Genetic variation of Golgi membrane protein 1 is associated with COVID-19 disease

Abstract

•There is an causality between GOLM1 and COVID-19.•GOLM1 levels may be linked to high glucose levels during COVID-19 infection.•GOLM1 might be a novel biomarker for COVID-19. We read with interest a recent work by Zoha Kamali and colleagues, who found IL-13 as a risk factor for severe COVID-19.1Kamali Z Vonk JM Thio CHL Vaez A Snieder H. A Mendelian randomization cytokine screen reveals IL-13 as causal factor in risk of severe COVID-19.J Infect. 2022 May 23; (PubMed PMID: 35618154. Pubmed Central PMCID: PMC9126023 interests. Epub 2022/05/27. eng)Abstract Full Text Full Text PDF PubMed Scopus (1) Google Scholar Similarly, other investigators discovered that interleukin (IL) pathways, including IL-1, IL-1R1, and IL-6, etc, were associated with the severity of COVID-19 disease.2Wang R. Genetic variation of interleukin-1 receptor type 1 is associated with severity of COVID-19 disease.J Infect. 2022 Feb; 84 (PubMed PMID: 34952040. Pubmed Central PMCID: PMC8690223 interest to disclose. Epub 2021/12/25. eng): e19-e21Abstract Full Text Full Text PDF PubMed Scopus (5) Google Scholar,3Giannitrapani L Augello G Mirarchi L Amodeo S Veronese N Sasso BL et al.Outcome predictors in SARS-CoV-2 disease (COVID-19): The prominent role of IL-6 levels and an IL-6 gene polymorphism in a western Sicilian population.J Infect. 2022 Apr 29; (PubMed PMID: 35490738. Pubmed Central PMCID: PMC9050196. Epub 2022/05/02. eng)Abstract Full Text Full Text PDF PubMed Scopus (1) Google ScholarIn the present work, we used the previously identified association of single-nucleotide polymorphisms (SNPs) for circulating Golgi membrane protein 1 (GOLM1) levels to evaluate its causal role in COVID-19.4Sun BB Maranville JC Peters JE Stacey D Staley JR Blackshaw J et al.Genomic atlas of the human plasma proteome.Nature. 2018; 558 (Jun PubMed PMID: 29875488. Pubmed Central PMCID: PMC6697541. Epub 2018/06/08. eng): 73-79Crossref PubMed Scopus (513) Google Scholar GOLM1, also known as GOLPH2 and GP73, is a type II transmembrane protein that cycles across membrane compartments. Once considered a valuable serum marker for hepatocellular carcinoma,5Mao Y Yang H Xu H Lu X Sang X Du S et al.Golgi protein 73 (GOLPH2) is a valuable serum marker for hepatocellular carcinoma.Gut. 2010; 59 (Dec PubMed PMID: 20876776. Epub 2010/09/30. eng): 1687-1693Crossref PubMed Scopus (196) Google Scholar GOLM1 was shown to exacerbate CD8+ T cell suppression in liver cancer by facilitating exosomal PD-L1 trafficking into tumor-associated macrophages.6Chen J Lin Z Liu L Zhang R Geng Y Fan M et al.GOLM1 exacerbates CD8(+) T cell suppression in hepatocellular carcinoma by promoting exosomal PD-L1 transport into tumor-associated macrophages.Signal Transduct Target Ther. 2021 Nov 19; 6 (PubMed PMID: 34795203. Pubmed Central PMCID: PMC8602261. Epub 2021/11/20. eng): 397Crossref PubMed Scopus (13) Google Scholar More recently, it was discovered that GOLM1 connects SARS-CoV-2 infection with dysglycemia.7Coate KC. GP73 links SARS-CoV-2 infection with dysglycaemia.Nat Metab. 2022; 4 (Jan PubMed PMID: 34992300. Epub 2022/01/08. eng): 9-10Crossref PubMed Scopus (1) Google ScholarIn order to infer potential causality of risk factor-disease associations, we used the promising approach of Mendelian randomization (MR).8Hemani G Zheng J Elsworth B Wade KH Haberland V Baird D et al.The MR-Base platform supports systematic causal inference across the human phenome.Elife. 