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Miaskowski C, Conley YP, Levine JD, Cooper BA, Paul SM, Hammer MJ, Oppegaard K, Harris C, Shin J, Abrams G, Asakitogum D, Fu MR, Alismal S. Chronic Decrements in Energy in Women with Breast Cancer are Associated with Cytokine Gene Polymorphisms. Semin Oncol Nurs 2024; 40:151652. [PMID: 38834449 DOI: 10.1016/j.soncn.2024.151652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 06/06/2024]
Abstract
OBJECTIVES Decrements in energy were found in 67% of women who underwent breast cancer surgery. However, no information is available on chronic decrements in energy and associations with inflammation. Purposes were to identify latent classes of patients with distinct average energy profiles from prior to through 12 months after breast cancer surgery; evaluate for differences in demographic and clinical characteristics between the two extreme average energy classes; and evaluate for polymorphisms for cytokine genes associated with membership in the Low energy class. METHODS Women (n = 397) completed assessments of energy prior to and for 12 months following breast cancer surgery. Growth mixture modeling was used to identify classes of patients with distinct average energy profiles. Eighty-two single nucleotide polymorphisms (SNPs) among 15 cytokine genes were evaluated. RESULTS Three distinct energy profiles were identified (ie, Low [27.0%], Moderate [54.4%], Changing [18.6%]). Data from patients in the Low and Moderate energy classes were used in the candidate gene analyses. Five SNPs and one haplotype in six different genes remained significant in logistic regression analyses (ie, interleukin [IL]-1β rs1143623, IL1 receptor 1 rs3917332 IL4 rs2243263, IL6 HapA1 [that consisted of rs1800795, rs2069830, rs2069840, rs1554606, rs2069845, rs2069849, and rs2069861], nuclear factor kappa beta subunit 1 rs170731, tumor necrosis factor rs1799964). For several SNPs for IL6, expression quantitative trait locis were identified in subcutaneous and visceral adipose tissue and thyroid tissue. In addition, skeletal muscle was identified as an expression quantitative trait loci for nuclear factor kappa beta subunit 1. CONCLUSIONS Findings suggest that cytokine genes are involved in the mechanisms that underlie chronic decrements in energy in women following breast cancer surgery. Given the roles of subcutaneous and visceral adipose and thyroid tissues in metabolism and energy balance, the findings related to IL6 suggest that these polymorphisms may have a functional role in the development and maintenance of chronic decrements in energy.
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Affiliation(s)
- Christine Miaskowski
- School of Nursing, University of California, San Francisco; School of Medicine, University of California, San Francisco.
| | | | - Jon D Levine
- School of Medicine, University of California, San Francisco
| | - Bruce A Cooper
- School of Nursing, University of California, San Francisco
| | - Steven M Paul
- School of Nursing, University of California, San Francisco
| | | | | | - Carolyn Harris
- School of Nursing, University of Pittsburgh, Pittsburgh, PA
| | | | - Gary Abrams
- School of Medicine, University of California, San Francisco
| | | | - Mei R Fu
- University of Missouri, Kansas City
| | - Sarah Alismal
- Beckman Research Institute, City of Hope, Duarte, CA
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2
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da Costa ACA, Albarello Gellen LP, Fernandes MR, Coelho RDCC, Monte N, de Moraes FCA, Calderaro MCL, de Freitas LM, Matos JA, Fernandes TFDS, Aguiar KEC, Vinagre LWMS, dos Santos SEB, dos Santos NPC. Correlation between Genomic Variants and Worldwide COVID-19 Epidemiology. J Pers Med 2024; 14:579. [PMID: 38929800 PMCID: PMC11204818 DOI: 10.3390/jpm14060579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
COVID-19 is a systemic disease caused by the etiologic agent SARS-CoV-2, first reported in Hubei Province in Wuhan, China, in late 2019. The SARS-CoV-2 virus has evolved over time with distinct transmissibility subvariants from ancestral lineages. The clinical manifestations of the disease vary according to their severity and can range from asymptomatic to severe. Due to the rapid evolution to a pandemic, epidemiological studies have become essential to understand and effectively combat COVID-19, as the incidence and mortality of this disease vary between territories and populations. This study correlated epidemiological data on the incidence and mortality of COVID-19 with frequencies of important SNPs in GWAS studies associated with the susceptibility and mortality of this disease in different populations. Our results indicated significant correlations for 11 genetic variants (rs117169628, rs2547438, rs2271616, rs12610495, rs12046291, rs35705950, rs2176724, rs10774671, rs1073165, rs4804803 and rs7528026). Of these 11 variants, 7 (rs12046291, rs117169628, rs1073165, rs2547438, rs2271616, rs12610495 and rs35705950) were positively correlated with the incidence rate, these variants were more frequent in EUR populations, suggesting that this population is more susceptible to COVID-19. The rs2176724 variant was inversely related to incidence rates; therefore, the higher the frequency of the allele is, the lower the incidence rate. This variant was more frequent in the AFR population, which suggests a protective factor against SARS-CoV-2 infection in this population. The variants rs10774671, rs4804803, and rs7528026 showed a significant relationship with mortality rates. SNPs rs10774671 and rs4804803 were inversely related to mortality rates and are more frequently present in the AFR population. The rs7528026 variant, which is more frequent in the AMR population, was positively related to mortality rates. The study has the potential to identify and correlate the genetic profile with epidemiological data, identify populations that are more susceptible to severe forms of COVID-19, and relate them to incidence and mortality.
