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Cantalupo S, Lasorsa VA, Russo R, Andolfo I, D’Alterio G, Rosato BE, Frisso G, Abete P, Cassese GM, Servillo G, Gentile I, Piscopo C, Della Monica M, Fiorentino G, Russo G, Cerino P, Buonerba C, Pierri B, Zollo M, Iolascon A, Capasso M. Regulatory Noncoding and Predicted Pathogenic Coding Variants of CCR5 Predispose to Severe COVID-19. Int J Mol Sci 2021; 22:5372. [PMID: 34065289 PMCID: PMC8161088 DOI: 10.3390/ijms22105372] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/12/2021] [Accepted: 05/18/2021] [Indexed: 11/17/2022] Open
Abstract
Genome-wide association studies (GWAS) found locus 3p21.31 associated with severe COVID-19. CCR5 resides at the same locus and, given its known biological role in other infection diseases, we investigated if common noncoding and rare coding variants, affecting CCR5, can predispose to severe COVID-19. We combined single nucleotide polymorphisms (SNPs) that met the suggestive significance level (P ≤ 1 × 10-5) at the 3p21.31 locus in public GWAS datasets (6406 COVID-19 hospitalized patients and 902,088 controls) with gene expression data from 208 lung tissues, Hi-C, and Chip-seq data. Through whole exome sequencing (WES), we explored rare coding variants in 147 severe COVID-19 patients. We identified three SNPs (rs9845542, rs12639314, and rs35951367) associated with severe COVID-19 whose risk alleles correlated with low CCR5 expression in lung tissues. The rs35951367 resided in a CTFC binding site that interacts with CCR5 gene in lung tissues and was confirmed to be associated with severe COVID-19 in two independent datasets. We also identified a rare coding variant (rs34418657) associated with the risk of developing severe COVID-19. Our results suggest a biological role of CCR5 in the progression of COVID-19 as common and rare genetic variants can increase the risk of developing severe COVID-19 by affecting the functions of CCR5.
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Affiliation(s)
- Sueva Cantalupo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80136 Napoli, Italy; (S.C.); (V.A.L.); (R.R.); (I.A.); (B.E.R.); (G.F.); (M.Z.); (A.I.)
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy;
| | - Vito Alessandro Lasorsa
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80136 Napoli, Italy; (S.C.); (V.A.L.); (R.R.); (I.A.); (B.E.R.); (G.F.); (M.Z.); (A.I.)
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy;
| | - Roberta Russo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80136 Napoli, Italy; (S.C.); (V.A.L.); (R.R.); (I.A.); (B.E.R.); (G.F.); (M.Z.); (A.I.)
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy;
| | - Immacolata Andolfo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80136 Napoli, Italy; (S.C.); (V.A.L.); (R.R.); (I.A.); (B.E.R.); (G.F.); (M.Z.); (A.I.)
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy;
| | | | - Barbara Eleni Rosato
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80136 Napoli, Italy; (S.C.); (V.A.L.); (R.R.); (I.A.); (B.E.R.); (G.F.); (M.Z.); (A.I.)
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy;
| | - Giulia Frisso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80136 Napoli, Italy; (S.C.); (V.A.L.); (R.R.); (I.A.); (B.E.R.); (G.F.); (M.Z.); (A.I.)
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy;
| | - Pasquale Abete
- COVID Hospital, P.O.S. Anna e SS. Madonna della Neve di Boscotrecase, Ospedali Riuniti Area Vesuviana, 80042 Boscotrecase, Italy; (P.A.); (G.M.C.)
| | - Gian Marco Cassese
- COVID Hospital, P.O.S. Anna e SS. Madonna della Neve di Boscotrecase, Ospedali Riuniti Area Vesuviana, 80042 Boscotrecase, Italy; (P.A.); (G.M.C.)
| | - Giuseppe Servillo
- Dipartimento di Neuroscienze e Scienze Riproduttive ed Odontostomatologiche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy;
| | - Ivan Gentile
- Dipartimento di Medicina Clinica e Chirurgia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy;
| | - Carmelo Piscopo
- Medical and Laboratory Genetics Unit, A.O.R.N. ‘Antonio Cardarelli’, 80131 Napoli, Italy; (C.P.); (M.D.M.)
| | - Matteo Della Monica
- Medical and Laboratory Genetics Unit, A.O.R.N. ‘Antonio Cardarelli’, 80131 Napoli, Italy; (C.P.); (M.D.M.)
| | | | - Giuseppe Russo
- Unità di Radiologia, Casa di Cura Villa dei Fiori, 80011 Acerra, Italy;
| | - Pellegrino Cerino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (P.C.); (C.B.); (B.P.)
| | - Carlo Buonerba
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (P.C.); (C.B.); (B.P.)
| | - Biancamaria Pierri
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (P.C.); (C.B.); (B.P.)
