DOI: 10.5281/zenodo.10685544
title: Backpain exercise therapy remodels human epigenetic profiles in buccal and human peripheral blood mononuclear cells: An exploratory study in young male participants

description: ###### Files description #####
Notes. 1) "BT" refers to before therapy and "AT" to after therapy.
2) 0 refers to FALSE and 1 to TRUE for binary variables.
The provided files have tab-separated columns except the .RDS which is and R output of the mixOmics DIABLO integration analysis.

# Questionnaire
> participants_categories.tsv: per participant (rows), output of the clustering with the participant ("ID") category ("category") per class ("class") 
> questionnaire_agility_metrics.tsv: questionnaire and agility metrics per participant (rows) for the participants ("ID") with at least one 
paired AT+BT data in one type of biological sample (indicated in the columns "swab", "PBMC", and "plasma")

# PTMs
Samples´ names are encoded as PBMC_AT_8_batch1, i.e. cells origin_time upon therapy_ID_batch (we removed _batch column suffix for the processed files).
NA indicates an undetected intensity.
> raw_PBMC_light_labelled_intensities.tsv: raw intensity of light/endogenous peptides (row) by precursor per sample (column) from PBMC
> raw_swab_light_labelled_intensities.tsv: idem from buccal cells
> raw_PBMC_heavy_labelled_intensities.tsv: raw intensity of light/endogenous peptides (row) by precursor per sample (column) from PBMC
> raw_swab_heavy_labelled_intensities.tsv: idem from buccal cells
> raw_PBMC_heavynormalized_intensities.tsv: raw intensity of light peptides normalized by heavy peptides intensity (row) by precursor per sample (column)
> raw_swab_heavynormalized_labelled_intensities.tsv: idem from buccal cells
> processed_cleaned_PBMC_log2intensities.tsv: processed (heavy normalized, imputed, batch-corrected) intensity of peptides 
aggregated by modification (PTM, row) by precursor per sample (column) after log2-transformation. 
The relative abundances are computed from this file.
Rows without me/ac suffix represents the amount of unmodified peptide for the considered site.
> processed_cleaned_swab_log2intensities.tsv: idem from buccal cells
> rel_abundance_PTM_PBMC.tsv: relative abundance computed per precursor, e.g. for a given sample, the H3_K4+H3_K4me1+H3_K4me2+H3_K4me3 relative abundance values must sum to 100, with the relative abundance of H3_K4 representing the absence of modified K4.
> rel_abundance_PTM_swab.tsv: idem from buccal cells
> tests_from_rel_abundance_PTM_swab_PBMC.tsv: per type of samples ("Sample.origin", i.e.swab of PBMC) and per PTM (rows, "PTM"), report the output of classic (p-values, adjusted with Benjamini-Hochberg (BH), or Benjamini-Yekutieli procedure (BY), from raw and arcsin square root transformed percentage) and PLS-DA tests (VIP - Variable Importance score - and its 95% confidence interval). The percentage of changeof each PTM after therapy relative tobefore therapy is reported in "perc_change.AT.over.BT" column.
The "is_candidate" indicates if the PTM has been considered as a hit in the swab or PBMC.

# Plasma
Samples´ names are encoded as PLASMA_AT_8_batch1, i.e. cells origin_time upon therapy_ID_batch.
NA indicates an undetected intensity.
> raw_plasma_maxquant_log2ibaq_intensities.tsv: raw data from protein group MaxQuant file. The iBAQ columns are used in later steps.
> processed_cleaned_plasma_log2intensities.tsv: processed (imputed, batch-corrected) intensity of protein groups after log2-transformation. 
> tests_from_intens_plasma.tsv: per protein group ("Proteins.ID"), report the output of classic (p-values, adjusted Benjamini-Hochberg (BH),or Benjamini-Yekutieli procedure (BY), from log2-transformed intensities) and PLS-DA tests (VIP and its 95% confidence interval). The log2 fold change after therapy relative to before therapy is reported in "log2FC.AT.over.BT" column.
The "is_candidate" indicates if the protein group has been considered as a hit.

# Integration
> circos_input: output of DIABLO analysis with correlation threshold set to 0.7. Use the readRDS R function to open.

 
description: Background

With its high and increasing lifetime prevalence, back pain represents a contemporary challenge for patients and healthcare providers. Monitored exercise therapy is a commonly prescribed treatment to relieve pain and functional limitations. However, the benefits of exercise are often gradual, subtle, and evaluated by subjective self-reported scores. Back pain pathogenesis is interlinked with epigenetically mediated processes that modify gene expression without altering the DNA sequence. Therefore, we hypothesize that therapy effects can be objectively evaluated by measurable epigenetic histone posttranslational modifications and proteome expression. Because epigenetic modifications are dynamic and responsive to environmental exposure, lifestyle choices—such as physical activity—can alter epigenetic profiles, subsequent gene expression, and health traits. Instead of invasive sampling (e.g., muscle biopsy), we collect easily accessible buccal swabs and plasma. The plasma proteome provides a systemic understandingof a person’s current health state and is an ideal snapshot of downstream, epigenetically regulated, changes upon therapy. This study investigates how molecular profiles evolve in response to standardized sport therapy and noncontrolled lifestyle choices.

Results

We report that the therapy improves agility, attenuates back pain, and triggers healthier habits. We find that a subset of participants’ histone methylation and acetylation profiles cluster samples according to their therapy status, before or after therapy. Integrating epigenetic reprogramming of both buccal cells and peripheral blood mononuclear cells (PBMCs) reveals that these concomitant changes are concordant with higher levels of self-rated back pain improvement and agility gain. Additionally, epigenetic changes correlate with changes in immune response plasma factors, reflecting their comparable ability to rate therapy effects at the molecular level. We also performed an exploratory analysis to confirm the usability of molecular profiles in (1) mapping lifestyle choices and (2) evaluating the distance of a given participant to an optimal health state.

Conclusion

This pre-post cohort study highlights the potential of integrated molecular profiles to score therapy efficiency. Our findings reflect the complex interplay of an individual’s background and lifestyle upon therapeutic exposure. Future studies are needed to provide mechanistic insights into back pain pathogenesis and lifestyle-based epigenetic reprogramming upon sport therapy intervention to maintain therapeutic effects in the long run.