall bladder cell carcinogenesis: Implications in targeted therapy of gall bladder cancer. World J Gastrointest Oncol 2023; 15:2053-2063. [PMID: 38173427 PMCID: PMC10758643 DOI: 10.4251/wjgo.v15.i12.2053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/11/2023] [Accepted: 11/10/2023] [Indexed: 12/14/2023] Open
Abstract
Gall bladder cancer (GBC) is becoming a very devastating form of hepatobiliary cancer in India. Every year new cases of GBC are quite high in India. Despite recent advanced multimodality treatment options, the survival of GBC patients is very low. If the disease is diagnosed at the advanced stage (with local nodal metastasis or distant metastasis) or surgical resection is inoperable, the prognosis of those patients is very poor. So, perspectives of targeted therapy are being taken. Targeted therapy includes hormone therapy, proteasome inhibitors, signal transduction and apoptosis inhibitors, angiogenesis inhibitors, and immunotherapeutic agents. One such signal transduction inhibitor is the specific short interfering RNA (siRNA) or short hairpin RNA (shRNA). For developing siRNA-mediated therapy shRNA, although several preclinical studies to evaluate the efficacy of these key molecules have been performed using gall bladder cells, many more clinical trials are required. To date, many such genes have been identified. This review will discuss the recently identified genes associated with GBC and those that have implications in its treatment by siRNA or shRNA.
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Affiliation(s)
- Ishita Ghosh
- Department of Molecular Biology, Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata 700094, India
| | - Ruma Dey Ghosh
- Department of Molecular Biology, Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata 700094, India
| | - Soma Mukhopadhyay
- Department of Molecular Biology, Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata 700094, India
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15
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Farahmandi F, Parhizgar P, Mozafari Komesh Tape P, Bizhannia F, Rohani FS, Bizhanzadeh M, Mostafavi Alhosseini ZS, Hosseinzade M, Farsi Y, Nasiri MJ. Implications and Mechanisms of Antiviral Effects of Lactic Acid Bacteria: A Systematic Review. Int J Microbiol 2023; 2023:9298363. [PMID: 38144900 PMCID: PMC10748726 DOI: 10.1155/2023/9298363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 10/09/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023] Open
Abstract
Background Lactic acid bacteria (LAB) are among the most important strains of probiotics. Some are normal flora of human mucous membranes in the gastrointestinal system, skin, urinary tract, and genitalia. There is evidence suggesting that LAB has an antiviral effect on viral infections. However, these studies are still controversial; a systematic review was conducted to evaluate the antiviral effects of LAB on viral infections. Methods The systematic search was conducted until the end of December 17, 2022, using international databases such as Scopus, Web of Science, and Medline (via PubMed). The keywords of our search were lactic acid bacteria, Lactobacillales, Lactobacillus (as well as its species), probiotics, antiviral, inhibitory effect, and virus. Results Of 15.408 potentially relevant articles obtained, 45 eligible in-vivo human studies were selected for inclusion in the study from databases, registers, and citation searching. We conducted a systematic review of the antiviral effects of the LAB based on the included articles. The most commonly investigated lactobacillus specie were Lactobacillus rhamnosus GG and Lactobacillus casei. Conclusion Our study indicates that 40 of the selected 45 of the included articles support the positive effect of LAB on viral infections, although some studies showed no significant positive effect of LABs on some viral infections.
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Affiliation(s)
- Fargol Farahmandi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parynaz Parhizgar
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parya Mozafari Komesh Tape
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fahimeh Bizhannia
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fateme Sadat Rohani
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marzieh Bizhanzadeh
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Maede Hosseinzade
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yeganeh Farsi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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16
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Liu J, Chen PJ, Mehta S, Dutra EH, Yadav S. Dynamic changes in transcriptome during orthodontic tooth movement. Orthod Craniofac Res 2023; 26 Suppl 1:73-81. [PMID: 36891648 DOI: 10.1111/ocr.12650] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 03/10/2023]
Abstract
OBJECTIVES The objective of this study was to determine global changes in gene expression with next generation sequencing (NGS) in order to assess the biological effects of orthodontic tooth movement (OTM) on alveolar bone in a rat model. MATERIALS AND METHODS Thirty-five Wistar rats (age 14 weeks) were used in the study. The OTM was performed using closed coil Nickel-Titanium spring to apply a mesial force on maxillary first molars of 8-10 g. Three hours, 1, 3, 7 and 14 days after the placement of the appliance, rats were killed at each time point respectively. The alveolar bone, around left maxillary first molar, were excised on compression side. The samples were immediately frozen in liquid nitrogen for subsequent RNA extraction. Total RNA samples were prepared for mRNA sequencing using the Illumina kit. RNA-Seq reads were aligned to the rat genomes using the STAR Aligner and bioinformatic analysis was performed. RESULTS A total of 18 192 genes were determined. Day 1 has the highest number of differentially expressed genes (DEGs) observed with more upregulated than downregulated genes. A total of 2719 DEGs were identified to use as input for the algorithm. Six distinct clusters of temporal patterns were observed representing proteins that were differentially regulated indicating different expression kinetics. Principal component analysis (PCA) showed distinct clustering by time points and days 3, 7 and 14 share similar gene expression pattern. CONCLUSIONS Distinct gene expression pattern was observed at different time points studied. Hypoxia, inflammation and bone remodelling pathways are major mechanisms behind OTM.
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Affiliation(s)
- Jia Liu
- Private Practice, Boston, Massachusetts, USA
| | - Po-Jung Chen
- Section of Orthodontics, Department of Growth and Development, University of Nebraska Medical Center, Lincoln, Nebraska, USA
| | - Shivam Mehta
- Department of Developmental Sciences/Orthodontics, Marquette University School of Dentistry, Milwaukee, Wisconsin, USA
| | - Eliane H Dutra
- Division of Orthodontics, University of Connecticut Health, Farmington, Connecticut, USA
| | - Sumit Yadav
- Department of Growth and Development, University of Nebraska Medical Center, Lincoln, Nebraska, USA
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17
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von Stromberg K, Seddar L, Ip WH, Günther T, Gornott B, Weinert SC, Hüppner M, Bertzbach LD, Dobner T. The human adenovirus E1B-55K oncoprotein coordinates cell transformation through regulation of DNA-bound host transcription factors. Proc Natl Acad Sci U S A 2023; 120:e2310770120. [PMID: 37883435 PMCID: PMC10622919 DOI: 10.1073/pnas.2310770120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/13/2023] [Indexed: 10/28/2023] Open
Abstract
The multifunctional adenovirus E1B-55K oncoprotein can induce cell transformation in conjunction with adenovirus E1A gene products. Previous data from transient expression studies and in vitro experiments suggest that these growth-promoting activities correlate with E1B-55K-mediated transcriptional repression of p53-targeted genes. Here, we analyzed genome-wide occupancies and transcriptional consequences of species C5 and A12 E1B-55Ks in transformed mammalian cells by combinatory ChIP and RNA-seq analyses. E1B-55K-mediated repression correlates with tethering of the viral oncoprotein to p53-dependent promoters via DNA-bound p53. Moreover, we found that E1B-55K also interacts with and represses transcription of numerous p53-independent genes through interactions with transcription factors that play central roles in cancer and stress signaling. Our results demonstrate that E1B-55K oncoproteins function as promiscuous transcriptional repressors of both p53-dependent and -independent genes and further support the model that manipulation of cellular transcription is central to adenovirus-induced cell transformation and oncogenesis.
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Affiliation(s)
| | - Laura Seddar
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Wing-Hang Ip
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Thomas Günther
- Virus Genomics, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Britta Gornott
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Sophie-Celine Weinert
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Max Hüppner
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Luca D. Bertzbach
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Thomas Dobner
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
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18
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Adir O, Sagi-Assif O, Meshel T, Ben-Menachem S, Pasmanik-Chor M, Hoon DSB, Witz IP, Izraely S. Heterogeneity in the Metastatic Microenvironment: JunB-Expressing Microglia Cells as Potential Drivers of Melanoma Brain Metastasis Progression. Cancers (Basel) 2023; 15:4979. [PMID: 37894348 PMCID: PMC10605008 DOI: 10.3390/cancers15204979] [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: 08/08/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Reciprocal signaling between melanoma brain metastatic (MBM) cells and microglia reprograms the phenotype of both interaction partners, including upregulation of the transcription factor JunB in microglia. Here, we aimed to elucidate the impact of microglial JunB upregulation on MBM progression. For molecular profiling, we employed RNA-seq and reverse-phase protein array (RPPA). To test microglial JunB functions, we generated microglia variants stably overexpressing JunB (JunBhi) or with downregulated levels of JunB (JunBlo). Melanoma-derived factors, namely leukemia inhibitory factor (LIF), controlled JunB upregulation through Janus kinase (JAK)/signal transducer and activator of transcription 3 (STAT3) signaling. The expression levels of JunB in melanoma-associated microglia were heterogeneous. Flow cytometry analysis revealed the existence of basal-level JunB-expressing microglia alongside microglia highly expressing JunB. Proteomic profiling revealed a differential protein expression in JunBhi and JunBlo cells, namely the expression of microglia activation markers Iba-1 and CD150, and the immunosuppressive molecules SOCS3 and PD-L1. Functionally, JunBhi microglia displayed decreased migratory capacity and phagocytic activity. JunBlo microglia reduced melanoma proliferation and migration, while JunBhi microglia preserved the ability of melanoma cells to proliferate in three-dimensional co-cultures, that was abrogated by targeting leukemia inhibitory factor receptor (LIFR) in control microglia-melanoma spheroids. Altogether, these data highlight a melanoma-mediated heterogenous effect on microglial JunB expression, dictating the nature of their functional involvement in MBM progression. Targeting microglia highly expressing JunB may potentially be utilized for MBM theranostics.
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Affiliation(s)
- Orit Adir
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel; (O.A.); (O.S.-A.); (T.M.); (S.B.-M.); (I.P.W.)
| | - Orit Sagi-Assif
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel; (O.A.); (O.S.-A.); (T.M.); (S.B.-M.); (I.P.W.)
| | - Tsipi Meshel
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel; (O.A.); (O.S.-A.); (T.M.); (S.B.-M.); (I.P.W.)
| | - Shlomit Ben-Menachem
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel; (O.A.); (O.S.-A.); (T.M.); (S.B.-M.); (I.P.W.)
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, The George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel;
| | - Dave S. B. Hoon
- Department of Translational Molecular Medicine, Saint John’s Cancer Institute, Providence Saint John’s Health Center, Santa Monica, CA 90404, USA;
| | - Isaac P. Witz
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel; (O.A.); (O.S.-A.); (T.M.); (S.B.-M.); (I.P.W.)
| | - Sivan Izraely
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel; (O.A.); (O.S.-A.); (T.M.); (S.B.-M.); (I.P.W.)