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Affiliation(s)
- Ana Caroline Alves da Costa
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Laura Patrícia Albarello Gellen
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Marianne Rodrigues Fernandes
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
- Ophir Loyola Hospital, Pará State Departament of Health, Belém 66063-240, PA, Brazil
| | - Rita de Cássia Calderaro Coelho
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Natasha Monte
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Francisco Cezar Aquino de Moraes
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Maria Clara Leite Calderaro
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Lilian Marques de Freitas
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Juliana Aires Matos
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Thamara Fernanda da Silva Fernandes
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Kaio Evandro Cardoso Aguiar
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Lui Wallacy Morikawa Souza Vinagre
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
- Ophir Loyola Hospital, Pará State Departament of Health, Belém 66063-240, PA, Brazil
| | - Sidney Emanuel Batista dos Santos
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belém 66077-830, PA, Brazil
| | - Ney Pereira Carneiro dos Santos
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
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Yin Y, Zhang Y, Sun L, Wang S, Zeng Y, Gong B, Huang L, He Y, Yang Z. Association analysis of genetic variants in critical patients with COVID-19 and validation in a Chinese population. Virol Sin 2024; 39:347-350. [PMID: 38403118 DOI: 10.1016/j.virs.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Affiliation(s)
- Yi Yin
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610213, China; Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Zhang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Lelin Sun
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Shuqiang Wang
- Infectious Disease Department, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Yong Zeng
- Department of Ophthalmology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Bo Gong
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Lulin Huang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
| | - Yongquan He
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
| | - Zhenglin Yang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610213, China; Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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4
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Cruz Cisneros MC, Anderson EJ, Hampton BK, Parotti B, Sarkar S, Taft-Benz S, Bell TA, Blanchard M, Dillard JA, Dinnon KH, Hock P, Leist SR, Madden EA, Shaw GD, West A, Baric RS, Baxter VK, Pardo-Manuel de Villena F, Heise MT, Ferris MT. Host Genetic Variation Impacts SARS-CoV-2 Vaccination Response in the Diversity Outbred Mouse Population. Vaccines (Basel) 2024; 12:103. [PMID: 38276675 PMCID: PMC10821422 DOI: 10.3390/vaccines12010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
The COVID-19 pandemic led to the rapid and worldwide development of highly effective vaccines against SARS-CoV-2. However, there is significant individual-to-individual variation in vaccine efficacy due to factors including viral variants, host age, immune status, environmental and host genetic factors. Understanding those determinants driving this variation may inform the development of more broadly protective vaccine strategies. While host genetic factors are known to impact vaccine efficacy for respiratory pathogens such as influenza and tuberculosis, the impact of host genetic variation on vaccine efficacy against COVID-19 is not well understood. To model the impact of host genetic variation on SARS-CoV-2 vaccine efficacy, while controlling for the impact of non-genetic factors, we used the Diversity Outbred (DO) mouse model. We found that DO mice immunized against SARS-CoV-2 exhibited high levels of variation in vaccine-induced neutralizing antibody responses. While the majority of the vaccinated mice were protected from virus-induced disease, similar to human populations, we observed vaccine breakthrough in a subset of mice. Importantly, we found that this variation in neutralizing antibody, virus-induced disease, and viral titer is heritable, indicating that the DO serves as a useful model system for studying the contribution of genetic variation of both vaccines and disease outcomes.
