1
|
Ahlström FH, Viisanen H, Karhinen L, Velagapudi V, Blomqvist KJ, Lilius TO, Rauhala PV, Kalso EA. Gene expression in the dorsal root ganglion and the cerebrospinal fluid metabolome in polyneuropathy and opioid tolerance in rats. IBRO Neurosci Rep 2024; 17:38-51. [PMID: 38933596 PMCID: PMC11201153 DOI: 10.1016/j.ibneur.2024.05.006] [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: 10/05/2023] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
First-line pharmacotherapy for peripheral neuropathic pain (NP) of diverse pathophysiology consists of antidepressants and gabapentinoids, but only a minority achieve sufficient analgesia with these drugs. Opioids are considered third-line analgesics in NP due to potential severe and unpredictable adverse effects in long-term use. Also, opioid tolerance and NP may have shared mechanisms, raising further concerns about opioid use in NP. We set out to further elucidate possible shared and separate mechanisms after chronic morphine treatment and oxaliplatin-induced and diabetic polyneuropathies, and to identify potential diagnostic markers and therapeutic targets. We analysed thermal nociceptive behaviour, the transcriptome of dorsal root ganglia (DRG) and the metabolome of cerebrospinal fluid (CSF) in these three conditions, in rats. Several genes were differentially expressed, most following oxaliplatin and least after chronic morphine treatment, compared with saline-treated rats. A few genes were differentially expressed in the DRGs in all three models (e.g. Csf3r and Fkbp5). Some, e.g. Alox15 and Slc12a5, were differentially expressed in both diabetic and oxaliplatin models. Other differentially expressed genes were associated with nociception, inflammation, and glial cells. The CSF metabolome was most significantly affected in the diabetic rats. Interestingly, we saw changes in nicotinamide metabolism, which has been associated with opioid addiction and withdrawal, in the CSF of morphine-tolerant rats. Our results offer new hypotheses for the pathophysiology and treatment of NP and opioid tolerance. In particular, the role of nicotinamide metabolism in opioid addiction deserves further study.
Collapse
Affiliation(s)
- Fredrik H.G. Ahlström
- Department of Pharmacology, Faculty of Medicine, Biomedicum 1, University of Helsinki, Haartmaninkatu 8, 00014, Finland
- Individualized Drug Therapy Research Programme, Faculty of Medicine, Biomedicum 1, University of Helsinki, Haartmaninkatu 8, 00014, Finland
| | - Hanna Viisanen
- Department of Pharmacology, Faculty of Medicine, Biomedicum 1, University of Helsinki, Haartmaninkatu 8, 00014, Finland
- Individualized Drug Therapy Research Programme, Faculty of Medicine, Biomedicum 1, University of Helsinki, Haartmaninkatu 8, 00014, Finland
| | - Leena Karhinen
- Department of Pharmacology, Faculty of Medicine, Biomedicum 1, University of Helsinki, Haartmaninkatu 8, 00014, Finland
| | - Vidya Velagapudi
- Metabolomics Unit, Institute for Molecular Medicine Finland FIMM, University of Helsinki, P.O. Box 20, FI-00014, Finland
| | - Kim J. Blomqvist
- Department of Pharmacology, Faculty of Medicine, Biomedicum 1, University of Helsinki, Haartmaninkatu 8, 00014, Finland
- Individualized Drug Therapy Research Programme, Faculty of Medicine, Biomedicum 1, University of Helsinki, Haartmaninkatu 8, 00014, Finland
| | - Tuomas O. Lilius
- Department of Pharmacology, Faculty of Medicine, Biomedicum 1, University of Helsinki, Haartmaninkatu 8, 00014, Finland
- Individualized Drug Therapy Research Programme, Faculty of Medicine, Biomedicum 1, University of Helsinki, Haartmaninkatu 8, 00014, Finland
- Department of Clinical Pharmacology, University of Helsinki and Helsinki University Hospital, Tukholmankatu 8C, 00014, Finland
- Department of Emergency Medicine and Services, University of Helsinki and HUS Helsinki University Hospital, Haartmaninkatu 4, Helsinki 00290, Finland
| | - Pekka V. Rauhala
- Department of Pharmacology, Faculty of Medicine, Biomedicum 1, University of Helsinki, Haartmaninkatu 8, 00014, Finland
- Individualized Drug Therapy Research Programme, Faculty of Medicine, Biomedicum 1, University of Helsinki, Haartmaninkatu 8, 00014, Finland
| | - Eija A. Kalso
- Department of Pharmacology, Faculty of Medicine, Biomedicum 1, University of Helsinki, Haartmaninkatu 8, 00014, Finland
- SleepWell Research Programme, Faculty of Medicine, , University of Helsinki, Haartmaninkatu 3, 00014, Finland
- Department of Anaesthesiology and Intensive Care Medicine, Helsinki University Hospital and University of Helsinki, HUS, Stenbäckinkatu 9, P.O. Box 440, 00029, Finland
| |
Collapse
|
2
|
Kremp M, Aberle T, Sock E, Bohl B, Hillgärtner S, Winkler J, Wegner M. Transcription factor Olig2 is a major downstream effector of histone demethylase Phf8 during oligodendroglial development. Glia 2024; 72:1435-1450. [PMID: 38613395 DOI: 10.1002/glia.24538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/26/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
The plant homeodomain finger protein Phf8 is a histone demethylase implicated by mutation in mice and humans in neural crest defects and neurodevelopmental disturbances. Considering its widespread expression in cell types of the central nervous system, we set out to determine the role of Phf8 in oligodendroglial cells to clarify whether oligodendroglial defects are a possible contributing factor to Phf8-dependent neurodevelopmental disorders. Using loss- and gain-of-function approaches in oligodendroglial cell lines and primary cell cultures, we show that Phf8 promotes the proliferation of rodent oligodendrocyte progenitor cells and impairs their differentiation to oligodendrocytes. Intriguingly, Phf8 has a strong positive impact on Olig2 expression by acting on several regulatory regions of the gene and changing their histone modification profile. Taking the influence of Olig2 levels on oligodendroglial proliferation and differentiation into account, Olig2 likely acts as an important downstream effector of Phf8 in these cells. In line with such an effector function, ectopic Olig2 expression in Phf8-deficient cells rescues the proliferation defect. Additionally, generation of human oligodendrocytes from induced pluripotent stem cells did not require PHF8 in a system that relies on forced expression of Olig2 during oligodendroglial induction. We conclude that Phf8 may impact nervous system development at least in part through its action in oligodendroglial cells.
Collapse
Affiliation(s)
- Marco Kremp
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Tim Aberle
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Elisabeth Sock
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Bettina Bohl
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Simone Hillgärtner
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jürgen Winkler
- Abteilung für Molekulare Neurologie, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Michael Wegner
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| |
Collapse
|
3
|
Bobis-Wozowicz S, Paw M, Sarna M, Kędracka-Krok S, Nit K, Błażowska N, Dobosz A, Hammad R, Cathomen T, Zuba-Surma E, Tyszka-Czochara M, Madeja Z. Hypoxic extracellular vesicles from hiPSCs protect cardiomyocytes from oxidative damage by transferring antioxidant proteins and enhancing Akt/Erk/NRF2 signaling. Cell Commun Signal 2024; 22:356. [PMID: 38982464 DOI: 10.1186/s12964-024-01722-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 06/21/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Stem cell-derived extracellular vesicles (EVs) are an emerging class of therapeutics with excellent biocompatibility, bioactivity and pro-regenerative capacity. One of the potential targets for EV-based medicines are cardiovascular diseases (CVD). In this work we used EVs derived from human induced pluripotent stem cells (hiPSCs; hiPS-EVs) cultured under different oxygen concentrations (21, 5 and 3% O2) to dissect the molecular mechanisms responsible for cardioprotection. METHODS EVs were isolated by ultrafiltration combined with size exclusion chromatography (UF + SEC), followed by characterization by nanoparticle tracking analysis, atomic force microscopy (AFM) and Western blot methods. Liquid chromatography and tandem mass spectrometry coupled with bioinformatic analyses were used to identify differentially enriched proteins in various oxygen conditions. We directly compared the cardioprotective effects of these EVs in an oxygen-glucose deprivation/reoxygenation (OGD/R) model of cardiomyocyte (CM) injury. Using advanced molecular biology, fluorescence microscopy, atomic force spectroscopy and bioinformatics techniques, we investigated intracellular signaling pathways involved in the regulation of cell survival, apoptosis and antioxidant response. The direct effect of EVs on NRF2-regulated signaling was evaluated in CMs following NRF2 inhibition with ML385. RESULTS We demonstrate that hiPS-EVs derived from physiological hypoxia at 5% O2 (EV-H5) exert enhanced cytoprotective function towards damaged CMs compared to EVs derived from other tested oxygen conditions (normoxia; EV-N and hypoxia 3% O2; EV-H3). This resulted from higher phosphorylation rates of Akt kinase in the recipient cells after transfer, modulation of AMPK activity and reduced apoptosis. Furthermore, we provide direct evidence for improved calcium signaling and sustained contractility in CMs treated with EV-H5 using AFM measurements. Mechanistically, our mass spectrometry and bioinformatics analyses revealed differentially enriched proteins in EV-H5 associated with the antioxidant pathway regulated by NRF2. In this regard, EV-H5 increased the nuclear translocation of NRF2 protein and enhanced its transcription in CMs upon OGD/R. In contrast, inhibition of NRF2 with ML385 abolished the protective effect of EVs on CMs. CONCLUSIONS In this work, we demonstrate a superior cardioprotective function of EV-H5 compared to EV-N and EV-H3. Such EVs were most effective in restoring redox balance in stressed CMs, preserving their contractile function and preventing cell death. Our data support the potential use of hiPS-EVs derived from physiological hypoxia, as cell-free therapeutics with regenerative properties for the treatment of cardiac diseases.
Collapse
Affiliation(s)
- Sylwia Bobis-Wozowicz
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Jagiellonian University, Kraków, Poland.
| | - Milena Paw
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Jagiellonian University, Kraków, Poland
| | - Michał Sarna
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Biophysics, Jagiellonian University, Krakow, Poland
| | - Sylwia Kędracka-Krok
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Krakow, Poland
| | - Kinga Nit
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Jagiellonian University, Kraków, Poland
| | - Natalia Błażowska
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Jagiellonian University, Kraków, Poland
| | - Anna Dobosz
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Jagiellonian University, Kraków, Poland
| | - Ruba Hammad
- Freiburg iPS Core Facility, Institute for Transfusion Medicine and Gene Therapy, Medical Center- University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), University of Freiburg, Freiburg, Germany
| | - Toni Cathomen
- Freiburg iPS Core Facility, Institute for Transfusion Medicine and Gene Therapy, Medical Center- University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), University of Freiburg, Freiburg, Germany
| | - Ewa Zuba-Surma
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Jagiellonian University, Kraków, Poland
| | - Małgorzata Tyszka-Czochara
- Faculty of Pharmacy, Department of Food Chemistry and Nutrition, Jagiellonian University Medical College, Kraków, Poland
| | - Zbigniew Madeja
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Jagiellonian University, Kraków, Poland
| |
Collapse
|
4
|
Grafinger OR, Hayward JJ, Meng Y, Geddes-McAlister J, Li Y, Mar S, Sheng M, Su B, Thillainadesan G, Lipsman N, Coppolino MG, Trant JF, Jerzak KJ, Leong HS. Cancer cell extravasation requires iplectin-mediated delivery of MT1-MMP at invadopodia. Br J Cancer 2024:10.1038/s41416-024-02782-9. [PMID: 38969866 DOI: 10.1038/s41416-024-02782-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/10/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND Invadopodia facilitate cancer cell extravasation, but the molecular mechanism whereby invadopodia-specific proteases such as MT1-MMP are called to invadopodia is unclear. METHODS Mass spectrometry and immunoprecipitation were used to identify interactors of MT1-MMP in metastatic breast cancer cells. After identification, siRNA and small molecule inhibitors were used to assess the effect these interactors had on cellular invasiveness. The chicken embryo chorioallantoic membrane (CAM) model was used to assess extravasation and invadopodia formation in vivo. RESULTS In metastatic breast cancer cells, MT1-MMP was found to associate with plectin, a cytolinker and scaffolding protein. Complex formation between plectin and MT1-MMP launches invadopodia formation, a subtype we termed iplectin (i = invadopodial). iPlectin delivers MT1-MMP to invadopodia and is indispensable for regulating cell surface levels of the enzyme. Genetic depletion of plectin with siRNA reduced invadopodia formation and cell invasion in vitro. In vivo extravasation efficiency assays and intravital imaging revealed iplectin to be a key contributor to invadopodia ultrastructure and essential for extravasation. Pharmacologic inhibition of plectin using the small molecule Plecstatin-1 (PST-1) abrogated MT1-MMP delivery to invadopodia and extravasation efficiency. CONCLUSIONS Anti-metastasis therapeutic approaches that target invadopodia are possible by disrupting interactions between MT1-MMP and iplectin. CLINICAL TRIAL REGISTRATION NUMBER NCT04608357.
Collapse
Affiliation(s)
- Olivia R Grafinger
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
| | - John J Hayward
- Department of Chemistry, University of Windsor, Windsor, ON, Canada
| | - Ying Meng
- Harquail Centre for Neuromodulation, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Division of Neurosurgery, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | | | - Yan Li
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Sara Mar
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Minzhi Sheng
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Boyang Su
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Gobi Thillainadesan
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Nir Lipsman
- Harquail Centre for Neuromodulation, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Division of Neurosurgery, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Marc G Coppolino
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - John F Trant
- Department of Chemistry, University of Windsor, Windsor, ON, Canada
| | - Katarzyna J Jerzak
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology, Sunnybrook Odette Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Hon S Leong
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada.
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
5
|
Huang M, Wang X, Chen Y, Pessoa MT, Terrell KC, Zhang J, Tian J, Xie Z, Pierre SV, Cai L. Role of Na/K-ATPase α1 caveolin-binding motif in adipogenesis. Am J Physiol Cell Physiol 2024; 327:C48-C64. [PMID: 38708522 DOI: 10.1152/ajpcell.00168.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/07/2024]
Abstract
Deficiencies in mice and in humans have brought to the fore the importance of the caveolar network in key aspects of adipocyte biology. The conserved N-terminal caveolin-binding motif (CBM) of the ubiquitous Na/K-ATPase (NKA) α1 isoform, which allows NKA/caveolin-1 (Cav1) interaction, influences NKA signaling and caveolar distribution. It has been shown to be critical for animal development and ontogenesis, as well as lineage-specific differentiation of human induced pluripotent stem cells (hiPSCs). However, its role in postnatal adipogenesis has not been fully examined. Using a genetic approach to alter CBM in hiPSC-derived adipocytes (iAdi-mCBM) and in mice (mCBM), we investigated the regulatory function of NKA CBM signaling in adipogenesis. Seahorse XF cell metabolism analyses revealed impaired glycolysis and decreased ATP synthesis-coupled respiration in iAdi-mCBM. These metabolic dysfunctions were accompanied by evidence of extensive remodeling of the extracellular matrix (ECM), including increased collagen staining, overexpression of ECM marker genes, and heightened TGF-β signaling uncovered by RNAseq analysis. Rescue of mCBM by lentiviral delivery of WT NKA α1 or treatment of mCBM hiPSCs with the TGF-β inhibitor SB431542 normalized ECM, suggesting that NKA CBM signaling integrity is required for adequate control of TGF-β signaling and ECM stiffness during adipogenesis. The physiological impact was revealed in mCBM male mice with reduced fat mass accompanied by histological and transcriptional evidence of elevated adipose fibrosis and decreased adipocyte size. Based on these findings, we propose that the genetic alteration of the NKA/Cav1 regulatory path uncovered in human iAdi leads to lipodystrophy in mice.NEW & NOTEWORTHY A Na/K-ATPase α1 caveolin-binding motif regulates adipogenesis. Mutation of this binding motif in the mouse leads to reduced fat with increased extracellular matrix production and inflammation. RNA-seq analysis and pharmacological interventions in human iPSC-derived adipocytes revealed that TGF-β signal, rather than Na/K-ATPase-mediated ion transport, is a key mediator of NKA regulation of adipogenesis.