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Wang X, Chen W, Yuan P, Xu H. RAGE acted as a new anti-inflammatory target for Icariin's treatment against vascular dementia based on network pharmacology-directed verification. J Biomol Struct Dyn 2023:1-21. [PMID: 37768122 DOI: 10.1080/07391102.2023.2256409] [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: 06/26/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023]
Abstract
Vascular dementia (VaD) ranks as the second most prevalent form of dementia and poses a considerable global health challenge. Icariin has been recognized for its robust neuroprotective effects in combating VaD. Nonetheless, the underlying mechanisms have not been fully elucidated. An integrated approach involving network pharmacology, molecular docking, and molecular dynamics simulations (MDS) was employed to systematically investigate the potential pharmacological actions of Icariin in counteracting VaD. The AGE/RAGE pathway was identified as a promising anti-inflammatory pathway. A chronic cerebral hypoperfusion mouse model was utilized to establish VaD. Both Icariin and FP S-ZM1 (a RAGE inhibitor) were administered through oral gavage and intraperitoneal injection, respectively. The Morris water maze (MWZ) was used to evaluate cognitive functions. Moreover, immunofluorescence, RT-qP CR, and Western blot analyses were carried out to evaluate the effects of FP S-ZM1 on neuroinflammation. Network analysis identified 14 crucial targets and highlighted the AGE-RAGE signaling cascade in diabetic complications as the foremost KEGG pathway with potential anti-neuroinflammatory property. MDS results suggested a stable binding of the RAGE-Icariin complex. Remarkably, Icariin was found to effectively mitigate cognitive deficits in VaD mice, which was correlated with the upregulation of the P I3K/AKT pathway and downregulation of the JNK/cJUN signaling cascade. Critically, co-administration of FP S-ZM1 enhanced Icariin's ameliorative effects on cognitive deficits, owing to bolstered anti-neuroinflammatory action. This study unveils the potential of Icariin in alleviating cognitive dysfunction and neuroinflammation in VaD, which may be attributed to the modulation of the AGE/RAGE pathway.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xiaohu Wang
- Department of Neurology, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Wei Chen
- Department of Neurology, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Ping Yuan
- Department of Neurology, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Hongbei Xu
- Department of Neurology, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
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20
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Huang M, Wu Z, Jia L, Wang Y, Gao S, Liu Y, Zhang Y, Li J. Bioinformatics and network pharmacology identify promotional effects and potential mechanisms of ethanol on esophageal squamous cell carcinoma and experimental validation. Toxicol Appl Pharmacol 2023; 474:116615. [PMID: 37406968 DOI: 10.1016/j.taap.2023.116615] [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: 04/06/2023] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Ethanol is an important risk factor for esophageal squamous cell carcinoma (ESCC); however, the molecular mechanisms behind how ethanol promotes ESCC development remain poorly understood. In this study, ethanol-ESCC-associated target genes were constructed and screened using network pharmacology and subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) and bioinformatics analysis. A mouse ethanol-exposed esophageal cancer model was constructed with 4-nitroquinoline-1-oxide (4-NQO) to assess its survival and tumor lesion status, and the mechanism of ethanol-promoted ESCC lesions was verified by qRT-PCR and Western blotting. The results showed that 126 ethanol-ESCC crossover genes were obtained, which were significantly enriched in the PI3K/AKT signaling pathway. Bioinformatics results showed that the target genes TNF, IL6, IL1β and JUN were highly expressed in esophageal tumor samples and positively correlated with tumor proliferation and apoptosis genes, and the genetic information of these genes was mutated to different degrees. Animal model experiments showed that ethanol decreased the survival rate and aggravated the occurrence of esophageal cancer in mice. qRT-PCR showed that ethanol promoted the expression of TNF, IL6, IL1β and JUN mRNA in mouse esophageal tumor tissues, and Western blotting showed that ethanol promoted p-PI3K and p-AKT protein expression in mouse esophageal tumor tissues. In conclusion, ethanol promotes esophageal carcinogenesis by increasing the expression of TNF, IL6, IL1β and JUN and activating the PI3K/AKT signaling pathway.
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Affiliation(s)
- Ming Huang
- College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, China
| | - Zhongbing Wu
- College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, China
| | - Lei Jia
- College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, China
| | - Yu Wang
- College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, China
| | - Shuang Gao
- College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, China
| | - Ying Liu
- College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, China
| | - Yushuang Zhang
- The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China.
| | - Jing Li
- College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, China; The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China.
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21
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Salem MA, Mohamed OG, Mosalam EM, Elberri AI, Abdel-Bar HM, Hassan M, Al-Karmalawy AA, Tripathi A, Ezzat SM, Abo Mansour HE. Investigation of the phytochemical composition, antioxidant, antibacterial, anti-osteoarthritis, and wound healing activities of selected vegetable waste. Sci Rep 2023; 13:13034. [PMID: 37563154 PMCID: PMC10415269 DOI: 10.1038/s41598-023-38591-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: 02/13/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
Agri-food wastes, produced following industrial food processing, are mostly discarded, leading to environmental hazards and losing the nutritional and medicinal values associated with their bioactive constituents. In this study, we performed a comprehensive analytical and biological evaluation of selected vegetable by-products (potato, onion, and garlic peels). The phytochemical analysis included UHPLC-ESI-qTOF-MS/MS in combination with molecular networking and determination of the total flavonoid and phenolic contents. Further, the antimicrobial, anti-osteoarthritis and wound healing potentials were also evaluated. In total, 47 compounds were identified, belonging to phenolic acids, flavonoids, saponins, and alkaloids as representative chemical classes. Onion peel extract (OPE) showed the higher polyphenolic contents, the promising antioxidant activity, the potential anti-osteoarthritis activity, and promising antimicrobial activity, especially against methicillin-resistant Staphylococcus aureus (MRSA). Furthermore, OPE revealed to have promising in vivo wound healing activity, restoring tissue physiology and integrity, mainly through the activation of AP-1 signaling pathway. Lastly, when OPE was loaded with nanocapsule based hydrogel, the nano-formulation revealed enhanced cellular viability. The affinities of the OPE major metabolites were evaluated against both p65 and ATF-2 targets using two different molecular docking processes revealing quercetin-3,4'-O-diglucoside, alliospiroside C, and alliospiroside D as the most promising entities with superior binding scores. These results demonstrate that vegetable by-products, particularly, those derived from onion peels can be incorporated as natural by-product for future evaluation against wounds and osteoarthritis.
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Affiliation(s)
- Mohamed A Salem
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University, Gamal Abd El Nasr st., Shibīn al-Kawm, 32511, Menoufia, Egypt.
| | - Osama G Mohamed
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Kasr el Aini St., Cairo, 11562, Egypt
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Esraa M Mosalam
- Biochemistry Department, Faculty of Pharmacy, Menoufia University, Gamal Abd El Nasr st., Shebin El-Koum, 32511, Egypt
| | - Aya Ibrahim Elberri
- Genetic Engineering and Molecular Biology Division, Department of Zoology, Faculty of Science, Menoufia University, Shebin El-Kom, 32511, Menoufia, Egypt
| | - Hend Mohamed Abdel-Bar
- Department of Pharmaceutics, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
| | - Mariam Hassan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr el Aini st., Cairo, 11562, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Galala University, New Galala City, Suez, Egypt
| | - Ahmed A Al-Karmalawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, 6th of October City, Giza, 12566, Egypt
| | - Ashootosh Tripathi
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Shahira M Ezzat
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Kasr el Aini St., Cairo, 11562, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, 12451, Egypt
| | - Hend E Abo Mansour
- Biochemistry Department, Faculty of Pharmacy, Menoufia University, Gamal Abd El Nasr st., Shebin El-Koum, 32511, Egypt
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Taha NA, Shafiq AM, Mohammed AH, Zaky AH, Omran OM, Ameen MG. FOS-Like Antigen 1 Expression Was Associated With Survival of Hepatocellular Carcinoma Patients. World J Oncol 2023; 14:285-299. [PMID: 37560339 PMCID: PMC10409557 DOI: 10.14740/wjon1608] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/10/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Early diagnosis and proper management of hepatocellular carcinoma (HCC) improve patient prognosis. Several studies attempted to discover new genes to understand the pathogenesis and identify the prognostic and predictive factors in HCC patients, to improve patient's overall survival (OS) and maintain their physical and social activity. The transcription factor FOS-like antigen 1 (FOSL1) acts as one of the important prognostic factors in different tumors, and its overexpression correlates with tumors' progression and worse patient survival. However, its expression and molecular mechanisms underlying its dysregulation in human HCC remain poorly understood. Our study was conducted to evaluate the expression of FOSL1 in HCC tissues and its relationship with various clinicopathological parameters besides OS. METHODS This study is a retrospective cohort study conducted among 113 patients with a proven diagnosis of HCC, who underwent tumor resection and received treatment at South Egypt Cancer Institute. Immunohistochemistry for FOSL1 expression and survival curves were conducted followed by statistical analysis. RESULTS HCC occurred at older age group and affected males more than females. There was a statistically significant correlation between combined cytoplasmic and nuclear expression of FOSL1 and worse prognosis in HCC patients. There was a statistically significant correlation of FOSL1 expression with histological grade, lymphovascular embolization, and tumor budding where high expression indicated potential deterioration of HCC patients. There was statistically significant correlation between tumor size, tumor grade and FOSL1 expression with the cumulative OS. CONCLUSIONS Combined cytoplasmic and nuclear FOSL1 expression has significant prognostic association with HCC and diagnostic importance, as it can identify cirrhosis and premalignant lesions that can progress to HCC. Furthermore, Kaplan-Meier survival analysis found that overexpressed FOSL1 was correlated with poor OS.
