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Bhushan V, Nita-Lazar A. Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology. J Proteome Res 2024; 23:2700-2722. [PMID: 38451675 PMCID: PMC11296931 DOI: 10.1021/acs.jproteome.3c00839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The mammalian cell is a complex entity, with membrane-bound and membrane-less organelles playing vital roles in regulating cellular homeostasis. Organellar protein niches drive discrete biological processes and cell functions, thus maintaining cell equilibrium. Cellular processes such as signaling, growth, proliferation, motility, and programmed cell death require dynamic protein movements between cell compartments. Aberrant protein localization is associated with a wide range of diseases. Therefore, analyzing the subcellular proteome of the cell can provide a comprehensive overview of cellular biology. With recent advancements in mass spectrometry, imaging technology, computational tools, and deep machine learning algorithms, studies pertaining to subcellular protein localization and their dynamic distributions are gaining momentum. These studies reveal changing interaction networks because of "moonlighting proteins" and serve as a discovery tool for disease network mechanisms. Consequently, this review aims to provide a comprehensive repository for recent advancements in subcellular proteomics subcontexting methods, challenges, and future perspectives for method developers. In summary, subcellular proteomics is crucial to the understanding of the fundamental cellular mechanisms and the associated diseases.
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Affiliation(s)
- Vanya Bhushan
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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2
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Galli J, Almiñana C, Wiesendanger M, Schuler G, Kowalewski MP, Klisch K. Bovine placental extracellular vesicles carry the fusogenic syncytin BERV-K1. Theriogenology 2024; 223:59-69. [PMID: 38678697 DOI: 10.1016/j.theriogenology.2024.04.012] [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: 02/27/2024] [Revised: 04/16/2024] [Accepted: 04/21/2024] [Indexed: 05/01/2024]
Abstract
Syncytins are endogenous retroviral envelope proteins which induce the fusion of membranes. A human representative of this group, endogenous retrovirus group W member 1 envelope (ERVW-1) or syncytin-1 is present in trophoblast-derived extracellular vesicles and supports the incorporation of these extracellular vesicles into recipient cells. During pregnancy, placenta-derived extracellular vesicles participate in feto-maternal communication. Bovine fetal binucleate trophoblast cells express the syncytin, bovine endogenous retroviral envelope protein K1 (BERV-K1). These cells release extracellular vesicles into the maternal stroma, but it is unclear whether BERV-K1 is included in these extracellular vesicles. Here, extracellular vesicles were isolated from bovine placental tissue using collagenase digestion, ultracentrifugation, and size exclusion chromatography. They were characterized with transmission electron microscopy, nanoparticle tracking analysis, immunoblotting and mass spectrometry. Immunohistochemistry and immunoelectron microscopy were used to localize BERV-K1 within the bovine placental tissue. The isolated extracellular vesicles range between 50 and 300 nm, carrying multiple extracellular vesicle biomarkers. Proteomic analysis and immunoelectron microscopy confirmed BERV-K1 presence on the isolated extracellular vesicles. Further, BERV-K1 was localized on intraluminal vesicles in secretory granules of binucleate trophoblast cells. The presence of BERV-K1 on bovine placental extracellular vesicles suggests their role in feto-maternal communication and potential involvement of BERV-K1 in uptake of extracellular vesicles by target cells.
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Affiliation(s)
- Jasmin Galli
- Institute of Veterinary Anatomy, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland
| | - Carmen Almiñana
- Institute of Veterinary Anatomy, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland; Department of Reproductive Endocrinology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Mahesa Wiesendanger
- Institute of Veterinary Anatomy, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland; Institute of Virology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, 8057, Zurich, Switzerland
| | - Gerhard Schuler
- Veterinary Clinic for Reproductive Medicine and Neonatology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, Frankfurter Strasse 106, 35392, Giessen, Germany
| | - Mariusz Pawel Kowalewski
- Institute of Veterinary Anatomy, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland; Center for Clinical Studies (ZKS), Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland
| | - Karl Klisch
- Institute of Veterinary Anatomy, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland; Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Länggass-Strasse 120, 3350, Bern, Switzerland.
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3
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Nadig A, Replogle JM, Pogson AN, McCarroll SA, Weissman JS, Robinson EB, O’Connor LJ. Transcriptome-wide characterization of genetic perturbations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601903. [PMID: 39005298 PMCID: PMC11244993 DOI: 10.1101/2024.07.03.601903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Single cell CRISPR screens such as Perturb-seq enable transcriptomic profiling of genetic perturbations at scale. However, the data produced by these screens are often noisy due to cost and technical constraints, limiting power to detect true effects with conventional differential expression analyses. Here, we introduce TRanscriptome-wide Analysis of Differential Expression (TRADE), a statistical framework which estimates the transcriptome-wide distribution of true differential expression effects from noisy gene-level measurements. Within TRADE, we derive multiple novel, interpretable statistical metrics, including the "transcriptome-wide impact", an estimator of the overall transcriptional effect of a perturbation which is stable across sampling depths. We analyze new and published large-scale Perturb-seq datasets to show that many true transcriptional effects are not statistically significant, but detectable in aggregate with TRADE. In a genome-scale Perturb-seq screen, we find that a typical gene perturbation affects an estimated 45 genes, whereas a typical essential gene perturbation affects over 500 genes. An advantage of our approach is its ability to compare the transcriptomic effects of genetic perturbations across contexts and dosages despite differences in power. We use this ability to identify perturbations with cell-type dependent effects and to find examples of perturbations where transcriptional responses are not only larger in magnitude, but also qualitatively different, as a function of dosage. Lastly, we expand our analysis to case/control comparison of gene expression for neuropsychiatric conditions, finding that transcriptomic effect correlations are greater than genetic correlations for these diagnoses. TRADE lays an analytic foundation for the systematic comparison of genetic perturbation atlases, as well as differential expression experiments more broadly.
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Affiliation(s)
- Ajay Nadig
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Joseph M. Replogle
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Angela N. Pogson
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jonathan S. Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Elise B. Robinson
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Luke J. O’Connor
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Luna HGC, Imasa MS, Juat N, Hernandez KV, Sayo TM, Cristal-Luna G, Asur-Galang SM, Bellengan M, Duga KJ, Buenaobra BB, De Los Santos MI, Medina D, Samo J, Literal VM, Sy-Naval S. NKX2‑1 copy number alterations are associated with oncogenic, immunological and prognostic remodeling in non‑small cell lung cancer. Oncol Lett 2024; 28:303. [PMID: 38774453 PMCID: PMC11106692 DOI: 10.3892/ol.2024.14436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/05/2023] [Indexed: 05/24/2024] Open
Abstract
NK2 homeobox 1 (NKX2-1) copy number alterations (CNAs) are frequently observed in lung cancer. However, little is known about the complete landscape of focal alterations in NKX2-1 copy number (CN), their clinical significance and their therapeutic implications in non-small cell lung cancer (NSCLC). The correlations between NKX2-1 expression and EGFR driver mutations and programmed death ligand 1 (PD-L1) co-expression were studied using immunohistochemistry and PCR from the tumors of recruited Filipino patients (n=45). Clinical features of NSCLC with NKX2-1 CNAs were resolved at the tumor and clonal levels using the molecular profiles of patients with lung adenocarcinoma and lung squamous cell carcinoma from The Cancer Genome Atlas (n=1,130), and deconvoluted single-cell RNA-seq data from the Bivona project (n=1,654), respectively. Despite a significant and positive correlation between expression and CN (r=0.264; P<0.001), NKX2-1 CNAs exerted a stronger influence on the combined EGFR and PD-L1 status of NSCLC tumors than expression. NKX2-1 CN gain was prognostic of favorable survival (P=0.018) and a better response to targeted therapy. NKX2-1 CN loss predicted a worse survival (P=0.041). Mutational architecture in the Y-chromosome differentiated the two prognostic groups. There were 19,941 synonymous mutations and 1,408 genome-wide CN perturbations associated with NKX2-1 CNAs. Tumors with NKX2-1 CN gain expressed lymphocyte markers more heterogeneously than those with CN loss. Higher expression of tumor-infiltrating lymphocyte gene signatures in CN gain was prognostic of longer disease-free survival (P=0.005). Tumors with NKX2-1 CN gain had higher B-cell (P<0.001) and total T-cell estimates (P=0.003). NKX2-1 CN loss was associated with immunologically colder tumors due to higher M2 macrophage infiltrates (P=0.011) and higher expression of immune checkpoint proteins, CD274 (P=0.025), VTCN1 (P<0.001) and LGALS9 (P=0.002). In conclusion, NKX2-1 CNAs are associated with tumors that exhibit clinically diverse characteristics, and with unique oncogenic, immunological and prognostic signatures.
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Affiliation(s)
- Herdee Gloriane C. Luna
- Department of Medical Oncology, Lung Center of The Philippines, Quezon City, Metro Manila 1100, Philippines
- Department of Internal Medicine, Section of Medical Oncology, National Kidney and Transplant Institute, Quezon City, Metro Manila 1101, Philippines
| | - Marcelo Severino Imasa
- Department of Medical Oncology, Lung Center of The Philippines, Quezon City, Metro Manila 1100, Philippines
| | - Necy Juat
- Department of Internal Medicine, Section of Medical Oncology, National Kidney and Transplant Institute, Quezon City, Metro Manila 1101, Philippines
| | - Katherine V. Hernandez
- Department of Internal Medicine, Section of Oncology, East Avenue Medical Center, Quezon City, Metro Manila 1100, Philippines
| | - Treah May Sayo
- Department of Pathology and Laboratory Medicine, Lung Center of The Philippines, Quezon City, Metro Manila 1100, Philippines
| | - Gloria Cristal-Luna
- Department of Internal Medicine, Section of Medical Oncology, National Kidney and Transplant Institute, Quezon City, Metro Manila 1101, Philippines
| | - Sheena Marie Asur-Galang
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Mirasol Bellengan
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Kent John Duga
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Bien Brian Buenaobra
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Marvin I. De Los Santos
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
- Globetek Science Foundation Inc., Makati, Metro Manila 1203, Philippines
| | - Daniel Medina
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Jamirah Samo
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Venus Minerva Literal
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Sullian Sy-Naval
- Department of Medical Oncology, Lung Center of The Philippines, Quezon City, Metro Manila 1100, Philippines
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Veszelyi K, Czegle I, Varga V, Németh CE, Besztercei B, Margittai É. Subcellular Localization of Thioredoxin/Thioredoxin Reductase System-A Missing Link in Endoplasmic Reticulum Redox Balance. Int J Mol Sci 2024; 25:6647. [PMID: 38928353 PMCID: PMC11204020 DOI: 10.3390/ijms25126647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
The lumen of the endoplasmic reticulum (ER) is usually considered an oxidative environment; however, oxidized thiol-disulfides and reduced pyridine nucleotides occur there parallelly, indicating that the ER lumen lacks components which connect the two systems. Here, we investigated the luminal presence of the thioredoxin (Trx)/thioredoxin reductase (TrxR) proteins, capable of linking the protein thiol and pyridine nucleotide pools in different compartments. It was shown that specific activity of TrxR in the ER is undetectable, whereas higher activities were measured in the cytoplasm and mitochondria. None of the Trx/TrxR isoforms were expressed in the ER by Western blot analysis. Co-localization studies of various isoforms of Trx and TrxR with ER marker Grp94 by immunofluorescent analysis further confirmed their absence from the lumen. The probability of luminal localization of each isoform was also predicted to be very low by several in silico analysis tools. ER-targeted transient transfection of HeLa cells with Trx1 and TrxR1 significantly decreased cell viability and induced apoptotic cell death. In conclusion, the absence of this electron transfer chain may explain the uncoupling of the redox systems in the ER lumen, allowing parallel presence of a reduced pyridine nucleotide and a probably oxidized protein pool necessary for cellular viability.
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Affiliation(s)
- Krisztina Veszelyi
- Institute of Translational Medicine, Semmelweis University, H-1085 Budapest, Hungary; (K.V.); (V.V.); (B.B.)
| | - Ibolya Czegle
- Department of Internal Medicine and Haematology, Semmelweis University, H-1085 Budapest, Hungary;
| | - Viola Varga
- Institute of Translational Medicine, Semmelweis University, H-1085 Budapest, Hungary; (K.V.); (V.V.); (B.B.)
| | - Csilla Emese Németh
- Institute of Biochemistry and Molecular Biology, Department of Molecular Biology, Semmelweis University, H-1085 Budapest, Hungary;
| | - Balázs Besztercei
- Institute of Translational Medicine, Semmelweis University, H-1085 Budapest, Hungary; (K.V.); (V.V.); (B.B.)
| | - Éva Margittai
- Institute of Translational Medicine, Semmelweis University, H-1085 Budapest, Hungary; (K.V.); (V.V.); (B.B.)
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Wurtz LI, Knyazhanskaya E, Sohaei D, Prassas I, Pittock S, Willrich MAV, Saadeh R, Gupta R, Atkinson HJ, Grill D, Stengelin M, Thebault S, Freedman MS, Diamandis EP, Scarisbrick IA. Identification of brain-enriched proteins in CSF as biomarkers of relapsing remitting multiple sclerosis. Clin Proteomics 2024; 21:42. [PMID: 38880880 PMCID: PMC11181608 DOI: 10.1186/s12014-024-09494-5] [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: 03/15/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024] Open
Abstract
BACKGROUND Multiple sclerosis (MS) is a clinically and biologically heterogenous disease with currently unpredictable progression and relapse. After the development and success of neurofilament as a cerebrospinal fluid (CSF) biomarker, there is reinvigorated interest in identifying other markers of or contributors to disease. The objective of this study is to probe the predictive potential of a panel of brain-enriched proteins on MS disease progression and subtype. METHODS This study includes 40 individuals with MS and 14 headache controls. The MS cohort consists of 20 relapsing remitting (RR) and 20 primary progressive (PP) patients. The CSF of all individuals was analyzed for 63 brain enriched proteins using a method of liquid-chromatography tandem mass spectrometry. Wilcoxon rank sum test, Kruskal-Wallis one-way ANOVA, logistic regression, and Pearson correlation were used to refine the list of candidates by comparing relative protein concentrations as well as relation to known imaging and molecular biomarkers. RESULTS We report 30 proteins with some relevance to disease, clinical subtype, or severity. Strikingly, we observed widespread protein depletion in the disease CSF as compared to control. We identified numerous markers of relapsing disease, including KLK6 (kallikrein 6, OR = 0.367, p < 0.05), which may be driven by active disease as defined by MRI enhancing lesions. Other oligodendrocyte-enriched proteins also appeared at reduced levels in relapsing disease, namely CNDP1 (carnosine dipeptidase 1), LINGO1 (leucine rich repeat and Immunoglobin-like domain-containing protein 1), MAG (myelin associated glycoprotein), and MOG (myelin oligodendrocyte glycoprotein). Finally, we identified three proteins-CNDP1, APLP1 (amyloid beta precursor like protein 1), and OLFM1 (olfactomedin 1)-that were statistically different in relapsing vs. progressive disease raising the potential for use as an early biomarker to discriminate clinical subtype. CONCLUSIONS We illustrate the utility of targeted mass spectrometry in generating potential targets for future biomarker studies and highlight reductions in brain-enriched proteins as markers of the relapsing remitting disease stage.
