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Ren Z, Ren Y, Li Z, Xu H. TCMM: A unified database for traditional Chinese medicine modernization and therapeutic innovations. Comput Struct Biotechnol J 2024; 23:1619-1630. [PMID: 38680873 PMCID: PMC11047297 DOI: 10.1016/j.csbj.2024.04.016] [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: 01/21/2024] [Revised: 03/30/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024] Open
Abstract
Mining the potential of traditional Chinese medicine (TCM) in treating modern diseases requires a profound understanding of its action mechanism and a comprehensive knowledge system that seamlessly bridges modern medical insights with traditional theories. However, existing databases for modernizing TCM are plagued by varying degrees of information loss, which impede the multidimensional dissection of pharmacological effects. To address this challenge, we introduce traditional Chinese medicine modernization (TCMM), the currently largest modernized TCM database that integrates pioneering intelligent pipelines. By aligning high-quality TCM and modern medicine data, TCMM boasts the most extensive TCM modernization knowledge, including 20 types of modernized TCM concepts such as prescription, ingredient, target and 46 biological relations among them, totaling 3,447,023 records. We demonstrate the efficacy and reliability of TCMM with two features, prescription generation and knowledge discovery, the outcomes show consistency with biological experimental results. A publicly available web interface is at https://www.tcmm.net.cn/.
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Affiliation(s)
- Zhixiang Ren
- Peng Cheng Laboratory, Shenzhen, 518055, Guangdong Province, China
| | - Yiming Ren
- Peng Cheng Laboratory, Shenzhen, 518055, Guangdong Province, China
| | - Zeting Li
- Peng Cheng Laboratory, Shenzhen, 518055, Guangdong Province, China
| | - Huan Xu
- School of Public Health, Anhui University of Science and Technology, Hefei, 231131, Anhui Province, China
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Park JH, Hothi P, de Lomana ALG, Pan M, Calder R, Turkarslan S, Wu WJ, Lee H, Patel AP, Cobbs C, Huang S, Baliga NS. Gene regulatory network topology governs resistance and treatment escape in glioma stem-like cells. SCIENCE ADVANCES 2024; 10:eadj7706. [PMID: 38848360 PMCID: PMC11160475 DOI: 10.1126/sciadv.adj7706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
Poor prognosis and drug resistance in glioblastoma (GBM) can result from cellular heterogeneity and treatment-induced shifts in phenotypic states of tumor cells, including dedifferentiation into glioma stem-like cells (GSCs). This rare tumorigenic cell subpopulation resists temozolomide, undergoes proneural-to-mesenchymal transition (PMT) to evade therapy, and drives recurrence. Through inference of transcriptional regulatory networks (TRNs) of patient-derived GSCs (PD-GSCs) at single-cell resolution, we demonstrate how the topology of transcription factor interaction networks drives distinct trajectories of cell-state transitions in PD-GSCs resistant or susceptible to cytotoxic drug treatment. By experimentally testing predictions based on TRN simulations, we show that drug treatment drives surviving PD-GSCs along a trajectory of intermediate states, exposing vulnerability to potentiated killing by siRNA or a second drug targeting treatment-induced transcriptional programs governing nongenetic cell plasticity. Our findings demonstrate an approach to uncover TRN topology and use it to rationally predict combinatorial treatments that disrupt acquired resistance in GBM.
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Affiliation(s)
| | - Parvinder Hothi
- Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | | | - Min Pan
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | - Wei-Ju Wu
- Institute for Systems Biology, Seattle, WA, USA
| | - Hwahyung Lee
- Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | - Anoop P. Patel
- Department of Neurosurgery, Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Charles Cobbs
- Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | - Sui Huang
- Institute for Systems Biology, Seattle, WA, USA
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, WA, USA
- Departments of Microbiology, Biology, and Molecular Engineering Sciences, University of Washington, Seattle, WA, USA
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Divya D, Robin AHK, Cho LH, Kim D, Lee DJ, Kim CK, Chung MY. Genome-wide characterization and expression profiling of E2F/DP gene family members in response to abiotic stress in tomato (Solanum lycopersicum L.). BMC PLANT BIOLOGY 2024; 24:436. [PMID: 38773361 PMCID: PMC11110339 DOI: 10.1186/s12870-024-05107-3] [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: 06/19/2023] [Accepted: 05/05/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND E2F/DP (Eukaryotic 2 transcription factor/dimerization partner) family proteins play an essential function in the cell cycle development of higher organisms. E2F/DP family genes have been reported only in a few plant species. However, comprehensive genome-wide characterization analysis of the E2F/DP gene family of Solanum lycopersicum has not been reported so far. RESULTS This study identified eight nonredundant SlE2F/DP genes that were classified into seven groups in the phylogenetic analysis. All eight genes had a single E2F-TDP domain and few genes had additional domains. Two segmental duplication gene pairs were observed within tomato, in addition to cis-regulatory elements, miRNA target sites and phosphorylation sites which play an important role in plant development and stress response in tomato. To explore the three-dimensional (3D) models and gene ontology (GO) annotations of SlE2F/DP proteins, we pointed to their putative transporter activity and their interaction with several putative ligands. The localization of SlE2F/DP-GFP fused proteins in the nucleus and endoplasmic reticulum suggested that they may act in other biological functions. Expression studies revealed the differential expression pattern of most of the SlE2F/DP genes in various organs. Moreover, the expression of E2F/DP genes against abiotic stress, particularly SlE2F/DP2 and/or SlE2F/DP7, was upregulated in response to heat, salt, cold and ABA treatment. Furthermore, the co-expression analysis of SlE2F/DP genes with multiple metabolic pathways was co-expressed with defence genes, transcription factors and so on, suggested their crucial role in various biological processes. CONCLUSIONS Overall, our findings provide a way to understand the structure and function of SlE2F/DP genes; it might be helpful to improve fruit development and tolerance against abiotic stress through marker-assisted selection or transgenic approaches.
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Affiliation(s)
- Dhanasekar Divya
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea
| | - Arif Hasan Khan Robin
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang-si, Gyeongsangnam-do, 50463, Republic of Korea
| | - Dohyeon Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang-si, Gyeongsangnam-do, 50463, Republic of Korea
| | - Do-Jin Lee
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea
| | - Chang-Kil Kim
- Department of Horticulture, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea.
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Thottakara T, Padmanabhan A, Tanriverdi T, Thambidurai T, Diaz-Rg JA, Amonkar SR, Olgin JE, Long CS, Abraham MR. Single-nucleus RNA/ATAC-seq in early-stage HCM models predicts SWI/SNF-activation in mutant-myocytes, and allele-specific differences in fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.589078. [PMID: 38903075 PMCID: PMC11188105 DOI: 10.1101/2024.04.24.589078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Hypertrophic cardiomyopathy (HCM) is associated with phenotypic variability. To gain insights into transcriptional regulation of cardiac phenotype, single-nucleus linked RNA-/ATAC-seq was performed in 5-week-old control mouse-hearts (WT) and two HCM-models (R92W-TnT, R403Q-MyHC) that exhibit differences in heart size/function and fibrosis; mutant data was compared to WT. Analysis of 23,304 nuclei from mutant hearts, and 17,669 nuclei from WT, revealed similar dysregulation of gene expression, activation of AP-1 TFs (FOS, JUN) and the SWI/SNF complex in both mutant ventricular-myocytes. In contrast, marked differences were observed between mutants, for gene expression/TF enrichment, in fibroblasts, macrophages, endothelial cells. Cellchat predicted activation of pro-hypertrophic IGF-signaling in both mutant ventricular-myocytes, and profibrotic TGFβ-signaling only in mutant-TnT fibroblasts. In summary, our bioinformatics analyses suggest that activation of IGF-signaling, AP-1 TFs and the SWI/SNF chromatin remodeler complex promotes myocyte hypertrophy in early-stage HCM. Selective activation of TGFβ-signaling in mutant-TnT fibroblasts contributes to genotype-specific differences in cardiac fibrosis.
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Ito T, Saito A, Kamikawa Y, Nakazawa N, Imaizumi K. AIbZIP/CREB3L4 Promotes Cell Proliferation via the SKP2-p27 Axis in Luminal Androgen Receptor Subtype Triple-Negative Breast Cancer. Mol Cancer Res 2024; 22:373-385. [PMID: 38236913 PMCID: PMC10985479 DOI: 10.1158/1541-7786.mcr-23-0629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/05/2023] [Accepted: 01/16/2024] [Indexed: 04/04/2024]
Abstract
Breast cancer ranks first in incidence and fifth in cancer-related deaths among all types of cancer globally. Among breast cancer, triple-negative breast cancer (TNBC) has few known therapeutic targets and a poor prognosis. Therefore, new therapeutic targets and strategies against TNBC are required. We found that androgen-induced basic leucine zipper (AIbZIP), also known as cyclic AMP-responsive element-binding protein 3-like protein 4 (CREB3L4), which is encoded by Creb3l4, is highly upregulated in a particular subtype of TNBC, luminal androgen receptor (LAR) subtype. We analyzed the function of AIbZIP through depletion of AIbZIP by siRNA knockdown in LAR subtype TNBC cell lines, MFM223 and MDAMB453. In AIbZIP-depleted cells, the proliferation ratios of cells were greatly suppressed. Moreover, G1-S transition was inhibited in AIbZIP-depleted cells. We comprehensively analyzed the expression levels of proteins that regulate G1-S transition and found that p27 was specifically upregulated in AIbZIP-depleted cells. Furthermore, we identified that this p27 downregulation was caused by protein degradation modulated by the ubiquitin-proteasome system via F-box protein S-phase kinase-associated protein 2 (SKP2) upregulation. Our findings demonstrate that AIbZIP is a novel p27-SKP2 pathway-regulating factor and a potential molecule that contributes to LAR subtype TNBC progression. IMPLICATIONS This research shows a new mechanism for the proliferation of LAR subtype TNBC regulated by AIbZIP, that may provide novel insight into the LAR subtype TNBC progression and the molecular mechanisms involved in cell proliferation.
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Affiliation(s)
- Taichi Ito
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Atsushi Saito
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasunao Kamikawa
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Nayuta Nakazawa
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazunori Imaizumi
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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Xu J, Hörner M, Nagel M, Korneck M, Noß M, Hauser S, Schöls L, Admard J, Casadei N, Schüle R. Unraveling Axonal Transcriptional Landscapes: Insights from iPSC-Derived Cortical Neurons and Implications for Motor Neuron Degeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586780. [PMID: 38585749 PMCID: PMC10996649 DOI: 10.1101/2024.03.26.586780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Neuronal function and pathology are deeply influenced by the distinct molecular profiles of the axon and soma. Traditional studies have often overlooked these differences due to the technical challenges of compartment specific analysis. In this study, we employ a robust RNA-sequencing (RNA-seq) approach, using microfluidic devices, to generate high-quality axonal transcriptomes from iPSC-derived cortical neurons (CNs). We achieve high specificity of axonal fractions, ensuring sample purity without contamination. Comparative analysis revealed a unique and specific transcriptional landscape in axonal compartments, characterized by diverse transcript types, including protein-coding mRNAs, ribosomal proteins (RPs), mitochondrial-encoded RNAs, and long non-coding RNAs (lncRNAs). Previous works have reported the existence of transcription factors (TFs) in the axon. Here, we detect a subset of previously unreported TFs specific to the axon and indicative of their active participation in transcriptional regulation. To investigate transcripts and pathways essential for central motor neuron (MN) degeneration and maintenance we analyzed KIF1C-knockout (KO) CNs, modeling hereditary spastic paraplegia (HSP), a disorder associated with prominent length-dependent degeneration of central MN axons. We found that several key factors crucial for survival and health were absent in KIF1C-KO axons, highlighting a possible role of these also in other neurodegenerative diseases. Taken together, this study underscores the utility of microfluidic devices in studying compartment-specific transcriptomics in human neuronal models and reveals complex molecular dynamics of axonal biology. The impact of KIF1C on the axonal transcriptome not only deepens our understanding of MN diseases but also presents a promising avenue for exploration of compartment specific disease mechanisms.
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Batel A, Polović M, Glumac M, Šuman O, Jadrijević S, Lozić B, Petrović M, Samardžija B, Bradshaw NJ, Skube K, Palada V, Acman M, Marinović Terzić I. SPRTN is involved in hepatocellular carcinoma development through the ER stress response. Cancer Gene Ther 2024; 31:376-386. [PMID: 38086993 DOI: 10.1038/s41417-023-00708-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 03/16/2024]
Abstract
Endoplasmic reticulum (ER) stress, prompted by the accumulation of misfolded or unfolded proteins, triggers the activation of the unfolded protein response (UPR) pathway to restore ER homeostasis. This stress response is implicated in the development of hepatocellular carcinoma (HCC). A biallelic mutation in SPRTN is currently the only known single-gene mutation implicated in the early onset of HCC. However, the exact mechanism linking SPRTN mutations to HCC remains unclear. In our study, we analyzed SPRTN and UPR in 21 human HCC tissue samples using RT-qPCR, immunoblot, and immunohistochemistry. We found alterations in the expression levels of SPRTN and UPR-related genes and proteins in HCC samples. The impact of SPRTN on the ER stress response was assessed in SPRTN-depleted HepG2 cells through RNA sequencing, pull-down assay, comet assay, and mitotic index calculation. We demonstrated that SPRTN interacts with the UPR sensor GRP78. Furthermore, we observed a decrease in SPRTN levels during ER stress, and increased sensitivity to ER stress in SPRTN-depleted cells. These findings suggest an essential role for SPRTN in the ER stress response and provide new insights into HCC pathogenesis. This newly discovered function of SPRTN could significantly enhance our understanding and treatment of HCC.
