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Tao S, Cao P, Jin M, Suo P, Chen Y, Li Y. Integrated analysis of long non-coding RNAs and mRNAs associated with condyloma acuminatum. J Dermatol 2024; 51:671-683. [PMID: 38421728 DOI: 10.1111/1346-8138.17133] [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: 05/18/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 03/02/2024]
Abstract
Condyloma acuminatum (CA) is a prevalent sexually transmitted disease caused by low-risk human papillomavirus infection, characterized by high transmission and recurrence rates. Long non-coding RNAs (lncRNAs) play a crucial role in regulating gene transcription and are involved in various biological processes. Although recent studies have demonstrated the involvement of lncRNAs in cervical cancer, their expression profile and function in CA remain poorly understood. In this study, we aimed to identify messenger RNA (mRNA) and lncRNA expression patterns in CA using high-throughput lncRNA sequencing. We found that 3033 differentially expressed genes (DEGs) and 1090 differentially expressed lncRNAs (DELs) were significantly altered in CA compared to healthy controls. The results from quantitative reverse transcription polymerase chain reaction and immunohistochemical staining are in accordance with the observed trends in the sequencing data. Functional enrichment analysis revealed that upregulated DEGs in CA were involved in biological processes such as virus response, immune response, cell cycle regulation, the tumor necrosis factor signaling pathway, and the P53 signaling pathway. Co-expression network analysis identified potential target genes of DELs, with enrichment in biological processes such as cell differentiation, the intrinsic apoptotic signaling pathway, and pathways such as virus infection, pathways in cancer, T helper 17 cell differentiation, the mitogen-activated protein kinase signaling pathway, and the Wnt signaling pathway. Collectively, our findings indicate significant changes in the transcriptome profile, including mRNAs and lncRNAs, in CA compared to healthy controls. Our study provides new insights into the potential functions of lncRNAs in the pathogenesis of CA and identifies potential therapeutic targets for this disease.
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Affiliation(s)
- Sizheng Tao
- Department of Dermatology, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Ping Cao
- Department of Dermatology, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Mei Jin
- Department of Dermatology, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Peiyan Suo
- Department of Plastic Surgery, Kunming Angel Women and Children's Hospital, Kunming, Yunnan, China
| | - Yuan Chen
- Department of Dermatology, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yuye Li
- Department of Dermatology and Venereology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
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2
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Deo R, Dubin RF, Ren Y, Murthy AC, Wang J, Zheng H, Zheng Z, Feldman H, Shou H, Coresh J, Grams M, Surapaneni AL, Bhat Z, Cohen JB, Rahman M, He J, Saraf SL, Go AS, Kimmel PL, Vasan RS, Segal MR, Li H, Ganz P. Proteomic cardiovascular risk assessment in chronic kidney disease. Eur Heart J 2023; 44:2095-2110. [PMID: 37014015 PMCID: PMC10281556 DOI: 10.1093/eurheartj/ehad115] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 01/21/2023] [Accepted: 02/16/2023] [Indexed: 04/05/2023] Open
Abstract
AIMS Chronic kidney disease (CKD) is widely prevalent and independently increases cardiovascular risk. Cardiovascular risk prediction tools derived in the general population perform poorly in CKD. Through large-scale proteomics discovery, this study aimed to create more accurate cardiovascular risk models. METHODS AND RESULTS Elastic net regression was used to derive a proteomic risk model for incident cardiovascular risk in 2182 participants from the Chronic Renal Insufficiency Cohort. The model was then validated in 485 participants from the Atherosclerosis Risk in Communities cohort. All participants had CKD and no history of cardiovascular disease at study baseline when ∼5000 proteins were measured. The proteomic risk model, which consisted of 32 proteins, was superior to both the 2013 ACC/AHA Pooled Cohort Equation and a modified Pooled Cohort Equation that included estimated glomerular filtrate rate. The Chronic Renal Insufficiency Cohort internal validation set demonstrated annualized receiver operating characteristic area under the curve values from 1 to 10 years ranging between 0.84 and 0.89 for the protein and 0.70 and 0.73 for the clinical models. Similar findings were observed in the Atherosclerosis Risk in Communities validation cohort. For nearly half of the individual proteins independently associated with cardiovascular risk, Mendelian randomization suggested a causal link to cardiovascular events or risk factors. Pathway analyses revealed enrichment of proteins involved in immunologic function, vascular and neuronal development, and hepatic fibrosis. CONCLUSION In two sizeable populations with CKD, a proteomic risk model for incident cardiovascular disease surpassed clinical risk models recommended in clinical practice, even after including estimated glomerular filtration rate. New biological insights may prioritize the development of therapeutic strategies for cardiovascular risk reduction in the CKD population.
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Affiliation(s)
- Rajat Deo
- Division of Cardiovascular Medicine, Electrophysiology Section, Perelman School of Medicine at the University of Pennsylvania, One Convention Avenue, Level 2 / City Side, Philadelphia, PA 19104, USA
| | - Ruth F Dubin
- Division of Nephrology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Yue Ren
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Ashwin C Murthy
- Division of Cardiovascular Medicine, Electrophysiology Section, Perelman School of Medicine at the University of Pennsylvania, One Convention Avenue, Level 2 / City Side, Philadelphia, PA 19104, USA
| | - Jianqiao Wang
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Haotian Zheng
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Zihe Zheng
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Harold Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Haochang Shou
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Josef Coresh
- Department of Epidemiology; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University, 2024 E. Monument Street, Room 2-635, Suite 2-600, Baltimore, MD 21287, USA
| | - Morgan Grams
- Department of Epidemiology; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University, 2024 E. Monument Street, Room 2-635, Suite 2-600, Baltimore, MD 21287, USA
| | - Aditya L Surapaneni
- Department of Epidemiology; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA
| | - Zeenat Bhat
- Division of Nephrology, University of Michigan, 5100 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105, USA
| | - Jordana B Cohen
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
- Renal, Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, 831 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Mahboob Rahman
- Department of Medicine, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Wearn Bldg. 3 Floor. Rm 352, Cleveland, OH 44106, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street, SL 18, New Orleans, LA 70112, USA
| | - Santosh L Saraf
- Division of Hematology and Oncology, University of Illinois at Chicago, 1740 West Taylor Street, Chicago, IL 60612, USA
| | - Alan S Go
- Division of Research, Kaiser Permanente Northern California, 2000 Broadway, Oakland, CA 94612, USA
- Departments of Epidemiology, Biostatistics and Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Paul L Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Ramachandran S Vasan
- Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Section of Cardiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Mark R Segal
- Department of Epidemiology and Biostatistics, University of California, 550 16th Street, 2nd Floor, Box #0560, San Francisco, CA 94143, USA
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 215 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Peter Ganz
- Division of Cardiology, Zuckerberg San Francisco General Hospital and Department of Medicine, University of California, San Francisco, 1001 Potrero Avenue, 5G1, San Francisco, CA 94110, USA
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3
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Venuto S, Coda ARD, González-Pérez R, Laselva O, Tolomeo D, Storlazzi CT, Liso A, Conese M. IGFBP-6 Network in Chronic Inflammatory Airway Diseases and Lung Tumor Progression. Int J Mol Sci 2023; 24:ijms24054804. [PMID: 36902237 PMCID: PMC10003725 DOI: 10.3390/ijms24054804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
The lung is an accomplished organ for gas exchanges and directly faces the external environment, consequently exposing its large epithelial surface. It is also the putative determinant organ for inducing potent immune responses, holding both innate and adaptive immune cells. The maintenance of lung homeostasis requires a crucial balance between inflammation and anti-inflammation factors, and perturbations of this stability are frequently associated with progressive and fatal respiratory diseases. Several data demonstrate the involvement of the insulin-like growth factor (IGF) system and their binding proteins (IGFBPs) in pulmonary growth, as they are specifically expressed in different lung compartments. As we will discuss extensively in the text, IGFs and IGFBPs are implicated in normal pulmonary development but also in the pathogenesis of various airway diseases and lung tumors. Among the known IGFBPs, IGFBP-6 shows an emerging role as a mediator of airway inflammation and tumor-suppressing activity in different lung tumors. In this review, we assess the current state of IGFBP-6's multiple roles in respiratory diseases, focusing on its function in the inflammation and fibrosis in respiratory tissues, together with its role in controlling different types of lung cancer.
