Download - GENOMEWIDE - edisciplinas.usp.br
GENOMEWIDEASSOCIATIONSTUDY OFSEVERECOVID-19 WITHRESPIRATORYFAILURE
Estudo de associação ampla do genoma com Covid-19
grave e insuficiência respiratóriaSeminar 3 - Genetics
Seminário 3 - Genética
Ana Clara Germano TostesDiego Ferreira CaldasGabriel Garcia SchmittHenrique LarssenKamilla Dolgoff Santana
Profº Jeremy Andrew SquireThe Severe Covid-19 GWAS GroupFrom the NEW ENGLAND JOURNAL of MEDICINE
Summary
◦ Abstract
◦ Background
◦ Methods
◦ Results
◦ Conclusions
◦ Methods
◦ Study participants and recruitment
◦ Ethics committee aproval
◦ Sample processing, genotyping and imputation
◦ Statistical analysis
◦ Results
◦ Patients, genotyping and quality control
◦ Genomewide association analysis
◦ Chromosome 3P21.31
◦ ABO Locus
◦ HLA Analysis
◦ Discussion
AbstractResumo
BACKGROUND METHODS RESULTS CONCLUSIONS
Contexto Métodos Resultados Conclusões
Presenter: Kamilla Dolgoff Santana
BackgroundContexto
Severe acuterespiratory syndrome
coronavirus 2 wasdiscovered in Wuhan,
China, in late 2019;
Covid-19 rapidlyevolved into a global
pandemic;
More than 8.03 millionconfirmed cases
worldwide, with total deaths exceeding 435
thousand;
The relative role ofclinical risk factors in
determining theseverity of Covid-19 has
not yet been clarified.
Presenter: Kamilla Dolgoff Santana
◦ It was performed a genomewide association study
(GWAS) in an attempt to delineate host genetic factors
contributing to severe Covid-19 with respiratory failure.
◦ Since there is considerable variation in disease behavior
among patients infected with severe acute respiratory
syndrome coronavirus 2, genomewide association
analysis may allow for the identification of potential
genetic factors involved in the development of Covid-19.
Methods; Results and ConclusionsMétodos; Resultados e Conclusões
◦ 1980 patients with Covid-19 and
severe disease at seven hospitals
in the Italian and Spanish
epicenters of the SARS-CoV-2
pandemic;
◦ 8,582,968 singlenucleotide
polymorphisms analyzed and a
meta-analysis of the two case-
control panels conducted.
Presenter: Kamilla Dolgoff Santana
◦ Higher risk in blood group A than
in other blood groups;
◦ Protective effect in blood group
O as compared with other blood
groups;
◦ Cross-replicating associations
with rs11385942 at locus 3p21.31
and with rs657152 at locus 9q34.2
detected:
◦ Locus 3p21.31: the association
signal spanned the genes
SLC6A20, LZTFLl, CCR9,
FYCOl, CXCR6 and XCRl;
◦ Locus 9q34.2: coincided with
the ABO blood group locus.
Confirmed a potential involvementof the ABO blood-group system.
MethodsMétodos
Study participants and recruitment
Ethics committee aproval
Sample processing, genotyping and imputation
Statistical analysis
Participantes do estudo e recrutamento
Processamento de amostras, genotipagem e imputação
Análises estatísticas
Aprovação do Comitê de Ética
Presenter: Diego Ferreira Caldas
Study participants and recruitment
◦ 7 hospitals in four cities in pandemic epicenters in Italy and Spain
◦ 1980 patients with severe Covid-19 (hospitalization, respiratory failure and confirmed SARS-CoV-2 RNA
PCR test)
◦ Respiratory failure defined as use of oxygen supplementation and mechanical ventilation, and severity
graded according to the maximum respiratory support received at any time (supplemental oxygen therapy,
noninvasive ventilatory support, invasive ventilatory support and extracorporeal membrane oxygenation)
◦ 2381 control participants from Italy and Spain (998 randomly selected blood donors and two previous
studies` control panels)
Presenter: Diego Ferreira Caldas
Ethics Committee Approval
◦ No additional project related procedures (clinically indicated venipunctures), anonimity
(minimal data set)
◦ Local differences due to local regulations or larger biobanking efforts
◦ Written informed consent obtained when possible, verbal and from next of kin in some
instances, exeption from informed consent for some severely ill patients afforded by local
regulations.
Presenter: Diego Ferreira Caldas
Sample Processing, Genotyping and Imputation
◦ DNA extraction with Chemagic 360
◦ Genotyping with Global Screening Array 2.0
◦ Single-nucleotide polymorphism (SNP) on genome build GRCh38 with Michigan Imputation
Server and haplotypes from the Trans-Omics for Precision Medicine program
◦ Exclusion of samples in quality control mostly due to population outliers, resulting in 835
patients and 1255 control participants from Italy and 775 patients and 950 control
participants from Spain.
