Brief Communication

Multiorgan injuries are a major complication of severe Coronavirus Disease 2019 (COVID-19). However, its pathogenesis is barely understood. Herein, we profiled the host responses to fatal SARS-CoV-2 infection by performing quantitative proteomics of 19 postmortem samples of 8 different organs or tissues, including lung, liver, intestine, kidney, spleen, brain, heart and muscle, from 3 decreased COVID-19 victims during the first wave of pandemic (Supplementary Fig. S1A and B, Table S1-S3).

We analyzed the pulmonary autopsy specimens, and found that the main pathological change of COVID-19 lungs was diffuse alveolar damage (Supplementary Fig. S1C and D). The immunofluorescent staining of SARS-CoV-2 nucleocapsid protein (NP) confirmed the presence of SARS-CoV-2 antigens in COVID-19 lung tissues (Supplementary Fig. S1E). For the proteomic profiling, we used tandem mass tag (TMT) 11-plex labeling and liquid chromatography with tandem mass spectrometry (LC-MS/MS), while a pooling mixture of the 19 COVID-19 samples was used as an internal control to eliminate the batch effect (Table S2 and S3).

From the LC-MS/MS analysis, we obtained 49,815 non-redundant peptides (Fig. 1A), which were unambiguously mapped to 5,346 human proteins quantified in at least one sample (Fig. 1B, Table S4). We evaluated the quality of the proteomic data by checking the original MS/MS data, and found that the average spectral counts of all peptides were 2.66, with 29,618 peptides (59.5%) matched by ≥ 2 spectral counts. Thus, the results indicate that the proteomic profiling is highly reliable at the peptide level.

To enable protein expressions of all samples following a similar distribution, z-score transformation plus min-max and median centering normalizations were used to individually normalize the proteomic data for each sample, and the normalized protein expression (NPE) value was determined for each protein (Supplementary Fig. S2A, Table S5). Using NPE values of proteins, a principal component analysis (PCA) revealed that different COVID-19 postmortem tissue types could be roughly separated (Supplementary Fig. S2B).