Virus Expression Database

GSE157103

Large-scale Multi-omic Analysis of COVID-19 Severity

Submitted by Adolfo Ariel Jaitovich (Albany Medical Center, USA) on Aug 28 2020

Platform: ngs – Illumina NovaSeq 6000 (Homo sapiens)

Pubmed: 33096051

Summary Using RNA-seq and high-resolution mass spectrometry we performed a comprehensive systems analysis on 128 plasma and leukocyte samples from hospitalized patients with or without COVID-19 (n=102 and 26 respectively) and with differing degrees of disease severity. We generated abundance measurements for over 17,000 transcripts, proteins, metabolites, and lipids and compiled them with clinical data into a curated relational database. This resource offers the unique opportunity to perform systems analysis and cross-ome correlations to both molecules and patient outcomes. In total 219 molecular features were mapped with high significance to COVID-19 status and severity, including those involved in processes such as complement system activation, dysregulated lipid transport, and B cell activation. In one example, we detected a trio of covarying molecules – citrate, plasmenyl-phosphatidylcholines, and gelsolin (GSN) – that offer both pathophysiological insight and potential novel therapeutic targets. Further, our data revealed in some cases, and supported in others, that several biological processes were dysregulated in COVID-19 patients including vessel damage, platelet activation and degranulation, blood coagulation, and acute phase response. For example, we observed that the coagulation-related protein, cellular fibronectin (cFN), was highly increased within COVID-19 patients and provide new evidence that the upregulated proteoform stems from endothelial cells, consistent with endothelial injury as a major activator of the coagulation cascade. The abundance of prothrombin, which is cleaved to form thrombin during clotting, was significantly reduced and correlated with severity and might help to explain the hyper coagulative environment of SARS-CoV-2 infection. From transcriptomic analysis of leukocytes, we concluded that COVID-19 patients with acute respiratory distress syndrome (ARDS) demonstrated a phenotype that overlapped with, but was distinct from, that found in patients with non-COVID-19-ARDS. To aid in the global efforts toward elucidation of disease pathophysiology and therapeutic development, we created a web-based tool with interactive visualizations allowing for easy navigation of this systems-level compendium of biomolecule abundance in relation to COVID-19 status and severity. Finally, we leveraged these multi-omic data to predict COVID-19 patient outcomes with machine learning, which highlighted the predictive power of these expansive molecular measurements beyond the standardized clinical estimate of 10-year survival Charlson score.