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Affiliation(s)
- Marta C. Cruz Cisneros
- Genetics and Molecular Biology Curriculum, University of North Carolina, Chapel Hill, NC 27599, USA; (M.C.C.C.); (B.K.H.)
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Elizabeth J. Anderson
- Division of Comparative Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (E.J.A.); (V.K.B.)
| | - Brea K. Hampton
- Genetics and Molecular Biology Curriculum, University of North Carolina, Chapel Hill, NC 27599, USA; (M.C.C.C.); (B.K.H.)
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Breantié Parotti
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Sanjay Sarkar
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Sharon Taft-Benz
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Timothy A. Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Matthew Blanchard
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Jacob A. Dillard
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
| | - Kenneth H. Dinnon
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Sarah R. Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.)
| | - Emily A. Madden
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
| | - Ginger D. Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.)
| | - Ralph S. Baric
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.)
| | - Victoria K. Baxter
- Division of Comparative Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (E.J.A.); (V.K.B.)
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mark T. Heise
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; (J.A.D.); (E.A.M.); (R.S.B.)
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; (B.P.); (S.S.); (S.T.-B.); (T.A.B.); (M.B.); (P.H.); (G.D.S.); (F.P.-M.d.V.); (M.T.H.)
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López-Bielma MF, Falfán-Valencia R, Abarca-Rojano E, Pérez-Rubio G. Participation of Single-Nucleotide Variants in IFNAR1 and IFNAR2 in the Immune Response against SARS-CoV-2 Infection: A Systematic Review. Pathogens 2023; 12:1320. [PMID: 38003785 PMCID: PMC10675296 DOI: 10.3390/pathogens12111320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/22/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Host genetic factors significantly influence susceptibility to SARS-CoV-2 infection and COVID-19 severity. Among these genetic factors are single-nucleotide variants (SNVs). IFNAR2 and IFNAR1 genes have been associated with severe COVID-19 in populations from the United Kingdom, Africa, and Latin America. IFNAR1 and IFNAR2 are subunits forming the type I interferon receptor (IFNAR). SNVs in the IFNAR genes impact protein function, affecting antiviral response and disease phenotypes. This systematic review aimed to describe IFNAR1 and IFNAR2 variants associated with COVID-19 susceptibility and severity. Accordingly, the current review focused on IFNAR1 and IFNAR2 studies published between January 2021 and February 2023, utilizing the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) protocol. The electronic search was conducted in PubMed databases using Boolean operators and inclusion and exclusion criteria. Of the 170 literature pieces, 11 studies were included. We include case reports of rare SNVs, defined by minor allele frequency (MAF) < 1%, and genome-wide associated studies (GWAS). Variants in IFNAR1 and IFNAR2 could potentially be new targets for therapies that limit the infection and the resulting inflammation by SARS-CoV-2 infection.
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Affiliation(s)
- María Fernanda López-Bielma
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico (R.F.-V.)
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico (R.F.-V.)
| | - Edgar Abarca-Rojano
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico (R.F.-V.)
