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Rajeh A, Cornman HL, Gupta A, Szeto MD, Kambala A, Oladipo O, Parthasarathy V, Deng J, Wheelan S, Pritchard T, Kwatra MM, Semenov YR, Gusev A, Yegnasubramanian S, Kwatra SG. Somatic mutations reveal hyperactive Notch signaling and racial disparities in prurigo nodularis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.25.23295810. [PMID: 37808834 PMCID: PMC10557842 DOI: 10.1101/2023.09.25.23295810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Prurigo nodularis (PN) is a chronic inflammatory skin disease that disproportionately affects African Americans and is characterized by pruritic skin nodules of unknown etiology. Little is known about genetic alterations in PN pathogenesis, especially relating to somatic events which are often implicated in inflammatory conditions. We thus performed whole-exome sequencing on 54 lesional and nonlesional skin biopsies from 17 PN patients and 10 atopic dermatitis (AD) patients for comparison. Somatic mutational analysis revealed that PN lesional skin harbors pervasive somatic mutations in fibrotic, neurotropic, and cancer-associated genes. Nonsynonymous mutations were most frequent in NOTCH1 and the Notch signaling pathway, a regulator of cellular proliferation and tissue fibrosis, and NOTCH1 mutations were absent in AD. Somatic copy-number analysis, combined with expression data, showed that recurrently deleted and downregulated genes in PN lesional skin are associated with axonal guidance and extension. Follow-up immunofluorescence validation demonstrated increased NOTCH1 expression in PN lesional skin fibroblasts and increased Notch signaling in PN lesional dermis. Finally, multi-center data revealed a significantly increased risk of NOTCH1-associated diseases in PN patients. In characterizing the somatic landscape of PN, we uncover novel insights into its pathophysiology and identify a role for dysregulated Notch signaling in PN.
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Affiliation(s)
- Ahmad Rajeh
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hannah L Cornman
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anuj Gupta
- The Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Mindy D Szeto
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anusha Kambala
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olusola Oladipo
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Varsha Parthasarathy
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Junwen Deng
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah Wheelan
- Present affiliation: National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA
| | - Thomas Pritchard
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Madan M Kwatra
- Department of Anesthesiology, Duke University School of Medicine, Durham, NC, USA
| | - Yevgeniy R Semenov
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alexander Gusev
- Division of Genetics, Brigham & Women's Hospital, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Srinivasan Yegnasubramanian
- The Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shawn G Kwatra
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Veenstra BT, Veenstra TD. Proteomic applications in identifying protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:1-48. [PMID: 38220421 DOI: 10.1016/bs.apcsb.2023.04.001] [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: 01/16/2024]
Abstract
There are many things that can be used to characterize a protein. Size, isoelectric point, hydrophobicity, structure (primary to quaternary), and subcellular location are just a few parameters that are used. The most important feature of a protein, however, is its function. While there are many experiments that can indicate a protein's role, identifying the molecules it interacts with is probably the most definitive way of determining its function. Owing to technology limitations, protein interactions have historically been identified on a one molecule per experiment basis. The advent of high throughput multiplexed proteomic technologies in the 1990s, however, made identifying hundreds and thousands of proteins interactions within single experiments feasible. These proteomic technologies have dramatically increased the rate at which protein-protein interactions (PPIs) are discovered. While the improvement in mass spectrometry technology was an early driving force in the rapid pace of identifying PPIs, advances in sample preparation and chromatography have recently been propelling the field. In this chapter, we will discuss the importance of identifying PPIs and describe current state-of-the-art technologies that demonstrate what is currently possible in this important area of biological research.
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Affiliation(s)
- Benjamin T Veenstra
- Department of Math and Sciences, Cedarville University, Cedarville, OH, United States
| | - Timothy D Veenstra
- School of Pharmacy, Cedarville University, Cedarville, OH, United States.
