Multi-omics integration identifies MT2A as a biomarker and a candidate host target linking zinc dysregulation to COVID-19 mortality

Abstract

Identifying host programs that connect micronutrient biology to COVID-19 immunopathology may enable more precise host-directed strategies. Zinc deficiency is linked to worse outcomes, yet the intracellular mediators that couple metal/redox stress to disease severity remain unclear. In this study, a PRISMA-guided meta-analysis of zinc supplementation was performed in hospitalized COVID-19 (seven studies; 1,972 participants), and observed reduced mortality (OR 0.48, 95% CI 0.36-0.64). Statistical heterogeneity was low, although regimens varied substantially in formulation, elemental dose, route, and duration. The study then integrated single-cell and bulk transcriptomes across blood and respiratory compartments, to map zinc-homeostasis pattern across disease states. In a large single-cell atlas (GSE158055; 1,462,702 cells from 196 individuals) spanning PBMC, bronchoalveolar lavage fluid, sputum, in bulk RNA-seq from postmortem lung tissue (GSE183533), and longitudinal peripheral blood (GSE198449), MT2A showed the most reproducible association with disease severity among metallothioneins, and was enriched in myeloid lineages. Its associations were compartment- and state-dependent, and SARS-CoV-2-relevant entry/processing and innate-sensing are involved, including TMPRSS2, CTSB/CTSL, and RNA-sensing pathways. In a longitudinal subset with complete timepoints (n = 9; days 0, 1, 8, and 12), MT2A peaked early after infection and declined thereafter, consistent with an inducible acute-phase response. Together, these results prioritize MT2A as a cross-compartment marker of metal/redox immune stress and a testable host node for biomarker-guided stratification and intervention timing, pending perturbation-based causal validation.

Keywords

COVID-19 / SARS-CoV-2 / Zinc homeostasis / MT2A / Single-cell transcriptome

Ethical statements

The data used in this study were provided by the Gene Expression Omnibus (GEO) database (Accession Nos GSE158055, GSE183533, and GSE198449), and public literature databases (PubMed, Embase, Web of Science, Cochrane Library, and ClinicalTrials.gov). Therefore, no ethics committee approval or informed consent was required for this study.

Author contributions

The authors confirm contributions to the paper as follows: study conception and design: Zhu B, Hua S, Li Z; data collection: Li Z, Hua S, Zhu B, Luo Y; analysis and interpretation of results: Li Z, Hua S, Zhu B, Luo Y, Qian W, Song S, Li J; draft manuscript preparation: Zhu B, Li Z, Hua S, Liu L. All authors reviewed the results and approved the final version of the manuscript.

Data availability

Raw bulk or single-cell RNA-seq data supporting this study are publicly available from the GEO database (www.ncbi.nlm.nih.gov/geo) under accession numbers GSE158055, GSE183533, and GSE198449. All other datasets generated and/or analyzed during the current study are available from the corresponding author upon reasonable request

Acknowledgments

Not applicable.

Conflict of interest

The authors declare no competing interests.

Supplementary information accompanies this paper online at: https://doi.org/10.48130/targetome-0026-0006

References

[1] Aw DZH, Zhang DX, Vignuzzi M. 2025. Strategies and efforts in circum-venting the emergence of antiviral resistance against conventional antivirals. npj Antimicrobials and Resistance 3:54

[2] Nature Microbiology. 2024. Considering the host in host-pathogen interactions. Nature Microbiology 9:1149-49

[3] Chen B, Yu P, Chan WN, Xie F, Zhang Y, et al. 2024. Cellular zinc metabolism and zinc signaling: from biological functions to diseases and therapeutic targets. Signal Transduction and Targeted Therapy 9:6

[4] Read SA, Obeid S, Ahlenstiel C, Ahlenstiel G. 2019. The role of zinc in antiviral immunity. Advances in Nutrition 10:696-710

[5] Jothimani D, Kailasam E, Danielraj S, Nallathambi B, Ramachandran H, et al. 2020. COVID-19: poor outcomes in patients with zinc deficiency. International Journal of Infectious Diseases 100:343-49

[6] Santos HO. 2022. Therapeutic supplementation with zinc in the management of COVID-19-related diarrhea and ageusia/dysgeusia: mechanisms and clues for a personalized dosage regimen. Nutrition Reviews 80:1086-1093

[7] Briassoulis G, Briassoulis P, Ilia S, Miliaraki M, Briassouli E. 2023. The anti-oxidative, anti-inflammatory, anti-apoptotic, and anti-necroptotic role of zinc in COVID-19 and sepsis. Antioxidants 12:1942

[8] Chu A, Foster M, Ward S, Zaman K, Hancock D, et al. 2015. Zinc-induced upregulation of metallothionein (MT)-2A is predicted by gene expres-sion of zinc transporters in healthy adults. Genes & Nutrition 10:44