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Affiliation(s)
- Lincoln I Wurtz
- Medical Scientist Training Program, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Alix School of Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Dorsa Sohaei
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Ioannis Prassas
- Mount Sinai Hospital, Toronto, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Canada
| | - Sean Pittock
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
- Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, USA
| | | | - Ruba Saadeh
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ruchi Gupta
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Hunter J Atkinson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Diane Grill
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | - Simon Thebault
- Department of Medicine and The Ottawa Research Institute, Ottawa, Canada
- Division of Multiple Sclerosis, Department of Neurology, The University of Pennsylvania, Philadelphia, USA
| | - Mark S Freedman
- Department of Medicine and The Ottawa Research Institute, Ottawa, Canada
| | | | - Isobel A Scarisbrick
- Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, USA.
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, 55905, USA.
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Klomp JE, Diehl JN, Klomp JA, Edwards AC, Yang R, Morales AJ, Taylor KE, Drizyte-Miller K, Bryant KL, Schaefer A, Johnson JL, Huntsman EM, Yaron TM, Pierobon M, Baldelli E, Prevatte AW, Barker NK, Herring LE, Petricoin EF, Graves LM, Cantley LC, Cox AD, Der CJ, Stalnecker CA. Determining the ERK-regulated phosphoproteome driving KRAS-mutant cancer. Science 2024; 384:eadk0850. [PMID: 38843329 DOI: 10.1126/science.adk0850] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 04/17/2024] [Indexed: 06/16/2024]
Abstract
To delineate the mechanisms by which the ERK1 and ERK2 mitogen-activated protein kinases support mutant KRAS-driven cancer growth, we determined the ERK-dependent phosphoproteome in KRAS-mutant pancreatic cancer. We determined that ERK1 and ERK2 share near-identical signaling and transforming outputs and that the KRAS-regulated phosphoproteome is driven nearly completely by ERK. We identified 4666 ERK-dependent phosphosites on 2123 proteins, of which 79 and 66%, respectively, were not previously associated with ERK, substantially expanding the depth and breadth of ERK-dependent phosphorylation events and revealing a considerably more complex function for ERK in cancer. We established that ERK controls a highly dynamic and complex phosphoproteome that converges on cyclin-dependent kinase regulation and RAS homolog guanosine triphosphatase function (RHO GTPase). Our findings establish the most comprehensive molecular portrait and mechanisms by which ERK drives KRAS-dependent pancreatic cancer growth.
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Affiliation(s)
- Jennifer E Klomp
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffrey A Klomp
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - A Cole Edwards
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Runying Yang
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexis J Morales
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Khalilah E Taylor
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kristina Drizyte-Miller
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kirsten L Bryant
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Antje Schaefer
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jared L Johnson
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | | | - Elisa Baldelli
- School of Systems Biology, George Mason University, Fairfax, VA 22030, USA
| | - Alex W Prevatte
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie K Barker
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura E Herring
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Lee M Graves
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lewis C Cantley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Adrienne D Cox
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Channing J Der
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Clint A Stalnecker
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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8
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Lu P, Tian J. ACDMBI: A deep learning model based on community division and multi-source biological information fusion predicts essential proteins. Comput Biol Chem 2024; 112:108115. [PMID: 38865861 DOI: 10.1016/j.compbiolchem.2024.108115] [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: 04/03/2024] [Revised: 05/15/2024] [Accepted: 05/28/2024] [Indexed: 06/14/2024]
Abstract
Accurately identifying essential proteins is vital for drug research and disease diagnosis. Traditional centrality methods and machine learning approaches often face challenges in accurately discerning essential proteins, primarily relying on information derived from protein-protein interaction (PPI) networks. Despite attempts by some researchers to integrate biological data and PPI networks for predicting essential proteins, designing effective integration methods remains a challenge. In response to these challenges, this paper presents the ACDMBI model, specifically designed to overcome the aforementioned issues. ACDMBI is comprised of two key modules: feature extraction and classification. In terms of capturing relevant information, we draw insights from three distinct data sources. Initially, structural features of proteins are extracted from the PPI network through community division. Subsequently, these features are further optimized using Graph Convolutional Networks (GCN) and Graph Attention Networks (GAT). Moving forward, protein features are extracted from gene expression data utilizing Bidirectional Long Short-Term Memory networks (BiLSTM) and a multi-head self-attention mechanism. Finally, protein features are derived by mapping subcellular localization data to a one-dimensional vector and processing it through fully connected layers. In the classification phase, we integrate features extracted from three different data sources, crafting a multi-layer deep neural network (DNN) for protein classification prediction. Experimental results on brewing yeast data showcase the ACDMBI model's superior performance, with AUC reaching 0.9533 and AUPR reaching 0.9153. Ablation experiments further reveal that the effective integration of features from diverse biological information significantly boosts the model's performance.
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Affiliation(s)
- Pengli Lu
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou 730050, China.
| | - Jialong Tian
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou 730050, China.
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9
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Shraim R, Mooney B, Conkrite KL, Weiner AK, Morin GB, Sorensen PH, Maris JM, Diskin SJ, Sacan A. IMMUNOTAR - Integrative prioritization of cell surface targets for cancer immunotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597422. [PMID: 38895237 PMCID: PMC11185603 DOI: 10.1101/2024.06.04.597422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Cancer remains a leading cause of mortality globally. Recent improvements in survival have been facilitated by the development of less toxic immunotherapies; however, identifying targets for immunotherapies remains a challenge in the field. To address this challenge, we developed IMMUNOTAR, a computational tool that systematically prioritizes and identifies candidate immunotherapeutic targets. IMMUNOTAR integrates user-provided RNA-sequencing or proteomics data with quantitative features extracted from publicly available databases based on predefined optimal immunotherapeutic target criteria and quantitatively prioritizes potential surface protein targets. We demonstrate the utility and flexibility of IMMUNOTAR using three distinct datasets, validating its effectiveness in identifying both known and new potential immunotherapeutic targets within the analyzed cancer phenotypes. Overall, IMMUNOTAR enables the compilation of data from multiple sources into a unified platform, allowing users to simultaneously evaluate surface proteins across diverse criteria. By streamlining target identification, IMMUNOTAR empowers researchers to efficiently allocate resources and accelerate immunotherapy development.
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Affiliation(s)
- Rawan Shraim
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- School of Biomedical Engineering, Science and Health System, Drexel University, Philadelphia, PA 19104, USA
| | - Brian Mooney
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Karina L. Conkrite
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Amber K. Weiner
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Gregg B. Morin
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Poul H. Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ahmet Sacan
- School of Biomedical Engineering, Science and Health System, Drexel University, Philadelphia, PA 19104, USA
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10
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Ibragimov E, Eriksen EØ, Nielsen JP, Jørgensen CB, Fredholm M, Karlskov-Mortensen P. Towards identification of new genetic determinants for post-weaning diarrhea in piglets. Anim Genet 2024; 55:387-395. [PMID: 38343028 DOI: 10.1111/age.13406] [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: 05/02/2023] [Revised: 10/17/2023] [Accepted: 01/31/2024] [Indexed: 05/04/2024]
Abstract
Post-weaning diarrhea in pigs is a considerable challenge in the pig farming industry due to its effect on animal welfare and production costs, as well as the large volume of antibiotics, which are used to treat diarrhea in pigs after weaning. Previous studies have revealed loci on SSC6 and SSC13 associated with susceptibility to specific diarrhea causing pathogens. This study aimed to identify new genetic loci for resistance to diarrhea based on phenotypic data. In depth clinical characterization of diarrhea was performed in 257 pigs belonging to two herds during the first 14 days post weaning. The daily diarrhea assessments were used for the classification of pigs into case and control groups. Pigs were assigned to case and control groups based only on the incidence of diarrhea in the second week of the study in order to differentiate between differences in etiology. Genome-wide association studies and metabolomics association analysis were performed in order to identify new biological determinants for diarrhea susceptibility. With the present work, we revealed a new locus for diarrhea resistance on SSC16. Furthermore, studies of metabolomics in the same pigs revealed one metabolite associated with diarrhea.
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Affiliation(s)
- Emil Ibragimov
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Esben Østergaard Eriksen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jens Peter Nielsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Claus B Jørgensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Merete Fredholm
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Peter Karlskov-Mortensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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11
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Li Z, Wang S, Cui H, Liu X, Zhang Y. Spatiotemporal constrained RNA-protein heterogeneous network for protein complex identification. Brief Bioinform 2024; 25:bbae280. [PMID: 38856171 PMCID: PMC11163383 DOI: 10.1093/bib/bbae280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/05/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024] Open
Abstract
The identification of protein complexes from protein interaction networks is crucial in the understanding of protein function, cellular processes and disease mechanisms. Existing methods commonly rely on the assumption that protein interaction networks are highly reliable, yet in reality, there is considerable noise in the data. In addition, these methods fail to account for the regulatory roles of biomolecules during the formation of protein complexes, which is crucial for understanding the generation of protein interactions. To this end, we propose a SpatioTemporal constrained RNA-protein heterogeneous network for Protein Complex Identification (STRPCI). STRPCI first constructs a multiplex heterogeneous protein information network to capture deep semantic information by extracting spatiotemporal interaction patterns. Then, it utilizes a dual-view aggregator to aggregate heterogeneous neighbor information from different layers. Finally, through contrastive learning, STRPCI collaboratively optimizes the protein embedding representations under different spatiotemporal interaction patterns. Based on the protein embedding similarity, STRPCI reweights the protein interaction network and identifies protein complexes with core-attachment strategy. By considering the spatiotemporal constraints and biomolecular regulatory factors of protein interactions, STRPCI measures the tightness of interactions, thus mitigating the impact of noisy data on complex identification. Evaluation results on four real PPI networks demonstrate the effectiveness and strong biological significance of STRPCI. The source code implementation of STRPCI is available from https://github.com/LI-jasm/STRPCI.
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Affiliation(s)
- Zeqian Li
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Shilong Wang
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Hai Cui
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Xiaoxia Liu
- Department of Neurology and Neurological Sciences, Stanford University, CA 94305, USA
| | - Yijia Zhang
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
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12
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Shaw TI, Wagner J, Tian L, Wickman E, Poudel S, Wang J, Paul R, Koo SC, Lu M, Sheppard H, Fan Y, O'Neill FH, Lau CC, Zhou X, Zhang J, Gottschalk S. Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression. Nat Commun 2024; 15:3732. [PMID: 38702309 PMCID: PMC11068777 DOI: 10.1038/s41467-024-47649-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/09/2024] [Indexed: 05/06/2024] Open
Abstract
Immunotherapy with chimeric antigen receptor T cells for pediatric solid and brain tumors is constrained by available targetable antigens. Cancer-specific exons present a promising reservoir of targets; however, these have not been explored and validated systematically in a pan-cancer fashion. To identify cancer specific exon targets, here we analyze 1532 RNA-seq datasets from 16 types of pediatric solid and brain tumors for comparison with normal tissues using a newly developed workflow. We find 2933 exons in 157 genes encoding proteins of the surfaceome or matrisome with high cancer specificity either at the gene (n = 148) or the alternatively spliced isoform (n = 9) level. Expression of selected alternatively spliced targets, including the EDB domain of fibronectin 1, and gene targets, such as COL11A1, are validated in pediatric patient derived xenograft tumors. We generate T cells expressing chimeric antigen receptors specific for the EDB domain or COL11A1 and demonstrate that these have antitumor activity. The full target list, explorable via an interactive web portal ( https://cseminer.stjude.org/ ), provides a rich resource for developing immunotherapy of pediatric solid and brain tumors using gene or AS targets with high expression specificity in cancer.
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Affiliation(s)
- Timothy I Shaw
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Jessica Wagner
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Elizabeth Wickman
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Suresh Poudel
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jian Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Robin Paul
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Selene C Koo
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Meifen Lu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Heather Sheppard
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Francis H O'Neill
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Ching C Lau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Connecticut Children's Medical Center, Hartford, CT, 06106, USA
- University of Connecticut School of Medicine, Farmington, CT, 06032, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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13
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Cabrera-Romero E, Ochoa JP, Barriales-Villa R, Bermúdez-Jiménez FJ, Climent-Payá V, Zorio E, Espinosa MA, Gallego-Delgado M, Navarro-Peñalver M, Arana-Achaga X, Piqueras-Flores J, Espejo-Bares V, Rodríguez-Palomares JF, Lacuey-Lecumberri G, López J, Tiron C, Peña-Peña ML, García-Pinilla JM, Lorca R, Ripoll-Vera T, Díez-López C, Mogollon MV, García-Álvarez A, Martínez-Dolz L, Brion M, Larrañaga-Moreira JM, Jiménez-Jáimez J, García-Álvarez MI, Vilches S, Villacorta E, Sabater-Molina M, Solla-Ruiz I, Royuela A, Domínguez F, Mirelis JG, Garcia-Pavia P. Penetrance of Dilated Cardiomyopathy in Genotype-Positive Relatives. J Am Coll Cardiol 2024; 83:1640-1651. [PMID: 38658103 DOI: 10.1016/j.jacc.2024.02.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Disease penetrance in genotype-positive (G+) relatives of families with dilated cardiomyopathy (DCM) and the characteristics associated with DCM onset in these individuals are unknown. OBJECTIVES This study sought to determine the penetrance of new DCM diagnosis in G+ relatives and to identify factors associated with DCM development. METHODS The authors evaluated 779 G+ patients (age 35.8 ± 17.3 years; 459 [59%] females; 367 [47%] with variants in TTN) without DCM followed at 25 Spanish centers. RESULTS After a median follow-up of 37.1 months (Q1-Q3: 16.3-63.8 months), 85 individuals (10.9%) developed DCM (incidence rate of 2.9 per 100 person-years; 95% CI: 2.3-3.5 per 100 person-years). DCM penetrance and age at DCM onset was different according to underlying gene group (log-rank P = 0.015 and P <0.01, respectively). In a multivariable model excluding CMR parameters, independent predictors of DCM development were: older age (HR per 1-year increase: 1.02; 95% CI: 1.0-1.04), an abnormal electrocardiogram (HR: 2.13; 95% CI: 1.38-3.29); presence of variants in motor sarcomeric genes (HR: 1.92; 95% CI: 1.05-3.50); lower left ventricular ejection fraction (HR per 1% increase: 0.86; 95% CI: 0.82-0.90) and larger left ventricular end-diastolic diameter (HR per 1-mm increase: 1.10; 95% CI: 1.06-1.13). Multivariable analysis in individuals with cardiac magnetic resonance and late gadolinium enhancement assessment (n = 360, 45%) identified late gadolinium enhancement as an additional independent predictor of DCM development (HR: 2.52; 95% CI: 1.43-4.45). CONCLUSIONS Following a first negative screening, approximately 11% of G+ relatives developed DCM during a median follow-up of 3 years. Older age, an abnormal electrocardiogram, lower left ventricular ejection fraction, increased left ventricular end-diastolic diameter, motor sarcomeric genetic variants, and late gadolinium enhancement are associated with a higher risk of developing DCM.