- Dipartimento di Medicina, Chirurgia e Odontoiatria “Scuola Medica Salernitana”, Università di Salerno, 84081 Baronissi, Italy
| | - Massimo Zollo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80136 Napoli, Italy; (S.C.); (V.A.L.); (R.R.); (I.A.); (B.E.R.); (G.F.); (M.Z.); (A.I.)
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy;
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80136 Napoli, Italy; (S.C.); (V.A.L.); (R.R.); (I.A.); (B.E.R.); (G.F.); (M.Z.); (A.I.)
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy;
| | - Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80136 Napoli, Italy; (S.C.); (V.A.L.); (R.R.); (I.A.); (B.E.R.); (G.F.); (M.Z.); (A.I.)
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy;
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Almeida MJ, Matos A. Designer Nucleases: Gene-Editing Therapies using CCR5 as an Emerging Target in HIV. Curr HIV Res 2020; 17:306-323. [PMID: 31652113 DOI: 10.2174/1570162x17666191025112918] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 02/08/2023]
Abstract
Acquired Immunodeficiency Syndrome (AIDS), caused by the Human Immunodeficiency Virus (HIV), is a life-threatening disorder that persists worldwide as a severe health problem. Since it was linked with the HIV attachment process, the Chemokine receptor, CCR5, has been at the development leading edge of several gene-based therapies. Given the shortcomings of the current antiretroviral treatment procedure and the non-availability of a licensed vaccine, the aptitude to modify complex genomes with Designer Nucleases has had a noteworthy impact on biotechnology. Over the last years, ZFN, TALEN and CRISPR/Cas9 gene-editing technology have appeared as a promising solution that mimics the naturally occurring CCR5/Δ32 mutation and permanently guarantees the absence of CCR5-expression on the surface of HIV target-cells, leading to a continuous resistance to the virus entry and, ultimately, proving that cellular immunization from infection could be, in fact, a conceivable therapeutic approach to finally achieve the long-awaited functional cure of HIV.
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Affiliation(s)
- Maria João Almeida
- Laboratory of Microbiology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Ana Matos
- Laboratory of Microbiology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.,Research Centre on Chemical Processes Engineering and Forest Products (CIEPQF), Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
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Ellwanger JH, Kulmann-Leal B, Kaminski VDL, Rodrigues AG, Bragatte MADS, Chies JAB. Beyond HIV infection: Neglected and varied impacts of CCR5 and CCR5Δ32 on viral diseases. Virus Res 2020; 286:198040. [PMID: 32479976 PMCID: PMC7260533 DOI: 10.1016/j.virusres.2020.198040] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022]
Abstract
CCR5 regulates multiple cell types (e.g., T regulatory and Natural Killer cells) and immune responses. The effects of CCR5, CCR5Δ32 (variant associated with reduced CCR5 expression) and CCR5 antagonists vary between infections. CCR5 affects the pathogenesis of flaviviruses, especially in the brain. The genetic variant CCR5Δ32 increases the risk of symptomatic West Nile virus infection. The triad “CCR5, extracellular vesicles and infections” is an emerging topic.
