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Srinivasan G, Davis M, LeBoeuf M, Fatemi M, Azher Z, Lu Y, Diallo A, Montivero MS, Kolling F, Perrard L, Salas L, Christensen B, Palisoul S, Tsongalis G, Vaickus L, Preum S, Levy J. Potential to Enhance Large Scale Molecular Assessments of Skin Photoaging through Virtual Inference of Spatial Transcriptomics from Routine Staining. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.30.551188. [PMID: 37577612 PMCID: PMC10418044 DOI: 10.1101/2023.07.30.551188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The advent of spatial transcriptomics technologies has heralded a renaissance in research to advance our understanding of the spatial cellular and transcriptional heterogeneity within tissues. Spatial transcriptomics allows investigation of the interplay between cells, molecular pathways and the surrounding tissue architecture and can help elucidate developmental trajectories, disease pathogenesis, and various niches in the tumor microenvironment. Photoaging is the histological and molecular skin damage resulting from chronic/acute sun exposure and is a major risk factor for skin cancer. Spatial transcriptomics technologies hold promise for improving the reliability of evaluating photoaging and developing new therapeutics. Current challenges, including limited focus on dermal elastosis variations and reliance on self-reported measures, can introduce subjectivity and inconsistency. Spatial transcriptomics offer an opportunity to assess photoaging objectively and reproducibly in studies of carcinogenesis and discern the effectiveness of therapies that intervene on photoaging and prevent cancer. Evaluation of distinct histological architectures using highly-multiplexed spatial technologies can identify specific cell lineages that have been understudied due to their location beyond the depth of UV penetration. However, the cost and inter-patient variability using state-of-the-art assays such as the 10x Genomics Spatial Transcriptomics assays limits the scope and scale of large-scale molecular epidemiologic studies. Here, we investigate the inference of spatial transcriptomics information from routine hematoxylin and eosin-stained (H&E) tissue slides. We employed the Visium CytAssist spatial transcriptomics assay to analyze over 18,000 genes at a 50-micron resolution for four patients from a cohort of 261 skin specimens collected adjacent to surgical resection sites for basal and squamous keratinocyte tumors. The spatial transcriptomics data was co-registered with 40x resolution whole slide imaging (WSI) information. We developed machine learning models that achieved a macro-averaged median AUC and F1 score of 0.80 and 0.61 and Spearman coefficient of 0.60 in inferring transcriptomic profiles across the slides, and accurately captured biological pathways across various tissue architectures.
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Mikhailova SV, Shcherbakova LV, Logvinenko NI, Logvinenko II, Voevoda MI. Polymorphism of genes associated with infectious lung diseases in Northern Asian populations and in patients with community-acquired pneumonia. Vavilovskii Zhurnal Genet Selektsii 2021; 25:301-309. [PMID: 35083399 PMCID: PMC8698094 DOI: 10.18699/vj21.51-o] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/12/2020] [Accepted: 09/28/2020] [Indexed: 11/29/2022] Open
Abstract
The innate immune system is the first to respond to invading pathogens. It is responsible for invader recognition, immune-cell recruitment, adaptive-immunity activation, and regulation of inflammation intensity. Previously, two single-nucleotide polymorphisms of innate-immunity genes – rs5743708 (Arg753Gln) of the TLR2 gene
and rs8177374 (Ser180Leu) of the TIRAP gene – have been shown to be associated with both pneumonia and tuberculosis in humans, but the data are contradictory among different ethnic groups. It has also been reported that
rs10902158 at the PKP3-SIGGIR-TMEM16J genetic locus belongs to a haplotype race-specifically associated with tuberculosis. Meanwhile, a gradient of its frequency is observed in Asia. The aim of this work was to assess the effect of
selection for the genotypes of the above-mentioned SNPs on the gene pools of populations living in harsh climatic
conditions that contribute to the development of infectious lung diseases. We estimated the prevalence of these
variants in white and Asian (Chukchis and Yakuts) population samples from Northern Asia and among patients with
community-acquired pneumonia (CAP). Carriage of the rs5743708 A allele was found to predispose to severe CAP
(odds ratio 2.77, p = 0.021), whereas the GG/CT genotype of rs5743708/rs8177374 proved to be protective against
it (odds ratio 0.478, p = 0.022) in white patients. No association of rs10902158 with CAP (total or severe) was found
among whites. Stratification of CAP by causative pathogen may help eliminate the current discrepancies between
different studies. No significant difference in rs5743708 or rs8177374 was found between adolescent and long-lived
white samples. Carriage of the alleles studied is probably not associated with predisposition to longevity among
whites in Siberia. Both white and Asian populations studied were different from Western European and East Asian
populations in the variants’ prevalence. The frequency of the rs8177374 T (Ser180Leu) variant was significantly higher
in the Chukchi sample (p = 0, χ2 = 63.22) relative to the East Asian populations. This result may confirm the hypothesis
about the selection of this allele in the course of human migration into areas with unfavorable climatic conditions.
