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Ladas P, Porfyridis I, Tryfonos C, Ioannou A, Adamide T, Christodoulou C, Richter J. Aetiology of Community-Acquired Pneumonia and the Role of Genetic Host Factors in Hospitalized Patients in Cyprus. Microorganisms 2023; 11:2051. [PMID: 37630611 PMCID: PMC10458012 DOI: 10.3390/microorganisms11082051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/25/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Community-acquired pneumonia (CAP) remains the leading cause of hospitalization among infectious disease in Europe, and a major cause of morbidity and mortality. In order to determine and characterize the aetiology of CAP in hospitalized adults in Cyprus, respiratory and blood samples were obtained from hospitalized patients with CAP, and analyzed using Multiplex Real-Time PCR/RT-PCR, and ID/AMR enrichment panel (RPIP) analysis. Probe-based allelic discrimination was used to investigate genetic host factors in patients. The aetiology could be established in 87% of patients. The most prevalent viral pathogens detected were influenza A, SARS-CoV-2, and human rhinovirus. The most common bacterial pathogens detected were Streptococcus pneumoniae, Staphylococcus aureus, and Haemophilus influenzae. Antimicrobial resistance genes were identified in 23 patients. S. aureus was the most common AMR correlated strain in our study. A positive correlation was detected between bacterial infections and the NOS3 rs1799983 G allele and the FCGR2A rs1801274 G allele. A positive correlation was also detected between the TNF-α rs1800629 A allele and sepsis, while a negative correlation was detected with the ACE rs1799752 insertion genotype and the severity of pneumonia. In conclusion, the targeted NGS panel approach applied provides highly sensitive, comprehensive pathogen detection, in combination with antimicrobial resistance AMR insights that can guide treatment choices. In addition, several host factors have been identified that impact the disease progression and outcome.
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Affiliation(s)
- Petros Ladas
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, 2371 Egkomi, Nicosia, Cyprus; (P.L.); (C.T.); (C.C.)
| | - Ilias Porfyridis
- Pulmonary Department, Nicosia General Hospital, Lemesou 215, 2029 Strovolos, Nicosia, Cyprus; (I.P.); (A.I.); (T.A.)
| | - Christina Tryfonos
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, 2371 Egkomi, Nicosia, Cyprus; (P.L.); (C.T.); (C.C.)
| | - Anna Ioannou
- Pulmonary Department, Nicosia General Hospital, Lemesou 215, 2029 Strovolos, Nicosia, Cyprus; (I.P.); (A.I.); (T.A.)
| | - Tonia Adamide
- Pulmonary Department, Nicosia General Hospital, Lemesou 215, 2029 Strovolos, Nicosia, Cyprus; (I.P.); (A.I.); (T.A.)
| | - Christina Christodoulou
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, 2371 Egkomi, Nicosia, Cyprus; (P.L.); (C.T.); (C.C.)
| | - Jan Richter
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, 2371 Egkomi, Nicosia, Cyprus; (P.L.); (C.T.); (C.C.)
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Karnaushkina MA, Sviridov PS, Korchagin VI, Salamaikina SA, Vasilyeva IS, Litvinova MM, Vatsik-Gorodetskaya MV. Genetic factors contributing to a severe course of pneumonia: a systematic review. BULLETIN OF SIBERIAN MEDICINE 2023. [DOI: 10.20538/1682-0363-2022-4-160-169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The article presents a systematic review of publications devoted to the study of genetic markers of severe pneumonia.The aim of the study was to compile a list of genetic markers that contribute to a severe course of pneumonia on the basis of the published data.In the current study, we searched for and analyzed articles published between January 2000 and April 2021. Following the search for and subsequent selection of articles, a list of 10 publications was compiled, which demonstrated a clear association of certain gene variants with severe and complicated pneumonia. Finally, we made a list of genetic markers of severe pneumonia consisting of 16 polymorphisms in 12 genes (CD86, IL6, IL10, PAI1, TNFα, HMGB1, ATG16L1, AGTR1, GCLC, CAT, IFNγ, FCGR2A).These genetic markers of severe and complicated pneumonia are responsible for various innate immune responses. The odds ratio for complicated pneumonia with a risk allele in the polymorphisms in the mentioned genes ranges from 1.39 to 4.28. To understand molecular and genetic mechanisms of severe pneumonia, further investigation of the effect of these genetic factors on the outcomes of pneumonia in different groups of patients with a simultaneous assessment of the cumulative effect of genetic variants and genetic interactions is required.
