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Aumer T, Däther M, Bergmayr L, Kartika S, Zeng T, Ge Q, Giorgio G, Hess AJ, Michalakis S, Traube FR. The type of DNA damage response after decitabine treatment depends on the level of DNMT activity. Life Sci Alliance 2024; 7:e202302437. [PMID: 38906675 PMCID: PMC11192838 DOI: 10.26508/lsa.202302437] [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: 10/15/2023] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
Decitabine and azacytidine are considered as epigenetic drugs that induce DNA methyltransferase (DNMT)-DNA crosslinks, resulting in DNA hypomethylation and damage. Although they are already applied against myeloid cancers, important aspects of their mode of action remain unknown, highly limiting their clinical potential. Using a combinatorial approach, we reveal that the efficacy profile of both compounds primarily depends on the level of induced DNA damage. Under low DNMT activity, only decitabine has a substantial impact. Conversely, when DNMT activity is high, toxicity and cellular response to both compounds are dramatically increased, but do not primarily depend on DNA hypomethylation or RNA-associated processes. By investigating proteome dynamics on chromatin, we show that decitabine induces a strictly DNMT-dependent multifaceted DNA damage response based on chromatin recruitment, but not expression-level changes of repair-associated proteins. The choice of DNA repair pathway hereby depends on the severity of decitabine-induced DNA lesions. Although under moderate DNMT activity, mismatch (MMR), base excision (BER), and Fanconi anaemia-dependent DNA repair combined with homologous recombination are activated in response to decitabine, high DNMT activity and therefore immense replication stress induce activation of MMR and BER followed by non-homologous end joining.
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Affiliation(s)
- Tina Aumer
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Maike Däther
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Linda Bergmayr
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Stephanie Kartika
- Department of Biochemistry, University of Munich (LMU), München, Germany
| | - Theodor Zeng
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Qingyi Ge
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Grazia Giorgio
- Department of Ophthalmology, University Hospital LMU Munich, München, Germany
| | - Alexander J Hess
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | | | - Franziska R Traube
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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2
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Lukovic D, Gyöngyösi M, Pavo IJ, Mester-Tonczar J, Einzinger P, Zlabinger K, Kastner N, Spannbauer A, Traxler D, Pavo N, Goliasch G, Pils D, Jakab A, Szankai Z, Michel-Behnke I, Zhang L, Devaux Y, Graf S, Beitzke D, Winkler J. Increased [ 18F]FDG uptake in the infarcted myocardial area displayed by combined PET/CMR correlates with snRNA-seq-detected inflammatory cell invasion. Basic Res Cardiol 2024:10.1007/s00395-024-01064-y. [PMID: 38922408 DOI: 10.1007/s00395-024-01064-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
Combined [18F]FDG PET-cardiac MRI imaging (PET/CMR) is a useful tool to assess myocardial viability and cardiac function in patients with acute myocardial infarction (AMI). Here, we evaluated the prognostic value of PET/CMR in a porcine closed-chest reperfused AMI (rAMI) model. Late gadolinium enhancement by PET/CMR imaging displayed tracer uptake defect at the infarction site by 3 days after the rAMI in the majority of the animals (group Match, n = 28). Increased [18F]FDG uptake at the infarcted area (metabolism/contractility mismatch) with reduced tracer uptake in the remote viable myocardium (group Mismatch, n = 12) 3 days after rAMI was observed in the animals with larger infarct size and worse left ventricular ejection fraction (LVEF) (34 ± 8.7 vs 42.0 ± 5.2%), with lower LVEF also at the 1-month follow-up (35.8 ± 9.5 vs 43.0 ± 6.3%). Transcriptome analyses by bulk and single-nuclei RNA sequencing of the infarcted myocardium and border zones (n = 3 of each group, and 3 sham-operated controls) revealed a strong inflammatory response with infiltration of monocytes and macrophages in the infarcted and border areas in Mismatch animals. Our data indicate a high prognostic relevance of combined PET/MRI in the subacute phase of rAMI for subsequent impairment of heart function and underline the adverse effects of an excessive activation of the innate immune system in the initial phase after rAMI.
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Affiliation(s)
- Dominika Lukovic
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria
| | - Mariann Gyöngyösi
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria.
| | - Imre J Pavo
- Division of Pediatric Cardiology, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Julia Mester-Tonczar
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria
| | - Patrick Einzinger
- Institute of Information Systems Engineering, Research Unit of Information and Software Engineering, Vienna University of Technology, 1040, Vienna, Austria
| | - Katrin Zlabinger
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria
| | - Nina Kastner
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria
| | - Andreas Spannbauer
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria
| | - Denise Traxler
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria
| | - Noemi Pavo
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria
| | - Georg Goliasch
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria
| | - Dietmar Pils
- Division of General Surgery, Department of Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Andras Jakab
- Center for MR-Research, University Children's Hospital Zurich, Zurich, Switzerland
| | | | - Ina Michel-Behnke
- Division of Pediatric Cardiology, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Lu Zhang
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Senta Graf
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria
| | - Dietrich Beitzke
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Johannes Winkler
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria
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3
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Heidari Horestani M, Atri Roozbahani G, Baniahmad A. The clock gene BHLHE40 and atypical CCNG2 control androgen-induced cellular senescence as a novel tumor suppressive pathway in prostate cancer. J Exp Clin Cancer Res 2024; 43:174. [PMID: 38902772 PMCID: PMC11188219 DOI: 10.1186/s13046-024-03097-6] [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: 04/19/2024] [Accepted: 06/08/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND The androgen receptor (AR) is a drug target used to inhibit AR and prostate cancer (PCa) growth. Surprisingly, treatment with supraphysiological androgen level (SAL), used in bipolar androgen therapy, inhibits growth of PCa suggesting a tumor-suppressive activity by SAL. SAL was shown to induce cellular senescence in PCa. METHODS RNA-seq and transcriptome analysis, ChIP-seq, human 3D PCa spheroids, mouse xenografted castration-resistant PCa, knockdown and overexpression, Co-immunoprecipitation (Co-IP), translocation analysis, immune detection, qRT-PCR, protein-protein interaction modelling. RESULTS Here, mice xenografts with castration-resistant PCa tumors show that SAL inhibits cancer growth in vivo suggesting that SAL activates a tumor-suppressive mechanism. RNA-seq and ChIP-seq revealed the clock gene BHLHE40 is a novel direct AR target. Compared to adjacent human prostate tissues, the expression of BHLHE40 is reduced in PCa tumors and associated with reduced survival. Knockdown suggests that BHLHE40 mediates SAL-induced cellular senescence including tumor spheroids. Interestingly, a large overlap of differentially expressed gene sets was identified between BHLHE40 and SAL leading to the identification of four classes of SAL-BHLHE40 transcriptome landscapes. Co-IP and modelling suggest binding of BHLHE40 to AR and their co-translocation into nucleus by SAL treatment. Further, RNA-seq and ChIP-seq analysis indicate that the atypical tumor suppressive cyclin G2 emerged as a novel downstream target of BHLHE40 and a mediator of SAL-induced cellular senescence. CONCLUSIONS The data provide evidence of the tumor suppressive activity of SAL and a novel signaling by the AR-BHLHE40-CCNG2 axis for androgen-induced cellular senescence, linking circadian rhythm factor to androgen signaling as a novel tumor suppressive pathway.
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Affiliation(s)
| | - Golnaz Atri Roozbahani
- Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, 07740, Jena, Germany
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, 07740, Jena, Germany.
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Abbas M, Goodney G, Vargas JD, Gaye A. Transcriptome Study of 2 Black Cohorts Reveals cis Long Noncoding RNAs Associated With Hypertension-Related mRNAs. J Am Heart Assoc 2024; 13:e034417. [PMID: 38818927 DOI: 10.1161/jaha.124.034417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/06/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) have emerged as critical regulators of the expression of genes involved in cardiovascular diseases. This project aims to identify circulating lncRNAs associated with protein-coding mRNAs differentially expressed between hypertensive and normotensive individuals and establish their link with hypertension. METHODS AND RESULTS The analyses were conducted in 3 main steps: (1) an unbiased whole blood transcriptome-wide analysis was conducted to identify and replicate protein-coding genes differentially expressed by hypertension status in 497 and 179 Black individuals from the GENE-FORECAST (Genomics, Environmental Factors and the Social Determinants of Cardiovascular Disease in African-Americans Study) and MH-GRID (Minority Health Genomics and Translational Research Bio-Repository Database) studies, respectively. Subsequently, (2) proximal lncRNAs, termed cis lncRNA quantitative trait loci, associated with each mRNA were identified in the GENE-FORECAST study and replicated in the MH-GRID study. Finally, (3) the lncRNA quantitative trait loci were used as predictors in a random forest model to predict hypertension in both data sets. A total of 129 mRNAs were significantly differentially expressed between normotensive and hypertensive individuals in both data sets. The lncRNA-mRNA association analysis revealed 249 cis lncRNA quantitative trait loci associated with 102 mRNAs, including VAMP2 (vesicle-associated membrane protein 2), mitogen-activated protein kinase kinase 3, CCAAT enhancer binding protein beta, and lymphocyte antigen 6 complex, locus E. The 249 lncRNA quantitative trait loci predicted hypertension with an area under the curve of 0.79 and 0.71 in GENE-FORECAST and MH-GRID studies, respectively. CONCLUSIONS This study leveraged a significant sample of Black individuals, a population facing a disproportionate burden of hypertension. The analyses unveiled a total of 271 lncRNA-mRNA relationships involving mRNAs that play critical roles in vascular pathways relevant to blood pressure regulation. The compelling findings, consistent across 2 independent data sets, establish a reliable foundation for designing in vitro/in vivo experiments.
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Affiliation(s)
- Malak Abbas
- National Human Genome Research Institute, National Institutes of Health Bethesda MD
| | - Gabriel Goodney
- National Human Genome Research Institute, National Institutes of Health Bethesda MD
| | | | - Amadou Gaye
- National Human Genome Research Institute, National Institutes of Health Bethesda MD
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5
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Aguadé-Gorgorió J, Jami-Alahmadi Y, Calvanese V, Kardouh M, Fares I, Johnson H, Rezek V, Ma F, Magnusson M, Wang Y, Shin JE, Nance KJ, Goodridge HS, Liebscher S, Schenke-Layland K, Crooks GM, Wohlschlegel JA, Mikkola HKA. MYCT1 controls environmental sensing in human haematopoietic stem cells. Nature 2024; 630:412-420. [PMID: 38839950 PMCID: PMC11168926 DOI: 10.1038/s41586-024-07478-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: 05/30/2023] [Accepted: 04/26/2024] [Indexed: 06/07/2024]
Abstract
The processes that govern human haematopoietic stem cell (HSC) self-renewal and engraftment are poorly understood and challenging to recapitulate in culture to reliably expand functional HSCs1-3. Here we identify MYC target 1 (MYCT1; also known as MTLC) as a crucial human HSC regulator that moderates endocytosis and environmental sensing in HSCs. MYCT1 is selectively expressed in undifferentiated human haematopoietic stem and progenitor cells (HSPCs) and endothelial cells but becomes markedly downregulated during HSC culture. Lentivirus-mediated knockdown of MYCT1 prevented human fetal liver and cord blood (CB) HSPC expansion and engraftment. By contrast, restoring MYCT1 expression improved the expansion and engraftment of cultured CB HSPCs. Single-cell RNA sequencing of human CB HSPCs in which MYCT1 was knocked down or overexpressed revealed that MYCT1 governs important regulatory programmes and cellular properties essential for HSC stemness, such as ETS factor expression and low mitochondrial activity. MYCT1 is localized in the endosomal membrane in HSPCs and interacts with vesicle trafficking regulators and signalling machinery. MYCT1 loss in HSPCs led to excessive endocytosis and hyperactive signalling responses, whereas restoring MYCT1 expression balanced culture-induced endocytosis and dysregulated signalling. Moreover, sorting cultured CB HSPCs on the basis of lowest endocytosis rate identified HSPCs with preserved MYCT1 expression and MYCT1-regulated HSC stemness programmes. Our work identifies MYCT1-moderated endocytosis and environmental sensing as essential regulatory mechanisms required to preserve human HSC stemness. Our data also pinpoint silencing of MYCT1 as a cell-culture-induced vulnerability that compromises human HSC expansion.
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Affiliation(s)
- Júlia Aguadé-Gorgorió
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA.
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
- Pfizer, Cambridge, MA, USA
| | - Vincenzo Calvanese
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
- Laboratory for Molecular Cell Biology, University College London, London, UK
- Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Maya Kardouh
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Oakland University William Beaumont School of Medicine, Rochester, MI, USA
| | - Iman Fares
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Kite Pharma, Santa Monica, CA, USA
| | - Haley Johnson
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Valerie Rezek
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- UCLA AIDS Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Feiyang Ma
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
- Amgen, Thousand Oaks, CA, USA
| | - Mattias Magnusson
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Yanling Wang
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Juliana E Shin
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Karina J Nance
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Helen S Goodridge
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Simone Liebscher
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University, Tübingen, Germany
| | - Katja Schenke-Layland
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University, Tübingen, Germany
- NMI Natural and Medical Sciences Institute at the University Tübingen, Reutlingen, Germany
| | - Gay M Crooks
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Hanna K A Mikkola
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA.
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Nowrouzi B, Torres-Montero P, Kerkhoven EJ, Martínez JL, Rios-Solis L. Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production. Metab Eng Commun 2024; 18:e00229. [PMID: 38098801 PMCID: PMC10716015 DOI: 10.1016/j.mec.2023.e00229] [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: 09/01/2023] [Revised: 10/09/2023] [Accepted: 11/04/2023] [Indexed: 12/17/2023] Open
Abstract
Saccharomyces cerevisiae has been conveniently used to produce Taxol® anticancer drug early precursors. However, the harmful impact of oxidative stress by the first cytochrome P450-reductase enzymes (CYP725A4-POR) of Taxol® pathway has hampered sufficient progress in yeast. Here, we evolved an oxidative stress-resistant yeast strain with three-fold higher titre of their substrate, taxadiene. The performance of the evolved and parent strains were then evaluated in galactose-limited chemostats before and under the oxidative stress by an oxidising agent. The interaction of evolution and oxidative stress was comprehensively evaluated through transcriptomics and metabolite profiles integration in yeast enzyme-constrained genome scale model. Overall, the evolved strain showed improved respiration, reduced overflow metabolites production and oxidative stress re-induction tolerance. The cross-protection mechanism also potentially contributed to better heme, flavin and NADPH availability, essential for CYP725A4 and POR optimal activity in yeast. The results imply that the evolved strain is a robust cell factory for future efforts towards Taxol© production.
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Affiliation(s)
- Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Pablo Torres-Montero
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Eduard J. Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- SciLifeLab, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - José L. Martínez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
- Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, United Kingdom
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Choksey A, Carter RD, Thackray BD, Ball V, Kennedy BWC, Ha LHT, Sharma E, Broxholme J, Castro-Guarda M, Murphy MP, Heather LC, Tyler DJ, Timm KN. AICAR confers prophylactic cardioprotection in doxorubicin-induced heart failure in rats. J Mol Cell Cardiol 2024; 191:12-22. [PMID: 38643934 DOI: 10.1016/j.yjmcc.2024.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 04/23/2024]
Abstract
Doxorubicin (DOX) is a widely used chemotherapeutic agent that can cause serious cardiotoxic side effects, leading to heart failure (HF). Impaired mitochondrial function is thought to be key factor driving progression into HF. We have previously shown in a rat model of DOX-HF that heart failure with reduced ejection fraction correlates with mitochondrial loss and dysfunction. Adenosine monophosphate-dependent kinase (AMPK) is a cellular energy sensor, regulating mitochondrial biogenesis and energy metabolism, including fatty acid oxidation. We hypothesised that AMPK activation could restore mitochondrial function and therefore be a novel cardioprotective strategy for the prevention of DOX-HF. Consequently, we set out to assess whether 5-aminoimidazole-4-carboxamide 1-β-D-ribofuranoside (AICAR), an activator of AMPK, could prevent cardiac functional decline in this chronic intravenous rat model of DOX-HF. In line with our hypothesis, AICAR improved cardiac systolic function. AICAR furthermore improved cardiac mitochondrial fatty acid oxidation, independent of mitochondrial number, and in the absence of observable AMPK-activation. In addition, we found that AICAR prevented loss of myocardial mass. RNAseq analysis showed that this may be driven by normalisation of pathways associated with ribosome function and protein synthesis, which are impaired in DOX-treated rat hearts. AICAR furthermore prevented dyslipidemia and excessive body-weight loss in DOX-treated rats, which may contribute to preservation of myocardial mass. Though it is unclear whether AICAR exerted its cardioprotective effect through cardiac or extra-cardiac AMPK-activation or via an AMPK-independent effect, these results show promise for the use of AICAR as a cardioprotective agent in DOX-HF to both preserve cardiac function and mass.
