Additional file 2: Figure S2. Blunting neuronal nuclear calcium signaling did not alter IBA1+/TMEM119+ cell density and percentage in the perilesional area post-TBI. A) Depiction of the regions of interest: the core area of the injury and the perilesional areas 200µm away from the injury axis. Scale bar 200µm. B) No significant difference in IBA1+ and IBA1+/CD169+ cell density in the perilesional area 24h post injury (IBA1+: CS= 4.10 ± 0.47, CT = 6.73 ±...

Additional file 2: Figure S2. Blunting neuronal nuclear calcium signaling did not alter IBA1+/TMEM119+ cell density and percentage in the perilesional area post-TBI. A) Depiction of the regions of interest: the core area of the injury and the perilesional areas 200µm away from the injury axis. Scale bar 200µm. B) No significant difference in IBA1+ and IBA1+/CD169+ cell density in the perilesional area 24h post injury (IBA1+: CS= 4.10 ± 0.47, CT = 6.73 ±...

Additional file 4: Figure S4. Neuronal expression of osteoprotegerin is upregulated by nuclear calcium signaling and neuronal activity in TBI. A) Negative Control, baseline OPG (TNFRSF11B) signal and a positive Control of the in situ hybridization 24h post injury. B) OPG (TNFRSF11B) in situ signal is mainly found in neuronal sources (neuronal vs non-neuronal 75.38 ± 1.83% vs 24.62% ± 1.83%). N=5. C)-D) Significant increase of OPG (TNFRSF11b) mRNA density 24h post-TBI compared to sham...

Additional file 10: Fig. S6. Expression correlation between BCL11B & C14ORF64 (LINC01550). Expression correlation between BCL11B & C14ORF64 (LINC01550) in 426 human datasets with 42563 samples from R2: Genomics analysis and visualization platform (https://hgserver1.amc.nl/cgi-bin/r2/main.cgi).

Additional file 4: Fig. S3A. Gene Ontology analysis of genes hyper- (A) and hypomethylated (B) of T-LGL patients. Significant Biological processes (GO database) enriched in genes associated with significantly differentially methylated CpG loci in T-LGL. Enrichment represented as odds ratio. Point size represents the gene count of each pathway. Enrichment p value obtained by overrepresentation analysis [30], represented by point color. A Gene Ontology analysis of hypermethylated genes in T-LGL.

Additional file 6: Fig. S4. Differential gene expression of IL6 between T-LGL and healthy donor-derived CD8+ memory T cells. Differential gene expression for IL6 was measured by qPCR. Bulk CD8+ cells from two healthy donors were used for comparison. In line with previous publications, the T-LGLL cohort analyzed exhibits a higher IL6 expression compared to healthy donor-derived C8+ cells. HD Healthy donor.

Additional file 7: Fig. S5A. (A and B): Location of differentially methylated CpG loci in the genes BCL11B and C14orf64 (LINC01550). A Significant differentially methylated CpGs in BCL11B (T-LGLL compared to CD8+. memory T cells) were located in the gene body and assigned as enhancers by ENCODE, which match as enhancers in CD8-positive memory cells.

Additional file 8: Fig. S5B. (A and B): Location of differentially methylated CpG loci in the genes BCL11B and C14orf64 (LINC01550). B Significant differentially methylated CpGs in C14orf64 (LINC01550) (T-LGL compared to CD8 pos. memory T cells).

Supplementary Figure S1. Barplots depicting the metagenome bins recovered after each step from P. lutea and I. palifera skeleton samples. Only High-quality bins were used for performing all the analysis.

Supplementary Figure S1. Barplots depicting the metagenome bins recovered after each step from P. lutea and I. palifera skeleton samples. Only High-quality bins were used for performing all the analysis.

Supplementary Figure S3.Stacked barplots for Relative abundance (>1%) of MAGs taxonomic classes for P. lutea and I. palifera. p_Aenigmatarchaeota, p_Nanoarchaeota, p_Thermoproteota represents the Archaea domain.

Additional file 1: Figure S1. Glial CREB phosphorylation post injury is limited to IBA1+ cells. A)-B) AAVs are able to infect 89.98 ± 14.47% of cortical neurons. Data are shown as mean ± SD (Red dots represent individual animals). N=8. Scale bar: 50µm. C)-D) Non-neuronal pCREB signal is mainly found in IBA1+ cells (IBA1+ cells: 97.76 ± 0.83% vs. GFAP+ cells: 1.24 ± 0.83%). Data are shown as mean ± SD. N=4. Scale Bar: 50µm.E-F)...

Additional file 5: Figure S5. Re-expression of osteoprotegerin together with nuclear calcium buffering massively induces neuronal OPG mRNA intensity. A)-B) Significant increase in neuronal OPG (TNFRSF11b) mRNA intensity (CS vs CT; 181.8 ± 24.34 vs 224.3 ± 35.87). Buffering of nuclear calcium signaling decreased neuronal OPG mRNA intensity (CT vs PT; 224.3 ± 35.87 vs 184.1 ± 24.11). Re-expression of OPG together with nuclear calcium buffering increased the neuronal OPG mRNA intensity massively (PT vs...