Collapse
Affiliation(s)
- Minqi Huang
- Marshall Institute for Interdisciplinary Research, Marshall University, Huntington, West Virginia, United States
| | - Xiaoliang Wang
- Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, United States
| | - Yiliang Chen
- Versiti Blood Research Institute, Milwaukee, West Virginia, United States
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Marco T Pessoa
- Marshall Institute for Interdisciplinary Research, Marshall University, Huntington, West Virginia, United States
| | - Kayleigh C Terrell
- Marshall Institute for Interdisciplinary Research, Marshall University, Huntington, West Virginia, United States
| | - Jue Zhang
- Versiti Blood Research Institute, Milwaukee, West Virginia, United States
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Jiang Tian
- Marshall Institute for Interdisciplinary Research, Marshall University, Huntington, West Virginia, United States
- Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, United States
| | - Zijian Xie
- Marshall Institute for Interdisciplinary Research, Marshall University, Huntington, West Virginia, United States
| | - Sandrine V Pierre
- Marshall Institute for Interdisciplinary Research, Marshall University, Huntington, West Virginia, United States
| | - Liquan Cai
- Marshall Institute for Interdisciplinary Research, Marshall University, Huntington, West Virginia, United States
| |
Collapse
|
6
|
Yen H, Chen P, Huang RY, Jeng J, Lai I. Clinicopathological features and cancer transcriptomic profiling of poorly cohesive gastric carcinoma subtypes. J Pathol Clin Res 2024; 10:e12387. [PMID: 38860888 PMCID: PMC11165978 DOI: 10.1002/2056-4538.12387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/12/2024]
Abstract
Gastric poorly cohesive carcinoma (PCC) manifests with a diffuse pattern and diverse tumor cell morphologies, often indicating a more unfavorable prognosis. Recent consensus has reclassified PCC based on the proportion of signet-ring cells (SRCs) in tumors for research purposes. The two most distinct subtypes, poorly cohesive carcinoma not otherwise specified (PCC-NOS) and signet-ring cell carcinoma (SRCC), are characterized by less than 10% and more than 90% SRCs, respectively. However, research comparing the clinicopathological and transcriptomic differences between these subtypes remains limited. In this study, we conducted a comparative analysis of clinicopathological features in 55 advanced-stage PCCs, consisting of 43 PCC-NOS and 12 SRCC cases. Subsequently, 12 PCC-NOS and 5 SRCC cases were randomly selected for initial cancer-related gene expression profiling and pathway enrichment analysis using the GeoMx digital spatial profiler, followed by validation in a separate validation group comprising 16 PCC-NOS and 6 SRCC cases. These transcriptomic findings were then correlated with tumor morphology and clinicopathological data. PCC-NOS cases exhibited larger tumor size, a higher prevalence of pathological N3 disease, and a worse 1-year progression-free survival rate compared to SRCC cases. Clustering of PCC-NOS and SRCC was successfully achieved using the GeoMx Cancer Transcriptome Atlas. Among all studied genes, only MMP7 showed differential expression, with its overexpression significantly associated with the PCC-NOS subtype, increased perineural invasion, and earlier disease progression. Pathway analysis revealed significantly enriched pathways in PCC-NOS related to vesicle-mediated transport, adaptive immune systems, oncogenic signaling, and extracellular matrix organization, while SRCC displayed significant enrichment in pathways associated with respiratory electron transport and the cell cycle. In conclusion, this study compares and correlates clinicopathological features and transcriptomic data between PCC-NOS and SRCC at advanced stages, employing the latest consensus classification and a novel platform for analysis.
Collapse
Affiliation(s)
- Hung‐Hsuan Yen
- Department of SurgeryNational Taiwan University Hospital Hsin‐Chu BranchHsinchuTaiwan
- Department of SurgeryNational Taiwan University HospitalTaipeiTaiwan
| | - Pin‐Yu Chen
- Graduate Institute of Anatomy and Cell Biology, College of MedicineNational Taiwan UniversityTaipeiTaiwan
| | - Ruby Yun‐Ju Huang
- School of Medicine, College of MedicineNational Taiwan UniversityTaipeiTaiwan
| | - Jung‐Ming Jeng
- Department of PathologyNational Taiwan University HospitalTaipeiTaiwan
| | - I‐Rue Lai
- Department of SurgeryNational Taiwan University HospitalTaipeiTaiwan
- Graduate Institute of Anatomy and Cell Biology, College of MedicineNational Taiwan UniversityTaipeiTaiwan
| |
Collapse
|
7
|
Schmidt AL, Kremp M, Aratake T, Cui S, Lin Y, Zhong X, Lu QR, Zhang C, Qiu M, Aberle T, Wegner M. The myelination-associated G protein-coupled receptor 37 is regulated by Zfp488, Nkx2.2, and Sox10 during oligodendrocyte differentiation. Glia 2024; 72:1304-1318. [PMID: 38546197 DOI: 10.1002/glia.24530] [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: 10/12/2023] [Revised: 03/13/2024] [Accepted: 03/19/2024] [Indexed: 05/12/2024]
Abstract
Oligodendrocyte differentiation and myelination in the central nervous system are controlled and coordinated by a complex gene regulatory network that contains several transcription factors, including Zfp488 and Nkx2.2. Despite the proven role in oligodendrocyte differentiation little is known about the exact mode of Zfp488 and Nkx2.2 action, including their target genes. Here, we used overexpression of Zfp488 and Nkx2.2 in differentiating CG4 cells to identify aspects of the oligodendroglial expression profile that depend on these transcription factors. Although both transcription factors are primarily described as repressors, the detected changes argue for an additional function as activators. Among the genes activated by both Zfp488 and Nkx2.2 was the G protein-coupled receptor Gpr37 that is important during myelination. In agreement with a positive effect on Gpr37 expression, downregulation of the G protein-coupled receptor was observed in Zfp488- and in Nkx2.2-deficient oligodendrocytes in the mouse. We also identified several potential regulatory regions of the Gpr37 gene. Although Zfp488 and Nkx2.2 both bind to one of the regulatory regions downstream of the Gpr37 gene in vivo, none of the regulatory regions was activated by either transcription factor alone. Increased activation by Zfp488 or Nkx2.2 was only observed in the presence of Sox10, a transcription factor continuously present in oligodendroglial cells. Our results argue that both Zfp488 and Nkx2.2 also act as transcriptional activators during oligodendrocyte differentiation and cooperate with Sox10 to allow the expression of Gpr37 as a modulator of the myelination process.
Collapse
Affiliation(s)
- Antonia L Schmidt
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Marco Kremp
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Takaaki Aratake
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Siying Cui
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yifeng Lin
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiaowen Zhong
- Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio, USA
| | - Q Richard Lu
- Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio, USA
| | - Chengfu Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Life Sciences, Key Laboratory of Organ Development and Regeneration of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Mengsheng Qiu
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Life Sciences, Key Laboratory of Organ Development and Regeneration of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Tim Aberle
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Michael Wegner
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| |
Collapse
|
8
|
Luna HGC, Imasa MS, Juat N, Hernandez KV, Sayo TM, Cristal-Luna G, Asur-Galang SM, Bellengan M, Duga KJ, Buenaobra BB, De Los Santos MI, Medina D, Samo J, Literal VM, Sy-Naval S. NKX2‑1 copy number alterations are associated with oncogenic, immunological and prognostic remodeling in non‑small cell lung cancer. Oncol Lett 2024; 28:303. [PMID: 38774453 PMCID: PMC11106692 DOI: 10.3892/ol.2024.14436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/05/2023] [Indexed: 05/24/2024] Open
Abstract
NK2 homeobox 1 (NKX2-1) copy number alterations (CNAs) are frequently observed in lung cancer. However, little is known about the complete landscape of focal alterations in NKX2-1 copy number (CN), their clinical significance and their therapeutic implications in non-small cell lung cancer (NSCLC). The correlations between NKX2-1 expression and EGFR driver mutations and programmed death ligand 1 (PD-L1) co-expression were studied using immunohistochemistry and PCR from the tumors of recruited Filipino patients (n=45). Clinical features of NSCLC with NKX2-1 CNAs were resolved at the tumor and clonal levels using the molecular profiles of patients with lung adenocarcinoma and lung squamous cell carcinoma from The Cancer Genome Atlas (n=1,130), and deconvoluted single-cell RNA-seq data from the Bivona project (n=1,654), respectively. Despite a significant and positive correlation between expression and CN (r=0.264; P<0.001), NKX2-1 CNAs exerted a stronger influence on the combined EGFR and PD-L1 status of NSCLC tumors than expression. NKX2-1 CN gain was prognostic of favorable survival (P=0.018) and a better response to targeted therapy. NKX2-1 CN loss predicted a worse survival (P=0.041). Mutational architecture in the Y-chromosome differentiated the two prognostic groups. There were 19,941 synonymous mutations and 1,408 genome-wide CN perturbations associated with NKX2-1 CNAs. Tumors with NKX2-1 CN gain expressed lymphocyte markers more heterogeneously than those with CN loss. Higher expression of tumor-infiltrating lymphocyte gene signatures in CN gain was prognostic of longer disease-free survival (P=0.005). Tumors with NKX2-1 CN gain had higher B-cell (P<0.001) and total T-cell estimates (P=0.003). NKX2-1 CN loss was associated with immunologically colder tumors due to higher M2 macrophage infiltrates (P=0.011) and higher expression of immune checkpoint proteins, CD274 (P=0.025), VTCN1 (P<0.001) and LGALS9 (P=0.002). In conclusion, NKX2-1 CNAs are associated with tumors that exhibit clinically diverse characteristics, and with unique oncogenic, immunological and prognostic signatures.
Collapse
Affiliation(s)
- Herdee Gloriane C. Luna
- Department of Medical Oncology, Lung Center of The Philippines, Quezon City, Metro Manila 1100, Philippines
- Department of Internal Medicine, Section of Medical Oncology, National Kidney and Transplant Institute, Quezon City, Metro Manila 1101, Philippines
| | - Marcelo Severino Imasa
- Department of Medical Oncology, Lung Center of The Philippines, Quezon City, Metro Manila 1100, Philippines
| | - Necy Juat
- Department of Internal Medicine, Section of Medical Oncology, National Kidney and Transplant Institute, Quezon City, Metro Manila 1101, Philippines
| | - Katherine V. Hernandez
- Department of Internal Medicine, Section of Oncology, East Avenue Medical Center, Quezon City, Metro Manila 1100, Philippines
| | - Treah May Sayo
- Department of Pathology and Laboratory Medicine, Lung Center of The Philippines, Quezon City, Metro Manila 1100, Philippines
| | - Gloria Cristal-Luna
- Department of Internal Medicine, Section of Medical Oncology, National Kidney and Transplant Institute, Quezon City, Metro Manila 1101, Philippines
| | - Sheena Marie Asur-Galang
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Mirasol Bellengan
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Kent John Duga
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Bien Brian Buenaobra
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Marvin I. De Los Santos
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
- Globetek Science Foundation Inc., Makati, Metro Manila 1203, Philippines
| | - Daniel Medina
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Jamirah Samo
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Venus Minerva Literal
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Sullian Sy-Naval
- Department of Medical Oncology, Lung Center of The Philippines, Quezon City, Metro Manila 1100, Philippines
| |
Collapse
|
9
|
Pechous RD, Malaviarachchi PA, Banerjee SK, Byrum SD, Alkam DH, Ghaffarieh A, Kurten RC, Kennedy JL, Zhang X. An ex vivo human precision-cut lung slice platform provides insight into SARS-CoV-2 pathogenesis and antiviral drug efficacy. J Virol 2024:e0079424. [PMID: 38940558 DOI: 10.1128/jvi.00794-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) has claimed millions of lives since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and lung disease appears the primary cause of death in COVID-19 patients. However, the underlying mechanisms of COVID-19 pathogenesis remain elusive, and there is no existing model where human disease can be faithfully recapitulated and conditions for the infection process can be experimentally controlled. Herein we report the establishment of an ex vivo human precision-cut lung slice (hPCLS) platform for studying SARS-CoV-2 pathogenicity and innate immune responses, and for evaluating the efficacy of antiviral drugs against SARS-CoV-2. We show that while SARS-CoV-2 continued to replicate during the course of infection of hPCLS, infectious virus production peaked within 2 days, and rapidly declined thereafter. Although most proinflammatory cytokines examined were induced by SARS-CoV-2 infection, the degree of induction and types of cytokines varied significantly among hPCLS from individual donors. Two cytokines in particular, IP-10 and IL-8, were highly and consistently induced, suggesting a role in the pathogenesis of COVID-19. Histopathological examination revealed focal cytopathic effects late in the infection. Transcriptomic and proteomic analyses identified molecular signatures and cellular pathways that are largely consistent with the progression of COVID-19 in patients. Furthermore, we show that homoharringtonine, a natural plant alkaloid derived from Cephalotoxus fortunei, not only inhibited virus replication but also production of pro-inflammatory cytokines, and thus ameliorated the histopathological changes caused by SARS-CoV-2 infection, demonstrating the usefulness of the hPCLS platform for evaluating antiviral drugs. IMPORTANCE Here, established an ex vivo human precision-cut lung slice platform for assessing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, viral replication kinetics, innate immune response, disease progression, and antiviral drugs. Using this platform, we identified early induction of specific cytokines, especially IP-10 and IL-8, as potential predictors for severe coronavirus disease 2019 (COVID-19), and uncovered a hitherto unrecognized phenomenon that while infectious virus disappears at late times of infection, viral RNA persists and lung histopathology commences. This finding may have important clinical implications for both acute and post-acute sequelae of COVID-19. This platform recapitulates some of the characteristics of lung disease observed in severe COVID-19 patients and is therefore a useful platform for understanding mechanisms of SARS-CoV-2 pathogenesis and for evaluating the efficacy of antiviral drugs.
Collapse
Affiliation(s)
- Roger D Pechous
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Priyangi A Malaviarachchi
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Srijon K Banerjee
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - Duah H Alkam
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Alireza Ghaffarieh
- Department of Ophthalmology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Richard C Kurten
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Lung Cell Biology Laboratory, Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - Joshua L Kennedy
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Lung Cell Biology Laboratory, Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - Xuming Zhang
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| |
Collapse
|
10
|
Ahmadi M, Abdollahi R, Otogara M, Taherkhani A. Exploring molecular targets: herbal isolates in cervical cancer therapy. Genomics Inform 2024; 22:9. [PMID: 38926832 PMCID: PMC11201312 DOI: 10.1186/s44342-024-00008-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 06/28/2024] Open
Abstract
OBJECTIVE Cervical cancer (CxCa) stands as a significant global health challenge, ranking fourth in cancer-related mortality among the female population. While chemotherapy regimens have demonstrated incremental progress in extending overall survival, the outlook for recurrent CxCa patients remains disheartening. An imperative necessity arises to delve into innovative therapeutic avenues, with molecular targeted therapy emerging as a promising candidate. Previous investigations have shed light on the therapeutic effectiveness of five distinct herbal compounds, epicatechin, curcumin, myricetin, jatrorrhizine, and arborinine, within the context of CxCa. METHODS A systems biology approach was employed to discern differentially expressed genes (DEGs) in CxCa tissues relative to healthy cervical epithelial tissues. A protein-protein interaction network (PPIN) was constructed, anchored in the genes related to CxCa. The central genes were discerned within the PPIN, and Kaplan-Meier survival curves explored their prognostic significance. An assessment of the binding affinity of the selected herbal compounds to the master regulator of prognostic markers in CxCa was conducted. RESULTS A significant correlation between the overexpression of MYC, IL6, JUN, RRM2, and VEGFA and an adverse prognosis in CxCa was indicated. The regulation of these markers is notably influenced by the transcription factor CEBPD. Molecular docking analysis indicated that the binding affinity between myricetin and the CEBPD DNA binding site was robust. CONCLUSION The findings presented herein have unveiled pivotal genes and pathways that play a central role in the malignant transformation of CxCa. CEBPD has emerged as a potential target for harnessing the therapeutic potential of myricetin in this context.
Collapse
Affiliation(s)
- Maryam Ahmadi
- Clinical Research Development Unit of Fatemiyeh Hospital, Department of Gynecology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Razieh Abdollahi
- Clinical Research Development Unit of Fatemiyeh Hospital, Department of Gynecology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Marzieh Otogara
- Mother and Child Care Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| |
Collapse
|
11
|
Subramanian V, Juhr D, Johnson LS, Yem JB, Giansanti P, Grumbach IM. Changes in the Proteome of the Circle of Willis during Aging Reveal Signatures of Vascular Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2024; 2024:4887877. [PMID: 38962180 PMCID: PMC11221951 DOI: 10.1155/2024/4887877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 04/22/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024]
Abstract
Approximately 70% of all strokes occur in patients over 65 years old, and stroke increases the risk of developing dementia. The circle of Willis (CoW), the ring of arteries at the base of the brain, links the intracerebral arteries to one another to maintain adequate cerebral perfusion. The CoW proteome is affected in cerebrovascular and neurodegenerative diseases, but changes related to aging have not been described. Here, we report on a quantitative proteomics analysis comparing the CoW from five young (2-3-month-old) and five aged male (18-20-month-old) mice using gene ontology (GO) enrichment, ingenuity pathway analysis (IPA), and iPathwayGuide tools. This revealed 242 proteins that were significantly dysregulated with aging, among which 189 were upregulated and 53 downregulated. GO enrichment-based analysis identified blood coagulation as the top biological function that changed with age and integrin binding and extracellular matrix constituents as the top molecular functions. Consistent with these findings, iPathwayGuide-based impact analysis revealed associations between aging and the complement and coagulation, platelet activation, ECM-receptor interaction, and metabolic process pathways. Furthermore, IPA analysis revealed the enrichment of 97 canonical pathways that contribute to inflammatory responses, as well as 59 inflammation-associated upstream regulators including 39 transcription factors and 20 cytokines. Thus, aging-associated changes in the CoW proteome in male mice demonstrate increases in metabolic, thrombotic, and inflammatory processes.
