DOI: 10.5061/dryad.b2rbnzsq2
title: Olink proteomic data for RESERVE-U-1-EBB and RESERVE-U-2-TOR

description: Rationale: The global burden of sepsis is concentrated in sub-Saharan
 Africa, where inciting pathogens are diverse and HIV co-infection is a
 major driver of poor outcomes. Biological heterogeneity inherent to sepsis
 in this setting is poorly defined. Objectives: To identify dominant
 pathobiological signatures of sepsis in sub-Saharan Africa and their
 relationship to clinical phenotypes, patient outcomes, and biological
 classifications of sepsis identified in high-income countries (HICs).
 Methods: We analyzed two prospective cohorts of adults hospitalized with
 sepsis (severe infection with qSOFA score≥1) at disparate settings in
 Uganda (discovery cohort [Entebbe, urban], N=242; validation cohort
 [Tororo, rural], N=253). To identify pathobiological signatures in the
 discovery cohort, we applied unsupervised clustering to 173 soluble
 proteins reflecting key domains of the host response to severe infection.
 A random forest-derived classifier was used to predict signature
 assignment in the validation cohort. Measurements and Main Results: Two
 signatures (Uganda Sepsis Signature [USS]-1 and USS-2) were identified in
 the discovery cohort, distinguished by expression of proteins involved in
 myeloid cell and inflammasome activation, T cell co-stimulation and
 exhaustion, and endothelial barrier dysfunction. A five-protein classifier
 (AUROC 0.97) reproduced two signatures in the validation cohort with
 similar biological profiles. In both cohorts, USS-2 mapped to a more
 severe clinical phenotype associated with HIV and related
 immunosuppression, severe tuberculosis, and increased risk of 30-day
 mortality. Substantial biological overlap was observed between USS-2 and
 hyperinflammatory and reactive sepsis phenotypes identified in
 HICs.   Conclusions: We identified
 prognostically-enriched pathobiological signatures among sepsis patients
 with diverse infections and high HIV prevalence in Uganda. Globally
 inclusive investigations are needed to define generalizable and
 context-specific mechanisms of sepsis pathobiology, with the goal of
 improving access to precision medicine treatment strategies.
description: In cryopreserved serum samples, Olink proteomics (Olink
 Proteomics AB, Uppsala, Sweden) was performed at the Human Immune
 Monitoring Center of the Icahn School of Medicine at Mount Sinai (New
 York, NY, USA) using Target Immunooncology and Cardiometabolic panels.
 These panels, each of which include 92 proteins, were selected to broadly
 capture pathobiological domains implicated in the host response to severe
 infection (i.e., innate and adaptive immune activation and exhaustion,
 endothelial and cellular metabolic dysfunction, dysregulated coagulation).
 Comprehensive descriptions of each panel including validation data are
 available at
 https://olink.com/products-services/target/immune-response-panel/ and
 https://olink.com/products-services/target/cardiometabolic-panel/. Samples
 from RESERVE-U-1-EBB and RESERVE-U-2-TOR were analyzed separately. For
 each cohort, samples were analyzed in a single batch, randomized across
 plates, and analyzed by technicians blinded to clinical data. For each
 panel, proteins were quantified via the Olink Proximity Extension Assay.
 The Proximity Extension Assay uses dual oligonucleotide-labelled
 antibodies to bind target proteins, creating a unique double stranded DNA
 barcode which is quantitatively proportional to the initial concentration
 of the target protein. This barcode then serves as a template for a DNA
 polymerase-dependent extension step, which is followed by PCR
 amplification (T100 Thermal Cycle, Bio-Rad Laboratories, Inc., Hercules,
 CA, USA). Resulting DNA amplicons are quantified by microfluidic qPCR
 (Fluidigm Biomark HD and JUNO Systems, Standard BioTools Inc., San
 Francisco, CA, USA) and normalized across batch plates. Intensity
 normalization was used for RESERVE-U-1-EBB assays and reference sample
 normalization was used for RESERVE-U-2-TOR assays. Relative protein
 abundance was calculated from cycle threshold values and expressed in
 log<sub>2</sub>-normalized protein expression (NPX) units by
 Olink’s NPX Manager software. Missing NPX values, which were rare, were
 multiply imputed for each panel using chained equations, predictive mean
 matching, and all other proteins as predictors (<em>mice</em>
 R package). Five imputed datasets were reviewed for convergence and
 plausibility after which one was randomly selected for use. 
description: # Olink proteomic data for RESERVE-U-1-EBB and RESERVE-U-2-TOR Cohorts
 **Description of the Data and File structure:** Two files are provided
 corresponding to adult patients (age &gt;=18 years) enrolled in the
 RESERVE-U-1-EBB (2017-2019) and RESERVE-U-2-TOR (2021-2023) cohorts.
