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Updated: Mar 14, 2026
Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
Published on: July 29, 2022
Consensus co-expression analysis identifies a common set of co-expressed genes associated with diabetic peripheral
Kord Kober1,2,3, Esther Chavez-Iglesias1, Nam Woo Cho2,4
1Department of Physiological Nursing, University of California, San Francisco, CA, USA.
Background:
Diabetic peripheral neuropathy (DPN) and chemotherapy-induced peripheral neuropathy (CIPN) are major clinical challenges with limited therapeutic options. While these conditions arise from different causes, they may share common molecular mechanisms that could be targeted for intervention.
Methods:
We performed consensus weighted gene co-expression network analysis (WGCNA) on two publicly available datasets: GSE185011 (DPN vs healthy controls in peripheral blood mononuclear cells) and GSE173610 (paclitaxel-treated vs control iPSC-derived sensory neurons). After filtering all but the most variable genes, consensus analysis was used to identify conserved co-expression modules across both conditions.
Results:
Consensus analysis identified a 193-gene module (ME3/brown) significantly associated with both DPN (correlation = 0.817, p = 0.0040) and CIPN (correlation = 0.971, p = 0.0060). Functional enrichment analysis of this module revealed pathways related to Glycolysis, FoxO signaling, Apoptosis, and Autophagy.
Conclusions:
Our analysis reveals a convergent molecular signature underlying both DPN and CIPN, centered on metabolic reprogramming, transcriptional stress, and programmed cell death. These findings provide a systems-level framework for developing therapies targeting shared pathological mechanisms.
Insights
Diabetic peripheral neuropathy (DPN) and chemotherapy-induced peripheral neuropathy (CIPN) share molecular pathways. Targeting these common mechanisms, including metabolism and cell death, may offer new therapeutic strategies for both conditions.
Area of Science:
- Neuroscience
- Genomics
- Systems Biology
Background:
- Diabetic peripheral neuropathy (DPN) and chemotherapy-induced peripheral neuropathy (CIPN) present significant clinical challenges with limited treatment options.
- Despite different etiologies, DPN and CIPN may involve shared molecular pathways amenable to therapeutic intervention.
Purpose of the Study:
- To identify conserved molecular mechanisms underlying both DPN and CIPN.
- To establish a systems-level framework for developing novel therapies targeting shared pathological pathways.
Main Methods:
- Consensus weighted gene co-expression network analysis (WGCNA) was applied to two independent datasets: GSE185011 (DPN) and GSE173610 (CIPN).
- Analysis focused on identifying conserved gene co-expression modules associated with both DPN and CIPN.
Main Results:
- A significant 193-gene module (ME3/brown) was identified, strongly correlated with both DPN and CIPN.
- Functional enrichment analysis of this module highlighted key pathways including Glycolysis, FoxO signaling, Apoptosis, and Autophagy.
Conclusions:
- A convergent molecular signature involving metabolic reprogramming, transcriptional stress, and programmed cell death underlies both DPN and CIPN.
- These findings provide a foundation for developing targeted therapies addressing the common pathological mechanisms of DPN and CIPN.