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Affiliation(s)
- Anja Batel
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
| | - Mirjana Polović
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
| | - Mateo Glumac
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
| | - Oliver Šuman
- Department of Abdominal Surgery, Merkur Clinical Hospital, Zajčeva 19, 10000, Zagreb, Croatia
| | - Stipislav Jadrijević
- Department of Abdominal Surgery, Merkur Clinical Hospital, Zajčeva 19, 10000, Zagreb, Croatia
| | - Bernarda Lozić
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
- Laboratory for Human Genetics, University Hospital Split, Spinčićeva 1, 21000, Split, Croatia
| | - Marija Petrović
- Laboratory for Human Genetics, University Hospital Split, Spinčićeva 1, 21000, Split, Croatia
| | - Bobana Samardžija
- Faculty of Biotechnology & Drug Development, University of Rijeka, Radmile Matejčić 2, 51000, Rijeka, Croatia
| | - Nicholas J Bradshaw
- Faculty of Biotechnology & Drug Development, University of Rijeka, Radmile Matejčić 2, 51000, Rijeka, Croatia
| | - Karlo Skube
- Selvita, Prilaz baruna Filipovića 29, 10000, Zagreb, Croatia
| | - Vinko Palada
- Department of Physiology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
| | - Mislav Acman
- Omics solutions, trg 101. Brigade HV 1, 10000, Zagreb, Croatia
| | - Ivana Marinović Terzić
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia.
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Zhang A, He X, Zhang C, Tang X. Molecular subtype identification and prognosis stratification based on golgi apparatus-related genes in head and neck squamous cell carcinoma. BMC Med Genomics 2024; 17:53. [PMID: 38365684 PMCID: PMC10870608 DOI: 10.1186/s12920-024-01823-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Abnormal dynamics of the Golgi apparatus reshape the tumor microenvironment and immune landscape, playing a crucial role in the prognosis and treatment response of cancer. This study aims to investigate the potential role of Golgi apparatus-related genes (GARGs) in the heterogeneity and prognosis of head and neck squamous cell carcinoma (HNSCC). METHODS Transcriptional data and corresponding clinical information of HNSCC were obtained from public databases for differential expression analysis, consensus clustering, survival analysis, immune infiltration analysis, immune therapy response assessment, gene set enrichment analysis, and drug sensitivity analysis. Multiple machine learning algorithms were employed to construct a prognostic model based on GARGs. A nomogram was used to integrate and visualize the multi-gene model with clinical pathological features. RESULTS A total of 321 GARGs that were differentially expressed were identified, out of which 69 were associated with the prognosis of HNSCC. Based on these prognostic genes, two molecular subtypes of HNSCC were identified, which showed significant differences in prognosis. Additionally, a risk signature consisting of 28 GARGs was constructed and demonstrated good performance for assessing the prognosis of HNSCC. This signature divided HNSCC into the high-risk and low-risk groups with significant differences in multiple clinicopathological characteristics, including survival outcome, grade, T stage, chemotherapy. Immune response-related pathways were significantly activated in the high-risk group with better prognosis. There were significant differences in chemotherapy drug sensitivity and immune therapy response between the high-risk and low-risk groups, with the low-risk group being more suitable for receiving immunotherapy. Riskscore, age, grade, and radiotherapy were independent prognostic factors for HNSCC and were used to construct a nomogram, which had good clinical applicability. CONCLUSIONS We successfully identified molecular subtypes and prognostic signature of HNSCC that are derived from GARGs, which can be used for the assessment of HNSCC prognosis and treatment responses.
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Affiliation(s)
- Aichun Zhang
- Department of Otolaryngology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), 310006, Hangzhou, Zhejiang Province, P. R. China
| | - Xiao He
- Department of Otolaryngology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), 310006, Hangzhou, Zhejiang Province, P. R. China
| | - Chen Zhang
- Department of Otolaryngology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), 310006, Hangzhou, Zhejiang Province, P. R. China
| | - Xuxia Tang
- Department of Otolaryngology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), 310006, Hangzhou, Zhejiang Province, P. R. China.
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Jiang Z, Shi B, Zhang Y, Yu T, Cheng Y, Zhu J, Zhang G, Zhong M, Hu S, Ma X. CREB3L4 promotes hepatocellular carcinoma progression and decreases sorafenib chemosensitivity by promoting RHEB-mTORC1 signaling pathway. iScience 2024; 27:108843. [PMID: 38303702 PMCID: PMC10831937 DOI: 10.1016/j.isci.2024.108843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 11/09/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024] Open
Abstract
This study was designed to explore the roles of CREB3L4 in the pathogenesis and drug resistance of hepatocellular carcinoma (HCC). The proliferation of HCC lines was determined in the presence of CREB3L4 over-expression and silencing. Chromatin immunoprecipitation (ChIP) assay and dual-luciferase reporter assay were performed to screen the potential target of CREB3L4 on mTORC1. Xenografted tumor model was established to define the regulatory effects of CREB3L4 in the tumorigenesis. Then we evaluated the roles of CREB3L4 in chemosensitivity to sorafenib treatment. CREB3L4 significantly induced the HCC cell proliferation by modulating the activation of mTROC1-S6K1 signaling pathway via binding with RHEB promoter. Moreover, CREB3L4 dramatically inhibited the chemosensitivity to sorafenib treatment via up-regulating RHEB-mTORC1 signaling. CREB3L4 promoted HCC progression and decreased its chemosensitivity to sorafenib through up-regulating RHEB-mTORC1 signaling pathway, indicating a potential treatment strategy for HCC through targeting CREB3L4.
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Affiliation(s)
- Zhengchen Jiang
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China
- Department of Gastric Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou 310022, China
| | - Bowen Shi
- Department of General Surgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250014, China
| | - Yun Zhang
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China
| | - Tianming Yu
- Department of General Surgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250014, China
| | - Yang Cheng
- Department of General Surgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250014, China
| | - Jiankang Zhu
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China
| | - Guangyong Zhang
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China
| | - Mingwei Zhong
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China
| | - Sanyuan Hu
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China
| | - Xiaomin Ma
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China
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Girolamo DD, Benavente-Diaz M, Murolo M, Grimaldi A, Lopes PT, Evano B, Kuriki M, Gioftsidi S, Laville V, Tinevez JY, Letort G, Mella S, Tajbakhsh S, Comai G. Extraocular muscle stem cells exhibit distinct cellular properties associated with non-muscle molecular signatures. Development 2024; 151:dev202144. [PMID: 38240380 DOI: 10.1242/dev.202144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/27/2023] [Indexed: 02/22/2024]
Abstract
Skeletal muscle stem cells (MuSCs) are recognised as functionally heterogeneous. Cranial MuSCs are reported to have greater proliferative and regenerative capacity when compared with those in the limb. A comprehensive understanding of the mechanisms underlying this functional heterogeneity is lacking. Here, we have used clonal analysis, live imaging and single cell transcriptomic analysis to identify crucial features that distinguish extraocular muscle (EOM) from limb muscle stem cell populations. A MyogeninntdTom reporter showed that the increased proliferation capacity of EOM MuSCs correlates with deferred differentiation and lower expression of the myogenic commitment gene Myod. Unexpectedly, EOM MuSCs activated in vitro expressed a large array of extracellular matrix components typical of mesenchymal non-muscle cells. Computational analysis underscored a distinct co-regulatory module, which is absent in limb MuSCs, as driver of these features. The EOM transcription factor network, with Foxc1 as key player, appears to be hardwired to EOM identity as it persists during growth, disease and in vitro after several passages. Our findings shed light on how high-performing MuSCs regulate myogenic commitment by remodelling their local environment and adopting properties not generally associated with myogenic cells.
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Affiliation(s)
- Daniela Di Girolamo
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Maria Benavente-Diaz
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Sorbonne Universités, Complexité du Vivant, F-75005 Paris, France
| | - Melania Murolo
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Alexandre Grimaldi
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Sorbonne Universités, Complexité du Vivant, F-75005 Paris, France
| | - Priscilla Thomas Lopes
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Brendan Evano
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Mao Kuriki
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Stamatia Gioftsidi
- Université Paris-Est, 77420 Champs-sur- Marne, France
- Freie Universität Berlin, 14195 Berlin, Germany
- Inserm, IMRB U955-E10, 94000 Créteil, France
| | - Vincent Laville
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, 75015 Paris, France
| | - Gaëlle Letort
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 rue du Dr Roux, 75015 Paris, France
| | - Sebastian Mella
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Shahragim Tajbakhsh
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Glenda Comai
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
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11
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Zeylan M, Senyuz S, Picón-Pagès P, García-Elías A, Tajes M, Muñoz FJ, Oliva B, Garcia-Ojalvo J, Barbu E, Vicente R, Nattel S, Ois A, Puig-Pijoan A, Keskin O, Gursoy A. Shared Proteins and Pathways of Cardiovascular and Cognitive Diseases: Relation to Vascular Cognitive Impairment. J Proteome Res 2024; 23:560-573. [PMID: 38252700 PMCID: PMC10846560 DOI: 10.1021/acs.jproteome.3c00289] [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: 05/12/2023] [Revised: 09/29/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024]
Abstract
One of the primary goals of systems medicine is the detection of putative proteins and pathways involved in disease progression and pathological phenotypes. Vascular cognitive impairment (VCI) is a heterogeneous condition manifesting as cognitive impairment resulting from vascular factors. The precise mechanisms underlying this relationship remain unclear, which poses challenges for experimental research. Here, we applied computational approaches like systems biology to unveil and select relevant proteins and pathways related to VCI by studying the crosstalk between cardiovascular and cognitive diseases. In addition, we specifically included signals related to oxidative stress, a common etiologic factor tightly linked to aging, a major determinant of VCI. Our results show that pathways associated with oxidative stress are quite relevant, as most of the prioritized vascular cognitive genes and proteins were enriched in these pathways. Our analysis provided a short list of proteins that could be contributing to VCI: DOLK, TSC1, ATP1A1, MAPK14, YWHAZ, CREB3, HSPB1, PRDX6, and LMNA. Moreover, our experimental results suggest a high implication of glycative stress, generating oxidative processes and post-translational protein modifications through advanced glycation end-products (AGEs). We propose that these products interact with their specific receptors (RAGE) and Notch signaling to contribute to the etiology of VCI.
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Affiliation(s)
- Melisa
E. Zeylan
- Computational
Sciences and Engineering, Graduate School of Science and Engineering, Koç University, Istanbul 34450, Türkiye
| | - Simge Senyuz
- Computational
Sciences and Engineering, Graduate School of Science and Engineering, Koç University, Istanbul 34450, Türkiye
| | - Pol Picón-Pagès
- Laboratory
of Molecular Physiology, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08002, Spain
| | - Anna García-Elías
- Laboratory
of Molecular Physiology, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08002, Spain
| | - Marta Tajes
- Laboratory
of Molecular Physiology, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08002, Spain
| | - Francisco J. Muñoz
- Laboratory
of Molecular Physiology, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08002, Spain
| | - Baldomero Oliva
- Laboratory
of Structural Bioinformatics (GRIB), Department of Medicine and Life
Sciences, Universitat Pompeu Fabra, Barcelona 08002, Spain
| | - Jordi Garcia-Ojalvo
- Laboratory
of Dynamical Systems Biology, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08002, Spain
| | - Eduard Barbu
- Institute
of Computer Science, University of Tartu, Tartu, 50090, Estonia
| | - Raul Vicente
- Institute
of Computer Science, University of Tartu, Tartu, 50090, Estonia
| | - Stanley Nattel
- Department
of Medicine and Research Center, Montreal Heart Institute and Université
de Montréal; Institute of Pharmacology, West German Heart and
Vascular Center, University Duisburg-Essen,
Germany; IHU LIRYC and Fondation Bordeaux Université, Bordeaux 33000, France
| | - Angel Ois
- Department
of Neurology, Hospital Del Mar. Hospital
Del Mar - Medical Research Institute and Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Albert Puig-Pijoan
- Department
of Neurology, Hospital Del Mar. Hospital
Del Mar - Medical Research Institute and Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Ozlem Keskin
- Department
of Chemical and Biological Engineering, Koç University, Istanbul 34450, Türkiye
| | - Attila Gursoy
- Department
of Computer Engineering, Koç University, Istanbul 34450, Türkiye
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12
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He J, Zhou Y, Sun L. Emerging mechanisms of the unfolded protein response in therapeutic resistance: from chemotherapy to Immunotherapy. Cell Commun Signal 2024; 22:89. [PMID: 38297380 PMCID: PMC10832166 DOI: 10.1186/s12964-023-01438-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/12/2023] [Indexed: 02/02/2024] Open
Abstract
The accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) causes ER stress and activates the unfolded protein response (UPR). As an adaptive cellular response to hostile microenvironments, such as hypoxia, nutrient deprivation, oxidative stress, and chemotherapeutic drugs, the UPR is activated in diverse cancer types and functions as a dynamic tumour promoter in cancer development; this role of the UPR indicates that regulation of the UPR can be utilized as a target for tumour treatment. T-cell exhaustion mainly refers to effector T cells losing their effector functions and expressing inhibitory receptors, leading to tumour immune evasion and the loss of tumour control. Emerging evidence suggests that the UPR plays a crucial role in T-cell exhaustion, immune evasion, and resistance to immunotherapy. In this review, we summarize the molecular basis of UPR activation, the effect of the UPR on immune evasion, the emerging mechanisms of the UPR in chemotherapy and immunotherapy resistance, and agents that target the UPR for tumour therapeutics. An understanding of the role of the UPR in immune evasion and therapeutic resistance will be helpful to identify new therapeutic modalities for cancer treatment. Video Abstract.