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Affiliation(s)
- Noura Ali Taha
- Department of Medical Oncology and Hematological Malignancies, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Ahmed Mahran Shafiq
- Department of Medical Oncology and Hematological Malignancies, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Abdallah Hedia Mohammed
- Department of Medical Oncology and Hematological Malignancies, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Amen Hamdy Zaky
- Department of Medical Oncology and Hematological Malignancies, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Ola M. Omran
- Department of Pathology, Faculty of Medicine, Assiut University, Assiut, Egypt
- Department of Pathology, College of Medicine, Qassim University, KSA
| | - Mahmoud Gamal Ameen
- Department of Oncologic Pathology, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
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23
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Wang Y, Li J, Wang F, Cui Y, Song L, Ruan B, Yu Y. Analysis of ceRNA Regulatory Mechanism of Rape Pollen Allergy Based on Whole-Transcriptome Sequencing of Peripheral Blood Mononuclear Cells. J Asthma Allergy 2023; 16:775-788. [PMID: 37534326 PMCID: PMC10390718 DOI: 10.2147/jaa.s416772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/12/2023] [Indexed: 08/04/2023] Open
Abstract
Background Rape pollen allergy is a common allergic reaction disorder that affects the health and life of patients seriously. The research on ceRNA regulatory network in rape pollen allergy is poor. Methods High throughput whole-transcriptome sequencing was conducted on rape pollen allergic samples and non-allergic samples. Differentially expressed microRNAs (DEmiRNAs), circRNAs (DEcircRNAs), long non-coding RNA (DElncRNAs), mRNA (DEmRNAs) were identified and a ceRNA regulatory network was constructed by Cytoscape. Functional enrichment analyses were performed on DEmRNAs in the ceRNA network. Then, the least absolute shrinkage and selection operator (LASSO) regression model was used to identify characteristic genes for rape pollen allergy. The receiver operating characteristic (ROC) curve was used to evaluate the diagnostic ability of characteristic genes. Results A total of 25 DEmiRNAs, 258 DEcircRNAs, 304 DElncRNAs, and 383 DEmRNAs in the allergic group compared with the non-allergic group were uncovered, respectively. A ceRNA network containing 21 miRNAs, 57 circRNAs, 28 lncRNAs, and 33 mRNAs was generated with 139 nodes and 160 edges. The signal transduction-related processes, immune-related processes, the ion, inorganic substance, and hormone regulation processes were associated with mRNAs in the ceRNA network. The results of pathway enrichment illustrated that mRNAs in the ceRNA were significantly linked to IL-17 signaling pathway, inflammatory mediator regulation of trp channels, GMP-PKG signaling pathway, signaling by GPCR, and GPCR downstream signaling pathway. Then, five characteristic genes (KCNQ3, CCR5, FOSB, CFAP43, and PRKG1) were defined by the LASSO algorithm. The AUC values of these genes indicated that these genes had a powerful discrimination ability in discriminating allergic samples from non-allergic samples. Conclusion Taken together, we revealed the ceRNA regulatory network in rape pollen allergy and excavated five characteristic genes (KCNQ3, CCR5, FOSB, CFAP43, and PRKG1) with the diagnostic value that may be a potential target in diagnosis and treatment.
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Affiliation(s)
- Ya Wang
- Department of Otolaryngology, the First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Jianhua Li
- Department of Otolaryngology, the Sixth Affiliated Hospital of Kunming Medical University, Yuxi, People’s Republic of China
| | - Fang Wang
- Department of Otolaryngology, the First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Yunhua Cui
- Department of Otolaryngology, the First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Li Song
- Department of Otolaryngology, the First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Biao Ruan
- Department of Otolaryngology, the First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Yongmei Yu
- Department of Otolaryngology, the First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
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24
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Fan H, Wang F, Zeng A, Murison A, Tomczak K, Hao D, Jelloul FZ, Wang B, Barrodia P, Liang S, Chen K, Wang L, Zhao Z, Rai K, Jain AK, Dick J, Daver N, Futreal A, Abbas HA. Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance. Commun Biol 2023; 6:765. [PMID: 37479893 PMCID: PMC10362028 DOI: 10.1038/s42003-023-05120-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of therapy resistance. Since the cell of origin can impact response to therapy, it is crucial to understand the lineage composition of AML cells at time of therapy resistance. Here we leverage single-cell chromatin accessibility profiling of 22 AML bone marrow aspirates from eight patients at time of therapy resistance and following subsequent therapy to characterize their lineage landscape. Our findings reveal a complex lineage architecture of therapy-resistant AML cells that are primed for stem and progenitor lineages and spanning quiescent, activated and late stem cell/progenitor states. Remarkably, therapy-resistant AML cells are also composed of cells primed for differentiated myeloid, erythroid and even lymphoid lineages. The heterogeneous lineage composition persists following subsequent therapy, with early progenitor-driven features marking unfavorable prognosis in The Cancer Genome Atlas AML cohort. Pseudotime analysis further confirms the vast degree of heterogeneity driven by the dynamic changes in chromatin accessibility. Our findings suggest that therapy-resistant AML cells are characterized not only by stem and progenitor states, but also by a continuum of differentiated cellular lineages. The heterogeneity in lineages likely contributes to their therapy resistance by harboring different degrees of lineage-specific susceptibilities to therapy.
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Affiliation(s)
- Huihui Fan
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Feng Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Zeng
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alex Murison
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Katarzyna Tomczak
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dapeng Hao
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fatima Zahra Jelloul
- Department of Hematopathology, University of Texas M D Anderson Cancer Center, Houston, TX, USA
| | - Bofei Wang
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Praveen Barrodia
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaoheng Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kunal Rai
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Dick
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Naval Daver
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hussein A Abbas
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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25
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Kim E, Rahmawati L, Aziz N, Kim HG, Kim JH, Kim KH, Yoo BC, Parameswaran N, Kang JS, Hur H, Manavalan B, Lee J, Cho JY. Protection of c-Fos from autophagic degradation by PRMT1-mediated methylation fosters gastric tumorigenesis. Int J Biol Sci 2023; 19:3640-3660. [PMID: 37564212 PMCID: PMC10411464 DOI: 10.7150/ijbs.85126] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 07/08/2023] [Indexed: 08/12/2023] Open
Abstract
Both AP-1 and PRMT1 are vital molecules in variety of cellular progresssion, but the interaction between these proteins in the context of cellular functions is less clear. Gastric cancer (GC) is one of the pernicious diseases worldwide. An in-depth understanding of the molecular mode of action underlying gastric tumorigenesis is still elusive. In this study, we found that PRMT1 directly interacts with c-Fos and enhances AP-1 activation. PRMT1-mediated arginine methylation (mono- and dimethylation) of c-Fos synergistically enhances c-Fos-mediated AP-1 liveliness and consequently increases c-Fos protein stabilization. Consistent with this finding, PRMT1 knockdown decreases the protein level of c-Fos. We discovered that the c-Fos protein undergoes autophagic degradation and found that PRMT1-mediated methylation at R287 protects c-Fos from autophagosomal degradation and is linked to clinicopathologic variables as well as prognosis in stomach tumor. Together, our data demonstrate that PRMT1-mediated c-Fos protein stabilization promotes gastric tumorigenesis. We contend that targeting this modification could constitute a new therapeutic strategy in gastric cancer.
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Affiliation(s)
- Eunji Kim
- Department of Integrative Biotechnology and Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
- R&D Center, Yungjin Pharmaceutical Co, Suwon 16229, Republic of Korea
| | - Laily Rahmawati
- Department of Integrative Biotechnology and Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
- Emergency Department, Hermina Hospital Tangkubanprahu, Malang 65119, Indonesia
| | - Nur Aziz
- Department of Integrative Biotechnology and Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
- Pharmacy Program, Faculty of Science and Engineering, Universitas Ma Chung, Malang 65151, Indonesia
| | - Han Gyung Kim
- Department of Integrative Biotechnology and Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ji Hye Kim
- Department of Integrative Biotechnology and Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Kyung-Hee Kim
- Proteomic Analysis Team, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea
| | - Byong Chul Yoo
- Division of Translational Science, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea
| | - Narayana Parameswaran
- Department of Physiology and Division of Pathology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Jong-Sun Kang
- Department of Molecular Cell Biology, Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Hoon Hur
- Department of Surgery, Department of Biomedical Sciences, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Balachandran Manavalan
- Department of Integrative Biotechnology and Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jongsung Lee
- Department of Integrative Biotechnology and Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jae Youl Cho
- Department of Integrative Biotechnology and Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
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26
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Ahn S, Kwon A, Oh Y, Rhee S, Song WK. Microtubule Acetylation-Specific Inhibitors Induce Cell Death and Mitotic Arrest via JNK/AP-1 Activation in Triple-Negative Breast Cancer Cells. Mol Cells 2023; 46:387-398. [PMID: 36794420 PMCID: PMC10258459 DOI: 10.14348/molcells.2023.2192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 02/17/2023] Open
Abstract
Microtubule acetylation has been proposed as a marker of highly heterogeneous and aggressive triple-negative breast cancer (TNBC). The novel microtubule acetylation inhibitors GM-90257 and GM-90631 (GM compounds) cause TNBC cancer cell death but the underlying mechanisms are currently unknown. In this study, we demonstrated that GM compounds function as anti-TNBC agents through activation of the JNK/AP-1 pathway. RNA-seq and biochemical analyses of GM compound-treated cells revealed that c-Jun N-terminal kinase (JNK) and members of its downstream signaling pathway are potential targets for GM compounds. Mechanistically, JNK activation by GM compounds induced an increase in c-Jun phosphorylation and c-Fos protein levels, thereby activating the activator protein-1 (AP-1) transcription factor. Notably, direct suppression of JNK with a pharmacological inhibitor alleviated Bcl2 reduction and cell death caused by GM compounds. TNBC cell death and mitotic arrest were induced by GM compounds through AP-1 activation in vitro. These results were reproduced in vivo, validating the significance of microtubule acetylation/JNK/AP-1 axis activation in the anti-cancer activity of GM compounds. Moreover, GM compounds significantly attenuated tumor growth, metastasis, and cancer-related death in mice, demonstrating strong potential as therapeutic agents for TNBC.
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Affiliation(s)
- Suyeon Ahn
- Cell Logistics Research Center, School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Ahreum Kwon
- Cell Logistics Research Center, School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Youngsoo Oh
- Cell Logistics Research Center, School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Sangmyung Rhee
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Woo Keun Song
- Cell Logistics Research Center, School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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Mendes C, Lemos I, Francisco I, Almodôvar T, Cunha F, Albuquerque C, Gonçalves LG, Serpa J. NSCLC presents metabolic heterogeneity, and there is still some leeway for EGF stimuli in EGFR-mutated NSCLC. Lung Cancer 2023; 182:107283. [PMID: 37379672 DOI: 10.1016/j.lungcan.2023.107283] [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: 04/20/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND Metabolic remodeling is crucial in carcinogenesis and cancer progression. Oncogenic mutations may promote metabolic reprogramming in cancer cells to support their energy and biomass requirements. EGFR mutations are commonly found in non-small cell lung cancer (NSCLC) and may induce NSCLC metabolic rewiring. Whether EGFR-driven metabolic reprogramming triggers cell vulnerabilities with therapeutic potential remains unknown. METHODS The role of EGFR signaling activation by EGF was investigated using NSCLC cell lines with different EGFR and KRAS status: A549 (EGFR WT and KRAS c.34G > A), H292 (EGFR WT and KRAS WT) and PC-9 (EGFR exon 19 E746-A750 deletion and KRAS WT). The effect of EGF on NSCLC cell death and cell cycle was evaluated using flow cytometry, and cell migration was assessed through wound healing. EGFR, HER2, MCT1, and MCT4 expression was analyzed through immunofluorescence or western blotting. We explored the impact of glucose and lactate bioavailability on NSCLC cells' metabolic profile using nuclear magnetic resonance (NMR) spectroscopy. Moreover, the expression of several relevant metabolic genes in NSCLC cells or patient samples was determined by RT-qPCR. RESULTS We showed that cell lines presented different metabolic profiles, and PC-9 cells were the most responsive to EGF stimulus, as they showed higher rates of cell proliferation and migration, together with altered metabolic behavior. By inhibiting EGFR with gefitinib, a decrease in glucose consumption was observed, which may be related to the fact that despite PC-9 harbor EGFR mutation, they still express the EGFR WT allele. The analysis of NSCLC patients' RNA showed a correlation between MCT1/MCT4 and GLUT1 expression in most cases, indicating that the metabolic information can serve as a reference in patients' follow-up. CONCLUSION Together, this study shows that NSCLC cell lines have heterogeneous metabolic profiles, which may be underlaid by different genetic profiles, revealing an opportunity to identify and stratify patients who can benefit from metabolism-targeted therapies.