Collapse
Affiliation(s)
- Vikram Subramanian
- Abboud Cardiovascular Research CenterDepartment of Internal MedicineCarver College of MedicineUniversity of Iowa, Iowa City, USA
| | - Denise Juhr
- Abboud Cardiovascular Research CenterDepartment of Internal MedicineCarver College of MedicineUniversity of Iowa, Iowa City, USA
| | - Lydia S. Johnson
- Abboud Cardiovascular Research CenterDepartment of Internal MedicineCarver College of MedicineUniversity of Iowa, Iowa City, USA
| | - Justin B. Yem
- Abboud Cardiovascular Research CenterDepartment of Internal MedicineCarver College of MedicineUniversity of Iowa, Iowa City, USA
| | - Piero Giansanti
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS@MRI)Technical University of Munich, Munich, Germany
| | - Isabella M. Grumbach
- Abboud Cardiovascular Research CenterDepartment of Internal MedicineCarver College of MedicineUniversity of Iowa, Iowa City, USA
- Free Radical and Radiation Biology ProgramDepartment of Radiation OncologyCarver College of MedicineUniversity of Iowa, Iowa City, USA
- Iowa City VA Healthcare System, Iowa City, IA, USA
| |
Collapse
|
12
|
Pénzes Z, Horváth D, Molnár P, Fekete T, Pázmándi K, Bácsi A, Szöllősi AG. Anandamide modulation of monocyte-derived Langerhans cells: implications for immune homeostasis and skin inflammation. Front Immunol 2024; 15:1423776. [PMID: 38979427 PMCID: PMC11228147 DOI: 10.3389/fimmu.2024.1423776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/06/2024] [Indexed: 07/10/2024] Open
Abstract
Introduction The endocannabinoid system (ECS), named after the chemical compounds found in the cannabis plant, is a regulatory network of neurotransmitters, receptors, and enzymes that plays crucial roles in skin health and disease. Endogenous ligands of the ECS, called endocannabinoids, have proven to be important regulators of immune responses. One of the most prevalent endocannabinoids, arachidonoylethanolamide (also known as anandamide), is known for its anti-inflammatory effects. Langerhans cells (LCs) are the sole antigen-presenting cells present in the human epidermis. They serve as the first line of defense against pathogens and are essential for the skin's specific immune responses and play a critical role in maintaining tissue homeostasis; however, little is known about the effect of endocannabinoids on these cells. Our research aimed to provide the connection between monocyte-derived Langerhans cells (moLCs) and the ECS, shedding light on their collaborative roles in immune homeostasis and inflammation. Methods Human monocytes were differentiated into moLCs using established protocols. Anandamide was applied during the differentiation process to test its effect on the viability, marker expression, and cytokine production of the cells, as well as in short term treatments for intracellular calcium measurement. TLR ligands applied after the differentiation protocol were used to activate moLCs. The impact of anandamide on the functionality of moLCs was further assessed using differential gene expression analysis of bulk RNA-Seq data, moLC-T cell cocultures, while ELISpot was employed to determine polarization of T cells activated in the aforementioned cocultures. Results Anandamide did not significantly affect the viability of moLCs up to 10 µM. When applied during the differentiation process it had only a negligible effect on CD207 expression, the prototypic marker of LCs; however, there was an observed reduction in CD1a expression by moLCs. Anandamide had no significant effects on the maturation status of moLCs, nor did it affect the maturation induced by TLR3 and TLR7/8 agonists. MoLCs differentiated in the presence of anandamide did however show decreased production of CXCL8, IL-6, IL-10 and IL-12 cytokines induced by TLR3 and TLR7/8 activation. Anandamide-treated moLCs showed an increased capability to activate naïve T cells; however, not to the level seen with combined TLR agonism. RNA sequencing analysis of moLCs differentiated with anandamide showed modest changes compared to control cells but did reveal an inhibitory effect on oxidative phosphorylation specifically in activated moLCs. Anandamide also promoted the polarization of naïve T cells towards a Th1 phenotype. Discussion Our results show that anandamide has nuanced effects on the differentiation, maturation, cytokine secretion, metabolism and function of activated moLCs. Among these changes the decrease in CD1a expression on moLCs holds promise to selectively dampen inflammation induced by CD1a restricted T cells, which have been implicated as drivers of inflammation in common inflammatory skin conditions such as psoriasis, atopic dermatitis and contact dermatitis.
Collapse
Affiliation(s)
- Zsófia Pénzes
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - Dorottya Horváth
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - Petra Molnár
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - Tünde Fekete
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Kitti Pázmándi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Bácsi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- ELKH-DE Allergology Research Group, Debrecen, Hungary
| | - Attila Gábor Szöllősi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| |
Collapse
|
13
|
Cox D, Hatters DM. PERCEPT: Replacing binary p-value thresholding with scaling for more nuanced identification of sample differences. iScience 2024; 27:109891. [PMID: 38832020 PMCID: PMC11145341 DOI: 10.1016/j.isci.2024.109891] [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: 08/14/2023] [Revised: 04/16/2024] [Accepted: 04/30/2024] [Indexed: 06/05/2024] Open
Abstract
Key to a biologists' capacity to understand data is the ability to make meaningful conclusions about differences in experimental observations. Typically, data are noisy, and conventional methods rely on replicates to average out noise and enable univariate statistical tests to assign p-values. Yet thresholding p-values to determine significance is controversial and often misleading, especially for omics datasets with few replicates. This study introduces PERCEPT, an alternative that transforms data using an ad-hoc scaling factor derived from p-values. By applying this method, low confidence effects are suppressed compared to high confidence ones, enabling clearer patterns to emerge from noisy datasets. The effectiveness of PERCEPT scaling is demonstrated using simulated datasets and published omics studies. The approach reduces the exclusion of datapoints, enhances accuracy, and enables nuanced interpretation of data. PERCEPT is easy to apply for the non-expert in statistics and provides researchers a straightforward way to improve data-driven analyses.
Collapse
Affiliation(s)
- Dezerae Cox
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
- Molecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2500 Australia
| | - Danny M. Hatters
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| |
Collapse
|
14
|
Laragione T, Harris C, Rice N, Gulko PS. DUSP6 deletion protects mice and reduces disease severity in autoimmune arthritis. iScience 2024; 27:110158. [PMID: 38974475 PMCID: PMC11225809 DOI: 10.1016/j.isci.2024.110158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/26/2024] [Accepted: 05/28/2024] [Indexed: 07/09/2024] Open
Abstract
Receptor tyrosine kinases (RTKs) have an important role in arthritis severity and in models of rheumatoid arthritis (RA), but their regulation is not fully understood. The dual specificity phosphatase 6 (DUSP6) has been implicated in the regulation of RTK signaling, but never in the context of arthritis and autoimmunity. We used the KRN serum-induced arthritis (KSIA) model of RA and showed that DUSP6-/- mice were protected and had a 50% lower maximum arthritis score (p = 0.006) and reduced joint damage than C57BL/6 DUSP6+/+ controls. Serum levels of interleukin (IL) 10 were significantly increased (>2-fold), and IL6 decreased in DUSP6-/- mice. DUSP6-/- mice had increased numbers of IL10+ cells including Tr1 regulatory cells (p < 0.01). Introduction of the IL10-/- into DUSP6-/- (double knockout [KO]) reversed the DUSP6-/- protection. In conclusion, this study reports a pro-arthritic role for DUSP6. This discovery has the potential to generate a previously unknown target for therapies for RA and inflammatory diseases.
Collapse
Affiliation(s)
- Teresina Laragione
- Division of Rheumatology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carolyn Harris
- Division of Rheumatology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Natasha Rice
- Division of Rheumatology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Percio S. Gulko
- Division of Rheumatology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
15
|
Hulahan TS, Spruill L, Wallace EN, Park Y, West RB, Marks JR, Hwang ES, Drake RR, Angel PM. Extracellular Microenvironment Alterations in Ductal Carcinoma In Situ and Invasive Breast Cancer Pathologies by Multiplexed Spatial Proteomics. Int J Mol Sci 2024; 25:6748. [PMID: 38928454 PMCID: PMC11203487 DOI: 10.3390/ijms25126748] [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: 05/07/2024] [Revised: 06/10/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
Ductal carcinoma in situ (DCIS) is a heterogeneous breast disease that remains challenging to treat due to its unpredictable progression to invasive breast cancer (IBC). Contemporary literature has become increasingly focused on extracellular matrix (ECM) alterations with breast cancer progression. However, the spatial regulation of the ECM proteome in DCIS has yet to be investigated in relation to IBC. We hypothesized that DCIS and IBC present distinct ECM proteomes that could discriminate between these pathologies. Tissue sections of pure DCIS, mixed DCIS-IBC, or pure IBC (n = 22) with detailed pathological annotations were investigated by multiplexed spatial proteomics. Across tissues, 1,005 ECM peptides were detected in pathologically annotated regions and their surrounding extracellular microenvironments. A comparison of DCIS to IBC pathologies demonstrated 43 significantly altered ECM peptides. Notably, eight fibrillar collagen peptides could distinguish with high specificity and sensitivity between DCIS and IBC. Lesion-targeted proteomic imaging revealed heterogeneity of the ECM proteome surrounding individual DCIS lesions. Multiplexed spatial proteomics reported an invasive cancer field effect, in which DCIS lesions in closer proximity to IBC shared a more similar ECM profile to IBC than distal counterparts. Defining the ECM proteomic microenvironment provides novel molecular insights relating to DCIS and IBC.
Collapse
Affiliation(s)
- Taylor S. Hulahan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Laura Spruill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Elizabeth N. Wallace
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Yeonhee Park
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53726, USA;
| | - Robert B. West
- Department of Pathology Clinical, Stanford University, Stanford, CA 94305, USA;
| | - Jeffrey R. Marks
- Department of Surgery, Duke University, Durham, NC 27710, USA; (J.R.M.); (E.S.H.)
| | - E. Shelley Hwang
- Department of Surgery, Duke University, Durham, NC 27710, USA; (J.R.M.); (E.S.H.)
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| |
Collapse
|
16
|
Zeng X, Lafferty TK, Sehrawat A, Chen Y, Ferreira PCL, Bellaver B, Povala G, Kamboh MI, Klunk WE, Cohen AD, Lopez OL, Ikonomovic MD, Pascoal TA, Ganguli M, Villemagne VL, Snitz BE, Karikari TK. Multi-analyte proteomic analysis identifies blood-based neuroinflammation, cerebrovascular and synaptic biomarkers in preclinical Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.15.24308975. [PMID: 38947065 PMCID: PMC11213097 DOI: 10.1101/2024.06.15.24308975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background Blood-based biomarkers are gaining grounds for Alzheimer's disease (AD) detection. However, two key obstacles need to be addressed: the lack of methods for multi-analyte assessments and the need for markers of neuroinflammation, vascular, and synaptic dysfunction. Here, we evaluated a novel multi-analyte biomarker platform, NULISAseq CNS disease panel, a multiplex NUcleic acid-linked Immuno-Sandwich Assay (NULISA) targeting ~120 analytes, including classical AD biomarkers and key proteins defining various disease hallmarks. Methods The NULISAseq panel was applied to 176 plasma samples from the MYHAT-NI cohort of cognitively normal participants from an economically underserved region in Western Pennsylvania. Classical AD biomarkers, including p-tau181 p-tau217, p-tau231, GFAP, NEFL, Aβ40, and Aβ42, were also measured using Single Molecule Array (Simoa). Amyloid pathology, tau pathology, and neurodegeneration were evaluated with [11C] PiB PET, [18F]AV-1451 PET, and MRI, respectively. Linear mixed models were used to examine cross-sectional and Wilcoxon rank sum tests for longitudinal associations between NULISA biomarkers and AD pathologies. Spearman correlations were used to compare NULISA and Simoa. Results NULISA concurrently measured 116 plasma biomarkers with good technical performance, and good correlation with Simoa measures. Cross-sectionally, p-tau217 was the top hit to identify Aβ pathology, with age, sex, and APOE genotype-adjusted AUC of 0.930 (95%CI: 0.878-0.983). Fourteen markers were significantly decreased in Aβ-PET+ participants, including TIMP3, which regulates brain Aβ production, the neurotrophic factor BDNF, the energy metabolism marker MDH1, and several cytokines. Longitudinally, FGF2, IL4, and IL9 exhibited Aβ PET-dependent yearly increases in Aβ-PET+ participants. Markers with tau PET-dependent longitudinal changes included the microglial activation marker CHIT1, the reactive astrogliosis marker CHI3L1, the synaptic protein NPTX1, and the cerebrovascular markers PGF, PDGFRB, and VEFGA; all previously linked to AD but only reliably measured in cerebrospinal fluid. SQSTM1, the autophagosome cargo protein, exhibited a significant association with neurodegeneration status after adjusting age, sex, and APOE ε4 genotype. Conclusions Together, our results demonstrate the feasibility and potential of immunoassay-based multiplexing to provide a comprehensive view of AD-associated proteomic changes. Further validation of the identified inflammation, synaptic, and vascular markers will be important for establishing disease state markers in asymptomatic AD.
Collapse
Affiliation(s)
- Xuemei Zeng
- Department of Psychiatry, School of Medicine, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
| | - Tara K. Lafferty
- Department of Psychiatry, School of Medicine, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
| | - Anuradha Sehrawat
- Department of Psychiatry, School of Medicine, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
| | - Yijun Chen
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Pamela C. L. Ferreira
- Department of Psychiatry, School of Medicine, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
| | - Bruna Bellaver
- Department of Psychiatry, School of Medicine, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
| | - Guilherme Povala
- Department of Psychiatry, School of Medicine, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
| | - M. Ilyas Kamboh
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - William E. Klunk
- Department of Psychiatry, School of Medicine, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
| | - Ann D. Cohen
- Department of Psychiatry, School of Medicine, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
| | - Oscar L. Lopez
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Milos D. Ikonomovic
- Department of Psychiatry, School of Medicine, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Geriatric Research Education and Clinical Center, VA Pittsburgh HS, Pittsburgh, PA, USA
| | - Tharick A. Pascoal
- Department of Psychiatry, School of Medicine, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
| | - Mary Ganguli
- Department of Psychiatry, School of Medicine, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Victor L. Villemagne
- Department of Psychiatry, School of Medicine, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
| | - Beth E. Snitz
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Thomas K. Karikari
- Department of Psychiatry, School of Medicine, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
| |
Collapse
|
17
|
Barrault M, Chabelskaya S, Coronel-Tellez RH, Toffano-Nioche C, Jacquet E, Bouloc P. Staphylococcal aconitase expression during iron deficiency is controlled by an sRNA-driven feedforward loop and moonlighting activity. Nucleic Acids Res 2024:gkae506. [PMID: 38869061 DOI: 10.1093/nar/gkae506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
Pathogenic bacteria employ complex systems to cope with metal ion shortage conditions and propagate in the host. IsrR is a regulatory RNA (sRNA) whose activity is decisive for optimum Staphylococcus aureus fitness upon iron starvation and for full virulence. IsrR down-regulates several genes encoding iron-containing enzymes to spare iron for essential processes. Here, we report that IsrR regulates the tricarboxylic acid (TCA) cycle by controlling aconitase (CitB), an iron-sulfur cluster-containing enzyme, and its transcriptional regulator, CcpE. This IsrR-dependent dual-regulatory mechanism provides an RNA-driven feedforward loop, underscoring the tight control required to prevent aconitase expression. Beyond its canonical enzymatic role, aconitase becomes an RNA-binding protein with regulatory activity in iron-deprived conditions, a feature that is conserved in S. aureus. Aconitase not only negatively regulates its own expression, but also impacts the enzymes involved in both its substrate supply and product utilization. This moonlighting activity concurrently upregulates pyruvate carboxylase expression, allowing it to compensate for the TCA cycle deficiency associated with iron scarcity. These results highlight the cascade of complex posttranscriptional regulations controlling S. aureus central metabolism in response to iron deficiency.