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Affiliation(s)
| | - L. V. Shcherbakova
- Institute of Internal and Preventive Medicine – Branch of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | | | - I. I. Logvinenko
- Institute of Internal and Preventive Medicine – Branch of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences;
Novosibirsk State Medical University
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A catenin of the plakophilin-subfamily, Pkp3, responds to canonical-Wnt pathway components and signals. Biochem Biophys Res Commun 2021; 563:31-39. [PMID: 34058472 DOI: 10.1016/j.bbrc.2021.05.043] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/21/2022]
Abstract
Vertebrate beta-catenin plays a key role as a transducer of canonical-Wnt signals. We earlier reported that, similar to beta-catenin, the cytoplasmic signaling pool of p120-catenin-isoform1 is stabilized in response to canonical-Wnt signals. To obtain a yet broader view of the Wnt-pathway's impact upon catenin proteins, we focused upon plakophilin3 (plakophilin-3; Pkp3) as a representative of the plakophilin-catenin subfamily. Promoting tissue integrity, the plakophilins assist in linking desmosomal cadherins to intermediate filaments at desmosome junctions, and in common with other catenins they perform additional functions including in the nucleus. In this report, we test whether canonical-Wnt pathway components modulate Pkp3 protein levels. We find that in common with beta-catenin and p120-catenin-isoform1, Pkp3 is stabilized in the presence of a Wnt-ligand or a dominant-active form of the LRP6 receptor. Pkp3's levels are conversely lowered upon expressing destruction-complex components such as GSK3β and Axin, and in further likeness to beta-catenin and p120-isoform1, Pkp3 associates with GSK3beta and Axin. Finally, we note that Pkp3-catenin trans-localizes into the nucleus in response to Wnt-ligand and its exogenous expression stimulates an accepted Wnt reporter. These findings fit an expanded model where context-dependent Wnt-signals or pathway components modulate Pkp3-catenin levels. Future studies will be needed to assess potential gene regulatory, cell adhesive, or cytoskeletal effects.
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Zimmer SE, Kowalczyk AP. The desmosome as a model for lipid raft driven membrane domain organization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183329. [PMID: 32376221 DOI: 10.1016/j.bbamem.2020.183329] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 01/14/2023]
Abstract
Desmosomes are cadherin-based adhesion structures that mechanically couple the intermediate filament cytoskeleton of adjacent cells to confer mechanical stress resistance to tissues. We have recently described desmosomes as mesoscale lipid raft membrane domains that depend on raft dynamics for assembly, function, and disassembly. Lipid raft microdomains are regions of the plasma membrane enriched in sphingolipids and cholesterol. These domains participate in membrane domain heterogeneity, signaling and membrane trafficking. Cellular structures known to be dependent on raft dynamics include the post-synaptic density in neurons, the immunological synapse, and intercellular junctions, including desmosomes. In this review, we discuss the current state of the desmosome field and put forward new hypotheses for the role of lipid rafts in desmosome adhesion, signaling and epidermal homeostasis. Furthermore, we propose that differential lipid raft affinity of intercellular junction proteins is a central driving force in the organization of the epithelial apical junctional complex.