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Affiliation(s)
- Cindy Mendes
- NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal; Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Isabel Lemos
- NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal; Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Inês Francisco
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Teresa Almodôvar
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Fernando Cunha
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Cristina Albuquerque
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Luís G Gonçalves
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB Nova), Oeiras, Portugal
| | - Jacinta Serpa
- NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal; Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal.
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28
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Kechin AA, Koryukov MA, Smertina MA, Borobova VS, Oscorbin IP, Ivanov AA, Bakharev SY, Boyarskikh UA, Kushlinskii NE, Filipenko ML. Differences in Transcriptomic Profiles of Brain and Thyroid Tumors with NTRK Gene Rearrangement. Bull Exp Biol Med 2023:10.1007/s10517-023-05815-0. [PMID: 37335445 DOI: 10.1007/s10517-023-05815-0] [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: 11/18/2022] [Indexed: 06/21/2023]
Abstract
For tumors with chimeric NTRK genes, entrectinib and larotrectinib can be prescribed regardless of tumor localization. We compared changes in the transcriptional activity of genes in brain tumors (BT) and thyroid cancer (TC) with rearrangement (NTRK+) and without rearrangement (NTRK-) of the NTRK genes using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. We revealed an increase in the transcription of the JUN gene in NTRK+ samples in comparison with NTRK- samples: by 1.6 times for BT (p=0.239) and by 2.5 times for TC (p=0.003). The transcription of eight HOX genes in NTRK+ BT samples was also increased (by 85-725 times, p<0.05) in comparison with NTRK-. In NTRK+ TC samples, the level of miR-31 and miR-542 was statistically significantly higher (by 3 and 2.5 times, respectively) than in NTRK-samples. For the NTRK+ BT samples, the levels of miR-10b, miR-182, and miR-21 more than 5-fold surpassed the corresponding values in NTRK-samples (p<0.05). These findings reflect differences in activation of gene transcription resulting from NTRK gene rearrangement in BT and TC.
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Affiliation(s)
- A A Kechin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia.
- Novosibirsk National Research State University, Novosibirsk, Russia.
| | - M A Koryukov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk National Research State University, Novosibirsk, Russia
| | - M A Smertina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V S Borobova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk National Research State University, Novosibirsk, Russia
| | - I P Oscorbin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Ivanov
- Altai Regional Oncological Center, Barnaul, Russia
| | | | - U A Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N E Kushlinskii
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - M L Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
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Kashyap D, Rele S, Bagde PH, Saini V, Chatterjee D, Jain AK, Pandey RK, Jha HC. Comprehensive insight into altered host cell-signaling cascades upon Helicobacter pylori and Epstein-Barr virus infections in cancer. Arch Microbiol 2023; 205:262. [PMID: 37310490 DOI: 10.1007/s00203-023-03598-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/14/2023]
Abstract
Cancer is characterized by mutagenic events that lead to disrupted cell signaling and cellular functions. It is one of the leading causes of death worldwide. Literature suggests that pathogens, mainly Helicobacter pylori and Epstein-Barr virus (EBV), have been associated with the etiology of human cancer. Notably, their co-infection may lead to gastric cancer. Pathogen-mediated DNA damage could be the first and crucial step in the carcinogenesis process that modulates numerous cellular signaling pathways. Altogether, it dysregulates the metabolic pathways linked with cell growth, apoptosis, and DNA repair. Modulation in these pathways leads to abnormal growth and proliferation. Several signaling pathways such RTK, RAS/MAPK, PI3K/Akt, NFκB, JAK/STAT, HIF1α, and Wnt/β-catenin are known to be altered in cancer. Therefore, this review focuses on the oncogenic roles of H. pylori, EBV, and its associated signaling cascades in various cancers. Scrutinizing these signaling pathways is crucial and may provide new insights and targets for preventing and treating H. pylori and EBV-associated cancers.
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Affiliation(s)
- Dharmendra Kashyap
- Lab No. POD 1B 602, Infection Bio-Engineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India
| | - Samiksha Rele
- Lab No. POD 1B 602, Infection Bio-Engineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India
| | - Pranit Hemant Bagde
- Lab No. POD 1B 602, Infection Bio-Engineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India
| | - Vaishali Saini
- Lab No. POD 1B 602, Infection Bio-Engineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India
| | | | | | - Rajan Kumar Pandey
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177, Solna, Sweden
| | - Hem Chandra Jha
- Lab No. POD 1B 602, Infection Bio-Engineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India.
- Centre for Rural Development and Technology, Indian Institute of Technology Indore, Madhya Pradesh, 453552, Indore, India.
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30
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Ishikawa C, Mori N. Heat shock factor 1 is a promising therapeutic target against adult T-cell leukemia. Med Oncol 2023; 40:172. [PMID: 37165174 DOI: 10.1007/s12032-023-02042-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/28/2023] [Indexed: 05/12/2023]
Abstract
Patients with adult T-cell leukemia (ATL), which is caused by human T-cell leukemia virus type 1 (HTLV-1), show poor prognosis because of drug resistance. Heat shock protein (HSP) 90 is reportedly essential for ATL cell survival as it regulates important signaling pathways, thereby making HSP90 inhibitors new therapeutic candidates for ATL. However, HSP90 inhibition increases the expression of other HSPs, suggesting that HSPs may contribute to drug resistance. The heat shock factor 1 (HSF1) transcription factor is the primary regulator of the expression of HSPs. Furthermore, targeting HSF1 disrupts the HSP90 chaperone function. Herein, we demonstrated that HSF1 is overexpressed in HTLV-1-infected T cells. HSF1 knockdown inhibited the proliferation of HTLV-1-infected T cells. HSF1 inhibitor KRIBB11 reduced the expression and phosphorylation of HSF1, downregulated HSP70 and HSP27 expression, and suppressed Akt, nuclear factor-κB, and AP-1 signals. KRIBB11 treatment induced DNA damage, upregulated p53 and p21, and reduced the expression of cyclin D2/E, CDK2/4, c-Myc, MDM2, and β-catenin, thereby preventing retinoblastoma protein phosphorylation and inhibiting G1-S cell cycle progression. KRIBB11 also induced caspase-mediated apoptosis concomitant with the suppression of Bcl-xL, Mcl-1, XIAP, c-IAP1/2, and survivin expression. KRIBB11 inhibited HSP70 and HSP90 upregulation through treatment with AUY922, an HSP90 inhibitor, and enhanced the cytotoxic effect of AUY922, suggesting a salvage role of HSF1-dependent HSP induction in response to drug treatment. Finally, treatment of mice with KRIBB11 reduced ATL tumor growth. Therefore, this study provides a strong rationale to target HSF1 and validates the anti-ATL activity of KRIBB11.
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Affiliation(s)
- Chie Ishikawa
- Department of Microbiology and Oncology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan
- Division of Health Sciences, Transdisciplinary Research Organization for Subtropics and Island Studies, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Naoki Mori
- Department of Microbiology and Oncology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan.
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Kavousi N, Tonge DP, Mourtada-Maarabouni M. New insights into the functional role of protein phosphatase 4 regulatory subunit PP4R3A/SMEK1 in the regulation of leukemic cell fate. Int J Biol Macromol 2023; 233:123467. [PMID: 36731689 DOI: 10.1016/j.ijbiomac.2023.123467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/08/2023] [Accepted: 01/25/2023] [Indexed: 02/01/2023]
Abstract
The serine/threonine protein phosphatase 4 holoenzyme consists of a PP4 catalytic subunit (PP4c), which interacts with four different regulatory subunits. Previous studies have shown that PP4c acts as a tumour suppressor. Emerging evidence suggests that the protein phosphatase 4 regulatory subunits might regulate cell fate independently of PP4c. To this end, we investigated the role of PP4R3A (SMEK1) in Jurkat and CEM-C7 leukemic cell lines. SMEK1 overexpression decreased cell growth, increased spontaneous apoptosis, and reduced the colony forming ability of leukemic cells. Conversely, siRNA-mediated silencing of SMEK1 led to increased short and long-term survival in these cells. Phospho-protein arrays revealed that increased expression of SMEK1 affected the phosphorylation of key proteins involved in MAPK3, AKT, JAK/STAT, NFκB and TGFβ signalling pathways. These proteins include transcription factors such as NFκB, STAT3, c-JUN, SMAD1, and SMAD5, suggesting a role for SMEK1 in the regulation of gene expression. RNA sequencing confirmed the role of SMEK1 in the regulation of gene expression. RNA sequencing also confirmed the tumour suppressor role of SMEK1. Taken together, this study shows that SMEK1 regulates leukemic T cell survival, indicating that SMEK1 dysfunction may be important in the development and progression of leukemia.
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Affiliation(s)
- Nadieh Kavousi
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, UK
| | - Daniel P Tonge
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, UK
| | - Mirna Mourtada-Maarabouni
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, UK.
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32
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Cuarental L, Ribagorda M, Ceballos MI, Pintor-Chocano A, Carriazo SM, Dopazo A, Vazquez E, Suarez-Alvarez B, Cannata-Ortiz P, Sanz AB, Ortiz A, Sanchez-Niño MD. The transcription factor Fosl1 preserves Klotho expression and protects from acute kidney injury. Kidney Int 2023; 103:686-701. [PMID: 36565807 DOI: 10.1016/j.kint.2022.11.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 11/02/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022]
Abstract
Increased expression of AP-1 transcription factor components has been reported in acute kidney injury (AKI). However, the role of specific components, such as Fosl1, in tubular cells or AKI is unknown. Upstream regulator analysis of murine nephrotoxic AKI transcriptomics identified AP-1 as highly upregulated. Among AP-1 canonical components, Fosl1 was found to be upregulated in two transcriptomics datasets from nephrotoxic murine AKI induced by folic acid or cisplatin and from proximal tubular cells exposed to TWEAK, a cytokine mediator of AKI. Fosl1 was minimally expressed in the kidneys of control uninjured mice. Increased Fosl1 protein was localized to proximal tubular cell nuclei in AKI. In human AKI, FOSL1 was found present in proximal tubular cells in kidney sections and in urine along with increased urinary FOSL1 mRNA. Selective Fosl1 deficiency in proximal tubular cells (Fosl1Δtub) increased the severity of murine cisplatin- or folate-induced AKI as characterized by lower kidney function, more severe kidney inflammation and Klotho downregulation. Indeed, elevated AP-1 activity was observed after cisplatin-induced AKI in Fosl1Δtub mice compared to wild-type mice. More severe Klotho downregulation preceded more severe kidney dysfunction. The Klotho promoter was enriched in Fosl1 binding sites and Fosl1 bound to the Klotho promoter in cisplatin-AKI. In cultured proximal tubular cells, Fosl1 targeting increased the proinflammatory response and downregulated Klotho. In vivo, recombinant Klotho administration protected Fosl1Δtub mice from cisplatin-AKI. Thus, increased proximal tubular Fosl1 expression during AKI is an adaptive response, preserves Klotho, and limits the severity of tubular cell injury and AKI.