Collapse
Affiliation(s)
- Maxime Barrault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Svetlana Chabelskaya
- Université de Rennes 1, BRM (Bacterial regulatory RNAs and Medicine) UMR_S 1230, 35000 Rennes, France
| | - Rodrigo H Coronel-Tellez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Claire Toffano-Nioche
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Eric Jacquet
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR2301, 91198 Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| |
Collapse
|
18
|
Gardner R, Kyle M, Hughes K, Zhao LR. Single cell RNA sequencing reveals immunomodulatory effects of stem cell factor and granulocyte colony-stimulating factor treatment in the brains of aged APP/PS1 mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593359. [PMID: 38766064 PMCID: PMC11100789 DOI: 10.1101/2024.05.09.593359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Alzheimers disease leads to progressive neurodegeneration and dementia. Alzheimers disease primarily affects older adults with neuropathological changes including amyloid beta deposition, neuroinflammation, and neurodegeneration. We have previously demonstrated that systemic treatment with combined stem cell factor, SCF, and granulocyte colony stimulating factor, GCSF, reduces amyloid beta load, increases amyloid beta uptake by activated microglia and macrophages, reduces neuroinflammation, and restores dendrites and synapses in the brains of aged APP-PS1 mice. However, the mechanisms underlying SCF-GCSF-enhanced brain repair in aged APP-PS1 mice remain unclear. This study used a transcriptomic approach to identify potential mechanisms by which SCF-GCSF treatment modulates microglia and peripheral myeloid cells to mitigate Alzheimers disease pathology in the aged brain. After injections of SCF-GCSF for 5 consecutive days, single cell RNA sequencing was performed on CD11b positive cells isolated from the brains of 28-month-old APP-PS1 mice. The vast majority of cell clusters aligned with transcriptional profiles of microglia in various activation states. However, SCF-GCSF treatment dramatically increased a cell population showing upregulation of marker genes related to peripheral myeloid cells. Flow cytometry data also revealed an SCF-GCSF-induced increase of cerebral CD45high-CD11b positive active phagocytes. SCF-GCSF treatment robustly increased the transcription of genes implicated in immune cell activation, including gene sets that regulate inflammatory processes and cell migration. Expression of S100a8 and S100a9 were robustly enhanced following SCF-GCSF treatment in all CD11b positive cell clusters. Moreover, the topmost genes differentially expressed with SCF-GCSF treatment were largely upregulated in S100a8-S100a9 positive cells, suggesting a well-conserved transcriptional profile related to SCF-GCSF treatment in resident and peripherally derived CD11b positive immune cells. This S100a8-S100a9-associated transcriptional profile contained notable genes related to proinflammatory and antiinflammatory responses, neuroprotection, and amyloid beta plaque inhibition or clearance. Altogether, this study reveals immunomodulatory effects of SCF-GCSF treatment in the aged brain with Alzheimers disease pathology, which will guide future studies to further uncover the therapeutic mechanisms.
Collapse
|
19
|
Bedi K, Magnuson B, Narayanan IV, McShane A, Ashaka M, Paulsen MT, Wilson TE, Ljungman M. Isoform and pathway-specific regulation of post-transcriptional RNA processing in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598705. [PMID: 38915566 PMCID: PMC11195214 DOI: 10.1101/2024.06.12.598705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Steady-state levels of RNA transcripts are controlled by their rates of synthesis and degradation. Here we used nascent RNA Bru-seq and BruChase-seq to profile RNA dynamics across 16 human cell lines as part of ENCODE4 Deeply Profiled Cell Lines collection. We show that RNA turnover dynamics differ widely between transcripts of different genes and between different classes of RNA. Gene set enrichment analysis (GSEA) revealed that transcripts encoding proteins belonging to the same pathway often show similar turnover dynamics. Furthermore, transcript isoforms show distinct dynamics suggesting that RNA turnover is important in regulating mRNA isoform choice. Finally, splicing across newly made transcripts appears to be cooperative with either all or none type splicing. These data sets generated as part of ENCODE4 illustrate the intricate and coordinated regulation of RNA dynamics in controlling gene expression to allow for the precise coordination of cellular functions.
Collapse
Affiliation(s)
- Karan Bedi
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brian Magnuson
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology and Department of Human Genetics, University of Michigan Medical School, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Ariel McShane
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mario Ashaka
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas E Wilson
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology and Department of Human Genetics, University of Michigan Medical School, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
20
|
Karaselek MA, Duran T, Kuccukturk S, Vatansev H, Oltulu P. Changes in T-cell subsets occur in interstitial lung disease and may contribute to pathology via complicated immune cascade. APMIS 2024. [PMID: 38860355 DOI: 10.1111/apm.13445] [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: 03/20/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
The study aimed to investigate the expression profiles of transcription factors, cytokines, and co-stimulatory molecules in helper T (Th)-cell subsets within bronchoalveolar lavage (BAL) samples of patients with interstitial lung diseases (ILDs). Twenty ILDs patients were included in the study, comprising those with idiopathic pulmonary fibrosis (IPF) (n:8), autoimmune-related ILDs (auto-ILD) (n:4), and orphan diseases (O-ILD) (n:8), alongside five control subjects. Flow cytometry was employed to evaluate the Th to cytotoxic T cell (CTL) ratio in BAL fluid, while cytopathological examination assessed macrophages, lymphocytes, and neutrophils. Quantitative real-time polymerase chain reaction was utilized to investigate the expressions in Th1, Th2, Th17, and regulatory T (Treg) cells. Results revealed elevated Th cell to CTL ratios across all patient groups compared to controls. Furthermore, upregulation of Th1, Th2, Th17, and T-cell factors was observed in all patient groups compared to controls. Interestingly, upregulation of CD28 and downregulation of CTLA-4 and PD-1 gene expression were consistent across all ILDs groups, highlighting potential immune dysregulation. This study provides a comprehensive exploration of molecular immunological mechanisms in ILDs patients, underscoring the dominance of Th2 and Th17 responses and revealing novel findings regarding the dysregulation of CD28, CTLA-4, and PD-1 expressions in ILDs for the first time.
Collapse
Affiliation(s)
- Mehmet Ali Karaselek
- Department of Pediatric Immunology and Allergy, Medicine Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Tugce Duran
- Department of Medical Genetic, Medicine Faculty, KTO Karatay University, Konya, Turkey
| | - Serkan Kuccukturk
- Department of Medical Biology, Medicine Faculty, Karamanoğlu Mehmetbey University, Karaman, Turkey
| | - Hulya Vatansev
- Department of Chest Disease, Medicine Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Pembe Oltulu
- Department of Pathology, Medicine Faculty, Necmettin Erbakan University, Konya, Turkey
| |
Collapse
|
21
|
Krusenstjerna AC, Jusufovic N, Saylor TC, Stevenson B. DnaA modulates gene expression and morphologyof the Lyme Disease spirochete. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.08.598065. [PMID: 38895450 PMCID: PMC11185795 DOI: 10.1101/2024.06.08.598065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
All bacteria encode a multifunctional DNA-binding protein, DnaA, which initiates chromosomal replication. Despite having the most complex, segmented bacterial genome, little is known about Borrelia burgdorferi DnaA and its role in maintaining the spirochete's physiology. We utilized inducible CRISPR-interference and overexpression to modulate cellular levels of DnaA to better understand this essential protein. Dysregulation of DnaA, either up or down, significantly slowed replication and increased or decreased cell lengths. Using fluorescent microscopy, we found the DnaA CRISPRi mutants had increased numbers of chromosomes with irregular spacing patterns. The DnaA-depleted spirochetes also exhibited a significant defect in helical morphology. RNA-seq of the conditional mutants showed significant changes in the levels of transcripts involved with flagellar synthesis, elongation, cell division, virulence, and other functions. These findings demonstrate that the DnaA plays a commanding role in maintaining borrelial growth dynamics and protein expression, which are essential for the survival of the Lyme disease spirochete.
Collapse
Affiliation(s)
- Andrew C Krusenstjerna
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Nerina Jusufovic
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Timothy C Saylor
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Brian Stevenson
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| |
Collapse
|
22
|
Hoang PM, Torre D, Jaynes P, Ho J, Mohammed K, Alvstad E, Lam WY, Khanchandani V, Lee JM, Toh CMC, Lee RX, Anbuselvan A, Lee S, Sebra RP, Martin J Walsh, Marazzi I, Kappei D, Guccione E, Jeyasekharan AD. A PRMT5-ZNF326 axis mediates innate immune activation upon replication stress. SCIENCE ADVANCES 2024; 10:eadm9589. [PMID: 38838142 DOI: 10.1126/sciadv.adm9589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/25/2024] [Indexed: 06/07/2024]
Abstract
DNA replication stress (RS) is a widespread phenomenon in carcinogenesis, causing genomic instability and extensive chromatin alterations. DNA damage leads to activation of innate immune signaling, but little is known about transcriptional regulators mediating such signaling upon RS. Using a chemical screen, we identified protein arginine methyltransferase 5 (PRMT5) as a key mediator of RS-dependent induction of interferon-stimulated genes (ISGs). This response is also associated with reactivation of endogenous retroviruses (ERVs). Using quantitative mass spectrometry, we identify proteins with PRMT5-dependent symmetric dimethylarginine (SDMA) modification induced upon RS. Among these, we show that PRMT5 targets and modulates the activity of ZNF326, a zinc finger protein essential for ISG response. Our data demonstrate a role for PRMT5-mediated SDMA in the context of RS-induced transcriptional induction, affecting physiological homeostasis and cancer therapy.
Collapse
Affiliation(s)
- Phuong Mai Hoang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Denis Torre
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jessica Ho
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Kevin Mohammed
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erik Alvstad
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Wan Yee Lam
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vartika Khanchandani
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jie Min Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Chin Min Clarissa Toh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Rui Xue Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Akshaya Anbuselvan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, South Korea
| | - Robert P Sebra
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martin J Walsh
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ivan Marazzi
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Haematology-Oncology, National University Hospital, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| |
Collapse
|
23
|
Anderson CL, Brown KA, North RJ, Walters JK, Kaska ST, Wolff MR, Kamp TJ, Ge Y, Eckhardt LL. Global Proteomic Analysis Reveals Alterations in Differentially Expressed Proteins between Cardiopathic Lamin A/C Mutations. J Proteome Res 2024; 23:1970-1982. [PMID: 38718259 PMCID: PMC11218822 DOI: 10.1021/acs.jproteome.3c00853] [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] [Indexed: 05/15/2024]
Abstract
Lamin A/C (LMNA) is an important component of nuclear lamina. Mutations cause arrhythmia, heart failure, and sudden cardiac death. While LMNA-associated cardiomyopathy typically has an aggressive course that responds poorly to conventional heart failure therapies, there is variability in severity and age of penetrance between and even within specific mutations, which is poorly understood at the cellular level. Further, this heterogeneity has not previously been captured to mimic the heterozygous state, nor have the hundreds of clinical LMNA mutations been represented. Herein, we have overexpressed cardiopathic LMNA variants in HEK cells and utilized state-of-the-art quantitative proteomics to compare the global proteomic profiles of (1) aggregating Q353 K alone, (2) Q353 K coexpressed with WT, (3) aggregating N195 K coexpressed with WT, and (4) nonaggregating E317 K coexpressed with WT to help capture some of the heterogeneity between mutations. We analyzed each data set to obtain the differentially expressed proteins (DEPs) and applied gene ontology (GO) and KEGG pathway analyses. We found a range of 162 to 324 DEPs from over 6000 total protein IDs with differences in GO terms, KEGG pathways, and DEPs important in cardiac function, further highlighting the complexity of cardiac laminopathies. Pathways disrupted by LMNA mutations were validated with redox, autophagy, and apoptosis functional assays in both HEK 293 cells and in induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs) for LMNA N195 K. These proteomic profiles expand our repertoire for mutation-specific downstream cellular effects that may become useful as druggable targets for personalized medicine approach for cardiac laminopathies.
Collapse
Affiliation(s)
- Corey L. Anderson
- Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705
| | - Ryan J. North
- Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Janay K. Walters
- Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Sara T. Kaska
- Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Mathew R. Wolff
- Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Timothy J. Kamp
- Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705
| | - Lee L. Eckhardt
- Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI 53705
| |
Collapse
|
24
|
Geethadevi A, Ku Z, Tsaih SW, Parashar D, Kadamberi IP, Xiong W, Deng H, George J, Kumar S, Mittal S, Zhang N, Pradeep S, An Z, Chaluvally-Raghavan P. Blocking Oncostatin M receptor abrogates STAT3 mediated integrin signaling and overcomes chemoresistance in ovarian cancer. NPJ Precis Oncol 2024; 8:127. [PMID: 38839865 PMCID: PMC11153533 DOI: 10.1038/s41698-024-00593-y] [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: 01/07/2024] [Accepted: 04/30/2024] [Indexed: 06/07/2024] Open
Abstract
Chemotherapy such as cisplatin is widely used to treat ovarian cancer either before or after surgical debulking. However, cancer relapse due to chemotherapy resistance is a major challenge in the treatment of ovarian cancer. The underlying mechanisms related to chemotherapy resistance remain largely unclear. Therefore, identification of effective therapeutic strategies is urgently needed to overcome therapy resistance. Transcriptome-based analysis, in vitro studies and functional assays identified that cisplatin-resistant ovarian cancer cells express high levels of OSMR compared to cisplatin sensitive cells. Furthermore, OSMR expression associated with a module of integrin family genes and predominantly linked with integrin αV (ITGAV) and integrin β3 (ITGB3) for cisplatin resistance. Using ectopic expression and knockdown approaches, we proved that OSMR directly regulates ITGAV and ITGB3 gene expression through STAT3 activation. Notably, targeting OSMR using anti-OSMR human antibody inhibited the growth and metastasis of ovarian cancer cells and sensitized cisplatin treatment. Taken together, our results underscore the pivotal role of OSMR as a requirement for cisplatin resistance in ovarian cancer. Notably, OSMR fostered the expression of a distinct set of integrin genes, which in turn resulted into a crosstalk between OSMR and integrins for signaling activation that is critical for cisplatin resistance. Therefore, targeting OSMR emerges as a promising and viable strategy to reverse cisplatin-resistance in ovarian cancer.
Collapse
Affiliation(s)
- Anjali Geethadevi
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical College of Wisconsin Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Shirng-Wern Tsaih
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical College of Wisconsin Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Deepak Parashar
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical College of Wisconsin Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Medicine, Division of Hematology & Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ishaque P Kadamberi
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical College of Wisconsin Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Wei Xiong
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Hui Deng
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Jasmine George
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical College of Wisconsin Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Sudhir Kumar
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical College of Wisconsin Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Sonam Mittal
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical College of Wisconsin Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Sunila Pradeep
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical College of Wisconsin Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA.
| | - Pradeep Chaluvally-Raghavan
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA.
- Medical College of Wisconsin Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA.
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
| |
Collapse
|
25
|
Feierman ER, Louzon S, Prescott NA, Biaco T, Gao Q, Qiu Q, Choi K, Palozola KC, Voss AJ, Mehta SD, Quaye CN, Lynch KT, Fuccillo MV, Wu H, David Y, Korb E. Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.575103. [PMID: 38352334 PMCID: PMC10862743 DOI: 10.1101/2024.01.29.575103] [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: 02/22/2024]
Abstract
Regulation of histone proteins affects gene expression through multiple mechanisms including exchange with histone variants. However, widely expressed variants of H2B remain elusive. Recent findings link histone variants to neurological disorders, yet few are well studied in the brain. We applied new tools including novel antibodies, biochemical assays, and sequencing approaches to reveal broad expression of the H2B variant H2BE, and defined its role in regulating chromatin structure, neuronal transcription, and mouse behavior. We find that H2BE is enriched at promoters and a single unique amino acid allows it to dramatically enhance chromatin accessibility. Lastly, we show that H2BE is critical for synaptic gene expression and long-term memory. Together, these data reveal a novel mechanism linking histone variants to chromatin regulation, neuronal function, and memory. This work further identifies the first widely expressed H2B variant and uncovers a single histone amino acid with profound effects on genomic structure.