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Affiliation(s)
- Jiang He
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, 410008, Huan, China.
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Changsha, 410008, China.
- Center for Molecular Imaging of Central, South University, Xiangya Hospital, Changsha, 410008, China.
| | - You Zhou
- Department of Pathology, Tongji Medical College Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Lunquan Sun
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, 410008, Huan, China.
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Changsha, 410008, China.
- Center for Molecular Imaging of Central, South University, Xiangya Hospital, Changsha, 410008, China.
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13
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Zhao Y, Yu Z, Song Y, Fan L, Lei T, He Y, Hu S. The Regulatory Network of CREB3L1 and Its Roles in Physiological and Pathological Conditions. Int J Med Sci 2024; 21:123-136. [PMID: 38164349 PMCID: PMC10750332 DOI: 10.7150/ijms.90189] [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] [Received: 09/15/2023] [Accepted: 10/26/2023] [Indexed: 01/03/2024] Open
Abstract
CREB3 subfamily belongs to the bZIP transcription factor family and comprises five members. Normally they are located on the endoplasmic reticulum (ER) membranes and proteolytically activated through RIP (regulated intramembrane proteolysis) on Golgi apparatus to liberate the N-terminus to serve as transcription factors. CREB3L1 acting as one of them transcriptionally regulates the expressions of target genes and exhibits distinct functions from the other members of CREB3 family in eukaryotes. Physiologically, CREB3L1 involves in the regulation of bone morphogenesis, neurogenesis, neuroendocrine, secretory cell differentiation, and angiogenesis. Pathologically, CREB3L1 implicates in the modulation of osteogenesis imperfecta, low grade fibro myxoid sarcoma (LGFMS), sclerosing epithelioid fibrosarcoma (SEF), glioma, breast cancer, thyroid cancer, and tissue fibrosis. This review summarizes the upstream and downstream regulatory network of CREB3L1 and thoroughly presents our current understanding of CREB3L1 research progress in both physiological and pathological conditions with special focus on the novel findings of CREB3L1 in cancers.
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Affiliation(s)
- Ying Zhao
- Department of Anesthesiology and Perioperative Medicine, Xi'an People's Hospital (Xi'an Fourth Hospital), Northwest University, Xi'an, Shaanxi Province, China
| | - Zhou Yu
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Yajuan Song
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Liumeizi Fan
- Department of Anesthesiology and Perioperative Medicine, Xi'an People's Hospital (Xi'an Fourth Hospital), Northwest University, Xi'an, Shaanxi Province, China
| | - Ting Lei
- Department of Anesthesiology and Perioperative Medicine, Xi'an People's Hospital (Xi'an Fourth Hospital), Northwest University, Xi'an, Shaanxi Province, China
| | - Yinbin He
- Department of Anesthesiology and Perioperative Medicine, Xi'an People's Hospital (Xi'an Fourth Hospital), Northwest University, Xi'an, Shaanxi Province, China
| | - Sheng Hu
- Department of Anesthesiology and Perioperative Medicine, Xi'an People's Hospital (Xi'an Fourth Hospital), Northwest University, Xi'an, Shaanxi Province, China
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14
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Zhan S, Qiu M, Wei X, Wei J, Qin L, Jiang B, Wen Q, Chen P, Lin Q, Wei X, Zhou Z, Jiang Y, Liang X, Li R, Liu Y, Yu H. Potentially functional genetic variants in ferroptosis-related CREB3 and GALNT14 genes predict survival of hepatitis B virus-related hepatocellular carcinoma. Cancer Med 2023; 13:e6848. [PMID: 38151984 PMCID: PMC10807646 DOI: 10.1002/cam4.6848] [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: 09/09/2023] [Revised: 11/19/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND Ferroptosis is a known crucial player in the development of cancers. However, the effect of single nucleotide polymorphisms (SNPs) in ferroptosis-related genes on survival in hepatitis B virus (HBV)-related hepatocellular carcinoma (HBV-HCC) patients remains unknown. METHODS We used two-stage multivariable Cox proportional hazards regression analyses to estimate the associations between 48,774 SNPs in 480 ferroptosis-related genes and overall survival (OS) of 866 HBV-HCC patients. RESULTS We identified that two potentially functional SNPs (CREB3 rs10814274 C > T and GALNT14 rs17010547 T > C) were significantly independently associated with the OS of HBV-HCC patients (CT + TT verse CC, hazards ratio (HR) = 0.77, 95% confidence interval (CI) = 0.67-0.89, p < 0.001 for rs10814274 and TC + CC verse TT, HR = 0.66, 95% CI = 0.53-0.82, p < 0.001 for rs17010547, respectively). Additional joint assessment of protective genotypes of these two SNPs showed that patients with 1-2 protective genotypes had a significantly better OS compared with those carrying 0 protective genotypes (HR = 0.56, 95% CI = 0.45-0.70, p < 0.001). Moreover, the expression quantitative trait loci (eQTL) analysis revealed that the survival-associated SNP rs10814274 T allele was significantly correlated with reduced CREB3 transcript levels in both normal liver tissues and whole blood cells, while the GALNT14 rs17010547 C allele had a significant correlation with increased GALNT14 transcript levels in whole blood cells. CONCLUSION These results suggest that genetic variants of CREB3 and GALNT14 may affect the survival of HBV-HCC patients, likely via transcriptional regulation of respective genes. However, further studies are required to confirm these findings.
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Affiliation(s)
- Shicheng Zhan
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
- Department of Epidemiology and Health Statistics, School of Public HealthGuangxi Medical UniversityNanningChina
| | - Moqin Qiu
- Department of Respiratory OncologyGuangxi Medical University Cancer HospitalNanningChina
| | - Xueyan Wei
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
- Department of Epidemiology and Health Statistics, School of Public HealthGuangxi Medical UniversityNanningChina
| | - Junjie Wei
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
- Department of Epidemiology and Health Statistics, School of Public HealthGuangxi Medical UniversityNanningChina
| | - Liming Qin
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
- Department of Epidemiology and Health Statistics, School of Public HealthGuangxi Medical UniversityNanningChina
| | - Binbin Jiang
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Qiuping Wen
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Peiqin Chen
- Editorial Department of Chinese Journal of Oncology Prevention and TreatmentGuangxi Medical University Cancer HospitalNanningChina
| | - Qiuling Lin
- Department of Clinical ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Xiaoxia Wei
- Department of Clinical ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Zihan Zhou
- Department of Cancer Prevention and ControlGuangxi Medical University Cancer HospitalNanningChina
| | - Yanji Jiang
- Scientific Research DepartmentGuangxi Medical University Cancer HospitalNanningChina
| | - Xiumei Liang
- Department of Disease Process ManagementGuangxi Medical University Cancer HospitalNanningChina
| | - Runwei Li
- Department of Civil Engineering, College of EngineeringNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Yingchun Liu
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
- Key Cultivated Laboratory of Cancer Molecular Medicine of Guangxi Health CommissionGuangxi Medical University Cancer HospitalNanningChina
| | - Hongping Yu
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
- Key Cultivated Laboratory of Cancer Molecular Medicine of Guangxi Health CommissionGuangxi Medical University Cancer HospitalNanningChina
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University)Ministry of EducationNanningChina
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15
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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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16
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Lee GE, Byun J, Lee CJ, Cho YY. Molecular Mechanisms for the Regulation of Nuclear Membrane Integrity. Int J Mol Sci 2023; 24:15497. [PMID: 37895175 PMCID: PMC10607757 DOI: 10.3390/ijms242015497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023] Open
Abstract
The nuclear membrane serves a critical role in protecting the contents of the nucleus and facilitating material and signal exchange between the nucleus and cytoplasm. While extensive research has been dedicated to topics such as nuclear membrane assembly and disassembly during cell division, as well as interactions between nuclear transmembrane proteins and both nucleoskeletal and cytoskeletal components, there has been comparatively less emphasis on exploring the regulation of nuclear morphology through nuclear membrane integrity. In particular, the role of type II integral proteins, which also function as transcription factors, within the nuclear membrane remains an area of research that is yet to be fully explored. The integrity of the nuclear membrane is pivotal not only during cell division but also in the regulation of gene expression and the communication between the nucleus and cytoplasm. Importantly, it plays a significant role in the development of various diseases. This review paper seeks to illuminate the biomolecules responsible for maintaining the integrity of the nuclear membrane. It will delve into the mechanisms that influence nuclear membrane integrity and provide insights into the role of type II membrane protein transcription factors in this context. Understanding these aspects is of utmost importance, as it can offer valuable insights into the intricate processes governing nuclear membrane integrity. Such insights have broad-reaching implications for cellular function and our understanding of disease pathogenesis.
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Affiliation(s)
- Ga-Eun Lee
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
| | - Jiin Byun
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
| | - Cheol-Jung Lee
- Research Center for Materials Analysis, Korea Basic Science Institute, 169-148, Gwahak-ro, Yuseong-gu, Daejeon 34133, Chungcheongnam-do, Republic of Korea
| | - Yong-Yeon Cho
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
- RCD Control and Material Research Institute, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea
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17
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Li Y, Zhang J, Cai W, Wang C, Yu Z, Jiang Z, Lai K, Wang Y, Yang G. CREB3L2 Regulates Hemidesmosome Formation during Epithelial Sealing. J Dent Res 2023; 102:1199-1209. [PMID: 37555472 DOI: 10.1177/00220345231176520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023] Open
Abstract
The long-term success rate of dental implants can be improved by establishing a favorable biological sealing with a high-quality epithelial attachment. The application of mesenchymal stem cells (MSCs) holds promise for facilitating the soft tissue integration around implants, but the molecular mechanism is still unclear and the general application of MSC sheet for soft tissue integration is also relatively unexplored. We found that gingival tissue-derived MSC (GMSC) sheet treatment significantly promoted the expression of hemidesmosome (HD)-related genes and proteins in gingival epithelial cells (GECs). The formation of HDs played a key role in strengthening peri-implant epithelium (PIE) sealing. Further, high-throughput transcriptome sequencing showed that GMSC sheet significantly upregulated the PI3K/AKT pathway, confirming that cell adhesion and HD expression in GECs were regulated by GMSC sheet. We observed that the expression of transcription factor CREB3L2 in GECs was downregulated. After treatment with PI3K pathway inhibitor LY294002, CREB3L2 messenger RNA and protein expression levels were upregulated. Further experiments showed that overexpression or knockdown of CREB3L2 could significantly inhibit or promote HD-related genes and proteins, respectively. We confirmed that CREB3L2 was a transcription factor downstream of the PI3K/AKT pathway and participated in the formation of HDs regulated by GMSC sheet. Finally, through the establishment of early implant placement model in rats, we clarified the molecular function of CREB3L2 in PIE sealing as a mechanical transmission molecule in GECs. The application of GMSC sheet-implant complex could enhance the formation of HDs at the implant-PIE interface and decrease the penetration distance of horseradish peroxidase between the implant and PIE. Meanwhile, GMSC sheet reduced the length of CREB3L2 protein expression on PIE. These findings elucidate the potential function and molecular mechanism of MSC sheet regulating the epithelial sealing around implants, providing new insights and ideas for the application of stem cell therapy in regenerative medicine.
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Affiliation(s)
- Y Li
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - J Zhang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - W Cai
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - C Wang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Z Yu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Z Jiang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - K Lai
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Y Wang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - G Yang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
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18
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Yuxiong W, Faping L, Bin L, Yanghe Z, Yao L, Yunkuo L, Yishu W, Honglan Z. Regulatory mechanisms of the cAMP-responsive element binding protein 3 (CREB3) family in cancers. Biomed Pharmacother 2023; 166:115335. [PMID: 37595431 DOI: 10.1016/j.biopha.2023.115335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023] Open
Abstract
The CREB3 family of proteins, encompassing CREB3 and its four homologs (CREB3L1, CREB3L2, CREB3L3, and CREB3L4), exerts pivotal control over cellular protein metabolism in response to unfolded protein reactions. Under conditions of endoplasmic reticulum stress, activation of the CREB3 family occurs through regulated intramembrane proteolysis within the endoplasmic reticulum membrane. Perturbations in the function and expression of the CREB3 family have been closely associated with the development of diverse diseases, with a particular emphasis on cancer. Recent investigations have shed light on the indispensable role played by CREB3 family members in modulating the onset and progression of various human cancers. This comprehensive review endeavors to provide an in-depth examination of the involvement of CREB3 family members in distinct human cancer types, accentuating their significance in the pathogenesis of cancer and the manifestation of malignant phenotypes.
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Affiliation(s)
- Wang Yuxiong
- Department of Urology II, The First Hospital of Jilin University, Changchun 130011, China
| | - Li Faping
- Department of Urology II, The First Hospital of Jilin University, Changchun 130011, China
| | - Liu Bin
- Department of Urology II, The First Hospital of Jilin University, Changchun 130011, China
| | - Zhang Yanghe
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130011, China
| | - Li Yao
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130011, China
| | - Li Yunkuo
- Department of Urology II, The First Hospital of Jilin University, Changchun 130011, China
| | - Wang Yishu
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130011, China.
| | - Zhou Honglan
- Department of Urology II, The First Hospital of Jilin University, Changchun 130011, China,.