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Affiliation(s)
| | - P. S. Sviridov
- Peoples' Friendship University of Russia (RUDN University);
Research Centre for Medical Genetics
| | | | | | - I. S. Vasilyeva
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University)
| | - M. M. Litvinova
- The Loginov Moscow Clinical Scientific Center;
I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University)
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Guin D, Yadav S, Singh P, Singh P, Thakran S, Kukal S, Kanojia N, Paul PR, Pattnaik B, Sardana V, Grover S, Hasija Y, Saso L, Agrawal A, Kukreti R. Human genetic factors associated with pneumonia risk, a cue for COVID-19 susceptibility. INFECTION, GENETICS AND EVOLUTION 2022; 102:105299. [PMID: 35545162 PMCID: PMC9080029 DOI: 10.1016/j.meegid.2022.105299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/30/2022] [Accepted: 05/02/2022] [Indexed: 01/08/2023]
Abstract
Pneumonia, an acute respiratory tract infection, is one of the major causes of mortality worldwide. Depending on the site of acquisition, pneumonia can be community acquired pneumonia (CAP) or nosocomial pneumonia (NP). The risk of pneumonia, is partially driven by host genetics. CYP1A1 is a widely studied pulmonary CYP family gene primarily expressed in peripheral airway epithelium. The CYP1A1 genetic variants, included in this study, alter the gene activity and are known to contribute in lung inflammation, which may cause pneumonia pathogenesis. In this study, we performed a meta-analysis to establish the possible contribution of CYP1A1 gene, and its three variants (rs2606345, rs1048943 and rs4646903) towards the genetic etiology of pneumonia risk. Using PRISMA guidelines, we systematically reviewed and meta-analysed case-control studies, evaluating risk of pneumonia in patients carrying the risk alleles of CYP1A1 variants. Heterogeneity across the studies was evaluated using I2 statistics. Based on heterogeneity, a random-effect (using maximum likelihood) or fixed-effect (using inverse variance) model was applied to estimate the effect size. Pooled odds ratio (OR) was calculated to estimate the overall effect of the risk allele association with pneumonia susceptibility. Egger's regression test and funnel plot were used to assess publication bias. Subgroup analysis was performed based on pneumonia type (CAP and NP), population, as well as age group. A total of ten articles were identified as eligible studies, which included 3049 cases and 2249 healthy controls. The meta-analysis findings revealed CYP1A1 variants, rs2606345 [T vs G; OR = 1.12 (0.75–1.50); p = 0.02; I2 = 84.89%], and rs1048943 [G vs T; OR = 1.19 (0.76–1.61); p = 0.02; I2 = 0.00%] as risk markers whereas rs4646903 showed no statistical significance for susceptibility to pneumonia. On subgroup analysis, both the genetic variants showed significant association with CAP but not with NP. We additionally performed a spatial analysis to identify the key factors possibly explaining the variability across countries in the prevalence of the coronavirus disease 2019 (COVID-19), a viral pneumonia. We observed a significant association between the risk allele of rs2606345 and rs1048943, with a higher COVID-19 prevalence worldwide, providing us important links in understanding the variability in COVID-19 prevalence.