Collapse
Affiliation(s)
- Emily R. Feierman
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Sean Louzon
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Nicholas A. Prescott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Tracy Biaco
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Qingzeng Gao
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Kyuhyun Choi
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katherine C. Palozola
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Anna J. Voss
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Shreya D. Mehta
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Camille N. Quaye
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katherine T. Lynch
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Marc V. Fuccillo
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Erica Korb
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| |
Collapse
|
26
|
Wakasugi D, Kondo S, Ferdousi F, Mizuno S, Yada A, Tominaga K, Takahashi S, Isoda H. A rare olive compound oleacein functions as a TrkB agonist and mitigates neuroinflammation both in vitro and in vivo. Cell Commun Signal 2024; 22:309. [PMID: 38835076 PMCID: PMC11151522 DOI: 10.1186/s12964-024-01691-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/28/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Neuroinflammation is widely acknowledged as a characteristic feature of almost all neurological disorders and specifically in depression- and anxiety-like disorders. In recent years, there has been significant attention on natural compounds with potent anti-inflammatory effects due to their potential in mitigating neuroinflammation and neuroplasticity. METHODS In the present study, we aimed to evaluate the neuroprotective effects of oleacein (OC), a rare secoiridoid derivative found in extra virgin olive oil. Our goal was to explore the BDNF/TrkB neurotrophic activity of OC and subsequently assess its potential for modulating neuroinflammatory response using human neuroblastoma cells (SH-SY5Y cells) and an in vivo model of depression induced by lipopolysaccharide (LPS)-mediated inflammation. RESULTS In SH-SY5Y cells, OC exhibited a significant dose-dependent increase in BDNF expression. This enhancement was absent when cells were co-treated with inhibitors of BDNF's receptor TrkB, as well as downstream molecules PI3K and MEK. Whole-transcriptomics analysis revealed that OC upregulated cell cycle-related genes under normal conditions, while downregulating inflammation-associated genes in LPS-induced conditions. Furthermore, surface plasmon resonance (SPR) assays demonstrated that OC exhibited a stronger and more stable binding affinity to TrkB compared to the positive control, 7,8-dihydroxyflavone. Importantly, bioluminescence imaging revealed that a single oral dose of OC significantly increased BDNF expression in the brains of Bdnf-IRES-AkaLuc mice. Furthermore, oral administration of OC at a dosage of 10 mg/kg body weight for 10 days significantly reduced immobility time in the tail suspension test compared to the LPS-treated group. RT-qPCR analysis revealed that OC significantly decreased the expression of pro-inflammatory cytokines Tnfα, Il6, and Il1β, while simultaneously enhancing Bdnf expression, as well as both pro and mature BDNF protein levels in mice hippocampus. These changes were comparable to those induced by the positive control antidepressant drug fluoxetine. Additionally, microarray analysis of mouse brains confirmed that OC could counteract LPS-induced inflammatory biological events. CONCLUSION Altogether, our study represents the first report on the potential antineuroinflammatory and antidepressant properties of OC via modulation of BDNF/TrkB neurotrophic activity. This finding underscores the potential of OC as a natural therapeutic agent for depression- and anxiety-related disorders.
Collapse
Affiliation(s)
- Daiki Wakasugi
- Tsukuba Life Science Innovation Program (T-LSI), University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Shinji Kondo
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Farhana Ferdousi
- Tsukuba Life Science Innovation Program (T-LSI), University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center (LARC) in Transborder Medical Research Center (TMRC), Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Akira Yada
- Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-0821, Japan
- Interdisciplinary Research Center for Catalytic Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Ibaraki, 305-8565, Japan
| | - Kenichi Tominaga
- Tsukuba Life Science Innovation Program (T-LSI), University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
- Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-0821, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center (LARC) in Transborder Medical Research Center (TMRC), Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Hiroko Isoda
- Tsukuba Life Science Innovation Program (T-LSI), University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan.
- Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-0821, Japan.
| |
Collapse
|
27
|
Jongen M, Reddin I, Cave S, Cashmore L, Pond J, Cleal JK, Hall NJ, Lewis RM. Gastroschisis associated changes in the placental transcriptome. Placenta 2024; 154:38-41. [PMID: 38870840 DOI: 10.1016/j.placenta.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/16/2024] [Accepted: 06/02/2024] [Indexed: 06/15/2024]
Abstract
The congenital condition gastroschisis is associated with delayed villous development and placental malperfusion, suggesting placental involvement. This study uses RNA sequencing to compare the placental transcriptome in pregnancies with and without gastroschisis. 180 coding genes were differentially expressed, mapping to multiple gene ontology pathways. Altered placental gene expression may represent fetal signalling to the placenta, and these changes could contribute to the pathogenesis of gastroschisis and associated morbidities, including fetal growth restriction.
Collapse
Affiliation(s)
| | - Ian Reddin
- University of Southampton, Faculty of Medicine, UK; Bio-R Bioinformatics Research Facility, University of Southampton, Southampton, UK
| | - Sharon Cave
- Neonatal Unit, Southampton Children's Hospital, UK
| | | | - Jenny Pond
- Neonatal Unit, Southampton Children's Hospital, UK
| | - Jane K Cleal
- University of Southampton, Faculty of Medicine, UK; Institute for Life Sciences, UK
| | - Nigel J Hall
- University of Southampton, Faculty of Medicine, UK; Neonatal Unit, Southampton Children's Hospital, UK; NIHR Southampton BRC, UK
| | - Rohan M Lewis
- University of Southampton, Faculty of Medicine, UK; Institute for Life Sciences, UK; NIHR Southampton BRC, UK.
| |
Collapse
|
28
|
Mwando NL, Khamis FM, Ndlela S, Meyhöfer R, Ombura FLO, Wamalwa M, Subramanian S, Mohamed SA. Comparative transcriptome analysis of false codling moth, Thaumatotibia leucotreta in response to high and low-temperature treatments. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101199. [PMID: 38330807 DOI: 10.1016/j.cbd.2024.101199] [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: 11/30/2023] [Revised: 01/07/2024] [Accepted: 01/27/2024] [Indexed: 02/10/2024]
Abstract
The false codling moth (FCM), Thaumatotibia leucotreta, is a major quarantine pest native to Africa. Physical postharvest phytosanitary measures such as cold and heat treatments are championed to control its spread to new regions. However, the molecular changes that T. leucotreta undergoes as it attempts to adjust to its surroundings during the treatments and withstand the extreme temperatures remain largely unknown. The current study employs RNA-seq using the next-generation Illumina HiSeq platform to produce transcriptome profiles for differential gene expression analysis of T. leucotreta larvae under thermal stress. The transcriptome assembly analysis revealed 226,067 transcripts, clustering into 127,018 unigenes. In comparison to the 25 °C treated group, 874, 91, 159, and 754 individual differentially expressed genes (DEGs) co-regulated at -10, 0, 40, and 50 °C, respectively were discovered. Annotation of the DEGs by gene ontology (GO) revealed several genes, previously implicated in low and high-temperature stresses, including heat shock proteins, cytochrome P450, cuticle proteins, odorant binding proteins, and immune system genes. Kyoto Encyclopedia of Genes and Genomics (KEGG) classification analysis revealed that substantive DEGs were those involved in metabolic pathways such as thiamine, purine, folate, and glycerolipid metabolism pathways. The RT-qPCR validation of several significantly up- and down-regulated DEGs showed congruence between RNA-seq and qPCR data. This baseline study lays a foundation for future research into the molecular mechanisms underlying T. leucotreta's cold/heat tolerance by providing a thorough differential gene expression analysis that has identified multiple genes that may be associated with the insect's ability to withstand cold and heat.
Collapse
Affiliation(s)
- Nelson L Mwando
- International Centre of Insect Physiology and Ecology, icipe, 30772-00100, Nairobi, Kenya; Leibniz Universität Hannover, Institute of Horticultural Production Systems, Sect. Phytomedicine - Applied Entomology, Herrenhäuser Strasse 2, D-30419 Hannover, Germany.
| | - Fathiya M Khamis
- International Centre of Insect Physiology and Ecology, icipe, 30772-00100, Nairobi, Kenya
| | - Shepard Ndlela
- International Centre of Insect Physiology and Ecology, icipe, 30772-00100, Nairobi, Kenya
| | - Rainer Meyhöfer
- Leibniz Universität Hannover, Institute of Horticultural Production Systems, Sect. Phytomedicine - Applied Entomology, Herrenhäuser Strasse 2, D-30419 Hannover, Germany
| | - Fidelis L O Ombura
- International Centre of Insect Physiology and Ecology, icipe, 30772-00100, Nairobi, Kenya
| | - Mark Wamalwa
- International Centre of Insect Physiology and Ecology, icipe, 30772-00100, Nairobi, Kenya
| | - Sevgan Subramanian
- International Centre of Insect Physiology and Ecology, icipe, 30772-00100, Nairobi, Kenya
| | - Samira A Mohamed
- International Centre of Insect Physiology and Ecology, icipe, 30772-00100, Nairobi, Kenya
| |
Collapse
|
29
|
Pinto N, Nissa MU, Yashwanth BS, Sathiyanarayanan A, Pai MGJ, Srivastava S, Goswami M. Proteomics analysis of differentially abundant proteins in the rohu kidney infected with Edwardsiella tarda. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101221. [PMID: 38430708 DOI: 10.1016/j.cbd.2024.101221] [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: 11/22/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024]
Abstract
Edwardsiella tarda (Et) is a zoonotic gram-negative pathogen with a diverse host range, including fish. However, the in-depth molecular mechanisms underlying the response of Labeo rohita (rohu) kidney to Et are poorly understood. A proteomic and histopathological analysis was performed for the rohu kidney after Et infection. The histopathology of the infected rohu kidney showed vacuolation and necrosis. After LC-MS/MS analysis, ~1240 proteins were identified with ≥2 unique peptides. A total of 96 differentially abundant proteins (DAPs) were observed between the control and Et infected group (ET). Metascape and STRING analysis were used for the gene ontology (GO), and protein-protein interaction network (PPI) for the significant pathways of DAPs. In PPI, low-abundant proteins were mapped to metabolic pathways and oxidative phosphorylation (cox5ab, uqcrfs1). High-abundance proteins were mapped to ribosomes (rplp2), protein process in the ER (hspa8), and immune system (ptgdsb.1, muc2). Our label-free proteomic approach in the rohu kidney revealed abundant enriched proteins involved in vesicle coat (ehd4), complement activation (c3a.1, c9, c7a), phagosome (thbs4, mapk1), metabolic reprogramming (hao1, glud1a), wound healing (vim, alox5), and the immune system (psap) after Et infection. A targeted proteomics approach of multiple reaction monitoring (MRM) validated the DAPs (nprl3, ambp, vmo1a, hspg2, muc2, hao1 and glud1a) between control and ET. Overall, the current analysis of histology and proteome in the rohu kidney provides comprehensive data on pathogenicity and the potential immune proteins against Et.
Collapse
Affiliation(s)
- Nevil Pinto
- Indian Council of Agricultural Research - Central Institute of Fisheries Education, Versova, Mumbai, Maharashtra 400061, India. https://twitter.com/pintonevil8
| | - Mehar Un Nissa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - B S Yashwanth
- Indian Council of Agricultural Research - Central Institute of Fisheries Education, Versova, Mumbai, Maharashtra 400061, India
| | - A Sathiyanarayanan
- Indian Council of Agricultural Research - Central Institute of Fisheries Education, Versova, Mumbai, Maharashtra 400061, India
| | - Medha Gayathri J Pai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India. https://twitter.com/Sanjeeva_IITB
| | - Mukunda Goswami
- Indian Council of Agricultural Research - Central Institute of Fisheries Education, Versova, Mumbai, Maharashtra 400061, India.
| |
Collapse
|
30
|
Patil S, Cremosnik G, Dötsch L, Flegel J, Schulte B, Maier KC, Žumer K, Cramer P, Janning P, Sievers S, Ziegler S, Waldmann H. The Pseudo-Natural Product Tafbromin Selectively Targets the TAF1 Bromodomain 2. Angew Chem Int Ed Engl 2024:e202404645. [PMID: 38801173 DOI: 10.1002/anie.202404645] [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: 03/07/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Phenotypic assays detect small-molecule bioactivity at functionally relevant cellular sites, and inherently cover a variety of targets and mechanisms of action. They can uncover new small molecule-target pairs and may give rise to novel biological insights. By means of an osteoblast differentiation assay which employs a Hedgehog (Hh) signaling agonist as stimulus and which monitors an endogenous marker for osteoblasts, we identified a pyrrolo[3,4-g]quinoline (PQ) pseudo-natural product (PNP) class of osteogenesis inhibitors. The most potent PQ, termed Tafbromin, impairs canonical Hh signaling and modulates osteoblast differentiation through binding to the bromodomain 2 of the TATA-box binding protein-associated factor 1 (TAF1). Tafbromin is the most selective TAF1 bromodomain 2 ligand and promises to be an invaluable tool for the study of biological processes mediated by TAF1(2) bromodomains.
Collapse
Affiliation(s)
- Sohan Patil
- Max-Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
| | - Gregor Cremosnik
- Max-Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
| | - Lara Dötsch
- Max-Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, Dortmund, 44227, Germany
| | - Jana Flegel
- Max-Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
| | - Britta Schulte
- Max-Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
| | - Kerstin C Maier
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077, Göttingen, Germany
| | - Kristina Žumer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077, Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077, Göttingen, Germany
| | - Petra Janning
- Max-Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
| | - Sonja Sievers
- Max-Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
| | - Slava Ziegler
- Max-Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
| | - Herbert Waldmann
- Max-Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, Dortmund, 44227, Germany
| |
Collapse
|
31
|
Salas-Lloret D, García-Rodríguez N, Soto-Hidalgo E, González-Vinceiro L, Espejo-Serrano C, Giebel L, Mateos-Martín ML, de Ru AH, van Veelen PA, Huertas P, Vertegaal ACO, González-Prieto R. BRCA1/BARD1 ubiquitinates PCNA in unperturbed conditions to promote continuous DNA synthesis. Nat Commun 2024; 15:4292. [PMID: 38769345 PMCID: PMC11106271 DOI: 10.1038/s41467-024-48427-6] [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: 08/03/2023] [Accepted: 04/30/2024] [Indexed: 05/22/2024] Open
Abstract
Deficiencies in the BRCA1 tumor suppressor gene are the main cause of hereditary breast and ovarian cancer. BRCA1 is involved in the Homologous Recombination DNA repair pathway and, together with BARD1, forms a heterodimer with ubiquitin E3 activity. The relevance of the BRCA1/BARD1 ubiquitin E3 activity for tumor suppression and DNA repair remains controversial. Here, we observe that the BRCA1/BARD1 ubiquitin E3 activity is not required for Homologous Recombination or resistance to Olaparib. Using TULIP2 methodology, which enables the direct identification of E3-specific ubiquitination substrates, we identify substrates for BRCA1/BARD1. We find that PCNA is ubiquitinated by BRCA1/BARD1 in unperturbed conditions independently of RAD18. PCNA ubiquitination by BRCA1/BARD1 avoids the formation of ssDNA gaps during DNA replication and promotes continuous DNA synthesis. These results provide additional insight about the importance of BRCA1/BARD1 E3 activity in Homologous Recombination.
Collapse
Grants
- KWF-KIG 11367/2017-2 KWF Kankerbestrijding (Dutch Cancer Society)
- EMERGIA20_00276 Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)
- EMERGIA21_00057 Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)
- 310913 EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))
- MICIU/AEI/10.13039/501100011033 and by European Union NextGenerationEU/PRTR - Grants: CNS2022-135216 ; MICIU/AEI/10.13039/501100011033 and by European Union : PID2021-122361NA-I00
Collapse
Affiliation(s)
- Daniel Salas-Lloret
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Néstor García-Rodríguez
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Emily Soto-Hidalgo
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Lourdes González-Vinceiro
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Carmen Espejo-Serrano
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Lisanne Giebel
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - María Luisa Mateos-Martín
- Institute of Biomedicine of Seville, IBiS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Proteomics Facility, Sevilla, Spain
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pablo Huertas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands.
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain.
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain.
| |
Collapse
|
32
|
Plaza-Florido A, Liem RI, Haddad F, Radom-Aizik S. Whole-blood transcriptome analysis reveals distinct gene expression signatures in paediatric patients with sickle cell anaemia before and after exercise. Br J Haematol 2024. [PMID: 38768976 DOI: 10.1111/bjh.19533] [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: 01/03/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Sickle cell anaemia (SCA) patients display elevated levels of circulating pro-inflammatory cytokines and endothelial activation markers compared to healthy peers. The impact of exercise on the pro-inflammatory state in SCA remains unclear. This study aimed to characterize the whole-blood transcriptome profile in response to an acute bout of exercise in paediatric SCA patients. Twenty-three SCA participants (13 ± 3 years, 52% girls) and 17 healthy controls (14 ± 3 years, 29% girls) performed eight 2-min bouts of cycle ergometry interspersed with 1-min rest intervals. Whole-blood transcriptome profile (RNA-seq) was performed before and after exercise. At baseline, gene pathways associated with gas transport in erythrocytes were up-regulated in SCA patients compared to controls. Following exercise, gene pathways associated with innate immunity were altered in both groups. Interaction analyses revealed 160 annotated genes (101 up- and 59 down-regulated) that differentially altered by exercise in SCA patients. Moreover, genes that exhibited a blunted response to exercise in SCA patients were enriched in the IL-17 signalling pathway, suggesting an impaired innate immune response to exercise. This data will contribute to the development of evidence-based exercise prescription guidelines for this patient population.