 Although analyses presented in the manuscript were restricted to patients
 with qSOFA score &gt;=1, data is provided for patients enrolled in the
 above cohorts regardless of qSOFA score. In each file, the "pid"
 column reflects the persistent unique identifier for each sample. The
 remainder of columns reflect relative protein abundance as quantified in
 serum using the Olink Target Immunooncology and Cardiometabolic panels
 (Olink Proteomics AB, Uppsala, Sweden). Relative protein abundance is
 expressed in log2-normalized protein expression (NPX) units as generated
 by Olink’s NPX Manager software. Details of all quantified proteins
 (protein name, Uniprot code, and proportion of missing values in each
 cohort) are presented below. As described in the Methods section, missing
 NPX values were imputed for each panel using chained equations, predictive
 mean matching, and all other proteins as predictors. **Olink
 Immunooncology Panel** | **Protein** | **Uniprot Code** | **Proportion of
 missing NPX values in RESERVE-U-1-EBB (%)** | **Proportion of missing NPX
 values in RESERVE-U-2-TOR (%)** | | :------------- | :--------------- |
 :---------------------------------------------------------- |
 :---------------------------------------------------------- | | IL-8 |
 P10145 | 0.0 | 0.0 | | TNFRSF9 | Q07011 | 0.0 | 0.0 | | TIE2 | Q02763 |
 0.0 | 0.0 | | MCP-3 | P80098 | 0.0 | 0.0 | | CD40-L | P29965 | 0.0 | 0.0 |
 | IL-1α# | P01583 | 0.0 | 0.3 | | CD244 | Q9BZW8 | 0.0 | 0.0 | | EGF |
 P01133 | 0.0 | 0.0 | | ANGPT1 | Q15389 | 0.0 | 0.0 | | IL-7 | P13232 | 0.0
 | 0.0 | | PGF | P49763 | 0.0 | 0.0 | | IL-6 | P05231 | 0.0 | 0.0 | |
 ADGRG1 | Q9Y653 | 0.0 | 0.0 | | MCP-1 | P13500 | 0.0 | 0.0 | | CRTAM |
 O95727 | 0.0 | 0.0 | | CXCL11 | O14625 | 0.0 | 0.0 | | MCP-4 | Q99616 |
 0.0 | 0.0 | | TRAIL | P50591 | 0.0 | 0.0 | | FGF2 | P09038 | 0.0 | 0.0 | |
 CXCL9 | Q07325 | 0.0 | 0.0 | | CD8A | P01732 | 0.0 | 0.0 | | CAIX | Q16790
 | 0.0 | 0.0 | | MUC-16 | Q8WXI7 | 0.0 | 0.0 | | ADA | P00813 | 0.0 | 0.0 |
 | CD4 | P01730 | 0.0 | 0.0 | | NOS3 | P29474 | 0.0 | 0.0 | | IL-2# |
 P60568 | 0.0 | 1.4 | | Gal-9 | O00182 | 0.0 | 0.0 | | VEGFR-2 | P35968 |
 0.0 | 0.0 | | CD40 | P25942 | 0.0 | 0.0 | | IL-18 | Q14116 | 0.0 | 0.0 | |
 GZMH | P20718 | 0.0 | 0.0 | | KIR3DL1 | P43629 | 0.0 | 0.0 | | LAP TGF-β
 -1 | P01137 | 0.0 | 0.0 | | CXCL1 | P09341 | 0.0 | 0.0 | | TNFSF14 |
 O43557 | 0.0 | 0.0 | | IL-33# | O95760 | 0.0 | 0.0 | | TWEAK | O43508 |
 0.0 | 0.0 | | PDGF subunit B | P01127 | 0.0 | 0.0 | | PDCD1 | Q15116 | 0.0