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Affiliation(s)
- Anurag Choksey
- Department of Physiology Anatomy and Genetics, University of Oxford, UK
| | - Ryan D Carter
- Department of Physiology Anatomy and Genetics, University of Oxford, UK; Doctoral Training Centre, University of Oxford, Keble Road, Oxford, OX1 3NP, UK
| | | | - Vicky Ball
- Department of Physiology Anatomy and Genetics, University of Oxford, UK
| | - Brett W C Kennedy
- Department of Physiology Anatomy and Genetics, University of Oxford, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, UK
| | | | - Eshita Sharma
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Dr, Headington, Oxford OX3 7BN, UK
| | - John Broxholme
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Dr, Headington, Oxford OX3 7BN, UK
| | | | | | - Lisa C Heather
- Department of Physiology Anatomy and Genetics, University of Oxford, UK
| | - Damian J Tyler
- Department of Physiology Anatomy and Genetics, University of Oxford, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, UK
| | - Kerstin N Timm
- Department of Physiology Anatomy and Genetics, University of Oxford, UK; Department of Pharmacology, University of Oxford, UK.
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8
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Captur G, Doykov I, Chung SC, Field E, Barnes A, Zhang E, Heenan I, Norrish G, Moon JC, Elliott PM, Heywood WE, Mills K, Kaski JP. Novel Multiplexed Plasma Biomarker Panel Has Diagnostic and Prognostic Potential in Children With Hypertrophic Cardiomyopathy. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004448. [PMID: 38847081 PMCID: PMC11188636 DOI: 10.1161/circgen.123.004448] [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: 10/11/2023] [Accepted: 04/16/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is defined clinically by pathological left ventricular hypertrophy. We have previously developed a plasma proteomics biomarker panel that correlates with clinical markers of disease severity and sudden cardiac death risk in adult patients with HCM. The aim of this study was to investigate the utility of adult biomarkers and perform new discoveries in proteomics for childhood-onset HCM. METHODS Fifty-nine protein biomarkers were identified from an exploratory plasma proteomics screen in children with HCM and augmented into our existing multiplexed targeted liquid chromatography-tandem/mass spectrometry-based assay. The association of these biomarkers with clinical phenotypes and outcomes was prospectively tested in plasma collected from 148 children with HCM and 50 healthy controls. Machine learning techniques were used to develop novel pediatric plasma proteomic biomarker panels. RESULTS Four previously identified adult HCM markers (aldolase fructose-bisphosphate A, complement C3a, talin-1, and thrombospondin 1) and 3 new markers (glycogen phosphorylase B, lipoprotein a and profilin 1) were elevated in pediatric HCM. Using supervised machine learning applied to training (n=137) and validation cohorts (n=61), this 7-biomarker panel differentiated HCM from healthy controls with an area under the curve of 1.0 in the training data set (sensitivity 100% [95% CI, 95-100]; specificity 100% [95% CI, 96-100]) and 0.82 in the validation data set (sensitivity 75% [95% CI, 59-86]; specificity 88% [95% CI, 75-94]). Reduced circulating levels of 4 other peptides (apolipoprotein L1, complement 5b, immunoglobulin heavy constant epsilon, and serum amyloid A4) found in children with high sudden cardiac death risk provided complete separation from the low and intermediate risk groups and predicted mortality and adverse arrhythmic outcomes (hazard ratio, 2.04 [95% CI, 1.0-4.2]; P=0.044). CONCLUSIONS In children, a 7-biomarker proteomics panel can distinguish HCM from controls with high sensitivity and specificity, and another 4-biomarker panel identifies those at high risk of adverse arrhythmic outcomes, including sudden cardiac death.
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Affiliation(s)
- Gabriella Captur
- UCL MRC Unit for Lifelong Health & Ageing, UCL, London, United Kingdom (G.C.)
- UCL Institute of Cardiovascular Science, UCL, London, United Kingdom (G.C., J.C.M., P.M.E.)
- The Royal Free Hospital, Centre for Inherited Heart Muscle Conditions, Cardiology Department, UCL, London, United Kingdom (G.C.)
| | - Ivan Doykov
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health, London, United Kingdom (I.D., E.Z., W.E.H., K.M.)
| | - Sheng-Chia Chung
- UCL Institute of Health Informatics Research, Division of Infection and Immunity, London, United Kingdom (S.-C.C.)
| | - Ella Field
- Centre for Paediatric Inherited & Rare Cardiovascular Disease, Institute of Cardiovascular Science, London, United Kingdom (E.F., A.B., I.H., G.N., J.P.K.)
- Centre for Inherited Cardiovascular Diseases, Great Ormond Street Hospital, London, United Kingdom (E.F., A.B., I.H., G.N., J.P.K.)
| | - Annabelle Barnes
- Centre for Paediatric Inherited & Rare Cardiovascular Disease, Institute of Cardiovascular Science, London, United Kingdom (E.F., A.B., I.H., G.N., J.P.K.)
- Centre for Inherited Cardiovascular Diseases, Great Ormond Street Hospital, London, United Kingdom (E.F., A.B., I.H., G.N., J.P.K.)
| | - Enpei Zhang
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health, London, United Kingdom (I.D., E.Z., W.E.H., K.M.)
- UCL Medical School, University College London, London, United Kingdom (E.Z.)
| | - Imogen Heenan
- Centre for Paediatric Inherited & Rare Cardiovascular Disease, Institute of Cardiovascular Science, London, United Kingdom (E.F., A.B., I.H., G.N., J.P.K.)
- Centre for Inherited Cardiovascular Diseases, Great Ormond Street Hospital, London, United Kingdom (E.F., A.B., I.H., G.N., J.P.K.)
| | - Gabrielle Norrish
- Centre for Paediatric Inherited & Rare Cardiovascular Disease, Institute of Cardiovascular Science, London, United Kingdom (E.F., A.B., I.H., G.N., J.P.K.)
- Centre for Inherited Cardiovascular Diseases, Great Ormond Street Hospital, London, United Kingdom (E.F., A.B., I.H., G.N., J.P.K.)
| | - James C. Moon
- Barts Heart Centre, the Cardiovascular Magnetic Resonance Unit, London, United Kingdom (J.C.M.)
| | - Perry M. Elliott
- Barts Heart Centre, the Inherited Cardiovascular Diseases Unit, St Bartholomew’s Hospital, London, United Kingdom (P.M.E.)
| | - Wendy E. Heywood
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health, London, United Kingdom (I.D., E.Z., W.E.H., K.M.)
| | - Kevin Mills
- Translational Mass Spectrometry Research Group, UCL Institute of Child Health, London, United Kingdom (I.D., E.Z., W.E.H., K.M.)
| | - Juan Pablo Kaski
- Centre for Paediatric Inherited & Rare Cardiovascular Disease, Institute of Cardiovascular Science, London, United Kingdom (E.F., A.B., I.H., G.N., J.P.K.)
- Centre for Inherited Cardiovascular Diseases, Great Ormond Street Hospital, London, United Kingdom (E.F., A.B., I.H., G.N., J.P.K.)
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9
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Elovitz M, Anton L, Cristancho A, Ferguson B, Joseph A, Ravel J. Vaginal microbes alter epithelial transcriptome and induce epigenomic modifications providing insight into mechanisms for susceptibility to adverse reproductive outcomes. RESEARCH SQUARE 2024:rs.3.rs-4385224. [PMID: 38854063 PMCID: PMC11160883 DOI: 10.21203/rs.3.rs-4385224/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The cervicovaginal microbiome is highly associated with women's health, with microbial communities dominated by Lactobacillus species considered optimal. Conversely, a lack of lactobacilli and a high abundance of strict and facultative anaerobes, including Gardnerella vaginalis, have been associated with adverse reproductive outcomes. However, how host-microbial interactions alter specific molecular pathways and impact cervical and vaginal epithelial function remains unclear. Using RNA-sequencing, we characterized the in vitro cervicovaginal epithelial transcriptional response to different vaginal bacteria and their culture supernatants. We showed that G. vaginalis upregulates genes associated with an activated innate immune response. Unexpectedly, G. vaginalis specifically induced inflammasome pathways through activation of NLRP3-mediated increases in caspase-1, IL-1β and cell death, while live L. crispatus had minimal transcriptomic changes on epithelial cells. L. crispatus culture supernatants resulted in a shift in the epigenomic landscape of cervical epithelial cells that was confirmed by ATAC-sequencing showing reduced chromatin accessibility. This study reveals new insights into host-microbe interactions in the lower reproductive tract and suggests potential therapeutic strategies leveraging the vaginal microbiome to improve reproductive health.
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10
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Powell RT, Rinkenbaugh AL, Guo L, Cai S, Shao J, Zhou X, Zhang X, Jeter-Jones S, Fu C, Qi Y, Baameur Hancock F, White JB, Stephan C, Davies PJ, Moulder S, Symmans WF, Chang JT, Piwnica-Worms H. Targeting neddylation and sumoylation in chemoresistant triple negative breast cancer. NPJ Breast Cancer 2024; 10:37. [PMID: 38802426 PMCID: PMC11130334 DOI: 10.1038/s41523-024-00644-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Triple negative breast cancer (TNBC) accounts for 15-20% of breast cancer cases in the United States. Systemic neoadjuvant chemotherapy (NACT), with or without immunotherapy, is the current standard of care for patients with early-stage TNBC. However, up to 70% of TNBC patients have significant residual disease once NACT is completed, which is associated with a high risk of developing recurrence within two to three years of surgical resection. To identify targetable vulnerabilities in chemoresistant TNBC, we generated longitudinal patient-derived xenograft (PDX) models from TNBC tumors before and after patients received NACT. We then compiled transcriptomes and drug response profiles for all models. Transcriptomic analysis identified the enrichment of aberrant protein homeostasis pathways in models from post-NACT tumors relative to pre-NACT tumors. This observation correlated with increased sensitivity in vitro to inhibitors targeting the proteasome, heat shock proteins, and neddylation pathways. Pevonedistat, a drug annotated as a NEDD8-activating enzyme (NAE) inhibitor, was prioritized for validation in vivo and demonstrated efficacy as a single agent in multiple PDX models of TNBC. Pharmacotranscriptomic analysis identified a pathway-level correlation between pevonedistat activity and post-translational modification (PTM) machinery, particularly involving neddylation and sumoylation targets. Elevated levels of both NEDD8 and SUMO1 were observed in models exhibiting a favorable response to pevonedistat compared to those with a less favorable response in vivo. Moreover, a correlation emerged between the expression of neddylation-regulated pathways and tumor response to pevonedistat, indicating that targeting these PTM pathways may prove effective in combating chemoresistant TNBC.
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Affiliation(s)
- Reid T Powell
- Center for Translational Cancer Research, Institute of Bioscience and Technology Texas A&M Health Science Center, Houston, TX, USA
| | - Amanda L Rinkenbaugh
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lei Guo
- Center for Translational Cancer Research, Institute of Bioscience and Technology Texas A&M Health Science Center, Houston, TX, USA
| | - Shirong Cai
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jiansu Shao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xinhui Zhou
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaomei Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sabrina Jeter-Jones
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chunxiao Fu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuan Qi
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Faiza Baameur Hancock
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason B White
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Clifford Stephan
- Center for Translational Cancer Research, Institute of Bioscience and Technology Texas A&M Health Science Center, Houston, TX, USA
| | - Peter J Davies
- Center for Translational Cancer Research, Institute of Bioscience and Technology Texas A&M Health Science Center, Houston, TX, USA
| | - Stacy Moulder
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Eli Lilly and Company, Indianapolis, IN, USA
| | - W Fraser Symmans
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeffrey T Chang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Helen Piwnica-Worms
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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11
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Braun J, Hu Y, Jauch AT, Gronauer TF, Mergner J, Bach NC, Traube FR, Zahler S, Sieber SA. Neocarzilin Inhibits Cancer Cell Proliferation via BST-2 Degradation, Resulting in Lipid Raft-Trapped EGFR. JACS AU 2024; 4:1833-1840. [PMID: 38818080 PMCID: PMC11134574 DOI: 10.1021/jacsau.4c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 06/01/2024]
Abstract
Neocarzilin (NCA) is a natural product exhibiting potent antimigratory as well as antiproliferative effects. While vesicle amine transport protein 1 (VAT-1) was previously shown to inhibit migration upon NCA binding, the molecular mechanisms responsible for impaired proliferation remained elusive. We here introduce a chemical probe closely resembling the structural and stereochemical features of NCA and unravel bone marrow stromal antigen 2 (BST-2) as one of the targets responsible for the antiproliferative effect of NCA in cancer cells. The antiproliferative mechanism of NCA was confirmed in corresponding BST-2 knockout (KO) HeLa cells, which were less sensitive to compound treatment. Vice versa, reconstitution of BST-2 in the KO cells again reduced proliferation upon NCA addition, comparable to that of wild-type (wt) HeLa cells. Whole proteome mass spectrometric (MS) analysis of NCA-treated wt and KO cancer cells revealed regulated pathways and showed reduced levels of BST-2 upon NCA treatment. In-depth analysis of BST-2 levels in response to proteasome and lysosome inhibitors unraveled a lysosomal degradation path upon NCA treatment. As BST-2 mediates the release of epidermal growth factor receptor (EGFR) from lipid rafts to turn on proliferation signaling pathways, reduced BST-2 levels led to attenuated phosphorylation of STAT3. Furthermore, fluorescence microscopy confirmed increased colocalization of EGFR and lipid rafts in the presence of NCA. Overall, NCA represents a versatile anticancer natural product with a unique dual mode of action and unconventional inhibition of proliferation via BST-2 degradation.
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Affiliation(s)
- Josef Braun
- TUM School of Natural Sciences, Department of Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Straße 8, Garching near Munich D-85748, Germany
| | - Yudong Hu
- Department of Pharmacy, Pharmaceutical Biology, Ludwig-Maximilians-University in Munich (LMU), Butenandtstraße 5-13, Munich D-81377, Germany
| | - Adrian T Jauch
- Department of Pharmacy, Pharmaceutical Biology, Ludwig-Maximilians-University in Munich (LMU), Butenandtstraße 5-13, Munich D-81377, Germany
| | - Thomas F Gronauer
- TUM School of Natural Sciences, Department of Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Straße 8, Garching near Munich D-85748, Germany
- Metabolomics and Proteomics Core (MPC), Helmholtz Zentrum München GmbH German Research Center for Environmental Health, Heidemannstr. 1, Munich D-80939, Germany
| | - Julia Mergner
- Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar (BayBioMS@MRI), Technical University of Munich (TUM), Einsteinstraße 25 Munich, D-81675, Germany
| | - Nina C Bach
- TUM School of Natural Sciences, Department of Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Straße 8, Garching near Munich D-85748, Germany
| | - Franziska R Traube
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart D-70569, Germany
| | - Stefan Zahler
- Department of Pharmacy, Pharmaceutical Biology, Ludwig-Maximilians-University in Munich (LMU), Butenandtstraße 5-13, Munich D-81377, Germany
| | - Stephan A Sieber
- TUM School of Natural Sciences, Department of Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Straße 8, Garching near Munich D-85748, Germany
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12
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Langerud J, Eilertsen IA, Moosavi SH, Klokkerud SMK, Reims HM, Backe IF, Hektoen M, Sjo OH, Jeanmougin M, Tejpar S, Nesbakken A, Lothe RA, Sveen A. Multiregional transcriptomics identifies congruent consensus subtypes with prognostic value beyond tumor heterogeneity of colorectal cancer. Nat Commun 2024; 15:4342. [PMID: 38773143 PMCID: PMC11109119 DOI: 10.1038/s41467-024-48706-2] [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: 08/23/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
Intra-tumor heterogeneity compromises the clinical value of transcriptomic classifications of colorectal cancer. We investigated the prognostic effect of transcriptomic heterogeneity and the potential for classifications less vulnerable to heterogeneity in a single-hospital series of 1093 tumor samples from 692 patients, including multiregional samples from 98 primary tumors and 35 primary-metastasis sets. We show that intra-tumor heterogeneity of the consensus molecular subtypes (CMS) is frequent and has poor-prognostic associations independently of tumor microenvironment markers. Multiregional transcriptomics uncover cancer cell-intrinsic and low-heterogeneity signals that recapitulate the intrinsic CMSs proposed by single-cell sequencing. Further subclassification identifies congruent CMSs that explain a larger proportion of variation in patient survival than intra-tumor heterogeneity. Plasticity is indicated by discordant intrinsic phenotypes of matched primary and metastatic tumors. We conclude that multiregional sampling reconciles the prognostic power of tumor classifications from single-cell and bulk transcriptomics in the context of intra-tumor heterogeneity, and phenotypic plasticity challenges the reconciliation of primary and metastatic subtypes.