Collapse
Affiliation(s)
- Abel Plaza-Florido
- Department of Pediatrics, School of Medicine, Pediatric Exercise and Genomics Research Center, University of California Irvine, Irvine, California, USA
| | - Robert I Liem
- Division of Hematology, Oncology & Stem Cell Transplant, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Fadia Haddad
- Department of Pediatrics, School of Medicine, Pediatric Exercise and Genomics Research Center, University of California Irvine, Irvine, California, USA
| | - Shlomit Radom-Aizik
- Department of Pediatrics, School of Medicine, Pediatric Exercise and Genomics Research Center, University of California Irvine, Irvine, California, USA
| |
Collapse
|
33
|
Henningfield CM, Soni N, Lee RW, Sharma R, Cleland JL, Green KN. Selective targeting and modulation of plaque associated microglia via systemic hydroxyl dendrimer administration in an Alzheimer's disease mouse model. Alzheimers Res Ther 2024; 16:101. [PMID: 38711159 DOI: 10.1186/s13195-024-01470-3] [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: 10/26/2023] [Accepted: 04/29/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND In Alzheimer's disease (AD), microglia surround extracellular plaques and mount a sustained inflammatory response, contributing to the pathogenesis of the disease. Identifying approaches to specifically target plaque-associated microglia (PAMs) without interfering in the homeostatic functions of non-plaque associated microglia would afford a powerful tool and potential therapeutic avenue. METHODS Here, we demonstrated that a systemically administered nanomedicine, hydroxyl dendrimers (HDs), can cross the blood brain barrier and are preferentially taken up by PAMs in a mouse model of AD. As proof of principle, to demonstrate biological effects in PAM function, we treated the 5xFAD mouse model of amyloidosis for 4 weeks via systemic administration (ip, 2x weekly) of HDs conjugated to a colony stimulating factor-1 receptor (CSF1R) inhibitor (D-45113). RESULTS Treatment resulted in significant reductions in amyloid-beta (Aβ) and a stark reduction in the number of microglia and microglia-plaque association in the subiculum and somatosensory cortex, as well as a downregulation in microglial, inflammatory, and synaptic gene expression compared to vehicle treated 5xFAD mice. CONCLUSIONS This study demonstrates that systemic administration of a dendranib may be utilized to target and modulate PAMs.
Collapse
Affiliation(s)
- Caden M Henningfield
- Department of Neurobiology and Behavior, University of California, 3208 Biological Sciences III, Irvine, CA, 92697, USA
| | - Neelakshi Soni
- Department of Neurobiology and Behavior, University of California, 3208 Biological Sciences III, Irvine, CA, 92697, USA
| | - Ryan W Lee
- Department of Neurobiology and Behavior, University of California, 3208 Biological Sciences III, Irvine, CA, 92697, USA
| | - Rishi Sharma
- Ashvattha Therapeutics, Inc, Redwood City, CA, 94065, USA
| | | | - Kim N Green
- Department of Neurobiology and Behavior, University of California, 3208 Biological Sciences III, Irvine, CA, 92697, USA.
| |
Collapse
|
34
|
Potter SJ, Zhang L, Kotliar M, Wu Y, Schafer C, Stefan K, Boukas L, Qu’d D, Bodamer O, Simpson BN, Barski A, Lindsley AW, Bjornsson HT. KMT2D regulates activation, localization, and integrin expression by T-cells. Front Immunol 2024; 15:1341745. [PMID: 38765012 PMCID: PMC11099208 DOI: 10.3389/fimmu.2024.1341745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/26/2024] [Indexed: 05/21/2024] Open
Abstract
Individuals with Kabuki syndrome present with immunodeficiency; however, how pathogenic variants in the gene encoding the histone-modifying enzyme lysine methyltransferase 2D (KMT2D) lead to immune alterations remain poorly understood. Following up on our prior report of KMT2D-altered integrin expression in B-cells, we performed targeted analyses of KMT2D's influence on integrin expression in T-cells throughout development (thymocytes through peripheral T-cells) in murine cells with constitutive- and conditional-targeted Kmt2d deletion. Using high-throughput RNA-sequencing and flow cytometry, we reveal decreased expression (both at the transcriptional and translational levels) of a cluster of leukocyte-specific integrins, which perturb aspects of T-cell activation, maturation, adhesion/localization, and effector function. H3K4me3 ChIP-PCR suggests that these evolutionary similar integrins are under direct control of KMT2D. KMT2D loss also alters multiple downstream programming/signaling pathways, including integrin-based localization, which can influence T-cell populations. We further demonstrated that KMT2D deficiency is associated with the accumulation of murine CD8+ single-positive (SP) thymocytes and shifts in both human and murine peripheral T-cell populations, including the reduction of the CD4+ recent thymic emigrant (RTE) population. Together, these data show that the targeted loss of Kmt2d in the T-cell lineage recapitulates several distinct features of Kabuki syndrome-associated immune deficiency and implicates epigenetic mechanisms in the regulation of integrin signaling.
Collapse
Affiliation(s)
- Sarah J. Potter
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Li Zhang
- McKusick-Nathans Department of Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Michael Kotliar
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Yuehong Wu
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Caitlin Schafer
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Kurtis Stefan
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Leandros Boukas
- McKusick-Nathans Department of Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Dima Qu’d
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Olaf Bodamer
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, United States
- The Roya Kabuki Program, Boston Children’s Hospital, Boston, MA, United States
- Division of Genetics and Genomics, Broad Institute of MIT and Harvard University, Cambridge, MA, United States
| | - Brittany N. Simpson
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Artem Barski
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Andrew W. Lindsley
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Hans T. Bjornsson
- McKusick-Nathans Department of Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Faculty of Medicine, The University of Iceland, Reykjavik, Iceland
- Department of Genetics and Molecular Medicine, Landspitali University Hospital, Reykjavik, Iceland
| |
Collapse
|
35
|
Nelson ZM, Kadiri O, Fehl C. GlycoID Proximity Labeling to Identify O-GlcNAcylated Protein Interactomes in Live Cells. Curr Protoc 2024; 4:e1052. [PMID: 38752278 PMCID: PMC11101149 DOI: 10.1002/cpz1.1052] [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] [Indexed: 05/19/2024]
Abstract
Cells continuously remodel their intracellular proteins with the monosaccharide O-linked N-acetylglucosamine (O-GlcNAc) to regulate metabolism, signaling, and stress. This protocol describes the use of GlycoID tools to capture O-GlcNAc dynamics in live cells. GlycoID constructs contain an O-GlcNAc binding domain linked to a proximity labeling domain and a subcellular localization sequence. When expressed in mammalian cells, GlycoID tracks changes in O-GlcNAc-modified proteins and their interactomes in response to chemical induction with biotin over time. Pairing the subcellular localization of GlycoID with the chemical induction of activity enables spatiotemporal studies of O-GlcNAc biology during cellular events such as insulin signaling. However, optimizing intracellular labeling experiments requires attention to several variables. Here, we describe two protocols to adapt GlycoID methods to a cell line and biological process of interest. Next, we describe how to conduct a semiquantitative proteomic analysis of O-GlcNAcylated proteins and their interactomes using insulin versus glucagon signaling as a sample application. This articles aims to establish baseline GlycoID protocols for new users and set the stage for widespread use over diverse cellular applications for the functional study of O-GlcNAc glycobiology. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Expression of targeted GlycoID constructs to verify subcellular location and labeling activity in mammalian cells Basic Protocol 2: GlycoID labeling in live HeLa cells for O-GlcNAc proteomic comparisons.
Collapse
Affiliation(s)
- Zachary M. Nelson
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, United States
| | - Oseni Kadiri
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, United States
| | - Charlie Fehl
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, United States
| |
Collapse
|
36
|
Robinson JF, Das S, Khan W, Khanam R, Price JT, Rahman A, Ahmed S, Ali SM, Deb S, Deveale B, Dutta A, Gormley M, Hall SC, Hasan ASMT, Hotwani A, Juma MH, Kasaro MP, Khalid J, Kshetrapal P, McMaster MT, Mehmood U, Nisar I, Pervin J, Rahman S, Raqib R, San A, Sarker P, Tuomivaara ST, Zhang G, Zhou Y, Aktar S, Baqui AH, Jehan F, Sazawal S, Stringer JSA, Fisher SJ. High rates of placental inflammation among samples collected by the Multi-Omics for Mothers and Infants consortium. Am J Obstet Gynecol 2024:S0002-9378(24)00560-X. [PMID: 38697337 DOI: 10.1016/j.ajog.2024.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/04/2024]
Abstract
BACKGROUND The Multi-Omics for Mothers and Infants consortium aims to improve birth outcomes. Preterm birth is a major obstetrical complication globally and causes significant infant and childhood morbidity and mortality. OBJECTIVE We analyzed placental samples (basal plate, placenta or chorionic villi, and the chorionic plate) collected by the 5 Multi-Omics for Mothers and Infants sites, namely The Alliance for Maternal and Newborn Health Improvement Bangladesh, The Alliance for Maternal and Newborn Health Improvement Pakistan, The Alliance for Maternal and Newborn Health Improvement Tanzania, The Global Alliance to Prevent Prematurity and Stillbirth Bangladesh, and The Global Alliance to Prevent Prematurity and Stillbirth Zambia. The goal was to analyze the morphology and gene expression of samples collected from preterm and uncomplicated term births. STUDY DESIGN The teams provided biopsies from 166 singleton preterm (<37 weeks' gestation) and 175 term (≥37 weeks' gestation) deliveries. The samples were fixed in formalin and paraffin embedded. Tissue sections from these samples were stained with hematoxylin and eosin and subjected to morphologic analyses. Other placental biopsies (n=35 preterm, 21 term) were flash frozen, which enabled RNA purification for bulk transcriptomics. RESULTS The morphologic analyses revealed a surprisingly high rate of inflammation that involved the basal plate, placenta or chorionic villi, and the chorionic plate. The rate of inflammation in chorionic villus samples, likely attributable to chronic villitis, ranged from 25% (Pakistan site) to 60% (Zambia site) of cases. Leukocyte infiltration in this location vs in the basal plate or chorionic plate correlated with preterm birth. Our transcriptomic analyses identified 267 genes that were differentially expressed between placentas from preterm vs those from term births (123 upregulated, 144 downregulated). Mapping the differentially expressed genes onto single-cell RNA sequencing data from human placentas suggested that all the component cell types, either singly or in subsets, contributed to the observed dysregulation. Consistent with the histopathologic findings, gene ontology analyses highlighted the presence of leukocyte infiltration or activation and inflammatory responses in both the fetal and maternal compartments. CONCLUSION The relationship between placental inflammation and preterm birth is appreciated in developed countries. In this study, we showed that this link also exists in developing geographies. In addition, among the participating sites, we found geographic- and population-based differences in placental inflammation and preterm birth, suggesting the importance of local factors.
Collapse
Affiliation(s)
- Joshua F Robinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA
| | - Sayan Das
- Public Health Laboratory Ivo de Carneri, Wawi, Chake, Pemba, Zanzibar, Tanzania
| | - Waqasuddin Khan
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan; Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Rasheda Khanam
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Joan T Price
- UNC Global Projects - Zambia, Lusaka, Zambia; Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Anisur Rahman
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | | | - Said Mohammed Ali
- Public Health Laboratory Ivo de Carneri, Wawi, Chake, Pemba, Zanzibar, Tanzania
| | - Saikat Deb
- Public Health Laboratory Ivo de Carneri, Wawi, Chake, Pemba, Zanzibar, Tanzania; Center for Public Health Kinetics, Vinoba Puri, Lajpatnagar II, New Delhi, India
| | - Brian Deveale
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA; Department of Urology, University of California, San Francisco, San Francisco, CA
| | - Arup Dutta
- Center for Public Health Kinetics, Vinoba Puri, Lajpatnagar II, New Delhi, India
| | - Matthew Gormley
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA; Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, San Francisco, CA
| | - Steven C Hall
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA; Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, San Francisco, CA
| | - A S M Tarik Hasan
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Mohamed Hamid Juma
- Public Health Laboratory Ivo de Carneri, Wawi, Chake, Pemba, Zanzibar, Tanzania
| | - Margaret P Kasaro
- UNC Global Projects - Zambia, Lusaka, Zambia; Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC; Department of Gynaecology and Obstetrics, University of Zambia School of Medicine, Lusaka, Zambia
| | - Javairia Khalid
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan; Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Pallavi Kshetrapal
- Maternal and Child Health, Translational Health Science and Technology Institute, Faridabad, India
| | - Michael T McMaster
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
| | - Usma Mehmood
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Imran Nisar
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan; Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Jesmin Pervin
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Sayedur Rahman
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh; Projahnmo Research Foundation, Dhaka, Bangladesh
| | - Rubhana Raqib
- International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Ali San
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA
| | - Protim Sarker
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Sami T Tuomivaara
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA; Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, San Francisco, CA
| | - Ge Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH; Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Yan Zhou
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA
| | - Shaki Aktar
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Abdullah H Baqui
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Fyezah Jehan
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan; Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Sunil Sazawal
- Center for Public Health Kinetics, Vinoba Puri, Lajpatnagar II, New Delhi, India
| | - Jeffrey S A Stringer
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Susan J Fisher
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA; Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, San Francisco, CA.
| |
Collapse
|
37
|
Laragione T, Harris C, Gulko PS. KIF1C and new Huntingtin-interacting protein 1 binding proteins regulate rheumatoid arthritis fibroblast-like synoviocytes' phenotypes. Front Immunol 2024; 15:1323410. [PMID: 38726004 PMCID: PMC11079228 DOI: 10.3389/fimmu.2024.1323410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/18/2024] [Indexed: 05/12/2024] Open
Abstract
Background Huntingtin-interacting protein-1 (HIP1) is a new arthritis severity gene implicated in the regulation of the invasive properties of rheumatoid arthritis (RA) fibroblast-like synoviocytes (FLS). These invasive properties of FLS strongly correlate with radiographic and histology damage in patients with RA and rodent models of arthritis. While HIP1 has several intracellular functions, little is known about its binding proteins, and identifying them has the potential to expand our understanding of its role in cell invasion and other disease-contributing phenotypes, and potentially identify new targets for therapy. Methods FLS cell lines from arthritic DA (highly invasive) and from arthritis-protected congenic rats R6 (minimally invasive), which differ in an amino-acid changing HIP1 SNP, were cultured and lysed, and proteins were immunoprecipitated with an anti-HIP1 antibody. Immunoprecipitates were analyzed by mass spectrometry. Differentially detected (bound) proteins were selected for functional experiments using siRNA knockdown in human RA FLS to examine their effect in cell invasiveness, adhesion, cell migration and proliferation, and immunofluorescence microscopy. Results Proteins detected included a few known HIP1-binding proteins and several new ones. Forty-five proteins differed in levels detected in the DA versus R6 congenic mass spectrometry analyses. Thirty-two of these proteins were knocked down and studied in vitro, with 10 inducing significant changes in RA FLS phenotypes. Specifically, knockdown of five HIP1-binding protein genes (CHMP4BL1, COPE, KIF1C, YWHAG, and YWHAH) significantly decreased FLS invasiveness. Knockdown of KIF1C also reduced RA FLS migration. The binding of four selected proteins to human HIP1 was confirmed. KIF1C colocalized with lamellipodia, and its knockdown prevented RA FLS from developing an elongated morphology with thick linearized actin fibers or forming polarized lamellipodia, all required for cell mobility and invasion. Unlike HIP1, KIF1C knockdown did not affect Rac1 signaling. Conclusion We have identified new HIP1-binding proteins and demonstrate that 10 of them regulate key FLS phenotypes. These HIP1-binding proteins have the potential to become new therapeutic targets and help better understand the RA FLS pathogenic behavior. KIF1C knockdown recapitulated the morphologic changes previously seen in the absence of HIP1, but did not affect the same cell signaling pathway, suggesting involvement in the regulation of different processes.