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19
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Seetharam SM, Liu Y, Wu J, Fechter L, Murugesan K, Maecker H, Gotlib J, Zehnder J, Paulmurugan R, Krishnan A. Enkurin: a novel marker for myeloproliferative neoplasms from platelet, megakaryocyte, and whole blood specimens. Blood Adv 2023; 7:5433-5445. [PMID: 37315179 PMCID: PMC10509670 DOI: 10.1182/bloodadvances.2022008939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/10/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023] Open
Abstract
Impaired protein homeostasis, though well established in age-related disorders, has been recently linked with the pathogenesis of myeloproliferative neoplasms (MPNs). However, little is known about MPN-specific modulators of proteostasis, thus impeding our ability for increased mechanistic understanding and discovery of additional therapeutic targets. Loss of proteostasis, in itself, is traced to dysregulated mechanisms in protein folding and intracellular calcium signaling at the endoplasmic reticulum (ER). Here, using ex vivo and in vitro systems (including CD34+ cultures from patient bone marrow and healthy cord/peripheral blood specimens), we extend our prior data from platelet RNA sequencing in patients with MPN and discover select proteostasis-associated markers at RNA and/or protein levels in each of platelet, parent megakaryocyte, and whole blood specimens. Importantly, we identify a novel role in MPNs for enkurin (ENKUR), a calcium mediator protein originally implicated only in spermatogenesis. Our data reveal consistent ENKUR downregulation at both RNA and protein levels across specimens from patients with MPN and experimental models (including upon treatment with thapsigargin, an agent that causes protein misfolding in the ER by selective loss of calcium), with a concomitant upregulation of a cell cycle marker, CDC20. Silencing of ENKUR using short hairpin RNA in CD34+-derived megakaryocytes further confirms this association with CDC20 at both RNA and protein levels and indicates a likely role for the PI3K/Akt pathway. Together, our work sheds light on enkurin as a novel marker of MPN pathogenesis and indicates further mechanistic investigation into a role for dysregulated calcium homeostasis and ER and protein folding stress in MPN transformation.
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Affiliation(s)
| | - Yi Liu
- Department of Radiology, Stanford University, Stanford, CA
| | - Jason Wu
- High-Throughput Bioscience Center and Stanford Genomics, Stanford University School of Medicine, Stanford, CA
| | - Lenn Fechter
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | | | - Holden Maecker
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA
| | - Jason Gotlib
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - James Zehnder
- Department of Pathology, Stanford University, Stanford, CA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | | | - Anandi Krishnan
- Department of Pathology, Stanford University, Stanford, CA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
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20
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Sołek P, Czechowska E, Sowa-Kućma M, Stachowicz K, Kaczka P, Tabęcka-Łonczyńska A. Elucidating the molecular mechanisms underlying the induction of autophagy by antidepressant-like substances in C57BL/6J mouse testis model upon LPS challenge. Cell Commun Signal 2023; 21:251. [PMID: 37735683 PMCID: PMC10512556 DOI: 10.1186/s12964-023-01270-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/13/2023] [Indexed: 09/23/2023] Open
Abstract
The treatment of depression with pharmaceuticals is associated with many adverse side effects, including male fertility problems. The precise mechanisms by which these agents affect testicular cells remain largely unknown, but they are believed to induce cellular stress, which is sensed by the endoplasmic reticulum (ER) and the Golgi apparatus. These organelles are responsible for maintaining cellular homeostasis and regulating signal pathways that lead to autophagy or apoptosis. Therefore, in this study, we aimed to investigate the autophagy, ER, and Golgi stress-related pathways in mouse testis following treatment with antidepressant-like substances (ALS) and ALS combined with lipopolysaccharide (LPS). We found that most ALS and activated proteins are associated with the induction of apoptosis. However, when imipramine (IMI) was combined with NS-398 (a cyclooxygenase-2 inhibitor) after LPS administration, we observed a marked increase in the BECLIN1, Bcl-2, ATG16L, and LC3 expression, which are marker proteins of autophagosome formation. The expression of the BECN1 and ATG16L genes was also high compared to the control, indicating the induction of autophagy processes that may potentially protect mouse testicular cells from death and regulate metabolism in the testis. Our findings may provide a better understanding of the stress-related effects of specific ALS on the testis. Video Abstract.
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Affiliation(s)
- Przemysław Sołek
- Department of Biopharmacy, Medical University of Lublin, 4a Chodźki, 20-093, Lublin, Poland
| | - Ewelina Czechowska
- Department of Human Physiology, Institute of Medical Sciences, Medical College of Rzeszow University, 2a Kopisto, 35-959, Rzeszow, Poland
| | - Magdalena Sowa-Kućma
- Department of Human Physiology, Institute of Medical Sciences, Medical College of Rzeszow University, 2a Kopisto, 35-959, Rzeszow, Poland
| | - Katarzyna Stachowicz
- Maj Institute of Pharmacology Polish Academy of Sciences, 12 Smetna, 31-343, Krakow, Poland
| | - Piotr Kaczka
- PRO-NOO-BIOTICS Sp. z o.o., 39 Warszawska, 35-205, Rzeszow, Poland
| | - Anna Tabęcka-Łonczyńska
- Department of Biotechnology and Cell Biology, Medical College, University of Information Technology and Management in Rzeszow, 2 Sucharskiego, 35-225, Rzeszow, Poland.
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21
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Sarrafha L, Neavin DR, Parfitt GM, Kruglikov IA, Whitney K, Reyes R, Coccia E, Kareva T, Goldman C, Tipon R, Croft G, Crary JF, Powell JE, Blanchard J, Ahfeldt T. Novel human pluripotent stem cell-derived hypothalamus organoids demonstrate cellular diversity. iScience 2023; 26:107525. [PMID: 37646018 PMCID: PMC10460991 DOI: 10.1016/j.isci.2023.107525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/19/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023] Open
Abstract
The hypothalamus is a region of the brain that plays an important role in regulating body functions and behaviors. There is a growing interest in human pluripotent stem cells (hPSCs) for modeling diseases that affect the hypothalamus. Here, we established an hPSC-derived hypothalamus organoid differentiation protocol to model the cellular diversity of this brain region. Using an hPSC line with a tyrosine hydroxylase (TH)-TdTomato reporter for dopaminergic neurons (DNs) and other TH-expressing cells, we interrogated DN-specific pathways and functions in electrophysiologically active hypothalamus organoids. Single-cell RNA sequencing (scRNA-seq) revealed diverse neuronal and non-neuronal cell types in mature hypothalamus organoids. We identified several molecularly distinct hypothalamic DN subtypes that demonstrated different developmental maturities. Our in vitro 3D hypothalamus differentiation protocol can be used to study the development of this critical brain structure and can be applied to disease modeling to generate novel therapeutic approaches for disorders centered around the hypothalamus.
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Affiliation(s)
- Lily Sarrafha
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Drew R. Neavin
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Gustavo M. Parfitt
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | | | - Kristen Whitney
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Molecular, and Cell-Based Medicine, Mount Sinai, New York, NY 10029, USA
| | - Ricardo Reyes
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Elena Coccia
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Tatyana Kareva
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Camille Goldman
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Regine Tipon
- New York Stem Cell Foundation, New York, NY 10019, USA
| | - Gist Croft
- New York Stem Cell Foundation, New York, NY 10019, USA
| | - John F. Crary
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Molecular, and Cell-Based Medicine, Mount Sinai, New York, NY 10029, USA
- Windreich Department of Artificial Intelligence and Human Health, Mount Sinai, New York, NY 10029, USA
| | - Joseph E. Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Kensington, Sydney, NSW 2052, Australia
| | - Joel Blanchard
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
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22
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Dumitru AV, Stoica EE, Covache-Busuioc RA, Bratu BG, Cirstoiu MM. Unraveling the Intricate Link: Deciphering the Role of the Golgi Apparatus in Breast Cancer Progression. Int J Mol Sci 2023; 24:14073. [PMID: 37762375 PMCID: PMC10531533 DOI: 10.3390/ijms241814073] [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: 08/23/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Breast cancer represents a paramount global health challenge, warranting intensified exploration of the molecular underpinnings influencing its progression to facilitate the development of precise diagnostic instruments and customized therapeutic regimens. Historically, the Golgi apparatus has been acknowledged for its primary role in protein sorting and trafficking within cellular contexts. However, recent findings suggest a potential link between modifications in Golgi apparatus function and organization and the pathogenesis of breast cancer. This review delivers an exhaustive analysis of this correlation. Specifically, we examine the consequences of disrupted protein glycosylation, compromised protein transport, and inappropriate oncoprotein processing on breast cancer cell dynamics. Furthermore, we delve into the impacts of Golgi-mediated secretory routes on the release of pro-tumorigenic factors during the course of breast cancer evolution. Elucidating the nuanced interplay between the Golgi apparatus and breast cancer can pave the way for innovative therapeutic interventions and the discovery of biomarkers, potentially enhancing the diagnostic, prognostic, and therapeutic paradigms for afflicted patients. The advancement of such research could substantially expedite the realization of these objectives.
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Affiliation(s)
- Adrian Vasile Dumitru
- Department of Pathology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
- Department of Pathology, University Emergency Hospital, 050098 Bucharest, Romania
| | - Evelina-Elena Stoica
- Department of Obstetrics and Gynaecology, University Emergency Hospital, 050098 Bucharest, Romania;
| | | | - Bogdan-Gabriel Bratu
- Department of Neurosurgery, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Monica-Mihaela Cirstoiu
- Department of Obstetrics and Gynaecology, University Emergency Hospital, 050098 Bucharest, Romania;
- Department of Obstetrics and Gynaecology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
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23
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Morishita S, Komatsu N. Diagnosis- and Prognosis-Related Gene Alterations in BCR::ABL1-Negative Myeloproliferative Neoplasms. Int J Mol Sci 2023; 24:13008. [PMID: 37629188 PMCID: PMC10455804 DOI: 10.3390/ijms241613008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
BCR::ABL1-negative myeloproliferative neoplasms (MPNs) are a group of hematopoietic malignancies in which somatic mutations are acquired in hematopoietic stem/progenitor cells, resulting in an abnormal increase in blood cells in peripheral blood and fibrosis in bone marrow. Mutations in JAK2, MPL, and CALR are frequently found in BCR::ABL1-negative MPNs, and detecting typical mutations in these three genes has become essential for the diagnosis of BCR::ABL1-negative MPNs. Furthermore, comprehensive gene mutation and expression analyses performed using massively parallel sequencing have identified gene mutations associated with the prognosis of BCR::ABL1-negative MPNs such as ASXL1, EZH2, IDH1/2, SRSF2, and U2AF1. Furthermore, single-cell analyses have partially elucidated the effect of the order of mutation acquisition on the phenotype of BCR::ABL1-negative MPNs and the mechanism of the pathogenesis of BCR::ABL1-negative MPNs. Recently, specific CREB3L1 overexpression has been identified in megakaryocytes and platelets in BCR::ABL1-negative MPNs, which may be promising for the development of diagnostic applications. In this review, we describe the genetic mutations found in BCR::ABL1-negative MPNs, including the results of analyses conducted by our group.
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Affiliation(s)
- Soji Morishita
- Development of Therapies against MPNs, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Advanced Hematology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkuo-ku, Tokyo 113-8421, Japan
| | - Norio Komatsu
- Development of Therapies against MPNs, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Advanced Hematology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkuo-ku, Tokyo 113-8421, Japan
- PharmaEssentia Japan, Akasaka Center Building 12 Fl, 1-3-13 Motoakasaka, Minato-ku, Tokyo 107-0051, Japan
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24
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Klyosova E, Azarova I, Buikin S, Polonikov A. Differentially Expressed Genes Regulating Glutathione Metabolism, Protein-Folding, and Unfolded Protein Response in Pancreatic β-Cells in Type 2 Diabetes Mellitus. Int J Mol Sci 2023; 24:12059. [PMID: 37569434 PMCID: PMC10418503 DOI: 10.3390/ijms241512059] [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: 03/28/2023] [Revised: 07/12/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Impaired redox homeostasis in the endoplasmic reticulum (ER) may contribute to proinsulin misfolding and thus to activate the unfolded protein response (UPR) and apoptotic pathways, culminating in pancreatic β-cell loss and type 2 diabetes (T2D). The present study was designed to identify differentially expressed genes (DEGs) encoding enzymes for glutathione metabolism and their impact on the expression levels of genes regulating protein folding and UPR in β-cells of T2D patients. The GEO transcriptome datasets of β-cells of diabetics and non-diabetics, GSE20966 and GSE81608, were analyzed for 142 genes of interest using limma and GREIN software, respectively. Diabetic β-cells showed dataset-specific patterns of DEGs (FDR ≤ 0.05) implicated in the regulation of glutathione metabolism (ANPEP, PGD, IDH2, and CTH), protein-folding (HSP90AB1, HSP90AA1, HSPA1B, HSPA8, BAG3, NDC1, NUP160, RLN1, and RPS19BP1), and unfolded protein response (CREB3L4, ERP27, and BID). The GCLC gene, encoding the catalytic subunit of glutamate-cysteine ligase, the first rate-limiting enzyme of glutathione biosynthesis, was moderately down-regulated in diabetic β-cells from both datasets (p ≤ 0.05). Regression analysis established that genes involved in the de novo synthesis of glutathione, GCLC, GCLM, and GSS affect the expression levels of genes encoding molecular chaperones and those involved in the UPR pathway. This study showed for the first time that diabetic β-cells exhibit alterations in the expression of genes regulating glutathione metabolism, protein-folding, and UPR and provided evidence for the molecular crosstalk between impaired redox homeostasis and abnormal protein folding, underlying ER stress in type 2 diabetes.