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Tian LX, Tang X, Zhu JY, Luo L, Ma XY, Cheng SW, Zhang W, Tang WQ, Ma W, Yang X, Lv CZ, Liang HP. Cytochrome P450 1A1 enhances inflammatory responses and impedes phagocytosis of bacteria in macrophages during sepsis. Cell Commun Signal 2020; 18:70. [PMID: 32366266 PMCID: PMC7199371 DOI: 10.1186/s12964-020-0523-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/29/2020] [Indexed: 01/28/2023] Open
Abstract
Abstract The hydroxylase cytochrome P450 1A1 (CYP1A1) is regulated by the inflammation-limiting aryl hydrocarbon receptor (AhR), but CYP1A1 immune functions remain unclear. We observed CYP1A1 overexpression in peritoneal macrophages (PMs) isolated from mice following LPS or heat-killed Escherichia. coli (E. coli) challenge. CYP1A1 overexpression augmented TNF-α and IL-6 production in RAW264.7 cells (RAW) by enhancing JNK/AP-1 signalling. CYP1A1 overexpression also promoted 12S-hydroxy-5Z,8Z,10E,14Z-eicosatetraenoic acid (12(S)-HETE) production in activated RAW, while a 12(S)-HETE antibody attenuated and 12(S)-HETE alone induced inflammatory responses. Macrophages harbouring hydroxylase-deficient CYP1A1 demonstrated reduced 12(S)-HETE generation and LPS-induced TNF-α/IL-6 secretion. CYP1A1 overexpression also impaired phagocytosis of bacteria via decreasing the expression of scavenger receptor A (SR-A) in PMs. Mice injected with CYP1A1-overexpressing PMs were more susceptible to CLP- or E. coli-induced mortality and bacteria invading, while Rhapontigenin, a selective CYP1A1 inhibitor, improved survival and bacteria clearance of mice in sepsis. CYP1A1 and 12(S)-HETE were also elevated in monocytes and plasma of septic patients and positively correlated with SOFA scores. Macrophage CYP1A1 disruption could be a promising strategy for treating sepsis. Video abstract
Graphical abstract ![]()
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Affiliation(s)
- Li-Xing Tian
- State Key Laboratory of Trauma, Burns and Combined Injury, Department of Wound Infection and Drug, Daping Hospital, Army Medical University, Yuzhong District, Chongqing, China
| | - Xin Tang
- State Key Laboratory of Trauma, Burns and Combined Injury, Department of Wound Infection and Drug, Daping Hospital, Army Medical University, Yuzhong District, Chongqing, China
| | - Jun-Yu Zhu
- State Key Laboratory of Trauma, Burns and Combined Injury, Department of Wound Infection and Drug, Daping Hospital, Army Medical University, Yuzhong District, Chongqing, China
| | - Li Luo
- State Key Laboratory of Trauma, Burns and Combined Injury, Department of Wound Infection and Drug, Daping Hospital, Army Medical University, Yuzhong District, Chongqing, China
| | - Xiao-Yuan Ma
- State Key Laboratory of Trauma, Burns and Combined Injury, Department of Wound Infection and Drug, Daping Hospital, Army Medical University, Yuzhong District, Chongqing, China
| | - Shao-Wen Cheng
- Trauma Center, The First Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Wei Zhang
- Emergency and Trauma College of Hainan Medical University, Haikou, China
| | - Wan-Qi Tang
- State Key Laboratory of Trauma, Burns and Combined Injury, Department of Wound Infection and Drug, Daping Hospital, Army Medical University, Yuzhong District, Chongqing, China
| | - Wei Ma
- State Key Laboratory of Trauma, Burns and Combined Injury, Department of Wound Infection and Drug, Daping Hospital, Army Medical University, Yuzhong District, Chongqing, China
| | - Xue Yang
- State Key Laboratory of Trauma, Burns and Combined Injury, Department of Wound Infection and Drug, Daping Hospital, Army Medical University, Yuzhong District, Chongqing, China
| | - Chuan-Zhu Lv
- Trauma Center, The First Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Hua-Ping Liang
- State Key Laboratory of Trauma, Burns and Combined Injury, Department of Wound Infection and Drug, Daping Hospital, Army Medical University, Yuzhong District, Chongqing, China.