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Affiliation(s)
- Leticia Cuarental
- Department of Nephrology and Hypertension, Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz, Universidad Autonoma de Madrid, Madrid, Spain; RICORS2040 (Redes de Investigación Cooperativa Orientadas a Resultados en Salud), Madrid, Spain
| | - Marta Ribagorda
- Department of Nephrology and Hypertension, Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz, Universidad Autonoma de Madrid, Madrid, Spain; RICORS2040 (Redes de Investigación Cooperativa Orientadas a Resultados en Salud), Madrid, Spain
| | - Maria I Ceballos
- Department of Nephrology and Hypertension, Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz, Universidad Autonoma de Madrid, Madrid, Spain; RICORS2040 (Redes de Investigación Cooperativa Orientadas a Resultados en Salud), Madrid, Spain
| | - Aranzazu Pintor-Chocano
- Department of Nephrology and Hypertension, Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz, Universidad Autonoma de Madrid, Madrid, Spain; RICORS2040 (Redes de Investigación Cooperativa Orientadas a Resultados en Salud), Madrid, Spain
| | - Sol M Carriazo
- Department of Nephrology and Hypertension, Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz, Universidad Autonoma de Madrid, Madrid, Spain; RICORS2040 (Redes de Investigación Cooperativa Orientadas a Resultados en Salud), Madrid, Spain
| | - Ana Dopazo
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Enrique Vazquez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Beatriz Suarez-Alvarez
- Translational Immunology, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Pablo Cannata-Ortiz
- Department of Pathology, IIS-Fundacion Jimenez Diaz, Universidad Autonoma de Madrid, Madrid, Spain
| | - Ana B Sanz
- Department of Nephrology and Hypertension, Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz, Universidad Autonoma de Madrid, Madrid, Spain; RICORS2040 (Redes de Investigación Cooperativa Orientadas a Resultados en Salud), Madrid, Spain
| | - Alberto Ortiz
- Department of Nephrology and Hypertension, Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz, Universidad Autonoma de Madrid, Madrid, Spain; RICORS2040 (Redes de Investigación Cooperativa Orientadas a Resultados en Salud), Madrid, Spain; Departamento de Medicina, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Maria D Sanchez-Niño
- Department of Nephrology and Hypertension, Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz, Universidad Autonoma de Madrid, Madrid, Spain; RICORS2040 (Redes de Investigación Cooperativa Orientadas a Resultados en Salud), Madrid, Spain; Departamento de Farmacología, Universidad Autonoma de Madrid (UAM), Madrid, Spain.
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33
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Alkaabi D, Arafat K, Sulaiman S, Al-Azawi AM, Attoub S. PD-1 Independent Role of PD-L1 in Triple-Negative Breast Cancer Progression. Int J Mol Sci 2023; 24:ijms24076420. [PMID: 37047395 PMCID: PMC10094894 DOI: 10.3390/ijms24076420] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 04/01/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a type of breast malignancy characterized by a high proliferative rate and metastatic potential leading to treatment failure, relapse, and poor prognosis. Therefore, efforts are continuously being devoted to understanding its biology and identifying new potential targets. Programmed death-ligand 1 (PD-L1) is an immunosuppressive protein that inactivates T cells by binding to the inhibitory receptor programmed death-1 (PD-1). PD-L1 overexpression in cancer cells contributes to immune evasion and, subsequently, poor survival and prognosis in several cancers, including breast cancer. Apart from its inhibitory impact on T cells, this ligand is believed to have an intrinsic role in cancer cells. This study was performed to clarify the PD-1 independent role of PD-L1 in TNBC MDA-MB-231 cells by knocking out the PD-L1 using three designs of CRISPR-Cas9 lentiviral particles. Our study revealed that PD-L1 knockout significantly inhibited MDA-MB-231 cell proliferation and colony formation in vitro and tumor growth in the chick embryo chorioallantoic membrane (CAM) model in vivo. PD-L1 knockout also decreased the migration and invasion of MDA-MB-231 cells in vitro. We have shown that PD-L1 knockout MDA-MB-231 cells have low levels of p-Akt and p-ERK in addition to some of their downstream proteins, c-Fos, c-Myc, p21, survivin, and COX-2. Furthermore, PD-L1 knockout significantly decreased the expression of Snail and RhoA. This study shows the intrinsic role of PD-L1 in TNBC independently of its binding to PD-1 receptors on T cells. It may pave the way for developing novel therapeutic strategies using PD-L1 inhibitors alone and in combination to treat TNBC more effectively.
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Affiliation(s)
- Duaa Alkaabi
- Department of Pharmacology & Therapeutics, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
| | - Kholoud Arafat
- Department of Pharmacology & Therapeutics, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
| | - Shahrazad Sulaiman
- Department of Pharmacology & Therapeutics, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
| | - Aya Mudhafar Al-Azawi
- Department of Pharmacology & Therapeutics, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
| | - Samir Attoub
- Department of Pharmacology & Therapeutics, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
- Institut National de la Santé et de la Recherche Médicale (INSERM), 75013 Paris, France
- Correspondence:
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34
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Kumari S, Kumar P. Design and Computational Analysis of an MMP9 Inhibitor in Hypoxia-Induced Glioblastoma Multiforme. ACS OMEGA 2023; 8:10565-10590. [PMID: 36969457 PMCID: PMC10035023 DOI: 10.1021/acsomega.3c00441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The main therapeutic difficulties in treating hypoxia-induced glioblastoma multiforme (GBM) are toxicity of current treatments and the resistance brought on by the microenvironment. More effective therapeutic alternatives are urgently needed to reduce tumor lethality. Hence, we screened plant-based natural product panels intending to identify novel drugs without elevating drug resistance. We explored GEO for the hypoxia GBM model and compared hypoxic genes to non-neoplastic brain cells. A total of 2429 differentially expressed genes expressed exclusively in hypoxia were identified. The functional enrichment analysis demonstrated genes associated with GBM, further PPI network was constructed, and biological pathways associated with them were explored. Seven webtools, including GEPIA2.0, TIMER2.0, TCGA-GBM, and GlioVis, were used to validate 32 hub genes discovered using Cytoscape tool in GBM patient samples. Four GBM-specific hypoxic hub genes, LYN, MMP9, PSMB9, and TIMP1, were connected to the tumor microenvironment using TIMER analysis. 11 promising hits demonstrated positive drug-likeness with nontoxic characteristics and successfully crossed blood-brain barrier and ADMET analyses. Top-ranking hits have stable intermolecular interactions with the MMP9 protein according to molecular docking, MD simulation, MM-PBSA, PCA, and DCCM analyses. Herein, we have reported flavonoids, 7,4'-dihydroxyflavan, (3R)-3-(4-hydroxybenzyl)-6-hydroxy-8-methoxy-3,4-dihydro-2H-1-benzopyran, and 4'-hydroxy-7-methoxyflavan, to inhibit MMP9, a novel hypoxia gene signature that could serve as a promising predictor in various clinical applications, including GBM diagnosis, prognosis, and targeted therapy.
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35
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Akcan TS, Vilov S, Heinig M. Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures. Nucleic Acids Res 2023; 51:1608-1624. [PMID: 36727445 PMCID: PMC9976927 DOI: 10.1093/nar/gkac1272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/09/2022] [Accepted: 01/12/2023] [Indexed: 02/03/2023] Open
Abstract
Promoter-proximal Polymerase II (Pol II) pausing is a key rate-limiting step for gene expression. DNA and RNA-binding trans-acting factors regulating the extent of pausing have been identified. However, we lack a quantitative model of how interactions of these factors determine pausing, therefore the relative importance of implicated factors is unknown. Moreover, previously unknown regulators might exist. Here we address this gap with a machine learning model that accurately predicts the extent of promoter-proximal Pol II pausing from large-scale genome and transcriptome binding maps and gene annotation and sequence composition features. We demonstrate high accuracy and generalizability of the model by validation on an independent cell line which reveals the model's cell line agnostic character. Model interpretation in light of prior knowledge about molecular functions of regulatory factors confirms the interconnection of pausing with other RNA processing steps. Harnessing underlying feature contributions, we assess the relative importance of each factor, quantify their predictive effects and systematically identify previously unknown regulators of pausing. We additionally identify 16 previously unknown 7SK ncRNA interacting RNA-binding proteins predictive of pausing. Our work provides a framework to further our understanding of the regulation of the critical early steps in transcriptional elongation.
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Affiliation(s)
- Toray S Akcan
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Department of Computer Science, TUM School of Computation, Information and Technology, Technical University Munich, Munich, Germany
| | - Sergey Vilov
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Department of Computer Science, TUM School of Computation, Information and Technology, Technical University Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Munich Heart Association, Partner Site Munich, 10785 Berlin, Germany
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Roura AJ, Szadkowska P, Poleszak K, Dabrowski MJ, Ellert-Miklaszewska A, Wojnicki K, Ciechomska IA, Stepniak K, Kaminska B, Wojtas B. Regulatory networks driving expression of genes critical for glioblastoma are controlled by the transcription factor c-Jun and the pre-existing epigenetic modifications. Clin Epigenetics 2023; 15:29. [PMID: 36850002 PMCID: PMC9972689 DOI: 10.1186/s13148-023-01446-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM, WHO grade IV) is an aggressive, primary brain tumor. Despite extensive tumor resection followed by radio- and chemotherapy, life expectancy of GBM patients did not improve over decades. Several studies reported transcription deregulation in GBMs, but regulatory mechanisms driving overexpression of GBM-specific genes remain largely unknown. Transcription in open chromatin regions is directed by transcription factors (TFs) that bind to specific motifs, recruit co-activators/repressors and the transcriptional machinery. Identification of GBM-related TFs-gene regulatory networks may reveal new and targetable mechanisms of gliomagenesis. RESULTS We predicted TFs-regulated networks in GBMs in silico and intersected them with putative TF binding sites identified in the accessible chromatin in human glioma cells and GBM patient samples. The Cancer Genome Atlas and Glioma Atlas datasets (DNA methylation, H3K27 acetylation, transcriptomic profiles) were explored to elucidate TFs-gene regulatory networks and effects of the epigenetic background. In contrast to the majority of tumors, c-Jun expression was higher in GBMs than in normal brain and c-Jun binding sites were found in multiple genes overexpressed in GBMs, including VIM, FOSL2 or UPP1. Binding of c-Jun to the VIM gene promoter was stronger in GBM-derived cells than in cells derived from benign glioma as evidenced by gel shift and supershift assays. Regulatory regions of the majority of c-Jun targets have distinct DNA methylation patterns in GBMs as compared to benign gliomas, suggesting the contribution of DNA methylation to the c-Jun-dependent gene expression. CONCLUSIONS GBM-specific TFs-gene networks identified in GBMs differ from regulatory pathways attributed to benign brain tumors and imply a decisive role of c-Jun in controlling genes that drive glioma growth and invasion as well as a modulatory role of DNA methylation.