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Affiliation(s)
- Jonas Langerud
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Seyed H Moosavi
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Solveig M K Klokkerud
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Henrik M Reims
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Ingeborg F Backe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Merete Hektoen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ole H Sjo
- Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Marine Jeanmougin
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Sabine Tejpar
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Arild Nesbakken
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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13
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Brown PA. Genes Differentially Expressed Across Major Arteries Are Enriched in Endothelial Dysfunction-Related Gene Sets: Implications for Relative Inter-artery Atherosclerosis Risk. Bioinform Biol Insights 2024; 18:11779322241251563. [PMID: 38765020 PMCID: PMC11100403 DOI: 10.1177/11779322241251563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/13/2024] [Indexed: 05/21/2024] Open
Abstract
Atherosclerosis differs across major arteries. Although the biological basis is not fully understood, limited evidence of genetic differences has been documented. This study, therefore, was aimed to identify differentially expressed genes between clinically relevant major arteries and investigate their enrichment in endothelial dysfunction-related gene sets. A bioinformatic analysis of publicly available gene-level read counts for coronary, aortic, and tibial arteries was performed. Differential gene expression was conducted with DeSeq2 at a false discovery rate of 0.05. Differentially expressed genes were then subjected to over-representation analysis and active-subnetwork-oriented enrichment analysis, both at a false discovery rate of 0.005. Enriched terms common to both analyses were categorized for each contrast into immunity/inflammation-, membrane biology-, lipid metabolism-, and coagulation-related terms, and the top differentially expressed genes validated against Swiss Institute of Bioinformatics' Bgee database. There was mostly upregulation of differentially expressed genes for the coronary/tibial and aorta/tibial contrasts, but milder changes for the coronary/aorta contrast. Transcriptomic differences between coronary or aortic versus tibial samples largely involved immunity/inflammation-, membrane biology-, lipid metabolism-, and coagulation-related genes, suggesting potential to modulate endothelial dysfunction and atherosclerosis. These results imply atheroprone coronary and aortic environments compared with tibial artery tissue, which may explain observed relative inter-artery atherosclerosis risk.
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Affiliation(s)
- Paul A Brown
- Department of Basic Medical Sciences, Faculty of Medical Sciences Teaching and Research Complex, The University of the West Indies, Kingston, Jamaica
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14
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Seo J, Liu H, Young K, Zhang X, Keku TO, Jones CD, North KE, Sandler RS, Peery AF. Genetic and transcriptomic landscape of colonic diverticulosis. Gut 2024; 73:932-940. [PMID: 38443061 PMCID: PMC11088512 DOI: 10.1136/gutjnl-2023-331267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024]
Abstract
OBJECTIVE Colonic diverticulosis is a prevalent condition among older adults, marked by the presence of thin-walled pockets in the colon wall that can become inflamed, infected, haemorrhage or rupture. We present a case-control genetic and transcriptomic study aimed at identifying the genetic and cellular determinants underlying this condition and the relationship with other gastrointestinal disorders. DESIGN We conducted DNA and RNA sequencing on colonic tissue from 404 patients with (N=172) and without (N=232) diverticulosis. We investigated variation in the transcriptome associated with diverticulosis and further integrated this variation with single-cell RNA-seq data from the human intestine. We also integrated our expression quantitative trait loci with genome-wide association study using Mendelian randomisation (MR). Furthermore, a Polygenic Risk Score analysis gauged associations between diverticulosis severity and other gastrointestinal disorders. RESULTS We discerned 38 genes with differential expression and 17 with varied transcript usage linked to diverticulosis, indicating tissue remodelling as a primary diverticula formation mechanism. Diverticula formation was primarily linked to stromal and epithelial cells in the colon including endothelial cells, myofibroblasts, fibroblasts, goblet, tuft, enterocytes, neurons and glia. MR highlighted five genes including CCN3, CRISPLD2, ENTPD7, PHGR1 and TNFSF13, with potential causal effects on diverticulosis. Notably, ENTPD7 upregulation was confirmed in diverticulosis cases. Additionally, diverticulosis severity was positively correlated with genetic predisposition to diverticulitis. CONCLUSION Our results suggest that tissue remodelling is a primary mechanism for diverticula formation. Individuals with an increased genetic proclivity to diverticulitis exhibit a larger numbers of diverticula on colonoscopy.
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Affiliation(s)
- Jungkyun Seo
- Department of Epidemiology, The University of North Carolina, Chapel Hill, North Carolina, USA
| | - Hongwei Liu
- Department of Genetics, The University of North Carolina, Chapel Hill, North Carolina, USA
| | - Kristin Young
- Department of Epidemiology, The University of North Carolina, Chapel Hill, North Carolina, USA
| | - Xinruo Zhang
- Department of Epidemiology, The University of North Carolina, Chapel Hill, North Carolina, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, The University of North Carolina, Chapel Hill, North Carolina, USA
| | - Corbin D Jones
- Department of Biology and Integrative Program for Biological and Genome Sciences, The University of North Carolina, Chapel Hill, North Carolina, USA
| | - Kari E North
- Department of Epidemiology, The University of North Carolina, Chapel Hill, North Carolina, USA
| | - Robert S Sandler
- Gastroenterology and Hepatology, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Anne F Peery
- Center for Gastrointestinal Biology and Disease, The University of North Carolina, Chapel Hill, North Carolina, USA
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15
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Kaimala S, Lootah SS, Mehra N, Kumar CA, Marzooqi SA, Sampath P, Ansari SA, Emerald BS. The Long Non-Coding RNA Obesity-Related (Obr) Contributes To Lipid Metabolism Through Epigenetic Regulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401939. [PMID: 38704700 DOI: 10.1002/advs.202401939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Indexed: 05/07/2024]
Abstract
Obesity is a multifactorial disease that is part of today's epidemic and also increases the risk of other metabolic diseases. Long noncoding RNAs (lncRNAs) provide one tier of regulatory mechanisms to maintain metabolic homeostasis. Although lncRNAs are a significant constituent of the mammalian genome, studies aimed at their metabolic significance, including obesity, are only beginning to be addressed. Here, a developmentally regulated lncRNA, termed as obesity related (Obr), whose expression in metabolically relevant tissues such as skeletal muscle, liver, and pancreas is altered in diet-induced obesity, is identified. The Clone 9 cell line and high-fat diet-induced obese Wistar rats are used as a model system to verify the function of Obr. By using stable expression and antisense oligonucleotide-mediated downregulation of the expression of Obr followed by different molecular biology experiments, its role in lipid metabolism is verified. It is shown that Obr associates with the cAMP response element-binding protein (Creb) and activates different transcription factors involved in lipid metabolism. Its association with the Creb histone acetyltransferase complex, which includes the cAMP response element-binding protein (CBP) and p300, positively regulates the transcription of genes involved in lipid metabolism. In addition, Obr is regulated by Pparγ in response to lipid accumulation.
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Affiliation(s)
- Suneesh Kaimala
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
| | - Shareena Saeed Lootah
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
| | - Neha Mehra
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
| | - Challagandla Anil Kumar
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
| | - Saeeda Al Marzooqi
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
| | - Prabha Sampath
- A*STAR Skin Research Laboratory, Agency for Science Technology & Research (A*STAR), Singapore, 138648, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Genome Institute of Singapore, Agency for Science Technology & Research (A*STAR), Singapore, 138672, Singapore
| | - Suraiya Anjum Ansari
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
- ASPIRE Precision Medicine, Research Institute Abu Dhabi, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
- ASPIRE Precision Medicine, Research Institute Abu Dhabi, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
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16
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Al-Dalahmah O, Lam M, McInvale JJ, Qu W, Nguyen T, Mun JY, Kwon S, Ifediora N, Mahajan A, Humala N, Winters T, Angeles E, Jakubiak KA, Kühn R, Kim YA, De Rosa MC, Doege CA, Paryani F, Flowers X, Dovas A, Mela A, Lu H, DeTure MA, Vonsattel JP, Wszolek ZK, Dickson DW, Kuhlmann T, Zaehres H, Schöler HR, Sproul AA, Siegelin MD, De Jager PL, Goldman JE, Menon V, Canoll P, Hargus G. Osteopontin drives neuroinflammation and cell loss in MAPT-N279K frontotemporal dementia patient neurons. Cell Stem Cell 2024; 31:676-693.e10. [PMID: 38626772 DOI: 10.1016/j.stem.2024.03.013] [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: 04/04/2023] [Revised: 01/07/2024] [Accepted: 03/19/2024] [Indexed: 05/05/2024]
Abstract
Frontotemporal dementia (FTD) is an incurable group of early-onset dementias that can be caused by the deposition of hyperphosphorylated tau in patient brains. However, the mechanisms leading to neurodegeneration remain largely unknown. Here, we combined single-cell analyses of FTD patient brains with a stem cell culture and transplantation model of FTD. We identified disease phenotypes in FTD neurons carrying the MAPT-N279K mutation, which were related to oxidative stress, oxidative phosphorylation, and neuroinflammation with an upregulation of the inflammation-associated protein osteopontin (OPN). Human FTD neurons survived less and elicited an increased microglial response after transplantation into the mouse forebrain, which we further characterized by single nucleus RNA sequencing of microdissected grafts. Notably, downregulation of OPN in engrafted FTD neurons resulted in improved engraftment and reduced microglial infiltration, indicating an immune-modulatory role of OPN in patient neurons, which may represent a potential therapeutic target in FTD.
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Affiliation(s)
- Osama Al-Dalahmah
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease & the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Matti Lam
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julie J McInvale
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Wenhui Qu
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Trang Nguyen
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Jeong-Yeon Mun
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Sam Kwon
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Nkechime Ifediora
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Aayushi Mahajan
- Department of Neurosurgery, Columbia University, New York, NY 10032, USA
| | - Nelson Humala
- Department of Neurosurgery, Columbia University, New York, NY 10032, USA
| | - Tristan Winters
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Ellen Angeles
- Taub Institute for Research on Alzheimer's Disease & the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Kelly A Jakubiak
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Rebekka Kühn
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Yoon A Kim
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Maria Caterina De Rosa
- Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Claudia A Doege
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Fahad Paryani
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xena Flowers
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Athanassios Dovas
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Angeliki Mela
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Hong Lu
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Michael A DeTure
- Department of Neuroscience, The Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Jean Paul Vonsattel
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Zbigniew K Wszolek
- Department of Neurology, The Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, The Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Tanja Kuhlmann
- Institute of Neuropathology, University Hospital Münster, Münster 48149, Germany
| | - Holm Zaehres
- Institute of Anatomy, Ruhr University Bochum, Medical Faculty, Bochum 44801, Germany; Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany
| | - Andrew A Sproul
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease & the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Markus D Siegelin
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Philip L De Jager
- Taub Institute for Research on Alzheimer's Disease & the Aging Brain, Columbia University, New York, NY 10032, USA; Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - James E Goldman
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease & the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Vilas Menon
- Taub Institute for Research on Alzheimer's Disease & the Aging Brain, Columbia University, New York, NY 10032, USA; Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter Canoll
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Gunnar Hargus
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease & the Aging Brain, Columbia University, New York, NY 10032, USA.
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Regina-Ferreira L, Valdivieso-Rivera F, Angelim MKSC, Menezes Dos Reis L, Furino VO, Morari J, Maia de Sousa L, Consonni SR, Sponton CH, Moraes-Vieira PM, Velloso LA. Inhibition of Crif1 protects fatty acid-induced POMC neuron-like cell-line damage by increasing CPT-1 function. Am J Physiol Endocrinol Metab 2024; 326:E681-E695. [PMID: 38597829 DOI: 10.1152/ajpendo.00420.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/07/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024]
Abstract
Hypothalamic proopiomelanocortin (POMC) neurons are sensors of signals that reflect the energy stored in the body. Inducing mild stress in proopiomelanocortin neurons protects them from the damage promoted by the consumption of a high-fat diet, mitigating the development of obesity; however, the cellular mechanisms behind these effects are unknown. Here, we induced mild stress in a proopiomelanocortin neuron cell line by inhibiting Crif1. In proopiomelanocortin neurons exposed to high levels of palmitate, the partial inhibition of Crif1 reverted the defects in mitochondrial respiration and ATP production; this was accompanied by improved mitochondrial fusion/fission cycling. Furthermore, the partial inhibition of Crif1 resulted in increased reactive oxygen species production, increased fatty acid oxidation, and reduced dependency on glucose for mitochondrial respiration. These changes were dependent on the activity of CPT-1. Thus, we identified a CPT-1-dependent metabolic shift toward greater utilization of fatty acids as substrates for respiration as the mechanism behind the protective effect of mild stress against palmitate-induced damage of proopiomelanocortin neurons.NEW & NOTEWORTHY Saturated fats can damage hypothalamic neurons resulting in positive energy balance, and this is mitigated by mild cellular stress; however, the mechanisms behind this protective effect are unknown. Using a proopiomelanocortin cell line, we show that under exposure to a high concentration of palmitate, the partial inhibition of the mitochondrial protein Crif1 results in protection due to a metabolic shift warranted by the increased expression and activity of the mitochondrial fatty acid transporter CPT-1.
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Affiliation(s)
| | - Fernando Valdivieso-Rivera
- Obesity and Comorbidities Research Center, São Paulo, Brazil
- Department of Structural and Functional Biology, Institute of Biology (IB), University of Campinas, São Paulo, Brazil
| | - Monara K S C Angelim
- Laboratory of Immunometabolism, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, São Paulo, Brazil
| | - Larissa Menezes Dos Reis
- Laboratory of Immunometabolism, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, São Paulo, Brazil
| | | | - Joseane Morari
- Obesity and Comorbidities Research Center, São Paulo, Brazil
| | - Lizandra Maia de Sousa
- Laboratory of Cytochemistry and Immunocytochemistry, Department of Biochemistry and Tissue Biology, Institute of Biology (IB), University of Campinas, São Paulo, Brazil
| | - Sílvio Roberto Consonni
- Laboratory of Cytochemistry and Immunocytochemistry, Department of Biochemistry and Tissue Biology, Institute of Biology (IB), University of Campinas, São Paulo, Brazil
| | - Carlos H Sponton
- Obesity and Comorbidities Research Center, São Paulo, Brazil
- Department of Structural and Functional Biology, Institute of Biology (IB), University of Campinas, São Paulo, Brazil
| | - Pedro M Moraes-Vieira
- Obesity and Comorbidities Research Center, São Paulo, Brazil
- Laboratory of Immunometabolism, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, São Paulo, Brazil
| | - Lício A Velloso
- Obesity and Comorbidities Research Center, São Paulo, Brazil
- National Institute of Science and Technology on Neuroimmunomodulation, São Paulo, Brazil
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18
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Tang S, Lu Y, Sun F, Qin Y, Harypursat V, Deng R, Zhang G, Chen Y, Wang T. Transcriptomic crosstalk between viral and host factors drives aberrant homeostasis of T-cell proliferation and cell death in HIV-infected immunological non-responders. J Infect 2024; 88:106151. [PMID: 38582127 DOI: 10.1016/j.jinf.2024.106151] [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: 06/15/2023] [Revised: 03/13/2024] [Accepted: 03/28/2024] [Indexed: 04/08/2024]
Abstract
BACKGROUND Immunological non-responders (INRs) among people living with HIV have inherently higher mortality and morbidity rates. The underlying immunological mechanisms whereby failure of immune reconstitution occurs in INRs require elucidation. METHOD HIV-1 DNA and HIV-1 cell-associated RNA (CA-HIV RNA) quantifications were conducted via RT-qPCR. Transcriptome sequencing (RNA-seq), bioinformatics, and biological verifications were performed to discern the crosstalk between host and viral factors. Flow cytometry was employed to analyze cellular activation, proliferation, and death. RESULTS HIV-1 DNA and CA-HIV RNA levels were observed to be significantly higher in INRs compared to immunological responders (IRs). Evaluation of CD4/CD8 ratios showed a significantly negative correlation with HIV-1 DNA in IRs, but not in INRs. Bioinformatics analyses and biological verifications showed IRF7/INF-α regulated antiviral response was intensified in INRs. PBMCs of INRs expressed significantly more HIV integrase-mRNA (p31) than IRs. Resting (CD4+CD69- T-cells) and activated (CD4+CD69+ T-cells) HIV-1 reservoir harboring cells were significantly higher in INRs, with the co-occurrence of significantly higher cellular proliferation and cell death in CD4+ T-cells of INRs. CONCLUSION In INRs, the systematic crosstalk between the HIV-1 reservoir and host cells tends to maintain a persistent antiviral response-associated inflammatory environment, which drives aberrant cellular activation, proliferation, and death of CD4+ T-cells.