2018 May 30; 7 (PubMed PMID: 29846171. Pubmed Central PMCID: PMC5976434. Epub 2018/05/31. eng)Crossref PubMed Scopus (1260) Google Scholar This strategy is based on the premise that genetic variations are distributed randomly during meiosis, hence minimizing confounding bias. The design for this MR study is shown in Suppl. Fig. 1.The GOLM1 genetic instrumental variables (IVs) were selected on the basis of cis-protein quantitative trait loci (cis-pQTLs) identified in recent proteomics genome-wide association study (GWAS) including 3,301 European individuals.4Sun BB Maranville JC Peters JE Stacey D Staley JR Blackshaw J et al.Genomic atlas of the human plasma proteome.Nature. 2018; 558 (Jun PubMed PMID: 29875488. Pubmed Central PMCID: PMC6697541. Epub 2018/06/08. eng): 73-79Crossref PubMed Scopus (513) Google Scholar pQTLs strongly associated with GOLM1 at a threshold of p < 5e-6 were chosen. Linkage disequilibrium (LD) analysis by the LDlinkR package was used to eliminate cis-pQTLs (r2 > 0.1) based on the 1000-genome European reference panel. F statistics were assessed to determine the instrument strength, and F ≥ 10 indicates strong instruments. Finally, the candidate GOLM1 genetic IVs were listed in Suppl. Table 1.Table 1Corona Virus Disease 2019 (COVID-19) GWAS datasets.GWAS IDtraitncasencontrolnsnppopulationebi-a-GCST011074COVID-19 (RELEASE 5)3249413162078666451Europeanebi-a-GCST010776COVID-19 (RELEASE 4)14134128487611435708Europeanebi-a-GCST010780COVID-19 (RELEASE 4)14134128487612508741Europeanebi-a-GCST011072COVID-19 (RELEASE 5)3156210268487750967Europeanebi-a-GCST011073COVID-19 (RELEASE 5)3898416447848660177Europeanebi-a-GCST011071COVID-19 (RELEASE 5)2907115597128103014Europeanebi-a-GCST010781COVID-19 (predicted covid from self-reported symptoms vs predicted or self-reported non-covid) RELEASE 432043572811379674Europeanebi-a-GCST010778COVID-19 (covid vs lab/self reported negative) RELEASE 4881810180612832272Europeanebi-a-GCST011075COVID-19 (very severe respiratory confirmed vs population) RELEASE 5510113832419739225Europeanebi-a-GCST011076COVID-19 (very severe respiratory confirmed vs population) RELEASE 546067028017475770Europeanebi-a-GCST011078COVID-19 (very severe respiratory confirmed vs population) RELEASE 5479210546649817241Europeanebi-a-GCST010783COVID-19 (very severe respiratory confirmed vs population) RELEASE 4388662226511678750Europeanebi-a-GCST010777COVID-19 (hospitalized vs population) RELEASE 4640690208812832272Europeanebi-a-GCST010779COVID-19 (hospitalized vs population) RELEASE 4640690208811272365Europeanebi-a-GCST011077COVID-19 (very severe respiratory confirmed vs population) RELEASE 5479210546647496658Europeanebi-a-GCST011084COVID-19 (hospitalized vs population) RELEASE 5937311972567534178Europeanebi-a-GCST90000256Severe COVID-19 infection with respiratory failure (analysis II)161021808095992Europeanebi-a-GCST90000255Severe COVID-19 infection with respiratory failure (analysis I)161022058095360Europeanebi-a-GCST011082COVID-19 (hospitalized vs population) RELEASE 5831615490956814406EuropeanGWAS ID: Genome wide association study identity; ncase: the number of COVID-19 case; ncontrol: the number of the control; nsnp: the number of single-nucleotide polymorphism. Open table in a new tab The instrumental variables for COVID-19 were retrieved at the genome-wide significance (p < 5e-8) from the largest GWAS meta-analysis of COVID-19 to date, by the COVID-19 Host Genetics Initiative.9COVID-19 Host Genetics InitiativeThe COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic.Eur J Hum Genet. 