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Affiliation(s)
- Elena Klyosova
- Laboratory of Biochemical Genetics and Metabolomics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia; (E.K.); (I.A.)
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, 305041 Kursk, Russia
| | - Iuliia Azarova
- Laboratory of Biochemical Genetics and Metabolomics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia; (E.K.); (I.A.)
- Department of Biological Chemistry, Kursk State Medical University, 3 Karl Marx Street, 305041 Kursk, Russia
| | - Stepan Buikin
- Centre of Omics Technology, I.M. Sechenov First Moscow State Medical University, 8-2 Trubetskaya Street, 119991 Moscow, Russia;
- Department of Internal Diseases, Yaroslav the Wise Novgorod State University, 41 Bolshaya St. Petersburg Street, 173003 Veliky Novgorod, Russia
| | - Alexey Polonikov
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, 305041 Kursk, Russia
- Laboratory of Statistical Genetics and Bioinformatics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia
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25
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Xiong Y, Zhang Y, Liu N, Li Y, Liu H, Yang Q, Chen Y, Xia Z, Chen X, Wanggou S, Li X. Integration of single-cell regulon atlas and multi-omics data for prognostic stratification and personalized treatment prediction in human lung adenocarcinoma. J Transl Med 2023; 21:499. [PMID: 37491302 PMCID: PMC10369768 DOI: 10.1186/s12967-023-04331-z] [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: 05/07/2023] [Accepted: 07/07/2023] [Indexed: 07/27/2023] Open
Abstract
Transcriptional programs are often dysregulated in cancers. A comprehensive investigation of potential regulons is critical to the understanding of tumorigeneses. We first constructed the regulatory networks from single-cell RNA sequencing data in human lung adenocarcinoma (LUAD). We next introduce LPRI (Lung Cancer Prognostic Regulon Index), a precision oncology framework to identify new biomarkers associated with prognosis by leveraging the single cell regulon atlas and bulk RNA sequencing or microarray datasets. We confirmed that LPRI could be a robust biomarker to guide prognosis stratification across lung adenocarcinoma cohorts. Finally, a multi-omics data analysis to characterize molecular alterations associated with LPRI was performed from The Cancer Genome Atlas (TCGA) dataset. Our study provides a comprehensive chart of regulons in LUAD. Additionally, LPRI will be used to help prognostic prediction and developing personalized treatment for future studies.
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Affiliation(s)
- Yi Xiong
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Yihao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Na Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Postdoctoral Research Workstation, Xiangya Hospital, Central South University, Hunan, 410078, China
| | - Yueshuo Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Postdoctoral Research Workstation, Xiangya Hospital, Central South University, Hunan, 410078, China
| | - Hongwei Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Qi Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yu Chen
- Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Zhizhi Xia
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Xin Chen
- Songjiang Research Institute, Shanghai Songjiang District Central Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 201600, China.
| | - Siyi Wanggou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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26
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Easton ZJW, Sarr O, Zhao L, Buzatto AZ, Luo X, Zhao S, Li L, Regnault TRH. An Integrated Multi-OMICS Approach Highlights Elevated Non-Esterified Fatty Acids Impact BeWo Trophoblast Metabolism and Lipid Processing. Metabolites 2023; 13:883. [PMID: 37623828 PMCID: PMC10456680 DOI: 10.3390/metabo13080883] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 08/26/2023] Open
Abstract
Maternal obesity and gestational diabetes mellitus (GDM) are linked with impaired placental function and early onset of non-communicable cardiometabolic diseases in offspring. Previous studies have highlighted that the dietary non-esterified fatty acids (NEFAs) palmitate (PA) and oleate (OA), key dietary metabolites associated with maternal obesity and GDM, are potential modulators of placental lipid processing. Using the BeWo cell line model, the current study integrated transcriptomic (mRNA microarray), metabolomic, and lipidomic readouts to characterize the underlying impacts of exogenous PA and OA on placental villous trophoblast cell metabolism. Targeted gas chromatography and thin-layer chromatography highlighted that saturated and monounsaturated NEFAs differentially impact BeWo cell lipid profiles. Furthermore, cellular lipid profiles differed when exposed to single and multiple NEFA species. Additional multi-omic analyses suggested that PA exposure is associated with enrichment in β-oxidation pathways, while OA exposure is associated with enrichment in anti-inflammatory and antioxidant pathways. Overall, this study further demonstrated that dietary PA and OA are important regulators of placental lipid metabolism. Encouraging appropriate dietary advice and implementing dietary interventions to maintain appropriate placental function by limiting excessive exposure to saturated NEFAs remain crucial in managing at-risk obese and GDM pregnancies.
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Affiliation(s)
- Zachary J. W. Easton
- Department of Physiology and Pharmacology, Western University, Medical Sciences Building Room 216, London, ON N6A 5C1, Canada; (Z.J.W.E.); (O.S.); (L.Z.)
| | - Ousseynou Sarr
- Department of Physiology and Pharmacology, Western University, Medical Sciences Building Room 216, London, ON N6A 5C1, Canada; (Z.J.W.E.); (O.S.); (L.Z.)
| | - Lin Zhao
- Department of Physiology and Pharmacology, Western University, Medical Sciences Building Room 216, London, ON N6A 5C1, Canada; (Z.J.W.E.); (O.S.); (L.Z.)
| | - Adriana Zardini Buzatto
- The Metabolomics Innovation Centre (TMIC), University of Alberta, Edmonton, AB T6G 2G2, Canada; (A.Z.B.); (X.L.); (S.Z.); (L.L.)
| | - Xian Luo
- The Metabolomics Innovation Centre (TMIC), University of Alberta, Edmonton, AB T6G 2G2, Canada; (A.Z.B.); (X.L.); (S.Z.); (L.L.)
| | - Shuang Zhao
- The Metabolomics Innovation Centre (TMIC), University of Alberta, Edmonton, AB T6G 2G2, Canada; (A.Z.B.); (X.L.); (S.Z.); (L.L.)
| | - Liang Li
- The Metabolomics Innovation Centre (TMIC), University of Alberta, Edmonton, AB T6G 2G2, Canada; (A.Z.B.); (X.L.); (S.Z.); (L.L.)
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Timothy R. H. Regnault
- Department of Physiology and Pharmacology, Western University, Medical Sciences Building Room 216, London, ON N6A 5C1, Canada; (Z.J.W.E.); (O.S.); (L.Z.)
- Department of Obstetrics and Gynaecology, Western University, B2-401 London Health Science Centre-Victoria Hospital, 800 Commissioners Rd E, London, ON N6H 5W9, Canada
- Children’s Health Research Institute, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
- Lawson Health Research Institute, 750 Base Line Rd E, London, ON N6C 2R5, Canada
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27
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Li G, Yu X, Portela Fontoura AB, Javaid A, de la Maza-Escolà VS, Salandy NS, Fubini SL, Grilli E, McFadden JW, Duan JE. Transcriptomic regulations of heat stress response in the liver of lactating dairy cows. BMC Genomics 2023; 24:410. [PMID: 37474909 PMCID: PMC10360291 DOI: 10.1186/s12864-023-09484-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/24/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND The global dairy industry is currently facing the challenge of heat stress (HS). Despite the implementation of various measures to mitigate the negative impact of HS on milk production, the cellular response of dairy cows to HS is still not well understood. Our study aims to analyze transcriptomic dynamics and functional changes in the liver of cows subjected to heat stress (HS). To achieve this, a total of 9 Holstein dairy cows were randomly selected from three environmental conditions - heat stress (HS), pair-fed (PF), and thermoneutral (TN) groups - and liver biopsies were obtained for transcriptome analysis. RESULTS Both the dry matter intake (DMI) and milk yield of cows in the HS group exhibited significant reduction compared to the TN group. Through liver transcriptomic analysis, 483 differentially expressed genes (DEGs) were identified among three experimental groups. Especially, we found all the protein coding genes in mitochondria were significantly downregulated under HS and 6 heat shock proteins were significant upregulated after HS exposure, indicating HS may affect mitochondria integrity and jeopardize the metabolic homeostasis in liver. Furthermore, Gene ontology (GO) enrichment of DEGs revealed that the protein folding pathway was upregulated while oxidative phosphorylation was downregulated in the HS group, corresponding to impaired energy production caused by mitochondria dysfunction. CONCLUSIONS The liver transcriptome analysis generated a comprehensive gene expression regulation network upon HS in lactating dairy cows. Overall, this study provides novel insights into molecular and metabolic changes of cows conditioned under HS. The key genes and pathways identified in this study provided further understanding of transcriptome regulation of HS response and could serve as vital references to mitigate the HS effects on dairy cow health and productivity.
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Affiliation(s)
- Guangsheng Li
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, 14853, USA
| | - Xingtan Yu
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, 14853, USA
| | - Ananda B Portela Fontoura
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, 14853, USA
| | - Awais Javaid
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, 14853, USA
| | - Víctor Sáinz de la Maza-Escolà
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, 14853, USA
- Dipartamento di Scienze Mediche Veterinarie, Università di Bologna, Bologna, 40064, Italy
| | - Nia S Salandy
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, 14853, USA
- Department of Agriculture and Environmental Sciences, Tuskegee University, Tuskegee, 36088, USA
| | - Susan L Fubini
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, 14853, USA
| | - Ester Grilli
- Dipartamento di Scienze Mediche Veterinarie, Università di Bologna, Bologna, 40064, Italy
- VetAgro S.p.A, Reggio Emilia, 42124, Italy
| | - Joseph W McFadden
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, 14853, USA.
| | - Jingyue Ellie Duan
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, 14853, USA.
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Nandanpawar P, Sahoo L, Sahoo B, Murmu K, Chaudhari A, Pavan kumar A, Das P. Identification of differentially expressed genes and SNPs linked to harvest body weight of genetically improved rohu carp, Labeo rohita. Front Genet 2023; 14:1153911. [PMID: 37359361 PMCID: PMC10285081 DOI: 10.3389/fgene.2023.1153911] [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: 01/30/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
In most of the aquaculture selection programs, harvest body weight has been a preferred performance trait for improvement. Molecular interplay of genes linked to higher body weight is not elucidated in major carp species. The genetically improved rohu carp with 18% average genetic gain per generation with respect to harvest body weight is a promising candidate for studying genes' underlying performance traits. In the present study, muscle transcriptome sequencing of two groups of individuals, with significant difference in breeding value, belonging to the tenth generation of rohu carp was performed using the Illumina HiSeq 2000 platform. A total of 178 million paired-end raw reads were generated to give rise to 173 million reads after quality control and trimming. The genome-guided transcriptome assembly and differential gene expression produced 11,86,119 transcripts and 451 upregulated and 181 downregulated differentially expressed genes (DEGs) between high-breeding value and low-breeding value (HB & LB) groups, respectively. Similarly, 39,158 high-quality coding SNPs were identified with the Ts/Tv ratio of 1.23. Out of a total of 17 qPCR-validated transcripts, eight were associated with cellular growth and proliferation and harbored 13 SNPs. The gene expression pattern was observed to be positively correlated with RNA-seq data for genes such as myogenic factor 6, titin isoform X11, IGF-1 like, acetyl-CoA, and thyroid receptor hormone beta. A total of 26 miRNA target interactions were also identified to be associated with significant DETs (p-value < 0.05). Genes such as Myo6, IGF-1-like, and acetyl-CoA linked to higher harvest body weight may serve as candidate genes in marker-assisted breeding and SNP array construction for genome-wide association studies and genomic selection.
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Affiliation(s)
- P. Nandanpawar
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - L. Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - B. Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - K. Murmu
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - A. Chaudhari
- ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - A. Pavan kumar
- ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - P. Das
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
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29
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Örd T, Lönnberg T, Nurminen V, Ravindran A, Niskanen H, Kiema M, Õunap K, Maria M, Moreau PR, Mishra PP, Palani S, Virta J, Liljenbäck H, Aavik E, Roivainen A, Ylä-Herttuala S, Laakkonen JP, Lehtimäki T, Kaikkonen MU. Dissecting the polygenic basis of atherosclerosis via disease-associated cell state signatures. Am J Hum Genet 2023; 110:722-740. [PMID: 37060905 PMCID: PMC10183377 DOI: 10.1016/j.ajhg.2023.03.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/21/2023] [Indexed: 04/17/2023] Open
Abstract
Coronary artery disease (CAD) is a pandemic disease where up to half of the risk is explained by genetic factors. Advanced insights into the genetic basis of CAD require deeper understanding of the contributions of different cell types, molecular pathways, and genes to disease heritability. Here, we investigate the biological diversity of atherosclerosis-associated cell states and interrogate their contribution to the genetic risk of CAD by using single-cell and bulk RNA sequencing (RNA-seq) of mouse and human lesions. We identified 12 disease-associated cell states that we characterized further by gene set functional profiling, ligand-receptor prediction, and transcription factor inference. Importantly, Vcam1+ smooth muscle cell state genes contributed most to SNP-based heritability of CAD. In line with this, genetic variants near smooth muscle cell state genes and regulatory elements explained the largest fraction of CAD-risk variance between individuals. Using this information for variant prioritization, we derived a hybrid polygenic risk score (PRS) that demonstrated improved performance over a classical PRS. Our results provide insights into the biological mechanisms associated with CAD risk, which could make a promising contribution to precision medicine and tailored therapeutic interventions in the future.