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Affiliation(s)
- Shengquan Tang
- The First Affiliated Hospital, MOE Key Laboratory of Tumor Molecular Biology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong 510632, China; Department of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Shapingba District, Chongqing 400036, China
| | - Yanqiu Lu
- Department of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Shapingba District, Chongqing 400036, China
| | - Feng Sun
- Department of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Shapingba District, Chongqing 400036, China
| | - Yuanyuan Qin
- Department of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Shapingba District, Chongqing 400036, China
| | - Vijay Harypursat
- Department of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Shapingba District, Chongqing 400036, China
| | - Renni Deng
- Department of Clinical Laboratory, Chongqing Public Health Medical Center, 109 Baoyu Road, Shapingba District, Chongqing 400036, China
| | - Gong Zhang
- The First Affiliated Hospital, MOE Key Laboratory of Tumor Molecular Biology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong 510632, China
| | - Yaokai Chen
- Department of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Shapingba District, Chongqing 400036, China.
| | - Tong Wang
- The First Affiliated Hospital, MOE Key Laboratory of Tumor Molecular Biology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong 510632, China.
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19
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Kosnik MB, Antczak P, Fantke P. Data-Driven Characterization of Genetic Variability in Disease Pathways and Pesticide-Induced Nervous System Disease in the United States Population. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:57003. [PMID: 38752992 PMCID: PMC11098008 DOI: 10.1289/ehp14108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND Genetic susceptibility to chemicals is incompletely characterized. However, nervous system disease development following pesticide exposure can vary in a population, implying some individuals may have higher genetic susceptibility to pesticide-induced nervous system disease. OBJECTIVES We aimed to build a computational approach to characterize single-nucleotide polymorphisms (SNPs) implicated in chemically induced adverse outcomes and used this framework to assess the link between differential population susceptibility to pesticides and human nervous system disease. METHODS We integrated publicly available datasets of Chemical-Gene, Gene-Pathway, and SNP-Disease associations to build Chemical-Pathway-Gene-SNP-Disease linkages for humans. As a case study, we integrated these linkages with spatialized pesticide application data for the US from 1992 to 2018 and spatialized nervous system disease rates for 2018. Through this, we characterized SNPs that may be important in states with high disease occurrence based on the pesticides used there. RESULTS We found that the number of SNP hits per pesticide in US states positively correlated with disease incidence and prevalence for Alzheimer's disease, Parkinson disease, and multiple sclerosis. We performed frequent itemset mining to differentiate pesticides used over time in states with high and low disease occurrence and found that only 19% of pesticide sets overlapped between 10 states with high disease occurrence and 10 states with low disease occurrence rates, and more SNPs were implicated in pathways in high disease occurrence states. Through a cross-validation of subsets of five high and low disease occurrence states, we characterized SNPs, genes, pathways, and pesticides more frequently implicated in high disease occurrence states. DISCUSSION Our findings support that pesticides contribute to nervous system disease, and we developed priority lists of SNPs, pesticides, and pathways for further study. This data-driven approach can be adapted to other chemicals, diseases, and locations to characterize differential population susceptibility to chemical exposures. https://doi.org/10.1289/EHP14108.
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Affiliation(s)
- Marissa B. Kosnik
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Philipp Antczak
- Faculty of Medicine and Cologne University Hospital, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Cologne, Germany
| | - Peter Fantke
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
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20
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Huo L, Montano E, Tumurkhuu G, Bose M, Berman DS, Wallace D, Wei J, Ishimori M, Merz CNB, Jefferies C. Alterations in genes associated with cytosolic RNA sensing in whole blood are associated with coronary microvascular disease in SLE. RESEARCH SQUARE 2024:rs.3.rs-4171759. [PMID: 38746373 PMCID: PMC11092805 DOI: 10.21203/rs.3.rs-4171759/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Systemic lupus erythematosus (SLE) patients are 90% women and over three times more likely to die of cardiovascular disease than women in the general population. Chest pain with no obstructive cardiac disease is associated with coronary microvascular disease (CMD), where narrowing of the small blood vessels can lead to ischemia, and frequently reported by SLE patients. Using whole blood RNA samples, we asked whether gene signatures discriminate SLE patients with coronary microvascular dysfunction (CMD) on cardiac MRI (n=4) from those without (n=7) and whether any signaling pathway is linked to the underlying pathobiology of SLE CMD. RNA-seq analysis revealed 143 differentially expressed (DE) genes between the SLE and healthy control (HC) groups, with virus defense and interferon (IFN) signaling being the key pathways identified as enriched in SLE as expected. We next conducted a comparative analysis of genes differentially expressed in SLE-CMD and SLE-non-CMD relative to HC samples. Our analysis highlighted differences in IFN signaling, RNA sensing and ADP-ribosylation pathways between SLE-CMD and SLE-non-CMD. This is the first study to investigate possible gene signatures associating with CMD in SLE, and our data strongly suggests that distinct molecular mechanisms underly vascular changes in CMD and non-CMD involvement in SLE.
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21
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Touahri Y, Hanna J, Tachibana N, Okawa S, Liu H, David LA, Olender T, Vasan L, Pak A, Mehta DN, Chinchalongporn V, Balakrishnan A, Cantrup R, Dixit R, Mattar P, Saleh F, Ilnytskyy Y, Murshed M, Mains PE, Kovalchuk I, Lefebvre JL, Leong HS, Cayouette M, Wang C, Del Sol A, Brand M, Reese BE, Schuurmans C. Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina. Cell Rep 2024; 43:114005. [PMID: 38551961 DOI: 10.1016/j.celrep.2024.114005] [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: 09/08/2022] [Revised: 01/30/2024] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
The retina is exquisitely patterned, with neuronal somata positioned at regular intervals to completely sample the visual field. Here, we show that phosphatase and tensin homolog (Pten) controls starburst amacrine cell spacing by modulating vesicular trafficking of cell adhesion molecules and Wnt proteins. Single-cell transcriptomics and double-mutant analyses revealed that Pten and Down syndrome cell adhesion molecule Dscam) are co-expressed and function additively to pattern starburst amacrine cell mosaics. Mechanistically, Pten loss accelerates the endocytic trafficking of DSCAM, FAT3, and MEGF10 off the cell membrane and into endocytic vesicles in amacrine cells. Accordingly, the vesicular proteome, a molecular signature of the cell of origin, is enriched in exocytosis, vesicle-mediated transport, and receptor internalization proteins in Pten conditional knockout (PtencKO) retinas. Wnt signaling molecules are also enriched in PtencKO retinal vesicles, and the genetic or pharmacological disruption of Wnt signaling phenocopies amacrine cell patterning defects. Pten thus controls vesicular trafficking of cell adhesion and signaling molecules to establish retinal amacrine cell mosaics.
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Affiliation(s)
- Yacine Touahri
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada
| | - Joseph Hanna
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Nobuhiko Tachibana
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Satoshi Okawa
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; McGowan Institute for Regenerative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Hedy Liu
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Luke Ajay David
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Thomas Olender
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON K1H 8L6, Canada
| | - Lakshmy Vasan
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alissa Pak
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Dhruv Nimesh Mehta
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada
| | - Vorapin Chinchalongporn
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anjali Balakrishnan
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Robert Cantrup
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Rajiv Dixit
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Pierre Mattar
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada
| | - Fermisk Saleh
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Yaroslav Ilnytskyy
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Monzur Murshed
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC H3G 1A6, Canada
| | - Paul E Mains
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Julie L Lefebvre
- Department of Molecular Genetics, University of Toronto, Toronto ON M5S 1A8, Canada; Program for Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Hon S Leong
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada
| | - Chao Wang
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Immunology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON K1H 8L6, Canada
| | - Benjamin E Reese
- Department of Psychological and Brain Sciences, Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106-5060, USA
| | - Carol Schuurmans
- Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.
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22
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Baassiri A, Ghais A, Kurdi A, Rahal E, Nasr R, Shirinian M. The molecular signature of BCR::ABLP210 and BCR::ABLT315I in a Drosophila melanogaster chronic myeloid leukemia model. iScience 2024; 27:109538. [PMID: 38585663 PMCID: PMC10995885 DOI: 10.1016/j.isci.2024.109538] [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: 10/27/2023] [Revised: 02/01/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Chronic myeloid leukemia (CML) is a clonal hematopoietic stem cell disorder resulting from a balanced translocation leading to BCR::ABL1 oncogene with increased tyrosine kinase activity. Despite the advancements in the development of tyrosine kinase inhibitors (TKIs), the T315I gatekeeper point mutation in the BCR::ABL1 gene remains a challenge. We have previously reported in a Drosophila CML model an increased hemocyte count and disruption in sessile hemocyte patterns upon expression of BCR::ABL1p210 and BCR::ABL1T315I in the hemolymph. In this study, we performed RNA sequencing to determine if there is a distinct gene expression that distinguishes BCR::ABL1p210 and BCR::ABL1T315I. We identified six genes that were consistently upregulated in the fly CML model and validated in adult and pediatric CML patients and in a mouse cell line expressing BCR::ABL1T315I. This study provides a comprehensive analysis of gene signatures in BCR::ABL1p210 and BCR::ABL1T315I, laying the groundwork for targeted investigations into the role of these genes in CML pathogenesis.
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Affiliation(s)
- Amro Baassiri
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ali Ghais
- Department of Experimental Pathology and Immunology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Abdallah Kurdi
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Elias Rahal
- Department of Experimental Pathology and Immunology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Margret Shirinian
- Department of Experimental Pathology and Immunology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
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23
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Kim SC, Seo HY, Lee JO, Maeng JE, Shin YK, Lee SH, Jang JY, Ku JL. Establishment, characterization, and biobanking of 36 pancreatic cancer organoids: prediction of metastasis in resectable pancreatic cancer. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00939-5. [PMID: 38619751 DOI: 10.1007/s13402-024-00939-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 04/16/2024] Open
Abstract
PURPOSE Early dissemination of primary pancreatic ductal adenocarcinoma (PDAC) is the main cause of dismal prognosis as it highly limits possible treatment options. A number of PDAC patients experience distant metastasis even after treatment due to the metastatic clones. We aimed to demonstrate the molecular architecture of borderline resectable PDAC manifests cancer dissemination of PDAC. METHODS Here, 36 organoids isolated from primary tumor masses of PDAC patients with diverse metastatic statues are presented. Whole-exome sequencing and RNA sequencing were performed and drug responses to clinically relevant 18 compounds were assessed. RESULTS Our results revealed that borderline resectable PDAC organoids exhibited distinct patterns according to their metastatic potency highlighted by multiple genetic and transcriptional factors and strong variances in drug responses. CONCLUSIONS These data suggest that the presence of metastatic PDAC can be identified by integrating molecular compositions and drug responses of borderline resectable PDAC.
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Affiliation(s)
- Soon-Chan Kim
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Ha-Young Seo
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Ja-Oh Lee
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Ju Eun Maeng
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Young-Kyoung Shin
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Sang Hyub Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Korea.
| | - Jin-Young Jang
- Department of Surgery, Seoul National University College of Medicine, 103, Daehak-ro, Jongno-gu, Seoul, 03080, South Korea.
| | - Ja-Lok Ku
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea.
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.
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Urbiola-Salvador V, Lima de Souza S, Macur K, Czaplewska P, Chen Z. Plasma Proteomics Elucidated a Protein Signature in COVID-19 Patients with Comorbidities and Early-Diagnosis Biomarkers. Biomedicines 2024; 12:840. [PMID: 38672194 PMCID: PMC11048573 DOI: 10.3390/biomedicines12040840] [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: 03/10/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Despite great scientific efforts, deep understanding of coronavirus-19 disease (COVID-19) immunopathology and clinical biomarkers remains a challenge. Pre-existing comorbidities increase the mortality rate and aggravate the exacerbated immune response against the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, which can result in more severe symptoms as well as long-COVID and post-COVID complications. In this study, we applied proteomics analysis of plasma samples from 28 patients with SARS-CoV-2, with and without pre-existing comorbidities, as well as their corresponding controls to determine the systemic protein changes caused by the SARS-CoV-2 infection. As a result, the protein signature shared amongst COVID-19 patients with comorbidities was revealed to be characterized by alterations in the coagulation and complement pathways, acute-phase response proteins, tissue damage and remodeling, as well as cholesterol metabolism. These altered proteins may play a relevant role in COVID-19 pathophysiology. Moreover, several novel potential biomarkers for early diagnosis of the SARS-CoV-2 infection were detected, such as increased levels of keratin K22E, extracellular matrix protein-1 (ECM1), and acute-phase response protein α-2-antiplasmin (A2AP). Importantly, elevated A2AP may contribute to persistent clotting complications associated with the long-COVID syndrome in patients with comorbidities. This study provides new insights into COVID-19 pathogenesis and proposes novel potential biomarkers for early diagnosis that could be facilitated for clinical application by further validation studies.
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Affiliation(s)
- Víctor Urbiola-Salvador
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, 80-307 Gdańsk, Poland;
| | - Suiane Lima de Souza
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220 Oulu, Finland;
| | - Katarzyna Macur
- Laboratory of Mass Spectrometry-Core Facility Laboratories, Intercollegiate Faculty of Biotechnology University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, 80-309 Gdańsk, Poland; (K.M.); (P.C.)
| | - Paulina Czaplewska
- Laboratory of Mass Spectrometry-Core Facility Laboratories, Intercollegiate Faculty of Biotechnology University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, 80-309 Gdańsk, Poland; (K.M.); (P.C.)
| | - Zhi Chen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220 Oulu, Finland;
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25
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Atri Roozbahani G, Kokal-Ribaudo M, Heidari Horestani M, Pungsrinont T, Baniahmad A. The protein composition of exosomes released by prostate cancer cells is distinctly regulated by androgen receptor-antagonists and -agonist to stimulate growth of target cells. Cell Commun Signal 2024; 22:219. [PMID: 38589887 PMCID: PMC11000412 DOI: 10.1186/s12964-024-01584-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/23/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Prostate cancer (PCa) is a prevalent malignancy in men worldwide, ranking as the second leading cause of cancer-related death in Western countries. Various PCa hormone therapies, such as androgen receptor (AR)-antagonists or supraphysiological androgen level (SAL) reduce cancer cell proliferation. However, treated cells may influence the growth of neighboring cells through secreted exosomes in the tumor microenvironment (TME). Here, the change of protein content of exosomes secreted from PCa cells through treatment with different AR-antagonists or SAL has been analyzed. METHODS Isolation of exosomes via ultracentrifugation of treated human PCa LNCaP cells with AR-agonist and various AR-antagonists; analysis of cellular senescence by detection of senescence associated beta galactosidase activity (SA β-Gal); Western blotting and immunofluorescence staining; Mass spectrometry (MS-spec) of exosomes and bioinformatic analyses to identify ligand-specific exosomal proteins. Growth assays to analyze influence of exosomes on non-treated cells. RESULTS MS-spec analysis identified ligand-specific proteins in exosomes. One thousand seventy proteins were up- and 52 proteins downregulated by SAL whereas enzalutamide upregulated 151 proteins and downregulated 42 exosomal proteins. The bioinformatic prediction indicates an up-regulation of pro-proliferative pathways. AR ligands augment hub factors in exosomes that include AKT1, CALM1, PAK2 and CTNND1. Accordingly, functional assays confirmed that the isolated exosomes from AR-ligand treated cells promote growth of untreated PCa cells. CONCLUSION The data suggest that the cargo of exosomes is controlled by AR-agonist and -antagonists and distinct among the AR-antagonists. Further, exosomes promote growth that might influence the TME. This finding sheds light into the complex interplay between AR signaling and exosome-mediated communication between PCa cells.