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Affiliation(s)
- Eva Cabrera-Romero
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, IDIPHISA, Madrid, Spain; CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, ERN GUARD-Heart, Amsterdam, the Netherlands
| | - Juan Pablo Ochoa
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, ERN GUARD-Heart, Amsterdam, the Netherlands; Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; Health in Code, Madrid, Spain
| | - Roberto Barriales-Villa
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; Inherited Cardiac Diseases Unit, Department of Cardiology, Complexo Hospitalario Universitario A Coruña, A Coruña, Spain; Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
| | - Francisco José Bermúdez-Jiménez
- Department of Cardiology, Virgen de las Nieves University Hospital, Instituto de Investigación Biosanitaria (ibs.GRANADA), Granada, Spain
| | - Vicente Climent-Payá
- Heart Failure and Inherited Cardiac Diseases Unit, Cardiology Department, Hospital General Universitario Dr Balmis, Institute for Health and Biomedical Research of Alicante (ISABIAL), Alicante, Spain
| | - Esther Zorio
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; Department of Cardiology, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Clinical and Translational Research in Cardiology, Instituto de Investigación Sanitaria La Fe (IIS-La Fe), Valencia, Spain
| | - María Angeles Espinosa
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, ERN GUARD-Heart, Amsterdam, the Netherlands; Department of Cardiology, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - María Gallego-Delgado
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; Inherited Cardiovascular Disease Unit, Department of Cardiology, Complejo Asistencial Universitario de Salamanca, Institute for Biomedical Research of Salamanca (IBSAL), Gerencia Regional de Salud de Castilla y Leon (SACYL), Salamanca, Spain
| | - Marina Navarro-Peñalver
- Unidad CSUR/ERN de Cardiopatías Familiares, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Xabier Arana-Achaga
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Donostia University Hospital, Donostia, Spain; Biodonostia Health Research Institute, Donostia, Spain
| | - Jesús Piqueras-Flores
- Inherited Cardiac Diseases Unit, Cardiology Department, Hospital General Universitario de Ciudad Real, Ciudad Real, Spain; Department of Medicine, Universidad de Castilla La Mancha, Ciudad Real, Spain; Health Research Institute of Castilla La Mancha (IDISCAM), Ciudad Real, Spain
| | - Victoria Espejo-Bares
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario 12 de Octubre, Madrid, Spain; Instituto de investigación 12 de Octubre i+12, Madrid, Spain
| | - José F Rodríguez-Palomares
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, ERN GUARD-Heart, Amsterdam, the Netherlands; Cardiovascular Imaging Department and Inherited Cardiac Diseases Unit, Cardiology Department, Hospital Universitario Vall Hebrón, Barcelona, Spain; Vall Hebron Research Institute (VHIR), Universitat Autónoma de Barcelona (UAB), Barcelona, Spain
| | - Gemma Lacuey-Lecumberri
- Hospital Universitario de Navarra, Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Javier López
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; Hospital Clínico de Valladolid, Vallodolid, Spain; Instituto de Ciencias del Corazón (ICICOR), Valladolid, Spain
| | - Coloma Tiron
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitari Dr Josep Trueta, Girona, Spain; Medical Science Department, School of Medicine, University of Girona, Girona, Spain
| | - María Luisa Peña-Peña
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, ERN GUARD-Heart, Amsterdam, the Netherlands; Cardiovascular Imaging and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Virgen del Rocío, Sevilla, Spain
| | - Jose M García-Pinilla
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; Heart Failure and Inherited Cardiac Diseases Unit, Hospital Universitario Virgen de la Victoria, IBIMA, Málaga, Spain; Departamento de Medicina y Dermatología, Universidad de Málaga, Málaga, Spain
| | - Rebeca Lorca
- Inherited Cardiac Diseases Unit, Área del Corazón, Hospital Universitario Central Asturias (HUCA), Oviedo, Spain; de Fisiología, Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORs), Madrid, Spain
| | - Tomas Ripoll-Vera
- Hospital Universitario Son Llatzer, IdISBa, Palma de Mallorca, Spain
| | - Carles Díez-López
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; Inherited Cardiovascular Diseases Program, Hospital Universitari de Bellvitge, BioHeart Research Group, IDIBELL, Badalona, Spain
| | | | - Ana García-Álvarez
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, ERN GUARD-Heart, Amsterdam, the Netherlands; Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; Cardiology Department, Hospital Clínic Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Luis Martínez-Dolz
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; Department of Cardiology, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Clinical and Translational Research in Cardiology, Instituto de Investigación Sanitaria La Fe (IIS-La Fe), Valencia, Spain
| | - María Brion
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; Xenética Cardiovascular, Instituto de investigación Sanitaria de Santiago, Inherited Cardiac Diseases Unit, Department of Cardiology Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jose María Larrañaga-Moreira
- Inherited Cardiac Diseases Unit, Department of Cardiology, Complexo Hospitalario Universitario A Coruña, A Coruña, Spain; Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
| | - Juan Jiménez-Jáimez
- Department of Cardiology, Virgen de las Nieves University Hospital, Instituto de Investigación Biosanitaria (ibs.GRANADA), Granada, Spain
| | - María Isabel García-Álvarez
- Heart Failure and Inherited Cardiac Diseases Unit, Cardiology Department, Hospital General Universitario Dr Balmis, Institute for Health and Biomedical Research of Alicante (ISABIAL), Alicante, Spain
| | - Silvia Vilches
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, ERN GUARD-Heart, Amsterdam, the Netherlands; Department of Cardiology, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Eduardo Villacorta
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; Inherited Cardiovascular Disease Unit, Department of Cardiology, Complejo Asistencial Universitario de Salamanca, Institute for Biomedical Research of Salamanca (IBSAL), Gerencia Regional de Salud de Castilla y Leon (SACYL), Salamanca, Spain; Universidad de Salamanca, Salamanca, Spain
| | - María Sabater-Molina
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; Unidad CSUR/ERN de Cardiopatías Familiares, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain; Laboratorio de Cardiogenética, Instituto Murciano de Investigación Biosanitaria, Murcia, Spain; Departamento de Ciencias Sociosanitarias, Universidad de Murcia, Murcia, Spain
| | - Itziar Solla-Ruiz
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Donostia University Hospital, Donostia, Spain; Biodonostia Health Research Institute, Donostia, Spain
| | - Ana Royuela
- Biostatistics Unit, Hospital Universitario Puerta de Hierro Majadahonda, IDIPHISA, CIBERESP, Madrid, Spain
| | - Fernando Domínguez
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, IDIPHISA, Madrid, Spain; CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, ERN GUARD-Heart, Amsterdam, the Netherlands; Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Jesús G Mirelis
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, IDIPHISA, Madrid, Spain; CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
| | - Pablo Garcia-Pavia
- Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro, IDIPHISA, Madrid, Spain; CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, ERN GUARD-Heart, Amsterdam, the Netherlands; Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; Universidad Francisco de Vitoria (UFV), Pozuelo de Alarcón, Spain
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14
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Pan L, Wang H, Yang B, Li W. A protein network refinement method based on module discovery and biological information. BMC Bioinformatics 2024; 25:157. [PMID: 38643108 PMCID: PMC11031909 DOI: 10.1186/s12859-024-05772-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: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND The identification of essential proteins can help in understanding the minimum requirements for cell survival and development to discover drug targets and prevent disease. Nowadays, node ranking methods are a common way to identify essential proteins, but the poor data quality of the underlying PIN has somewhat hindered the identification accuracy of essential proteins for these methods in the PIN. Therefore, researchers constructed refinement networks by considering certain biological properties of interacting protein pairs to improve the performance of node ranking methods in the PIN. Studies show that proteins in a complex are more likely to be essential than proteins not present in the complex. However, the modularity is usually ignored for the refinement methods of the PINs. METHODS Based on this, we proposed a network refinement method based on module discovery and biological information. The idea is, first, to extract the maximal connected subgraph in the PIN, and to divide it into different modules by using Fast-unfolding algorithm; then, to detect critical modules according to the orthologous information, subcellular localization information and topology information within each module; finally, to construct a more refined network (CM-PIN) by using the identified critical modules. RESULTS To evaluate the effectiveness of the proposed method, we used 12 typical node ranking methods (LAC, DC, DMNC, NC, TP, LID, CC, BC, PR, LR, PeC, WDC) to compare the overall performance of the CM-PIN with those on the S-PIN, D-PIN and RD-PIN. The experimental results showed that the CM-PIN was optimal in terms of the identification number of essential proteins, precision-recall curve, Jackknifing method and other criteria, and can help to identify essential proteins more accurately.
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Affiliation(s)
- Li Pan
- Hunan Institute of Science and Technology, Yueyang, 414006, China
- Hunan Engineering Research Center of Multimodal Health Sensing and Intelligent Analysis, Yueyang, 414006, China
| | - Haoyue Wang
- Hunan Institute of Science and Technology, Yueyang, 414006, China.
| | - Bo Yang
- Hunan Institute of Science and Technology, Yueyang, 414006, China
- Hunan Engineering Research Center of Multimodal Health Sensing and Intelligent Analysis, Yueyang, 414006, China
| | - Wenbin Li
- Hunan Institute of Science and Technology, Yueyang, 414006, China.
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15
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Bai Z, Bartelo N, Aslam M, Murphy EA, Hale CR, Blachere NE, Parveen S, Spolaore E, DiCarlo E, Gravallese EM, Smith MH, Frank MO, Jiang CS, Zhang H, Pyrgaki C, Lewis MJ, Sikandar S, Pitzalis C, Lesnak JB, Mazhar K, Price TJ, Malfait AM, Miller RE, Zhang F, Goodman S, Darnell RB, Wang F, Orange DE. Synovial fibroblast gene expression is associated with sensory nerve growth and pain in rheumatoid arthritis. Sci Transl Med 2024; 16:eadk3506. [PMID: 38598614 DOI: 10.1126/scitranslmed.adk3506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/21/2024] [Indexed: 04/12/2024]
Abstract
It has been presumed that rheumatoid arthritis (RA) joint pain is related to inflammation in the synovium; however, recent studies reveal that pain scores in patients do not correlate with synovial inflammation. We developed a machine-learning approach (graph-based gene expression module identification or GbGMI) to identify an 815-gene expression module associated with pain in synovial biopsy samples from patients with established RA who had limited synovial inflammation at arthroplasty. We then validated this finding in an independent cohort of synovial biopsy samples from patients who had early untreated RA with little inflammation. Single-cell RNA sequencing analyses indicated that most of these 815 genes were most robustly expressed by lining layer synovial fibroblasts. Receptor-ligand interaction analysis predicted cross-talk between human lining layer fibroblasts and human dorsal root ganglion neurons expressing calcitonin gene-related peptide (CGRP+). Both RA synovial fibroblast culture supernatant and netrin-4, which is abundantly expressed by lining fibroblasts and was within the GbGMI-identified pain-associated gene module, increased the branching of pain-sensitive murine CGRP+ dorsal root ganglion neurons in vitro. Imaging of solvent-cleared synovial tissue with little inflammation from humans with RA revealed CGRP+ pain-sensing neurons encasing blood vessels growing into synovial hypertrophic papilla. Together, these findings support a model whereby synovial lining fibroblasts express genes associated with pain that enhance the growth of pain-sensing neurons into regions of synovial hypertrophy in RA.
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Affiliation(s)
- Zilong Bai
- Weill Cornell Medicine, New York, NY 10065, USA
| | | | | | | | - Caryn R Hale
- Rockefeller University, New York, NY 10065, USA
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nathalie E Blachere
- Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, Rockefeller University, New York, NY 10065, USA
| | | | | | | | | | | | | | | | | | | | - Myles J Lewis
- Queen Mary University of London & NIHR BRC Barts Health NHS Trust, London E1 4NS, UK
| | - Shafaq Sikandar
- Queen Mary University of London & NIHR BRC Barts Health NHS Trust, London E1 4NS, UK
| | - Costantino Pitzalis
- Queen Mary University of London & NIHR BRC Barts Health NHS Trust, London E1 4NS, UK
- Department of Biomedical Sciences, Humanitas University & IRCC Humanitas Research Hospital, Milan 20072, Italy
| | | | | | | | | | | | - Fan Zhang
- University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Susan Goodman
- Hospital for Special Surgery, New York, NY 10021, USA
| | - Robert B Darnell
- Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, Rockefeller University, New York, NY 10065, USA
| | - Fei Wang
- Weill Cornell Medicine, New York, NY 10065, USA
| | - Dana E Orange
- Rockefeller University, New York, NY 10065, USA
- Hospital for Special Surgery, New York, NY 10021, USA
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16
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Birkemeier M, Swindle A, Bowman J, Lynch VJ. Pervasive loss of regulated necrotic cell death genes in elephants, hyraxes, and sea cows ( Paenungualta). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588129. [PMID: 38617256 PMCID: PMC11014510 DOI: 10.1101/2024.04.04.588129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Gene loss can promote phenotypic differences between species, for example, if a gene constrains phenotypic variation in a trait, its loss allows for the evolution of a greater range of variation or even new phenotypes. Here, we explore the contribution of gene loss to the evolution of large bodies and augmented cancer resistance in elephants. We used genomes from 17 Afrotherian and Xenarthran species to identify lost genes, i.e., genes that have pseudogenized or been completely lost, and Dollo parsimony to reconstruct the evolutionary history of gene loss across species. We unexpectedly discovered a burst of gene losses in the Afrotherian stem lineage and found that the loss of genes with functions in regulated necrotic cell death modes was pervasive in elephants, hyraxes, and sea cows (Paenungulata). Among the lost genes are MLKL and RIPK3, which mediate necroptosis, and sensors that activate inflammasomes to induce pyroptosis, including AIM2, MEFV, NLRC4, NLRP1, and NLRP6. These data suggest that the mechanisms that regulate necrosis and pyroptosis are either extremely derived or potentially lost in these lineages, which may contribute to the repeated evolution of large bodies and cancer resistance in Paenungulates as well as susceptibility to pathogen infection.
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Affiliation(s)
- Meaghan Birkemeier
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, USA
| | - Arianna Swindle
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, USA
| | - Jacob Bowman
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, USA
| | - Vincent J. Lynch
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, USA
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17
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Wu CC, Tsantilas KA, Park J, Plubell D, Sanders JA, Naicker P, Govender I, Buthelezi S, Stoychev S, Jordaan J, Merrihew G, Huang E, Parker ED, Riffle M, Hoofnagle AN, Noble WS, Poston KL, Montine TJ, MacCoss MJ. Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.10.544439. [PMID: 38617345 PMCID: PMC11014469 DOI: 10.1101/2023.06.10.544439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Membrane-bound particles in plasma are composed of exosomes, microvesicles, and apoptotic bodies and represent ~1-2% of the total protein composition. Proteomic interrogation of this subset of plasma proteins augments the representation of tissue-specific proteins, representing a "liquid biopsy," while enabling the detection of proteins that would otherwise be beyond the dynamic range of liquid chromatography-tandem mass spectrometry of unfractionated plasma. We have developed an enrichment strategy (Mag-Net) using hyper-porous strong-anion exchange magnetic microparticles to sieve membrane-bound particles from plasma. The Mag-Net method is robust, reproducible, inexpensive, and requires <100 μL plasma input. Coupled to a quantitative data-independent mass spectrometry analytical strategy, we demonstrate that we can collect results for >37,000 peptides from >4,000 plasma proteins with high precision. Using this analytical pipeline on a small cohort of patients with neurodegenerative disease and healthy age-matched controls, we discovered 204 proteins that differentiate (q-value < 0.05) patients with Alzheimer's disease dementia (ADD) from those without ADD. Our method also discovered 310 proteins that were different between Parkinson's disease and those with either ADD or healthy cognitively normal individuals. Using machine learning we were able to distinguish between ADD and not ADD with a mean ROC AUC = 0.98 ± 0.06.