Additional file 2: Fig. S2. Differential methylation of CpG loci in the SOCS3 promoter in T-LGL samples. Comparison of CpG methylation (beta-value) for CpGs in the SOCS3 promoter between CD8+ memory cells (CD8mem) and T-LGLL samples (LGL). On top, adjusted p val of differential methylation analysis (dmpFDR, top left) and adjusted p value of differential variability analysis (dmVar, top right).

Additional file 4: Fig. S3A. Gene Ontology analysis of genes hyper- (A) and hypomethylated (B) of T-LGL patients. Significant Biological processes (GO database) enriched in genes associated with significantly differentially methylated CpG loci in T-LGL. Enrichment represented as odds ratio. Point size represents the gene count of each pathway. Enrichment p value obtained by overrepresentation analysis [30], represented by point color. A Gene Ontology analysis of hypermethylated genes in T-LGL.

Additional file 5: Fig. S3B. Gene Ontology analysis of genes hyper- (A) and hypomethylated (B) of T-LGL patients. Significant Biological processes (GO database) enriched in genes associated with significantly differentially methylated CpG loci in T-LGL. Enrichment represented as odds ratio. Point size represents the gene count of each pathway. Enrichment p value obtained by overrepresentation analysis [30], represented by point color. B Gene Ontology analysis of hypomethylated genes in T-LGL.

Additional file 7: Fig. S5A. (A and B): Location of differentially methylated CpG loci in the genes BCL11B and C14orf64 (LINC01550). A Significant differentially methylated CpGs in BCL11B (T-LGLL compared to CD8+. memory T cells) were located in the gene body and assigned as enhancers by ENCODE, which match as enhancers in CD8-positive memory cells.

Additional file 8: Fig. S5B. (A and B): Location of differentially methylated CpG loci in the genes BCL11B and C14orf64 (LINC01550). B Significant differentially methylated CpGs in C14orf64 (LINC01550) (T-LGL compared to CD8 pos. memory T cells).

Additional file 2: Fig. S2. Differential methylation of CpG loci in the SOCS3 promoter in T-LGL samples. Comparison of CpG methylation (beta-value) for CpGs in the SOCS3 promoter between CD8+ memory cells (CD8mem) and T-LGLL samples (LGL). On top, adjusted p val of differential methylation analysis (dmpFDR, top left) and adjusted p value of differential variability analysis (dmVar, top right).

Additional file 3: Fig. S2. Differential methylation of CpG loci in the SOCS3 promoter in T-LGL samples. Comparison of CpG methylation (beta-value) for CpGs in the SOCS3 promoter between CD8+ memory cells (CD8mem) and T-LGLL samples (LGL). On top, adjusted p val of differential methylation analysis (dmpFDR, top left) and adjusted p value of differential variability analysis (dmVar, top right).

Additional file 6: Fig. S4. Differential gene expression of IL6 between T-LGL and healthy donor-derived CD8+ memory T cells. Differential gene expression for IL6 was measured by qPCR. Bulk CD8+ cells from two healthy donors were used for comparison. In line with previous publications, the T-LGLL cohort analyzed exhibits a higher IL6 expression compared to healthy donor-derived C8+ cells. HD Healthy donor.

Additional file 9: Fig. S1. Correlation of bisulfite Pyrosequencing (BPS) and methylation Array DNA methylation levels. The correlation matrix shows the Pearson correlation coefficient (r: 1 (red) to − 1 (blue) among all CpG loci analyzed by BPS. The candidate genes LINC01550 and BCL11B contained multiple CpG sites. Columns and rows represent one CpG loci of the listed candidate gene.

Additional file 9: Fig. S1. Correlation of bisulfite Pyrosequencing (BPS) and methylation Array DNA methylation levels. The correlation matrix shows the Pearson correlation coefficient (r: 1 (red) to − 1 (blue) among all CpG loci analyzed by BPS. The candidate genes LINC01550 and BCL11B contained multiple CpG sites. Columns and rows represent one CpG loci of the listed candidate gene.

Additional file 3: Figure S3. Blunting neuronal nuclear calcium signaling did not alter amplitude and velocity of whisker movement post-TBI. A)-C) The amplitudes of the affected (CS = 0.88 ± 0.22; CT = 1.1 ± 0.19; PS = 0.93 ± 0.42; PT = 1.269 ± 0.56) or unaffected (CS = 1.07 ± 0.39; CT = 1.05 ± 0.35; PS = 1.14 ± 0.45; PT = 1.22 ± 0.45) whisker were not significantly changed 24h after...

Additional file 5: Figure S5. Re-expression of osteoprotegerin together with nuclear calcium buffering massively induces neuronal OPG mRNA intensity. A)-B) Significant increase in neuronal OPG (TNFRSF11b) mRNA intensity (CS vs CT; 181.8 ± 24.34 vs 224.3 ± 35.87). Buffering of nuclear calcium signaling decreased neuronal OPG mRNA intensity (CT vs PT; 224.3 ± 35.87 vs 184.1 ± 24.11). Re-expression of OPG together with nuclear calcium buffering increased the neuronal OPG mRNA intensity massively (PT vs...