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Affiliation(s)
- Golnaz Atri Roozbahani
- Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, 07740, Jena, Germany
| | - Miriam Kokal-Ribaudo
- Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, 07740, Jena, Germany
| | | | - Thanakorn Pungsrinont
- Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, 07740, Jena, Germany
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, 07740, Jena, Germany.
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26
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Akkouh IA, Ueland T, Szabo A, Hughes T, Smeland OB, Andreassen OA, Osete JR, Djurovic S. Longitudinal Transcriptomic Analysis of Human Cortical Spheroids Identifies Axonal Dysregulation in the Prenatal Brain as a Mediator of Genetic Risk for Schizophrenia. Biol Psychiatry 2024; 95:687-698. [PMID: 37661009 DOI: 10.1016/j.biopsych.2023.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/28/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023]
Abstract
BACKGROUND Schizophrenia (SCZ) has a known neurodevelopmental etiology, but limited access to human prenatal brain tissue hampers the investigation of basic disease mechanisms in early brain development. Here, we elucidate the molecular mechanisms contributing to SCZ risk in a disease-relevant model of the prenatal human brain. METHODS We generated induced pluripotent stem cell-derived organoids, termed human cortical spheroids (hCSs), from a large, genetically stratified sample of 14 SCZ cases and 14 age- and sex-matched controls. The hCSs were differentiated for 150 days, and comprehensive molecular characterization across 4 time points was carried out. RESULTS The transcriptional and cellular architecture of hCSs closely resembled that of fetal brain tissue at 10 to 24 postconception weeks, showing strongest spatial overlap with frontal regions of the cerebral cortex. A total of 3520 genes were differentially modulated between SCZ and control hCSs across organoid maturation, displaying a significant contribution of genetic loading, an overrepresentation of risk genes for autism spectrum disorder and SCZ, and the strongest enrichment for axonal processes in all hCS stages. The two axon guidance genes SEMA7A and SEMA5A, the first a promoter of synaptic functions and the second a repressor, were downregulated and upregulated, respectively, in SCZ hCSs. This expression pattern was confirmed at the protein level and replicated in a large postmortem sample. CONCLUSIONS Applying a disease-relevant model of the developing fetal brain, we identified consistent dysregulation of axonal genes as an early risk factor for SCZ, providing novel insights into the effects of genetic predisposition on the neurodevelopmental origins of the disorder.
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Affiliation(s)
- Ibrahim A Akkouh
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway.
| | - Thor Ueland
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; K.G. Jebsen Thrombosis Research and Expertise Center, University of Tromsø, Tromsø, Norway
| | - Attila Szabo
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Timothy Hughes
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Olav B Smeland
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Jordi Requena Osete
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Department of Clinical Science, University of Bergen, Bergen, Norway.
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Konstantis G, Tsaousi G, Pourzitaki C, Kasper-Virchow S, Zaun G, Kitsikidou E, Passenberg M, Tseriotis VS, Willuweit K, Schmidt HH, Rashidi-Alavijeh J. Identification of Key Genes Associated with Tumor Microenvironment Infiltration and Survival in Gastric Adenocarcinoma via Bioinformatics Analysis. Cancers (Basel) 2024; 16:1280. [PMID: 38610959 PMCID: PMC11010876 DOI: 10.3390/cancers16071280] [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: 02/17/2024] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
OBJECTIVE Gastric carcinoma (GC) is the fifth most commonly diagnosed cancer and the third leading cause of cancer-related deaths globally. The tumor microenvironment plays a significant role in the pathogenesis, prognosis, and response to immunotherapy. However, the immune-related molecular mechanisms underlying GC remain elusive. Bioinformatics analysis of the gene expression of GC and paracancerous healthy tissues from the same patient was performed to identify the key genes and signaling pathways, as well as their correlation to the infiltration of the tumor microenvironment (TME) by various immune cells related to GC development. METHODS We employed GSE19826, a gene expression profile from the Gene Expression Omnibus (GEO), for our analysis. Functional enrichment analysis of Differentially Expressed Genes (DEGs) was conducted using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes database. RESULTS Cytoscape software facilitated the identification of nine hub DEGs, namely, FN1, COL1A1, COL1A2, THBS2, COL3A1, COL5A1, APOE, SPP1, and BGN. Various network analysis algorithms were applied to determine their high connectivity. Among these hub genes, FN1, COL1A2, THBS2, COL3A1, COL5A1, and BGN were found to be associated with a poor prognosis for GC patients. Subsequent analysis using the TIMER database revealed the infiltration status of the TME concerning the overexpression of these six genes. Specifically, the abovementioned genes demonstrated direct correlations with cancer-associated fibroblasts, M1 and M2 macrophages, myeloid-derived suppressor cells, and activated dendritic cells. CONCLUSION Our findings suggest that the identified hub genes, particularly BGN, FN1, COL1A2, THBS2, COL3A1, and COL5A1, play crucial roles in GC prognosis and TME cell infiltration. This comprehensive analysis enhances our understanding of the molecular mechanisms underlying GC development and may contribute to the identification of potential therapeutic targets and prognostic markers for GC patients.
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Affiliation(s)
- Georgios Konstantis
- Clinical Pharmacology, Faculty of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (C.P.); (V.S.T.)
- Department of Gastroenterology, Hepatology and Transplant Medicine, Medical Faculty, University of Duisburg-Essen, 45141 Essen, Germany
| | - Georgia Tsaousi
- Department of Anesthesiology and ICU, Medical School, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
| | - Chryssa Pourzitaki
- Clinical Pharmacology, Faculty of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (C.P.); (V.S.T.)
| | - Stefan Kasper-Virchow
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Gregor Zaun
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Elisavet Kitsikidou
- Department of Internal Medicine, Evangelical Hospital Dusseldorf, 40217 Dusseldorf, Germany;
| | - Moritz Passenberg
- Department of Gastroenterology, Hepatology and Transplant Medicine, Medical Faculty, University of Duisburg-Essen, 45141 Essen, Germany
| | - Vasilis Spyridon Tseriotis
- Clinical Pharmacology, Faculty of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (C.P.); (V.S.T.)
| | - Katharina Willuweit
- Department of Gastroenterology, Hepatology and Transplant Medicine, Medical Faculty, University of Duisburg-Essen, 45141 Essen, Germany
| | - Hartmut H. Schmidt
- Department of Gastroenterology, Hepatology and Transplant Medicine, Medical Faculty, University of Duisburg-Essen, 45141 Essen, Germany
| | - Jassin Rashidi-Alavijeh
- Department of Gastroenterology, Hepatology and Transplant Medicine, Medical Faculty, University of Duisburg-Essen, 45141 Essen, Germany
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Irfan M, Solbiati J, Duran-Pinedo A, Rocha FG, Gibson FC, Frias-Lopez J. A Porphyromonas gingivalis hypothetical protein controlled by the type I-C CRISPR-Cas system is a novel adhesin important in virulence. mSystems 2024; 9:e0123123. [PMID: 38323815 PMCID: PMC10949514 DOI: 10.1128/msystems.01231-23] [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: 11/17/2023] [Accepted: 12/26/2023] [Indexed: 02/08/2024] Open
Abstract
The ability of many human pathogens to infect requires their ability to adhere to the host surfaces as a first step in the process. Porphyromonas gingivalis, a keystone oral pathogen, uses adhesins to adhere to the surface of the gingival epithelium and other members of the oral microbiome. In a previous study, we identified several proteins potentially linked to virulence whose mRNA levels are regulated by CRISPR-Cas type I-C. Among those, PGN_1547 was highly upregulated in the CRISPR-Cas 3 mutant. PGN_1547 is annotated as a hypothetical protein. Employing homology searching, our data support that PGN_1547 resembles an auto-transporter adhesin of P. gingivalis based on containing the DUF2807 domain. To begin to characterize the function of PGN_1547, we found that a deletion mutant displayed a significant decrease in virulence using a Galleria mellonela model. Furthermore, this mutant was significantly impaired in forming biofilms and attaching to the macrophage-like cell THP-1. Luminex revealed that the PGN_1547 mutant elicited a less robust cytokine and chemokine response from THP-1 cells, and TLR2 predominantly sensed that recombinant PGN_1547. Taken together, these findings broaden our understanding of the toolbox of virulence factors possessed by P. gingivalis. Importantly, PGN_1547, a hypothetical protein, has homologs in another member of the order Bacteroidales whose function is unknown, and our results could shed light on the role of this family of proteins as auto-transport adhesins in this phylogenetic group.IMPORTANCEPeriodontal diseases are among humans' most common infections, and besides their effect on the oral cavity, they have been associated with systemic inflammatory conditions. Among members of the oral microbiome implicated in the development of periodontitis, Porphyromonas gingivalis is considered a keystone pathogen. We have identified a new adhesin that acts as a virulence factor, PGN_1547, which contains the DUF2807 domain, which belongs to the putative auto-transporter adhesin, head GIN domain family. Deletion of this gene lowers the virulence of P. gingivalis and impacts the ability of P. gingivalis to form biofilm and attach to host cells. Furthermore, the broad distribution of these receptors in the order Bacteroidales suggests their importance in colonization by this important group of organisms.
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Affiliation(s)
- Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Jose Solbiati
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Ana Duran-Pinedo
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Fernanda Godoy Rocha
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Frank C. Gibson
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Jorge Frias-Lopez
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
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Bigger-Allen A, Gheinani AH, Adam RM. Investigation of the impact of bromodomain inhibition on cytoskeleton stability and contraction. Cell Commun Signal 2024; 22:184. [PMID: 38493137 PMCID: PMC10944605 DOI: 10.1186/s12964-024-01553-6] [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: 12/21/2023] [Accepted: 03/01/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Injury to contractile organs such as the heart, vasculature, urinary bladder and gut can stimulate a pathological response that results in loss of normal contractility. PDGF and TGFβ are among the most well studied initiators of the injury response and have been shown to induce aberrant contraction in mechanically active cells of hollow organs including smooth muscle cells (SMC) and fibroblasts. However, the mechanisms driving contractile alterations downstream of PDGF and TGFβ in SMC and fibroblasts are incompletely understood, limiting therapeutic interventions. METHODS To identify potential molecular targets, we have leveraged the analysis of publicly available data, comparing transcriptomic changes in mechanically active cells stimulated with PDGF and TGFβ. Additional Analysis of publicly available data sets were performed on SMC and fibroblasts treated in the presence or absence of the MYC inhibitor JQ1. Validation of in silico findings were performed with qPCR, immunoblots, and collagen gel contraction assays measure the effect of JQ1 on cytoskeleton associated genes, proteins and contractility in mechanically active cells. Likelihood ratio test and FDR adjusted p-values were used to determine significant differentially expressed genes. Student ttest were used to calculate statistical significance of qPCR and contractility analyses. RESULTS Comparing PDGF and TGFβ stimulated SMC and fibroblasts identified a shared molecular profile regulated by MYC and members of the AP-1 transcription factor complex. Additional in silico analysis revealed a unique set of cytoskeleton-associated genes that were sensitive to MYC inhibition with JQ1. In vitro validation demonstrated JQ1 was also able to attenuate TGFβ and PDGF induced changes to the cytoskeleton and contraction of smooth muscle cells and fibroblasts in vitro. CONCLUSIONS These findings identify MYC as a key driver of aberrant cytoskeletal and contractile changes in fibroblasts and SMC, and suggest that JQ1 could be used to restore normal contractile function in hollow organs.
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Affiliation(s)
- Alexander Bigger-Allen
- Urological Diseases Research Center, Boston Children's Hospital, Enders Bldg 1061.4, 300 Longwood Avenue, Boston, MA, 02115, USA
- Biological & Biomedical Sciences Program, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ali Hashemi Gheinani
- Urological Diseases Research Center, Boston Children's Hospital, Enders Bldg 1061.4, 300 Longwood Avenue, Boston, MA, 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, Bern, Switzerland
- Department of Urology, Inselspital University Hospital, 3010, Bern, Switzerland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rosalyn M Adam
- Urological Diseases Research Center, Boston Children's Hospital, Enders Bldg 1061.4, 300 Longwood Avenue, Boston, MA, 02115, USA.
- Department of Surgery, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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30
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Mikhael S, Kurdi A, Khoueiry-Zgheib N, Tahtouh R, Nasr R, Hilal G. Evaluating synergistic effects of metformin and simvastatin on ovarian cancer cells. PLoS One 2024; 19:e0298127. [PMID: 38489280 PMCID: PMC10942021 DOI: 10.1371/journal.pone.0298127] [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: 11/20/2023] [Accepted: 01/19/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Ovarian Cancer (OC) stands as the most lethal gynecological malignancy, presenting an urgent clinical challenge in the quest to improve response rates. One approach to address this challenge is through drug repurposing, exemplified by the investigation of metabolic-modulating drugs such as Metformin (MTF) and Simvastatin (SIM). This study aims to explore the molecular mechanisms contributing to the potential synergistic anti-cancer effects between MTF and SIM on ovarian cancer cells. METHODS We assessed the effects of the combination on the proliferation and viability of two cell lines OVCAR-3 and SKOV-3. IC50 concentrations of MTF and SIM were determined using a proliferation assay, followed by subtoxic concentrations to explore the potential synergistic effects on the viability of both cell lines. Transcriptomic analysis was conducted on OVCAR-3 treated cells, and the findings were validated by assessing the expression levels of differentially expressed genes (DEGs) through real-time PCR in both cell lines SK-OV-3 and OVCAR-3. RESULTS Cytotoxicity analysis guided the selection of treatment concentrations as such MTF 10 mM and SIM 5 μM. The combined treatment of MTF and SIM demonstrated a synergistic inhibition of proliferation and viability in both cell lines. In OVCAR-3, exclusive identification of 507 DEGs was seen in the combination arm. Upregulation of FOXO3, RhoA, and TNFα, along with downregulation of PIK3R1, SKP2, and ATP6V1D levels, was observed in OVCAR-3 treated cells. Real-time PCR validation confirmed the consistency of expression levels for the mentioned DEGs. CONCLUSION Our data strongly supports the presence of synergy between MTF and SIM in OC cells. The combination's effect is associated with the dysregulation of genes in the key regulators AMPK and mTOR alongside other interconnected pathways.
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Affiliation(s)
- Sara Mikhael
- Laboratory of Cancer and Metabolism, Faculty of Medicine, Saint-Joseph University, Beirut, Lebanon
| | - Abdullah Kurdi
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Nathalie Khoueiry-Zgheib
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Roula Tahtouh
- Laboratory of Cancer and Metabolism, Faculty of Medicine, Saint-Joseph University, Beirut, Lebanon
| | - Rihab Nasr
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - George Hilal
- Laboratory of Cancer and Metabolism, Faculty of Medicine, Saint-Joseph University, Beirut, Lebanon
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31
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Manzar N, Khan UK, Goel A, Carskadon S, Gupta N, Palanisamy N, Ateeq B. An integrative proteomics approach identifies tyrosine kinase KIT as a therapeutic target for SPINK1-positive prostate cancer. iScience 2024; 27:108794. [PMID: 38384854 PMCID: PMC10879682 DOI: 10.1016/j.isci.2024.108794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/05/2023] [Accepted: 01/02/2024] [Indexed: 02/23/2024] Open
Abstract
Elevated serine peptidase inhibitor, Kazal type 1 (SPINK1) levels in ∼10%-25% of prostate cancer (PCa) patients associate with aggressive phenotype, for which there are limited treatment choices and dismal clinical outcomes. Using an integrative proteomics approach involving label-free phosphoproteome and proteome profiling, we delineated the downstream signaling pathways involved in SPINK1-mediated tumorigenesis and identified tyrosine kinase KIT as highly enriched. Furthermore, high to moderate levels of KIT expression were detected in ∼85% of SPINK1-positive PCa specimens. We show KIT signaling orchestrates SPINK1-mediated oncogenesis, and treatment with KIT inhibitor reduces tumor growth and metastases in preclinical mice models. Mechanistically, KIT signaling modulates WNT/β-catenin pathway and confers stemness-related features in PCa. Notably, inhibiting KIT signaling led to restoration of AR/REST levels, forming a feedback loop enabling SPINK1 repression. Overall, we uncover the role of KIT signaling downstream of SPINK1 in maintaining lineage plasticity and provide distinct treatment modalities for advanced-stage SPINK1-positive patients.