2020; 28 (Jun PubMed PMID: 32404885. Pubmed Central PMCID: PMC7220587. Epub 2020/05/15. eng.): 715-718Crossref PubMed Scopus (315) Google Scholar In total, we used twenty COVID-19 GWASs for COVID-19 severity (e.g. “Severe COVID-19 infection with respiratory failure, id:ebi-a-GCST90000256”, etc) or susceptibility (e.g. “COVID-19 RELEASE 5, id:ebi-a-GCST011072”, etc) respectively. Summary statistics about twenty COVID-19 GWASs of persons with European ancestry are shown in Table 1, and GWAS summary datasets are available in https://gwas.mrcieu.ac.uk/datasets/.The independent GOLM1 genetic IVs from twenty COVID-2019 GWAS datasets were then standardized. Potential proxy SNPs were identified by the LD proxy tool (r2 > 0.80) when these IVs could not be found. The association of these IVs with the twenty COVID-19 GWAS datasets is shown in Suppl. Table 2.The MR-PRESSO, MR-Egger_intercept, MR-Egger, and Inverse variance weighted (IVW) methods in Cochran's Q statistic were used to examine the pleiotropy or heterogeneity of the independent GOLM1 genetic IVs in the COVID-19 GWASs. No evident pleiotropy or heterogeneity of these IVs was seen in the COVID-19 GWAS datasets (Suppl. Table 3). Consequently, all identified GOLM1 genetic variations may be regarded as effective IVs in our MR investigation.Further, we used MR to analyze the effect of the GOLM1 genetic IVs on the risk of contracting COVID-19. Interestingly, we found that as GOLM1 genetically increased, the risk of severe respiratory COVID-19 (ebi-a-GCST90000256) had an increased trend using MR Egger (Beta = 0.823, p = 6.96E-03; OR = 2.277), weighted mode (Beta = 0.587, p = 2.07E-03; OR = 1.799), weighted median (Beta = 0.573, p = 9.81E-06; OR = 1.773), and IVW (Beta = 0.410, p = 1.81E-04; OR = 1.507) (Fig. 1; Suppl. Table 4). In addition, the impact of a single SNP on COVID-19 risk rose as the effect of a single SNP on GOLM1 increased, as measured by IVW, weighted median, simple mode, and weighted mode (Fig. 1A). Critically, each effect size (Fig. 1B) and leave-one-out sensitivity (Fig. 1C) suggested that each effect of GOLM1-associated SNPs on COVID-19 risk were robust. Our MR results were replicated in other 19 COVID-19 GWASs to ensure robustness and reduce false positives (Suppl. Table 4; Suppl. Fig. 2-4).In summary, we found an OR of about 1.20 for COVID-19 per 1 SD increase in GOLM1 levels and replicated in multiple independent datasets (Fig. 1D). Warranting further investigations, severe cases of SARS-CoV-2 infection are related with high blood glucose levels and metabolic complications. Recent research suggested that GOLM1 is a glucogenic hormone that contributes to the SARS-CoV-2-induced change in systemic glucose metabolism and increased hepatic gluconeogenesis.10Wan L Gao Q Deng Y Ke Y Ma E Yang H et al.GP73 is a glucogenic hormone contributing to SARS-CoV-2-induced hyperglycemia.Nat Metab. 2022; 4 (Jan PubMed PMID: 34992299. Epub 2022/01/08. eng): 29-43Crossref PubMed Scopus (4) Google Scholar We then conducted a MR study to investigate the associations of genetically predicted GOLM1 with glucose (Suppl. Table 5). Our MR result of a favorable impact of GOLM1 on glucose levels is consistent with a prior finding that plasma GOLM1 levels are increased in COVID-19 patients and positively correlate with blood glucose levels.10Wan L Gao Q Deng Y Ke Y Ma E Yang H et al.GP73 is a glucogenic hormone contributing to SARS-CoV-2-induced hyperglycemia.Nat Metab. 2022; 4 (Jan PubMed PMID: 34992299. Epub 2022/01/08. eng): 29-43Crossref PubMed Scopus (4) Google ScholarThis study has several limitations. First, GOLM1 genetic IVs and COVID-19 GWAS are from European ancestry. Our conclusion need be proven in other ancestries. Second, GOLM1 blockade with an antibody inhibits excessive glucogenesis stimulated by SARS-CoV-2 in vitro and lowers elevated fasting blood glucose levels in infected mice.10Wan L Gao Q Deng Y Ke Y Ma E Yang H et al.GP73 is a glucogenic hormone contributing to SARS-CoV-2-induced hyperglycemia.Nat Metab. 