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Affiliation(s)
- Tiit Örd
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland.
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Valtteri Nurminen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Aarthi Ravindran
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Henri Niskanen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Miika Kiema
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Kadri Õunap
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Maleeha Maria
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Pierre R Moreau
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland
| | - Senthil Palani
- Turku PET Centre, University of Turku, Kiinamyllynkatu 4-8, 20520 Turku, Finland
| | - Jenni Virta
- Turku PET Centre, University of Turku, Kiinamyllynkatu 4-8, 20520 Turku, Finland
| | - Heidi Liljenbäck
- Turku PET Centre, University of Turku, Kiinamyllynkatu 4-8, 20520 Turku, Finland; Turku Center for Disease Modeling, University of Turku, 20520 Turku, Finland
| | - Einari Aavik
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Anne Roivainen
- Turku PET Centre, University of Turku, Kiinamyllynkatu 4-8, 20520 Turku, Finland; Turku Center for Disease Modeling, University of Turku, 20520 Turku, Finland; Turku PET Centre, Turku University Hospital, 20520 Turku, Finland
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Johanna P Laakkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland
| | - Minna U Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland.
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30
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Stevenson NL. The factory, the antenna and the scaffold: the three-way interplay between the Golgi, cilium and extracellular matrix underlying tissue function. Biol Open 2023; 12:287059. [PMID: 36802341 PMCID: PMC9986613 DOI: 10.1242/bio.059719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
The growth and development of healthy tissues is dependent on the construction of a highly specialised extracellular matrix (ECM) to provide support for cell growth and migration and to determine the biomechanical properties of the tissue. These scaffolds are composed of extensively glycosylated proteins which are secreted and assembled into well-ordered structures that can hydrate, mineralise, and store growth factors as required. The proteolytic processing and glycosylation of ECM components is vital to their function. These modifications are under the control of the Golgi apparatus, an intracellular factory hosting spatially organised, protein-modifying enzymes. Regulation also requires a cellular antenna, the cilium, which integrates extracellular growth signals and mechanical cues to inform ECM production. Consequently, mutations in either Golgi or ciliary genes frequently lead to connective tissue disorders. The individual importance of each of these organelles to ECM function is well-studied. However, emerging evidence points towards a more tightly linked system of interdependence between the Golgi, cilium and ECM. This review examines how the interplay between all three compartments underpins healthy tissue. As an example, it will look at several members of the golgin family of Golgi-resident proteins whose loss is detrimental to connective tissue function. This perspective will be important for many future studies looking to dissect the cause and effect of mutations impacting tissue integrity.
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Affiliation(s)
- Nicola L Stevenson
- Cell Biology Laboratories, School of Biochemistry, Faculty of Biomedical Sciences University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
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31
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Ai C, Rong T, Chen Z, Shen W, Huang K, Li Q, Xiong J, Li W. Cyclic AMP Responsive Element Binding Protein 3-like 4/AarF Domain Containing Kinase 5 Axis Facilitates Proliferation, Migration and Invasion of Lung Adenocarcinoma Cells by Modulating the TGFβ Pathway. BIOTECHNOL BIOPROC E 2023. [DOI: 10.1007/s12257-022-0248-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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32
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Kim H, Song Z, Zhang R, Davies BSJ, Zhang K. A hepatokine derived from the ER protein CREBH promotes triglyceride metabolism by stimulating lipoprotein lipase activity. Sci Signal 2023; 16:eadd6702. [PMID: 36649378 PMCID: PMC10080946 DOI: 10.1126/scisignal.add6702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 12/22/2022] [Indexed: 01/19/2023]
Abstract
The endoplasmic reticulum (ER)-tethered, liver-enriched stress sensor CREBH is processed in response to increased energy demands or hepatic stress to release an amino-terminal fragment that functions as a transcription factor for hepatic genes encoding lipid and glucose metabolic factors. Here, we discovered that the carboxyl-terminal fragment of CREBH (CREBH-C) derived from membrane-bound, full-length CREBH was secreted as a hepatokine in response to fasting or hepatic stress. Phosphorylation of CREBH-C mediated by the kinase CaMKII was required for efficient secretion of CREBH-C through exocytosis. Lipoprotein lipase (LPL) mediates the lipolysis of circulating triglycerides for tissue uptake and is inhibited by a complex consisting of angiopoietin-like (ANGPTL) 3 and ANGPTL8. Secreted CREBH-C blocked the formation of ANGPTL3-ANGPTL8 complexes, leading to increased LPL activity in plasma and metabolic tissues in mice. CREBH-C administration promoted plasma triglyceride clearance and partitioning into peripheral tissues and mitigated hypertriglyceridemia and hepatic steatosis in mice fed a high-fat diet. Individuals with obesity had higher circulating amounts of CREBH-C than control individuals, and human CREBH loss-of-function variants were associated with dysregulated plasma triglycerides. These results identify a stress-induced, secreted protein fragment derived from CREBH that functions as a hepatokine to stimulate LPL activity and triglyceride homeostasis.
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Affiliation(s)
- Hyunbae Kim
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Zhenfeng Song
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Ren Zhang
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Brandon S. J. Davies
- Department of Biochemistry, Fraternal Order of Eagles Diabetes Research Center, and Obesity Research and Education Initiative, University of Iowa, Iowa City, IA 52242, USA
| | - Kezhong Zhang
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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Mosale Seetharam S, Liu Y, Wu J, Fechter L, Murugesan K, Maecker H, Gotlib J, Zehnder J, Paulmurugan R, Krishnan A. Enkurin: A novel marker for myeloproliferative neoplasms from platelet, megakaryocyte, and whole blood specimens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.07.523111. [PMID: 36712071 PMCID: PMC9881897 DOI: 10.1101/2023.01.07.523111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Impaired protein homeostasis, though well established in age-related disorders, has been linked in recent research with the pathogenesis of myeloproliferative neoplasms (MPNs). As yet, however, little is known about MPN-specific modulators of proteostasis, thus impeding our ability for increased mechanistic understanding and discovery of additional therapeutic targets. Loss of proteostasis, in itself, is traced to dysregulated mechanisms in protein folding and intracellular calcium signaling at the endoplasmic reticulum (ER). Here, using ex vivo and in vitro systems (including CD34 + cultures from patient bone marrow, and healthy cord/peripheral blood specimens), we extend our prior data from MPN patient platelet RNA sequencing, and discover select proteostasis-associated markers at RNA and/or protein levels in each of platelets, parent megakaryocytes, and whole blood specimens. Importantly, we identify a novel role in MPNs for enkurin ( ENKUR ), a calcium mediator protein, implicated originally only in spermatogenesis. Our data reveal consistent ENKUR downregulation at both RNA and protein levels across MPN patient specimens and experimental models, with a concomitant upregulation of a cell cycle marker, CDC20 . Silencing of ENKUR by shRNA in CD34 + derived megakaryocytes further confirm this association with CDC20 at both RNA and protein levels; and indicate a likely role for the PI3K/Akt pathway. The inverse association of ENKUR and CDC20 expression was further confirmed upon treatment with thapsigargin (an agent that causes protein misfolding in the ER by selective loss of calcium) in both megakaryocyte and platelet fractions at RNA and protein levels. Together, our work sheds light on enkurin as a novel marker of MPN pathogenesis beyond the genetic alterations; and indicates further mechanistic investigation into a role for dysregulated calcium homeostasis, and ER and protein folding stress in MPN transformation. VISUAL ABSTRACT Key Points Enkurin, a calcium adaptor protein, is identified as a novel marker of pathogenesis in MPNs.MPN megakaryocyte and platelet expression of enkurin at RNA and protein levels is inversely associated with a cell differentiation cycle gene, CDC20.Likely role for dysregulated calcium homeostasis, and ER and protein folding stress in MPN transformation.
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Affiliation(s)
| | - Yi Liu
- Department of Radiology, Stanford University, Stanford, CA
| | - Jason Wu
- High-Throughput Bioscience Center (HTBC), Stanford University School of Medicine, Stanford, CA
| | - Lenn Fechter
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | | | - Holden Maecker
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA
| | - Jason Gotlib
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - James Zehnder
- Department of Pathology, Stanford University, Stanford, CA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | | | - Anandi Krishnan
- Department of Pathology, Stanford University, Stanford, CA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
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34
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Bilbao-Arribas M, Jugo BM. Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep. Front Genet 2022; 13:1067350. [PMID: 36482891 PMCID: PMC9725098 DOI: 10.3389/fgene.2022.1067350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in several biological processes, including the immune system response to pathogens and vaccines. The annotation and functional characterization of lncRNAs is more advanced in humans than in livestock species. Here, we take advantage of the increasing number of high-throughput functional experiments deposited in public databases in order to uniformly analyse, profile unannotated lncRNAs and integrate 422 ovine RNA-seq samples from the ovine immune system. We identified 12302 unannotated lncRNA genes with support from independent CAGE-seq and histone modification ChIP-seq assays. Unannotated lncRNAs showed low expression levels and sequence conservation across other mammal species. There were differences in expression levels depending on the genomic location-based lncRNA classification. Differential expression analyses between unstimulated and samples stimulated with pathogen infection or vaccination resulted in hundreds of lncRNAs with changed expression. Gene co-expression analyses revealed immune gene-enriched clusters associated with immune system activation and related to interferon signalling, antiviral response or endoplasmic reticulum stress. Besides, differential co-expression networks were constructed in order to find condition-specific relationships between coding genes and lncRNAs. Overall, using a diverse set of immune system samples and bioinformatic approaches we identify several ovine lncRNAs associated with the response to an external stimulus. These findings help in the improvement of the ovine lncRNA catalogue and provide sheep-specific evidence for the implication in the general immune response for several lncRNAs.
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Hartal-Benishay LH, Saadi E, Toubiana S, Shaked L, Lalzar M, Abu Hatoum O, Tal S, Selig S, Barki-Harrington L. MBTPS1 regulates proliferation of colorectal cancer primarily through its action on sterol regulatory element-binding proteins. Front Oncol 2022; 12:1004014. [PMID: 36300096 PMCID: PMC9592115 DOI: 10.3389/fonc.2022.1004014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Among the main metabolic pathways implicated in cancer cell proliferation are those of cholesterol and fatty acid synthesis, both of which are tightly regulated by sterol regulatory element-binding proteins (SREBPs). SREBPs are activated through specific cleavage by membrane-bound transcription factor protease 1 (MBTPS1), a serine protease that cleaves additional substrates (ATF6, BDNF, CREBs and somatostatin), some of which are also implicated in cell proliferation. The goal of this study was to determine whether MBTPS1 may serve as a master regulator in proliferation of colorectal cancer (CRC). Tumors from CRC patients showed variable levels of MBTPS1 mRNA, which were in positive correlation with the levels of SREBPs and ATF6, and in reverse correlation with BDNF levels. Chemical inhibition of MBTPS1 activity in two CRC-derived cell lines resulted in a marked decrease in the levels of SREBPs, but not of its other substrates and a marked decrease in cell proliferation, which suggested that MBTPS1 activity is critical for proliferation of these cells. In accordance, CRISPR/Cas9 targeted knockout (KO) of the MBTPS1 gene resulted in the survival of only a single clone that presented a phenotype of severely attenuated proliferation and marked downregulation of several energy metabolism pathways. We further showed that survival of the MBTPS1 KO clone was dependent upon significant upregulation of the type-1 interferon pathway, the inhibition of which halted proliferation entirely. Finally, rescue of the MBTPS1 KO cells, resulted in partial restoration of MBTPS1 levels, which was in accordance with partial recovery in proliferation and in SREBP levels. These finding suggest that MBTPS1 plays a critical role in regulating colon cancer proliferation primarily through SREBP-associated lipid metabolism, and as such may serve as a possible therapeutic target in CRC.
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Affiliation(s)
- Liat H. Hartal-Benishay
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Esraa Saadi
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Shir Toubiana
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa, Israel
| | - Lior Shaked
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Maya Lalzar
- Bioinformatics Service Unit, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Ossama Abu Hatoum
- Department of Surgery, Ha’emek Medical Center, Afula, Israel
- Department of Medicine, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa, Israel
| | - Sharon Tal
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Sara Selig
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa, Israel
- Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa, Israel
| | - Liza Barki-Harrington
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
- *Correspondence: Liza Barki-Harrington,
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Gorrell L, Makareeva E, Omari S, Otsuru S, Leikin S. ER, Mitochondria, and ISR Regulation by mt-HSP70 and ATF5 upon Procollagen Misfolding in Osteoblasts. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201273. [PMID: 35988140 PMCID: PMC9561870 DOI: 10.1002/advs.202201273] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Cellular response to protein misfolding underlies multiple diseases. Collagens are the most abundant vertebrate proteins, yet little is known about cellular response to misfolding of their procollagen precursors. Osteoblasts (OBs)-the cells that make bone-produce so much procollagen that it accounts for up to 40% of mRNAs in the cell, which is why bone bears the brunt of mutations causing procollagen misfolding in osteogenesis imperfecta (OI). The present study of a G610C mouse model of OI by multiple transcriptomic techniques provides first solid clues to how OBs respond to misfolded procollagen accumulation in the endoplasmic reticulum (ER) and how this response affects OB function. Surprisingly, misfolded procollagen escapes the quality control in the ER lumen and indirectly triggers the integrated stress response (ISR) through other cell compartments. In G610C OBs, the ISR is regulated by mitochondrial HSP70 (mt-HSP70) and ATF5 instead of their BIP and ATF4 paralogues, which normally activate and regulate ISR to secretory protein misfolding in the ER. The involvement of mt-HSP70 and ATF5 together with other transcriptomic findings suggest that mitochondria might initiate the ISR upon disruption of ER-mitochondria connections or might respond to the ISR activated by a yet unknown sensor.