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Affiliation(s)
- Nishat Manzar
- Molecular Oncology Laboratory, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, UP 208016, India
| | - Umar Khalid Khan
- Molecular Oncology Laboratory, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, UP 208016, India
| | - Ayush Goel
- Molecular Oncology Laboratory, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, UP 208016, India
| | - Shannon Carskadon
- Vattikuti Urology Institute, Department of Urology, Henry Ford Health System, Detroit, MI 48202, USA
| | - Nilesh Gupta
- Department of Pathology, Henry Ford Health System, Detroit, MI 48202, USA
| | - Nallasivam Palanisamy
- Vattikuti Urology Institute, Department of Urology, Henry Ford Health System, Detroit, MI 48202, USA
| | - Bushra Ateeq
- Molecular Oncology Laboratory, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, UP 208016, India
- Mehta Family Center for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, UP 208016, India
- Centre of Excellence for Cancer - Gangwal School of Medical Sciences and Technology, Indian Institute of Technology Kanpur, Kanpur, UP 208016, India
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32
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Lan Q, Trela E, Lindström R, Satta JP, Kaczyńska B, Christensen MM, Holzenberger M, Jernvall J, Mikkola ML. Mesenchyme instructs growth while epithelium directs branching in the mouse mammary gland. eLife 2024; 13:e93326. [PMID: 38441552 PMCID: PMC10959526 DOI: 10.7554/elife.93326] [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: 10/05/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024] Open
Abstract
The mammary gland is a unique organ that undergoes dynamic alterations throughout a female's reproductive life, making it an ideal model for developmental, stem cell and cancer biology research. Mammary gland development begins in utero and proceeds via a quiescent bud stage before the initial outgrowth and subsequent branching morphogenesis. How mammary epithelial cells transit from quiescence to an actively proliferating and branching tissue during embryogenesis and, importantly, how the branch pattern is determined remain largely unknown. Here, we provide evidence indicating that epithelial cell proliferation and onset of branching are independent processes, yet partially coordinated by the Eda signaling pathway. Through heterotypic and heterochronic epithelial-mesenchymal recombination experiments between mouse mammary and salivary gland tissues and ex vivo live imaging, we demonstrate that unlike previously concluded, the mode of branching is an intrinsic property of the mammary epithelium whereas the pace of growth and the density of ductal tree are determined by the mesenchyme. Transcriptomic profiling and ex vivo and in vivo functional studies in mice disclose that mesenchymal Wnt/ß-catenin signaling, and in particular IGF-1 downstream of it critically regulate mammary gland growth. These results underscore the general need to carefully deconstruct the different developmental processes producing branched organs.
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Affiliation(s)
- Qiang Lan
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of HelsinkiHelsinkiFinland
| | - Ewelina Trela
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of HelsinkiHelsinkiFinland
| | - Riitta Lindström
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of HelsinkiHelsinkiFinland
| | - Jyoti Prabha Satta
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of HelsinkiHelsinkiFinland
| | - Beata Kaczyńska
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of HelsinkiHelsinkiFinland
| | - Mona M Christensen
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of HelsinkiHelsinkiFinland
| | | | - Jukka Jernvall
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of HelsinkiHelsinkiFinland
- Department of Geosciences and Geography, University of HelsinkiHelsinkiFinland
| | - Marja L Mikkola
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of HelsinkiHelsinkiFinland
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Mehta D, Chaudhary S, Sunil S. Oxidative stress governs mosquito innate immune signalling to reduce chikungunya virus infection in Aedes-derived cells. J Gen Virol 2024; 105. [PMID: 38488850 DOI: 10.1099/jgv.0.001966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024] Open
Abstract
Arboviruses such as chikungunya, dengue and zika viruses cause debilitating diseases in humans. The principal vector species that transmits these viruses is the Aedes mosquito. Lack of substantial knowledge of the vector species hinders the advancement of strategies for controlling the spread of arboviruses. To supplement our information on mosquitoes' responses to virus infection, we utilized Aedes aegypti-derived Aag2 cells to study changes at the transcriptional level during infection with chikungunya virus (CHIKV). We observed that genes belonging to the redox pathway were significantly differentially regulated. Upon quantifying reactive oxygen species (ROS) in the cells during viral infection, we further discovered that ROS levels are considerably higher during the early hours of infection; however, as the infection progresses, an increase in antioxidant gene expression suppresses the oxidative stress in cells. Our study also suggests that ROS is a critical regulator of viral replication in cells and inhibits intracellular and extracellular viral replication by promoting the Rel2-mediated Imd immune signalling pathway. In conclusion, our study provides evidence for a regulatory role of oxidative stress in infected Aedes-derived cells.
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Affiliation(s)
- Divya Mehta
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sakshi Chaudhary
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sujatha Sunil
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Jones BA, Gisch DL, Myakala K, Sadiq A, Cheng YH, Taranenko E, Panov J, Korolowicz K, Wang X, Rosenberg AZ, Jain S, Eadon MT, Levi M. Nicotinamide riboside activates renal metabolism and protects the kidney in a model of Alport syndrome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.580911. [PMID: 38464264 PMCID: PMC10925224 DOI: 10.1101/2024.02.26.580911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Chronic kidney disease (CKD) is associated with renal metabolic disturbances, including impaired fatty acid oxidation (FAO). Nicotinamide adenine dinucleotide (NAD + ) is a small molecule that participates in hundreds of metabolism-related reactions. NAD + levels are decreased in CKD, and NAD + supplementation is protective. However, both the mechanism of how NAD + supplementation protects from CKD, as well as the cell types most responsible, are poorly understood. Using a mouse model of Alport syndrome, we show that nicotinamide riboside (NR), an NAD + precursor, stimulates renal peroxisome proliferator-activated receptor α signaling and restores FAO in the proximal tubules, thereby protecting from CKD in both sexes. Bulk RNA-sequencing shows that renal metabolic pathways are impaired in Alport mice and dramatically activated by NR in both sexes. These transcriptional changes are confirmed by orthogonal imaging techniques and biochemical assays. Single nuclei RNA-sequencing and spatial transcriptomics, both the first of their kind from Alport mice, show that NAD + supplementation restores FAO in the proximal tubules with minimal effects on the podocytes. Finally, we also report, for the first time, sex differences at the transcriptional level in this Alport model. Male Alport mice had more severe inflammation and fibrosis than female mice at the transcriptional level. In summary, the data herein identify both the protective mechanism and location of NAD + supplementation in this model of CKD.
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Zarrella JA, Tsurumi A. Genome-wide transcriptome profiling and development of age prediction models in the human brain. Aging (Albany NY) 2024; 16:4075-4094. [PMID: 38428408 DOI: 10.18632/aging.205609] [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: 05/02/2022] [Accepted: 03/28/2023] [Indexed: 03/03/2024]
Abstract
Aging-related transcriptome changes in various regions of the healthy human brain have been explored in previous works, however, a study to develop prediction models for age based on the expression levels of specific panels of transcripts is lacking. Moreover, studies that have assessed sexually dimorphic gene activities in the aging brain have reported discrepant results, suggesting that additional studies would be advantageous. The prefrontal cortex (PFC) region was previously shown to have a particularly large number of significant transcriptome alterations during healthy aging in a study that compared different regions in the human brain. We harmonized neuropathologically normal PFC transcriptome datasets obtained from the Gene Expression Omnibus (GEO) repository, ranging in age from 21 to 105 years, and found a large number of differentially regulated transcripts in the old and elderly, compared to young samples overall, and compared female and male-specific expression alterations. We assessed the genes that were associated with age by employing ontology, pathway, and network analyses. Furthermore, we applied various established (least absolute shrinkage and selection operator (Lasso) and Elastic Net (EN)) and recent (eXtreme Gradient Boosting (XGBoost) and Light Gradient Boosting Machine (LightGBM)) machine learning algorithms to develop accurate prediction models for chronological age and validated them. Studies to further validate these models in other large populations and molecular studies to elucidate the potential mechanisms by which the transcripts identified may be related to aging phenotypes would be advantageous.
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Affiliation(s)
- Joseph A Zarrella
- Department of Health Policy and Management, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Amy Tsurumi
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Shriner's Hospitals for Children-Boston, Boston, MA 02114, USA
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Mendes CB, da Rocha LS, de Carvalho Fraga CA, Ximenes-da-Silva A. Homeostatic status of thyroid hormones and brain water movement as determinant factors in biology of cerebral gliomas: a pilot study using a bioinformatics approach. Front Neurosci 2024; 18:1349421. [PMID: 38476871 PMCID: PMC10927765 DOI: 10.3389/fnins.2024.1349421] [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: 12/04/2023] [Accepted: 02/07/2024] [Indexed: 03/14/2024] Open
Abstract
Introduction The expression and localization of the water channel transporters, aquaporins (AQPs), in the brain are substantially modified in gliomas during tumorigenesis, cell migration, edema formation, and resolution. We hypothesized that the molecular changes associated with AQP1 and AQP4 in the brain may potentially be anticancer therapeutic targets. To test this hypothesis, a bioinformatics analysis of publicly available data from international consortia was performed. Methods We used RNA-seq as an experimental strategy and identified the number of differential AQP1 and AQP4 transcript expressions in glioma tissue compared to normal brain tissue. Results AQPs genes are overexpressed in patients with glioma. Among the glioma subtypes, AQP1 and AQP4 were overexpressed in astrocytoma (low-grade glioma) and classical (high-grade glioma). Overall survival analysis demonstrated that both AQP genes can be used as prognostic factors for patients with low-grade glioma. Additionally, we observed a correlation between the expression of genes involved in the tyrosine and thyroid hormone pathways and AQPs, namely: PNMT, ALDH1A3, AOC2, HGDATP1B1, ADCY5, PLCB4, ITPR1, ATP1A3, LRP2, HDAC1, MED24, MTOR, and ACTB1 (Spearman's coefficient = geq 0.20 and p-value = ≤ 0.05). Conclusion Our findings indicate that the thyroid hormone pathways and AQPs 1 and 4 are potential targets for new anti-tumor drugs and therapeutic biomarkers for malignant gliomas.
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Affiliation(s)
- Carmelita Bastos Mendes
- Laboratório de Eletrofisiologia e Metabolismo Cerebral, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Brazil
| | - Lanni Sarmento da Rocha
- Laboratório de Eletrofisiologia e Metabolismo Cerebral, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Brazil
| | | | - Adriana Ximenes-da-Silva
- Laboratório de Eletrofisiologia e Metabolismo Cerebral, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Brazil
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Broce IJ, Sirkis DW, Nillo RM, Bonham LW, Lee SE, Miller BL, Castruita PA, Sturm VE, Sugrue LS, Desikan RS, Yokoyama JS. C9orf72 gene networks in the human brain correlate with cortical thickness in C9-FTD and implicate vulnerable cell types. Front Neurosci 2024; 18:1258996. [PMID: 38469573 PMCID: PMC10925697 DOI: 10.3389/fnins.2024.1258996] [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: 07/14/2023] [Accepted: 01/15/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction A hexanucleotide repeat expansion (HRE) intronic to chromosome 9 open reading frame 72 (C9orf72) is recognized as the most common genetic cause of amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and ALS-FTD. Identifying genes that show similar regional co-expression patterns to C9orf72 may help identify novel gene targets and biological mechanisms that mediate selective vulnerability to ALS and FTD pathogenesis. Methods We leveraged mRNA expression data in healthy brain from the Allen Human Brain Atlas to evaluate C9orf72 co-expression patterns. To do this, we correlated average C9orf72 expression values in 51 regions across different anatomical divisions (cortex, subcortex, and cerebellum) with average gene expression values for 15,633 protein-coding genes, including 54 genes known to be associated with ALS, FTD, or ALS-FTD. We then performed imaging transcriptomic analyses to evaluate whether the identified C9orf72 co-expressed genes correlated with patterns of cortical thickness in symptomatic C9orf72 pathogenic HRE carriers (n = 19) compared to controls (n = 23). Lastly, we explored whether genes with significant C9orf72 imaging transcriptomic correlations (i.e., "C9orf72 imaging transcriptomic network") were enriched in specific cell populations in the brain and enriched for specific biological and molecular pathways. Results A total of 2,120 genes showed an anatomical distribution of gene expression in the brain similar to C9orf72 and significantly correlated with patterns of cortical thickness in C9orf72 HRE carriers. This C9orf72 imaging transcriptomic network was differentially expressed in cell populations previously implicated in ALS and FTD, including layer 5b cells, cholinergic neurons in the spinal cord and brainstem and medium spiny neurons of the striatum, and was enriched for biological and molecular pathways associated with protein ubiquitination, autophagy, cellular response to DNA damage, endoplasmic reticulum to Golgi vesicle-mediated transport, among others. Conclusion Considered together, we identified a network of C9orf72 associated genes that may influence selective regional and cell-type-specific vulnerabilities in ALS/FTD.
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Affiliation(s)
- Iris J. Broce
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, United States
- Department of Neurosciences, University of California San Diego, San Diego, CA, United States
| | - Daniel W. Sirkis
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, United States
| | - Ryan M. Nillo
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, United States
| | - Luke W. Bonham
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, United States
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, United States
| | - Suzee E. Lee
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, United States
| | - Bruce L. Miller
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, United States
| | - Patricia A. Castruita
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, United States
| | - Virginia E. Sturm
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, United States
- Global Brain Health Institute, University of California San Francisco, San Francisco, CA, United States
| | - Leo S. Sugrue
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, United States
| | - Rahul S. Desikan
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, United States
| | - Jennifer S. Yokoyama
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, United States
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, United States
- Global Brain Health Institute, University of California San Francisco, San Francisco, CA, United States
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Popescu RG, Dinischiotu A, Soare T, Vlase E, Marinescu GC. Nicotinamide Mononucleotide (NMN) Works in Type 2 Diabetes through Unexpected Effects in Adipose Tissue, Not by Mitochondrial Biogenesis. Int J Mol Sci 2024; 25:2594. [PMID: 38473844 DOI: 10.3390/ijms25052594] [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: 12/20/2023] [Revised: 02/01/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Nicotinamide mononucleotide (NMN) has emerged as a promising therapeutic intervention for age-related disorders, including type 2 diabetes. In this study, we confirmed the previously observed effects of NMN treatment on glucose uptake and investigated its underlying mechanisms in various tissues and cell lines. Through the most comprehensive proteomic analysis to date, we discovered a series of novel organ-specific effects responsible for glucose uptake as measured by the IPGTT: adipose tissue growing (suggested by increased protein synthesis and degradation and mTOR proliferation signaling upregulation). Notably, we observed the upregulation of thermogenic UCP1, promoting enhanced glucose conversion to heat in intermuscular adipose tissue while showing a surprising repressive effect on mitochondrial biogenesis in muscle and the brain. Additionally, liver and muscle cells displayed a unique response, characterized by spliceosome downregulation and concurrent upregulation of chaperones, proteasomes, and ribosomes, leading to mildly impaired and energy-inefficient protein synthesis machinery. Furthermore, our findings revealed remarkable metabolic rewiring in the brain. This involved increased production of ketone bodies, downregulation of mitochondrial OXPHOS and TCA cycle components, as well as the induction of well-known fasting-associated effects. Collectively, our data elucidate the multifaceted nature of NMN action, highlighting its organ-specific effects and their role in improving glucose uptake. These findings deepen our understanding of NMN's therapeutic potential and pave the way for novel strategies in managing metabolic disorders.