2022; 4 (Jan PubMed PMID: 34992299. Epub 2022/01/08. eng): 29-43Crossref PubMed Scopus (4) Google Scholar It is necessary to clarify whether inhibiting GOLM1 could reduce the risk of severe respiratory COVID-19 in the future research.To conclude, our study provides evidence for a causal effect of GOLM1 on COVID-19. As such, further investigation is warranted exploring GOLM1 as a potential novel biomarker and therapeutic target for COVID-19 patients or those at risk of acquiring severe symptoms.FundingThis study was supported by grants from National Natural Science Foundation of China (81772520). The funder had no role in the study design, collection, analysis and interpretation of data, in the writing of the manuscript or in the decision to submit the manuscript for publication.Authors’ contributionsJY conceived and initiated the project, and were responsible for the design of the study. F-JT, L-YX, FX and L-JM access all the data in the study and took responsibility for the accuracy of the data analysis. JY and F-JT performed the statistical analysis. All authors were involved in the writing and revision of the article, and all authors approved the submitted version to be published. We read with interest a recent work by Zoha Kamali and colleagues, who found IL-13 as a risk factor for severe COVID-19.1Kamali Z Vonk JM Thio CHL Vaez A Snieder H. A Mendelian randomization cytokine screen reveals IL-13 as causal factor in risk of severe COVID-19.J Infect. 2022 May 23; (PubMed PMID: 35618154. Pubmed Central PMCID: PMC9126023 interests. Epub 2022/05/27. eng)Abstract Full Text Full Text PDF PubMed Scopus (1) Google Scholar Similarly, other investigators discovered that interleukin (IL) pathways, including IL-1, IL-1R1, and IL-6, etc, were associated with the severity of COVID-19 disease.2Wang R. Genetic variation of interleukin-1 receptor type 1 is associated with severity of COVID-19 disease.J Infect. 2022 Feb; 84 (PubMed PMID: 34952040. Pubmed Central PMCID: PMC8690223 interest to disclose. Epub 2021/12/25. eng): e19-e21Abstract Full Text Full Text PDF PubMed Scopus (5) Google Scholar,3Giannitrapani L Augello G Mirarchi L Amodeo S Veronese N Sasso BL et al.Outcome predictors in SARS-CoV-2 disease (COVID-19): The prominent role of IL-6 levels and an IL-6 gene polymorphism in a western Sicilian population.J Infect. 2022 Apr 29; (PubMed PMID: 35490738. Pubmed Central PMCID: PMC9050196. Epub 2022/05/02. eng)Abstract Full Text Full Text PDF PubMed Scopus (1) Google Scholar In the present work, we used the previously identified association of single-nucleotide polymorphisms (SNPs) for circulating Golgi membrane protein 1 (GOLM1) levels to evaluate its causal role in COVID-19.4Sun BB Maranville JC Peters JE Stacey D Staley JR Blackshaw J et al.Genomic atlas of the human plasma proteome.Nature. 2018; 558 (Jun PubMed PMID: 29875488. Pubmed Central PMCID: PMC6697541. Epub 2018/06/08. eng): 73-79Crossref PubMed Scopus (513) Google Scholar GOLM1, also known as GOLPH2 and GP73, is a type II transmembrane protein that cycles across membrane compartments. Once considered a valuable serum marker for hepatocellular carcinoma,5Mao Y Yang H Xu H Lu X Sang X Du S et al.Golgi protein 73 (GOLPH2) is a valuable serum marker for hepatocellular carcinoma.Gut. 2010; 59 (Dec PubMed PMID: 20876776. Epub 2010/09/30. eng): 1687-1693Crossref PubMed Scopus (196) Google Scholar GOLM1 was shown to exacerbate CD8+ T cell suppression in liver cancer by facilitating exosomal PD-L1 trafficking into tumor-associated macrophages.6Chen J Lin Z Liu L Zhang R Geng Y Fan M et al.GOLM1 exacerbates CD8(+) T cell suppression in hepatocellular carcinoma by promoting exosomal PD-L1 transport into tumor-associated macrophages.Signal Transduct Target Ther. 2021 Nov 19; 6 (PubMed PMID: 34795203. Pubmed Central PMCID: PMC8602261. Epub 2021/11/20. eng): 397Crossref PubMed Scopus (13) Google Scholar More recently, it was discovered that GOLM1 connects SARS-CoV-2 infection with dysglycemia.7Coate KC. GP73 links SARS-CoV-2 infection with dysglycaemia.Nat Metab. 