 | 0.0 | | FASLG | P48023 | 0.0 | 0.0 | | CD28 | P10747 | 0.0 | 0.0 | |
 CCL19 | Q99731 | 0.0 | 0.0 | | MCP-2 | P80075 | 0.0 | 0.0 | | CCL4 |
 P13236 | 0.0 | 0.0 | | IL-15 | P40933 | 0.0 | 0.0 | | Gal-1 | P09382 | 0.0
 | 0.0 | | PD-L1 | Q9NZQ7 | 0.0 | 0.0 | | CD27 | P26842 | 0.0 | 0.0 | |
 CXCL5 | P42830 | 0.0 | 0.0 | | IL-5 | P05113 | 1.8 | 1.1 | | HGF | P14210
 | 0.0 | 0.0 | | GZMA | P12544 | 0.0 | 0.0 | | HO-1 | P09601 | 0.0 | 0.0 |
 | CX3CL1 | P78423 | 0.0 | 0.0 | | CXCL10 | P02778 | 0.0 | 0.0 | | CD70 |
 P32970 | 0.0 | 0.0 | | IL-10 | P22301 | 0.0 | 0.0 | | TNFRSF12A | Q9NP84 |
 0.0 | 0.0 | | CCL23 | P55773 | 0.0 | 0.0 | | CD5 | P06127 | 0.0 | 0.0 | |
 CCL3 | P10147 | 0.0 | 0.0 | | MMP7 | P09237 | 0.0 | 0.0 | | ARG1 | P05089
 | 0.0 | 0.0 | | NCR1 | O76036 | 0.0 | 0.0 | | DCN | P07585 | 0.0 | 0.0 | |
 TNFRSF21 | O75509 | 0.0 | 0.0 | | TNFRSF4 | P43489 | 0.0 | 0.0 | | MIC-A/B
 | Q29983,Q29980 | 0.0 | 0.0 | | CCL17 | Q92583 | 0.0 | 0.0 | | ANGPT2 |
 O15123 | 0.0 | 0.0 | | PTN | P21246 | 0.0 | 0.0 | | CXCL12 | P48061 | 0.0
 | 0.0 | | IFN-γ | P01579 | 0.0 | 0.0 | | LAMP3 | Q9UQV4 | 0.0 | 0.0 | |
 CASP-8 | Q14790 | 0.0 | 0.0 | | ICOSLG | O75144 | 0.0 | 0.0 | | MMP12 |
 P39900 | 0.0 | 0.0 | | CXCL13 | O43927 | 0.0 | 0.0 | | PD-L2 | Q9BQ51 |
 0.0 | 0.0 | | VEGFA | P15692 | 0.0 | 0.0 | | IL-4# | P05112 | 4.3 | 7.0 |
 | LAG3 | P18627 | 0.0 | 0.0 | | IL12RB1 | P42701 | 0.0 | 0.0 | | IL-13# |
 P35225 | 0.0 | 0.0 | | CCL20 | P78556 | 0.0 | 0.0 | | TNF | P01375 | 0.0 |
 0.0 | | KLRD1 | Q13241 | 0.0 | 0.0 | | GZMB | P10144 | 0.0 | 0.0 | | CD83
 | Q01151 | 0.0 | 0.0 | | IL-12 | P29459,P29460 | 0.0 | 0.0 | | CSF-1 |
 P09603 | 0.0 | 0.0 | Legend: #&lt;20% of NPX values above panel’s
 estimated limit of detection. **Olink Cardiometabolic Panel** |
 **Protein** | **Uniprot Code** | **Proportion of missing NPX values in
 RESERVE-U-1-EBB (%)** | **Proportion of missing NPX values in
 RESERVE-U-2-TOR (%)** | | :---------- | :--------------- |
 :---------------------------------------------------------- |
 :---------------------------------------------------------- | | PRCP# |
 P42785 | 0.0 | 0.0 | | CA1 | P00915 | 0.0 | 0.0 | | ICAM1 | P05362 | 0.0 |
 0.0 | | CHL1 | O00533 | 0.0 | 0.0 | | TGFBI | Q15582 | 0.0 | 0.0 | | ENG |
 P17813 | 0.0 | 0.0 | | PLTP | P55058 | 0.0 | 0.0 | | SERPINA7 | P05543 |
 0.0 | 0.0 | | IGFBP3 | P17936 | 0.0 | 0.0 | | CR2 | P20023 | 0.0 | 0.0 | |
 SERPINA5 | P05154 | 0.0 | 0.0 | | FCGR3B | O75015 | 0.0 | 0.0 | | IGFBP6 |
 P24592 | 0.0 | 0.0 | | CDH1 | P12830 | 0.0 | 0.0 | | CCL5 | P13501 | 0.0 |
 0.0 | | CCL14 | Q16627 | 0.0 | 0.0 | | GNLY | P22749 | 0.0 | 0.0 | |