Presenter: Diego Ferreira Caldas
Statistical Analysis
◦ Testing for phenotypic associations with allele dosage date separately for both Italianand Spanish case-control panels to account for imputation uncertainty
◦ Conducting two genomewide tests of association with adjustments to control forpotential population stratification and potential population stratification and age andsex
◦ Definition of 5x10^-8 threshold for joint P values for statistical significance
◦ Selection of three ABO SNPs to infer ABO blood type and calculated odds ratio
◦ Assessment of allelic distribution according to no mechanical ventilation compared tomechanical ventilation of any kind
Presenter: Diego Ferreira Caldas
Patients, genotyping and quality control
• Median age: 64 –69 • Sex prevalence: male• Most frequent: supplemental
oxygen only and ventilator
• High rate of hypertension• Low rate of coronary artery disease• Medium rate of diabetes
Presenter: Gabriel Garcia Schmitt
Genomewide association analysis
• P Values suggest 2 group of genes associated with severe Covid-19 and respiratory failure• rs11385942 ------ locus 3p21.31 ------ P = 1.15 x 10^-10• rs657152 --------- locus 9q34.2 ------- P = 4.95 x 10^-8
Presenter: Gabriel Garcia Schmitt
• P Value: indicates how likely a null hypothesys could happen, given the experimental data. The lower the P Value, the more likely is an alternative hypothesys .
SNP rs11385942, locus 3p21.31
◦ Comprises a group of six genes located in chromosome 3: SLC6A20, LZTFLI, CCR9, FYCOI,
CXCR6, and XCRl
◦ Risk allele GA of rs11385942:
◦ reduced expression of CXCR6 and increased expression of SLC6A20 and LZTFLI (in lung cells)
◦ higher frequency among pacients who needed ventilation than those who needed oxygen only
◦ homozygotic patients for the risk allele with respiratory failure were younger
Presenter: Gabriel Garcia Schmitt
Conclusion: the risk allele GA of rs11385942 is associated with more severe Covid-19
SNP rs657152, locus 9q34.2
◦ ABO blood group complex of genes
◦ Higher risk for blood group A
◦ Lower risk for blood group O
◦ Why?
◦ Antigen A interacts with viral protein S
◦ Anti-A antibodies limit viral interaction with host blood cell
Presenter: Gabriel Garcia Schmitt
OBS: HLA analysis (region in chromosome 6)Despite its important role in several viralinfections, the study did not find anysignificant SNPs related to Covid-19 severityor respiratory failure.
Locus 3p21.31
Several genes are associated
with this locus, such
as SLCGA20, LZTFL1,
CCR9, FYCO1, CXCR6 e
XCR1.
Principal candidates:
• SLCGA20
• CCR9
• CXCR6
Presenter: Henrique Larssen
The Covid-19 Host Genetics Consortium
◦ SLC6A20 functionally interacts with ACE2, the
receptor of the SARS-CoV-2 Spike protein that
is the key host gene for viral entry;
◦ CCR9 encodes the CC motif chemokine
receptor 9 , maturation of T cells;
◦ CXCR6 regulates the localization of resident
memory T (TRM) cells in the lung and
maintains a pool of airway TRM cells, critical
for cellular immunity against respiratory
pathogens.
Presenter: Henrique Larssen
Currently studies about locus 3p21.31
◦ To date, the locus with the most robust human
genetic association to COVID-19 severity is 3p21.31.
◦ The study identify SLC6A20 andCXCR6 as putative
causal genes that modulate COVID-19 risk
Presenter: Henrique Larssen
System ABO influence on Covid-19
Natural anti-A antibodies against SARS-CoV-2 infection:
◦ Group B or O has anti-A antibodies that slightly inhibits the entry of the virus into the host
cell.
ABO antigens in SARS-CoV-2:
◦ ABO antigens can trigger the virus spike protein attachment to the host cell receptor by
interactions with cell surface receptors, facilitating its entry, which occurs mainly with A
antigens.
Presenter: Ana Clara Germano Tostes
VonWillebrandfactor (vWF) andfactorVIII inCovid-19 risk:
◦ Coagulation factors such as factor VIII and von
Willebrand factor (vWF) increase the risk of thrombosis and
pulmonary embolism when in high levels in the blood plasma,
aggravating Covid-19;
◦ Pulmonary thromboembolism stops blood flow to the lungs,
making breathing difficult;
◦ In addition, VWF serves as a potential marker to predict the
endothelial activation that expresses the ACE2 receptor
(membrane protein through which the SARS-CoV-2 virus
enters);
Presenter: Ana Clara Germano Tostes
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8035048/
Impacts on blood donation Research difficulties
◦ The influence of the ABO system in
diseases such as Covid-19 can result
in a segregation of blood donors, with
greater appreciation for those with
type O, however, there are studies
that show that there is no
interference of donated blood in the
manifestation of the disease.
Presenter: Ana Clara Germano Tostes
◦ Short period (recent studies);
◦ Minimum of clinical metadata was requested –extensive genotype-phenotype elaboration ofcurrent findings could not be conducted;
◦ Limited information about the SARS-CoV-2infection status in the control participants;
◦ Few restrictions imposed during the formationof control group;
◦ Factors present at lower levels in type O individuals that has lower risk of thromboembolism
◦ This hypothesis supports FVIII and VWF in the ABO (H) determinants also shows the associationof the vulnerability of COVID-19 to the ABO blood group