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. 2020 Jan-Dec:16:1744806920936502.
doi: 10.1177/1744806920936502.

Differential methylation and expression of genes in the hypoxia-inducible factor 1 signaling pathway are associated with paclitaxel-induced peripheral neuropathy in breast cancer survivors and with preclinical models of chemotherapy-induced neuropathic pain

Kord M Kober  1   2   3 , Man-Cheung Lee  4 , Adam Olshen  2   5 , Yvette P Conley  6 , Marina Sirota  3   4 , Michael Keiser  3   4   7 , Marilyn J Hammer  8 , Gary Abrams  4 , Mark Schumacher  4 , Jon D Levine  4 , Christine Miaskowski  1   2
Affiliations

Differential methylation and expression of genes in the hypoxia-inducible factor 1 signaling pathway are associated with paclitaxel-induced peripheral neuropathy in breast cancer survivors and with preclinical models of chemotherapy-induced neuropathic pain

Kord M Kober et al. Mol Pain. 2020 Jan-Dec.

Abstract

Background: Paclitaxel is an important chemotherapeutic agent for the treatment of breast cancer. Paclitaxel-induced peripheral neuropathy (PIPN) is a major dose-limiting toxicity that can persist into survivorship. While not all survivors develop PIPN, for those who do, it has a substantial negative impact on their functional status and quality of life. No interventions are available to treat PIPN. In our previous studies, we identified that the HIF-1 signaling pathway (H1SP) was perturbed between breast cancer survivors with and without PIPN. Preclinical studies suggest that the H1SP is involved in the development of bortezomib-induced and diabetic peripheral neuropathy, and sciatic nerve injury. The purpose of this study was to identify H1SP genes that have both differential methylation and differential gene expression between breast cancer survivors with and without PIPN.

Methods: A multi-staged integrated analysis was performed. In peripheral blood, methylation was assayed using microarray and gene expression was assayed using RNA-seq. Candidate genes in the H1SP having both differentially methylation and differential expression were identified between survivors who received paclitaxel and did (n = 25) and did not (n = 25) develop PIPN. Then, candidate genes were evaluated for differential methylation and differential expression in public data sets of preclinical models of PIPN and sciatic nerve injury.

Results: Eight candidate genes were identified as both differential methylation and differential expression in survivors. Of the eight homologs identified, one was found to be differential expression in both PIPN and "normal" mice dorsal root ganglia; three were differential methylation in sciatic nerve injury versus sham rats in both pre-frontal cortex and T-cells; and two were differential methylation in sciatic nerve injury versus sham rats in the pre-frontal cortex.

Conclusions: This study is the first to evaluate for methylation in cancer survivors with chronic PIPN. The findings provide evidence that the expression of H1SP genes associated with chronic PIPN in cancer survivors may be regulated by epigenetic mechanisms and suggests genes for validation as potential therapeutic targets.

Keywords: Paclitaxel-induced peripheral neuropathy; breast cancer; chemotherapy; gene expression; hypoxia-inducible factor; integrated genomic analysis; methylation; survivor.

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Figures

Figure 1.
Figure 1.
STRING connectivity network analysis identified protein–protein interactions between cullin 2 (CUL2), egl-9 family hypoxia-inducible factor 1 (EGLN1), ring-box 1 (RBX1), lactate dehydrogenase A (LDHA), transferrin receptor (TFRC), and phosphofructokinase, liver type (PFKL). Nodes represent all proteins produced by a single protein coding gene locus. Edges represent specific or meaningful associations. Known or predicted 3D structures are presented within the nodes. Color of the edges connecting the nodes represents the types of evidence supporting the connections: predicted gene neighborhood (green), predicted gene fusions (red), known interactions from experimental evidence (pink), co-expression (black), and text-mining (green).
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