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Affiliation(s)
- Santina Venuto
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | | | - Ruperto González-Pérez
- Allergy Department, Hospital Universitario de Canarias, 38320 Tenerife, Spain
- Severe Asthma Unit, Hospital Universitario de Canarias, 38320 Tenerife, Spain
| | - Onofrio Laselva
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Doron Tolomeo
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy
| | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy
| | - Arcangelo Liso
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
- Correspondence:
| | - Massimo Conese
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
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4
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Jiang P, Wu Y, Liu L, Zhang L, Song Z. Combined application of dinitrofluorobenzene and ovalbumin induced AD-like dermatitis with an increase in helper T-cell cytokines and a prolonged Th2 response. BMC Immunol 2022; 23:60. [PMID: 36476273 PMCID: PMC9730685 DOI: 10.1186/s12865-022-00531-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The progression of acute-to-chronic atopic dermatitis is accompanied by multiple helper T-cell cytokine responses, but the mechanisms and relative importance of these changes remain unclear. There is no animal model for atopic dermatitis that recapitulates these cytokine responses. OBJECTIVE We sought to build a novel mouse model for atopic dermatitis (AD) that recapitulates these helper T-cell responses and some dynamic changes in cytokine responses in the progression of AD. METHODS Female BALB/c mice were subjected to the application of dinitrofluorobenzene (DNFB) and ovalbumin (OVA) to induce AD-like dermatitis. Skin lesions and serum were collected from mice in the acute and chronic phases to detect changes in cytokine responses and other features of AD. RESULTS Combined application of DNFB and OVA successfully induced AD-like dermatitis and histological changes as well as epidermal barrier dysfunction. In the acute phase of AD-like dermatitis, Th2-associated cytokines were mainly increased in serum and skin lesions. In the chronic phase of AD-like dermatitis, Th2-associated cytokines were still highly expressed, while Th1- and Th17-associated cytokines were also gradually increased. Compared with the acute phase, the JAK-STAT signaling pathway was highly expressed in the chronic phase of AD-like dermatitis. CONCLUSION The combined application of DNFB and OVA could be used to build a new mouse model for atopic dermatitis. This mouse model recapitulates the helper T-cell responses and some dynamic changes in cytokine responses in the progression of acute-to-chronic in human AD. The JAK-STAT signaling pathway plays a pivotal role in the chronicity of AD.
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Affiliation(s)
- Pengju Jiang
- grid.190737.b0000 0001 0154 0904School of Medicine, Chongqing University, Chongqing, 400030 China
| | - Yaguang Wu
- grid.410570.70000 0004 1760 6682Department of Dermatology, Southwest Hospital, Army Medical University, Chongqing, 400038 China
| | - Lu Liu
- grid.410570.70000 0004 1760 6682Department of Dermatology, Southwest Hospital, Army Medical University, Chongqing, 400038 China
| | - Lian Zhang
- grid.410570.70000 0004 1760 6682Department of Dermatology, Southwest Hospital, Army Medical University, Chongqing, 400038 China
| | - Zhiqiang Song
- grid.410570.70000 0004 1760 6682Department of Dermatology, Southwest Hospital, Army Medical University, Chongqing, 400038 China
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5
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Devall MA, Eaton S, Ali MW, Powell SM, Li L, Casey G. Insights into Early Onset Colorectal Cancer through Analysis of Normal Colon Organoids of Familial Adenomatous Polyposis Patients. Cancers (Basel) 2022; 14:4138. [PMID: 36077675 PMCID: PMC9454756 DOI: 10.3390/cancers14174138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 01/07/2023] Open
Abstract
Early onset colorectal cancer (EOCRC) rates have increased in recent decades. While lowering the recommended age for routine colonoscopies to 45 may reduce this burden, such measures do not address those who develop CRC before that age. Additional measures are needed to identify individuals at-risk for CRC. To better define transcriptomic events that precede the development of CRC, we performed RNA-sequencing analysis in colon organoids derived from seven healthy and six familial adenomatous polyposis (FAP) patients. This led to the identification of 2635 significant differentially expressed genes (FDR < 0.05). Through secondary analysis of publicly available datasets, we found that these genes were enriched for significant genes also present in FAP CRC and non-hereditary CRC datasets, including a subset that were unique to EOCRC. By exposing FAP colon organoids to a three-day ethanol treatment, we found that two EOCRC-relevant genes were also targets of CRC related lifestyle factors. Our data provides unique insight into the potential, early mechanisms of CRC development in colon epithelial cells, which may provide biomarkers for patient monitoring. We also show how modifiable lifestyle factors may further alter genes relevant to EOCRC, adding weight to the hypothesis that such factors represent an important contributor to increased EOCRC incidence.
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Affiliation(s)
- Matthew A. Devall
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen Eaton
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Mourad W. Ali
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Steven M. Powell
- Digestive Health Center, University of Virginia, Charlottesville, VA 22903, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22911, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22911, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
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6
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Sologova SS, Zavadskiy SP, Mokhosoev IM, Moldogazieva NT. Short Linear Motifs Orchestrate Functioning of Human Proteins during Embryonic Development, Redox Regulation, and Cancer. Metabolites 2022; 12:metabo12050464. [PMID: 35629968 PMCID: PMC9144484 DOI: 10.3390/metabo12050464] [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: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/16/2022] Open
Abstract
Short linear motifs (SLiMs) are evolutionarily conserved functional modules of proteins that represent amino acid stretches composed of 3 to 10 residues. The biological activities of two short peptide segments of human alpha-fetoprotein (AFP), a major embryo-specific and cancer-related protein, have been confirmed experimentally. This is a heptapeptide segment LDSYQCT in domain I designated as AFP14–20 and a nonapeptide segment EMTPVNPGV in domain III designated as GIP-9. In our work, we searched the UniprotKB database for human proteins that contain SLiMs with sequence similarity to the both segments of human AFP and undertook gene ontology (GO)-based functional categorization of retrieved proteins. Gene set enrichment analysis included GO terms for biological process, molecular function, metabolic pathway, KEGG pathway, and protein–protein interaction (PPI) categories. We identified the SLiMs of interest in a variety of non-homologous proteins involved in multiple cellular processes underlying embryonic development, cancer progression, and, unexpectedly, the regulation of redox homeostasis. These included transcription factors, cell adhesion proteins, ubiquitin-activating and conjugating enzymes, cell signaling proteins, and oxidoreductase enzymes. They function by regulating cell proliferation and differentiation, cell cycle, DNA replication/repair/recombination, metabolism, immune/inflammatory response, and apoptosis. In addition to the retrieved genes, new interacting genes were identified. Our data support the hypothesis that conserved SLiMs are incorporated into non-homologous proteins to serve as functional blocks for their orchestrated functioning.
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Affiliation(s)
- Susanna S. Sologova
- Nelyubin Institute of Pharmacy, Sechenov First Moscow State Medical University, (Sechenov University), 119991 Moscow, Russia; (S.S.S.); (S.P.Z.)
| | - Sergey P. Zavadskiy
- Nelyubin Institute of Pharmacy, Sechenov First Moscow State Medical University, (Sechenov University), 119991 Moscow, Russia; (S.S.S.); (S.P.Z.)
| | - Innokenty M. Mokhosoev
- Department of Biochemistry and Molecular Biology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;
| | - Nurbubu T. Moldogazieva
- Nelyubin Institute of Pharmacy, Sechenov First Moscow State Medical University, (Sechenov University), 119991 Moscow, Russia; (S.S.S.); (S.P.Z.)