2022; 4 (Jan PubMed PMID: 34992300. Epub 2022/01/08. eng): 9-10Crossref PubMed Scopus (1) Google Scholar In order to infer potential causality of risk factor-disease associations, we used the promising approach of Mendelian randomization (MR).8Hemani G Zheng J Elsworth B Wade KH Haberland V Baird D et al.The MR-Base platform supports systematic causal inference across the human phenome.Elife. 2018 May 30; 7 (PubMed PMID: 29846171. Pubmed Central PMCID: PMC5976434. Epub 2018/05/31. eng)Crossref PubMed Scopus (1260) Google Scholar This strategy is based on the premise that genetic variations are distributed randomly during meiosis, hence minimizing confounding bias. The design for this MR study is shown in Suppl. Fig. 1. The GOLM1 genetic instrumental variables (IVs) were selected on the basis of cis-protein quantitative trait loci (cis-pQTLs) identified in recent proteomics genome-wide association study (GWAS) including 3,301 European individuals.4Sun BB Maranville JC Peters JE Stacey D Staley JR Blackshaw J et al.Genomic atlas of the human plasma proteome.Nature. 2018; 558 (Jun PubMed PMID: 29875488. Pubmed Central PMCID: PMC6697541. Epub 2018/06/08. eng): 73-79Crossref PubMed Scopus (513) Google Scholar pQTLs strongly associated with GOLM1 at a threshold of p < 5e-6 were chosen. Linkage disequilibrium (LD) analysis by the LDlinkR package was used to eliminate cis-pQTLs (r2 > 0.1) based on the 1000-genome European reference panel. F statistics were assessed to determine the instrument strength, and F ≥ 10 indicates strong instruments. Finally, the candidate GOLM1 genetic IVs were listed in Suppl. Table 1. GWAS ID: Genome wide association study identity; ncase: the number of COVID-19 case; ncontrol: the number of the control; nsnp: the number of single-nucleotide polymorphism. The instrumental variables for COVID-19 were retrieved at the genome-wide significance (p < 5e-8) from the largest GWAS meta-analysis of COVID-19 to date, by the COVID-19 Host Genetics Initiative.9COVID-19 Host Genetics InitiativeThe COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic.Eur J Hum Genet. 2020; 28 (Jun PubMed PMID: 32404885. Pubmed Central PMCID: PMC7220587. Epub 2020/05/15. eng.): 715-718Crossref PubMed Scopus (315) Google Scholar In total, we used twenty COVID-19 GWASs for COVID-19 severity (e.g. “Severe COVID-19 infection with respiratory failure, id:ebi-a-GCST90000256”, etc) or susceptibility (e.g. “COVID-19 RELEASE 5, id:ebi-a-GCST011072”, etc) respectively. Summary statistics about twenty COVID-19 GWASs of persons with European ancestry are shown in Table 1, and GWAS summary datasets are available in https://gwas.mrcieu.ac.uk/datasets/. The independent GOLM1 genetic IVs from twenty COVID-2019 GWAS datasets were then standardized. Potential proxy SNPs were identified by the LD proxy tool (r2 > 0.80) when these IVs could not be found. The association of these IVs with the twenty COVID-19 GWAS datasets is shown in Suppl. Table 2. The MR-PRESSO, MR-Egger_intercept, MR-Egger, and Inverse variance weighted (IVW) methods in Cochran's Q statistic were used to examine the pleiotropy or heterogeneity of the independent GOLM1 genetic IVs in the COVID-19 GWASs. No evident pleiotropy or heterogeneity of these