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6
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Willett JDS, Lu T, Nakanishi T, Yoshiji S, Butler-Laporte G, Zhou S, Farjoun Y, Richards JB. Colocalization of expression transcripts with COVID-19 outcomes is rare across cell states, cell types and organs. Hum Genet 2023; 142:1461-1476. [PMID: 37640912 PMCID: PMC10511363 DOI: 10.1007/s00439-023-02590-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 06/30/2023] [Indexed: 08/31/2023]
Abstract
Identifying causal genes at GWAS loci can help pinpoint targets for therapeutic interventions. Expression studies can disentangle such loci but signals from expression quantitative trait loci (eQTLs) often fail to colocalize-which means that the genetic control of measured expression is not shared with the genetic control of disease risk. This may be because gene expression is measured in the wrong cell type, physiological state, or organ. We tested whether Mendelian randomization (MR) could identify genes at loci influencing COVID-19 outcomes and whether the colocalization of genetic control of expression and COVID-19 outcomes was influenced by cell type, cell stimulation, and organ. We conducted MR of cis-eQTLs from single cell (scRNA-seq) and bulk RNA sequencing. We then tested variables that could influence colocalization, including cell type, cell stimulation, RNA sequencing modality, organ, symptoms of COVID-19, and SARS-CoV-2 status among individuals with symptoms of COVID-19. The outcomes used to test colocalization were COVID-19 severity and susceptibility as assessed in the Host Genetics Initiative release 7. Most transcripts identified using MR did not colocalize when tested across cell types, cell state and in different organs. Most that did colocalize likely represented false positives due to linkage disequilibrium. In general, colocalization was highly variable and at times inconsistent for the same transcript across cell type, cell stimulation and organ. While we identified factors that influenced colocalization for select transcripts, identifying 33 that mediate COVID-19 outcomes, our study suggests that colocalization of expression with COVID-19 outcomes is partially due to noisy signals even after following quality control and sensitivity testing. These findings illustrate the present difficulty of linking expression transcripts to disease outcomes and the need for skepticism when observing eQTL MR results, even accounting for cell types, stimulation state and different organs.
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Affiliation(s)
- Julian Daniel Sunday Willett
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, QC, Canada
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Tianyuan Lu
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, QC, Canada
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Tomoko Nakanishi
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Graduate School of Medicine, Kyoto-McGill International Collaborative Program in Genomic Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Satoshi Yoshiji
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Graduate School of Medicine, Kyoto-McGill International Collaborative Program in Genomic Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Guillaume Butler-Laporte
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
| | - Sirui Zhou
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Yossi Farjoun
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- Genome Centre, McGill University, Montreal, QC, Canada
| | - J Brent Richards
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada.
- McGill University, Montreal, QC, Canada.
- Genome Centre, McGill University, Montreal, QC, Canada.
- Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal, QC, Canada.
- Department of Twin Research, King's College London, London, UK.
- Five Prime Sciences Inc, Montréal, Québec, Canada.
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7
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Biancolella M, Colona VL, Luzzatto L, Watt JL, Mattiuz G, Conticello SG, Kaminski N, Mehrian-Shai R, Ko AI, Gonsalves GS, Vasiliou V, Novelli G, Reichardt JKV. COVID-19 annual update: a narrative review. Hum Genomics 2023; 17:68. [PMID: 37488607 PMCID: PMC10367267 DOI: 10.1186/s40246-023-00515-2] [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: 06/08/2023] [Accepted: 07/16/2023] [Indexed: 07/26/2023] Open
Abstract
Three and a half years after the pandemic outbreak, now that WHO has formally declared that the emergency is over, COVID-19 is still a significant global issue. Here, we focus on recent developments in genetic and genomic research on COVID-19, and we give an outlook on state-of-the-art therapeutical approaches, as the pandemic is gradually transitioning to an endemic situation. The sequencing and characterization of rare alleles in different populations has made it possible to identify numerous genes that affect either susceptibility to COVID-19 or the severity of the disease. These findings provide a beginning to new avenues and pan-ethnic therapeutic approaches, as well as to potential genetic screening protocols. The causative virus, SARS-CoV-2, is still in the spotlight, but novel threatening virus could appear anywhere at any time. Therefore, continued vigilance and further research is warranted. We also note emphatically that to prevent future pandemics and other world-wide health crises, it is imperative to capitalize on what we have learnt from COVID-19: specifically, regarding its origins, the world's response, and insufficient preparedness. This requires unprecedented international collaboration and timely data sharing for the coordination of effective response and the rapid implementation of containment measures.
