The Transcriptional Network Structure of a Myeloid Cell: A Computational Approach

ZHX2 in health and disease

As a transcriptional factor and the negative regulator of alpha fetal protein (AFP), Zinc fingers and homeoboxes 2 (ZHX2) has a well-established role in protection against hepatocellular carcinoma (HCC). However, recent studies have suggested ZHX2 as an oncogene in clear cell renal cell carcinoma (ccRCC) and triple-negative breast cancer (TNBC). Moreover, mounting evidence has illustrated a much broader role of ZHX2 in multiple cellular processes, including cell proliferation, cell differentiation, lipid metabolism, and immunoregulation. This comprehensive review emphasizes the role of ZHX2 in health and diseases which have been more recently uncovered.

Transcription factor Zhx2 restricts NK cell maturation and suppresses their antitumor immunity

The maturation and functional competence of natural killer (NK) cells is a tightly controlled process that relies on transcription factors (TFs). Here, we identify transcriptional repressor zinc fingers and homeoboxes 2 (Zhx2) as a novel regulator that restricts NK cell maturation and function. Mice with Zhx2 conditional deletion in NK cells (Zhx2Δ/Δ) showed accumulation of matured NK cells. Loss of Zhx2 enhanced NK cell survival and NK cell response to IL-15. Transcriptomic analysis revealed Zeb2, a key TF in NK cell terminal maturation, as a direct downstream target of Zhx2. Therapeutically, transfer of Zhx2-deficient NK cells resulted in inhibition of tumor growth and metastasis in different murine models. Our findings collectively unmask a previously unrecognized role of Zhx2 as a novel negative regulator in NK cell maturation and highlight its therapeutic potential as a promising strategy to enhance NK cell-mediated tumor surveillance.

Predicted regulatory SNPs reveal potential drug targets and novel companion diagnostics in psoriasis

Psoriasis is an autoimmune disease associated with interleukins, their receptors, key transcription factors and more recently, antimicrobial peptides (AMPs). Cathelicidin LL-37 is an AMP proposed to play a fundamental role in psoriasis etiology. With our proprietary software SNPClinic v.1.0, we analyzed 203 common SNPs (MAF frequency ​> ​1%) in proximal promoters of 22 genes associated with psoriasis. These include nine genes which protein products are classic drug targets for psoriasis (TNF, IL17A, IL17B, IL17C, IL17F, IL17RA, IL12A, IL12B and IL23A). SNPClinic predictions were run with DNAseI-HUP chromatin accessibility data in eight psoriasis/epithelia-relevant cell lines from ENCODE including keratinocytes (NHEK), T_H1 and T_H17 lymphocytes. Results were ranked quantitatively by transcriptional relevance according to our novel Functional Impact Factor (FIF) parameter. We found six rSNPs in five genes (CAMP/cathelicidin, S100A7/psoriasin, IL17C, IL17RA and TNF) and each was confirmed as true rSNP in at least one public eQTL database including GTEx portal and ENCODE (Phase 3). Predicted regulatory SNPs in cathelicidin, IL17C and IL17RA genes may explain hyperproliferation of keratinocytes. Predicted rSNPs in psoriasin, IL17C and cathelicidin may contribute to activation and polarization of lymphocytes. Predicted rSNPs in TNF gene are concordant with the epithelium-mesenchymal transition. In spite that these results must be validated in vitro and in vivo with a functional genomics approach, we propose FOXP2, RUNX2, NR2F1, ELF1 and HESX1 transcription factors (those with the highest FIF on each gene) as novel drug targets for psoriasis. Furthermore, four out of six rSNPs uncovered by SNPClinic v.1.0 software, could also be validated in the clinic as companion diagnostics/pharmacogenetics assays for psoriasis prescribed drugs that block TNF-α (e.g. Etanercept), IL-17 (e.g. Secukinumab) and IL-17 receptor (Brodalumab).

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We found six putative regulatory SNPs in cathelicidin (LL-37), psoriasin (S100A7), IL17C, IL17RA and TNF genes.

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These rSNPs could be validated also as companion diagnostics/pharmacogenetics assays for most approved psoriasis drugs.

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Regulatory SNPs in TNF gene are concordant with the epithelial-mesenchymal transition.

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Regulatory SNPs in IL17C and IL17RA may partially explain hyperproliferation of keratinocytes.

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Regulatory SNP rs12049559 in psoriasin (S100A7) may contribute to T-cell polarization.