Profiling Immunological Phenotypes in Individuals During the First Year After Traumatic Spinal Cord Injury: A Longitudinal Analysis.

"de-identified rna-seq data from this study are available in the geo repository accession gse226238."

"Author Disclosure Statement No competing financial interests exist."

"The authors wish to thank Paige Herman, MD and Anthony A. Arcese for initial efforts on the bioinformatics pipeline and Dr. Martin Lesser for consultations on the initial study design and biostatistical plan. This work was supported by the Office of the Assistant Secretary of Defense for Health Affairs under Award No. W81XWH-15-1-0614 (grant to OB). Opinions, interpretations, conclusions and recommendations are those of the author and are not necessarily endorsed by the Department of Defense. This work was also supported by grants to OB from the New York State Spinal Cord Injury Research Board (DOH01-ISSCI6-2016-00018, DOH01-FLLOW2-2016). Authors' Contributions: Conceptualization and Study Design: OB, CS, AL, PG, GF, SK, SH, MAB, BK, AS, MB. Methodology: DM, CP, AL, CS, PG, OB, JS. Formal analyses: DM, CP, AL, CS, OB. Investigation: DM, CP, AL, CS, AC, GF, MAB, MB, JH, TB, BK, AS, OB. Data curation: OB, AC. Writing Original Draft: DM, OB, CS, AS, MAB. Editing: PG, SK, JH, TB, JS, BK, MB. All authors reviewed and approved manuscript. Funding acquisition: OB."

"Transparency, Rigor, and Reproducibility Summary: This observational study was registered on Clinicialtrials.gov (NCT02731027). The analysis plan was not pre-registered. Key inclusion criteria and outcome measures are established standards in the field (time from injury, AIS grade, neurological level of injury). A sample size of 100 participants was assumed based on the average number of patients admitted to study sites and using a simplified power calculation for estimating Spearman correlations between AIS grade and a given biomarker level, a sample of 100 would have yielded 80% power to detect a correlation of 0.28 or greater (2-tailed alpha = 0.05, with no adjustment for multiple testing.) There were 1117 individuals assessed for eligibility. Of these, 33 declined to enroll, 47 were excluded due to medical reasons, and 998 did not meet inclusion/exclusion criteria. There were 42 participants who were enrolled, but one was withdrawn due to lesion level criteria ineligibility. Of the remaining 41, the following number completed these study visits with RNA-Seq samples that passed quality controls: V1 (N = 38, V2 (N = 14), V3 (N = 14), V4 (N = 8). In total, 12 participants were selected for this longitudinal analysis because they had sequential non-missing biological samples for study visits 1-3. Participants were not told and were unable to guess results of the fluid biomarkers measurements. Sample handling and quality control decisions were performed by personnel blinded to participant characteristics. De-identified participant IDs were used for all analyses. Equipment and analytical resources were from commercial suppliers described in methods. There were no analytic codes generated; all statistical analyses were performed in Prism GraphPad and Partek Genomics Flow, using algorithms and methods pre-specified by the commercial software. Biological samples used in this study were obtained by the investigators and are being used for additional analyses; limited quantities of some samples remain. We are not conducting replication studies. De-identified RNA-Seq data from this study are available in the GEO repository, accession GSE226238.: For single and multiplex ELISAs, samples were assayed in duplicate, and performed with standards according to manufactures' protocols. For singleplex ELISAs, avg. R2 values and %CVs were: CRP: R2 = 0.999, %CV = 6.5; HMGB1: (0-10 ng/ml), R2 = 0.998, %CV = 6.6. For multiplex ELISAs, the avg. lower limits of quantification (LLOQ, pg/ml) were: CTACK (0.948), Eotaxin (0.126), FGF basic (3.518), G-CSF (7.171), GROa (13.207), HGF (9.151), IFN-g (16.912), IL-13 (0.359), IL-16 (1.525), IL-18 (0.716), IL-1b (0.25), IL-1ra (4.211), IL-2Ra (1.358), IL-4 (0.145), IL-6 (0.326), IL-8 (0.535), IL-9 (2.311), IP-10 (2.516), M-CSF (0.751), MCP-1(0.473), MIF (3.477), MIG (4.794), MIP-1a (0.067), MIP-1b (0.668), PDGF-bb (6.515), RANTES (2.065), SCF (1.736), SCGF-b (76.926), SDF-1a (5.245), TNF-a (2.485), TNF-b (0.714), TRAIL (0.576).: The inter-assay %CVs for samples described here were: CTACK (5.5%), Eotaxin (5.7%), FGF basic (6.0%), G-CSF (5.7%), GROa (4.4%), HGF (4.5%), IFN-g (7.1%), IL-13 (6.1%), IL-16 (5.1%), IL-18 (5.1%), IL-1b (5.7%), IL-1ra (8.0%), IL-2Ra (5.5%), IL-4 (6.1%), IL-6 (4.8%), IL-8 (7.1%), IL-9 (6.1%), IP-10 (6.2%), M-CSF (5.3%), MCP-1 (5.8%), MIF (5.0%), MIG (6.1%), MIP-1a (5.8%), MIP-1b (6.4%), PDGF-bb (5.5%), RANTES (5.4%), SCF (5.1%), SCGF-b (5.0%), SDF-1a (5.0%), TNF-a (4.2%), TNF-b (8.1%), TRAIL (5.6%)."