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Ge L, Huang P, Miao H, Yu H, Wu D, Chen F, Lin Y, Lin Y, Li W, Hua J. The new landscape of differentially expression proteins in placenta tissues of gestational diabetes based on iTRAQ proteomics. Placenta 2023; 131:36-48. [PMID: 36473392 DOI: 10.1016/j.placenta.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 10/26/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Gestational diabetes mellitus (GDM) refers to abnormal glucose tolerance that occurs or is firstly diagnosed during pregnancy. GDM is related to various adverse pregnancy outcomes, but GDM pathogeny has not been fully elucidated. Nevertheless, previous studies have observed that many proteins in the placentas of patients with GDM are dysregulated. The present study aimed to establish a novel differentially expressed protein (DEP) landscape of GDM and normal maternal placentas and to explore the possible connection between DEPs and GDM pathogenesis. This study provides new insights into the mechanism of GDM and should make an important contribution to the development of biomarkers. METHODS The morphological characteristics of the placenta were observed on 30 GDM and normal maternal placental tissues stained with haematoxylin and eosin. Isobaric tags for relative and absolute quantitation (iTRAQ) was used in the proteomics screening of the DEPs of the normal and GDM maternal placentas. Bioinformatics analysis was performed on the DEPs, and parallel reaction monitoring (PRM) was performed to verify the DEPs. Finally, the quantitative analysis of iTRAQ and PRM was verified by immunohistochemical assay. RESULTS A total of 68 DEPs in the GDM placenta were identified with iTRAQ proteomics experiment, comprising 21 up-regulated and 47 down-regulated DEPs. Bioinformatics analysis showed that the regulation of transport, catabolic process of non-coding RNA, cytoskeleton and cell binding were the most abundant Gene Ontology terms, and RNA degradation was an important pathway for significant enrichment. Protein-protein interaction network analysis showed that heterogeneous nuclear ribonucleoproteins A2/B1 (HNRNPA2B1), heterogeneous nuclear ribonucleoprotein A/B (HNRNPAB), heterogeneous nuclear ribonucleoprotein L (HNRNPL) and heterogeneous nuclear ribonucleoprotein A3 (HNRNPA3) were the cores of the up-regulated proteins. Band 3 anion transport protein (SLC4A1), spectrin beta chain erythrocytic (SPTB), ankyrin-1 (ANK1), spectrin beta chain non-erythrocytic 2 (SPTBN2), D-3-phosphoglycerate dehydrogenase (PHGDH) and exosome complex component RRP42 (EXOSC7) were the cores of the down-regulated proteins. These proteins are involved in the binding, splicing, processing, transport and degradation of RNA and in the formation and maintenance of the cytoskeleton. PRM verification results showed that seven proteins, namely, epiplakin (EPPK1), cold-inducible RNA-binding protein (CIRBP), HNRNPA2B1, HNRNPAB, HNRNPL, Ras-related protein Rab-21 (RAB21) and Ras-related protein Rab-3B (RAB3B), were up-regulated, whereas SPTB and SLC4A1 were down-regulated. The results of immunohistochemical assay also showed that the expression of five proteins, namely EPPK1, HNRNPA2B1, HNRNPAB, CIRBP and RAB21, were significantly higher in GDM placental tissues (P < 0.01). The GDM placentas showed changes in the morphological evaluation, including poor villous maturation, obvious increase in the number of syncytiotrophoblast nodules, thickening of the wall of dry villous arterioles with lumen stenosis, increased fibrinous exudation and excessive filling of villous interstitial vessels. DISCUSSION Differentially expressed proteins related to a variety of biological processes in the GDM placenta were found. Fourteen proteins, namely, HNRNPA2B1, HNRNPAB, HNRNPL, HNRNPA3, EPPK1, CIRBP, RAB21, RAB3B, SLC4A1, SPTB, ANK1, SPTBN2, PHGDH and EXOSC7, which were differentially expressed in the placenta, may play an important role in regulating the occurrence and development of gestational diabetes through multi-channel and multi-link regulation.