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Affiliation(s)
- Christine C. Wu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Jea Park
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Deanna Plubell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Justin A. Sanders
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Gennifer Merrihew
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Eric Huang
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Edward D. Parker
- Vision Core Lab, Department of Ophthalmology, University of Washington, Seattle, WA, USA
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Andrew N. Hoofnagle
- Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - William S. Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Kathleen L. Poston
- Department of Neurology & Neurological Sciences, Stanford University, Palo Alto CA, USA
| | | | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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18
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Koch B, Filzmayer M, Patyna S, Wetzstein N, Lampe S, Schmid T, Geiger H, Baer PC, Dolnik O. Transcriptomics of Marburg virus-infected primary proximal tubular cells reveals negative correlation of immune response and energy metabolism. Virus Res 2024; 342:199337. [PMID: 38346476 PMCID: PMC10875301 DOI: 10.1016/j.virusres.2024.199337] [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: 12/11/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024]
Abstract
Marburg virus, a member of the Filoviridae, is the causative agent of Marburg virus disease (MVD), a hemorrhagic fever with a case fatality rate of up to 90 %. Acute kidney injury is common in MVD and is associated with increased mortality, but its pathogenesis in MVD remains poorly understood. Interestingly, autopsies show the presence of viral proteins in different parts of the nephron, particularly in proximal tubular cells (PTC). These findings suggest a potential role for the virus in the development of MVD-related kidney injury. To shed light on this effect, we infected primary human PTC with Lake Victoria Marburg virus and conducted transcriptomic analysis at multiple time points. Unexpectedly, infection did not induce marked cytopathic effects in primary tubular cells at 20 and 40 h post infection. However, gene expression analysis revealed robust renal viral replication and dysregulation of genes essential for different cellular functions. The gene sets mainly downregulated in PTC were associated with the targets of the transcription factors MYC and E2F, DNA repair, the G2M checkpoint, as well as oxidative phosphorylation. Importantly, the downregulated factors comprise PGC-1α, a well-known factor in acute and chronic kidney injury. By contrast, the most highly upregulated gene sets were those related to the inflammatory response and cholesterol homeostasis. In conclusion, Marburg virus infects and replicates in human primary PTC and induces downregulation of processes known to be relevant for acute kidney injury as well as a strong inflammatory response.
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Affiliation(s)
- Benjamin Koch
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine 4, Nephrology, Theodor-Stern-Kai 7, Frankfurt am Main 60596, Germany.
| | - Maximilian Filzmayer
- Goethe University Frankfurt, University Hospital, Department of Urology, Frankfurt am Main 60596, Germany
| | - Sammy Patyna
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine 4, Nephrology, Theodor-Stern-Kai 7, Frankfurt am Main 60596, Germany
| | - Nils Wetzstein
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine, Infectious Diseases, Frankfurt am Main 60596, Germany
| | - Sebastian Lampe
- Goethe University Frankfurt, University Hospital, Faculty of Medicine, Institute for Biochemistry I, Frankfurt am Main 60596, Germany
| | - Tobias Schmid
- Goethe University Frankfurt, University Hospital, Faculty of Medicine, Institute for Biochemistry I, Frankfurt am Main 60596, Germany
| | - Helmut Geiger
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine 4, Nephrology, Theodor-Stern-Kai 7, Frankfurt am Main 60596, Germany
| | - Patrick C Baer
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine 4, Nephrology, Theodor-Stern-Kai 7, Frankfurt am Main 60596, Germany
| | - Olga Dolnik
- Philipps University Marburg, Institute of Virology, Hans-Meerwein-Str. 2, Marburg 35043, Germany.
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19
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Mohamed AS, Salama AF, Sabaa MA, Toraih E, Elshazli RM. GEMIN4 Variants: Risk Profiling, Bioinformatics, and Dynamic Simulations Uncover Susceptibility to Bladder Carcinoma. Arch Med Res 2024; 55:102970. [PMID: 38401326 DOI: 10.1016/j.arcmed.2024.102970] [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: 09/13/2023] [Revised: 01/11/2024] [Accepted: 02/13/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND The relationship between GEMIN4 genetic variants and cancer, especially bladder carcinoma (BLCA), has been explored without conclusive results. This study aims to elucidate the link between GEMIN4 polymorphisms and BLCA susceptibility through genetic analyses, bioinformatics, and molecular dynamics (MD) simulations. METHODS A cohort of 249 participants (121 BLCA patients and 128 unrelated controls) was enrolled. PCR was employed for allelic discrimination of GEMIN4 variants, followed by subgroup stratification, haplotype analyses, structural prediction using the AlphaFold2 prediction tool, subsequent MD simulations, structural analysis, and residue interaction mapping using Desmond, UCSF ChimeraX, and Cytoscape softwares. RESULTS The rs.2740348*G variant demonstrated a protective role against BLCA in allelic (OR = 0.55, p = 0.002) and recessive (OR = 0.54, p = 0.017) models, whereas the rs.7813*T variant increased BLCA risk under the recessive model (OR = 1.90, p = 0.019). Haplotype analysis revealed a significant association between GEMIN4 haplotype (rs.2740348*C/rs.7813*T) with increased BLCA risk (OR = 2.01, p = 0.004). Univariate analysis revealed associations of the variants with albumin levels and absolute neutrophil count in BLCA patients. Pathogenicity evaluation categorized p.Gln450Glu as neutral and p.Arg1033Cys as deleterious. MD simulations revealed structural alterations and conformational shifts in the GEMIN4 protein induced by the Glu450 and Cys1033 mutations. CONCLUSIONS The study highlights the dual role of GEMIN4 variants in BLCA susceptibility, with rs.2740348 conferring protection and rs.7813 increasing risk. The Glu450 residue positively impacted protein stability, while Cys1033 had a detrimental effect on protein function. These findings underscore the significance of GEMIN4 variants in BLCA susceptibility and pave the way for future diagnostic and therapeutic initiatives.
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Affiliation(s)
- Abdallah S Mohamed
- Biochemistry Division, Department of Chemistry, Faculty of Science, Tanta University, Tanta, Egypt
| | - Afrah F Salama
- Biochemistry Division, Department of Chemistry, Faculty of Science, Tanta University, Tanta, Egypt
| | - Magdy A Sabaa
- Department of Urology, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Eman Toraih
- Endocrine and Oncology Division, Department of Surgery, Tulane University School of Medicine, New Orleans, LA, USA; Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.
| | - Rami M Elshazli
- Biochemistry and Molecular Genetics Unit, Department of Basic Sciences, Faculty of Physical Therapy, Horus University - Egypt, New Damietta, Egypt.
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20
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Rosenberg FM, Kamali Z, Voorberg AN, Oude Munnink TH, van der Most PJ, Snieder H, Vaez A, Schuttelaar MLA. Transcriptomics- and Genomics-Guided Drug Repurposing for the Treatment of Vesicular Hand Eczema. Pharmaceutics 2024; 16:476. [PMID: 38675137 PMCID: PMC11054470 DOI: 10.3390/pharmaceutics16040476] [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: 02/19/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Vesicular hand eczema (VHE), a clinical subtype of hand eczema (HE), showed limited responsiveness to alitretinoin, the only approved systemic treatment for severe chronic HE. This emphasizes the need for alternative treatment approaches. Therefore, our study aimed to identify drug repurposing opportunities for VHE using transcriptomics and genomics data. We constructed a gene network by combining 52 differentially expressed genes (DEGs) from a VHE transcriptomics study with 3 quantitative trait locus (QTL) genes associated with HE. Through network analysis, clustering, and functional enrichment analyses, we investigated the underlying biological mechanisms of this network. Next, we leveraged drug-gene interactions and retrieved pharmaco-transcriptomics data from the DrugBank database to identify drug repurposing opportunities for (V)HE. We developed a drug ranking system, primarily based on efficacy, safety, and practical and pricing factors, to select the most promising drug repurposing candidates. Our results revealed that the (V)HE network comprised 78 genes that yielded several biological pathways underlying the disease. The drug-gene interaction search together with pharmaco-transcriptomics lookups revealed 123 unique drug repurposing opportunities. Based on our drug ranking system, our study identified the most promising drug repurposing opportunities (e.g., vitamin D analogues, retinoids, and immunomodulating drugs) that might be effective in treating (V)HE.
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Affiliation(s)
- Fieke M. Rosenberg
- Department of Dermatology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (F.M.R.); (A.N.V.)
| | - Zoha Kamali
- Department of Epidemiology, University Medical Centre Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands (H.S.)
- Department of Bioinformatics, School of Advanced Medical Technologies, Isfahan University of Medical Sciences, Isfahan P.O. Box 81746-7346, Iran
| | - Angelique N. Voorberg
- Department of Dermatology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (F.M.R.); (A.N.V.)
| | - Thijs H. Oude Munnink
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
| | - Peter J. van der Most
- Department of Epidemiology, University Medical Centre Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands (H.S.)
| | - Harold Snieder
- Department of Epidemiology, University Medical Centre Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands (H.S.)
| | - Ahmad Vaez
- Department of Epidemiology, University Medical Centre Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands (H.S.)
- Department of Bioinformatics, School of Advanced Medical Technologies, Isfahan University of Medical Sciences, Isfahan P.O. Box 81746-7346, Iran
| | - Marie L. A. Schuttelaar
- Department of Dermatology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (F.M.R.); (A.N.V.)
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21
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Xiao H, Zou Y, Wang J, Wan S. A Review for Artificial Intelligence Based Protein Subcellular Localization. Biomolecules 2024; 14:409. [PMID: 38672426 PMCID: PMC11048326 DOI: 10.3390/biom14040409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Proteins need to be located in appropriate spatiotemporal contexts to carry out their diverse biological functions. Mislocalized proteins may lead to a broad range of diseases, such as cancer and Alzheimer's disease. Knowing where a target protein resides within a cell will give insights into tailored drug design for a disease. As the gold validation standard, the conventional wet lab uses fluorescent microscopy imaging, immunoelectron microscopy, and fluorescent biomarker tags for protein subcellular location identification. However, the booming era of proteomics and high-throughput sequencing generates tons of newly discovered proteins, making protein subcellular localization by wet-lab experiments a mission impossible. To tackle this concern, in the past decades, artificial intelligence (AI) and machine learning (ML), especially deep learning methods, have made significant progress in this research area. In this article, we review the latest advances in AI-based method development in three typical types of approaches, including sequence-based, knowledge-based, and image-based methods. We also elaborately discuss existing challenges and future directions in AI-based method development in this research field.
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Affiliation(s)
- Hanyu Xiao
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Yijin Zou
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China;
| | - Jieqiong Wang
- Department of Neurological Sciences, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Shibiao Wan
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
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22
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Sun MA, Yao H, Yang Q, Pirozzi CJ, Chandramohan V, Ashley DM, He Y. Gene expression analysis suggests immunosuppressive roles of endolysosomes in glioblastoma. PLoS One 2024; 19:e0299820. [PMID: 38507437 PMCID: PMC10954093 DOI: 10.1371/journal.pone.0299820] [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: 10/17/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024] Open
Abstract
Targeting endolysosomes is a strategy extensively pursued for treating cancers, including glioblastomas (GBMs), on the basis that the intact function of these subcellular organelles is key to tumor cell autophagy and survival. Through gene expression analyses and cell type abundance estimation in GBMs, we showed that genes associated with the endolysosomal machinery are more prominently featured in non-tumor cells in GBMs than in tumor cells, and that tumor-associated macrophages represent the primary immune cell type that contributes to this trend. Further analyses found an enrichment of endolysosomal pathway genes in immunosuppressive (pro-tumorigenic) macrophages, such as M2-like macrophages or those associated with worse prognosis in glioma patients, but not in those linked to inflammation (anti-tumorigenic). Specifically, genes critical to the hydrolysis function of endolysosomes, including progranulin and cathepsins, were among the most positively correlated with immunosuppressive macrophages, and elevated expression of these genes is associated with worse patient survival in GBMs. Together, these results implicate the hydrolysis function of endolysosomes in shaping the immunosuppressive microenvironment of GBM. We propose that targeting endolysosomes, in addition to its detrimental effects on tumor cells, can be leveraged for modulating immunosuppression to render GBMs more amenable to immunotherapies.
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Affiliation(s)
- Michael A. Sun
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, United States of America
- Department of Pathology, Duke University Medical Center, Durham, NC, United States of America
- Pathology Graduate Program, Duke University Medical Center, Durham, NC, United States of America
| | - Haipei Yao
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, United States of America
- Department of Pathology, Duke University Medical Center, Durham, NC, United States of America
- Pathology Graduate Program, Duke University Medical Center, Durham, NC, United States of America
| | - Qing Yang
- Duke University School of Nursing, Durham, NC, United States of America
| | - Christopher J. Pirozzi
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, United States of America
- Department of Pathology, Duke University Medical Center, Durham, NC, United States of America
| | - Vidyalakshmi Chandramohan
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, United States of America
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States of America
| | - David M. Ashley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, United States of America
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States of America
| | - Yiping He
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, United States of America
- Department of Pathology, Duke University Medical Center, Durham, NC, United States of America
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23
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Fleischer S, Nash TR, Tamargo MA, Lock RI, Venturini G, Morsink M, Li V, Lamberti MJ, Graney PL, Liberman M, Kim Y, Zhuang RZ, Whitehead J, Friedman RA, Soni RK, Seidman JG, Seidman CE, Geraldino-Pardilla L, Winchester R, Vunjak-Novakovic G. An engineered human cardiac tissue model reveals contributions of systemic lupus erythematosus autoantibodies to myocardial injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583787. [PMID: 38559188 PMCID: PMC10979865 DOI: 10.1101/2024.03.07.583787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Systemic lupus erythematosus (SLE) is a highly heterogenous autoimmune disease that affects multiple organs, including the heart. The mechanisms by which myocardial injury develops in SLE, however, remain poorly understood. Here we engineered human cardiac tissues and cultured them with IgG fractions containing autoantibodies from SLE patients with and without myocardial involvement. We observed unique binding patterns of IgG from two patient subgroups: (i) patients with severe myocardial inflammation exhibited enhanced binding to apoptotic cells within cardiac tissues subjected to stress, and (ii) patients with systolic dysfunction exhibited enhanced binding to the surfaces of viable cardiomyocytes. Functional assays and RNA sequencing (RNA-seq) revealed that IgGs from patients with systolic dysfunction exerted direct effects on engineered tissues in the absence of immune cells, altering tissue cellular composition, respiration and calcium handling. Autoantibody target characterization by phage immunoprecipitation sequencing (PhIP-seq) confirmed distinctive IgG profiles between patient subgroups. By coupling IgG profiling with cell surface protein analyses, we identified four pathogenic autoantibody candidates that may directly alter the function of cells within the myocardium. Taken together, these observations provide insights into the cellular processes of myocardial injury in SLE that have the potential to improve patient risk stratification and inform the development of novel therapeutic strategies.