- Correspondence:
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7
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Konger RL, Derr-Yellin E, Zimmers TA, Katona T, Xuei X, Liu Y, Zhou HM, Simpson ER, Turner MJ. Epidermal PPARγ Is a Key Homeostatic Regulator of Cutaneous Inflammation and Barrier Function in Mouse Skin. Int J Mol Sci 2021; 22:ijms22168634. [PMID: 34445339 PMCID: PMC8395473 DOI: 10.3390/ijms22168634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 01/10/2023] Open
Abstract
Both agonist studies and loss-of-function models indicate that PPARγ plays an important role in cutaneous biology. Since PPARγ has a high level of basal activity, we hypothesized that epidermal PPARγ would regulate normal homeostatic processes within the epidermis. In this current study, we performed mRNA sequencing and differential expression analysis of epidermal scrapings from knockout mice and wildtype littermates. Pparg-/-epi mice exhibited a 1.5-fold or greater change in the expression of 11.8% of 14,482 identified transcripts. Up-regulated transcripts included those for a large number of cytokines/chemokines and their receptors, as well as genes associated with inflammasome activation and keratinization. Several of the most dramatically up-regulated pro-inflammatory genes in Pparg-/-epi mouse skin included Igfl3, 2610528A11Rik, and Il1f6. RT-PCR was performed from RNA obtained from non-lesional full-thickness skin and verified a marked increase in these transcripts, as well as transcripts for Igflr1, which encodes the receptor for Igfl3, and the 2610528A11Rik receptor (Gpr15). Transcripts for Il4 were detected in Pparg-/-epi mouse skin, but transcripts for Il17 and Il22 were not detected. Down-regulated transcripts included sebaceous gland markers and a number of genes associated with lipid barrier formation. The change in these transcripts correlates with an asebia phenotype, increased transepidermal water loss, alopecia, dandruff, and the appearance of spontaneous inflammatory skin lesions. Histologically, non-lesional skin showed hyperkeratosis, while inflammatory lesions were characterized by dermal inflammation and epidermal acanthosis, spongiosis, and parakeratosis. In conclusion, loss of epidermal Pparg alters a substantial set of genes that are associated with cutaneous inflammation, keratinization, and sebaceous gland function. The data indicate that epidermal PPARγ plays an important role in homeostatic epidermal function, particularly epidermal differentiation, barrier function, sebaceous gland development and function, and inflammatory signaling.
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Affiliation(s)
- Raymond L. Konger
- Department of Pathology & Laboratory Medicine, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN 46202, USA; (E.D.-Y.); (T.K.)
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- The Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (T.A.Z.); (Y.L.)
- Correspondence: ; Tel.: +1-317-274-4154
| | - Ethel Derr-Yellin
- Department of Pathology & Laboratory Medicine, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN 46202, USA; (E.D.-Y.); (T.K.)
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Teresa A. Zimmers
- The Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (T.A.Z.); (Y.L.)
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Terrence Katona
- Department of Pathology & Laboratory Medicine, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN 46202, USA; (E.D.-Y.); (T.K.)
| | - Xiaoling Xuei
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Yunlong Liu
- The Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (T.A.Z.); (Y.L.)
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Hong-Ming Zhou
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (H.-M.Z.); (M.J.T.)
| | - Ed Ronald Simpson
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (H.-M.Z.); (M.J.T.)
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Matthew J. Turner
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (H.-M.Z.); (M.J.T.)
- Department of Dermatology, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN 46202, USA
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8
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Wang H, Shi Y, Chen CH, Wen Y, Zhou Z, Yang C, Sun J, Du G, Wu J, Mao X, Liu R, Chen C. KLF5-induced lncRNA IGFL2-AS1 promotes basal-like breast cancer cell growth and survival by upregulating the expression of IGFL1. Cancer Lett 2021; 515:49-62. [PMID: 34052325 DOI: 10.1016/j.canlet.2021.04.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022]
Abstract
Basal-like breast cancer (BLBC) is the most malignant subtype of breast cancer and has a poor prognosis. Kruppel-like factor 5 (KLF5) is an oncogenic transcription factor in BLBCs. The mechanism by which KLF5 promotes BLBC by regulating the transcription of lncRNAs has not been fully elucidated. In this study, we discovered that lncRNA IGFL2-AS1 is a downstream target gene of KLF5 and that IGFL2-AS1 mediates the pro-proliferation and pro-survival functions of KLF5. Additionally, we demonstrated that IGFL2-AS1 functions by upregulating the transcription of its neighboring gene IGFL1 via two independent mechanisms. On the one hand, nuclear IGFL2-AS1 promotes the formation of a KLF5/TEAD4 transcriptional complex at the IGFL1 gene enhancer. On the other hand, cytoplasmic IGFL2-AS1 inhibits the expression of miR4795-3p, which targets the IGFL1 gene. TNFα induces the expression of IGFL2-AS1 and IGFL1 through KLF5. Taken together, the results of this study indicate that IGFL2-AS1 and IGFL1 may serve as new therapeutic targets for BLBCs.
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Affiliation(s)
- Haixia Wang
- School of Life Science, University of Science & Technology of China, Hefei, 230027, Anhui, China; Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yujie Shi
- Department of Pathology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
| | - Chuan-Huizi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yi Wen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhongmei Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Chuanyu Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jian Sun
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Guangshi Du
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jiao Wu
- Department of the Second Medical Oncology, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, 650118, China
| | - Xiaoyun Mao
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Rong Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China; Translational Cancer Research Center, Peking University First Hospital, Beijing, 100034, China.
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
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9
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Bashir NZ. The role of insulin-like growth factors in modulating the activity of dental mesenchymal stem cells. Arch Oral Biol 2020; 122:104993. [PMID: 33259987 DOI: 10.1016/j.archoralbio.2020.104993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/14/2020] [Accepted: 11/19/2020] [Indexed: 12/27/2022]
Abstract
Regenerative treatment protocols are an exciting prospect in the management of oral pathology, as they allow for tissues to be restored to their original form and function, as compared to the reparative healing mechanisms which currently govern the outcomes of the majority of dental treatment. Stem cell therapy presents with a great deal of untapped potential in this pursuit of tissue regeneration, and, in particular, mesenchymal stem cells (MSCs) derived from dental tissues are of specific relevance with regards to their applications in engineering craniofacial tissues. A number of mediatory factors are involved in modulating the actions of dental MSCs, and, of these, insulin like growth factors (IGFs) are known to have potent effects in governing the behavior of these cells. The IGF family comprises a number of primary ligands, receptors, and binding proteins which are known to modulate the key properties of dental MSCs, such as their proliferation rates, differentiation potential, and mineralisation. The aims of this review are three-fold: (i) to present an overview of dental MSCs and the role of growth factors in modulating their characteristics, (ii) to discuss in greater detail the specific role of IGFs and the benefits they may convey for tissue engineering, and (iii) to provide a summary of potential for in vivo clinical translation of the current in vitro body of evidence.
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10
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Song W, Shao Y, He X, Gong P, Yang Y, Huang S, Zeng Y, Wei L, Zhang J. IGFLR1 as a Novel Prognostic Biomarker in Clear Cell Renal Cell Cancer Correlating With Immune Infiltrates. Front Mol Biosci 2020; 7:565173. [PMID: 33324675 PMCID: PMC7726438 DOI: 10.3389/fmolb.2020.565173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022] Open
Abstract
Objective Insulin Growth Factor-Like receptor 1 (IGFLR1) reflects progressive disease and confers a poor prognosis in clear cell renal cell cancer (ccRCC). However, extensive studies highlighting the mechanisms involved in how IGFLR1 triggers the progression of ccRCC remain lacking. Methods In the present study, the expression level of IGFLR1 mRNA and correlation between IGFLR1 expression and prognosis of ccRCC were analyzed based on The Cancer Genome Atlas (TCGA) ccRCC cohort. Further, we analyzed methylation and copy number variation to try to explain the difference in IGFLR1 expression. Subsequently, we investigated the correlation between IGFLR1 and tumor-infiltrating immune cells with the aid of TIMER (Tumor Immune Estimation Resource). The potential candidates' genes associated with IGFLR1 were screened by variation analysis, which were used for further enrichment analysis of signaling pathways and immune gene sets to infer the certain function and corresponding mechanisms in which IGFLR1 was involved in ccRCC. Finally, we establish prognostic risk models using multivariate Cox regression analysis and analyzed the possible involvement of IGFLR1 in chemotherapeutic drug resistance. Results The results showed that upregulated IGFLR1 was detected in ccRCC compared with para-cancer tissues and significantly affected the prognosis of ccRCC (overall survival: Logrank p < 0.0001; disease free survival: Logrank p = 0.022). Univariate and multivariate analyses indicated that IGFLR1 was an independent prognostic factor for ccRCC (HR = 2.064, p = 0.006) and the risk prognostic model based on age, M, level of platelet and calcium and IGFLR1 expression had satisfying predictive ability. The correlation analysis showed that the expression level of IGFLR1 was positively correlated with the abundance of myeloid derived suppressor cell and their marker genes in ccRCC significantly. IGFLR1 may be related to the regulatory activation, intercellular adhesion of lymphocytes and drug resistance in cancer. Conclusion These findings suggested that IGFLR1 was significantly associated with the prognosis in a variety of cancers, particularly ccRCC. IGFLR1 may play an important role in tumor related immune infiltration and showed potential diagnostic, therapeutic and prognostic value in ccRCC.