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Mirzaev KB, Fedorinov DS, Ivashchenko DV, Sychev DA. ADME pharmacogenetics: future outlook for Russia. Pharmacogenomics 2019; 20:847-865. [DOI: 10.2217/pgs-2019-0013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
This systematic review reflects the results of pharmacogenetic studies in the Russian Federation aimed at studying the genes involved in the drug biotransformation system. The works of Russian researchers found by us are mostly devoted to microsomal liver oxidation enzymes (metabolism) and membrane transporter systems (absorption and excretion). This review presents population-ethnic and associative clinical studies on the genes of the CYP450 system, noncytochrome oxidation enzymes ( SULT1A1, CES1), membrane transporter system genes ( ABCB1, SLCO1B1) and warfarin biotransformation enzymes ( VKORC1, GGCX). The information is structured in the form of 11 tables, divided by regions of the Russian Federation.
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Affiliation(s)
- Karin B Mirzaev
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare, Moscow, Russian Federation
| | - Denis S Fedorinov
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare, Moscow, Russian Federation
| | - Dmitry V Ivashchenko
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare, Moscow, Russian Federation
| | - Dmitry A Sychev
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare, Moscow, Russian Federation
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Smelaya TV, Belopolskaya OB, Smirnova SV, Kuzovlev AN, Moroz VV, Golubev AM, Pabalan NA, Salnikova LE. Genetic dissection of host immune response in pneumonia development and progression. Sci Rep 2016; 6:35021. [PMID: 27725770 PMCID: PMC5057148 DOI: 10.1038/srep35021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/20/2016] [Indexed: 01/21/2023] Open
Abstract
The role of host genetic variation in pneumonia development and outcome is poorly understood. We studied common polymorphisms in the genes of proinflammatory cytokines (IL6 rs1800795, IL8 rs4073, IL1B rs16944), anti-inflammatory cytokines (IL10 rs1800896, IL4 rs2243250, IL13 rs20541) and toll-like receptors (TLR2 rs5743708 and rs4696480, TLR4 rs4986791, TLR9 rs352139, rs5743836 and rs187084) in patients with community-acquired pneumonia (CAP) (390 cases, 203 controls) and nosocomial pneumonia (355 cases, 216 controls). Experimental data were included in a series of 11 meta-analyses and eight subset analyses related to pneumonia susceptibility and outcome. TLR2 rs5743708 minor genotype appeared to be associated with CAP/Legionnaires’ disease/pneumococcal disease. In CAP patients, the IL6 rs1800795-C allele was associated with severe sepsis/septic shock/severe systemic inflammatory response, while the IL10 rs1800896-A allele protected against the development of these critical conditions. To contribute to deciphering of the above results, we performed an in silico analysis and a qualitative synthesis of literature data addressing basal and stimulated genotype-specific expression level. This data together with database information on transcription factors’ affinity changes caused by SNPs in putative promoter regions, the results of linkage disequilibrium analysis along with SNPs functional annotations supported assumptions about the complexity underlying the revealed associations.