The interactions between chemokine receptors and their ligands may affect susceptibility to infectious diseases as well as their clinical manifestations. These interactions mediate both the traffic of inflammatory cells and virus-associated immune responses. In the context of viral infections, the human C-C chemokine receptor type 5 (CCR5) receives great attention from the scientific community due to its role as an HIV-1 co-receptor. The genetic variant CCR5Δ32 (32 base-pair deletion in CCR5 gene) impairs CCR5 expression on the cell surface and is associated with protection against HIV infection in homozygous individuals. Also, the genetic variant CCR5Δ32 modifies the CCR5-mediated inflammatory responses in various conditions, such as inflammatory and infectious diseases. CCR5 antagonists mimic, at least in part, the natural effects of the CCR5Δ32 in humans, which explains the growing interest in the potential benefits of using CCR5 modulators for the treatment of different diseases. Nevertheless, beyond HIV infection, understanding the effects of the CCR5Δ32 variant in multiple viral infections is essential to shed light on the potential effects of the CCR5 modulators from a broader perspective. In this context, this review discusses the involvement of CCR5 and the effects of the CCR5Δ32 in human infections caused by the following pathogens: West Nile virus, Influenza virus, Human papillomavirus, Hepatitis B virus, Hepatitis C virus, Poliovirus, Dengue virus, Human cytomegalovirus, Crimean-Congo hemorrhagic fever virus, Enterovirus, Japanese encephalitis virus, and Hantavirus. Subsequently, this review addresses the impacts of CCR5 gene editing and CCR5 modulation on health and viral diseases. Also, this article connects recent findings regarding extracellular vesicles (e.g., exosomes), viruses, and CCR5. Neglected and emerging topics in “CCR5 research” are briefly described, with focus on Rocio virus, Zika virus, Epstein-Barr virus, and Rhinovirus. Finally, the potential influence of CCR5 on the immune responses to coronaviruses is discussed.
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Affiliation(s)
- Joel Henrique Ellwanger
- Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Bruna Kulmann-Leal
- Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Valéria de Lima Kaminski
- Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Programa de Pós-Graduação em Biotecnologia, Laboratório de Imunologia Aplicada, Instituto de Ciência e Tecnologia - ICT, Universidade Federal de São Paulo - UNIFESP, São José dos Campos, São Paulo, Brazil
| | - Andressa Gonçalves Rodrigues
- Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Marcelo Alves de Souza Bragatte
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Núcleo de Bioinformática do Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - José Artur Bogo Chies
- Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil.
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Ellwanger JH, Kaminski VDL, Rodrigues AG, Kulmann-Leal B, Chies JAB. CCR5 and CCR5Δ32 in bacterial and parasitic infections: Thinking chemokine receptors outside the HIV box. Int J Immunogenet 2020; 47:261-285. [PMID: 32212259 DOI: 10.1111/iji.12485] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 12/14/2022]
Abstract
The CCR5 molecule was reported in 1996 as the main HIV-1 co-receptor. In that same year, the CCR5Δ32 genetic variant was described as a strong protective factor against HIV-1 infection. These findings led to extensive research regarding the CCR5, culminating in critical scientific advances, such as the development of CCR5 inhibitors for the treatment of HIV infection. Recently, the research landscape surrounding CCR5 has begun to change. Different research groups have realized that, since CCR5 has such important effects in the chemokine system, it could also affect other different physiological systems. Therefore, the effect of reduced CCR5 expression due to the presence of the CCR5Δ32 variant began to be further studied. Several studies have investigated the role of CCR5 and the impacts of CCR5Δ32 on autoimmune and inflammatory diseases, various types of cancer, and viral diseases. However, the role of CCR5 in diseases caused by bacteria and parasites is still poorly understood. Therefore, the aim of this article is to review the role of CCR5 and the effects of CCR5Δ32 on bacterial (brucellosis, osteomyelitis, pneumonia, tuberculosis and infection by Chlamydia trachomatis) and parasitic infections (toxoplasmosis, leishmaniasis, Chagas disease and schistosomiasis). Basic information about each of these infections was also addressed. The neglected role of CCR5 in fungal disease and emerging studies regarding the action of CCR5 on regulatory T cells are briefly covered in this review. Considering the "renaissance of CCR5 research," this article is useful for updating researchers who develop studies involving CCR5 and CCR5Δ32 in different infectious diseases.
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Affiliation(s)
- Joel Henrique Ellwanger
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Valéria de Lima Kaminski
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Andressa Gonçalves Rodrigues
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Bruna Kulmann-Leal
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - José Artur Bogo Chies
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
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Abstract
We use the genotyping and death register information of 409,693 individuals of British ancestry to investigate fitness effects of the CCR5-∆32 mutation. We estimate a 21% increase in the all-cause mortality rate in individuals who are homozygous for the ∆32 allele. A deleterious effect of the ∆32/∆32 mutation is also independently supported by a significant deviation from the Hardy-Weinberg equilibrium (HWE) due to a deficiency of ∆32/∆32 individuals at the time of recruitment.
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