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Affiliation(s)
- Sharon Fleischer
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Trevor R Nash
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Manuel A Tamargo
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Roberta I Lock
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Margaretha Morsink
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Vanessa Li
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Morgan J Lamberti
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Pamela L Graney
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Martin Liberman
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Youngbin Kim
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Richard Z Zhuang
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jaron Whitehead
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Richard A Friedman
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Robert Winchester
- Department of Medicine, Columbia University, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University, New York, NY, USA
- College of Dental Medicine, Columbia University, New York, NY, USA
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24
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Flümann R, Hansen J, Meinel J, Pfeiffer P, Goldfarb Wittkopf H, Lütz A, Wirtz J, Möllmann M, Zhou T, Tabatabai A, Lohmann T, Jauch M, Beleggia F, Pelzer B, Ullrich F, Höfmann S, Arora A, Persigehl T, Büttner R, von Tresckow B, Klein S, Jachimowicz RD, Reinhardt HC, Knittel G. An inducible Cd79b mutation confers ibrutinib sensitivity in mouse models of Myd88-driven diffuse large B-cell lymphoma. Blood Adv 2024; 8:1063-1074. [PMID: 38060829 PMCID: PMC10907402 DOI: 10.1182/bloodadvances.2023011213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/26/2023] [Indexed: 02/29/2024] Open
Abstract
ABSTRACT Diffuse large B-cell lymphoma (DLBCL) is the most common aggressive lymphoma and constitutes a highly heterogenous disease. Recent comprehensive genomic profiling revealed the identity of numerous molecularly defined DLBCL subtypes, including a cluster which is characterized by recurrent aberrations in MYD88, CD79B, and BCL2, as well as various lesions promoting a block in plasma cell differentiation, including PRDM1, TBL1XR1, and SPIB. Here, we generated a series of autochthonous mouse models to mimic this DLBCL cluster and specifically focused on the impact of Cd79b mutations in this setting. We show that canonical Cd79b immunoreceptor tyrosine-based activation motif (ITAM) mutations do not accelerate Myd88- and BCL2-driven lymphomagenesis. Cd79b-mutant murine DLBCL were enriched for IgM surface expression, reminiscent of their human counterparts. Moreover, Cd79b-mutant lymphomas displayed a robust formation of cytoplasmic signaling complexes involving MYD88, CD79B, MALT1, and BTK. These complexes were disrupted upon pharmacological BTK inhibition. The BTK inhibitor-mediated disruption of these signaling complexes translated into a selective ibrutinib sensitivity of lymphomas harboring combined Cd79b and Myd88 mutations. Altogether, this in-depth cross-species comparison provides a framework for the development of molecularly targeted therapeutic intervention strategies in DLBCL.
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Affiliation(s)
- Ruth Flümann
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Julia Hansen
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Jörn Meinel
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Pauline Pfeiffer
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Hannah Goldfarb Wittkopf
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Anna Lütz
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Jessica Wirtz
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Michael Möllmann
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Tanja Zhou
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Areya Tabatabai
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Tim Lohmann
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Maximilian Jauch
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Filippo Beleggia
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Benedikt Pelzer
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY
| | - Fabian Ullrich
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Svenja Höfmann
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Aastha Arora
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Thorsten Persigehl
- Department of Radiology and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Bastian von Tresckow
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sebastian Klein
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ron D. Jachimowicz
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Gero Knittel
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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25
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Ip JY, Wijaya I, Lee LT, Lim Y, Teoh DEJ, Chan CSC, Cui L, Begley TJ, Dedon PC, Guo H. ROS-induced translational regulation-through spatiotemporal differences in codon recognition-is a key driver of brown adipogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.22.572954. [PMID: 38463965 PMCID: PMC10925207 DOI: 10.1101/2023.12.22.572954] [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
The role of translational regulation in brown adipogenesis is relatively unknown. Localized translation of mRNAs encoding mitochondrial components enables swift mitochondrial responses, but whether this occurs during brown adipogenesis, which involves massive mitochondrial biogenesis, has not been explored. Here, we used ribosome profiling and RNA-Seq, coupled with cellular fractionation, to obtain spatiotemporal insights into translational regulation. During brown adipogenesis, a translation bias towards G/C-ending codons is triggered first in the mitochondrial vicinity by reactive oxygen species (ROS), which later spreads to the rest of the cell. This translation bias is induced through ROS modulating the activity of the tRNA modification enzyme, ELP3. Intriguingly, functionally relevant mRNAs, including those encoding ROS scavengers, benefit from this bias; in so doing, ROS-induced translation bias both fuels differentiation and concurrently minimizes oxidative damage. These ROS-induced changes could enable sustained mitochondrial biogenesis during brown adipogenesis, and explain in part, the molecular basis for ROS hormesis.
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26
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Plessner M, Thiele L, Hofhuis J, Thoms S. Tissue-specific roles of peroxisomes revealed by expression meta-analysis. Biol Direct 2024; 19:14. [PMID: 38365851 PMCID: PMC10873952 DOI: 10.1186/s13062-024-00458-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
Peroxisomes are primarily studied in the brain, kidney, and liver due to the conspicuous tissue-specific pathology of peroxisomal biogenesis disorders. In contrast, little is known about the role of peroxisomes in other tissues such as the heart. In this meta-analysis, we explore mitochondrial and peroxisomal gene expression on RNA and protein levels in the brain, heart, kidney, and liver, focusing on lipid metabolism. Further, we evaluate a potential developmental and heart region-dependent specificity of our gene set. We find marginal expression of the enzymes for peroxisomal fatty acid oxidation in cardiac tissue in comparison to the liver or cardiac mitochondrial β-oxidation. However, the expression of peroxisome biogenesis proteins in the heart is similar to other tissues despite low levels of peroxisomal fatty acid oxidation. Strikingly, peroxisomal targeting signal type 2-containing factors and plasmalogen biosynthesis appear to play a fundamental role in explaining the essential protective and supporting functions of cardiac peroxisomes.
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Affiliation(s)
- Matthias Plessner
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Leonie Thiele
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Julia Hofhuis
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Sven Thoms
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany.
- Department of Child and Adolescent Health, University Medical Center, Göttingen, Germany.
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27
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Wagstyl K, Adler S, Seidlitz J, Vandekar S, Mallard TT, Dear R, DeCasien AR, Satterthwaite TD, Liu S, Vértes PE, Shinohara RT, Alexander-Bloch A, Geschwind DH, Raznahan A. Transcriptional cartography integrates multiscale biology of the human cortex. eLife 2024; 12:RP86933. [PMID: 38324465 PMCID: PMC10945526 DOI: 10.7554/elife.86933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
Abstract
The cerebral cortex underlies many of our unique strengths and vulnerabilities, but efforts to understand human cortical organization are challenged by reliance on incompatible measurement methods at different spatial scales. Macroscale features such as cortical folding and functional activation are accessed through spatially dense neuroimaging maps, whereas microscale cellular and molecular features are typically measured with sparse postmortem sampling. Here, we integrate these distinct windows on brain organization by building upon existing postmortem data to impute, validate, and analyze a library of spatially dense neuroimaging-like maps of human cortical gene expression. These maps allow spatially unbiased discovery of cortical zones with extreme transcriptional profiles or unusually rapid transcriptional change which index distinct microstructure and predict neuroimaging measures of cortical folding and functional activation. Modules of spatially coexpressed genes define a family of canonical expression maps that integrate diverse spatial scales and temporal epochs of human brain organization - ranging from protein-protein interactions to large-scale systems for cognitive processing. These module maps also parse neuropsychiatric risk genes into subsets which tag distinct cyto-laminar features and differentially predict the location of altered cortical anatomy and gene expression in patients. Taken together, the methods, resources, and findings described here advance our understanding of human cortical organization and offer flexible bridges to connect scientific fields operating at different spatial scales of human brain research.
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Affiliation(s)
- Konrad Wagstyl
- Wellcome Centre for Human Neuroimaging, University College LondonLondonUnited Kingdom
| | - Sophie Adler
- UCL Great Ormond Street Institute for Child HealthHolbornUnited Kingdom
| | - Jakob Seidlitz
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Simon Vandekar
- Department of Biostatistics, Vanderbilt UniversityNashvilleUnited States
| | - Travis T Mallard
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Psychiatry, Harvard Medical SchoolBostonUnited States
| | - Richard Dear
- Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Alex R DeCasien
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
| | - Theodore D Satterthwaite
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Lifespan Informatics and Neuroimaging Center, University of Pennsylvania School of MedicinePhiladelphiaUnited States
| | - Siyuan Liu
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
| | - Petra E Vértes
- Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Aaron Alexander-Bloch
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Daniel H Geschwind
- Center for Autism Research and Treatment, Semel Institute, Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Armin Raznahan
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
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28
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Matveev EV, Ponomarev GV, Kazanov MD. Genome-wide bioinformatics analysis of human protease capacity for proteolytic cleavage of the SARS-CoV-2 spike glycoprotein. Microbiol Spectr 2024; 12:e0353023. [PMID: 38189333 PMCID: PMC10846095 DOI: 10.1128/spectrum.03530-23] [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: 10/03/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) primarily enters the cell by binding the virus's spike (S) glycoprotein to the angiotensin-converting enzyme 2 receptor on the cell surface, followed by proteolytic cleavage by host proteases. Studies have identified furin and transmembrane protease serine 2 proteases in priming and triggering cleavages of the S glycoprotein, converting it into a fusion-competent form and initiating membrane fusion, respectively. Alternatively, SARS-CoV-2 can enter the cell through the endocytic pathway, where activation is triggered by lysosomal cathepsin L. However, other proteases are also suspected to be involved in both entry routes. In this study, we conducted a genome-wide bioinformatics analysis to explore the capacity of human proteases in hydrolyzing peptide bonds of the S glycoprotein. Predictive models of sequence specificity for 169 human proteases were constructed and applied to the S glycoprotein together with the method for predicting structural susceptibility to proteolysis of protein regions. After validating our approach on extensively studied S2' and S1/S2 cleavage sites, we applied our method to each peptide bond of the S glycoprotein across all 169 proteases. Our results indicate that various members of the proprotein convertase subtilisin/kexin type, type II transmembrane family serine protease, and kallikrein families, as well as specific coagulation factors, are capable of cleaving S2' or S1/S2 sites. We have also identified a potential cleavage site of cathepsin L at the K790 position within the S2' loop. Structural analysis suggests that cleavage of this site induces conformational changes similar to the cleavage at the R815 (S2') position, leading to the exposure of the fusion peptide and subsequent fusion with the membrane. Other potential cleavage sites and the influence of mutations in common SARS-CoV-2 variants on proteolytic efficiency are discussed.IMPORTANCEThe entry of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) into the cell, activated by host proteases, is considerably more complex in coronaviruses than in most other viruses and is not fully understood. There is evidence that other proteases beyond the known furin and transmembrane protease serine 2 can activate the spike protein. Another example of uncertainty is the cleavage site for the alternative endocytic route of SARS-CoV-2 entrance, which is still unknown. Bioinformatics methods, modeling protease specificity and estimating the structural susceptibility of protein regions to proteolysis, can aid in studying this topic by predicting the involved proteases and their cleavage sites, thereby substantially reducing the amount of experimental work. Elucidating the mechanisms of spike protein activation is crucial for preventing possible future coronavirus pandemics and developing antiviral drugs.
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Affiliation(s)
- Evgenii V. Matveev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Research and Training Center on Bioinformatics, A.A.Kharkevich Institute for Information Transmission Problems, Moscow, Russia
- Laboratory of Cytogenetics and Molecular Genetics, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Gennady V. Ponomarev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Research and Training Center on Bioinformatics, A.A.Kharkevich Institute for Information Transmission Problems, Moscow, Russia
| | - Marat D. Kazanov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Research and Training Center on Bioinformatics, A.A.Kharkevich Institute for Information Transmission Problems, Moscow, Russia
- Laboratory of Cytogenetics and Molecular Genetics, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
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29
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Ualiyeva S, Lemire E, Wong C, Perniss A, Boyd A, Avilés EC, Minichetti DG, Maxfield A, Roditi R, Matsumoto I, Wang X, Deng W, Barrett NA, Buchheit KM, Laidlaw TM, Boyce JA, Bankova LG, Haber AL. A nasal cell atlas reveals heterogeneity of tuft cells and their role in directing olfactory stem cell proliferation. Sci Immunol 2024; 9:eabq4341. [PMID: 38306414 PMCID: PMC11127180 DOI: 10.1126/sciimmunol.abq4341] [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: 04/07/2022] [Accepted: 12/08/2023] [Indexed: 02/04/2024]
Abstract
The olfactory neuroepithelium serves as a sensory organ for odors and forms part of the nasal mucosal barrier. Olfactory sensory neurons are surrounded and supported by epithelial cells. Among them, microvillous cells (MVCs) are strategically positioned at the apical surface, but their specific functions are enigmatic, and their relationship to the other specialized epithelial cells is unclear. Here, we establish that the family of MVCs comprises tuft cells and ionocytes in both mice and humans. Integrating analysis of the respiratory and olfactory epithelia, we define the distinct receptor expression of TRPM5+ tuft-MVCs compared with Gɑ-gustducinhigh respiratory tuft cells and characterize a previously undescribed population of glandular DCLK1+ tuft cells. To establish how allergen sensing by tuft-MVCs might direct olfactory mucosal responses, we used an integrated single-cell transcriptional and protein analysis. Inhalation of Alternaria induced mucosal epithelial effector molecules including Chil4 and a distinct pathway leading to proliferation of the quiescent olfactory horizontal basal stem cell (HBC) pool, both triggered in the absence of olfactory apoptosis. Alternaria- and ATP-elicited HBC proliferation was dependent on TRPM5+ tuft-MVCs, identifying these specialized epithelial cells as regulators of olfactory stem cell responses. Together, our data provide high-resolution characterization of nasal tuft cell heterogeneity and identify a function of TRPM5+ tuft-MVCs in directing the olfactory mucosal response to allergens.