IVs was seen in the COVID-19 GWAS datasets (Suppl. Table 3). Consequently, all identified GOLM1 genetic variations may be regarded as effective IVs in our MR investigation. Further, we used MR to analyze the effect of the GOLM1 genetic IVs on the risk of contracting COVID-19. Interestingly, we found that as GOLM1 genetically increased, the risk of severe respiratory COVID-19 (ebi-a-GCST90000256) had an increased trend using MR Egger (Beta = 0.823, p = 6.96E-03; OR = 2.277), weighted mode (Beta = 0.587, p = 2.07E-03; OR = 1.799), weighted median (Beta = 0.573, p = 9.81E-06; OR = 1.773), and IVW (Beta = 0.410, p = 1.81E-04; OR = 1.507) (Fig. 1; Suppl. Table 4). In addition, the impact of a single SNP on COVID-19 risk rose as the effect of a single SNP on GOLM1 increased, as measured by IVW, weighted median, simple mode, and weighted mode (Fig. 1A). Critically, each effect size (Fig. 1B) and leave-one-out sensitivity (Fig. 1C) suggested that each effect of GOLM1-associated SNPs on COVID-19 risk were robust. Our MR results were replicated in other 19 COVID-19 GWASs to ensure robustness and reduce false positives (Suppl. Table 4; Suppl. Fig. 2-4). In summary, we found an OR of about 1.20 for COVID-19 per 1 SD increase in GOLM1 levels and replicated in multiple independent datasets (Fig. 1D). Warranting further investigations, severe cases of SARS-CoV-2 infection are related with high blood glucose levels and metabolic complications. Recent research suggested that GOLM1 is a glucogenic hormone that contributes to the SARS-CoV-2-induced change in systemic glucose metabolism and increased hepatic gluconeogenesis.10Wan L Gao Q Deng Y Ke Y Ma E Yang H et al.GP73 is a glucogenic hormone contributing to SARS-CoV-2-induced hyperglycemia.Nat Metab. 2022; 4 (Jan PubMed PMID: 34992299. Epub 2022/01/08. eng): 29-43Crossref PubMed Scopus (4) Google Scholar We then conducted a MR study to investigate the associations of genetically predicted GOLM1 with glucose (Suppl. Table 5). Our MR result of a favorable impact of GOLM1 on glucose levels is consistent with a prior finding that plasma GOLM1 levels are increased in COVID-19 patients and positively correlate with blood glucose levels.10Wan L Gao Q Deng Y Ke Y Ma E Yang H et al.GP73 is a glucogenic hormone contributing to SARS-CoV-2-induced hyperglycemia.Nat Metab. 2022; 4 (Jan PubMed PMID: 34992299. Epub 2022/01/08. eng): 29-43Crossref PubMed Scopus (4) Google Scholar This study has several limitations. First, GOLM1 genetic IVs and COVID-19 GWAS are from European ancestry. Our conclusion need be proven in other ancestries. Second, GOLM1 blockade with an antibody inhibits excessive glucogenesis stimulated by SARS-CoV-2 in vitro and lowers elevated fasting blood glucose levels in infected mice.10Wan L Gao Q Deng Y Ke Y Ma E Yang H et al.GP73 is a glucogenic hormone contributing to SARS-CoV-2-induced hyperglycemia.Nat Metab. 2022; 4 (Jan PubMed PMID: 34992299. Epub 2022/01/08. eng): 29-43Crossref PubMed Scopus (4) Google Scholar It is necessary to clarify whether inhibiting GOLM1 could reduce the risk of severe respiratory COVID-19 in the future research. To conclude, our study provides evidence for a causal effect of GOLM1 on COVID-19. As such, further investigation is warranted exploring GOLM1 as a potential novel biomarker and therapeutic target for COVID-19 patients or those at risk of acquiring severe symptoms. FundingThis study was supported by grants from National Natural Science Foundation of China (81772520). The funder had no role in the study design, collection, analysis and interpretation of data, in the writing of the manuscript or in the decision to submit the manuscript for publication.