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Affiliation(s)
- Stephanie E Zimmer
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, GA 30322, United States of America; Department of Cell Biology, Emory University, Atlanta, GA 30322, United States of America
| | - Andrew P Kowalczyk
- Department of Cell Biology, Emory University, Atlanta, GA 30322, United States of America; Department of Dermatology, Emory University, Atlanta, GA 30322, United States of America.
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The Barrier Molecules Junction Plakoglobin, Filaggrin, and Dystonin Play Roles in Melanoma Growth and Angiogenesis. Ann Surg 2020; 270:712-722. [PMID: 31425296 DOI: 10.1097/sla.0000000000003522] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To understand role of barrier molecules in melanomas. BACKGROUND We have reported poor patient survival and low immune infiltration of melanomas that overexpress a set of genes that include filaggrin (FLG), dystonin (DST), junction plakoglobin (JUP), and plakophilin-3 (PKP3), and are involved in cell-cell adhesions. We hypothesized that these associations are causal, either by interfering with immune cell infiltration or by enhancing melanoma cell growth. METHODS FLG and DST were knocked out by CRISPR/Cas9 in human DM93 and murine B16-F1 melanoma cells. PKP3 and JUP were overexpressed in murine B16-AAD and human VMM39 melanoma cells by lentiviral transduction. These cell lines were evaluated in vitro for cell proliferation and in vivo for tumor burden, immune composition, cytokine expression, and vascularity. RESULTS Immune infiltrates were not altered by these genes. FLG/DST knockout reduced proliferation of human DM93 melanoma in vitro, and decreased B16-F1 tumor burden in vivo. Overexpression of JUP, but not PKP3, in B16-AAD significantly increased tumor burden, increased VEGF-A, reduced IL-33, and enhanced vascularity. CONCLUSIONS FLG and DST support melanoma cell growth in vitro and in vivo. Growth effects of JUP were only evident in vivo, and may be mediated, in part, by enhancing angiogenesis. In addition, growth-promoting effects of FLG and DST in vitro suggest that these genes may also support melanoma cell proliferation through angiogenesis-independent pathways. These findings identify FLG, DST, and JUP as novel therapeutic targets whose down-regulation may provide clinical benefit to patients with melanoma.
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Fuchs M, Foresti M, Radeva MY, Kugelmann D, Keil R, Hatzfeld M, Spindler V, Waschke J, Vielmuth F. Plakophilin 1 but not plakophilin 3 regulates desmoglein clustering. Cell Mol Life Sci 2019; 76:3465-3476. [PMID: 30949721 PMCID: PMC11105395 DOI: 10.1007/s00018-019-03083-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/15/2019] [Accepted: 03/25/2019] [Indexed: 12/25/2022]
Abstract
Plakophilins (Pkp) are desmosomal plaque proteins crucial for desmosomal adhesion and participate in the regulation of desmosomal turnover and signaling. However, direct evidence that Pkps regulate clustering and molecular binding properties of desmosomal cadherins is missing. Here, keratinocytes lacking either Pkp1 or 3 in comparison to wild type (wt) keratinocytes were characterized with regard to their desmoglein (Dsg) 1- and 3-binding properties and their capability to induce Dsg3 clustering. As revealed by atomic force microscopy (AFM), both Pkp-deficient keratinocyte cell lines showed reduced membrane availability and binding frequency of Dsg1 and 3 at cell borders. Extracellular crosslinking and AFM cluster mapping demonstrated that Pkp1 but not Pkp3 is required for Dsg3 clustering. Accordingly, Dsg3 overexpression reconstituted cluster formation in Pkp3- but not Pkp1-deficient keratinocytes as shown by AFM and STED experiments. Taken together, these data demonstrate that both Pkp1 and 3 regulate Dsg membrane availability, whereas Pkp1 but not Pkp3 is required for Dsg3 clustering.