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Affiliation(s)
- Roua Gabriela Popescu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- Independent Research Association, 012416 Bucharest, Romania
- Blue Screen SRL, 012416 Bucharest, Romania
| | - Anca Dinischiotu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
| | - Teodoru Soare
- Pathology Department, Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 050097 Bucharest, Romania
| | - Ene Vlase
- Animals Facility Laboratory, Cantacuzino National Institute for Medico-Military Research and Development, 013821 Bucharest, Romania
| | - George Cătălin Marinescu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- Independent Research Association, 012416 Bucharest, Romania
- Blue Screen SRL, 012416 Bucharest, Romania
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Schuurman AR, Chouchane O, Butler JM, Peters-Sengers H, Joosten S, Brands X, Haak BW, Otto NA, Uhel F, Klarenbeek A, van Linge CC, van Kampen A, Pras-Raves M, van Weeghel M, van Eijk M, Ferraz MJ, Faber DR, de Vos A, Scicluna BP, Vaz FM, Wiersinga WJ, van der Poll T. The shifting lipidomic landscape of blood monocytes and neutrophils during pneumonia. JCI Insight 2024; 9:e164400. [PMID: 38385743 DOI: 10.1172/jci.insight.164400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/17/2024] [Indexed: 02/23/2024] Open
Abstract
The lipidome of immune cells during infection has remained unexplored, although evidence of the importance of lipids in the context of immunity is mounting. In this study, we performed untargeted lipidomic analysis of blood monocytes and neutrophils from patients hospitalized for pneumonia and age- and sex-matched noninfectious control volunteers. We annotated 521 and 706 lipids in monocytes and neutrophils, respectively, which were normalized to an extensive set of internal standards per lipid class. The cellular lipidomes were profoundly altered in patients, with both common and distinct changes between the cell types. Changes involved every level of the cellular lipidome: differential lipid species, class-wide shifts, and altered saturation patterns. Overall, differential lipids were mainly less abundant in monocytes and more abundant in neutrophils from patients. One month after hospital admission, lipidomic changes were fully resolved in monocytes and partially in neutrophils. Integration of lipidomic and concurrently collected transcriptomic data highlighted altered sphingolipid metabolism in both cell types. Inhibition of ceramide and sphingosine-1-phosphate synthesis in healthy monocytes and neutrophils resulted in blunted cytokine responses upon stimulation with lipopolysaccharide. These data reveal major lipidomic remodeling in immune cells during infection, and link the cellular lipidome to immune functionality.
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Affiliation(s)
- Alex R Schuurman
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Osoul Chouchane
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Joe M Butler
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Hessel Peters-Sengers
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Sebastiaan Joosten
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Xanthe Brands
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Bastiaan W Haak
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Natasja A Otto
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Fabrice Uhel
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker-Enfants Malades, Paris, France
- Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, Colombes, France
| | - Augustijn Klarenbeek
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Christine Ca van Linge
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Antoine van Kampen
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Mia Pras-Raves
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, Netherlands
- Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, Netherlands
| | - Michel van Weeghel
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, Netherlands
- Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, Netherlands
| | - Marco van Eijk
- Leiden Institute of Chemistry, University of Leiden, Netherlands
| | - Maria J Ferraz
- Leiden Institute of Chemistry, University of Leiden, Netherlands
| | - Daniël R Faber
- Department of Internal Medicine, BovenIJ Hospital, Amsterdam, Netherlands
| | - Alex de Vos
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Brendon P Scicluna
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Applied Biomedical Science, Faculty of Health Sciences, Mater Dei Hospital, and
- Center for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Frédéric M Vaz
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, Netherlands
- Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, Netherlands
| | - W Joost Wiersinga
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Division of Infectious Diseases, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Division of Infectious Diseases, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
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Rocque B, Guion K, Singh P, Bangerth S, Pickard L, Bhattacharjee J, Eguizabal S, Weaver C, Chopra S, Zhou S, Kohli R, Sher L, Akbari O, Ekser B, Emamaullee JA. Technical optimization of spatially resolved single-cell transcriptomic datasets to study clinical liver disease. Sci Rep 2024; 14:3612. [PMID: 38351241 PMCID: PMC10864257 DOI: 10.1038/s41598-024-53993-2] [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: 08/29/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
Single cell and spatially resolved 'omic' techniques have enabled deep characterization of clinical pathologies that remain poorly understood, providing unprecedented insights into molecular mechanisms of disease. However, transcriptomic platforms are costly, limiting sample size, which increases the possibility of pre-analytical variables such as tissue processing and storage procedures impacting RNA quality and downstream analyses. Furthermore, spatial transcriptomics have not yet reached single cell resolution, leading to the development of multiple deconvolution methods to predict individual cell types within each transcriptome 'spot' on tissue sections. In this study, we performed spatial transcriptomics and single nucleus RNA sequencing (snRNAseq) on matched specimens from patients with either histologically normal or advanced fibrosis to establish important aspects of tissue handling, data processing, and downstream analyses of biobanked liver samples. We observed that tissue preservation technique impacts transcriptomic data, especially in fibrotic liver. Single cell mapping of the spatial transcriptome using paired snRNAseq data generated a spatially resolved, single cell dataset with 24 unique liver cell phenotypes. We determined that cell-cell interactions predicted using ligand-receptor analysis of snRNAseq data poorly correlated with cellular relationships identified using spatial transcriptomics. Our study provides a framework for generating spatially resolved, single cell datasets to study gene expression and cell-cell interactions in biobanked clinical samples with advanced liver disease.
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Affiliation(s)
- Brittany Rocque
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Kate Guion
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Pranay Singh
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Sarah Bangerth
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Lauren Pickard
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Jashdeep Bhattacharjee
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Sofia Eguizabal
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Carly Weaver
- Division of Abdominal Organ Transplantation, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Shefali Chopra
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shengmei Zhou
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California Los Angeles, Los Angeles, CA, USA
| | - Rohit Kohli
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Linda Sher
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Omid Akbari
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Burcin Ekser
- Division of Transplant Surgery, Department of Surgery, Indiana University School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Juliet A Emamaullee
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA.
- Division of Abdominal Organ Transplantation, Children's Hospital Los Angeles, Los Angeles, CA, USA.
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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Petrin AL, Machado-Paula L, Hinkle A, Hovey L, Awotoye W, Chimenti M, Darbro B, Ribeiro-Bicudo LA, Dabdoub SM, Peter T, Murray J, Van Otterloo E, Rengasamy Venugopalan S, Moreno-Uribe LM. Whole genome sequencing of a family with autosomal dominant features within the oculoauriculovertebral spectrum. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.07.24301824. [PMID: 38370836 PMCID: PMC10871465 DOI: 10.1101/2024.02.07.24301824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Background Oculoauriculovertebral Spectrum (OAVS) encompasses a wide variety of anomalies on derivatives from the first and second pharyngeal arches including macrostomia, hemifacial microsomia, micrognathia, preauricular tags, ocular and vertebral anomalies. We present the genetic findings of a large three-generation family with multiple members affected with macrostomia, preauricular tags and uni- or bilateral ptosis following an autosomal dominant segregation pattern. Methods We generated whole genome sequencing data for the proband, affected parent and unaffected paternal grandparent followed by Sanger sequencing on 23 family members for the top 10 candidate genes: KCND2, PDGFRA, CASP9, NCOA3, WNT10A, SIX1, MTF1, KDR/VEGFR2, LRRK1, and TRIM2. We performed parent and sibling-based transmission disequilibrium tests and burden analysis to explore segregation and burden of candidate gene mutations. Bioinformatic analyses investigated the biological connection between genes and the abnormal phenotypes. Results Overall, rare missense mutations in SIX1, KDR/VEGFR2, and PDGFRA showed the best evidence of segregation with the OAV phenotypes in this family. When considering affection with any of the 3 OAVS phenotypes as an outcome, parent-TDTs and sib-TDTs (unadjusted p-values) found that SIX1 (p=0.025, p=0.052), followed by PDGFRA (p=0.180, p=0.069) and KDR/VEGFR2 (p=0.180, p=0.069) have the strongest associations in this family. Burden analysis via a penalized linear mixed model identified SIX1 (RC=0.87) and PDGFRA (RC=0.98) as having the strongest association with OAVS severity. Using phenotype-specific ogfrautcomes, sib-TDTs identified associations between (1) SIX1 with uni- or bilateral ptosis (p=0.049) and ear tags (p=0.01), (2) PDGFRA and KDR/VEGFR2 with ear tags (both p<0.01). Conclusion Our study reports the genomic findings of a large family with multiple individuals affected with OAVS phenotypes with autosomal dominant inheritance. Our findings narrow down to three potential candidate genes, SIX1, PDGFRA, and KDR/VEGFR2. Among these, SIX1 has been previously associated with OAVS ear malformations and it is co-expressed with EYA1 during ear development. Attempts to strengthen the genotype-phenotype co-relation underlying the OAVS of phenotypes are essential to discover the etiological factors leading to this complex and burdensome condition as well as for family counseling and prevention efforts.
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Affiliation(s)
- A L Petrin
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - Lam Machado-Paula
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - A Hinkle
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - L Hovey
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - W Awotoye
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - M Chimenti
- Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - B Darbro
- Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | | | - S M Dabdoub
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - T Peter
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - J Murray
- Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - E Van Otterloo
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | | | - L M Moreno-Uribe
- College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
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Williams AS, Crown SB, Lyons SP, Koves TR, Wilson RJ, Johnson JM, Slentz DH, Kelly DP, Grimsrud PA, Zhang GF, Muoio DM. Ketone flux through BDH1 supports metabolic remodeling of skeletal and cardiac muscles in response to intermittent time-restricted feeding. Cell Metab 2024; 36:422-437.e8. [PMID: 38325337 PMCID: PMC10961007 DOI: 10.1016/j.cmet.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/20/2023] [Accepted: 01/10/2024] [Indexed: 02/09/2024]
Abstract
Time-restricted feeding (TRF) has gained attention as a dietary regimen that promotes metabolic health. This study questioned if the health benefits of an intermittent TRF (iTRF) schedule require ketone flux specifically in skeletal and cardiac muscles. Notably, we found that the ketolytic enzyme beta-hydroxybutyrate dehydrogenase 1 (BDH1) is uniquely enriched in isolated mitochondria derived from heart and red/oxidative skeletal muscles, which also have high capacity for fatty acid oxidation (FAO). Using mice with BDH1 deficiency in striated muscles, we discover that this enzyme optimizes FAO efficiency and exercise tolerance during acute fasting. Additionally, iTRF leads to robust molecular remodeling of muscle tissues, and muscle BDH1 flux does indeed play an essential role in conferring the full adaptive benefits of this regimen, including increased lean mass, mitochondrial hormesis, and metabolic rerouting of pyruvate. In sum, ketone flux enhances mitochondrial bioenergetics and supports iTRF-induced remodeling of skeletal muscle and heart.
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Affiliation(s)
- Ashley S Williams
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Scott B Crown
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Scott P Lyons
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Timothy R Koves
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Medicine, Division of Geriatrics, Duke University Medical Center, Durham, NC 27710, USA
| | - Rebecca J Wilson
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Jordan M Johnson
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Dorothy H Slentz
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Daniel P Kelly
- Cardiovascular Institute and Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Paul A Grimsrud
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC 27710, USA
| | - Guo-Fang Zhang
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC 27710, USA
| | - Deborah M Muoio
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC 27710, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.
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Trang KB, Pahl MC, Pippin JA, Su C, Littleton SH, Sharma P, Kulkarni NN, Ghanem LR, Terry NA, O’Brien JM, Wagley Y, Hankenson KD, Jermusyk A, Hoskins JW, Amundadottir LT, Xu M, Brown KM, Anderson SA, Yang W, Titchenell PM, Seale P, Cook L, Levings MK, Zemel BS, Chesi A, Wells AD, Grant SF. 3D genomic features across >50 diverse cell types reveal insights into the genomic architecture of childhood obesity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.08.30.23294092. [PMID: 37693606 PMCID: PMC10491377 DOI: 10.1101/2023.08.30.23294092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The prevalence of childhood obesity is increasing worldwide, along with the associated common comorbidities of type 2 diabetes and cardiovascular disease in later life. Motivated by evidence for a strong genetic component, our prior genome-wide association study (GWAS) efforts for childhood obesity revealed 19 independent signals for the trait; however, the mechanism of action of these loci remains to be elucidated. To molecularly characterize these childhood obesity loci we sought to determine the underlying causal variants and the corresponding effector genes within diverse cellular contexts. Integrating childhood obesity GWAS summary statistics with our existing 3D genomic datasets for 57 human cell types, consisting of high-resolution promoter-focused Capture-C/Hi-C, ATAC-seq, and RNA-seq, we applied stratified LD score regression and calculated the proportion of genome-wide SNP heritability attributable to cell type-specific features, revealing pancreatic alpha cell enrichment as the most statistically significant. Subsequent chromatin contact-based fine-mapping was carried out for genome-wide significant childhood obesity loci and their linkage disequilibrium proxies to implicate effector genes, yielded the most abundant number of candidate variants and target genes at the BDNF, ADCY3, TMEM18 and FTO loci in skeletal muscle myotubes and the pancreatic beta-cell line, EndoC-BH1. One novel implicated effector gene, ALKAL2 - an inflammation-responsive gene in nerve nociceptors - was observed at the key TMEM18 locus across multiple immune cell types. Interestingly, this observation was also supported through colocalization analysis using expression quantitative trait loci (eQTL) derived from the Genotype-Tissue Expression (GTEx) dataset, supporting an inflammatory and neurologic component to the pathogenesis of childhood obesity. Our comprehensive appraisal of 3D genomic datasets generated in a myriad of different cell types provides genomic insights into pediatric obesity pathogenesis.
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Affiliation(s)
- Khanh B. Trang
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Matthew C. Pahl
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - James A. Pippin
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Chun Su
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sheridan H. Littleton
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Prabhat Sharma
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nikhil N. Kulkarni
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Louis R. Ghanem
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, PA, USA
| | - Natalie A. Terry
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, PA, USA
| | - Joan M. O’Brien
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA, USA
- Penn Medicine Center for Ophthalmic Genetics in Complex Disease
| | - Yadav Wagley
- Department of Orthopedic Surgery University of Michigan Medical School Ann Arbor, MI, USA
| | - Kurt D. Hankenson
- Department of Orthopedic Surgery University of Michigan Medical School Ann Arbor, MI, USA
| | - Ashley Jermusyk
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jason W. Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Laufey T. Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Mai Xu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Stewart A. Anderson
- Department of Child and Adolescent Psychiatry, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wenli Yang
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul M. Titchenell
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrick Seale
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Cook
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Critical Care, Melbourne Medical School, University of Melbourne, Melbourne, VIC, Australia
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Megan K. Levings
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Babette S. Zemel
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew D. Wells
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division Endocrinology and Diabetes, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Garcia-Bonilla L, Shahanoor Z, Sciortino R, Nazarzoda O, Racchumi G, Iadecola C, Anrather J. Analysis of brain and blood single-cell transcriptomics in acute and subacute phases after experimental stroke. Nat Immunol 2024; 25:357-370. [PMID: 38177281 DOI: 10.1038/s41590-023-01711-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/13/2023] [Indexed: 01/06/2024]
Abstract
Cerebral ischemia triggers a powerful inflammatory reaction involving peripheral leukocytes and brain resident cells that contribute to both tissue injury and repair. However, their dynamics and diversity remain poorly understood. To address these limitations, we performed a single-cell transcriptomic study of brain and blood cells 2 or 14 days after ischemic stroke in mice. We observed a strong divergence of post-ischemic microglia, monocyte-derived macrophages and neutrophils over time, while endothelial cells and brain-associated macrophages showed altered transcriptomic signatures at 2 days poststroke. Trajectory inference predicted the in situ trans-differentiation of macrophages from blood monocytes into day 2 and day 14 phenotypes, while neutrophils were projected to be continuously de novo recruited from the blood. Brain single-cell transcriptomes from both female and male aged mice were similar to that of young male mice, but aged and young brains differed in their immune cell composition. Although blood leukocyte analysis also revealed altered transcriptomes after stroke, brain-infiltrating leukocytes displayed higher transcriptomic divergence than their circulating counterparts, indicating that phenotypic diversification occurs within the brain in the early and recovery phases of ischemic stroke. A portal ( https://anratherlab.shinyapps.io/strokevis/ ) is provided to allow user-friendly access to our data.