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Affiliation(s)
- Laura Gorrell
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)National Institutes of Health (NIH)BethesdaMD20892USA
- Department of Biomedical EngineeringRensselaer Polytechnic InstituteTroyNY12180USA
| | | | - Shakib Omari
- NICHDNIHBethesdaMD20892USA
- Sanford Burnham Prebys Medical Discovery InstituteLa JollaCA92037USA
| | - Satoru Otsuru
- Department of OrthopaedicsUniversity of Maryland School of MedicineBaltimoreMD21201USA
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Homoharringtonine demonstrates a cytotoxic effect against triple-negative breast cancer cell lines and acts synergistically with paclitaxel. Sci Rep 2022; 12:15663. [PMID: 36123435 PMCID: PMC9485251 DOI: 10.1038/s41598-022-19621-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/31/2022] [Indexed: 11/08/2022] Open
Abstract
The lack of targeted therapies for triple-negative breast cancer (TNBC) contributes to their high mortality rates and high risk of relapse compared to other subtypes of breast cancer. Most TNBCs (75%) have downregulated the expression of CREB3L1 (cAMP-responsive element binding protein 3 like 1), a transcription factor and metastasis suppressor that represses genes that promote cancer progression and metastasis. In this report, we screened an FDA-approved drug library and identified four drugs that were highly cytotoxic towards HCC1806 CREB3L1-deficient TNBC cells. These four drugs were: (1) palbociclib isethionate, a CDK4/6 inhibitor, (2) lanatocide C (also named isolanid), a Na+/K+-ATPase inhibitor, (3) cladribine, a nucleoside analog, and (4) homoharringtonine (also named omacetaxine mepesuccinate), a protein translation inhibitor. Homoharringtonine consistently showed the most cytotoxicity towards an additional six TNBC cell lines (BT549, HCC1395, HCC38, Hs578T, MDA-MB-157, MDA-MB-436), and several luminal A breast cancer cell lines (HCC1428, MCF7, T47D, ZR-75-1). All four drugs were then separately evaluated for possible synergy with the chemotherapy agents, doxorubicin (an anthracycline) and paclitaxel (a microtubule stabilizing agent). A strong synergy was observed using the combination of homoharringtonine and paclitaxel, with high cytotoxicity towards TNBC cells at lower concentrations than when each was used separately.
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38
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Fels JA, Dash J, Leslie K, Manfredi G, Kawamata H. Effects of
PB‐TURSO
on the transcriptional and metabolic landscape of sporadic
ALS
fibroblasts. Ann Clin Transl Neurol 2022; 9:1551-1564. [PMID: 36083004 PMCID: PMC9539390 DOI: 10.1002/acn3.51648] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/02/2022] [Accepted: 07/22/2022] [Indexed: 11/09/2022] Open
Abstract
Objective Methods Results Interpretation
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Affiliation(s)
- Jasmine A. Fels
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine 407 East 61st Street New York New York 10065 USA
- Neuroscience Graduate Program Weill Cornell Graduate School of Medical Sciences 1300 York Ave New York New York 10065 USA
| | - Jalia Dash
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine 407 East 61st Street New York New York 10065 USA
| | - Kent Leslie
- Amylyx Pharmaceuticals 43 Thorndike Street Cambridge Massachusetts 02141 USA
| | - Giovanni Manfredi
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine 407 East 61st Street New York New York 10065 USA
| | - Hibiki Kawamata
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine 407 East 61st Street New York New York 10065 USA
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Lin Z, Wu Y, Xiao X, Zhang X, Wan J, Zheng T, Chen H, Liu T, Tang X. Pan-cancer analysis of CREB3L1 as biomarker in the prediction of prognosis and immunotherapeutic efficacy. Front Genet 2022; 13:938510. [PMID: 36171879 PMCID: PMC9511413 DOI: 10.3389/fgene.2022.938510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
Background: CAMP response element binding protein 3-like 1 (CREB3L1) has been indicated as a critical biomarker and can modulate multifaced behaviors of tumor cells in diverse cancers. However, a systematic assessment of CREB3L1 in pan-cancer is of absence, and the predictive value of CREB3L1 in cancer prognosis, the tumor immune microenvironment and the efficacy of immunotherapy remains unexplored.Methods: CREB3L1 expression in 33 different cancer types was investigated using RNAseq data from The Cancer Genome Atlas (TCGA) database. The characteristics of CREB3L1 alternations were illustrated in cBioPortal database. The prognostic and clinicopathological value of CREB3L1 was analyzed through clinical data downloaded from the TCGA database. The potential role of CREB3L1 in the tumor immune microenvironment was illustrated by utilizing CIBERSORT and ESTIMATE algorithms, and TISIDB online database. The associations between CREB3L1 expression and tumor mutation burden (TMB), and microsatellite instability (MSI) were assessed by spearman’s rank correlation coefficient. Furthermore, Gene Set Enrichment Analysis (GSEA) was conducted to explore the potential biological functions and downstream pathways of CREB3L1 in different human cancers. The correlations of CREB3L1 expression with PD-1/PD-L1 inhibitors efficacy and drug sensitivity were also investigated.Results: The expression of CREB3L1 was abnormally high or low in several different cancer types, and was also strictly associated with the prognosis of cancer patients. CREB3L1 expression levels have a strong relationship with infiltrating immune cells, including regulatory T cells, CD8+ T cells, macrophages, B naïve cells, dendritic cells and mast cells. CREB3L1 expression was also correlated with the expression of multiple immune-related biomolecules, TMB, and MSI in several cancers. Moreover, CREB3L1 had promising applications in predicting the immunotherapeutic benefits and drug sensitivity in cancer management.Conclusions: Our results highlight the value of CREB3L1 as a predictive biomarker for the prognosis and immunotherapy efficacy in multiple cancers, and CREB3L1 seems to play key roles in the tumor immune microenvironment, suggesting the role of CREB3L1 as a promising biomarker for predicting the prognosis and immune-related signatures in diverse cancers.
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Affiliation(s)
- Zhengjun Lin
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yanlin Wu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - XunGang Xiao
- Department of Orthopedics, Chenzhou No. 1 People’s Hospital, Chenzhou, Hunan, China
| | - Xianghong Zhang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jia Wan
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tao Zheng
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongxuan Chen
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- *Correspondence: Tang Liu, ; Xianzhe Tang,
| | - Xianzhe Tang
- Department of Orthopedics, Chenzhou No. 1 People’s Hospital, Chenzhou, Hunan, China
- *Correspondence: Tang Liu, ; Xianzhe Tang,
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40
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Vriend J, Klonisch T. Genes of the Ubiquitin Proteasome System Qualify as Differential Markers in Malignant Glioma of Astrocytic and Oligodendroglial Origin. Cell Mol Neurobiol 2022; 43:1425-1452. [PMID: 35896929 PMCID: PMC10079750 DOI: 10.1007/s10571-022-01261-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022]
Abstract
We have mined public genomic datasets to identify genes coding for components of the ubiquitin proteasome system (UPS) that may qualify as potential diagnostic and therapeutic targets in the three major glioma types, astrocytoma (AS), glioblastoma (GBM), and oligodendroglioma (ODG). In the Sun dataset of glioma (GEO ID: GSE4290), expression of the genes UBE2S and UBE2C, which encode ubiquitin conjugases important for cell-cycle progression, distinguished GBM from AS and ODG. KEGG analysis showed that among the ubiquitin E3 ligase genes differentially expressed, the Notch pathway was significantly over-represented, whereas among the E3 ligase adaptor genes the Hippo pathway was over-represented. We provide evidence that the UPS gene contributions to the Notch and Hippo pathway signatures are related to stem cell pathways and can distinguish GBM from AS and ODG. In the Sun dataset, AURKA and TPX2, two cell-cycle genes coding for E3 ligases, and the cell-cycle gene coding for the E3 adaptor CDC20 were upregulated in GBM. E3 ligase adaptor genes differentially expressed were also over-represented for the Hippo pathway and were able to distinguish classic, mesenchymal, and proneural subtypes of GBM. Also over-expressed in GBM were PSMB8 and PSMB9, genes encoding subunits of the immunoproteasome. Our transcriptome analysis provides a strong rationale for UPS members as attractive therapeutic targets for the development of more effective treatment strategies in malignant glioma. Ubiquitin proteasome system and glioblastoma: E1-ubiquitin-activating enzyme, E2-ubiquitin-conjugating enzyme, E3-ubiquitin ligase. Ubiquitinated substrates of E3 ligases may be degraded by the proteasome. Expression of genes for specific E2 conjugases, E3 ligases, and genes for proteasome subunits may serve as differential markers of subtypes of glioblastoma.
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Affiliation(s)
- Jerry Vriend
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Max Rady Faculty of Health Sciences, University of Manitoba, Rm34, BMSB, 745 Bannatyne Ave, Winnipeg, MB, R3E0J9, Canada.
| | - Thomas Klonisch
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Max Rady Faculty of Health Sciences, University of Manitoba, Rm34, BMSB, 745 Bannatyne Ave, Winnipeg, MB, R3E0J9, Canada
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Identification of a Hydrogen-Sulfide-Releasing Isochroman-4-One Hybrid as a Cardioprotective Candidate for the Treatment of Cardiac Hypertrophy. Molecules 2022; 27:molecules27134114. [PMID: 35807360 PMCID: PMC9268299 DOI: 10.3390/molecules27134114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
Cardiac pathological hypertrophy is associated with undesirable epigenetic changes and causes maladaptive cardiac remodeling and heart failure, leading to high mortality rates. Specific drugs for the treatment of cardiac hypertrophy are still in urgent need. In the present study, a hydrogen-sulfide-releasing hybrid 13-E was designed and synthesized by appending p-hydroxythiobenzamide (TBZ), an H2S-releasing donor, to an analog of our previously discovered cardioprotective natural product XJP, 7,8-dihydroxy-3-methyl-isochromanone-4. This hybrid 13-E exhibited excellent H2S-generating ability and low cellular toxicity. The 13-E protected against cardiomyocyte hypertrophy In Vitro and reduced the induction of Anp and Bnp. More importantly, 13-E could reduce TAC-induced cardiac hypertrophy In Vivo, alleviate cardiac interstitial fibrosis and restore cardiac function. Unbiased transcriptomic analysis showed that 13-E regulated the AMPK signaling pathway and influenced fatty acid metabolic processes, which may be attributed to its cardioprotective activities.
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Zhang Q, Guo Z. SEC61G participates in endoplasmic reticulum stress by interacting with CREB3 to promote the malignant progression of lung adenocarcinoma. Oncol Lett 2022; 24:233. [PMID: 35720482 PMCID: PMC9178705 DOI: 10.3892/ol.2022.13316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022] Open
Abstract
As the most common type of lung cancer, lung adenocarcinoma (LUAD) poses a great threat to human health worldwide and severely compromises the quality of life of the patients. The present study aimed to explore the potential pathogenesis of LUAD. Reverse transcription-quantitative PCR and western blotting were applied to measure the expression levels of SEC61 translocon subunit γ (SEC61G) and cyclic AMP-responsive element-binding protein 3 (CREB3). Western blotting was also used to determine the expression of endoplasmic reticulum (ER) stress-, apoptosis- and migration-related proteins. Cell Counting Kit-8, colony formation, TUNEL, wound healing and Transwell assays were used, respectively, to determine the viability, proliferation, apoptosis, migration and invasion of LUAD A549 cells. The association between SEC61G and CREB3 was verified by co-immunoprecipitation assay. The results revealed that SEC61G was upregulated in A549 cells and its downregulation could activate ER stress. It was also found that silencing SEC61G inhibited the malignant development of LUAD through ER stress. In addition, SEC61G was verified to participate in ER stress in LUAD via CREB3 and silencing SEC61G exerted inhibitory effects on the malignant progression of LUAD by regulating CREB3. In summary, SEC61G participated in ER stress and its knockdown exerted inhibitory effects on A549 cells via regulating CREB3, which suggests that SEC61G may be a potential therapy for patients with LUAD.
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Affiliation(s)
- Qian Zhang
- Shanghai East Clinical Medical College, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Zhongliang Guo
- Shanghai East Clinical Medical College, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
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43
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CREB3 Plays an Important Role in HPSE-Facilitated HSV-1 Release in Human Corneal Epithelial Cells. Viruses 2022; 14:v14061171. [PMID: 35746643 PMCID: PMC9227461 DOI: 10.3390/v14061171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/10/2022] [Accepted: 05/26/2022] [Indexed: 01/16/2023] Open
Abstract
Herpes simplex virus type-1 (HSV-1) exploits several host factors to enhance its replication and release from infected cells. It induces the production of host enzyme heparanase (HPSE) to aid in egress. While the mechanism by which HPSE assists in viral release is well-characterized, other host factors that are recruited along with HPSE for viral release are less well understood. In this study, we identify cyclic-AMP-responsive element-binding protein3 (CREB3) as a key player in HPSE-facilitated HSV-1 egress. When CREB3 is transiently upregulated in human corneal epithelial cells, HSV-1 release from the infected cells is correspondingly enhanced. This activity is linked to HPSE expression such that HPSE-transfected corneal epithelial (HCE) cells more highly express CREB3 than wild-type cells while the cells knocked out for HPSE show very little CREB3 expression. CREB3-transfected HCE cells showed significantly higher export of HPSE upon infection than wild-type cells. Our data suggests that coat protein complex II (COPII), which mediates HPSE trafficking, is also upregulated via a CREB3-dependent pathway during HSV-1 infection. Finally, the co-transfection of CREB3 and HPSE in HCE cells shows the highest viral release compared to either treatment alone, establishing CREB3 as a key player in HPSE-facilitated HSV-1 egress.