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Affiliation(s)
- Adria-Jaume Roura
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Paulina Szadkowska
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
- grid.13339.3b0000000113287408Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Katarzyna Poleszak
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Michal J. Dabrowski
- grid.425308.80000 0001 2158 4832Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Aleksandra Ellert-Miklaszewska
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Kamil Wojnicki
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Iwona A. Ciechomska
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Karolina Stepniak
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bozena Kaminska
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bartosz Wojtas
- grid.419305.a0000 0001 1943 2944Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
- grid.419305.a0000 0001 1943 2944Laboratory of Sequencing, Nencki Institute of Experimental Biology, ul. Ludwika Pasteura 3, 02-093 Warsaw, Poland
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37
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Xu H, Jia J, Jeong HH, Zhao Z. Deep learning for detecting and elucidating human T-cell leukemia virus type 1 integration in the human genome. PATTERNS (NEW YORK, N.Y.) 2023; 4:100674. [PMID: 36873907 PMCID: PMC9982299 DOI: 10.1016/j.patter.2022.100674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/02/2022] [Accepted: 12/13/2022] [Indexed: 02/12/2023]
Abstract
Human T-cell leukemia virus type 1 (HTLV-1), a retrovirus, is the causative agent for adult T cell leukemia/lymphoma and many other human diseases. Accurate and high throughput detection of HTLV-1 virus integration sites (VISs) across the host genomes plays a crucial role in the prevention and treatment of HTLV-1-associated diseases. Here, we developed DeepHTLV, the first deep learning framework for VIS prediction de novo from genome sequence, motif discovery, and cis-regulatory factor identification. We demonstrated the high accuracy of DeepHTLV with more efficient and interpretive feature representations. Decoding the informative features captured by DeepHTLV resulted in eight representative clusters with consensus motifs for potential HTLV-1 integration. Furthermore, DeepHTLV revealed interesting cis-regulatory elements in regulation of VISs that have significant association with the detected motifs. Literature evidence demonstrated nearly half (34) of the predicted transcription factors enriched with VISs were involved in HTLV-1-associated diseases. DeepHTLV is freely available at https://github.com/bsml320/DeepHTLV.
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Affiliation(s)
- Haodong Xu
- Center for Precision Health, School of Biomedical Informatics, UTHealth Science Center at Houston, Houston, TX 77030, USA
| | - Johnathan Jia
- Center for Precision Health, School of Biomedical Informatics, UTHealth Science Center at Houston, Houston, TX 77030, USA.,MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Hyun-Hwan Jeong
- Center for Precision Health, School of Biomedical Informatics, UTHealth Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, UTHealth Science Center at Houston, Houston, TX 77030, USA.,MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
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38
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Naldurtiker A, Batchu P, Kouakou B, Terrill TH, McCommon GW, Kannan G. Differential gene expression analysis using RNA-seq in the blood of goats exposed to transportation stress. Sci Rep 2023; 13:1984. [PMID: 36737466 PMCID: PMC9898539 DOI: 10.1038/s41598-023-29224-5] [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: 07/17/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Transportation stress causes significant changes in physiological responses in goats; however, studies exploring the transcriptome of stress are very limited. The objective of this study was to determine the differential gene expressions and related pathways in the blood samples using RNA-seq procedure in Spanish goats subjected to different durations of transportation stress. Fifty-four male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg) were randomly subjected to one of three treatments (TRT; n = 18 goats/treatment): (1) transported for 180 min, (2) transported for 30 min, or (3) held in pens (control). Blood samples were collected before and after treatment for stress hormone, metabolite, and transcriptomic analysis. RNA-seq technology was used to obtain the transcriptome profiles of blood. Analysis of physiological data using SAS showed that plasma cortisol concentrations were higher (P < 0.01) in 180 min and 30 min groups compared to the control group. Enrichment analysis of DEGs related to transportation stress through Gene Ontology and KEGG databases revealed that the differentially expressed genes related to inflammatory pathways, caspases, and apoptosis such as IL1R2, CASP14, CD14, TLR4, and MAPK14 were highly enriched in the transported group of goats compared to non-transported goats. Stress in goats leads to a sequence of events at cellular and molecular levels that causes inflammation and apoptosis.
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Affiliation(s)
- Aditya Naldurtiker
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - Phaneendra Batchu
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - Brou Kouakou
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - Thomas H Terrill
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - George W McCommon
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - Govind Kannan
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA.
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Upreti A, Padula SL, Tangeman JA, Wagner BD, O’Connell MJ, Jaquish TJ, Palko RK, Mantz CJ, Anand D, Lovicu FJ, Lachke SA, Robinson ML. Lens Epithelial Explants Treated with Vitreous Humor Undergo Alterations in Chromatin Landscape with Concurrent Activation of Genes Associated with Fiber Cell Differentiation and Innate Immune Response. Cells 2023; 12:501. [PMID: 36766843 PMCID: PMC9914805 DOI: 10.3390/cells12030501] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Lens epithelial explants are comprised of lens epithelial cells cultured in vitro on their native basement membrane, the lens capsule. Biologists have used lens epithelial explants to study many different cellular processes including lens fiber cell differentiation. In these studies, fiber differentiation is typically measured by cellular elongation and the expression of a few proteins characteristically expressed by lens fiber cells in situ. Chromatin and RNA was collected from lens epithelial explants cultured in either un-supplemented media or media containing 50% bovine vitreous humor for one or five days. Chromatin for ATAC-sequencing and RNA for RNA-sequencing was prepared from explants to assess regions of accessible chromatin and to quantitatively measure gene expression, respectively. Vitreous humor increased chromatin accessibility in promoter regions of genes associated with fiber differentiation and, surprisingly, an immune response, and this was associated with increased transcript levels for these genes. In contrast, vitreous had little effect on the accessibility of the genes highly expressed in the lens epithelium despite dramatic reductions in their mRNA transcripts. An unbiased analysis of differentially accessible regions revealed an enrichment of cis-regulatory motifs for RUNX, SOX and TEAD transcription factors that may drive differential gene expression in response to vitreous.
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Affiliation(s)
- Anil Upreti
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Stephanie L. Padula
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Jared A. Tangeman
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Brad D. Wagner
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | | | - Tycho J. Jaquish
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Raye K. Palko
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Courtney J. Mantz
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Frank J. Lovicu
- Molecular and Cellular Biomedicine, School of Medical Sciences, and Save Sight Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Michael L. Robinson
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
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40
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Liu JP, Liu SC, Hu SQ, Lu JF, Wu CL, Hu DX, Zhang WJ. ATP ion channel P2X purinergic receptors in inflammation response. Biomed Pharmacother 2023; 158:114205. [PMID: 36916431 DOI: 10.1016/j.biopha.2022.114205] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/19/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Different studies have confirmed that P2X purinergic receptors play a key role in inflammation. Activation of P2X purinergic receptors can release inflammatory cytokines and participate in the progression of inflammatory diseases. In an inflammatory microenvironment, cells can release a large amount of ATP to activate P2X receptors, open non-selective cation channels, activate multiple intracellular signaling, release multiple inflammatory cytokines, amplify inflammatory response. While P2X4 and P2X7 receptors play an important role in the process of inflammation. P2X4 receptor can mediate the activation of microglia involved in neuroinflammation, and P2X7 receptor can mediate different inflammatory cells to mediate the progression of tissue-wide inflammation. At present, the role of P2X receptors in inflammatory response has been widely recognized and affirmed. Therefore, in this paper, we discussed the role of P2X receptors-mediated inflammation. Moreover, we also described the effects of some antagonists (such as A-438079, 5-BDBD, A-804598, A-839977, and A-740003) on inflammation relief by antagonizing the activities of P2X receptors.
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Affiliation(s)
- Ji-Peng Liu
- Department of Gastrointestinal surgery, The Second Affiliated Hospital, Nanchang University, Nanchang City, Jiangxi Province 343000, China
| | - Si-Cheng Liu
- Department of Gastrointestinal surgery, The Second Affiliated Hospital, Nanchang University, Nanchang City, Jiangxi Province 343000, China
| | - Shi-Qi Hu
- Queen Mary College, Nanchang University, Nanchang City, Jiangxi Province 343000, China
| | - Jia-Feng Lu
- Basic medical school, Nanchang University, Nanchang City, Jiangxi Province 343000, China
| | - Chang-Lei Wu
- Department of Gastrointestinal surgery, The Second Affiliated Hospital, Nanchang University, Nanchang City, Jiangxi Province 343000, China
| | - Dong-Xia Hu
- Department of Rehabilitation Medicine, The Second Affiliated Hospital, Nanchang University, Nanchang City, Jiangxi Province 343000, China.
| | - Wen-Jun Zhang
- Department of Rehabilitation Medicine, The Second Affiliated Hospital, Nanchang University, Nanchang City, Jiangxi Province 343000, China.
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41
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Hu FJ, Li YJ, Zhang L, Ji DB, Liu XZ, Chen YJ, Wang L, Wu AW. Single-cell profiling reveals differences between human classical adenocarcinoma and mucinous adenocarcinoma. Commun Biol 2023; 6:85. [PMID: 36690709 PMCID: PMC9870908 DOI: 10.1038/s42003-023-04441-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
Colorectal cancer is a highly heterogeneous disease. Most colorectal cancers are classical adenocarcinoma, and mucinous adenocarcinoma is a unique histological subtype that is known to respond poorly to chemoradiotherapy. The difference in prognosis between mucinous adenocarcinoma and classical adenocarcinoma is controversial. Here, to gain insight into the differences between classical adenocarcinoma and mucinous adenocarcinoma, we analyse 7 surgical tumour samples from 4 classical adenocarcinoma and 3 mucinous adenocarcinoma patients by single-cell RNA sequencing. Our results indicate that mucinous adenocarcinoma cancer cells have goblet cell-like properties, and express high levels of goblet cell markers (REG4, SPINK4, FCGBP and MUC2) compared to classical adenocarcinoma cancer cells. TFF3 is essential for the transcriptional regulation of these molecules, and may cooperate with RPS4X to eventually lead to the mucinous adenocarcinoma mucus phenotype. The observed molecular characteristics may be critical in the specific biological behavior of mucinous adenocarcinoma.
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Affiliation(s)
- Fang-Jie Hu
- Department of Gastroenterology, Beijing Chaoyang Hospital, Capital Medical University, Chaoyang District, Beijing, 100020, China
| | - Ying-Jie Li
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery III, Peking University Cancer Hospital & Institute, No. 52 Fucheng Rd., Haidian District, Beijing, 100142, China
| | - Li Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Deng-Bo Ji
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery III, Peking University Cancer Hospital & Institute, No. 52 Fucheng Rd., Haidian District, Beijing, 100142, China
| | - Xin-Zhi Liu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery III, Peking University Cancer Hospital & Institute, No. 52 Fucheng Rd., Haidian District, Beijing, 100142, China
| | - Yong-Jiu Chen
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery III, Peking University Cancer Hospital & Institute, No. 52 Fucheng Rd., Haidian District, Beijing, 100142, China
| | - Lin Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery III, Peking University Cancer Hospital & Institute, No. 52 Fucheng Rd., Haidian District, Beijing, 100142, China.
| | - Ai-Wen Wu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery III, Peking University Cancer Hospital & Institute, No. 52 Fucheng Rd., Haidian District, Beijing, 100142, China.
