A total of 2,489 blood samples were collected from 552 athletes amongst all groups. Participants without baseline samples in the CCT and INJ groups were filtered, leaving 130 CCT, 230 INJ, and 102 NCC individuals with a combined total of 2,125 blood samples. Participant demographics are in Table 1. Because some sample collections were missed, unaccounted for, improperly recorded, or failed quality control, the number of samples at each timepoint differed between groups. During the study, nine CCT participants sustained a concussion and were subsequently reclassified as INJ participants; as a result, samples from these athletes were present in both CCT and INJ groups. Therefore, the baseline samples for these nine participants were duplicated for the reclassified sample sets, while the other blood draws for these participants (40 CCT and 33 INJ) remained unique in the dataset. In addition, one CCT athlete served as a control in two different seasons; the first CCT sample set consisted of five blood draws and the second set consisted of two blood draws. The same baseline sample was used for both of these sample sets.
Table 1
Cohort demographics of CARE participants.
Factor | NCC | CCT | INJ |
Total | 102 | 130 | 230 |
Sex | | | |
Male | 82 (80.4%) | 99 (76.2%) | 182 (79.1%) |
Female | 20 (19.6%) | 31 (23.8%) | 48 (20.9%) |
Age (SD) | 19.3 (1.2) | 19 (1.2) | 18.9 (1.2) |
Race | | | |
African American | 13 (12.7%) | 30 (23.1%) | 45 (19.6%) |
Asian | 0 | 1 (0.7%) | 3 (1.3%) |
Hawaiian/Pac. Isl. | 1 (1%) | 1 (0.8%) | 4 (1.7%) |
Indian/Alaskan | 3 (2.9%) | 0 | 0 |
MSU | 7 (6.9%) | 9 (6.9%) | 21 (9.1%) |
White | 78 (76.5%) | 89 (68.5) | 157 (68.3) |
Ethnicity | | | |
Hispanic | 8 (7.8%) | 9 (6.9%) | 13 (5.7%) |
MSU | 1 (1%) | 12 (9.2%) | 29 (12.6%) |
Non-Hispanic | 93 (91.2%) | 109 (83.8%) | 188 (81.7%) |
Injury Sustained | | | |
Competition | | | 88 (38.3%) |
Practice/Training | | | 132 (57.4%) |
Outside Sport | | | 10 (4.3%) |
Sport | | | |
Football | | 61 (46.9%) | 101 (43.9%) |
Ice Hockey | | 10 (7.7%) | 20 (8.7%) |
Soccer | | 29 (22.3%) | 47 (20.4%) |
Lacrosse | | 8 (6.2%) | 16 (7.0%) |
Rugby | | 9 (6.9%) | 27 (11.7%) |
Wrestling | | 2 (1.5%) | 7 (3.0%) |
Cross Country/Track | 37 (36.3%) | 1 (0.8%) | 2 (0.9%) |
Intramurals | | 6 (4.6%) | 9 (3.9%) |
Softball | 7 (6.9%) | | 1 (0.4%) |
Baseball | 37 (36.3%) | | |
Basketball | 13 (12.7%) | | |
Field | 8 (7.8%) | | |
Other | | 3 (2.3%) | |
Unknown | | 1 (0.8%) | |
“Other” includes skiing, boxing and handball. SD, Standard Deviation; Pac. Isl, Pacific Islander; MSU, Multiple, skipped, or unknown. |
We constructed 130 CCT and 230 INJ sample sets, each having a baseline blood draw and at least one or more samples from a later timepoint. A summary of sample numbers is provided in Table 2 and the distribution of participant sample sets is shown in Fig. 1. NCC samples were used to represent time-based gene expression variance. For each of the 102 NCC participants, the first sample drawn was designated as the Base sample and each subsequent sample for that participant was individually paired with the Base sample as a separate sample set. As a result, there were 428 NCC sample sets, each with only two samples where the baseline sample may have been duplicated in another NCC sample set from the same athlete.
Table 2
Sample number at each timepoint
| CCT | INJ |
PostInj | 125 | 96 |
24h | 117 | 173 |
Asymp | 123 | 194 |
7PostUR | 115 | 171 |
6Mo | 85 | 138 |
To investigate how sport-related concussion altered gene expression patterns in peripheral blood over time, we performed differential gene expression analysis on the RNA-seq data at each of the sampled timepoints. The highest number of differentially expressed genes occurred at the PostInj timepoint (N = 860, FDR ≤ 0.05) and that number was reduced 100-fold by the 24h timepoint (N = 8). Volcano plots of differentially expressed genes at all follow-up timepoints are shown in Fig. 2. Lists of differentially expressed genes, fold-changes, and significance values for each timepoint are provided in Supplementary Data 1.
A known consequence of brain injury is membrane damage in neuronal cells that triggers ionic flux and disrupts calcium metabolism and calcium dependent signaling.19 The cellular response to restore homeostasis entails activating ion pumps, including calcium pumps, which in turn consume ATP and starve the brain of energy.19 Amongst the differentially expressed genes, we observed that multiple genes related to calcium metabolism were altered at the PostInj timepoint, including CAMK2G, CAMKK2, and CAMKK1, which were all upregulated in INJ participants. Additionally, expression of many solute transporters was altered, including four members of the SLC22 family (SLC22A15, SLC22A16, SLC22A1, and SLC22A4) that transport carnitine, which is used in cells to transport long-chain fatty acids into mitochondria for energy production.20 Together, the upregulated genes we observed related to calcium and energy metabolism suggested a compensatory effect following injury, and matched the pathophysiology reported for concussions.