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Affiliation(s)
- Tamara V Smelaya
- V. A. Negovsky Research Institute of General Reanimatology, Russian Academy of Sciences, 25 Petrovka str., build.2, Moscow 107031, Russia
| | - Olesya B Belopolskaya
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin street, Moscow 117971, Russia
| | - Svetlana V Smirnova
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin street, Moscow 117971, Russia
| | - Artem N Kuzovlev
- V. A. Negovsky Research Institute of General Reanimatology, Russian Academy of Sciences, 25 Petrovka str., build.2, Moscow 107031, Russia
| | - Viktor V Moroz
- V. A. Negovsky Research Institute of General Reanimatology, Russian Academy of Sciences, 25 Petrovka str., build.2, Moscow 107031, Russia
| | - Arkadiy M Golubev
- V. A. Negovsky Research Institute of General Reanimatology, Russian Academy of Sciences, 25 Petrovka str., build.2, Moscow 107031, Russia
| | - Noel A Pabalan
- Center for Research and Development, Angeles University Foundation, Angeles City 2009, Philippines
| | - Lyubov E Salnikova
- V. A. Negovsky Research Institute of General Reanimatology, Russian Academy of Sciences, 25 Petrovka str., build.2, Moscow 107031, Russia.,N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin street, Moscow 117971, Russia
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Epistatic interaction between common AGT G(-6)A (rs5051) and AGTR1 A1166C (rs5186) variants contributes to variation in kidney size at birth. Gene 2015; 572:72-78. [PMID: 26142106 DOI: 10.1016/j.gene.2015.06.071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 06/02/2015] [Accepted: 06/29/2015] [Indexed: 11/22/2022]
Abstract
Low nephron number has been recognised as an important cardiovascular risk factor and recently a strong correlation between renal mass and nephron number has been demonstrated in newborns. The aim of this study was to investigate individual, as well as combined, effects of common variants of genes which encode for major components of the renin-angiotensin system (REN G10601A, AGT G(-6)A, ACE I/D, AGTR1 A1166C) on kidney size in healthy, full-term newborns. A significant additive main effect of the ACE I/D polymorphism, as well as an additive-by-additive interaction between AGT G(-6)A and AGTR1 A1166C variants, were found. The variance attributed to the epistatic effect was 27.9 ml(2)/m(4), which accounted for 73.8% of the interaction variance (37.8 ml(2)/m(4)), 66.4% of the genetic variance (42.0 ml(2)/m(4)) and 4.4% to the total phenotypic variance (628 ml(2)/m(4)). No other statistically significant main or epistatic effects were detected. Our results highlight the importance of considering gene-gene interactions as part of the genetic architecture of congenital nephron number, even when the loci do not show significant single locus effects. Unravelling the genetic determinants of low nephron number, along with early molecular screening, may well help to identify children at risk for cardiovascular disease.
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Wang H, Zhang K, Qin H, Yang L, Zhang L, Cao Y. Genetic Association Between CD143 rs4340 Polymorphism and Pneumonia risk: A Meta Analysis. Medicine (Baltimore) 2015; 94:e883. [PMID: 26222869 PMCID: PMC4554131 DOI: 10.1097/md.0000000000000883] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
rs4340 polymorphism at intron 16 of the angiotensin-converting enzyme (CD143) gene was reported to repress cough reflex by reducing bradykinin and substance P levels, thus increasing the likelihood to develop pneumonia. There have been different reports regarding the correlation of CD143 rs4340 genotypes with pneumonia risk, which prompted us to perform a meta-analysis to determine the elusive association.We combined multiple keywords to identify the studies addressing the association between CD143 rs4340 genotypes and pneumonia risk covered in the EMBASE, Google Scholar, PubMed, and CNKI databases. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the risk of pneumonia. The fixed-effects model (FEM) was used.A total of 10 studies were analyzed in this quantitative analysis. We found a strong association between rs4340 single nucleotide polymorphism (SNP) and pneumonia risk using the recessive model (FEM: OR 1.33, 95% CI 1.13-1.57). A significantly increased risk was also indicated under the recessive model in Asian populations (FEM: OR 1.57, 95% CI 1.19-2.07), community-acquired pneumonia (CAP) (FEM: OR 1.31, 95% CI 1.08-1.60), and nosocomial pneumonia (NP) (FEM: OR 1.52, 95% CI 1.06-2.19).Our meta-analysis demonstrates that CD143 rs4340 polymorphism may represent a risk factor for pneumonia.
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Affiliation(s)
- Hong Wang
- Department of Lung Cancer, 307 Hospital of PLA, Affiliated Hospital of Academy of Military Medical Sciences, Beijing, China
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