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Affiliation(s)
- Saltanat Ualiyeva
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Evan Lemire
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Caitlin Wong
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Alexander Perniss
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Amelia Boyd
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Evelyn C. Avilés
- Department of Neurobiology, Harvard Medical School, Boston, MA; currently at Faculty of Biological Sciences, Pontificia Universidad Católica de Chile
| | - Dante G. Minichetti
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Alice Maxfield
- Division of Otolaryngology-Head and Neck Surgery, Brigham and Women’s Hospital and Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA
| | - Rachel Roditi
- Division of Otolaryngology-Head and Neck Surgery, Brigham and Women’s Hospital and Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA
| | | | - Xin Wang
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Wenjiang Deng
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Nora A. Barrett
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Kathleen M. Buchheit
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Tanya M. Laidlaw
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Joshua A. Boyce
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Lora G. Bankova
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Adam L. Haber
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA
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30
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Janeckova L, Knotek T, Kriska J, Hermanova Z, Kirdajova D, Kubovciak J, Berkova L, Tureckova J, Camacho Garcia S, Galuskova K, Kolar M, Anderova M, Korinek V. Astrocyte-like subpopulation of NG2 glia in the adult mouse cortex exhibits characteristics of neural progenitor cells. Glia 2024; 72:245-273. [PMID: 37772368 DOI: 10.1002/glia.24471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023]
Abstract
Glial cells expressing neuron-glial antigen 2 (NG2), also known as oligodendrocyte progenitor cells (OPCs), play a critical role in maintaining brain health. However, their ability to differentiate after ischemic injury is poorly understood. The aim of this study was to investigate the properties and functions of NG2 glia in the ischemic brain. Using transgenic mice, we selectively labeled NG2-expressing cells and their progeny in both healthy brain and after focal cerebral ischemia (FCI). Using single-cell RNA sequencing, we classified the labeled glial cells into five distinct subpopulations based on their gene expression patterns. Additionally, we examined the membrane properties of these cells using the patch-clamp technique. Of the identified subpopulations, three were identified as OPCs, whereas the fourth subpopulation had characteristics indicative of cells likely to develop into oligodendrocytes. The fifth subpopulation of NG2 glia showed astrocytic markers and had similarities to neural progenitor cells. Interestingly, this subpopulation was present in both healthy and post-ischemic tissue; however, its gene expression profile changed after ischemia, with increased numbers of genes related to neurogenesis. Immunohistochemical analysis confirmed the temporal expression of neurogenic genes and showed an increased presence of NG2 cells positive for Purkinje cell protein-4 at the periphery of the ischemic lesion 12 days after FCI, as well as NeuN-positive NG2 cells 28 and 60 days after injury. These results suggest the potential development of neuron-like cells arising from NG2 glia in the ischemic tissue. Our study provides insights into the plasticity of NG2 glia and their capacity for neurogenesis after stroke.
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Affiliation(s)
- Lucie Janeckova
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomas Knotek
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Kriska
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zuzana Hermanova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Denisa Kirdajova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Kubovciak
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Linda Berkova
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Tureckova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Sara Camacho Garcia
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Katerina Galuskova
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Kolar
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Miroslava Anderova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vladimir Korinek
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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31
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Mejia-Garcia A, Bonilla DA, Ramirez CM, Escobar-Díaz FA, Combita AL, Forero DA, Orozco C. Genes and Pathways Involved in the Progression of Malignant Pleural Mesothelioma: A Meta-analysis of Genome-Wide Expression Studies. Biochem Genet 2024; 62:352-370. [PMID: 37347449 DOI: 10.1007/s10528-023-10426-5] [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: 12/01/2022] [Accepted: 06/07/2023] [Indexed: 06/23/2023]
Abstract
Malignant pleural mesothelioma (MPM) is a rare and aggressive neoplasm of the pleural tissue that lines the lungs and is mainly associated with long latency from asbestos exposure. This tumor has no effective therapeutic opportunities nowadays and has a very low five-year survival rate. In this sense, identifying molecular events that trigger the development and progression of this tumor is highly important to establish new and potentially effective treatments. We conducted a meta-analysis of genome-wide expression studies publicly available at the Gene Expression Omnibus (GEO) and ArrayExpress databases. The differentially expressed genes (DEGs) were identified, and we performed functional enrichment analysis and protein-protein interaction networks (PPINs) to gain insight into the biological mechanisms underlying these genes. Additionally, we constructed survival prediction models for selected DEGs and predicted the minimum drug inhibition concentration of anticancer drugs for MPM. In total, 115 MPM tumor transcriptomes and 26 pleural tissue controls were analyzed. We identified 1046 upregulated DEGs in the MPM samples. Cellular signaling categories in tumor samples were associated with the TNF, PI3K-Akt, and AMPK pathways. The inflammatory response, regulation of cell migration, and regulation of angiogenesis were overrepresented biological processes. Expression of SOX17 and TACC1 were associated with reduced survival rates. This meta-analysis identified a list of DEGs in MPM tumors, cancer-related signaling pathways, and biological processes that were overrepresented in MPM samples. Some therapeutic targets to treat MPM are suggested, and the prognostic potential of key genes is shown.
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Affiliation(s)
- Alejandro Mejia-Garcia
- Molecular Genetics Research Group (GENMOL), Universidad de Antioquia, Medellín, Colombia
| | - Diego A Bonilla
- Research Division, Dynamical Business & Science Society - DBSS International SAS, Bogotá, Colombia
- Research Group in Physical Activity, Sports and Health Sciences (GICAFS), Universidad de Córdoba, Montería, Colombia
- Sport Genomics Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - Claudia M Ramirez
- Health and Sport Sciences Research Group, School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Fabio A Escobar-Díaz
- Public Health and Epidemiology Research Group, School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Alba Lucia Combita
- Cancer Biology Research Group, Instituto Nacional de Cancerología, Bogotá, Colombia
- Department of Microbiology, School of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Diego A Forero
- Health and Sport Sciences Research Group, School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
- Professional Program in Respiratory Therapy, School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Carlos Orozco
- Health and Sport Sciences Research Group, School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia.
- Professional Program in Surgical Instrumentation, Professional Program in Optometry and Technical Program in Radiology and Diagnostic Imaging, School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia.
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Tu KJ, Roy SK, Keepers Z, Gartia MR, Shukla HD, Biswal NC. Docetaxel radiosensitizes castration-resistant prostate cancer by downregulating CAV-1. Int J Radiat Biol 2024; 100:256-267. [PMID: 37747697 DOI: 10.1080/09553002.2023.2263553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Abstract
PURPOSE Docetaxel (DXL), a noted radiosensitizer, is one of the few chemotherapy drugs approved for castration-resistant prostate cancer (CRPC), though only a fraction of CRPCs respond to it. CAV-1, a critical regulator of radioresistance, has been known to modulate DXL and radiation effects. Combining DXL with radiotherapy may create a synergistic anticancer effect through CAV-1 and improve CRPC patients' response to therapy. Here, we investigate the effectiveness and molecular characteristics of DXL and radiation combination therapy in vitro. MATERIALS AND METHODS We used live/dead assays to determine the IC50 of DXL for PC3, DU-145, and TRAMP-C1 cells. Colony formation assay was used to determine the radioresponse of the same cells treated with radiation with/without IC50 DXL (4, 8, and 12 Gy). We performed gene expression analysis on public transcriptomic data collected from human-derived prostate cancer cell lines (C4-2, PC3, DU-145, and LNCaP) treated with DXL for 8, 16, and 72 hours. Cell cycle arrest and protein expression were assessed using flow cytometry and western blot, respectively. RESULTS Compared to radiation alone, combination therapy with DXL significantly increased CRPC death in PC3 (1.48-fold, p < .0001), DU-145 (1.64-fold, p < .05), and TRAMP-C1 (1.13-fold, p < .05) at 4 Gy of radiation. Gene expression of CRPC treated with DXL revealed downregulated genes related to cell cycle regulation and upregulated genes related to immune activation and oxidative stress. Confirming the results, G2/M cell cycle arrest was significantly increased after treatment with DXL and radiation. CAV-1 protein expression was decreased after DXL treatment in a dose-dependent manner; furthermore, CAV-1 copy number was strongly associated with poor response to therapy in CRPC patients. CONCLUSIONS Our results suggest that DXL sensitizes CRPC cells to radiation by downregulating CAV-1. DXL + radiation combination therapy may be effective at treating CRPC, especially subtypes associated with high CAV-1 expression, and should be studied further.
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Affiliation(s)
- Kevin J Tu
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Sanjit K Roy
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Zachery Keepers
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Manas R Gartia
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Hem D Shukla
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nrusingh C Biswal
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
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Ye C, Wu Q, Chen S, Zhang X, Xu W, Wu Y, Zhang Y, Yue Y. ECDEP: identifying essential proteins based on evolutionary community discovery and subcellular localization. BMC Genomics 2024; 25:117. [PMID: 38279081 PMCID: PMC10821549 DOI: 10.1186/s12864-024-10019-5] [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: 12/07/2023] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND In cellular activities, essential proteins play a vital role and are instrumental in comprehending fundamental biological necessities and identifying pathogenic genes. Current deep learning approaches for predicting essential proteins underutilize the potential of gene expression data and are inadequate for the exploration of dynamic networks with limited evaluation across diverse species. RESULTS We introduce ECDEP, an essential protein identification model based on evolutionary community discovery. ECDEP integrates temporal gene expression data with a protein-protein interaction (PPI) network and employs the 3-Sigma rule to eliminate outliers at each time point, constructing a dynamic network. Next, we utilize edge birth and death information to establish an interaction streaming source to feed into the evolutionary community discovery algorithm and then identify overlapping communities during the evolution of the dynamic network. SVM recursive feature elimination (RFE) is applied to extract the most informative communities, which are combined with subcellular localization data for classification predictions. We assess the performance of ECDEP by comparing it against ten centrality methods, four shallow machine learning methods with RFE, and two deep learning methods that incorporate multiple biological data sources on Saccharomyces. Cerevisiae (S. cerevisiae), Homo sapiens (H. sapiens), Mus musculus, and Caenorhabditis elegans. ECDEP achieves an AP value of 0.86 on the H. sapiens dataset and the contribution ratio of community features in classification reaches 0.54 on the S. cerevisiae (Krogan) dataset. CONCLUSIONS Our proposed method adeptly integrates network dynamics and yields outstanding results across various datasets. Furthermore, the incorporation of evolutionary community discovery algorithms amplifies the capacity of gene expression data in classification.
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Affiliation(s)
- Chen Ye
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China
| | - Qi Wu
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China
| | - Shuxia Chen
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China
| | - Xuemei Zhang
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China
| | - Wenwen Xu
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China
| | - Yunzhi Wu
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China
| | - Youhua Zhang
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China
| | - Yi Yue
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China.
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China.
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Wardman JH, Andreassen SN, Toft-Bertelsen TL, Jensen MN, Wilhjelm JE, Styrishave B, Hamann S, Heegaard S, Sinclair AJ, MacAulay N. CSF hyperdynamics in rats mimicking the obesity and androgen excess characteristic of patients with idiopathic intracranial hypertension. Fluids Barriers CNS 2024; 21:10. [PMID: 38273331 PMCID: PMC10810013 DOI: 10.1186/s12987-024-00511-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Idiopathic intracranial hypertension (IIH) is a syndrome exhibiting elevated intracranial pressure (ICP), visual disturbances, and severe headache. IIH primarily affects young obese women, though it can occur in individuals of any age, BMI, and sex. IIH is characterized by systemic metabolic dysregulation with a profile of increased androgen hormones. However, the contribution of obesity/hormonal perturbations to cerebrospinal fluid (CSF) dynamics remains unresolved. METHODS We employed obese female Zucker rats and adjuvant testosterone to reveal IIH causal drivers. ICP and CSF dynamics were determined with in vivo experimentation and magnetic resonance imaging, testosterone levels assessed with mass spectrometry, and choroid plexus function revealed with transcriptomics. RESULTS Obese rats had undisturbed CSF testosterone levels and no changes in ICP or CSF dynamics. Adjuvant testosterone treatment of obese rats elevated the CSF secretion rate, although with no effect on the ICP, due to elevated CSF drainage capacity of these rats. CONCLUSIONS Obesity in itself therefore does not suffice to recapitulate the IIH symptoms in rats, but modulation of CSF dynamics appears with adjuvant testosterone treatment, which mimics the androgen excess observed in female IIH patients. Obesity-induced androgen dysregulation may thus contribute to the disease mechanism of IIH and could potentially serve as a future therapeutic target.
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Affiliation(s)
- Jonathan H Wardman
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, Copenhagen, DK-2200, Denmark
| | - Søren Norge Andreassen
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, Copenhagen, DK-2200, Denmark
| | - Trine L Toft-Bertelsen
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, Copenhagen, DK-2200, Denmark
| | - Mette Nyholm Jensen
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, Copenhagen, DK-2200, Denmark
| | - Jens E Wilhjelm
- Department of Neurophysiology, Rigshospitalet, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Bjarne Styrishave
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Steffen Hamann
- Department of Ophthalmology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Steffen Heegaard
- Department of Ophthalmology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra J Sinclair
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nanna MacAulay
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, Copenhagen, DK-2200, Denmark.
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Koller A, Filosi M, Weissensteiner H, Fazzini F, Gorski M, Pattaro C, Schönherr S, Forer L, Herold JM, Stark KJ, Döttelmayer P, Hicks AA, Pramstaller PP, Würzner R, Eckardt KU, Heid IM, Fuchsberger C, Lamina C, Kronenberg F. Nuclear and mitochondrial genetic variants associated with mitochondrial DNA copy number. Sci Rep 2024; 14:2083. [PMID: 38267512 PMCID: PMC10808213 DOI: 10.1038/s41598-024-52373-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/17/2024] [Indexed: 01/26/2024] Open
Abstract
Mitochondrial DNA copy number (mtDNA-CN) is a biomarker for mitochondrial dysfunction associated with several diseases. Previous genome-wide association studies (GWAS) have been performed to unravel underlying mechanisms of mtDNA-CN regulation. However, the identified gene regions explain only a small fraction of mtDNA-CN variability. Most of this data has been estimated from microarrays based on various pipelines. In the present study we aimed to (1) identify genetic loci for qPCR-measured mtDNA-CN from three studies (16,130 participants) using GWAS, (2) identify potential systematic differences between our qPCR derived mtDNA-CN measurements compared to the published microarray intensity-based estimates, and (3) disentangle the nuclear from mitochondrial regulation of the mtDNA-CN phenotype. We identified two genome-wide significant autosomal loci associated with qPCR-measured mtDNA-CN: at HBS1L (rs4895440, p = 3.39 × 10-13) and GSDMA (rs56030650, p = 4.85 × 10-08) genes. Moreover, 113/115 of the previously published SNPs identified by microarray-based analyses were significantly equivalent with our findings. In our study, the mitochondrial genome itself contributed only marginally to mtDNA-CN regulation as we only detected a single rare mitochondrial variant associated with mtDNA-CN. Furthermore, we incorporated mitochondrial haplogroups into our analyses to explore their potential impact on mtDNA-CN. However, our findings indicate that they do not exert any significant influence on our results.
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Affiliation(s)
- Adriana Koller
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria
| | - Michele Filosi
- Eurac Research, Institute for Biomedicine, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria
| | - Federica Fazzini
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria
| | - Mathias Gorski
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Cristian Pattaro
- Eurac Research, Institute for Biomedicine, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria
| | - Janina M Herold
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Klaus J Stark
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Patricia Döttelmayer
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria
| | - Andrew A Hicks
- Eurac Research, Institute for Biomedicine, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Peter P Pramstaller
- Eurac Research, Institute for Biomedicine, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Reinhard Würzner
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- German Chronic Kidney Disease Study, Erlangen, Germany
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Christian Fuchsberger
- Eurac Research, Institute for Biomedicine, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Claudia Lamina
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020, Innsbruck, Austria.