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Affiliation(s)
| | - Vito Luigi Colona
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy
| | - Lucio Luzzatto
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- University of Florence, 50121, Florence, Italy
| | - Jessica Lee Watt
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Smithfield, QLD, 4878, Australia
| | | | - Silvestro G Conticello
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Florence, Italy
- Institute of Clinical Physiology - National Council of Research (IFC-CNR), 56124, Pisa, Italy
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ruty Mehrian-Shai
- Pediatric Hemato-Oncology, Edmond and Lilly Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 2 Sheba Road, 52621, Ramat Gan, Israel
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
- Instituto Gonçalo MonizFundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Gregg S Gonsalves
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, USA
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy.
- IRCCS Neuromed, 86077, Pozzilli, IS, Italy.
- Department of Pharmacology, School of Medicine, University of Nevada, 89557, Reno, NV, USA.
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, QLD, 4878, Australia
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8
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Latini A, De Benedittis G, Colafrancesco S, Perricone C, Novelli G, Novelli L, Priori R, Ciccacci C, Borgiani P. PCSK3 Overexpression in Sjögren's Syndrome Patients May Be Regulated by rs4932178 SNP in Its Promoter Region and Correlates with IFN-γ Gene Expression. Genes (Basel) 2023; 14:genes14050981. [PMID: 37239341 DOI: 10.3390/genes14050981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND The PCSK3 gene encodes for the protease enzyme Furin, which promotes proteolytic maturation of important regulators of the immune response, and also enhances the secretion of interferon-γ (IFN). Several studies have suggested its possible involvement in the pathogenesis of chronic inflammatory diseases. METHODS We investigated the PCSK3 gene expression level in peripheral blood mononuclear cells isolated from Sjögren's Syndrome (SS) patients and healthy controls and we evaluated a possible correlation with IFN-γ gene expression. Moreover, we also explored the variability of two PCSK3 genetic polymorphisms (rs4932178 and rs4702) to evaluate a possible association between these polymorphisms and the expression levels of this gene. RESULTS We observed, by RT-qPCR, that the PCSK3 expression level was significantly higher in SS patients compared to the controls (p = 0.028), and we confirmed a positive correlation between PCSK3 and IFN-γ expression levels (p < 0.001). Moreover, we reported that the variant homozygous genotype of rs4932178 SNP is associated with a higher expression of the PCSK3 gene (p = 0.038) and with the SS susceptibility (p = 0.016). CONCLUSIONS Our data suggest that Furin could play a role in SS development, also promoting IFN-γ secretion.
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Affiliation(s)
- Andrea Latini
- Department of Biomedicine and Prevention, Genetics Section, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Giada De Benedittis
- Department of Biomedicine and Prevention, Genetics Section, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Serena Colafrancesco
- Division of Rheumatology, Department of Clinical Internal, Anaesthesiologic and Cardiovascular Sciences, Sapienza University, 00133 Rome, Italy
| | - Carlo Perricone
- Rheumatology, Department of Medicine, University of Perugia, Piazzale Giorgio Menghini 1, 06129 Perugia, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Genetics Section, University of Rome Tor Vergata, 00133 Rome, Italy
- IRCCS NEUROMED, 86077 Pozzilli, Italy
- School of Medicine, Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
| | - Lucia Novelli
- UniCamillus, Saint Camillus International University of Health Sciences, 00131 Rome, Italy
| | - Roberta Priori
- UniCamillus, Saint Camillus International University of Health Sciences, 00131 Rome, Italy
- AOU Policlinico Umberto 1, 00161 Rome, Italy
| | - Cinzia Ciccacci
- UniCamillus, Saint Camillus International University of Health Sciences, 00131 Rome, Italy
| | - Paola Borgiani
- Department of Biomedicine and Prevention, Genetics Section, University of Rome Tor Vergata, 00133 Rome, Italy
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