[9] Kwon CS, Kountouri AM, Mayer C, Gordon MJ, Kwun IS, et al. 2007. Mononuclear cell metallothionein mRNA levels in human subjects with poor zinc nutrition. The British Journal of Nutrition 97:247-254

[10] Page MJ, McKenzie JE, Bossuyt PM, Boutron I, Hoffmann TC, et al. 2021. The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. BMJ 372:n71

[11] Sterne JA, Hernán MA, Reeves BC, Savović J, Berkman ND, et al. 2016. ROBINS-I: a tool for assessing risk of bias in non-randomised studies of interventions. BMJ 355:i4919

[12] Higgins JPT, Altman DG, Gøtzsche PC, Jüni P, Moher D, et al. 2011. The Cochrane Collaboration's tool for assessing risk of bias in randomised trials. BMJ 343:d5928

[13] Ren X, Wen W, Fan X, Hou W, Su B, et al. 2021. COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas. Cell 184:1895-913.e19

[14] Wolf FA, Angerer P, Theis FJ. 2018. SCANPY: large-scale single-cell gene expression data analysis. Genome Biology 19:15

[15] Sauerwald N, Zhang Z, Ramos I, Nair VD, Soares-Schanoski A, et al. 2022. Pre-infection antiviral innate immunity contributes to sex diffe-rences in SARS-CoV-2 infection. Cell Systems 13:924-31.e4

[16] Budhraja A, Basu A, Gheware A, Abhilash D, Rajagopala S, et al. 2022. Molecular signature of postmortem lung tissue from COVID-19 patients suggests distinct trajectories driving mortality. Disease Models & Mechanisms 15:dmm049572

[17] Fang Z, Liu X, Peltz G. 2023. GSEApy: a comprehensive package for performing gene set enrichment analysis in Python. Bioinformatics 39:btac757

[18] Futschik ME, Carlisle B. 2005. Noise-robust soft clustering of gene expression time-course data. Journal of Bioinformatics and Computa-tional Biology 3:965-88

[19] Mahjoub L, Youssef R, Yaakoubi H, Ben Salah H, Jaballah R, et al. 2024. Melatonin, vitamins and minerals supplements for the treatment of Covid-19 and Covid-like illness: a prospective, randomized, double-blind multicenter study. Explore 20:95-100

[20] Thomas S, Patel D, Bittel B, Wolski K, Wang Q, et al. 2021. Effect of high-dose zinc and ascorbic acid supplementation vs usual care on symp-tom length and reduction among ambulatory patients with SARS-CoV-2 infection: the COVID A to Z randomized clinical trial. JAMA Network Open 4:e210369-e69

[21] Ben Abdallah S, Mhalla Y, Trabelsi I, Sekma A, Youssef R, et al. 2023. Twice-daily oral zinc in the treatment of patients with coronavirus disease 2019: a randomized double-blind controlled trial. Clinical Infec-tious Diseases 76:185-191

[22] Patel O, Chinni V, El-Khoury J, Perera M, Neto AS, et al. 2021. A pilot double-blind safety and feasibility randomized controlled trial of high-dose intravenous zinc in hospitalized COVID-19 patients. Journal of Medical Virology 93:3261-3267

[23] Ibrahim Alhajjaji G, Alotaibi N, Abutaleb N, Alotaibi MM, Alhajjaji A, et al. 2023. Effect of zinc supplementation on symptom reduction and length of hospital stay among pediatric patients with Coronavirus disease 2019 (COVID-19). Saudi Pharmaceutical Journal 31: 585-591

[24] Al Sulaiman K, Aljuhani O, Al Shaya AI, Kharbosh A, Kensara R, et al. 2021. Evaluation of zinc sulfate as an adjunctive therapy in COVID-19 critically ill patients: a two center propensity-score matched study. Critical Care 25:363

[25] Carlucci PM, Ahuja T, Petrilli C, Rajagopalan H, Jones S, et al. 2020. Zinc sulfate in combination with a zinc ionophore may improve outcomes in hospitalized COVID-19 patients. Journal of Medical Microbiology 69:1228-1234

[26] Maret W, Krezel A. 2007. Cellular zinc and redox buffering capacity of metallothionein/thionein in health and disease. Molecular Medicine 13:371-375

[27] Subramanian Vignesh K, Deepe GS, Jr. 2017. Metallothioneins: emerg-ing modulators in immunity and infection. International Journal of Molecular Sciences 18:2197

[28] Sato M, Sasaki M, Hojo H. 1994. Differential induction of metallo-thionein synthesis by interleukin-6 and tumor necrosis factor-α in rat tissues. International Journal of Immunopharmacology 16:187-195