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Tarallo D, Martínez J, Leyva A, Mónaco A, Perroni C, Tassano M, Gambini JP, Cappetta M, Durán R, Moreno M, Quijano C. Mitofusin 1 silencing decreases the senescent associated secretory phenotype, promotes immune cell recruitment and delays melanoma tumor growth after chemotherapy. Sci Rep 2024; 14:909. [PMID: 38195762 PMCID: PMC10776601 DOI: 10.1038/s41598-024-51427-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024] Open
Abstract
Cellular senescence is a therapy endpoint in melanoma, and the senescence-associated secretory phenotype (SASP) can affect tumor growth and microenvironment, influencing treatment outcomes. Metabolic interventions can modulate the SASP, and mitochondrial energy metabolism supports resistance to therapy in melanoma. In a previous report we showed that senescence, induced by the DNA methylating agent temozolomide, increased the level of fusion proteins mitofusin 1 and 2 in melanoma, and silencing Mfn1 or Mfn2 expression reduced interleukin-6 secretion by senescent cells. Here we expanded these observations evaluating the secretome of senescent melanoma cells using shotgun proteomics, and explored the impact of silencing Mfn1 on the SASP. A significant increase in proteins reported to reduce the immune response towards the tumor was found in the media of senescent cells. The secretion of several of these immunomodulatory proteins was affected by Mfn1 silencing, among them was galectin-9. In agreement, tumors lacking mitofusin 1 responded better to treatment with the methylating agent dacarbazine, tumor size was reduced and a higher immune cell infiltration was detected in the tumor. Our results highlight mitochondrial dynamic proteins as potential pharmacological targets to modulate the SASP in the context of melanoma treatment.
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Affiliation(s)
- Doménica Tarallo
- Departamento de Bioquímica, Facultad de Medicina, and Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Jennyfer Martínez
- Departamento de Bioquímica, Facultad de Medicina, and Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Alejandro Leyva
- Institut Pasteur de Montevideo and Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Amy Mónaco
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Carolina Perroni
- Area Radiofarmacia, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Marcos Tassano
- Area Radiofarmacia, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Juan Pablo Gambini
- Centro Uruguayo de Imagenología Molecular (CUDIM) and Centro de Medicina Nuclear (CMN), Hospital de Clínicas Dr. Manuel Quintela, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Mónica Cappetta
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rosario Durán
- Institut Pasteur de Montevideo and Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - María Moreno
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
| | - Celia Quijano
- Departamento de Bioquímica, Facultad de Medicina, and Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay.
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Weiner AK, Radaoui AB, Tsang M, Martinez D, Sidoli S, Conkrite KL, Delaidelli A, Modi A, Rokita JL, Patel K, Lane MV, Zhang B, Zhong C, Ennis B, Miller DP, Brown MA, Rathi KS, Raman P, Pogoriler J, Bhatti T, Pawel B, Glisovic-Aplenc T, Teicher B, Erickson SW, Earley EJ, Bosse KR, Sorensen PH, Krytska K, Mosse YP, Havenith KE, Zammarchi F, van Berkel PH, Smith MA, Garcia BA, Maris JM, Diskin SJ. A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.06.570390. [PMID: 38106022 PMCID: PMC10723418 DOI: 10.1101/2023.12.06.570390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Cancer immunotherapies have produced remarkable results in B-cell malignancies; however, optimal cell surface targets for many solid cancers remain elusive. Here, we present an integrative proteomic, transcriptomic, and epigenomic analysis of tumor specimens along with normal tissues to identify biologically relevant cell surface proteins that can serve as immunotherapeutic targets for neuroblastoma, an often-fatal childhood cancer of the developing nervous system. We apply this approach to human-derived cell lines (N=9) and cell/patient-derived xenograft (N=12) models of neuroblastoma. Plasma membrane-enriched mass spectrometry identified 1,461 cell surface proteins in cell lines and 1,401 in xenograft models, respectively. Additional proteogenomic analyses revealed 60 high-confidence candidate immunotherapeutic targets and we prioritized Delta-like canonical notch ligand 1 (DLK1) for further study. High expression of DLK1 directly correlated with the presence of a super-enhancer spanning the DLK1 locus. Robust cell surface expression of DLK1 was validated by immunofluorescence, flow cytometry, and immunohistochemistry. Short hairpin RNA mediated silencing of DLK1 in neuroblastoma cells resulted in increased cellular differentiation. ADCT-701, a DLK1-targeting antibody-drug conjugate (ADC), showed potent and specific cytotoxicity in DLK1-expressing neuroblastoma xenograft models. Moreover, DLK1 is highly expressed in several adult cancer types, including adrenocortical carcinoma (ACC), pheochromocytoma/paraganglioma (PCPG), hepatoblastoma, and small cell lung cancer (SCLC), suggesting potential clinical benefit beyond neuroblastoma. Taken together, our study demonstrates the utility of comprehensive cancer surfaceome characterization and credentials DLK1 as an immunotherapeutic target. Highlights Plasma membrane enriched proteomics defines surfaceome of neuroblastomaMulti-omic data integration prioritizes DLK1 as a candidate immunotherapeutic target in neuroblastoma and other cancersDLK1 expression is driven by a super-enhancer DLK1 silencing in neuroblastoma cells results in cellular differentiation ADCT-701, a DLK1-targeting antibody-drug conjugate, shows potent and specific cytotoxicity in DLK1-expressing neuroblastoma preclinical models.
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Shaw TI, Wagner J, Tian L, Wickman E, Poudel S, Wang J, Paul R, Koo SC, Lu M, Sheppard H, Fan Y, O’Neil F, Lau CC, Zhou X, Zhang J, Gottschalk S. Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression. RESEARCH SQUARE 2024:rs.3.rs-3821632. [PMID: 38260279 PMCID: PMC10802740 DOI: 10.21203/rs.3.rs-3821632/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: 01/24/2024]
Abstract
Immunotherapy with CAR T cells for pediatric solid and brain tumors is constrained by available targetable antigens. Cancer-specific exons (CSE) present a promising reservoir of targets; however, these have not been explored and validated systematically in a pan-cancer fashion. To identify CSE targets, we analyzed 1,532 RNA-seq datasets from 16 types of pediatric solid and brain tumors for comparison with normal tissues using a newly developed workflow. We found 2,933 exons in 157 genes encoding proteins of the surfaceome or matrisome with high cancer specificity either at the gene (n=148) or the alternatively spliced (AS) isoform (n=9) level. Expression of selected AS targets, including the EDB domain of FN1 (EDB), and gene targets, such as COL11A1, were validated in pediatric PDX tumors. We generated CAR T cells specific to EDB or COL11A1 and demonstrated that COL11A1-CAR T-cells have potent antitumor activity. The full target list, explorable via an interactive web portal (https://cseminer.stjude.org/), provides a rich resource for developing immunotherapy of pediatric solid and brain tumors using gene or AS targets with high expression specificity in cancer.
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Affiliation(s)
- Timothy I Shaw
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jessica Wagner
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Elizabeth Wickman
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Suresh Poudel
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jian Wang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robin Paul
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Selene C. Koo
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Meifen Lu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Heather Sheppard
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Francis O’Neil
- The Jackson Laboratory Cancer Center, Farmington, CT, USA
| | - Ching C. Lau
- The Jackson Laboratory Cancer Center, Farmington, CT, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Schmok JC, Jain M, Street LA, Tankka AT, Schafer D, Her HL, Elmsaouri S, Gosztyla ML, Boyle EA, Jagannatha P, Luo EC, Kwon EJ, Jovanovic M, Yeo GW. Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. Nat Biotechnol 2024:10.1038/s41587-023-02014-0. [PMID: 38168984 DOI: 10.1038/s41587-023-02014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/29/2023] [Indexed: 01/05/2024]
Abstract
RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we developed tethered function luciferase-based splicing reporters that provide rapid, scalable and robust readouts of exon inclusion changes and used these to evaluate 718 human RBPs. We performed enhanced cross-linking immunoprecipitation, RNA sequencing and affinity purification-mass spectrometry to investigate a subset of candidates with no prior association with splicing. Integrative analysis of these assays indicates surprising roles for TRNAU1AP, SCAF8 and RTCA in the modulation of hundreds of endogenous splicing events. We also leveraged our tethering assays and top candidates to identify potent and compact exon inclusion activation domains for splicing modulation applications. Using these identified domains, we engineered programmable fusion proteins that outperform current artificial splicing factors at manipulating inclusion of reporter and endogenous exons. This tethering approach characterizes the ability of RBPs to induce exon inclusion and yields new molecular parts for programmable splicing control.
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Affiliation(s)
- Jonathan C Schmok
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Manya Jain
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lena A Street
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Alex T Tankka
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Danielle Schafer
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hsuan-Lin Her
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sara Elmsaouri
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Maya L Gosztyla
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Evan A Boyle
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Pratibha Jagannatha
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - En-Ching Luo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ester J Kwon
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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40
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Zhang BC, Ma SY, Zhu P, Zhu LY, Zhao XX, Pu C. LINC00665 target let-7i/HMGA1 promotes the proliferation and invasion of hepatoma cells. Mutat Res 2024; 828:111852. [PMID: 38368811 DOI: 10.1016/j.mrfmmm.2024.111852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 02/04/2024] [Indexed: 02/20/2024]
Abstract
OBJECTIVES Our group previously found that LINC00665 was upregulated in hepatocellular carcinoma (HCC) tissues through database analysis; however, the potential molecular mechanism of LINC00665 in HCC progression still needs further study. METHODS qRTPCR was performed to determine the differential expression of LINC00665 and let-7i in HCC cells. Dual-luciferase reporter assays were performed to analyze the interaction of LINC00665 and let-7i. CCK-8 assays, scratch assays, Transwell invasion assays, qRTPCR and western blotting were performed to determine the regulatory mechanism of LINC00665/let-7i/HMGA1 in HCC cells. RESULTS LINC00665 was upregulated in HCC cells compared with normal hepatocytes. A potential binding site between LINC00665 and let-7i was confirmed by dual-luciferase reporter assay. In HCC cells, inhibition of LINC00665 significantly reduced cell proliferation, migration and invasion ability via the let-7i/HMGA1 signaling axis. CONCLUSION LINC00665 promotes the proliferation and invasion of HCC cells via the let-7i/HMGA1 signaling axis.
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Affiliation(s)
- Bo-Chao Zhang
- Clinical Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China; Clinical Laboratory, Anhui Province Suixi County Hospital, Huaibei 235100, Anhui, China
| | - Si-Yuan Ma
- Clinical Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China.
| | - Ping Zhu
- Clinical Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
| | - Liang-Yu Zhu
- Clinical Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
| | - Xiao-Xiao Zhao
- Clinical Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
| | - Chun Pu
- Clinical Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
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41
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Villanueva E, Smith T, Pizzinga M, Elzek M, Queiroz RML, Harvey RF, Breckels LM, Crook OM, Monti M, Dezi V, Willis AE, Lilley KS. System-wide analysis of RNA and protein subcellular localization dynamics. Nat Methods 2024; 21:60-71. [PMID: 38036857 PMCID: PMC10776395 DOI: 10.1038/s41592-023-02101-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023]
Abstract
Although the subcellular dynamics of RNA and proteins are key determinants of cell homeostasis, their characterization is still challenging. Here we present an integrative framework to simultaneously interrogate the dynamics of the transcriptome and proteome at subcellular resolution by combining two methods: localization of RNA (LoRNA) and a streamlined density-based localization of proteins by isotope tagging (dLOPIT) to map RNA and protein to organelles (nucleus, endoplasmic reticulum and mitochondria) and membraneless compartments (cytosol, nucleolus and cytosolic granules). Interrogating all RNA subcellular locations at once enables system-wide quantification of the proportional distribution of RNA. We obtain a cell-wide overview of localization dynamics for 31,839 transcripts and 5,314 proteins during the unfolded protein response, revealing that endoplasmic reticulum-localized transcripts are more efficiently recruited to cytosolic granules than cytosolic RNAs, and that the translation initiation factor eIF3d is key to sustaining cytoskeletal function. Overall, we provide the most comprehensive overview so far of RNA and protein subcellular localization dynamics.
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Affiliation(s)
- Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom Smith
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Mariavittoria Pizzinga
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
- Structural Biology Research Centre, Human Technopole, Milan, Italy
| | - Mohamed Elzek
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Rayner M L Queiroz
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Oliver M Crook
- Department of Statistics, University of Oxford, Oxford, UK
| | - Mie Monti
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Veronica Dezi
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK.
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
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42
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Zhu WS, Litterman AJ, Sekhon HS, Kageyama R, Arce MM, Taylor KE, Zhao W, Criswell LA, Zaitlen N, Erle DJ, Ansel KM. GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins. Genome Biol 2023; 24:281. [PMID: 38062486 PMCID: PMC10701951 DOI: 10.1186/s13059-023-03125-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
GCLiPP is a global RNA interactome capture method that detects RNA-binding protein (RBP) occupancy transcriptome-wide. GCLiPP maps RBP-occupied sites at a higher resolution than phase separation-based techniques. GCLiPP sequence tags correspond with known RBP binding sites and are enriched for sites detected by RBP-specific crosslinking immunoprecipitation (CLIP) for abundant cytosolic RBPs. Comparison of human Jurkat T cells and mouse primary T cells uncovers shared peaks of GCLiPP signal across homologous regions of human and mouse 3' UTRs, including a conserved mRNA-destabilizing cis-regulatory element. GCLiPP signal overlapping with immune-related SNPs uncovers stabilizing cis-regulatory regions in CD5, STAT6, and IKZF1.
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Affiliation(s)
- Wandi S Zhu
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam J Litterman
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Harshaan S Sekhon
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
- University of California Berkeley, Berkeley, CA, USA
| | - Robin Kageyama
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Maya M Arce
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Kimberly E Taylor
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, USA
| | - Wenxue Zhao
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Lung Biology Center, University of California San Francisco, San Francisco, USA
- School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China
| | - Lindsey A Criswell
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, USA
| | - Noah Zaitlen
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Lung Biology Center, University of California San Francisco, San Francisco, USA
| | - David J Erle
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Lung Biology Center, University of California San Francisco, San Francisco, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA.
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43
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Zhang AMY, Xia YH, Lin JSH, Chu KH, Wang WCK, Ruiter TJJ, Yang JCC, Chen N, Chhuor J, Patil S, Cen HH, Rideout EJ, Richard VR, Schaeffer DF, Zahedi RP, Borchers CH, Johnson JD, Kopp JL. Hyperinsulinemia acts via acinar insulin receptors to initiate pancreatic cancer by increasing digestive enzyme production and inflammation. Cell Metab 2023; 35:2119-2135.e5. [PMID: 37913768 DOI: 10.1016/j.cmet.2023.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 06/02/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023]
Abstract
The rising pancreatic cancer incidence due to obesity and type 2 diabetes is closely tied to hyperinsulinemia, an independent cancer risk factor. Previous studies demonstrated reducing insulin production suppressed pancreatic intraepithelial neoplasia (PanIN) pre-cancerous lesions in Kras-mutant mice. However, the pathophysiological and molecular mechanisms remained unknown, and in particular it was unclear whether hyperinsulinemia affected PanIN precursor cells directly or indirectly. Here, we demonstrate that insulin receptors (Insr) in KrasG12D-expressing pancreatic acinar cells are dispensable for glucose homeostasis but necessary for hyperinsulinemia-driven PanIN formation in the context of diet-induced hyperinsulinemia and obesity. Mechanistically, this was attributed to amplified digestive enzyme protein translation, triggering of local inflammation, and PanIN metaplasia in vivo. In vitro, insulin dose-dependently increased acinar-to-ductal metaplasia formation in a trypsin- and Insr-dependent manner. Collectively, our data shed light on the mechanisms connecting obesity-driven hyperinsulinemia and pancreatic cancer development.