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Affiliation(s)
- Lidia Garcia-Bonilla
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
| | - Ziasmin Shahanoor
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Rose Sciortino
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Omina Nazarzoda
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Gianfranco Racchumi
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Costantino Iadecola
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Josef Anrather
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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Sun J, Sepulveda JL, Komissarova EV, Hills C, Seckar TD, LeFevre NM, Simonyan H, Young C, Su G, Del Portillo A, Wang TC, Sepulveda AR. CDKN2A-p16 Deletion and Activated KRAS G12D Drive Barrett's-Like Gland Hyperplasia-Metaplasia and Synergize in the Development of Dysplasia Precancer Lesions. Cell Mol Gastroenterol Hepatol 2024; 17:769-784. [PMID: 38296052 PMCID: PMC10966774 DOI: 10.1016/j.jcmgh.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND & AIMS Barrett's esophagus is the precursor of esophageal dysplasia and esophageal adenocarcinoma. CDKN2A-p16 deletions were reported in 34%-74% of patients with Barrett's esophagus who progressed to dysplasia and esophageal adenocarcinoma, suggesting that p16 loss may drive neoplastic progression. KRAS activation frequently occurs in esophageal adenocarcinoma and precancer lesions. LGR5+ stem cells in the squamocolumnar-junction (SCJ) of mouse stomach contribute as Barrett's esophagus progenitors. We aimed to determine the functional effects of p16 loss and KRAS activation in Barrett's-like metaplasia and dysplasia development. METHODS We established mouse models with conditional knockout of CDKN2A-p16 (p16KO) and/or activated KRASG12D expression targeting SCJ LGR5+ cells in interleukin 1b transgenic mice and characterized histologic alterations (mucous-gland hyperplasia/metaplasia, inflammation, and dysplasia) in mouse SCJ. Gene expression was determined by microarray, RNA sequencing, and immunohistochemistry of SCJ tissues and cultured 3-dimensional organoids. RESULTS p16KO mice exhibited increased mucous-gland hyperplasia/metaplasia versus control mice (P = .0051). Combined p16KO+KRASG12D resulted in more frequent dysplasia and higher dysplasia scores (P = .0036), with 82% of p16KO+KRASG12D mice developing high-grade dysplasia. SCJ transcriptome analysis showed several activated pathways in p16KO versus control mice (apoptosis, tumor necrosis factor-α/nuclear factor-kB, proteasome degradation, p53 signaling, MAPK, KRAS, and G1-to-S transition). CONCLUSIONS p16 deletion in LGR5+ cell precursors triggers increased SCJ mucous-gland hyperplasia/metaplasia. KRASG12D synergizes with p16 deletion resulting in higher grades of SCJ glandular dysplasia, mimicking Barrett's high-grade dysplasia. These genetically modified mouse models establish a functional role of p16 and activated KRAS in the progression of Barrett's-like lesions to dysplasia in mice, representing an in vivo model of esophageal adenocarcinoma precancer. Derived 3-dimensional organoid models further provide in vitro modeling opportunities of esophageal precancer stages.
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Affiliation(s)
- Jing Sun
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Jorge L Sepulveda
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Elena V Komissarova
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Caitlin Hills
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Tyler D Seckar
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Narine M LeFevre
- Department of Pharmacology & Physiology, George Washington University, School of Medicine and Health Sciences, Washington, DC
| | - Hayk Simonyan
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Colin Young
- Department of Pharmacology & Physiology, George Washington University, School of Medicine and Health Sciences, Washington, DC
| | - Gloria Su
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Armando Del Portillo
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Timothy C Wang
- Division of Digestive and Liver diseases, Department of Medicine, Columbia University, New York, New York
| | - Antonia R Sepulveda
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC.
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Duijvelaar E, Gisby J, Peters JE, Bogaard HJ, Aman J. Longitudinal plasma proteomics reveals biomarkers of alveolar-capillary barrier disruption in critically ill COVID-19 patients. Nat Commun 2024; 15:744. [PMID: 38272877 PMCID: PMC10811341 DOI: 10.1038/s41467-024-44986-w] [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: 04/28/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
The pathobiology of respiratory failure in COVID-19 consists of a complex interplay between viral cytopathic effects and a dysregulated host immune response. In critically ill patients, imatinib treatment demonstrated potential for reducing invasive ventilation duration and mortality. Here, we perform longitudinal profiling of 6385 plasma proteins in 318 hospitalised patients to investigate the biological processes involved in critical COVID-19, and assess the effects of imatinib treatment. Nine proteins measured at hospital admission accurately predict critical illness development. Next to dysregulation of inflammation, critical illness is characterised by pathways involving cellular adhesion, extracellular matrix turnover and tissue remodelling. Imatinib treatment attenuates protein perturbations associated with inflammation and extracellular matrix turnover. These proteomic alterations are contextualised using external pulmonary RNA-sequencing data of deceased COVID-19 patients and imatinib-treated Syrian hamsters. Together, we show that alveolar capillary barrier disruption in critical COVID-19 is reflected in the plasma proteome, and is attenuated with imatinib treatment. This study comprises a secondary analysis of both clinical data and plasma samples derived from a clinical trial that was registered with the EU Clinical Trials Register (EudraCT 2020-001236-10, https://www.clinicaltrialsregister.eu/ctr-search/trial/2020-001236-10/NL ) and Netherlands Trial Register (NL8491, https://www.trialregister.nl/trial/8491 ).
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Affiliation(s)
- Erik Duijvelaar
- Department of Pulmonary Medicine, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands.
| | - Jack Gisby
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, UK
| | - James E Peters
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, UK
| | - Harm Jan Bogaard
- Department of Pulmonary Medicine, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Jurjan Aman
- Department of Pulmonary Medicine, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands.
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Gisch DL, Brennan M, Lake BB, Basta J, Keller MS, Melo Ferreira R, Akilesh S, Ghag R, Lu C, Cheng YH, Collins KS, Parikh SV, Rovin BH, Robbins L, Stout L, Conklin KY, Diep D, Zhang B, Knoten A, Barwinska D, Asghari M, Sabo AR, Ferkowicz MJ, Sutton TA, Kelly KJ, De Boer IH, Rosas SE, Kiryluk K, Hodgin JB, Alakwaa F, Winfree S, Jefferson N, Türkmen A, Gaut JP, Gehlenborg N, Phillips CL, El-Achkar TM, Dagher PC, Hato T, Zhang K, Himmelfarb J, Kretzler M, Mollah S, Jain S, Rauchman M, Eadon MT. The chromatin landscape of healthy and injured cell types in the human kidney. Nat Commun 2024; 15:433. [PMID: 38199997 PMCID: PMC10781985 DOI: 10.1038/s41467-023-44467-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. Comprehensive integration of gene expression with epigenetic features that define regulatory elements remains a significant challenge. We measure dual single nucleus RNA expression and chromatin accessibility, DNA methylation, and H3K27ac, H3K4me1, H3K4me3, and H3K27me3 histone modifications to decipher the chromatin landscape and gene regulation of the kidney in reference and adaptive injury states. We establish a spatially-anchored epigenomic atlas to define the kidney's active, silent, and regulatory accessible chromatin regions across the genome. Using this atlas, we note distinct control of adaptive injury in different epithelial cell types. A proximal tubule cell transcription factor network of ELF3, KLF6, and KLF10 regulates the transition between health and injury, while in thick ascending limb cells this transition is regulated by NR2F1. Further, combined perturbation of ELF3, KLF6, and KLF10 distinguishes two adaptive proximal tubular cell subtypes, one of which manifested a repair trajectory after knockout. This atlas will serve as a foundation to facilitate targeted cell-specific therapeutics by reprogramming gene regulatory networks.
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Affiliation(s)
- Debora L Gisch
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Blue B Lake
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Jeannine Basta
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | | | | | | | - Reetika Ghag
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Charles Lu
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Ying-Hua Cheng
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Samir V Parikh
- Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Brad H Rovin
- Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Lynn Robbins
- St. Louis Veteran Affairs Medical Center, St. Louis, MO, 63106, USA
| | - Lisa Stout
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Kimberly Y Conklin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Dinh Diep
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Bo Zhang
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Amanda Knoten
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Daria Barwinska
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mahla Asghari
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Angela R Sabo
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Timothy A Sutton
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | | | - Sylvia E Rosas
- Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
| | | | | | | | - Seth Winfree
- University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Nichole Jefferson
- Kidney Precision Medicine Project Community Engagement Committee, Dallas, TX, USA
| | - Aydın Türkmen
- Istanbul School of Medicine, Division of Nephrology, Istanbul, Turkey
| | - Joseph P Gaut
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | | | | | - Pierre C Dagher
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Takashi Hato
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Shamim Mollah
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Sanjay Jain
- Washington University in Saint Louis, St. Louis, MO, 63103, USA.
| | - Michael Rauchman
- Washington University in Saint Louis, St. Louis, MO, 63103, USA.
| | - Michael T Eadon
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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Morrone Parfitt G, Coccia E, Goldman C, Whitney K, Reyes R, Sarrafha L, Nam KH, Sohail S, Jones DR, Crary JF, Ordureau A, Blanchard J, Ahfeldt T. Disruption of lysosomal proteolysis in astrocytes facilitates midbrain organoid proteostasis failure in an early-onset Parkinson's disease model. Nat Commun 2024; 15:447. [PMID: 38200091 PMCID: PMC10781970 DOI: 10.1038/s41467-024-44732-2] [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: 10/05/2022] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Accumulation of advanced glycation end products (AGEs) on biopolymers accompanies cellular aging and drives poorly understood disease processes. Here, we studied how AGEs contribute to development of early onset Parkinson's Disease (PD) caused by loss-of-function of DJ1, a protein deglycase. In induced pluripotent stem cell (iPSC)-derived midbrain organoid models deficient for DJ1 activity, we find that lysosomal proteolysis is impaired, causing AGEs to accumulate, α-synuclein (α-syn) phosphorylation to increase, and proteins to aggregate. We demonstrated these processes are at least partly driven by astrocytes, as DJ1 loss reduces their capacity to provide metabolic support and triggers acquisition of a pro-inflammatory phenotype. Consistently, in co-cultures, we find that DJ1-expressing astrocytes are able to reverse the proteolysis deficits of DJ1 knockout midbrain neurons. In conclusion, astrocytes' capacity to clear toxic damaged proteins is critical to preserve neuronal function and their dysfunction contributes to the neurodegeneration observed in a DJ1 loss-of-function PD model.
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Affiliation(s)
- Gustavo Morrone Parfitt
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA.
| | - Elena Coccia
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Camille Goldman
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Kristen Whitney
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular, and Cell-Based Medicine at Mount Sinai, New York, NY, USA
| | - Ricardo Reyes
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Lily Sarrafha
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Ki Hong Nam
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Soha Sohail
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Drew R Jones
- Metabolomics Core Resource Laboratory, NYU Langone Health, New York, NY, USA
| | - John F Crary
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular, and Cell-Based Medicine at Mount Sinai, New York, NY, USA
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joel Blanchard
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA.
- Recursion Pharmaceuticals, Salt Lake City, UT, USA.
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49
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Weidemann BJ, Marcheva B, Kobayashi M, Omura C, Newman MV, Kobayashi Y, Waldeck NJ, Perelis M, Lantier L, McGuinness OP, Ramsey KM, Stein RW, Bass J. Repression of latent NF-κB enhancers by PDX1 regulates β cell functional heterogeneity. Cell Metab 2024; 36:90-102.e7. [PMID: 38171340 PMCID: PMC10793877 DOI: 10.1016/j.cmet.2023.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 07/17/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
Interactions between lineage-determining and activity-dependent transcription factors determine single-cell identity and function within multicellular tissues through incompletely known mechanisms. By assembling a single-cell atlas of chromatin state within human islets, we identified β cell subtypes governed by either high or low activity of the lineage-determining factor pancreatic duodenal homeobox-1 (PDX1). β cells with reduced PDX1 activity displayed increased chromatin accessibility at latent nuclear factor κB (NF-κB) enhancers. Pdx1 hypomorphic mice exhibited de-repression of NF-κB and impaired glucose tolerance at night. Three-dimensional analyses in tandem with chromatin immunoprecipitation (ChIP) sequencing revealed that PDX1 silences NF-κB at circadian and inflammatory enhancers through long-range chromatin contacts involving SIN3A. Conversely, Bmal1 ablation in β cells disrupted genome-wide PDX1 and NF-κB DNA binding. Finally, antagonizing the interleukin (IL)-1β receptor, an NF-κB target, improved insulin secretion in Pdx1 hypomorphic islets. Our studies reveal functional subtypes of single β cells defined by a gradient in PDX1 activity and identify NF-κB as a target for insulinotropic therapy.
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Affiliation(s)
- Benjamin J Weidemann
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Biliana Marcheva
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mikoto Kobayashi
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Chiaki Omura
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marsha V Newman
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yumiko Kobayashi
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nathan J Waldeck
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mark Perelis
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Louise Lantier
- Vanderbilt-NIH Mouse Metabolic Phenotyping Center, Nashville, TN 37232, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Owen P McGuinness
- Vanderbilt-NIH Mouse Metabolic Phenotyping Center, Nashville, TN 37232, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kathryn Moynihan Ramsey
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Roland W Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Joseph Bass
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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50
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Vergouwen DP, Kolijn PM, de Hoog J, de Boer JH, Los LI, Gijs M, Erckens RJ, de Jong PH, Rothova A, Ten Berge JC, Schreurs MW. Potential Biomarkers for Noninfectious Scleritis Identified by Serum and Tear Fluid Proteomics. OPHTHALMOLOGY SCIENCE 2024; 4:100407. [PMID: 38054106 PMCID: PMC10694766 DOI: 10.1016/j.xops.2023.100407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 12/07/2023]
Abstract
Purpose Scleritis is an extremely painful and potentially blinding inflammation of the sclera with unknown pathogenesis and unpredictable course. To gain insight in its disease process and identify biomarker candidates, we performed extensive proteomics in serum and tear fluid. Design Prospective multicenter cohort study. Participants A total of 121 patients with noninfectious scleritis (of which 39 active cases), 30 healthy controls, and 23 disease controls (uveitis and rheumatoid arthritis) were enrolled in the Netherlands from 2020 to 2022. Methods Serum, tear fluid of both eyes, and clinical data were gathered. The level of 368 inflammatory proteins was measured using proximity extension assays. Results were validated in an independent cohort of 15 patients with scleritis, and using addressable laser bead immunoassay, or enzyme-linked immunoassays. In addition, we studied an extended panel of matrix metalloproteinases in tear fluid of necrotizing scleritis with addressable laser bead immunoassay. Main Outcome Measures Statistically significant differences in the level of inflammatory proteins between patients with scleritis and control groups. Results Proteomics revealed 18 significantly upregulated or downregulated serum proteins in active scleritis cases compared with all control groups in both the discovery cohort and the validation cohort. The most upregulated protein was nuclear migration protein nudC (NudC; P = 0.0032), a protein involved in neurogenesis. The other significant hits included proteins involved in T-cell activation, apoptosis, epithelial barrier maintenance, and angiogenesis. Our tear fluid analysis showed matrix metalloproteinase 9 (MMP9) to be upregulated in the tear fluid of patients with scleral necrosis. Conclusions The results of our proteomics analysis suggest a role for neurogenesis, T-cell activation, disruption of epithelial barrier, and angiogenesis in the pathogenesis of scleritis, and highlight MMP9 and NudC as biomarkers with potential clinical relevance. Funding Disclosures The authors have no proprietary or commercial interest in any materials discussed in this article.
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Affiliation(s)
- Daphne P.C. Vergouwen
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - P. Martijn Kolijn
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joeri de Hoog
- Department of Ophthalmology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Joke H. de Boer
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leonoor I. Los
- Department of Ophthalmology, University Medical Center Groningen, Groningen, The Netherlands
| | - Marlies Gijs
- University Eye Clinic, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Roel J. Erckens
- University Eye Clinic, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Pascal H.P. de Jong
- Department of Rheumatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Aniki Rothova
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Josianne C. Ten Berge
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marco W.J. Schreurs
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
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