Collapse
Affiliation(s)
| | | | - Percio S. Gulko
- Division of Rheumatology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| |
Collapse
|
38
|
Chen K, Han Y, Wang Y, Zhou D, Wu F, Cai W, Zheng S, Xiao Q, Zhang H, Li W. scMoresDB: A comprehensive database of single-cell multi-omics data for human respiratory system. iScience 2024; 27:109567. [PMID: 38617561 PMCID: PMC11015448 DOI: 10.1016/j.isci.2024.109567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/26/2023] [Accepted: 03/22/2024] [Indexed: 04/16/2024] Open
Abstract
The human respiratory system is a complex and important system that can suffer a variety of diseases. Single-cell sequencing technologies, applied in many respiratory disease studies, have enhanced our ability in characterizing molecular and phenotypic features at a single-cell resolution. The exponentially increasing data from these studies have consequently led to difficulties in data sharing and analysis. Here, we present scMoresDB, a single-cell multi-omics database platform with extensive omics types tailored for human respiratory diseases. scMoresDB re-analyzes single-cell multi-omics datasets, providing a user-friendly interface with cross-omics search capabilities, interactive visualizations, and analytical tools for comprehensive data sharing and integrative analysis. Our example applications highlight the potential significance of BSG receptor in SARS-CoV-2 infection as well as the involvement of HHIP and TGFB2 in the development and progression of chronic obstructive pulmonary disease. scMoresDB significantly increases accessibility and utility of single-cell data relevant to human respiratory system and associated diseases.
Collapse
Affiliation(s)
- Kang Chen
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Yutong Han
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Yanni Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Dingli Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Fanjie Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Wenhao Cai
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Shikang Zheng
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Qinyuan Xiao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Haiyue Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Weizhong Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, Guangdong Province, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| |
Collapse
|
39
|
Zavala-Meneses SG, Firrincieli A, Chalova P, Pajer P, Checcucci A, Skultety L, Cappelletti M. Proteogenomic Characterization of Pseudomonas veronii SM-20 Growing on Phenanthrene as Only Carbon and Energy Source. Microorganisms 2024; 12:753. [PMID: 38674697 PMCID: PMC11052242 DOI: 10.3390/microorganisms12040753] [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: 03/18/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, we conducted an extensive investigation of the biodegradation capabilities and stress response of the newly isolated strain Pseudomonas veronii SM-20 in order, to assess its potential for bioremediation of sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Initially, phenotype microarray technology demonstrated the strain's proficiency in utilizing various carbon sources and its resistance to certain stressors. Genomic analysis has identified numerous genes involved in aromatic hydrocarbon metabolism. Biodegradation assay analyzed the depletion of phenanthrene (PHE) when it was added as a sole carbon and energy source. We found that P. veronii strain SM-20 degraded approximately 25% of PHE over a 30-day period, starting with an initial concentration of 600 µg/mL, while being utilized for growth. The degradation process involved PHE oxidation to an unstable arene oxide and 9,10-phenanthrenequinone, followed by ring-cleavage. Comparative proteomics provided a comprehensive understanding of how the entire proteome responded to PHE exposure, revealing the strain's adaptation in terms of aromatic metabolism, surface properties, and defense mechanism. In conclusion, our findings shed light on the promising attributes of P. veronii SM-20 and offer valuable insights for the use of P. veronii species in environmental restoration efforts targeting PAH-impacted sites.
Collapse
Affiliation(s)
- Sofía G. Zavala-Meneses
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
- Faculty of Science, Charles University, Vinicna 5, 12844 Prague, Czech Republic
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy or (A.F.); (M.C.)
| | - Petra Chalova
- Biomedical Research Center, Slovak Academy of Sciences, Dubravska c. 9, 845 05 Bratislava, Slovakia;
- Faculty of Pharmacy, Comenius University, Odbojarov 10, 832 32 Bratislava, Slovakia
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, U Vojenske Nemocnice 1200, 16902 Prague, Czech Republic;
| | - Alice Checcucci
- Department of Agriculture, Food, Environment and Forestry, University of Florence, 50100 Firenze, Italy;
| | - Ludovit Skultety
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
- Biomedical Research Center, Slovak Academy of Sciences, Dubravska c. 9, 845 05 Bratislava, Slovakia;
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy or (A.F.); (M.C.)
| |
Collapse
|
40
|
Bianco V, Svecla M, Vingiani GB, Kolb D, Schwarz B, Buerger M, Beretta G, Norata GD, Kratky D. Regional Differences in the Small Intestinal Proteome of Control Mice and of Mice Lacking Lysosomal Acid Lipase. J Proteome Res 2024; 23:1506-1518. [PMID: 38422518 PMCID: PMC7615810 DOI: 10.1021/acs.jproteome.4c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
The metabolic contribution of the small intestine (SI) is still unclear despite recent studies investigating the involvement of single cells in regional differences. Using untargeted proteomics, we identified regional characteristics of the three intestinal tracts of C57BL/6J mice and found that proteins abundant in the mouse ileum correlated with the high ileal expression of the corresponding genes in humans. In the SI of C57BL/6J mice, we also detected an increasing abundance of lysosomal acid lipase (LAL), which is responsible for degrading triacylglycerols and cholesteryl esters within the lysosome. LAL deficiency in patients and mice leads to lipid accumulation, gastrointestinal disturbances, and malabsorption. We previously demonstrated that macrophages massively infiltrated the SI of Lal-deficient (KO) mice, especially in the duodenum. Using untargeted proteomics (ProteomeXchange repository, data identifier PXD048378), we revealed a general inflammatory response and a common lipid-associated macrophage phenotype in all three intestinal segments of Lal KO mice, accompanied by a higher expression of GPNMB and concentrations of circulating sTREM2. However, only duodenal macrophages activated a metabolic switch from lipids to other pathways, which were downregulated in the jejunum and ileum of Lal KO mice. Our results provide new insights into the process of absorption in control mice and possible novel markers of LAL-D and/or systemic inflammation in LAL-D.
Collapse
Affiliation(s)
- Valentina Bianco
- Gottfried
Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, 8010 Graz, Austria
| | - Monika Svecla
- Department
of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy
| | - Giovanni Battista Vingiani
- Department
of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy
| | - Dagmar Kolb
- Core
Facility Ultrastructural Analysis, Medical
University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
- Gottfried
Schatz Research Center, Cell Biology, Histology and Embryology, Medical University of Graz, 8010 Graz, Austria
| | - Birgit Schwarz
- Gottfried
Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, 8010 Graz, Austria
| | - Martin Buerger
- Gottfried
Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, 8010 Graz, Austria
| | - Giangiacomo Beretta
- Department
of Environmental Science and Policy, Università
degli Studi di Milano, 20133 Milan, Italy
| | - Giuseppe Danilo Norata
- Department
of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy
- Centro
SISA per lo studio dell’Aterosclerosi, Ospedale Bassini, 20092 Cinisello Balsamo, Italy
| | - Dagmar Kratky
- Gottfried
Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| |
Collapse
|
41
|
Boisserand LSB, Geraldo LH, Bouchart J, El Kamouh MR, Lee S, Sanganahalli BG, Spajer M, Zhang S, Lee S, Parent M, Xue Y, Skarica M, Yin X, Guegan J, Boyé K, Saceanu Leser F, Jacob L, Poulet M, Li M, Liu X, Velazquez SE, Singhabahu R, Robinson ME, Askenase MH, Osherov A, Sestan N, Zhou J, Alitalo K, Song E, Eichmann A, Sansing LH, Benveniste H, Hyder F, Thomas JL. VEGF-C prophylaxis favors lymphatic drainage and modulates neuroinflammation in a stroke model. J Exp Med 2024; 221:e20221983. [PMID: 38442272 PMCID: PMC10913814 DOI: 10.1084/jem.20221983] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 11/13/2023] [Accepted: 01/25/2024] [Indexed: 03/07/2024] Open
Abstract
Meningeal lymphatic vessels (MLVs) promote tissue clearance and immune surveillance in the central nervous system (CNS). Vascular endothelial growth factor-C (VEGF-C) regulates MLV development and maintenance and has therapeutic potential for treating neurological disorders. Herein, we investigated the effects of VEGF-C overexpression on brain fluid drainage and ischemic stroke outcomes in mice. Intracerebrospinal administration of an adeno-associated virus expressing mouse full-length VEGF-C (AAV-mVEGF-C) increased CSF drainage to the deep cervical lymph nodes (dCLNs) by enhancing lymphatic growth and upregulated neuroprotective signaling pathways identified by single nuclei RNA sequencing of brain cells. In a mouse model of ischemic stroke, AAV-mVEGF-C pretreatment reduced stroke injury and ameliorated motor performances in the subacute stage, associated with mitigated microglia-mediated inflammation and increased BDNF signaling in brain cells. Neuroprotective effects of VEGF-C were lost upon cauterization of the dCLN afferent lymphatics and not mimicked by acute post-stroke VEGF-C injection. We conclude that VEGF-C prophylaxis promotes multiple vascular, immune, and neural responses that culminate in a protection against neurological damage in acute ischemic stroke.
Collapse
Affiliation(s)
| | - Luiz Henrique Geraldo
- Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, USA
| | - Jean Bouchart
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - Marie-Renee El Kamouh
- Paris Brain Institute, Université Pierre et Marie Curie Paris 06 UMRS1127, Sorbonne Université, Paris, France
| | - Seyoung Lee
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Myriam Spajer
- Paris Brain Institute, Université Pierre et Marie Curie Paris 06 UMRS1127, Sorbonne Université, Paris, France
| | - Shenqi Zhang
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Sungwoon Lee
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - Maxime Parent
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT, USA
| | - Yuechuan Xue
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA
| | - Mario Skarica
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Xiangyun Yin
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Justine Guegan
- Paris Brain Institute, Université Pierre et Marie Curie Paris 06 UMRS1127, Sorbonne Université, Paris, France
| | - Kevin Boyé
- Paris Cardiovascular Research Center, INSERM U970, Paris, France
| | - Felipe Saceanu Leser
- Paris Cardiovascular Research Center, INSERM U970, Paris, France
- Glial Cell Biology Laboratory, Biomedical Sciences Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Laurent Jacob
- Paris Cardiovascular Research Center, INSERM U970, Paris, France
| | - Mathilde Poulet
- Paris Cardiovascular Research Center, INSERM U970, Paris, France
| | - Mingfeng Li
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Xiodan Liu
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA
| | - Sofia E. Velazquez
- Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, USA
| | - Ruchith Singhabahu
- Paris Brain Institute, Université Pierre et Marie Curie Paris 06 UMRS1127, Sorbonne Université, Paris, France
| | - Mark E. Robinson
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | | | - Artem Osherov
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA
- Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT, USA
| | - Jiangbing Zhou
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Kari Alitalo
- Faculty of Medicine, Wihuri Research Institute and Translational Cancer Biology Program, University of Helsinki, Helsinki, Finland
| | - Eric Song
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Anne Eichmann
- Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, USA
- Paris Cardiovascular Research Center, INSERM U970, Paris, France
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | - Lauren H. Sansing
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
| | - Helene Benveniste
- Department of Anesthesiology, Yale School of Medicine, New Haven, CT, USA
| | - Fahmeed Hyder
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Jean-Leon Thomas
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
- Paris Brain Institute, Université Pierre et Marie Curie Paris 06 UMRS1127, Sorbonne Université, Paris, France
| |
Collapse
|
42
|
Ferreiro E, Monteiro M, Pereira F, Barroso C, Egas C, Macedo P, Valero J, Sardão VA, Oliveira PJ. Age-dependent energy metabolism and transcriptome changes in urine-derived stem cells. Mech Ageing Dev 2024; 218:111912. [PMID: 38266781 DOI: 10.1016/j.mad.2024.111912] [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: 09/25/2023] [Revised: 12/06/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
The global population over 60 years old is projected to reach 1.5 billion by 2050. Understanding age-related disorders and gender-specificities is crucial for a healthy aging. Reliable age-related biomarkers are needed, preferentially obtained through non-invasive methods. Urine-derived stem cells (UDSCs) can be easily obtained, although a detailed bioenergetic characterization, according to the donor aging, remain unexplored. UDSCs were isolated from young and elderly adult women (22-35 and 70-94 years old, respectively). Surprisingly, UDSCs from elderly subjects exhibited significantly higher maximal oxygen consumption and bioenergetic health index than those from younger individuals, evaluated through oxygen consumption rate. Exploratory data analysis methods were applied to engineer a minimal subset of features for the classification and stratification of UDSCs. Additionally, RNAseq of UDSCs was performed to identify age-related transcriptional changes. Transcriptional analysis revealed downregulation of genes related to glucuronidation and estrogen metabolism, and upregulation of inflammation-related genes in UDSCs from elderly individuals. This study demonstrates unexpected differences in the UDSCs' OCR between young and elderly individuals, revealing improved bioenergetics in concurrent with an aged-like transcriptome signature. UDSCs offer a non-invasive model for studying age-related changes, holding promise for aging research and therapeutic studies.
Collapse
Affiliation(s)
- Elisabete Ferreiro
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech, Cantanhede, Portugal; Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra 3000-548, Portugal.
| | - Mariana Monteiro
- CISUC - Centre for Informatics and Systems, University of Coimbra, Coimbra, Portugal
| | - Francisco Pereira
- CISUC - Centre for Informatics and Systems, University of Coimbra, Coimbra, Portugal; Polytechnic Institute of Coimbra, Coimbra Institute of Engineering, Coimbra, Portugal
| | - Cristina Barroso
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech, Cantanhede, Portugal; Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra 3000-548, Portugal; Biocant - Transfer Technology Association, BiocantPark, Cantanhede, Portugal
| | - Conceição Egas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech, Cantanhede, Portugal; Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra 3000-548, Portugal
| | - Paula Macedo
- CEDOC-Chronic Diseases Research Center, NOVA Medical School, NOVA University of Lisbon, Lisboa, Portugal
| | - Jorge Valero
- Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca, Spain; Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain; Department of Cell Biology and Pathology, University of Salamanca, Spain
| | - Vilma A Sardão
- Multidisciplinary Institute of Aging (MIA-Portugal), University of Coimbra, Portugal
| | - Paulo J Oliveira
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech, Cantanhede, Portugal; Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra 3000-548, Portugal.
| |
Collapse
|
43
|
Lu YZ, Nayer B, Singh SK, Alshoubaki YK, Yuan E, Park AJ, Maruyama K, Akira S, Martino MM. CGRP sensory neurons promote tissue healing via neutrophils and macrophages. Nature 2024; 628:604-611. [PMID: 38538784 PMCID: PMC11023938 DOI: 10.1038/s41586-024-07237-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/26/2024] [Indexed: 04/06/2024]
Abstract
The immune system has a critical role in orchestrating tissue healing. As a result, regenerative strategies that control immune components have proved effective1,2. This is particularly relevant when immune dysregulation that results from conditions such as diabetes or advanced age impairs tissue healing following injury2,3. Nociceptive sensory neurons have a crucial role as immunoregulators and exert both protective and harmful effects depending on the context4-12. However, how neuro-immune interactions affect tissue repair and regeneration following acute injury is unclear. Here we show that ablation of the NaV1.8 nociceptor impairs skin wound repair and muscle regeneration after acute tissue injury. Nociceptor endings grow into injured skin and muscle tissues and signal to immune cells through the neuropeptide calcitonin gene-related peptide (CGRP) during the healing process. CGRP acts via receptor activity-modifying protein 1 (RAMP1) on neutrophils, monocytes and macrophages to inhibit recruitment, accelerate death, enhance efferocytosis and polarize macrophages towards a pro-repair phenotype. The effects of CGRP on neutrophils and macrophages are mediated via thrombospondin-1 release and its subsequent autocrine and/or paracrine effects. In mice without nociceptors and diabetic mice with peripheral neuropathies, delivery of an engineered version of CGRP accelerated wound healing and promoted muscle regeneration. Harnessing neuro-immune interactions has potential to treat non-healing tissues in which dysregulated neuro-immune interactions impair tissue healing.
Collapse
Affiliation(s)
- Yen-Zhen Lu
- European Molecular Biology Laboratory Australia, Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Bhavana Nayer
- European Molecular Biology Laboratory Australia, Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Shailendra Kumar Singh
- Laboratory of Host Defense, World Premier International Research Center, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Yasmin K Alshoubaki
- European Molecular Biology Laboratory Australia, Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Elle Yuan
- European Molecular Biology Laboratory Australia, Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Anthony J Park
- European Molecular Biology Laboratory Australia, Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Kenta Maruyama
- Laboratory of Host Defense, World Premier International Research Center, Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Department of Pharmacology, School of Medicine, Aichi Medical University, Aichi, Japan
| | - Shizuo Akira
- Laboratory of Host Defense, World Premier International Research Center, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Mikaël M Martino
- European Molecular Biology Laboratory Australia, Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia.