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Affiliation(s)
- Wenjing Song
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Youcheng Shao
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xin He
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Pengju Gong
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Yan Yang
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Sirui Huang
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Yifan Zeng
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Lei Wei
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jingwei Zhang
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
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11
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An Ixodes scapularis Protein Disulfide Isomerase Contributes to Borrelia burgdorferi Colonization of the Vector. Infect Immun 2020; 88:IAI.00426-20. [PMID: 32928964 PMCID: PMC7671890 DOI: 10.1128/iai.00426-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 08/31/2020] [Indexed: 01/06/2023] Open
Abstract
Borrelia burgdorferi causes Lyme disease, the most common tick-transmitted illness in North America. When Ixodes scapularis feed on an infected vertebrate host, spirochetes enter the tick gut along with the bloodmeal and colonize the vector. Here, we show that a secreted tick protein, I. scapularis protein disulfide isomerase A3 (IsPDIA3), enhances B. burgdorferi colonization of the tick gut. I. scapularis ticks in which ispdiA3 has been knocked down using RNA interference have decreased spirochete colonization of the tick gut after engorging on B. burgdorferi-infected mice. Moreover, administration of IsPDIA3 antiserum to B. burgdorferi-infected mice reduced the ability of spirochetes to colonize the tick when feeding on these animals. We show that IsPDIA3 modulates inflammatory responses at the tick bite site, potentially facilitating spirochete survival at the vector-host interface as it exits the vertebrate host to enter the tick gut. These data provide functional insights into the complex interactions between B. burgdorferi and its arthropod vector and suggest additional targets to interfere with the spirochete life cycle.
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12
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Singh S, Marquardt Y, Rimal R, Nishiguchi A, Huth S, Akashi M, Moeller M, Baron JM. Long-Term and Clinically Relevant Full-Thickness Human Skin Equivalent for Psoriasis. ACS APPLIED BIO MATERIALS 2020; 3:6639-6647. [PMID: 35019390 PMCID: PMC9062876 DOI: 10.1021/acsabm.0c00202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Psoriasis
is an incurable, immune-mediated inflammatory disease
characterized by the hyperproliferation and abnormal differentiation
of keratinocytes. To study in depth the pathogenesis of this disease
and possible therapy options suitable, pre-clinical models are required.
Three-dimensional skin equivalents are a potential alternative to
simplistic monolayer cultures and immunologically different animal
models. However, current skin equivalents lack long-term stability,
which jeopardizes the possibility to simulate the complex disease-specific
phenotype followed by long-term therapeutic treatment. To overcome
this limitation, the cell coating technique was used to fabricate
full-thickness human skin equivalents (HSEs). This rapid and scaffold-free
fabrication method relies on coating cell membranes with nanofilms
using layer-by-layer assembly, thereby allowing extended cultivation
of HSEs up to 49 days. The advantage in time is exploited to develop
a model that not only forms a disease phenotype but can also be used
to monitor the effects of topical or systemic treatment. To generate
a psoriatic phenotype, the HSEs were stimulated with recombinant human
interleukin 17A (rhIL-17A). This was followed by systemic treatment
of the HSEs with the anti-IL-17A antibody secukinumab in the presence
of rhIL-17A. Microarray and RT-PCR analysis demonstrated that HSEs
treated with rhIL-17A showed downregulation of differentiation markers
and upregulation of chemokines and cytokines, while treatment with
anti-IL-17A antibody reverted these gene regulations. Gene ontology
analysis revealed the proinflammatory and chemotactic effects of rhIL-17A
on the established HSEs. These data demonstrated, at the molecular
level, the effects of anti-IL-17A antibody on rhIL-17A-induced gene
regulations. This shows the physiological relevance of the developed
HSE and opens venues for its use as an alternative to ex vivo skin explants and animal testing.
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Affiliation(s)
- Smriti Singh
- DWI-Leibniz Institute for Interactive Materials, Forkenbeckstrasse 50, Aachen 52074, Germany
| | - Yvonne Marquardt
- Department of Dermatology and Allergology, University Hospital, RWTH Aachen University, Aachen 52074, Germany
| | - Rahul Rimal
- DWI-Leibniz Institute for Interactive Materials, Forkenbeckstrasse 50, Aachen 52074, Germany
| | - Akihiro Nishiguchi
- DWI-Leibniz Institute for Interactive Materials, Forkenbeckstrasse 50, Aachen 52074, Germany
- Research Center for Functional Materials, National Institute for Materials Science, Tsukuba, Ibaraki 305-0044, Japan
| | - Sebastian Huth
- Department of Dermatology and Allergology, University Hospital, RWTH Aachen University, Aachen 52074, Germany
| | - Mitsuru Akashi
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Martin Moeller
- DWI-Leibniz Institute for Interactive Materials, Forkenbeckstrasse 50, Aachen 52074, Germany
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Science, Vavilova 28, Moscow 119991, Russia
| | - Jens M. Baron
- Department of Dermatology and Allergology, University Hospital, RWTH Aachen University, Aachen 52074, Germany
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13
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Zhang L, Zhang Z. Recharacterizing Tumor-Infiltrating Lymphocytes by Single-Cell RNA Sequencing. Cancer Immunol Res 2020; 7:1040-1046. [PMID: 31262773 DOI: 10.1158/2326-6066.cir-18-0658] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/06/2019] [Accepted: 05/02/2019] [Indexed: 11/16/2022]
Abstract
T cells are central players in cancer immunotherapy. Despite much concentrated effort on the study of tumor-infiltrating lymphocytes (TIL), such as T cells, a series of fundamental properties that include heterogeneity, clonal expansion, migration, and functional state transition remain elusive. Advances of single-cell sequencing have enabled the detailed characterization of immune cells in tumors and have vastly improved our understanding of less-defined cell subsets. Here, we discuss the current strategies for uncovering the heterogeneity of TILs, and how the deep transcriptome coupled with T-cell receptor analysis enhances the understanding of detailed properties of T-cell subsets. We further discuss the identification of novel T-cell markers with therapeutic or prognosis potentials, and highlight distinct T-cell properties among different cancer indications.
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Affiliation(s)
- Lei Zhang
- Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, BIOPIC and School of Life Sciences, Peking University, Beijing, China
| | - Zemin Zhang
- Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, BIOPIC and School of Life Sciences, Peking University, Beijing, China.