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42
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Lakhia R, Mishra A, Biggers L, Malladi V, Cobo-Stark P, Hajarnis S, Patel V. Enhancer and super-enhancer landscape in polycystic kidney disease. Kidney Int 2023; 103:87-99. [PMID: 36283570 PMCID: PMC9841439 DOI: 10.1016/j.kint.2022.08.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/15/2022] [Accepted: 08/19/2022] [Indexed: 11/07/2022]
Abstract
Widespread aberrant gene expression is a pathological hallmark of polycystic kidney disease (PKD). Numerous pathogenic signaling cascades, including c-Myc, Fos, and Jun, are transactivated. However, the underlying epigenetic regulators are poorly defined. Here we show that H3K27ac, an acetylated modification of DNA packing protein histone H3 that marks active enhancers, is elevated in mouse and human samples of autosomal dominant PKD. Using comparative H3K27ac ChIP-Seq analysis, we mapped over 16000 active intronic and intergenic enhancer elements in Pkd1-mutant mouse kidneys. We found that the cystic kidney epigenetic landscape resembles that of a developing kidney, and over 90% of upregulated genes in Pkd1-mutant kidneys are co-housed with activated enhancers in the same topologically associated domains. Furthermore, we identified an evolutionarily conserved enhancer cluster downstream of the c-Myc gene and super-enhancers flanking both Jun and Fos loci in mouse and human models of autosomal dominant PKD. Deleting these regulatory elements reduced c-Myc, Jun, or Fos abundance and suppressed proliferation and 3D cyst growth of Pkd1-mutant cells. Finally, inhibiting glycolysis and glutaminolysis or activating Ppara in Pkd1-mutant cells lowerd global H3K27ac levels and its abundance on c-Myc enhancers. Thus, our work suggests that epigenetic rewiring mediates the transcriptomic dysregulation in PKD, and the regulatory elements can be targeted to slow cyst growth.
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Affiliation(s)
- Ronak Lakhia
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, Texas, USA.
| | - Abheepsa Mishra
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Laurence Biggers
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Venkat Malladi
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Patricia Cobo-Stark
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Sachin Hajarnis
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Vishal Patel
- Department of Internal Medicine, Nephrology, UT Southwestern Medical Center, Dallas, Texas, USA
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Luo T, Pan Y, Liu Y, Zheng J, Zhuang Z, Ren Z, Zhu J, Gu Y, Zeng Y. LANA regulates miR-155/GATA3 signaling axis by enhancing c-Jun/c-Fos interaction to promote the proliferation and migration of KSHV-infected cells. J Med Virol 2023; 95:e28255. [PMID: 36284455 DOI: 10.1002/jmv.28255] [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: 07/19/2022] [Revised: 10/08/2022] [Accepted: 10/21/2022] [Indexed: 01/11/2023]
Abstract
Kaposi's sarcoma (KS) is the second most common tumor in people infected with human immunodeficiency virus worldwide, but its pathogenesis is still unclear. In this study, we discovered that the expression of GATA-binding protein 3 (GATA3) was lowly expressed in KS tissues and KSHV-infected cells, while microRNA-155 (miR-155) was highly expressed in KS serum and KSHV-infected cells. miR-155 promoted the proliferation, migration and invasion of KSHV infection by targeting GATA3. Further, The KSHV-encoded protein, the Latency associated nuclear antigen (LANA), promotes the proliferation, migration and invasion of KSHV-infected cells by regulating the miR-155/GATA3 axis. Regarding the molecular mechanism, c-Jun and c-Fos interact to form a complex. LANA upregulates the expression of c-Jun and c-Fos and enhances the formation of c-Jun/c-Fos complex. The complex binds to the -95∼-100 bp site of miR-155 promoter and transcriptionally activates miR-155. All in all, LANA enhances the c-Jun/c-Fos interaction, resulting in enhanced transcriptional regulation of miR-155 by the c-Jun/c-Fos complex, thereby downregulating GATA3 and promoting the proliferation, migration and invasion of KSHV-infected cells. The discovery of LANA/c-Jun/c-Fos/miR-155/GATA3 further refines the pathogenesis of KS, potentially opening a new avenue for developing effective drugs against KS.
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Affiliation(s)
- Ting Luo
- Precision Clinical Laboratory, Central People's Hospital of Zhanjiang, Zhanjiang, Guangdong, China.,Key Laboratory of Xinjiang Endemic and Ethnic Disease, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Yangyang Pan
- Precision Clinical Laboratory, Central People's Hospital of Zhanjiang, Zhanjiang, Guangdong, China.,Key Laboratory of Xinjiang Endemic and Ethnic Disease, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Yuhao Liu
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jun Zheng
- Key Laboratory of Xinjiang Endemic and Ethnic Disease, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Zhaowei Zhuang
- Key Laboratory of Xinjiang Endemic and Ethnic Disease, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Zuodong Ren
- Key Laboratory of Xinjiang Endemic and Ethnic Disease, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Jiaojiao Zhu
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yongqing Gu
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yan Zeng
- Precision Clinical Laboratory, Central People's Hospital of Zhanjiang, Zhanjiang, Guangdong, China.,Key Laboratory of Xinjiang Endemic and Ethnic Disease, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
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44
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Mazalmazraei T, Nejadsadeghi L, Mehdi Khanlou K, Ahmadi DN. Comparative analysis of differentially expressed miRNAs in leaves of three sugarcanes (Saacharum officinarum L.) cultivars during salinity stress. Mol Biol Rep 2023; 50:485-492. [PMID: 36350419 DOI: 10.1007/s11033-022-07349-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 03/05/2022] [Accepted: 03/09/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Sugarcane is an important industrial plant cultivated mostlyin the arid and semiarid regions. Due to climate change and anthropogenic activities, the sugarcane fieldsare prone to be damagedas a result of salt deposition. The consequence of such phenomena is turning to become a major thread in sugarcane cultivation. To address this issue, the identification of salinity tolerant cultivars would be a suitable strategy to minimize yield loss in the area. It is well known thatthe expression of abiotic stress-responsive genes including noncoding microRNAs (miRNAs) and their codingtargetscould lead to enhancement of stress tolerance in crops. Therefore, the expression study of those noncoding and coding genes under stress conditions is an appropriate approach to screen the tolerant cultivars. In addition, the examination of the expression of miRNA's target genes could provide deeper insight into the molecular stress mechanism and facilitate the identification of tolerant cultivars. METHODS AND RESULTS We aimedto assess the expression of nine candidate miRNAsand their corresponding targeted genes among the studied sugarcane cultivars under high salinity conditions, leading to the identification of the salt-tolerant cultivar. To achieve our goal, a two-factorial experiment with three sugarcane cultivars (CP-48, CP-57, CP-69) and two salinity levels (0 and 8 ds/m) was conducted. The result indicated significant differences in expression with in miRNAs and also their target genes. The highest reduction of miRNAs expression occurred in miR160 while the lowest oneappeared in miR1432. The data also indicated that the higher and the lowest expression of targeted genes occurred in miR160 and miR393 respectively. Among studied cultivars, the CP-57 showed poor performance while CP-69 expresses a superior tolerance to salt stress. CONCLUSIONS Taken together, these results suggested that the monitoring of microRNA expressioncould provide a new approach forthe screening of well-adapted cultivars under salt conditions. Such an approach would be the appropriate solutionto combat plant stress inhigh salinity region/soil. Our result indicated that the miR160 generates sugarcane tolerant to salt stress, can be potentially be used as a biomarker to salt stress.
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Affiliation(s)
- Tofigh Mazalmazraei
- Department of Plant Production and Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Leila Nejadsadeghi
- Department of Plant Production and Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Khosro Mehdi Khanlou
- Department of Plant Production and Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Daryoosh Nabati Ahmadi
- Department of Plant Production and Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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Oh ET, Kim HG, Kim CH, Lee J, Kim C, Lee JS, Cho Y, Park HJ. NQO1 regulates cell cycle progression at the G2/M phase. Theranostics 2023; 13:873-895. [PMID: 36793872 PMCID: PMC9925316 DOI: 10.7150/thno.77444] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/26/2022] [Indexed: 01/11/2023] Open
Abstract
Rationale: Overexpression of NAD(P)H:quinone oxidoreductase 1 (NQO1) is associated with tumor cell proliferation and growth in several human cancer types. However, the molecular mechanisms underlying the activity of NQO1 in cell cycle progression are currently unclear. Here, we report a novel function of NQO1 in modulation of the cell cycle regulator, cyclin-dependent kinase subunit-1 (CKS1), at the G2/M phase through effects on the stability of c‑Fos. Methods: The roles of the NQO1/c-Fos/CKS1 signaling pathway in cell cycle progression were analyzed in cancer cells using synchronization of the cell cycle and flow cytometry. The mechanisms underlying NQO1/c-Fos/CKS1-mediated regulation of cell cycle progression in cancer cells were studied using siRNA approaches, overexpression systems, reporter assays, co-immunoprecipitation, pull-down assays, microarray analysis, and CDK1 kinase assays. In addition, publicly available data sets and immunohistochemistry were used to investigate the correlation between NQO1 expression levels and clinicopathological features in cancer patients. Results: Our results suggest that NQO1 directly interacts with the unstructured DNA-binding domain of c-Fos, which has been implicated in cancer proliferation, differentiation, and development as well as patient survival, and inhibits its proteasome-mediated degradation, thereby inducing CKS1 expression and regulation of cell cycle progression at the G2/M phase. Notably, a NQO1 deficiency in human cancer cell lines led to suppression of c-Fos-mediated CKS1 expression and cell cycle progression. Consistent with this, high NQO1 expression was correlated with increased CKS1 and poor prognosis in cancer patients. Conclusions: Collectively, our results support a novel regulatory role of NQO1 in the mechanism of cell cycle progression at the G2/M phase in cancer through effects on c‑Fos/CKS1 signaling.