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44
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Unveiling OASIS family as a key player in hypoxia-ischemia cases induced by cocaine using generative adversarial networks. Sci Rep 2022; 12:6734. [PMID: 35469040 PMCID: PMC9038918 DOI: 10.1038/s41598-022-10772-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
Repeated cocaine use poses many serious health risks to users. One of the risks is hypoxia and ischemia (HI). To restore the biological system against HI, complex biological mechanisms operate at the gene level. Despite the complexity of biological mechanisms, there are common denominator genes that play pivotal roles in various defense systems. Among these genes, the cAMP response element-binding (Creb) protein contributes not only to various aspects of drug-seeking behavior and drug reward, but also to protective mechanisms. However, it is still unclear which Creb members are key players in the protection of cocaine-induced HI conditions. Herein, using one of the state-of-the-art deep learning methods, the generative adversarial network, we revealed that the OASIS family, one of the Creb family, is a key player in various defense mechanisms such as angiogenesis and unfolded protein response against the HI state by unveiling hidden mRNA expression profiles. Furthermore, we identified mysterious kinases in the OASIS family and are able to explain why the prefrontal cortex and hippocampus are vulnerable to HI at the genetic level.
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45
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Wood RK, Flory AR, Mann MJ, Talbot LJ, Hendershot LM. Secretory defects in pediatric osteosarcoma result from downregulation of selective COPII coatomer proteins. iScience 2022; 25:104100. [PMID: 35402877 PMCID: PMC8983387 DOI: 10.1016/j.isci.2022.104100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/11/2022] [Accepted: 03/15/2022] [Indexed: 12/05/2022] Open
Abstract
Pediatric osteosarcomas (OS) exhibit extensive genomic instability that has complicated the identification of new targeted therapies. We found the vast majority of 108 patient tumor samples and patient-derived xenografts (PDXs), which display an unusually dilated endoplasmic reticulum (ER), have reduced expression of four COPII vesicle components that trigger aberrant accumulation of procollagen-I protein within the ER. CRISPR activation technology was used to increase the expression of two of these, SAR1A and SEC24D, to physiological levels. This was sufficient to resolve the dilated ER morphology, restore collagen-I secretion, and enhance secretion of some extracellular matrix (ECM) proteins. However, orthotopic xenograft growth was not adversely affected by restoration of only SAR1A and SEC24D. Our studies reveal the mechanism responsible for the dilated ER that is a hallmark characteristic of OS and identify a highly conserved molecular signature for this genetically unstable tumor. Possible relationships of this phenotype to tumorigenesis are discussed.
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Affiliation(s)
- Rachael K. Wood
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ashley R. Flory
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Melissa J. Mann
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lindsay J. Talbot
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Linda M. Hendershot
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- University of Tennessee Health Science Center, Memphis, TN 38163, USA
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46
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Song G, Shi Y, Meng L, Ma J, Huang S, Zhang J, Wu Y, Li J, Lin Y, Yang S, Rao D, Cheng Y, Lin J, Ji S, Liu Y, Jiang S, Wang X, Zhang S, Ke A, Wang X, Cao Y, Ji Y, Zhou J, Fan J, Zhang X, Xi R, Gao Q. Single-cell transcriptomic analysis suggests two molecularly subtypes of intrahepatic cholangiocarcinoma. Nat Commun 2022; 13:1642. [PMID: 35347134 PMCID: PMC8960779 DOI: 10.1038/s41467-022-29164-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is a highly heterogeneous cancer with limited understanding of its classification and tumor microenvironment. Here, by performing single-cell RNA sequencing on 144,878 cells from 14 pairs of iCCA tumors and non-tumor liver tissues, we find that S100P and SPP1 are two markers for iCCA perihilar large duct type (iCCAphl) and peripheral small duct type (iCCApps). S100P + SPP1− iCCAphl has significantly reduced levels of infiltrating CD4+ T cells, CD56+ NK cells, and increased CCL18+ macrophages and PD1+CD8+ T cells compared to S100P-SPP1 + iCCApps. The transcription factor CREB3L1 is identified to regulate the S100P expression and promote tumor cell invasion. S100P-SPP1 + iCCApps has significantly more SPP1+ macrophage infiltration, less aggressiveness and better survival than S100P + SPP1− iCCAphl. Moreover, S100P-SPP1 + iCCApps harbors tumor cells at different status of differentiation, such as ALB + hepatocyte differentiation and ID3+ stemness. Our study extends the understanding of the diversity of tumor cells in iCCA. The molecular classification and tumour microenvironment in intrahepatic cholangiocarcinoma (iCCA) need further characterisation. Here, the authors perform single cell RNA-sequencing from 14 pairs of iCCA tumours and non-tumour liver tissues and propose S100P and SPP1 as markers for patient classification.
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Affiliation(s)
- Guohe Song
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Yang Shi
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, China
| | - Lu Meng
- Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Jiaqiang Ma
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China.,Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Siyuan Huang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Juan Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Yingcheng Wu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Jiaxin Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Youpei Lin
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Shuaixi Yang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Dongning Rao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Yifei Cheng
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Jian Lin
- Department of Cancer Center, Jin Shan Hospital, Fudan University, Shanghai, China
| | - Shuyi Ji
- Department of Cancer Center, Jin Shan Hospital, Fudan University, Shanghai, China
| | - Yuming Liu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Shan Jiang
- Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoliang Wang
- Department of General Surgery, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Shu Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Aiwu Ke
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Xiaoying Wang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China
| | - Ya Cao
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yuan Ji
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China.,Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China. .,Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Xiaoming Zhang
- Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.
| | - Ruibin Xi
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, China.
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, China.
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Rohli KE, Boyer CK, Blom SE, Stephens SB. Nutrient Regulation of Pancreatic Islet β-Cell Secretory Capacity and Insulin Production. Biomolecules 2022; 12:335. [PMID: 35204835 PMCID: PMC8869698 DOI: 10.3390/biom12020335] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 01/27/2023] Open
Abstract
Pancreatic islet β-cells exhibit tremendous plasticity for secretory adaptations that coordinate insulin production and release with nutritional demands. This essential feature of the β-cell can allow for compensatory changes that increase secretory output to overcome insulin resistance early in Type 2 diabetes (T2D). Nutrient-stimulated increases in proinsulin biosynthesis may initiate this β-cell adaptive compensation; however, the molecular regulators of secretory expansion that accommodate the increased biosynthetic burden of packaging and producing additional insulin granules, such as enhanced ER and Golgi functions, remain poorly defined. As these adaptive mechanisms fail and T2D progresses, the β-cell succumbs to metabolic defects resulting in alterations to glucose metabolism and a decline in nutrient-regulated secretory functions, including impaired proinsulin processing and a deficit in mature insulin-containing secretory granules. In this review, we will discuss how the adaptative plasticity of the pancreatic islet β-cell's secretory program allows insulin production to be carefully matched with nutrient availability and peripheral cues for insulin signaling. Furthermore, we will highlight potential defects in the secretory pathway that limit or delay insulin granule biosynthesis, which may contribute to the decline in β-cell function during the pathogenesis of T2D.
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Affiliation(s)
- Kristen E. Rohli
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; (K.E.R.); (C.K.B.); (S.E.B.)
- Division of Endocrinology and Metabolism, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Cierra K. Boyer
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; (K.E.R.); (C.K.B.); (S.E.B.)
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA 52242, USA
| | - Sandra E. Blom
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; (K.E.R.); (C.K.B.); (S.E.B.)
- Division of Endocrinology and Metabolism, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Samuel B. Stephens
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; (K.E.R.); (C.K.B.); (S.E.B.)
- Division of Endocrinology and Metabolism, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
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48
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Kalwat MA, Scheuner D, Rodrigues-dos-Santos K, Eizirik DL, Cobb MH. The Pancreatic ß-cell Response to Secretory Demands and Adaption to Stress. Endocrinology 2021; 162:bqab173. [PMID: 34407177 PMCID: PMC8459449 DOI: 10.1210/endocr/bqab173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Indexed: 02/06/2023]
Abstract
Pancreatic β cells dedicate much of their protein translation capacity to producing insulin to maintain glucose homeostasis. In response to increased secretory demand, β cells can compensate by increasing insulin production capability even in the face of protracted peripheral insulin resistance. The ability to amplify insulin secretion in response to hyperglycemia is a critical facet of β-cell function, and the exact mechanisms by which this occurs have been studied for decades. To adapt to the constant and fast-changing demands for insulin production, β cells use the unfolded protein response of the endoplasmic reticulum. Failure of these compensatory mechanisms contributes to both type 1 and 2 diabetes. Additionally, studies in which β cells are "rested" by reducing endogenous insulin demand have shown promise as a therapeutic strategy that could be applied more broadly. Here, we review recent findings in β cells pertaining to the metabolic amplifying pathway, the unfolded protein response, and potential advances in therapeutics based on β-cell rest.
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Affiliation(s)
- Michael A Kalwat
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
| | - Donalyn Scheuner
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
| | | | - Decio L Eizirik
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Melanie H Cobb
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
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Single-cell analysis reveals androgen receptor regulates the ER-to-Golgi trafficking pathway with CREB3L2 to drive prostate cancer progression. Oncogene 2021; 40:6479-6493. [PMID: 34611310 DOI: 10.1038/s41388-021-02026-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/29/2021] [Accepted: 09/16/2021] [Indexed: 02/06/2023]
Abstract
Androgen receptor (AR) plays a central role in driving prostate cancer (PCa) progression. How AR promotes this process is still not completely clear. Herein, we used single-cell transcriptome analysis to reconstruct the transcriptional network of AR in PCa. Our work shows AR directly regulates a set of signature genes in the ER-to-Golgi protein vesicle-mediated transport pathway. The expression of these genes is required for maximum androgen-dependent ER-to-Golgi trafficking, cell growth, and survival. Our analyses also reveal the signature genes are associated with PCa progression and prognosis. Moreover, we find inhibition of the ER-to-Golgi transport process with a small molecule enhanced antiandrogen-mediated tumor suppression of hormone-sensitive and insensitive PCa. Finally, we demonstrate AR collaborates with CREB3L2 in mediating ER-to-Golgi trafficking in PCa. In summary, our findings uncover a critical role for dysregulation of ER-to-Golgi trafficking expression and function in PCa progression, provide detailed mechanistic insights for how AR tightly controls this process, and highlight the prospect of targeting the ER-to-Golgi pathway as a therapeutic strategy for advanced PCa.
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Shen Z, Du W, Perkins C, Fechter L, Natu V, Maecker H, Rowley J, Gotlib J, Zehnder J, Krishnan A. Platelet transcriptome identifies progressive markers and potential therapeutic targets in chronic myeloproliferative neoplasms. Cell Rep Med 2021; 2:100425. [PMID: 34755136 PMCID: PMC8561315 DOI: 10.1016/j.xcrm.2021.100425] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/08/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022]
Abstract
Predicting disease progression remains a particularly challenging endeavor in chronic degenerative disorders and cancer, thus limiting early detection, risk stratification, and preventive interventions. Here, profiling the three chronic subtypes of myeloproliferative neoplasms (MPNs), we identify the blood platelet transcriptome as a proxy strategy for highly sensitive progression biomarkers that also enables prediction of advanced disease via machine-learning algorithms. The MPN platelet transcriptome reveals an incremental molecular reprogramming that is independent of patient driver mutation status or therapy. Subtype-specific markers offer mechanistic and therapeutic insights, and highlight impaired proteostasis and a persistent integrated stress response. Using a LASSO model with validation in two independent cohorts, we identify the advanced subtype MF at high accuracy and offer a robust progression signature toward clinical translation. Our platelet transcriptome snapshot of chronic MPNs demonstrates a proof-of-principle for disease risk stratification and progression beyond genetic data alone, with potential utility in other progressive disorders.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Blood Platelets/metabolism
- Blood Platelets/pathology
- Cellular Reprogramming
- Child
- Child, Preschool
- Cohort Studies
- Diagnosis, Differential
- Disease Progression
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Male
- Middle Aged
- Polycythemia Vera/diagnosis
- Polycythemia Vera/genetics
- Polycythemia Vera/metabolism
- Polycythemia Vera/pathology
- Primary Myelofibrosis/diagnosis
- Primary Myelofibrosis/genetics
- Primary Myelofibrosis/metabolism
- Primary Myelofibrosis/pathology
- Proteostasis/genetics
- Risk Assessment
- Thrombocythemia, Essential/diagnosis
- Thrombocythemia, Essential/genetics
- Thrombocythemia, Essential/metabolism
- Thrombocythemia, Essential/pathology
- Transcriptome
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Affiliation(s)
- Zhu Shen
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Wenfei Du
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Cecelia Perkins
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Lenn Fechter
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Vanita Natu
- Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA, USA
| | - Holden Maecker
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jesse Rowley
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Jason Gotlib
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - James Zehnder
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Anandi Krishnan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
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