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14
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PCDH7 interacts with GluN1 and regulates dendritic spine morphology and synaptic function. Sci Rep 2020; 10:10951. [PMID: 32616769 PMCID: PMC7331671 DOI: 10.1038/s41598-020-67831-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 06/12/2020] [Indexed: 01/28/2023] Open
Abstract
The N-terminal domain (NTD) of the GluN1 subunit (GluN1-NTD) is important for NMDA receptor structure and function, but the interacting proteins of the GluN1-NTD are not well understood. Starting with an unbiased screen of ~ 1,500 transmembrane proteins using the purified GluN1-NTD protein as a bait, we identify Protocadherin 7 (PCDH7) as a potential interacting protein. PCDH7 is highly expressed in the brain and has been linked to CNS disorders, including epilepsy. Using primary neurons and brain slice cultures, we find that overexpression and knockdown of PCDH7 induce opposing morphological changes of dendritic structures. We also find that PCDH7 overexpression reduces synaptic NMDA receptor currents. These data show that PCDH7 can regulate dendritic spine morphology and synaptic function, possibly via interaction with the GluN1 subunit.
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15
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Ehmann R, Brandes K, Antwerpen M, Walter M, V Schlippenbach K, Stegmaier E, Essbauer S, Bugert J, Teifke JP, Meyer H. Molecular and genomic characterization of a novel equine molluscum contagiosum-like virus. J Gen Virol 2020; 102. [PMID: 31922947 PMCID: PMC8515872 DOI: 10.1099/jgv.0.001357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cases of pox-like lesions in horses and donkeys have been associated with poxviruses belonging to different genera of the family Poxviridae. These include the orthopoxviruses vaccinia virus (VACV), horsepoxvirus (HPXV) and cowpoxvirus (CPXV), as well as a potentially novel parapoxvirus and molluscum contagiosum virus (MOCV). However, with the exception of VACV, HPXV and CPXV, the genomic characterization of the causative agents remains largely elusive with only single short genome fragments available. Here we present the first full-length genome sequence of an equine molluscum contagiosum-like virus (EMCLV) directly determined from skin biopsies of a horse with generalized papular dermatitis. Histopathological analysis of the lesions revealed severe epidermal hyperplasia with numerous eosinophilic inclusion bodies within keratinocytes. Virions were detected in the lesions in embedded tissue by transmission electron microscopy. The genome sequence determined by next- and third-generation sequencing comprises 166 843 nt with inverted terminal repeats (ITRs) of 3473 nt. Overall, 20 of the predicted 159 ORFs have no equivalents in other poxviruses. Intriguingly, two of these ORFs were identified to encode homologues of mammalian proteins involved in immune signalling pathways, namely secreted and transmembrane protein 1 (SECTM1) and insulin growth factor-like family receptor 1 (IGFLR1), that were not described in any virus family so far. Phylogenetic analysis with all relevant representatives of the Poxviridae suggests that EMCLV should be nominated as a new species within the genus Molluscipoxvirus.
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Affiliation(s)
- Rosina Ehmann
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - K Brandes
- Animal Pathology Augsburg, Augsburg, Germany
| | - M Antwerpen
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - M Walter
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | | | - S Essbauer
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - J Bugert
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - J P Teifke
- Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | - H Meyer
- Bundeswehr Institute of Microbiology, Munich, Germany
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16
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Alriyami M, Marchand L, Li Q, Du X, Olivier M, Polychronakos C. Clonal copy-number mosaicism in autoreactive T lymphocytes in diabetic NOD mice. Genome Res 2019; 29:1951-1961. [PMID: 31694869 PMCID: PMC6886509 DOI: 10.1101/gr.247882.118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 11/02/2019] [Indexed: 01/10/2023]
Abstract
Concordance for type 1 diabetes (T1D) is far from 100% in monozygotic twins and in inbred nonobese diabetic (NOD) mice, despite genetic identity and shared environment during incidence peak years. This points to stochastic determinants, such as postzygotic mutations (PZMs) in the expanding antigen-specific autoreactive T cell lineages, by analogy to their role in the expanding tumor lineage in cancer. Using comparative genomic hybridization of DNA from pancreatic lymph-node memory CD4+ T cells of 25 diabetic NOD mice, we found lymphocyte-exclusive mosaic somatic copy-number aberrations (CNAs) with highly nonrandom independent involvement of the same gene(s) across different mice, some with an autoimmunity association (e.g., Ilf3 and Dgka). We confirmed genes of interest using the gold standard approach for CNA quantification, multiplex ligation-dependent probe amplification (MLPA), as an independent method. As controls, we examined lymphocytes expanded during normal host defense (17 NOD and BALB/c mice infected with Leishmania major parasite). Here, CNAs found were fewer and significantly smaller compared to those in autoreactive cells (P = 0.0019). We determined a low T cell clonality for our samples suggesting a prethymic formation of these CNAs. In this study, we describe a novel, unexplored phenomenon of a potential causal contribution of PZMs in autoreactive T cells in T1D pathogenesis. We expect that exploration of point mutations and studies in human T cells will enable the further delineation of driver genes to target for functional studies. Our findings challenge the classical notions of autoimmunity and open conceptual avenues toward individualized prevention and therapeutics.
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Affiliation(s)
- Maha Alriyami
- The Endocrine Genetics Laboratory, Child Health and Human Development Program and Department of Pediatrics, McGill University Health Centre Research Institute, Montreal, Quebec H3H 1P3, Canada.,Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, 123, Muscat, Oman
| | - Luc Marchand
- The Endocrine Genetics Laboratory, Child Health and Human Development Program and Department of Pediatrics, McGill University Health Centre Research Institute, Montreal, Quebec H3H 1P3, Canada
| | - Quan Li
- The Endocrine Genetics Laboratory, Child Health and Human Development Program and Department of Pediatrics, McGill University Health Centre Research Institute, Montreal, Quebec H3H 1P3, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, ON M5G 2C1, Canada
| | - Xiaoyu Du
- The Endocrine Genetics Laboratory, Child Health and Human Development Program and Department of Pediatrics, McGill University Health Centre Research Institute, Montreal, Quebec H3H 1P3, Canada
| | - Martin Olivier
- Departments of Medicine, Microbiology, and Immunology, McGill University Health Centre Research Institute, Montreal, Quebec H3H 1P3, Canada
| | - Constantin Polychronakos
- The Endocrine Genetics Laboratory, Child Health and Human Development Program and Department of Pediatrics, McGill University Health Centre Research Institute, Montreal, Quebec H3H 1P3, Canada
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17
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Kitano J, Ishikawa A, Kusakabe M. Parallel transcriptome evolution in stream threespine sticklebacks. Dev Growth Differ 2018; 61:104-113. [DOI: 10.1111/dgd.12576] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/05/2018] [Accepted: 10/05/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Jun Kitano
- Division of Ecological Genetics; National Institute of Genetics; Mishima, Shizuoka Japan
| | - Asano Ishikawa
- Division of Ecological Genetics; National Institute of Genetics; Mishima, Shizuoka Japan
| | - Makoto Kusakabe
- Department of Biological Science; Faculty of Science; Shizuoka University; Surugaku, Shizuoka Japan
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18
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Lineage tracking reveals dynamic relationships of T cells in colorectal cancer. Nature 2018; 564:268-272. [PMID: 30479382 DOI: 10.1038/s41586-018-0694-x] [Citation(s) in RCA: 639] [Impact Index Per Article: 106.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 10/19/2018] [Indexed: 01/26/2023]
Abstract
T cells are key elements of cancer immunotherapy1 but certain fundamental properties, such as the development and migration of T cells within tumours, remain unknown. The enormous T cell receptor (TCR) repertoire, which is required for the recognition of foreign and self-antigens2, could serve as lineage tags to track these T cells in tumours3. Here we obtained transcriptomes of 11,138 single T cells from 12 patients with colorectal cancer, and developed single T cell analysis by RNA sequencing and TCR tracking (STARTRAC) indices to quantitatively analyse the dynamic relationships among 20 identified T cell subsets with distinct functions and clonalities. Although both CD8+ effector and 'exhausted' T cells exhibited high clonal expansion, they were independently connected with tumour-resident CD8+ effector memory cells, implicating a TCR-based fate decision. Of the CD4+ T cells, most tumour-infiltrating T regulatory (Treg) cells showed clonal exclusivity, whereas certain Treg cell clones were developmentally linked to several T helper (TH) cell clones. Notably, we identified two IFNG+ TH1-like cell clusters in tumours that were associated with distinct IFNγ-regulating transcription factors -the GZMK+ effector memory T cells, which were associated with EOMES and RUNX3, and CXCL13+BHLHE40+ TH1-like cell clusters, which were associated with BHLHE40. Only CXCL13+BHLHE40+ TH1-like cells were preferentially enriched in patients with microsatellite-instable tumours, and this might explain their favourable responses to immune-checkpoint blockade. Furthermore, IGFLR1 was highly expressed in both CXCL13+BHLHE40+ TH1-like cells and CD8+ exhausted T cells and possessed co-stimulatory functions. Our integrated STARTRAC analyses provide a powerful approach to dissect the T cell properties in colorectal cancer comprehensively, and could provide insights into the dynamic relationships of T cells in other cancers.