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Affiliation(s)
- Eun-Taex Oh
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon 22212, Republic of Korea
| | - Ha Gyeong Kim
- Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Chul Hoon Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jeonghun Lee
- Department of Polymer Science & Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Chulhee Kim
- Department of Polymer Science & Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Jae-Seon Lee
- Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea.,Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Republic of Korea.,Research Center for Controlling Intracellular Communication, College of Medicine, Inha University, Incheon 22212, Republic of Korea
| | - Yunmi Cho
- Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Heon Joo Park
- Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea.,Research Center for Controlling Intracellular Communication, College of Medicine, Inha University, Incheon 22212, Republic of Korea.,Department of Microbiology, College of Medicine, Inha University, Incheon 22212, Republic of Korea
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46
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Han RT, Vainchtein ID, Schlachetzki JC, Cho FS, Dorman LC, Ahn E, Kim DK, Barron JJ, Nakao-Inoue H, Molofsky AB, Glass CK, Paz JT, Molofsky AV. Microglial pattern recognition via IL-33 promotes synaptic refinement in developing corticothalamic circuits in mice. J Exp Med 2022; 220:213758. [PMID: 36520518 PMCID: PMC9757845 DOI: 10.1084/jem.20220605] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/21/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Microglia are critical regulators of brain development that engulf synaptic proteins during postnatal synapse remodeling. However, the mechanisms through which microglia sense the brain environment are not well defined. Here, we characterized the regulatory program downstream of interleukin-33 (IL-33), a cytokine that promotes microglial synapse remodeling. Exposing the developing brain to a supraphysiological dose of IL-33 altered the microglial enhancer landscape and increased binding of stimulus-dependent transcription factors including AP-1/FOS. This induced a gene expression program enriched for the expression of pattern recognition receptors, including the scavenger receptor MARCO. CNS-specific deletion of IL-33 led to increased excitatory/inhibitory synaptic balance, spontaneous absence-like epileptiform activity in juvenile mice, and increased seizure susceptibility in response to chemoconvulsants. We found that MARCO promoted synapse engulfment, and Marco-deficient animals had excess thalamic excitatory synapses and increased seizure susceptibility. Taken together, these data define coordinated epigenetic and functional changes in microglia and uncover pattern recognition receptors as potential regulators of postnatal synaptic refinement.
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Affiliation(s)
- Rafael T. Han
- Departments of Psychiatry and Behavioral Sciences/Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA,Rafael T. Han:
| | - Ilia D. Vainchtein
- Departments of Psychiatry and Behavioral Sciences/Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Frances S. Cho
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA,Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Leah C. Dorman
- Departments of Psychiatry and Behavioral Sciences/Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA,Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Eunji Ahn
- Departments of Psychiatry and Behavioral Sciences/Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Dong Kyu Kim
- Departments of Psychiatry and Behavioral Sciences/Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jerika J. Barron
- Departments of Psychiatry and Behavioral Sciences/Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Hiromi Nakao-Inoue
- Departments of Psychiatry and Behavioral Sciences/Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Ari B. Molofsky
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA,Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jeanne T. Paz
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA,Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA,Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Anna V. Molofsky
- Departments of Psychiatry and Behavioral Sciences/Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA,Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA,Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA,Correspondence to Anna V. Molofsky:
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47
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Maternal Undernutrition Induces Cell Signalling and Metabolic Dysfunction in Undifferentiated Mouse Embryonic Stem Cells. Stem Cell Rev Rep 2022; 19:767-783. [PMID: 36517693 PMCID: PMC10070223 DOI: 10.1007/s12015-022-10490-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
Abstract
Peri-conceptional environment can induce permanent changes in embryo phenotype which alter development and associate with later disease susceptibility. Thus, mouse maternal low protein diet (LPD) fed exclusively during preimplantation is sufficient to lead to cardiovascular, metabolic and neurological dysfunction in adult offspring. Embryonic stem cell (ESC) lines were generated from LPD and control NPD C57BL/6 blastocysts and characterised by transcriptomics, metabolomics, bioinformatics and molecular/cellular studies to assess early potential mechanisms in dietary environmental programming. Previously, we showed these lines retain cellular and epigenetic characteristics of LPD and NPD embryos after several passages. Here, three main changes were identified in LPD ESC lines. First, their derivation capacity was reduced but pluripotency marker expression was similar to controls. Second, LPD lines had impaired Mitogen-activated protein kinase (MAPK) pathway with altered gene expression of several regulators (e.g., Maff, Rassf1, JunD), reduced ERK1/2 signalling capacity and poorer cell survival characteristics which may contribute to reduced derivation. Third, LPD lines had impaired glucose metabolism comprising reduced upstream enzyme expression (e.g., Gpi, Mpi) and accumulation of metabolites (e.g., glucose-6-P, fructose-6-P) above the phosphofructokinase (PFK) gateway with PFK enzyme activity reduced. ESC lines may therefore permit investigation of peri-conceptional programming mechanisms with reduced need for animal experimentation.
Graphical Abstract
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Papazoglou A, Huang M, Bulik M, Lafyatis A, Tabib T, Morse C, Sembrat J, Rojas M, Valenzi E, Lafyatis R. Epigenetic Regulation of Profibrotic Macrophages in Systemic Sclerosis-Associated Interstitial Lung Disease. Arthritis Rheumatol 2022; 74:2003-2014. [PMID: 35849803 PMCID: PMC9771864 DOI: 10.1002/art.42286] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/26/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Systemic sclerosis-associated interstitial lung disease (SSc-ILD) is the leading cause of death in patients with SSc with unclear pathogenesis and limited treatment options. Evidence strongly supports an important role for profibrotic secreted phosphoprotein 1 (SPP1)-expressing macrophages in SSc-ILD. This study was undertaken to define the transcriptome and chromatin structural changes of SPP1 SSc-ILD macrophages in order to better understand their role in promoting fibrosis and to identify transcription factors associated with open chromatin driving their altered phenotype. METHODS We performed single-cell RNA sequencing (scRNA-Seq) on 11 explanted SSc-ILD and healthy control lung samples, as well as single-cell assay for transposase-accessible chromatin sequencing on 5 lung samples to define altered chromatin accessibility of SPP1 macrophages. We predicted transcription factors regulating SPP1 macrophages using single-cell regulatory network inference and clustering (SCENIC) and determined transcription factor binding sites associated with global alterations in SPP1 chromatin accessibility using Signac/Seurat. RESULTS We identified distinct macrophage subpopulations using scRNA-Seq analysis in healthy and SSc-ILD lungs and assessed gene expression changes during the change of healthy control macrophages into SPP1 macrophages. Analysis of open chromatin validated SCENIC predictions, indicating that microphthalmia-associated transcription factor, transcription factor EB, activating transcription factor 6, sterol regulatory element binding transcription factor 1, basic helix-loop-helix family member E40, Kruppel-like factor 6, ETS variant transcription factor 5, and/or members of the activator protein 1 family of transcription factors regulate SPP1 macrophage differentiation. CONCLUSION Our findings shed light on the underlying changes in chromatin structure and transcription factor regulation of profibrotic SPP1 macrophages in SSc-ILD. Similar alterations in SPP1 macrophages may underpin fibrosis in other organs involved in SSc and point to novel targets for the treatment of SSc-ILD, specifically targeting profibrotic macrophages.
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Affiliation(s)
- Anna Papazoglou
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mengqi Huang
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Melissa Bulik
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Annika Lafyatis
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Christina Morse
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - John Sembrat
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mauricio Rojas
- Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University, Columbus, OH, USA
| | - Eleanor Valenzi
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
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The Androgen Regulated lncRNA NAALADL2-AS2 Promotes Tumor Cell Survival in Prostate Cancer. Noncoding RNA 2022; 8:ncrna8060081. [PMID: 36548180 PMCID: PMC9787508 DOI: 10.3390/ncrna8060081] [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: 09/28/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 12/05/2022] Open
Abstract
Castration resistance is the leading cause of death in men with prostate cancer. Recent studies indicate long noncoding RNAs (lncRNAs) to be important drivers of therapy resistance. The aim of this study was to identify differentially expressed lncRNAs in castration-resistant prostate cancer (CRPC) and to functionally characterize them in vitro. Tumor-derived RNA-sequencing data were used to quantify and compare the expression of 11,469 lncRNAs in benign, primary prostate cancer, and CRPC samples. CRPC-associated lncRNAs were selected for semi-quantitative PCR validation on 68 surgical tumor specimens. In vitro functional studies were performed by antisense-oligonucleotide-mediated lncRNA knockdown in hormone-sensitive prostate cancer (HSPC) and CRPC cell line models. Subsequently, cell proliferation, apoptosis, cell cycle, transcriptome and pathway analyses were performed using the appropriate assays. Transcriptome analysis of a prostate cancer tumor specimens unveiled NAALADL2-AS2 as a novel CRPC-upregulated lncRNA. The expression of NAALADL2-AS2 was found to be particularly high in HSPC in vitro models and to increase under androgen deprived conditions. NAALADL2-AS2 knockdown decreased cell viability and increased caspase activity and apoptotic cells. Cellular fractionization and RNA fluorescent in situ hybridization identified NAALADL2-AS2 as a nuclear transcript. Transcriptome and pathway analyses revealed that NAALADL2-AS2 modulates the expression of genes involved with cell cycle control and glycogen metabolism. We hypothesize that the nuclear lncRNA, NAALADL2-AS2, functions as a pro-survival signal in prostate cancer cells under pressure of targeted hormone therapy.
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Tokunaga Y, Otsuyama KI, Kakuta S, Hayashida N. Heat Shock Transcription Factor 2 Is Significantly Involved in Neurodegenerative Diseases, Inflammatory Bowel Disease, Cancer, Male Infertility, and Fetal Alcohol Spectrum Disorder: The Novel Mechanisms of Several Severe Diseases. Int J Mol Sci 2022; 23:ijms232213763. [PMID: 36430241 PMCID: PMC9691173 DOI: 10.3390/ijms232213763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/03/2022] [Accepted: 11/05/2022] [Indexed: 11/10/2022] Open
Abstract
HSF (heat shock transcription factor or heat shock factor) was discovered as a transcription factor indispensable for heat shock response. Although four classical HSFs were discovered in mammals and two major HSFs, HSF1 and HSF2, were cloned in the same year of 1991, only HSF1 was intensively studied because HSF1 can give rise to heat shock response through the induction of various HSPs' expression. On the other hand, HSF2 was not well studied for some time, which was probably due to an underestimate of HSF2 itself. Since the beginning of the 21st century, HSF2 research has progressed and many biologically significant functions of HSF2 have been revealed. For example, the roles of HSF2 in nervous system protection, inflammation, maintenance of mitosis and meiosis, and cancer cell survival and death have been gradually unveiled. However, we feel that the fact HSF2 has a relationship with various factors is not yet widely recognized; therefore, the biological significance of HSF2 has been underestimated. We strongly hope to widely communicate the significance of HSF2 to researchers and readers in broad research fields through this review. In addition, we also hope that many readers will have great interest in the molecular mechanism in which HSF2 acts as an active transcription factor and gene bookmarking mechanism of HSF2 during cell cycle progression, as is summarized in this review.
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Affiliation(s)
- Yasuko Tokunaga
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Yamaguchi University, Yamaguchi 755-8505, Japan
- Institute of Gene Research, Yamaguchi University Science Research Center, Yamaguchi 755-8505, Japan
| | - Ken-Ichiro Otsuyama
- Department of Clinical Laboratory Science, Faculty of Health Science, Graduate School of Medicine, Yamaguchi University, Yamaguchi 755-8505, Japan
| | - Shigeru Kakuta
- Laboratory of Biomedical Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Naoki Hayashida
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Yamaguchi University, Yamaguchi 755-8505, Japan
- Correspondence: ; Tel.: +81-836-22-2359
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