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Affiliation(s)
- Anni M Y Zhang
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yi Han Xia
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jeffrey S H Lin
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Ken H Chu
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Wei Chuan K Wang
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Titine J J Ruiter
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jenny C C Yang
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nan Chen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Justin Chhuor
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Shilpa Patil
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Haoning Howard Cen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Elizabeth J Rideout
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Vincent R Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - Rene P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada; Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3A 1R9, Canada; Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB R3E 3P4, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A 3T2, Canada
| | - James D Johnson
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Janel L Kopp
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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Zhao H, Liu G, Cao X. A seed expansion-based method to identify essential proteins by integrating protein-protein interaction sub-networks and multiple biological characteristics. BMC Bioinformatics 2023; 24:452. [PMID: 38036960 PMCID: PMC10688502 DOI: 10.1186/s12859-023-05583-8] [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: 04/08/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND The identification of essential proteins is of great significance in biology and pathology. However, protein-protein interaction (PPI) data obtained through high-throughput technology include a high number of false positives. To overcome this limitation, numerous computational algorithms based on biological characteristics and topological features have been proposed to identify essential proteins. RESULTS In this paper, we propose a novel method named SESN for identifying essential proteins. It is a seed expansion method based on PPI sub-networks and multiple biological characteristics. Firstly, SESN utilizes gene expression data to construct PPI sub-networks. Secondly, seed expansion is performed simultaneously in each sub-network, and the expansion process is based on the topological features of predicted essential proteins. Thirdly, the error correction mechanism is based on multiple biological characteristics and the entire PPI network. Finally, SESN analyzes the impact of each biological characteristic, including protein complex, gene expression data, GO annotations, and subcellular localization, and adopts the biological data with the best experimental results. The output of SESN is a set of predicted essential proteins. CONCLUSIONS The analysis of each component of SESN indicates the effectiveness of all components. We conduct comparison experiments using three datasets from two species, and the experimental results demonstrate that SESN achieves superior performance compared to other methods.
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Affiliation(s)
- He Zhao
- College of Computer Science and Technology, Jilin University, Changchun, China
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Guixia Liu
- College of Computer Science and Technology, Jilin University, Changchun, China.
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China.
| | - Xintian Cao
- College of Computer Science and Technology, Jilin University, Changchun, China
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
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45
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Santos-Silva T, Hazar Ülgen D, Lopes CFB, Guimarães FS, Alberici LC, Sandi C, Gomes FV. Transcriptomic analysis reveals mitochondrial pathways associated with distinct adolescent behavioral phenotypes and stress response. Transl Psychiatry 2023; 13:351. [PMID: 37978166 PMCID: PMC10656500 DOI: 10.1038/s41398-023-02648-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Adolescent individuals exhibit great variability in cortical dynamics and behavioral outcomes. The developing adolescent brain is highly sensitive to social experiences and environmental insults, influencing how personality traits emerge. A distinct pattern of mitochondrial gene expression in the prefrontal cortex (PFC) during adolescence underscores the essential role of mitochondria in brain maturation and the development of mental illnesses. Mitochondrial features in certain brain regions account for behavioral differences in adulthood. However, it remains unclear whether distinct adolescent behavioral phenotypes and the behavioral consequences of early adolescent stress exposure in rats are accompanied by changes in PFC mitochondria-related genes and mitochondria respiratory chain capacity. We performed a behavioral characterization during late adolescence (postnatal day, PND 47-50), including naïve animals and a group exposed to stress from PND 31-40 (10 days of footshock and 3 restraint sessions) by z-normalized data from three behavioral domains: anxiety (light-dark box tests), sociability (social interaction test) and cognition (novel-object recognition test). Employing principal component analysis, we identified three clusters: naïve with higher-behavioral z-score (HBZ), naïve with lower-behavioral z-score (LBZ), and stressed animals. Genome-wide transcriptional profiling unveiled differences in the expression of mitochondria-related genes in both naïve LBZ and stressed animals compared to naïve HBZ. Genes encoding subunits of oxidative phosphorylation complexes were significantly down-regulated in both naïve LBZ and stressed animals and positively correlated with behavioral z-score of phenotypes. Our network topology analysis of mitochondria-associated genes found Ndufa10 and Cox6a1 genes as central identifiers for naïve LBZ and stressed animals, respectively. Through high-resolution respirometry analysis, we found that both naïve LBZ and stressed animals exhibited a reduced prefrontal phosphorylation capacity and redox dysregulation. Our findings identify an association between mitochondrial features and distinct adolescent behavioral phenotypes while also underscoring the detrimental functional consequences of adolescent stress on the PFC.
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Affiliation(s)
- Thamyris Santos-Silva
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Doğukan Hazar Ülgen
- Brain Mind Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Caio Fábio Baeta Lopes
- Ribeirão Preto Pharmaceutical Sciences School, University of São Paulo, Ribeirão Preto, Brazil
| | - Francisco S Guimarães
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luciane Carla Alberici
- Ribeirão Preto Pharmaceutical Sciences School, University of São Paulo, Ribeirão Preto, Brazil
| | - Carmen Sandi
- Brain Mind Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Felipe V Gomes
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
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Hunt LC, Pagala V, Stephan A, Xie B, Kodali K, Kavdia K, Wang YD, Shirinifard A, Curley M, Graca FA, Fu Y, Poudel S, Li Y, Wang X, Tan H, Peng J, Demontis F. An adaptive stress response that confers cellular resilience to decreased ubiquitination. Nat Commun 2023; 14:7348. [PMID: 37963875 PMCID: PMC10646096 DOI: 10.1038/s41467-023-43262-7] [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] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023] Open
Abstract
Ubiquitination is a post-translational modification initiated by the E1 enzyme UBA1, which transfers ubiquitin to ~35 E2 ubiquitin-conjugating enzymes. While UBA1 loss is cell lethal, it remains unknown how partial reduction in UBA1 activity is endured. Here, we utilize deep-coverage mass spectrometry to define the E1-E2 interactome and to determine the proteins that are modulated by knockdown of UBA1 and of each E2 in human cells. These analyses define the UBA1/E2-sensitive proteome and the E2 specificity in protein modulation. Interestingly, profound adaptations in peroxisomes and other organelles are triggered by decreased ubiquitination. While the cargo receptor PEX5 depends on its mono-ubiquitination for binding to peroxisomal proteins and importing them into peroxisomes, we find that UBA1/E2 knockdown induces the compensatory upregulation of other PEX proteins necessary for PEX5 docking to the peroxisomal membrane. Altogether, this study defines a homeostatic mechanism that sustains peroxisomal protein import in cells with decreased ubiquitination capacity.
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Affiliation(s)
- Liam C Hunt
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Department of Biology, Rhodes College, 2000 North Pkwy, Memphis, TN, 38112, USA
| | - Vishwajeeth Pagala
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Anna Stephan
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Boer Xie
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kiran Kodali
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kanisha Kavdia
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Abbas Shirinifard
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Michelle Curley
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Flavia A Graca
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yingxue Fu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Suresh Poudel
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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Liu Y, Yang J, Wang T, Luo M, Chen Y, Chen C, Ronai Z, Zhou Y, Ruppin E, Han L. Expanding PROTACtable genome universe of E3 ligases. Nat Commun 2023; 14:6509. [PMID: 37845222 PMCID: PMC10579327 DOI: 10.1038/s41467-023-42233-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 09/28/2023] [Indexed: 10/18/2023] Open
Abstract
Proteolysis-targeting chimera (PROTAC) and other targeted protein degradation (TPD) molecules that induce degradation by the ubiquitin-proteasome system (UPS) offer new opportunities to engage targets that remain challenging to be inhibited by conventional small molecules. One fundamental element in the degradation process is the E3 ligase. However, less than 2% amongst hundreds of E3 ligases in the human genome have been engaged in current studies in the TPD field, calling for the recruiting of additional ones to further enhance the therapeutic potential of TPD. To accelerate the development of PROTACs utilizing under-explored E3 ligases, we systematically characterize E3 ligases from seven different aspects, including chemical ligandability, expression patterns, protein-protein interactions (PPI), structure availability, functional essentiality, cellular location, and PPI interface by analyzing 30 large-scale data sets. Our analysis uncovers several E3 ligases as promising extant PROTACs. In total, combining confidence score, ligandability, expression pattern, and PPI, we identified 76 E3 ligases as PROTAC-interacting candidates. We develop a user-friendly and flexible web portal ( https://hanlaboratory.com/E3Atlas/ ) aimed at assisting researchers to rapidly identify E3 ligases with promising TPD activities against specifically desired targets, facilitating the development of these therapies in cancer and beyond.
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Affiliation(s)
- Yuan Liu
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Jingwen Yang
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Tianlu Wang
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Mei Luo
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Yamei Chen
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Chengxuan Chen
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Ze'ev Ronai
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, 20892, MD, USA.
| | - Leng Han
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA.
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN, USA.
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA.
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48
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Delaleu N, Marti HP, Strauss P, Sekulic M, Osman T, Tøndel C, Skrunes R, Leh S, Svarstad E, Nowak A, Gaspert A, Rusu E, Kwee I, Rinaldi A, Flatberg A, Eikrem O. Systems analyses of the Fabry kidney transcriptome and its response to enzyme replacement therapy identified and cross-validated enzyme replacement therapy-resistant targets amenable to drug repurposing. Kidney Int 2023; 104:803-819. [PMID: 37419447 DOI: 10.1016/j.kint.2023.06.029] [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: 06/03/2022] [Revised: 05/19/2023] [Accepted: 06/22/2023] [Indexed: 07/09/2023]
Abstract
Fabry disease is a rare disorder caused by variations in the alpha-galactosidase gene. To a degree, Fabry disease is manageable via enzyme replacement therapy (ERT). By understanding the molecular basis of Fabry nephropathy (FN) and ERT's long-term impact, here we aimed to provide a framework for selection of potential disease biomarkers and drug targets. We obtained biopsies from eight control individuals and two independent FN cohorts comprising 16 individuals taken prior to and after up to ten years of ERT, and performed RNAseq analysis. Combining pathway-centered analyses with network-science allowed computation of transcriptional landscapes from four nephron compartments and their integration with existing proteome and drug-target interactome data. Comparing these transcriptional landscapes revealed high inter-cohort heterogeneity. Kidney compartment transcriptional landscapes comprehensively reflected differences in FN cohort characteristics. With exception of a few aspects, in particular arteries, early ERT in patients with classical Fabry could lastingly revert FN gene expression patterns to closely match that of control individuals. Pathways nonetheless consistently altered in both FN cohorts pre-ERT were mostly in glomeruli and arteries and related to the same biological themes. While keratinization-related processes in glomeruli were sensitive to ERT, a majority of alterations, such as transporter activity and responses to stimuli, remained dysregulated or reemerged despite ERT. Inferring an ERT-resistant genetic module of expressed genes identified 69 drugs for potential repurposing matching the proteins encoded by 12 genes. Thus, we identified and cross-validated ERT-resistant gene product modules that, when leveraged with external data, allowed estimating their suitability as biomarkers to potentially track disease course or treatment efficacy and potential targets for adjunct pharmaceutical treatment.
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Affiliation(s)
- Nicolas Delaleu
- 2cSysBioMed, Contra, Switzerland; Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Philipp Strauss
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Miroslav Sekulic
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Tarig Osman
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Camilla Tøndel
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Rannveig Skrunes
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Sabine Leh
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Einar Svarstad
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Albina Nowak
- Department of Endocrinology and Clinical Nutrition, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Ariana Gaspert
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Elena Rusu
- Department of Nephrology, Fundeni Clinical Institute, Bucharest, Romania; Department of Nephrology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Ivo Kwee
- BigOmics Analytics, Lugano, Switzerland
| | - Andrea Rinaldi
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Arnar Flatberg
- Central Administration, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway; Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Oystein Eikrem
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway.
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49
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Takeuchi F, Liang YQ, Shimizu-Furusawa H, Isono M, Ang MY, Mori K, Mori T, Kakazu E, Yoshio S, Kato N. Gene-regulation modules in nonalcoholic fatty liver disease revealed by single-nucleus ATAC-seq. Life Sci Alliance 2023; 6:e202301988. [PMID: 37491046 PMCID: PMC10368228 DOI: 10.26508/lsa.202301988] [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: 02/13/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023] Open
Abstract
We investigated the progression of nonalcoholic fatty liver disease from fatty liver to steatohepatitis using single-nucleus and bulk ATAC-seq on the livers of rats fed a high-fat diet (HFD). Rats fed HFD for 4 wk developed fatty liver, and those fed HFD for 8 wk further progressed to steatohepatitis. We observed an increase in the proportion of inflammatory macrophages, consistent with the pathological progression. Utilizing machine learning, we divided global gene regulation into modules, wherein transcription factors within a module could regulate genes within the same module, reaffirming known regulatory relationships between transcription factors and biological processes. We identified core genes-central to co-expression and protein-protein interaction-for the biological processes discovered. Notably, a large part of the core genes overlapped with genes previously implicated in nonalcoholic fatty liver disease. Single-nucleus ATAC-seq, combined with data-driven statistical analysis, offers insight into in vivo global gene regulation as a combination of modules and assists in identifying core genes of relevant biological processes.
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Affiliation(s)
- Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Medical Genomics Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Systems Genomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Yi-Qiang Liang
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hana Shimizu-Furusawa
- Department of Hygiene and Public Health, School of Medicine, Teikyo University, Tokyo, Japan
| | - Masato Isono
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Mia Yang Ang
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Department of Clinical Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kotaro Mori
- Medical Genomics Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Taizo Mori
- Department of Liver Diseases, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan
| | - Eiji Kakazu
- Department of Liver Diseases, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan
| | - Sachiyo Yoshio
- Department of Liver Diseases, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Medical Genomics Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Department of Clinical Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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50
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Han Y, Liu M, Wang Z. Key protein identification by integrating protein complex information and multi-biological features. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:18191-18206. [PMID: 38052554 DOI: 10.3934/mbe.2023808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Identifying key proteins based on protein-protein interaction networks has emerged as a prominent area of research in bioinformatics. However, current methods exhibit certain limitations, such as the omission of subcellular localization information and the disregard for the impact of topological structure noise on the reliability of key protein identification. Moreover, the influence of proteins outside a complex but interacting with proteins inside the complex on complex participation tends to be overlooked. Addressing these shortcomings, this paper presents a novel method for key protein identification that integrates protein complex information with multiple biological features. This approach offers a comprehensive evaluation of protein importance by considering subcellular localization centrality, topological centrality weighted by gene ontology (GO) similarity and complex participation centrality. Experimental results, including traditional statistical metrics, jackknife methodology metric and key protein overlap or difference, demonstrate that the proposed method not only achieves higher accuracy in identifying key proteins compared to nine classical methods but also exhibits robustness across diverse protein-protein interaction networks.
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Affiliation(s)
- Yongyin Han
- School of Computer Science and Technology, China University of Mining and Technology, China
- Xuzhou College of Industrial Technology, China
| | - Maolin Liu
- School of Computer Science and Technology, China University of Mining and Technology, China
| | - Zhixiao Wang
- School of Computer Science and Technology, China University of Mining and Technology, China
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