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19
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Tracy KM, Tye CE, Page NA, Fritz AJ, Stein JL, Lian JB, Stein GS. Selective expression of long non-coding RNAs in a breast cancer cell progression model. J Cell Physiol 2017; 233:1291-1299. [PMID: 28488769 DOI: 10.1002/jcp.25997] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 01/01/2023]
Abstract
Long non-coding RNAs (lncRNAs) are acknowledged as regulators of cancer biology and pathology. Our goal was to perform a stringent profiling of breast cancer cell lines that represent disease progression. We used the MCF-10 series, which includes the normal-like MCF-10A, HRAS-transformed MCF-10AT1 (pre-malignant), and MCF-10CA1a (malignant) cells, to perform transcriptome wide sequencing. From these data, we have identified 346 lncRNAs with dysregulated expression across the progression series. By comparing lncRNAs from these datasets to those from an additional set of cell lines that represent different disease stages and subtypes, MCF-7 (early stage, luminal), and MDA-MB-231 (late stage, basal), 61 lncRNAs that are associated with breast cancer progression were identified. Querying breast cancer patient data from The Cancer Genome Atlas, we selected a lncRNA, IGF-like family member 2 antisense RNA 1 (IGFL2-AS1), of potential clinical relevance for functional characterization. Among the 61 lncRNAs, IGFL2-AS1 was the most significantly decreased. Our results indicate that this lncRNA plays a role in downregulating its nearest neighbor, IGFL1, and affects migration of breast cancer cells. Furthermore, the lncRNAs we identified provide a valuable resource to mechanistically and clinically understand the contribution of lncRNAs in breast cancer progression.
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Affiliation(s)
- Kirsten M Tracy
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Coralee E Tye
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Natalie A Page
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
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20
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Yeh FL, Wang Y, Tom I, Gonzalez LC, Sheng M. TREM2 Binds to Apolipoproteins, Including APOE and CLU/APOJ, and Thereby Facilitates Uptake of Amyloid-Beta by Microglia. Neuron 2016; 91:328-40. [DOI: 10.1016/j.neuron.2016.06.015] [Citation(s) in RCA: 466] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 05/14/2016] [Accepted: 06/07/2016] [Indexed: 11/30/2022]
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21
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Martinez-Martin N, Ramani SR, Hackney JA, Tom I, Wranik BJ, Chan M, Wu J, Paluch MT, Takeda K, Hass PE, Clark H, Gonzalez LC. The extracellular interactome of the human adenovirus family reveals diverse strategies for immunomodulation. Nat Commun 2016; 7:11473. [PMID: 27145901 PMCID: PMC4858740 DOI: 10.1038/ncomms11473] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 03/30/2016] [Indexed: 01/06/2023] Open
Abstract
Viruses encode secreted and cell-surface expressed proteins essential to modulate host immune defenses and establish productive infections. However, to date there has been no systematic study of the extracellular interactome of any human virus. Here we utilize the E3 proteins, diverse and rapidly evolving transmembrane-containing proteins encoded by human adenoviruses, as a model system to survey the extracellular immunomodulatory landscape. From a large-scale protein interaction screen against a microarray of more than 1,500 human proteins, we find and validate 51 previously unidentified virus–host interactions. Our results uncover conserved strategies as well as substantial diversity and multifunctionality in host targeting within and between viral species. Prominent modulation of the leukocyte immunoglobulin-like and signalling lymphocyte activation molecule families and a number of inhibitory receptors were identified as hubs for viral perturbation, suggesting unrecognized immunoregulatory strategies. We describe a virus–host extracellular interaction map of unprecedented scale that provides new insights into viral immunomodulation. Viruses interact with their hosts via secreted and membrane-bound proteins to affect host immune responses and virulence. Here the authors contribute to our understanding of this relationship with an extracellular interaction map of human and adenoviral E3 immunomodulatory proteins.
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Affiliation(s)
- Nadia Martinez-Martin
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Sree R Ramani
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Jason A Hackney
- Department of Bioinformatics and Computational Biology, Genentech, 455 East Grand Avenue, South San Francisco, California 94080, USA
| | - Irene Tom
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Bernd J Wranik
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Michelle Chan
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Johnny Wu
- Department of Bioinformatics and Computational Biology, Genentech, 455 East Grand Avenue, South San Francisco, California 94080, USA
| | - Maciej T Paluch
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Kentaro Takeda
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Philip E Hass
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Hilary Clark
- Department of Bioinformatics and Computational Biology, Genentech, 455 East Grand Avenue, South San Francisco, California 94080, USA
| | - Lino C Gonzalez
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
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Jaworski A, Tom I, Tong RK, Gildea HK, Koch AW, Gonzalez LC, Tessier-Lavigne M. Operational redundancy in axon guidance through the multifunctional receptor Robo3 and its ligand NELL2. Science 2015; 350:961-5. [PMID: 26586761 DOI: 10.1126/science.aad2615] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Axon pathfinding is orchestrated by numerous guidance cues, including Slits and their Robo receptors, but it remains unclear how information from multiple cues is integrated or filtered. Robo3, a Robo family member, allows commissural axons to reach and cross the spinal cord midline by antagonizing Robo1/2-mediated repulsion from midline-expressed Slits and potentiating deleted in colorectal cancer (DCC)-mediated midline attraction to Netrin-1, but without binding either Slits or Netrins. We identified a secreted Robo3 ligand, neural epidermal growth factor-like-like 2 (NELL2), which repels mouse commissural axons through Robo3 and helps steer them to the midline. These findings identify NELL2 as an axon guidance cue and establish Robo3 as a multifunctional regulator of pathfinding that simultaneously mediates NELL2 repulsion, inhibits Slit repulsion, and facilitates Netrin attraction to achieve a common guidance purpose.
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Affiliation(s)
- Alexander Jaworski
- Division of Research, Genentech, South San Francisco, CA 94080, USA. Laboratory of Brain Development and Repair, The Rockefeller University, New York, NY 10065, USA. Department of Neuroscience, Brown University, Providence, RI 02912, USA.
| | - Irene Tom
- Department of Protein Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Raymond K Tong
- Department of Protein Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Holly K Gildea
- Department of Neuroscience, Brown University, Providence, RI 02912, USA
| | - Alexander W Koch
- Department of Protein Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Lino C Gonzalez
- Department of Protein Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Marc Tessier-Lavigne
- Division of Research, Genentech, South San Francisco, CA 94080, USA. Laboratory of Brain Development and Repair, The Rockefeller University, New York, NY 10065, USA.