 NOTCH1 | P46531 | 0.0 | 0.0 | | PAM | P19021 | 0.0 | 0.0 | | PROC | P04070
 | 0.0 | 0.0 | | CST3 | P01034 | 0.0 | 0.0 | | NCAM1 | P13591 | 0.0 | 0.0 |
 | PCOLCE | Q15113 | 0.0 | 0.0 | | LILRB1 | Q8NHL6 | 0.0 | 0.0 | | MET |
 P08581 | 0.0 | 0.0 | | LTBP2# | Q14767 | 0.0 | 0.0 | | IL7R | P16871 | 0.0
 | 0.0 | | VCAM1 | P19320 | 0.0 | 0.0 | | SELL | P14151 | 0.0 | 0.0 | | F11
 | P03951 | 0.0 | 0.0 | | COMP | P49747 | 0.0 | 0.0 | | CA4 | P22748 | 0.0
 | 0.0 | | PTPRS | Q13332 | 0.0 | 0.0 | | MBL2 | P11226 | 0.0 | 0.0 | |
 TIMP1 | P01033 | 0.0 | 0.0 | | ANGPTL3 | Q9Y5C1 | 0.0 | 0.0 | | REG3A |
 Q06141 | 0.0 | 0.0 | | SOD1# | P00441 | 0.0 | 0.0 | | CD46 | P15529 | 0.0
 | 0.0 | | ITGAM# | P11215 | 0.0 | 0.0 | | TNC | P24821 | 0.0 | 0.0 | |
 NID1 | P14543 | 0.0 | 0.0 | | CFHR5 | Q9BXR6 | 0.0 | 0.0 | | SPARCL1 |
 Q14515 | 0.0 | 0.0 | | PLXNB2 | O15031 | 0.0 | 0.0 | | MEGF9 | Q9H1U4 |
 0.0 | 0.0 | | ANG | P03950 | 0.0 | 0.0 | | ST6GAL1 | P15907 | 0.0 | 0.0 |
 | DPP4 | P27487 | 0.0 | 0.0 | | REG1A | P05451 | 0.0 | 0.0 | | QPCT |
 Q16769 | 0.0 | 0.0 | | FCN2 | Q15485 | 0.0 | 0.0 | | FETUB | Q9UGM5 | 0.0
 | 0.0 | | CES1 | P23141 | 0.0 | 0.0 | | CRTAC1 | Q9NQ79 | 0.0 | 0.0 | |
 TCN2 | P20062 | 0.0 | 0.0 | | PRSS2 | P07478 | 0.0 | 0.0 | | ICAM3 |
 P32942 | 0.0 | 0.0 | | SAA4 | P35542 | 0.0 | 0.0 | | CNDP1 | Q96KN2 | 0.0
 | 0.0 | | FCGR2A | P12318 | 0.0 | 0.0 | | NRP1 | O14786 | 0.0 | 0.0 | |
 EFEMP1 | Q12805 | 0.0 | 0.0 | | TIMD4 | Q96H15 | 0.0 | 0.0 | | FAP# |
 Q12884 | 0.0 | 0.0 | | TIE1 | P35590 | 0.0 | 0.0 | | THBS4 | P35443 | 0.0
 | 0.0 | | F7 | P08709 | 0.0 | 0.0 | | GP1BA | P07359 | 0.0 | 0.0 | | LYVE1
 | Q9Y5Y7 | 0.0 | 0.0 | | CA3 | P07451 | 0.0 | 0.0 | | TGFBR3 | Q03167 |
 0.0 | 0.0 | | DEFA1 | P59665 | 0.0 | 0.0 | | CD59 | P13987 | 0.0 | 0.0 | |
 APOM | O95445 | 0.0 | 0.0 | | OSMR | Q99650 | 0.0 | 0.0 | | LILRB2 |
 Q8N423 | 0.0 | 0.0 | | UMOD | P07911 | 0.0 | 0.0 | | CCL18 | P55774 | 0.0
 | 0.0 | | COL18A1 | P39060 | 0.0 | 0.0 | | LCN2 | P80188 | 0.0 | 0.0 | |
 KIT | P10721 | 0.0 | 0.0 | | C1QTNF1 | Q9BXJ1 | 0.0 | 0.0 | | AOC3 |
 Q16853 | 0.0 | 0.0 | | GAS6 | Q14393 | 0.0 | 0.0 | | IGLC2 | P0DOY2 | 0.0
 | 0.0 | | PLA2G7 | Q13093 | 0.0 | 0.0 | | TNXB | P22105 | 0.0 | 0.0 | |
 MFAP5# | Q13361 | 0.0 | 0.0 | | VASN | Q6EMK4 | 0.0 | 0.0 | | LILRB5 |
 O75023 | 0.0 | 0.0 | | C2 | P06681 | 0.0 | 0.0 | Legend: #&lt;20% of NPX
 values above panel’s estimated limit of detection. **Sharing/access
 Information:** Links to other publicly accessible locations of the data:
 None Was data derived from another source? No