Study explores differentially expressed immune genes for COVID-19 patient stratification

In a recent pre-proof study posted to the journal Molecular Immunology, researchers determined the transcriptional signatures associated with the severity of coronavirus disease 2019 (COVID-19).

Study: Stratification of COVID-19 patients based on quantitative immune-related gene expression in whole blood. Image Credit: Yuganov Konstantin/Shutterstock

To date, there have been over 440 million COVID-19 cases and 5.9 million related deaths globally since the initial outbreak in Wuhan, China. COVID-19, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), typically leads to mild disease. Yet, it causes severe illness requiring hospitalization and oxygen support and may prove fatal in some cases. 

Severe COVID-19 and death might result from pneumonia with respiratory distress. It is believed that a dysregulated immune response coupled with inflammation might play a critical role in the pathogenesis of severe COVID-19. Studies have suggested that older people, males, obese individuals, and those with diabetes mellitus, among other comorbidities, are at an elevated risk for severe COVID-19 and mortality. Identifying early predictive biomarkers can allow risk stratification for COVID-19 patients and guide treatment and strategies.

The study

In the present study, researchers examined blood specimens collected from SARS-CoV-2-infected individuals after a week of symptom onset. The subjects had varying degrees of disease severity. The whole blood specimens were analyzed for the expression of about 143 immune-related genes by dual-color reverse transcriptase multiplex ligation-dependent probe amplification (dcRT-MLPA).

50 whole blood samples were collected from adults at the Sahlgrenska University Hospital, Sweden, between March 2020 and May 2020. Total ribonucleic acids (RNAs) were extracted using the PAXgene Blood RNA Kit and then quantified using NanoDrop. Gene expression profiles were determined by dual-color reverse transcriptase multiplex ligation-dependent probe amplification (dcRT-MLPA).

RNA was transcribed to complementary deoxyribose nucleic acid (cDNA) with a specific reverse transcription (RT) primer for each target gene followed by hybridization of cDNA to probes and polymerase chain reaction (PCR) amplification of the ligated product (cDNA: probe). Besides the immune genes, four housekeeping genes viz., glyceraldehyde-3-phosphate dehydrogenase (GAPDH), beta-2-microglobulin (B2M), glucuronidase beta (GUSB), and RhoGEF and GTPase activating protein (ABR), were profiled.


Among the 50 specimens, 35 specimens were PCR tested for confirmed SARS-CoV-2 infection, while the remaining samples were from healthy subjects verified by their PCR-negative status. Patients who had varying disease states – mild, moderate/severe, and critical – were classified accordingly. The mean age of those with the critical disease was approximately 10 years higher than other subjects. Consistent with other reports, the authors observed males and older people as more susceptible to disease.

Of the 143 immune genes, 10 genes were differentially expressed across the mild disease cohort, with seven upregulated and three downregulated genes. In the moderate/severe group, nine genes were downregulated while two were upregulated, while in the samples from the critical disease cohort, 14 and 13 genes were up- and down-regulated, respectively. The number of genes being differentially expressed increased with the disease severity. Across the three cohorts, there were three common genes – interferon alpha inducible protein (IFI6), interferon-induced transmembrane protein 3 (IFITM3), and nod-like receptor family pyrin domain containing 1 (NLRP1). IFITM3 and IFI6 expression were high across all infected individuals, while NLRP1 expression was low. 

Mild cases had five upregulated genes – interferon-induced protein 35 (IFI35), IFI44, 2'-5'-oligoadenylate synthetase 2 (OAS2), OAS3, and IFIT2 (IFI with tetratricopeptide repeats 2) that were common with critical patients. Moreover, these genes showed upregulation in moderate/severe cases, albeit insignificant. Critical cases had a few unique highly expressed genes – Fc-gamma receptor 1A (FCGR1A), signal transducer and activator of transcription (STAT1), guanylate-binding protein 1 (GBP1), GBP2, and antigen peptide transporter 1 (TAP1).

Gene expression profiles were compared among the patients across three COVID-19 cohorts. The authors found 15 genes significantly different between mild and critical patients. Of these, all except three genes (FCGR1A, toll-like receptor 2 [TLR2], and TAP1) had lower expression in critical cases. The expression profile in the moderate/severe group was similar to critical cases except for three genes (TLR2, TAP1, and C-C motif chemokine ligand 5 [CCL5]).


The researchers identified various immune genes with differential expression patterns in acute COVID-19 patients. Based on the observations, the authors theorized that critical cases of COVID-19 can be discerned by the reduced expression of T lymphocyte-associated genes in the peripheral blood.

Notably, tumor necrosis factor (TNF) receptor superfamily member 1A (TNFRS1A) expression was selectively lower in patients with mild COVID-19. Despite the smaller sample size limiting the study findings, they speculate that TNFRS1A could be helpful for COVID-19 patient stratification; nonetheless, more validation is required in larger COVID-19 cohorts.

Journal reference:
  • Josefine Persson, Björn Andersson, Suzanne van Veen, Mariëlle C. Haks, Ogonna Obudulu, Sara Torkzadeh, Tom H.M. Ottenhoff, Nelly Kanberg, Magnus Gisslén, Lars-Magnus Andersson, Ali M. Harandi. (2022). Stratification of COVID-19 patients based on quantitative immune-related gene expression in whole blood, Molecular Immunology. doi:

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Tags: Antigen, Blood, CCL5, Chemokine, Coronavirus, Coronavirus Disease COVID-19, covid-19, Diabetes, Diabetes Mellitus, Gene, Gene Expression, Genes, Hospital, Hybridization, Immune Response, Immunology, Inflammation, Interferon, Ligand, Ligation, Lymphocyte, Mortality, Necrosis, Nucleic Acid, Oxygen, Pneumonia, Polymerase, Polymerase Chain Reaction, Protein, Receptor, Respiratory, Reverse Transcriptase, RNA, SARS, SARS-CoV-2, Severe Acute Respiratory, Severe Acute Respiratory Syndrome, Syndrome, T Lymphocyte, Transcription, Tumor, Tumor Necrosis Factor

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Tarun Sai Lomte

Tarun is a writer based in Hyderabad, India. He has a Master’s degree in Biotechnology from the University of Hyderabad and is enthusiastic about scientific research. He enjoys reading research papers and literature reviews and is passionate about writing.

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