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23
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Frisch CM, Zimmermann K, Zilleßen P, Pfeifer A, Racké K, Mayer P. Non-small cell lung cancer cell survival crucially depends on functional insulin receptors. Endocr Relat Cancer 2015; 22:609-21. [PMID: 26113601 DOI: 10.1530/erc-14-0581] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/28/2015] [Indexed: 12/19/2022]
Abstract
Insulin plays an important role as a growth factor and its contribution to tumor proliferation is intensely discussed. It acts via the cognate insulin receptor (IR) but can also activate the IGF1 receptor (IGF1R). Apart from increasing proliferation, insulin might have additional effects in lung cancer. Therefore, we investigated insulin action and effects of IR knockdown (KD) in three (NCI-H292, NCI-H226 and NCI-H460) independent non-small cell lung cancer (NSCLC) cell lines. All lung cancer lines studied were found to express IR, albeit with marked differences in the ratio of the two variants IR-A and IR-B. Insulin activated the classical signaling pathway with IR autophosphorylation and Akt phosphorylation. Moreover, activation of MAPK was observed in H292 cells, accompanied by enhanced proliferation. Lentiviral shRNA IR KD caused strong decrease in survival of all three lines, indicating that the effects of insulin in lung cancer go beyond enhancing proliferation. Unspecific effects were ruled out by employing further shRNAs and different insulin-responsive cells (human pre-adipocytes) for comparison. Caspase assays demonstrated that IR KD strongly induced apoptosis in these lung cancer cells, providing the physiological basis of the rapid cell loss. In search for the underlying mechanism, we analyzed alterations in the gene expression profile in response to IR KD. A strong induction of certain cytokines (e.g. IL20 and tumour necrosis factor) became obvious and it turned out that these cytokines trigger apoptosis in the NSCLC cells tested. This indicates a novel role of IR in tumor cell survival via suppression of pro-apoptotic cytokines.
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Affiliation(s)
- Carolin Maria Frisch
- Institute of Pharmacology and ToxicologyUniversity of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, GermanyFederal Institute for Drugs and Medical Devices (BfArM)Kurt-Georg-Kiesinger-Allee 3, 53175 Bonn, Germany
| | - Katrin Zimmermann
- Institute of Pharmacology and ToxicologyUniversity of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, GermanyFederal Institute for Drugs and Medical Devices (BfArM)Kurt-Georg-Kiesinger-Allee 3, 53175 Bonn, Germany
| | - Pia Zilleßen
- Institute of Pharmacology and ToxicologyUniversity of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, GermanyFederal Institute for Drugs and Medical Devices (BfArM)Kurt-Georg-Kiesinger-Allee 3, 53175 Bonn, Germany
| | - Alexander Pfeifer
- Institute of Pharmacology and ToxicologyUniversity of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, GermanyFederal Institute for Drugs and Medical Devices (BfArM)Kurt-Georg-Kiesinger-Allee 3, 53175 Bonn, Germany
| | - Kurt Racké
- Institute of Pharmacology and ToxicologyUniversity of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, GermanyFederal Institute for Drugs and Medical Devices (BfArM)Kurt-Georg-Kiesinger-Allee 3, 53175 Bonn, Germany
| | - Peter Mayer
- Institute of Pharmacology and ToxicologyUniversity of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, GermanyFederal Institute for Drugs and Medical Devices (BfArM)Kurt-Georg-Kiesinger-Allee 3, 53175 Bonn, Germany
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24
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Gordon WM, Zeller MD, Klein RH, Swindell WR, Ho H, Espetia F, Gudjonsson JE, Baldi PF, Andersen B. A GRHL3-regulated repair pathway suppresses immune-mediated epidermal hyperplasia. J Clin Invest 2014; 124:5205-18. [PMID: 25347468 DOI: 10.1172/jci77138] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/18/2014] [Indexed: 12/27/2022] Open
Abstract
Dermal infiltration of T cells is an important step in the onset and progression of immune-mediated skin diseases such as psoriasis; however, it is not known whether epidermal factors play a primary role in the development of these diseases. Here, we determined that the prodifferentiation transcription factor grainyhead-like 3 (GRHL3), which is essential during epidermal development, is dispensable for adult skin homeostasis, but required for barrier repair after adult epidermal injury. Consistent with activation of a GRHL3-regulated repair pathway in psoriasis, we found that GRHL3 is upregulated in lesional skin and binds known epidermal differentiation gene targets. Using an imiquimod-induced model of immune-mediated epidermal hyperplasia, we found that mice lacking GRHL3 have an exacerbated epidermal damage response, greater sensitivity to disease induction, delayed resolution of epidermal lesions, and resistance to anti-IL-22 therapy compared with WT animals. ChIP-Seq and gene expression profiling of murine skin revealed that while GRHL3 regulates differentiation pathways both during development and during repair from immune-mediated damage, it targets distinct sets of genes in the 2 processes. In particular, GRHL3 suppressed a number of alarmin and other proinflammatory genes after immune injury. This study identifies a GRHL3-regulated epidermal barrier repair pathway that suppresses disease initiation and helps resolve existing lesions in immune-mediated epidermal hyperplasia.
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25
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Haddick PCG, Tom I, Luis E, Quiñones G, Wranik BJ, Ramani SR, Stephan JP, Tessier-Lavigne M, Gonzalez LC. Defining the ligand specificity of the deleted in colorectal cancer (DCC) receptor. PLoS One 2014; 9:e84823. [PMID: 24400119 PMCID: PMC3882260 DOI: 10.1371/journal.pone.0084823] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 11/20/2013] [Indexed: 11/23/2022] Open
Abstract
The growth and guidance of many axons in the developing nervous system require Netrin-mediated activation of Deleted in Colorectal Cancer (DCC) and other still unknown signaling cues. Commissural axon guidance defects are more severe in DCC mutant mice than Netrin-1 mutant mice, suggesting additional DCC activating signals besides Netrin-1 are involved in proper axon growth. Here we report that interaction screens on extracellular protein microarrays representing over 1,000 proteins uniquely identified Cerebellin 4 (CBLN4), a member of the C1q-tumor necrosis factor (TNF) family, and Netrin-1 as extracellular DCC-binding partners. Immunofluorescence and radio-ligand binding studies demonstrate that Netrin-1 competes with CBLN4 binding at an overlapping site within the membrane-proximal fibronectin domains (FN) 4–6 of DCC and binds with ∼5-fold higher affinity. CBLN4 also binds to the DCC homolog, Neogenin-1 (NEO1), but with a lower affinity compared to DCC. CBLN4-null mice did not show a defect in commissural axons of the developing spinal cord but did display a transient increase in the number of wandering axons in the brachial plexus, consistent with a role in axon guidance. Overall, the data solidifies CBLN4 as a bona fide DCC ligand and strengthens its implication in axon guidance.
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Affiliation(s)
- Patrick C. G. Haddick
- Department of Neuroscience, Genentech, South San Francisco, California, United States of America
| | - Irene Tom
- Department of Protein Chemistry, Genentech, South San Francisco, California, United States of America
| | - Elizabeth Luis
- Department of Protein Chemistry, Genentech, South San Francisco, California, United States of America
| | - Gabriel Quiñones
- Department of Protein Chemistry, Genentech, South San Francisco, California, United States of America
| | - Bernd J. Wranik
- Department of Protein Chemistry, Genentech, South San Francisco, California, United States of America
| | - Sree R. Ramani
- Department of Protein Chemistry, Genentech, South San Francisco, California, United States of America
| | - Jean-Philippe Stephan
- Department of Protein Chemistry, Genentech, South San Francisco, California, United States of America
| | - Marc Tessier-Lavigne
- Department of Neuroscience, Genentech, South San Francisco, California, United States of America
| | - Lino C. Gonzalez
- Department of Protein Chemistry, Genentech, South San Francisco, California, United States of America
- * E-mail:
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26
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Guo P, Luo Y, Mai G, Zhang M, Wang G, Zhao M, Gao L, Li F, Zhou F. Gene expression profile based classification models of psoriasis. Genomics 2014; 103:48-55. [PMID: 24239985 DOI: 10.1016/j.ygeno.2013.11.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 08/13/2013] [Accepted: 11/01/2013] [Indexed: 02/05/2023]
Abstract
Psoriasis is an autoimmune disease, which symptoms can significantly impair the patient's life quality. It is mainly diagnosed through the visual inspection of the lesion skin by experienced dermatologists. Currently no cure for psoriasis is available due to limited knowledge about its pathogenesis and development mechanisms. Previous studies have profiled hundreds of differentially expressed genes related to psoriasis, however with no robust psoriasis prediction model available. This study integrated the knowledge of three feature selection algorithms that revealed 21 features belonging to 18 genes as candidate markers. The final psoriasis classification model was established using the novel Incremental Feature Selection algorithm that utilizes only 3 features from 2 unique genes, IGFL1 and C10orf99. This model has demonstrated highly stable prediction accuracy (averaged at 99.81%) over three independent validation strategies. The two marker genes, IGFL1 and C10orf99, were revealed as the upstream components of growth signal transduction pathway of psoriatic pathogenesis.