We also investigated gene expression of known potential protein biomarkers for traumatic brain injury diagnosis.21 Genes for two FDA-approved traumatic brain injury biomarkers used in the i-STAT TBI plasma test (Abbott), GFAP and UCH-L1, did not meet the minimum expression threshold for analysis at any timepoint. The MAPT gene encoding Tau also did not meet the minimum expression threshold for analysis at any timepoint. NEFL, encoding neurofilament light chain, was expressed at all timepoints but no significant differences were observed between INJ and CCT participants.
To explore the biological function of differentially expressed genes after concussion, we performed GO term and KEGG pathway enrichment analysis on the differentially expressed genes at the PostInj timepoint. The top two biological processes were neutrophil activation and neutrophil mediated immunity (Fig. 3A, Supplementary Data 2). Several other significant biological processes were also related to immune response, which is consistent with inflammation as a mechanism of neuronal tissue damage in concussion injuries.22,23 In addition, we also observed significant gene expression differences in multiple interleukin receptor genes at the PostInj timepoint, including IL1R1, IL1R2, IL1RAP, and IL2RB, which is consistent with an acute inflammatory response and upregulated cytokine production that has previously been reported in traumatic brain injury studies.24,25 Several other biological processes related to signal transduction pathways were found, such as regulation of GTPase activity and protein phosphorylation. Likewise, enriched KEGG pathways included natural killer cell mediated cytotoxicity, MAPK signaling pathway, and NOD-like receptor signaling activity (Fig. 3B, Supplementary Data 2).
The small number of differentially expressed genes after the 24h timepoint prohibited GO analysis. Therefore, to compare enriched cellular processes and pathways at all timepoints relative to the baseline, we performed GSEA. Enrichment results using hallmark gene sets are shown in Fig. 4A. Similar to the findings from GO analysis and KEGG pathways, GSEA also showed that the top-ranked pathways immediately following concussion were related to upregulation of immune-related signaling. For example, “TNFa signaling via NF-kB”, “inflammatory response”, and “IL6 JAK STAT3 signaling” were all significantly positively enriched (FDR ≤ 0.05); each of which has also been strongly associated with response to concussion.25–30 In addition, differentially expressed genes identified at the PostInj timepoint included multiple genes downstream of JAK, such as members of PI3K-AKT, MAPK and STAT signaling pathways. These genes include JAKMIP1, JAKMIP2, PRR5L, MAPK13, STAT6, and BCL6. Additionally, two regulatory subunits of protein phosphatase PP2, PPP2RB2 and PPP2R5E, were differentially expressed; PP2, a serine/threonine phosphatase, targets Raf, MEK and AKT signaling cascade pathways. At later timepoints, we also observed significant enrichment for “TNFa signaling via NF-kB”, “inflammatory response”, and “IL6 JAK STAT3 signaling”; however, the enrichment scores were now negative.
To determine whether the observed reversal in enriched pathway scores at later timepoints might be related to recovery of injured athletes after being removed from play, we compared enriched processes at the PostInj timepoint between CCT and NCC participants (Fig. 4B). Interestingly, we observed that the immune signaling processes “TNFa signaling via NF-kB”, inflammatory response, and “IL6 JAK STAT3 signaling”, were also positively enriched in CCT participants. Therefore, it appears that athletes participating in contact sports exhibit higher activation of certain immune signaling processes compared to athletes participating in non-contact sports. These immune signaling processes become further elevated immediately following concussion and are then downregulated below CCT levels during recovery. GSEA results also indicate that some altered immune signaling pathways in the INJ group appear to remain repressed compared to the CCT group up to 6 months following a concussion (Fig. 4A).
To confirm our observations from the GSEA Hallmark gene lists, we also performed GSEA with gene lists from WikiPathways and Biocarta.31,32 Similar findings were observed in both WikiPathways (Fig. 5A) and Biocarta (Fig. 5B), in that gene sets were positively enriched (FDR ≤ 0.05) at the PostInj timepoint and negatively enriched at later timepoints. Observed pathways included those associated with cytokine production and inflammatory response. Full results from GSEA analyses are provided in Supplementary Data 3.
Because we observed differential expression of genes that are important in immune signaling, we asked whether there were any changes in circulating cell type populations in response to concussion. To address this question, we performed deconvolution analysis on RNA-seq counts using CIBERSORT to identify immune cell proportions. We then evaluated differences in cell type proportions between INJ and CCT groups at all timepoints using a GLM. Only two cell types at the PostInj timepoint were determined to be differentially proportioned; neutrophils were more prevalent (FDR 2.3E-2) and natural killer cells were less prevalent (FDR 2.49E-5) in the INJ group. No differences in cell-type proportions were observed at later timepoints. Our finding that the neutrophil proportion increased within 6 hours following concussion is consistent with a previous report that also found an increase in neutrophils following mild traumatic brain injury at the site of injury.33