- Laboratory of Host Defense, World Premier International Research Center, Immunology Frontier Research Center, Osaka University, Osaka, Japan.
- Victorian Heart Institute, Monash University, Melbourne, Victoria, Australia.
| |
Collapse
|
44
|
Ghezellou P, von Bülow V, Luh D, Badin E, Albuquerque W, Roderfeld M, Roeb E, Grevelding CG, Spengler B. Schistosoma mansoni infection induces hepatic metallothionein and S100 protein expression alongside metabolic dysfunction in hamsters. PNAS NEXUS 2024; 3:pgae104. [PMID: 38562583 PMCID: PMC10983833 DOI: 10.1093/pnasnexus/pgae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/20/2024] [Indexed: 04/04/2024]
Abstract
Schistosomiasis, a widespread neglected tropical disease, presents a complex and multifaceted clinical-pathological profile. Using hamsters as final hosts, we dissected molecular events following Schistosoma mansoni infection in the liver-the organ most severely affected in schistosomiasis patients. Employing tandem mass tag-based proteomics, we studied alterations in the liver proteins in response to various infection modes and genders. We examined livers from female and male hamsters that were: noninfected (control), infected with either unisexual S. mansoni cercariae (single-sex) or both sexes (bisex). The infection induced up-regulation of proteins associated with immune response, cytoskeletal reorganization, and apoptotic signaling. Notably, S. mansoni egg deposition led to the down-regulation of liver factors linked to energy supply and metabolic processes. Gender-specific responses were observed, with male hamsters showing higher susceptibility, supported by more differentially expressed proteins than found in females. Of note, metallothionein-2 and S100a6 proteins exhibited substantial up-regulation in livers of both genders, suggesting their pivotal roles in the liver's injury response. Immunohistochemistry and real-time-qPCR confirmed strong up-regulation of metallothionein-2 expression in the cytoplasm and nucleus upon the infection. Similar findings were seen for S100a6, which localized around granulomas and portal tracts. We also observed perturbations in metabolic pathways, including down-regulation of enzymes involved in xenobiotic biotransformation, cellular energy metabolism, and lipid modulation. Furthermore, lipidomic analyses through liquid chromatography-tandem mass spectrometry and matrix-assisted laser desorption/ionization mass spectrometry imaging identified extensive alterations, notably in cardiolipin and triacylglycerols, suggesting specific roles of lipids during pathogenesis. These findings provide unprecedented insights into the hepatic response to S. mansoni infection, shedding light on the complexity of liver pathology in this disease.
Collapse
Affiliation(s)
- Parviz Ghezellou
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Verena von Bülow
- Department of Gastroenterology, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - David Luh
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Elisa Badin
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Wendell Albuquerque
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Martin Roderfeld
- Department of Gastroenterology, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Elke Roeb
- Department of Gastroenterology, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Christoph G Grevelding
- Institute of Parasitology, Biomedical Research Center Seltersberg (BFS), Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
| |
Collapse
|
45
|
Kuroiwa Y, Ito K, Nakayama J, Semba K, Yamamoto Y. Analysis of the responsiveness to antiandrogens in multiple breast cancer cell lines. Genes Cells 2024; 29:301-315. [PMID: 38366725 DOI: 10.1111/gtc.13105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Abstract
Antiandrogens were originally developed as therapeutic agents for prostate cancer but are also expected to be effective for breast cancer. However, the role of androgen signaling in breast cancer has long been controversial due to the limited number of experimental models. Our study aimed to comprehensively investigate the efficacy of antiandrogens on breast cancer. In the present study, a total of 18 breast cancer cell lines were treated with the agonist or antagonists of the androgen receptor (AR). Among the 18 cell lines tested, only T-47D cells proliferated in an androgen-dependent manner, while the other cell lines were almost irresponsive to AR stimulation. On the other hand, treatment with AR antagonists at relatively high doses suppressed the proliferation of not only T-47D cells but also some other cell lines including AR-low/negative cells. In addition, expression of the full-length AR and constitutively active AR splice variants, AR-V7 and ARV567es, was not correlated with sensitivity to AR antagonists. These data suggest that the antiproliferative effect of AR antagonists is AR-independent in some cases. Consistently, proliferation of AR-knockout BT-549 cells was inhibited by AR antagonists. Identification of biomarkers would be necessary to determine which breast cancer patients will benefit from these drugs.
Collapse
Affiliation(s)
- Yuka Kuroiwa
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Kagenori Ito
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Urology, The Jikei University School of Medicine, Tokyo, Japan
| | - Jun Nakayama
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kentaro Semba
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Translational Research Center, Fukushima Medical University, Fukushima, Japan
| | - Yusuke Yamamoto
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
| |
Collapse
|
46
|
Arya R, Shakya H, Chaurasia R, Haque MA, Kim JJ. Exploring the Role of Extracellular Vesicles in the Pathogenesis of Tuberculosis. Genes (Basel) 2024; 15:434. [PMID: 38674369 PMCID: PMC11049626 DOI: 10.3390/genes15040434] [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: 03/05/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Tuberculosis (TB) remains a significant global health concern, necessitating accurate diagnosis and treatment monitoring. Extracellular vesicles (EVs), including exosomes, play crucial roles in disease progression, with their associated genes serving as potential biomarkers and therapeutic targets. Leveraging publicly available RNA-Seq datasets of TB patients and healthy controls (HCs), to identify differentially expressed genes (DEGs) and their associated protein-protein interaction networks and immune cell profiles, the common EV-related DEGs were identified and validated in the GSE42830 and GSE40553 datasets. We have identified nine common EV-related DEGs (SERPINA1, TNFAIP6, MAPK14, STAT1, ITGA2B, VAMP5, CTSL, CEACAM1, and PLAUR) upregulated in TB patients. Immune cell infiltration analysis revealed significant differences between TB patients and HCs, highlighting increased proportions of various immune cells in TB patients. These DEGs are involved in crucial cellular processes and pathways related to exocytosis and immune response regulation. Notably, VAMP5 exhibited excellent diagnostic performance (AUC-0.993, sensitivity-93.8%, specificity-100%), with potential as a novel biomarker for TB. The EV-related genes can serve as novel potential biomarkers that can distinguish between TB and HCs. VAMP5, which functions in exosome biogenesis and showed significant upregulation in TB, can be targeted for therapeutic interventions and treatment outcomes.
Collapse
Affiliation(s)
- Rakesh Arya
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (R.A.); (M.A.H.)
| | - Hemlata Shakya
- Department of Biomedical Engineering, Shri G. S. Institute of Technology and Science, Indore 452003, Madhya Pradesh, India;
| | - Reetika Chaurasia
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Md Azizul Haque
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (R.A.); (M.A.H.)
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (R.A.); (M.A.H.)
| |
Collapse
|
47
|
Dötsch L, Davies C, Hennes E, Schönfeld J, Kumar A, Guita CDC, Ehrler JH, Hiesinger K, Thavam S, Janning P, Sievers S, Knapp S, Proschak E, Ziegler S, Waldmann H. Discovery of the sEH Inhibitor Epoxykynin as a Potent Kynurenine Pathway Modulator. J Med Chem 2024; 67:4691-4706. [PMID: 38470246 PMCID: PMC10983002 DOI: 10.1021/acs.jmedchem.3c02245] [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: 11/29/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/13/2024]
Abstract
Disease-related phenotypic assays enable unbiased discovery of novel bioactive small molecules and may provide novel insights into physiological systems and unprecedented molecular modes of action (MMOA). Herein, we report the identification and characterization of epoxykynin, a potent inhibitor of the soluble epoxide hydrolase (sEH). Epoxykynin was discovered by means of a cellular assay monitoring modulation of kynurenine (Kyn) levels in BxPC-3 cells upon stimulation with the cytokine interferon-γ (IFN-γ) and subsequent target identification employing affinity-based chemical proteomics. Increased Kyn levels are associated with immune suppression in the tumor microenvironment and, thus, the Kyn pathway and its key player indoleamine 2,3-dioxygenase 1 (IDO1) are appealing targets in immuno-oncology. However, targeting IDO1 directly has led to limited success in clinical investigations, demonstrating that alternative approaches to reduce Kyn levels are in high demand. We uncover a cross-talk between sEH and the Kyn pathway that may provide new opportunities to revert cancer-induced immune tolerance.
Collapse
Affiliation(s)
- Lara Dötsch
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Department
of Chemical Biology, Technical University
of Dortmund, Otto-Hahn-Strasse
6, Dortmund 44227, Germany
| | - Caitlin Davies
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Elisabeth Hennes
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Julia Schönfeld
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Adarsh Kumar
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
- Structural
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, Frankfurt 60438, Germany
| | - Celine Da Cruz
Lopes Guita
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Johanna H.M. Ehrler
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Kerstin Hiesinger
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Sasikala Thavam
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Petra Janning
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sonja Sievers
- Compound
Management and Screening Center (COMAS), Otto-Hahn-Strasse 15, Dortmund 44227, Germany
| | - Stefan Knapp
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
- Structural
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, Frankfurt 60438, Germany
| | - Ewgenij Proschak
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Slava Ziegler
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Herbert Waldmann
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Department
of Chemical Biology, Technical University
of Dortmund, Otto-Hahn-Strasse
6, Dortmund 44227, Germany
| |
Collapse
|
48
|
Palma FR, Coelho DR, Pulakanti K, Sakiyama MJ, Huang Y, Ogata FT, Danes JM, Meyer A, Furdui CM, Spitz DR, Gomes AP, Gantner BN, Rao S, Backman V, Bonini MG. Histone H3.1 is a chromatin-embedded redox sensor triggered by tumor cells developing adaptive phenotypic plasticity and multidrug resistance. Cell Rep 2024; 43:113897. [PMID: 38493478 PMCID: PMC11209755 DOI: 10.1016/j.celrep.2024.113897] [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: 06/26/2023] [Revised: 01/08/2024] [Accepted: 02/16/2024] [Indexed: 03/19/2024] Open
Abstract
Chromatin structure is regulated through posttranslational modifications of histone variants that modulate transcription. Although highly homologous, histone variants display unique amino acid sequences associated with specific functions. Abnormal incorporation of histone variants contributes to cancer initiation, therapy resistance, and metastasis. This study reports that, among its biologic functions, histone H3.1 serves as a chromatin redox sensor that is engaged by mitochondrial H2O2. In breast cancer cells, the oxidation of H3.1Cys96 promotes its eviction and replacement by H3.3 in specific promoters. We also report that this process facilitates the opening of silenced chromatin domains and transcriptional activation of epithelial-to-mesenchymal genes associated with cell plasticity. Scavenging nuclear H2O2 or amino acid substitution of H3.1(C96S) suppresses plasticity, restores sensitivity to chemotherapy, and induces remission of metastatic lesions. Hence, it appears that increased levels of H2O2 produced by mitochondria of breast cancer cells directly promote redox-regulated H3.1-dependent chromatin remodeling involved in chemoresistance and metastasis.
Collapse
Affiliation(s)
- Flavio R Palma
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Diego R Coelho
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Kirthi Pulakanti
- Versiti Blood Research Institute of Wisconsin, and Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marcelo J Sakiyama
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Yunping Huang
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Fernando T Ogata
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Jeanne M Danes
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA
| | - Alison Meyer
- Versiti Blood Research Institute of Wisconsin, and Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Douglas R Spitz
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52245, USA
| | - Ana P Gomes
- Molecular Oncology Program, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Benjamin N Gantner
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sridhar Rao
- Versiti Blood Research Institute of Wisconsin, and Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University McCormick School of Engineering, Evanston, IL 60208, USA
| | - Marcelo G Bonini
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
| |
Collapse
|
49
|
Duran T, Karaselek MA, Kuccukturk S, Kursunlu AN, Ozmen M. Water-soluble Pillar[5]arene-based drug candidates for lung and breast cancer. J Biomol Struct Dyn 2024:1-10. [PMID: 38525947 DOI: 10.1080/07391102.2024.2331629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
The objective of research was to examine the likely anticancer effectiveness of distinct pillar[5] arene derivatives, ws-penta-P[5] and ws-deca-P[5], on breast and lung cancer cell lines in vitro. To achieve this goal, breast cancer (MCF7) cells, lung cancer (A549) cells, healthy cells (HEK293) were utilized. The IC50 dose of ws-penta-P[5] and ws-deca-P[5] was determined using the MTT method. Both treatment (pillar[5] arene applied) and control (pillar[5] arene not applied) groups were established for all three cell lines. Real-time polymerase chain reaction (qPCR) was used to evaluate changes in gene expression following pillar[5] arene treatment. Flow cytometry analysis was used to determine apoptosis and cell cycle arrest. The treatment group and control group results were compared after the study. The results revealed that in both cell lines treated with ws-deca-P[5], proapoptotic gene expressions were upregulated, while antiapoptotic gene expressions and caspase activation gene expressions were down-regulated. The flow cytometry apoptosis and cell cycle analysis in treatment group compared to the control, it was observed that the apoptosis rate increased in the ws-deca-P[5] and ws-deca-P[5] were shown to cause G0/G1 phase arrest in both cell groups. Results from our study that pillar[5] arene derivatives had the potential for treating breast and lung cancer, and more research is required in this area.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Tugce Duran
- Medicine Faculty, Department of Medical Genetic, KTO Karatay University, Konya, Türkiye
| | - Mehmet Ali Karaselek
- Meram Medicine Faculty, Department of Internal Medicine, Necmettin Erbakan University, Konya, Türkiye
| | - Serkan Kuccukturk
- Medicine Faculty, Department of Medical Biology, Karamanoğlu Mehmetbey University, Konya, Türkiye
| | | | - Mustafa Ozmen
- Science Faculty, Department of Chemistry, Selçuk University, Konya, Türkiye
| |
Collapse
|
50
|
Leiva S, Cantoia A, Fabbri C, Bugnon Valdano M, Luppo V, Morales MA, Rosano G, Gardiol D. The Zika virus infection remodels the expression of the synaptotagmin-9 secretory protein. Biol Chem 2024; 405:189-201. [PMID: 37677740 DOI: 10.1515/hsz-2023-0165] [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: 03/20/2023] [Accepted: 08/08/2023] [Indexed: 09/09/2023]
Abstract
The exact mechanisms involved in flaviviruses virions' release and the specific secretion of viral proteins, such as the Non Structural protein-1 (NS1), are still unclear. While these processes might involve vesicular transport to the cell membrane, NS1 from some flaviviruses was shown to participate in viral assembly and release. Here, we assessed the effect of the Zika virus (ZIKV) NS1 expression on the cellular proteome to identify trafficking-related targets that may be altered in the presence of the viral protein. We detected an increase in the synaptotagmin-9 (SYT9) secretory protein, which participates in the intracellular transport of protein-laden vesicles. We confirmed the effect of NS1 on SYT9 levels by transfection models while also detecting a significant subcellular redistribution of SYT9. We found that ZIKV prM-Env proteins, required for the viral particle release, also increased SYT9 levels and changed its localization. Finally, we demonstrated that ZIKV cellular infection raises SYT9 levels and promotes changes in its subcellular localization, together with a co-distribution with both Env and NS1. Altogether, the data suggest SYT9's implication in the vesicular transport of viral proteins or virions during ZIKV infection, showing for the first time the association of synaptotagmins with the flavivirus' life cycle.
Collapse
Affiliation(s)
- Santiago Leiva
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario-CONICET, Universidad Nacional de Rosario, Suipacha 590, 2000, Rosario, Argentina
| | - Alejo Cantoia
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario-CONICET, Universidad Nacional de Rosario, Suipacha 590, 2000, Rosario, Argentina
| | - Cintia Fabbri
- Instituto Nacional de Enfermedades Virales Humanas "Dr. Julio Maiztegui" (INEVH-ANLIS), Monteagudo 2510, Pergamino, Buenos Aires, Argentina
| | - Marina Bugnon Valdano
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario-CONICET, Universidad Nacional de Rosario, Suipacha 590, 2000, Rosario, Argentina
| | - Victoria Luppo
- Instituto Nacional de Enfermedades Virales Humanas "Dr. Julio Maiztegui" (INEVH-ANLIS), Monteagudo 2510, Pergamino, Buenos Aires, Argentina
| | - María Alejandra Morales
- Instituto Nacional de Enfermedades Virales Humanas "Dr. Julio Maiztegui" (INEVH-ANLIS), Monteagudo 2510, Pergamino, Buenos Aires, Argentina
| | - Germán Rosano
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario-CONICET, Universidad Nacional de Rosario, Suipacha 590, 2000, Rosario, Argentina
| | - Daniela Gardiol
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario-CONICET, Universidad Nacional de Rosario, Suipacha 590, 2000, Rosario, Argentina
| |
Collapse
|