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Affiliation(s)
- Pi Guo
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Department of Public Health, Shantou University Medical College, No. 22 Xinling Road, Shantou, Guangdong 515041, PR China
| | - Youxi Luo
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China
| | - Guoqin Mai
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, Faculty of Infectious Diseases, University of Georgia, Athens, GA 30605, USA; Institute of Bioinformatics, University of Georgia, Athens, GA 30605, USA
| | - Guoqing Wang
- Department of Pathogeny Biology, Norman Bethune Medical College, Jilin University, Changchun, Jilin 130021, PR China; Department of Pathogeny Biology, Norman Bethune Medical College, Jilin University, Changchun, Jilin 130021, PR China
| | - Miaomiao Zhao
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China
| | - Liming Gao
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China
| | - Fan Li
- Department of Pathogeny Biology, Norman Bethune Medical College, Jilin University, Changchun, Jilin 130021, PR China; Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, Jilin 130021, PR China
| | - Fengfeng Zhou
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China.
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Advances in Mammalian cell line development technologies for recombinant protein production. Pharmaceuticals (Basel) 2013; 6:579-603. [PMID: 24276168 PMCID: PMC3817724 DOI: 10.3390/ph6050579] [Citation(s) in RCA: 199] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 03/28/2013] [Accepted: 04/10/2013] [Indexed: 01/20/2023] Open
Abstract
From 2006 to 2011, an average of 15 novel recombinant protein therapeutics have been approved by US Food and Drug Administration (FDA) annually. In addition, the expiration of blockbuster biologics has also spurred the emergence of biosimilars. The increasing numbers of innovator biologic products and biosimilars have thus fuelled the demand of production cell lines with high productivity. Currently, mammalian cell line development technologies used by most biopharmaceutical companies are based on either the methotrexate (MTX) amplification technology or the glutamine synthetase (GS) system. With both systems, the cell clones obtained are highly heterogeneous, as a result of random genome integration by the gene of interest and the gene amplification process. Consequently, large numbers of cell clones have to be screened to identify rare stable high producer cell clones. As such, the cell line development process typically requires 6 to 12 months and is a time, capital and labour intensive process. This article reviews established advances in protein expression and clone screening which are the core technologies in mammalian cell line development. Advancements in these component technologies are vital to improve the speed and efficiency of generating robust and highly productive cell line for large scale production of protein therapeutics.
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28
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Gonzalez LC. Protein microarrays, biosensors, and cell-based methods for secretome-wide extracellular protein-protein interaction mapping. Methods 2012; 57:448-58. [PMID: 22728035 DOI: 10.1016/j.ymeth.2012.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 06/02/2012] [Accepted: 06/08/2012] [Indexed: 12/15/2022] Open
Abstract
Approximately one quarter of all human genes encode proteins that function in the extracellular space or serve to bridge the extracellular and intracellular environments. Physical associations between these secretome proteins serve to regulate a wide range of biological activities and consequently represent important therapeutic targets. Moreover, some extracellular proteins are targeted by pathogens to allow host access or immune evasion. Despite the importance of extracellular protein-protein interactions, our knowledge in this area has remained sparse. Weak affinities and low abundance have often hindered efforts to identify these interactions using traditional methods such as biochemical purification and cDNA library expression cloning. Moreover, current large-scale protein-protein interaction mapping techniques largely under represent extracellular protein-protein interactions. This review highlights emerging biosensor and protein microarray technology, along with more traditional cell-based techniques, that are compatible with secretome-wide screens for extracellular protein-protein interaction discovery. A combination of these approaches will serve to rapidly expand our knowledge of the extracellular protein-protein interactome.
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Affiliation(s)
- Lino C Gonzalez
- Department of Protein Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, United States.
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29
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Udensi UK, Graham-Evans BE, Rogers C, Isokpehi RD. Cytotoxicity patterns of arsenic trioxide exposure on HaCaT keratinocytes. Clin Cosmet Investig Dermatol 2011; 4:183-90. [PMID: 22253543 PMCID: PMC3257883 DOI: 10.2147/ccid.s24677] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Arsenic is a ubiquitous environmental toxicant, and abnormalities of the skin are the most common outcomes of long-term, low-dose, chronic arsenic exposure. If the balance between keratinocyte proliferation, differentiation, and death is perturbed, pathologic changes of the epidermis may result, including psoriasis, atopic dermatitis, and certain forms of ichthyosis. Therefore, research investigations using in vitro human epidermal cells could help elucidate cellular and molecular processes in keratinocytes affected by arsenic. Data from such investigations could also provide the basis for developing cosmetic intervention for skin diseases caused by arsenic. METHODS The viability of HaCaT keratinocyte cultures with or without prior exposure to low-dose arsenic trioxide was compared for varying concentrations of arsenic trioxide over a time course of 14 days because in untreated control cultures, approximately 2 weeks is required to complete cell differentiation. Long-term cultures were established by culturing HaCaT cells on collagen IV, and cells were subsequently exposed to 0 parts per million (ppm), 1 ppm, 5 ppm, 7.5 ppm, 10 ppm, and 15 ppm of arsenic trioxide. The percentages of viable cells as well as DNA damage after exposure were determined on Day 2, Day 5, Day 8, and Day 14. RESULTS Using both statistical and visual analytics approaches for data analysis, we have observed a biphasic response at a 5 ppm dose with cell viability peaking on Day 8 in both chronic and acute exposures. Further, a low dose of 1 ppm arsenic trioxide enhanced HaCaT keratinocyte proliferation, whereas doses above 7.5 ppm inhibited growth. CONCLUSION The time course profiling of arsenic trioxide cytotoxicity using long-term HaCaT keratinocyte cultures presents an approach to modeling the human epidermal cellular responses to varying doses of arsenic trioxide treatment or exposure. A low dose of arsenic trioxide appears to aid cell growth but concomitantly disrupts the DNA transcription process.
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Affiliation(s)
- Udensi K Udensi
- RCMI-Center for Environmental Health, College of Science, Engineering and Technology, Jackson State University, Jackson, MS 39217
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Ramani SR, Tom I, Lewin-Koh N, Wranik B, Depalatis L, Zhang J, Eaton D, Gonzalez LC. A secreted protein microarray platform for extracellular protein interaction discovery. Anal Biochem 2011; 420:127-38. [PMID: 21982860 DOI: 10.1016/j.ab.2011.09.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 09/10/2011] [Accepted: 09/16/2011] [Indexed: 12/01/2022]
Abstract
Characterization of the extracellular protein interactome has lagged far behind that of intracellular proteins, where mass spectrometry and yeast two-hybrid technologies have excelled. Improved methods for identifying receptor-ligand and extracellular matrix protein interactions will greatly accelerate biological discovery in cell signaling and cellular communication. These technologies must be able to identify low-affinity binding events that are often observed between membrane-bound coreceptor molecules during cell-cell or cell-extracellular matrix contact. Here we demonstrate that functional protein microarrays are particularly well-suited for high-throughput screening of extracellular protein interactions. To evaluate the performance of the platform, we screened a set of 89 immunoglobulin (Ig)-type receptors against a highly diverse extracellular protein microarray with 686 genes represented. To enhance detection of low-affinity interactions, we developed a rapid method to assemble bait Fc fusion proteins into multivalent complexes using protein A microbeads. Based on these screens, we developed a statistical methodology for hit calling and identification of nonspecific interactions on protein microarrays. We found that the Ig receptor interactions identified using our methodology are highly specific and display minimal off-target binding, resulting in a 70% true-positive to false-positive hit ratio. We anticipate that these methods will be useful for a wide variety of functional protein microarray users.
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Affiliation(s)
- Sree R Ramani
- Department of Protein Chemistry, Genentech, South San Francisco, CA 94080, USA
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