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Affiliation(s)
- Li Ge
- School of Nursing, Fujian University of Traditional Chinese Medicine, Fuzhou, China.
| | - Pingping Huang
- School of Nursing, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Haiyan Miao
- Department of Obstetrics and Gynecology, The Second People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Honghong Yu
- School of Nursing, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Dongmei Wu
- Department of Obstetrics and Gynecology, The Second People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Fan Chen
- School of Nursing, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Yan Lin
- School of Nursing, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Yuzheng Lin
- School of Nursing, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Wenfang Li
- School of Nursing, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jinghe Hua
- School of Nursing, Fujian University of Traditional Chinese Medicine, Fuzhou, China
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Wesley T, Berzins S, Kannourakis G, Ahmed N. The attributes of plakins in cancer and disease: perspectives on ovarian cancer progression, chemoresistance and recurrence. Cell Commun Signal 2021; 19:55. [PMID: 34001250 PMCID: PMC8127266 DOI: 10.1186/s12964-021-00726-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/20/2021] [Indexed: 02/06/2023] Open
Abstract
The plakin family of cytoskeletal proteins play an important role in cancer progression yet are under-studied in cancer, especially ovarian cancer. These large cytoskeletal proteins have primary roles in the maintenance of cytoskeletal integrity but are also associated with scaffolds of intermediate filaments and hemidesmosomal adhesion complexes mediating signalling pathways that regulate cellular growth, migration, invasion and differentiation as well as stress response. Abnormalities of plakins, and the closely related spectraplakins, result in diseases of the skin, striated muscle and nervous tissue. Their prevalence in epithelial cells suggests that plakins may play a role in epithelial ovarian cancer progression and recurrence. In this review article, we explore the roles of plakins, particularly plectin, periplakin and envoplakin in disease-states and cancers with emphasis on ovarian cancer. We discuss the potential role the plakin family of proteins play in regulating cancer cell growth, survival, migration, invasion and drug resistance. We highlight potential relationships between plakins, epithelial-mesenchymal transition (EMT) and cancer stem cells (CSCs) and discuss how interaction of these processes may affect ovarian cancer progression, chemoresistance and ultimately recurrence. We propose that molecular changes in the expression of plakins leads to the transition of benign ovarian tumours to carcinomas, as well as floating cellular aggregates (commonly known as spheroids) in the ascites microenvironment, which may contribute to the sustenance and progression of the disease. In this review, attempts have been made to understand the crucial changes in plakin expression in relation to progression and recurrence of ovarian cancer. Video Abstract
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Affiliation(s)
- Tamsin Wesley
- Fiona Elsey Cancer Research Institute, Ballarat Technology Central Park, Suites 23-26, 106-110 Lydiard Street South, Ballarat, VIC, 3353, Australia.,School of Science, Psychology and Sport, Federation University Australia, Ballarat, VIC, 3010, Australia
| | - Stuart Berzins
- Fiona Elsey Cancer Research Institute, Ballarat Technology Central Park, Suites 23-26, 106-110 Lydiard Street South, Ballarat, VIC, 3353, Australia.,School of Science, Psychology and Sport, Federation University Australia, Ballarat, VIC, 3010, Australia
| | - George Kannourakis
- Fiona Elsey Cancer Research Institute, Ballarat Technology Central Park, Suites 23-26, 106-110 Lydiard Street South, Ballarat, VIC, 3353, Australia.,School of Science, Psychology and Sport, Federation University Australia, Ballarat, VIC, 3010, Australia
| | - Nuzhat Ahmed
- Fiona Elsey Cancer Research Institute, Ballarat Technology Central Park, Suites 23-26, 106-110 Lydiard Street South, Ballarat, VIC, 3353, Australia. .,School of Science, Psychology and Sport, Federation University Australia, Ballarat, VIC, 3010, Australia. .,Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC, 3052, Australia. .,Centre for Reproductive Health, The Hudson Institute of Medical Research and Department of Translational Medicine, Monash University, Melbourne, VIC, 3168, Australia.
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