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Affiliation(s)
- Michael Fuchs
- Faculty of Medicine, Institute of Anatomy, Ludwig-Maximilians-Universität Munich, Pettenkoferstr. 11, 80336, Munich, Germany
| | - Marco Foresti
- Faculty of Medicine, Institute of Anatomy, Ludwig-Maximilians-Universität Munich, Pettenkoferstr. 11, 80336, Munich, Germany
| | - Mariya Y Radeva
- Faculty of Medicine, Institute of Anatomy, Ludwig-Maximilians-Universität Munich, Pettenkoferstr. 11, 80336, Munich, Germany
| | - Daniela Kugelmann
- Faculty of Medicine, Institute of Anatomy, Ludwig-Maximilians-Universität Munich, Pettenkoferstr. 11, 80336, Munich, Germany
| | - Rene Keil
- Division of Pathobiochemistry, Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Mechthild Hatzfeld
- Division of Pathobiochemistry, Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Volker Spindler
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Jens Waschke
- Faculty of Medicine, Institute of Anatomy, Ludwig-Maximilians-Universität Munich, Pettenkoferstr. 11, 80336, Munich, Germany.
| | - Franziska Vielmuth
- Faculty of Medicine, Institute of Anatomy, Ludwig-Maximilians-Universität Munich, Pettenkoferstr. 11, 80336, Munich, Germany.
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Sun C, Wang L, Yang XX, Jiang YH, Guo XL. The aberrant expression or disruption of desmocollin2 in human diseases. Int J Biol Macromol 2019; 131:378-386. [DOI: 10.1016/j.ijbiomac.2019.03.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/21/2022]
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Fearnley GW, Young KA, Edgar JR, Antrobus R, Hay IM, Liang WC, Martinez-Martin N, Lin W, Deane JE, Sharpe HJ. The homophilic receptor PTPRK selectively dephosphorylates multiple junctional regulators to promote cell-cell adhesion. eLife 2019; 8:44597. [PMID: 30924770 PMCID: PMC6440744 DOI: 10.7554/elife.44597] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/23/2019] [Indexed: 12/20/2022] Open
Abstract
Cell-cell communication in multicellular organisms depends on the dynamic and reversible phosphorylation of protein tyrosine residues. The receptor-linked protein tyrosine phosphatases (RPTPs) receive cues from the extracellular environment and are well placed to influence cell signaling. However, the direct events downstream of these receptors have been challenging to resolve. We report here that the homophilic receptor PTPRK is stabilized at cell-cell contacts in epithelial cells. By combining interaction studies, quantitative tyrosine phosphoproteomics, proximity labeling and dephosphorylation assays we identify high confidence PTPRK substrates. PTPRK directly and selectively dephosphorylates at least five substrates, including Afadin, PARD3 and δ-catenin family members, which are all important cell-cell adhesion regulators. In line with this, loss of PTPRK phosphatase activity leads to disrupted cell junctions and increased invasive characteristics. Thus, identifying PTPRK substrates provides insight into its downstream signaling and a potential molecular explanation for its proposed tumor suppressor function.
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Affiliation(s)
- Gareth W Fearnley
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Katherine A Young
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Iain M Hay
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Wei-Ching Liang
- Antibody Engineering Department, Genentech, South San Francisco, United States
| | - Nadia Martinez-Martin
- Microchemistry, Proteomics and Lipidomics Department, Genentech, South San Francisco, United States
| | - WeiYu Lin
- Antibody Engineering Department, Genentech, South San Francisco, United States
| | - Janet E Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Hayley J Sharpe
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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