[29] Ling XB, Wei HW, Wang J, Kong YQ, Wu YY, et al. 2016. Mammalian metallothionein-2A and oxidative stress. International Journal of Mole-cular Sciences 17:1483

[30] Butcher HL, Kennette WA, Collins O, Zalups RK, Koropatnick J. 2004. Metallothionein mediates the level and activity of nuclear factor kappa B in murine fibroblasts. The Journal of Pharmacology and Experimental Therapeutics 310:589-598

[31] Saletta F, Suryo Rahmanto Y, Noulsri E, Richardson DR. 2010. Iron Chelator-mediated alterations in gene expression: identification of novel iron-regulated molecules that are molecular targets of hypoxia-inducible factor-1α and p53. Molecular Pharmacology 77:443-458

[32] Kim CH, Kim JH, Lee J, Ahn YS. 2003. Zinc-induced NF-κB inhibition can be modulated by changes in the intracellular metallothionein level. Toxicology and Applied Pharmacology 190( 2):189-196

[33] Stafford SL, Bokil NJ, Achard MES, Kapetanovic R, Schembri MA, et al. 2013. Metal ions in macrophage antimicrobial pathways: emerging roles for zinc and copper. Bioscience Reports 33:e00049

[34] Liu Y, Liu H, Chen W, Yang T, Zhang W. 2014. EOLA 1 protects lipopolysaccharide induced IL-6 production and apoptosis by regula-tion of MT2A in human umbilical vein endothelial cells. Molecular and Cellular Biochemistry 395:45-51

[35] Mussbacher M, Salzmann M, Brostjan C, Hoesel B, Schoergenhofer C, et al. 2019. Cell type-specific roles of NF-κB linking inflammation and thrombosis. Frontiers in Immunology 10:85

[36] Fekete R, Simats A, Bíró E, Pósfai B, Cserép C, et al. 2025. Microglia dysfunction, neurovascular inflammation and focal neuropathologies are linked to IL-1- and IL-6-related systemic inflammation in COVID-19. Nature Neuroscience 28:558-576

[37] Beckers M, Bloem BR, Helmich RC. 2023. Mask on, mask off: subclinical Parkinson's disease unveiled by COVID-19. Journal of Movement Disor-ders 16:55-58

[38] Padmanabhan P, Desikan R, Dixit NM. 2020. Targeting TMPRSS2 and Cathepsin B/L together may be synergistic against SARS-CoV-2 infec-tion. PLoS Computational Biology 16:e1008461

[39] Hashimoto R, Sakamoto A, Deguchi S, Yi R, Sano E, et al. 2021. Dual inhibition of TMPRSS2 and Cathepsin Bprevents SARS-CoV-2 infection in iPS cells. Molecular Therapy Nucleic Acids 26:1107-1114

[40] Zhao MM, Yang WL, Yang FY, Zhang L, Huang WJ, et al. 2021. Cathep-sin L plays a key role in SARS-CoV-2 infection in humans and humanized mice and is a promising target for new drug development. Signal Transduction and Targeted Therapy 6:134

[41] van der Made CI, Simons A, Schuurs-Hoeijmakers J, van den Heuvel G, Mantere T, et al. 2020. Presence of genetic variants among young men with severe COVID-19. JAMA 324:663-673

[42] Wang C, Khatun MS, Ellsworth CR, Chen Z, Islamuddin M, et al. 2024. Deficiency of Tlr7 and Irf 7 in mice increases the severity of COVID-19 through the reduced interferon production. Communications Biology 7:1162

[43] Lynes MA, Hidalgo J, Manso Y, Devisscher L, Laukens D, et al. 2014. Metallothionein and stress combine to affect multiple organ systems. Cell Stress and Chaperones 19:605-611

[44] Duprez J, Roma LP, Close AF, Jonas JC. 2012. Protective antioxidant and antiapoptotic effects of ZnCl 2 in rat pancreatic islets cultured in low and high glucose concentrations. PLoS One 7:e46831

[45] Borchert S, Suckrau PM, Walter RFH, Wessolly M, Mairinger E, et al. 2020. Impact of metallothionein-knockdown on cisplatin resistance in malignant pleural mesothelioma. Scientific Reports 10:18677

[46] Tarapore P, Shu Y, Guo P, Ho SM. 2011. Application of phi29 motor pRNA for targeted therapeutic delivery of siRNA silencing metallo-thionein-IIA and survivin in ovarian cancers. Molecular Therapy 19:386-394

[47] Racioppo B, Pechalrieu D, Abegg D, Dwyer B, Ramseier NT, et al. 2025. Chemoproteomics-enabled de novo proteolysis targeting chimera discovery platform identifies a metallothionein degrader to probe its role in cancer. Journal of the American Chemical Society 147:7817-7828