126 Samples

ID Title Cell Type Timepoint Reported Virus Virus Species Exclusion Reason
GSM4753021 COVID_01_39y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753022 COVID_02_63y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753023 COVID_03_33y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753024 COVID_04_49y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753025 COVID_05_49y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753026 COVID_06_:y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753027 COVID_07_38y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753028 COVID_08_78y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753029 COVID_09_64y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753030 COVID_10_62y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753031 COVID_11_52y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753032 COVID_12_50y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753033 COVID_13_37y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753034 COVID_14_55y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753035 COVID_15_68y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753036 COVID_16_48y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753037 COVID_17_54y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753038 COVID_18_70y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753039 COVID_19_51y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753040 COVID_20_62y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753041 COVID_21_66y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753042 COVID_22_43y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753043 COVID_23_76y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753044 COVID_24_55y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753045 COVID_25_55y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753046 COVID_26_41y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753047 COVID_27_71y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753048 COVID_28_63y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753049 COVID_29_63y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753050 COVID_30_54y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753051 COVID_31_50y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753052 COVID_32_72y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753053 COVID_33_81y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753054 COVID_34_64y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753055 COVID_35_58y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753056 COVID_36_68y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753057 COVID_37_87y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753058 COVID_38_68y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753059 COVID_39_80y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753060 COVID_40_66y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753061 COVID_41_74y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753062 COVID_42_21y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753063 COVID_43_83y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753064 COVID_44_46y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753065 COVID_45_62y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753066 COVID_46_62y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753067 COVID_47_78y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753068 COVID_48_72y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753069 COVID_49_73y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753070 COVID_50_37y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753071 COVID_51_58y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753072 COVID_52_71y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753073 COVID_53_35y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753074 COVID_55_62y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753075 COVID_56_33y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753076 COVID_57_30y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753077 COVID_58_62y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753078 COVID_59_55y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753079 COVID_60_49y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753080 COVID_61_54y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753081 COVID_62_78y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753082 COVID_63_39y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753083 COVID_64_65y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753084 COVID_65_84y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753085 COVID_66_66y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753086 COVID_67_57y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753087 COVID_68_79y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753088 COVID_69_77y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753089 COVID_70_81y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753090 COVID_71_37y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753091 COVID_72_50y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753092 COVID_73_82y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753093 COVID_74_55y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753094 COVID_75_55y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753095 COVID_76_73y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753096 COVID_77_55y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753097 COVID_78_80y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753098 COVID_79_27y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753099 COVID_80_71y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753100 COVID_82_67y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753101 COVID_83_85y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753102 COVID_84_75y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753103 COVID_85_62y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753104 COVID_86_52y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753105 COVID_87_61y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753106 COVID_89_90y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753107 COVID_90_86y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753108 COVID_91_29y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753109 COVID_92_82y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753110 COVID_93_81y_female_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753111 COVID_94_24y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753112 COVID_95_49y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753113 COVID_96_51y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753114 COVID_97_76y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753115 COVID_98_81y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753116 COVID_99_71y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753117 COVID_100_74y_female_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753118 COVID_101_58y_male_ICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753119 COVID_102_84y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753120 COVID_103_83y_male_NonICU leukocyte  COVID-19 Severe acute respiratory syndrome-related coronavirus
GSM4753121 NONCOVID_01_54y_female_NonICU leukocyte  Uninfected Uninfected
GSM4753122 NONCOVID_02_65y_male_ICU leukocyte  Uninfected Uninfected
GSM4753123 NONCOVID_03_65y_male_ICU leukocyte  Uninfected Uninfected
GSM4753124 NONCOVID_04_90y_male_NonICU leukocyte  Uninfected Uninfected
GSM4753125 NONCOVID_05_83y_female_NonICU leukocyte  Uninfected Uninfected
GSM4753126 NONCOVID_06_75y_female_ICU leukocyte  Uninfected Uninfected
GSM4753127 NONCOVID_07_50y_male_ICU leukocyte  Uninfected Uninfected
GSM4753128 NONCOVID_08_53y_female_ICU leukocyte  Uninfected Uninfected
GSM4753129 NONCOVID_09_49y_female_NonICU leukocyte  Uninfected Uninfected
GSM4753130 NONCOVID_10_67y_male_ICU leukocyte  Uninfected Uninfected
GSM4753131 NONCOVID_11_58y_female_NonICU leukocyte  Uninfected Uninfected
GSM4753132 NONCOVID_12_82y_male_ICU leukocyte  Uninfected Uninfected
GSM4753133 NONCOVID_13_65y_male_ICU leukocyte  Uninfected Uninfected
GSM4753134 NONCOVID_14_75y_female_ICU leukocyte  Uninfected Uninfected
GSM4753135 NONCOVID_15_83y_unknown_ICU leukocyte  Uninfected Uninfected
GSM4753136 NONCOVID_16_40y_female_ICU leukocyte  Uninfected Uninfected
GSM4753137 NONCOVID_17_84y_female_ICU leukocyte  Uninfected Uninfected
GSM4753138 NONCOVID_18_88y_male_ICU leukocyte  Uninfected Uninfected
GSM4753139 NONCOVID_19_66y_female_ICU leukocyte  Uninfected Uninfected
GSM4753140 NONCOVID_20_62y_female_ICU leukocyte  Uninfected Uninfected
GSM4753141 NONCOVID_21_71y_male_NonICU leukocyte  Uninfected Uninfected
GSM4753142 NONCOVID_22_63y_male_NonICU leukocyte  Uninfected Uninfected
GSM4753143 NONCOVID_23_42y_female_NonICU leukocyte  Uninfected Uninfected
GSM4753144 NONCOVID_24_32y_female_NonICU leukocyte  Uninfected Uninfected
GSM4753145 NONCOVID_25_62y_male_NonICU leukocyte  Uninfected Uninfected
GSM4753146 NONCOVID_26_36y_male_ICU leukocyte  Uninfected Uninfected