Biology subjects

Preston-Alp, S.

Publications and source records attributed to Preston-Alp, S..

6 recordsLinked to original sources

bioRxiv2026

NAD Metabolism Drives CTCF-Cohesin Chromatin Regulation in EBV-Transformed B-Cells

Chromatin architecture regulates gene expression, and it is maintained by architectural proteins such as CTCF and the cohesin complex. In Epstein Barr virus infected cells, viral chromatin organization is stabilized through the interaction between PARP1 and CTCF, ensuring maintenance of latent gene expression. EBV B cells exhibit elevated PARP1 activity, which imposes a substantial metabolic burden due to NAD consumption by PARP1 itself. We demonstrate that efficient EBV infection and B-cell transformation rely on the NAD salvage pathway to sustain PARP1 activity and CTCF and cohesin chromatin folding. Pharmacologic inhibition of the rate-limiting enzyme NAMPT with FK866 phenocopies the chromatin architectural disruption induced by PARP1 and changes in NAD levels affects CTCF/cohesin chromatin architectural remodeling and loop extrusion. Moreover, NAMPT inhibition reduces tumor burden in EBV xenograft models. These findings identify a critical metabolic dependency linking NAD homeostasis to CTCF-cohesin mediated chromatin architecture and reveal a therapeutic vulnerability in EBV-associated malignancies.

microbiology↗

bioRxiv2025

Integrated transcriptomic and methylome analysis reveals retinoic acid pathway activation after decitabine treatment in EBV associated gastric cancer

Epstein-Barr virus associated gastric cancer (EBVaGC) accounts for [~]9-10% of gastric cancers worldwide and is defined by a distinctive molecular profile, including extreme hypermethylation of the DNA. Targeting this aberrant methylation may be a potential therapeutic strategy. EBV+ gastric cancer cell lines (YCCEL1, SNU719) and EBV- lines (AGS, SNU16, MKN74) were treated with a DNA methyl-transferase inhibitor (DNMT), decitabine (DCB), for three days followed by RNA sequencing to identify EBV-specific responses. DNA methylation profiling by reduced representation bisulfite sequencing (RRBS) was performed in EBV+ cell-lines and integrated with expression data to identify epigenetically regulated networks. While DCB induced broad transcriptional changes across all lines, EBV+ cells exhibited the strongest transcriptional response, sharing many upregulated genes. Many of these EBV+ specific genes were expressed at lower baseline levels in EBV+ tumors from TCGA. DCB predominantly reduced methylation at highly methylated intergenic CpGs, with a subset of promoters undergoing significant demethylation. Integrated analysis revealed a strong inverse correlation between promoter demethylation and gene expression, implicating multiple cancer-relevant pathways. Upstream regulator analysis and motif enrichment indicated that regions losing methylation were enriched for retinoic acid receptor (RAR) binding motifs, suggesting that DCB-mediated demethylation restores RA pathway accessibility and transcriptional activity. Further, inhibiting RAR signaling reduced DCB induced apoptosis. Although DCB can induce both host gene re-expression and viral lytic gene activation in EBV-positive tumors, its impact on RA signaling in EBVaGC has not been studied. Decitabine promotes extensive epigenetic reprogramming in EBVaGC, with preferential effects in CIMP-positive, EBV-infected cell lines. ImportanceEBV+ gastric cancer contains hypermethylated DNA and despite this distinct molecular phenotype there are currently no EBV-specific treatments available. Using an FDA approved inhibitor to target hypermethylated DNA and multi-omics approach to study the cellular response, we uncovered epigenetically altered transcriptional networks that may be further exploited to improve potential therapy. Among the pathways disrupted, retinoic acid signaling is of particular interest, as retinoid receptors such as RAR and RAR{beta} are frequently hypermethylated and repressed in EBVaGC. Our findings indicate that DNMT inhibition can partially reverse RA receptor silencing, supporting further investigation of DNMTi-RA combination strategies as a novel therapy for EBV+ gastric cancer.

microbiology↗

bioRxiv2023

PARP1 Inhibition Halts EBV+ Lymphoma Progression by Disrupting the EBNA2/MYC Axis

PARP1 has been shown to regulate EBV latency. However, the therapeutic effect of PARP1 inhibitors on EBV+ lymphomagenesis has not yet been explored. Here, we show that PARPi BMN-673 has a potent anti-tumor effect on EBV-driven LCL in a mouse xenograft model. We found that PARP1 inhibition induces a dramatic transcriptional reprogramming of LCLs driven largely by the reduction of the MYC oncogene expression and dysregulation of MYC targets, both in vivo and in vitro. PARP1 inhibition also reduced the expression of viral oncoprotein EBNA2, which we previously demonstrated depends on PARP1 for activation of MYC. Further, we show that PARP1 inhibition blocks the chromatin association of MYC, EBNA2, and tumor suppressor p53. Overall, our study strengthens the central role of PARP1 in EBV malignant transformation and identifies the EBNA2/MYC pathway as a target of PARP1 inhibitors and its utility for the treatment of EBNA2-driven EBV-associated cancers. Significance StatementA promising approach to treating EBV-driven malignancies involves targeting cancer and EBV biology. However, investigating host factors that co-regulate EBV latent gene expression, such as PARP1, has been incomplete. Our study demonstrates that the PARP1 inhibitor BMN-673 effectively reduces EBV-driven tumors and metastasis in an LCL xenograft model. Additionally, we have identified potential dysregulated mechanisms associated with PARP1 inhibition. These findings strengthen the role of PARP1 in EBV+ lymphomas and establish a link between PARP1 and the EBNA2/MYC axis. This has important implications for developing therapeutic approaches to various EBV-associated malignancies.

cancer biology↗

bioRxiv2021

Interferon-Gamma Signaling Promotes Melanoma Progression and Metastasis

Interferon-gamma (IFNG) has long been regarded as the flag-bearer for the anti-cancer immunosurveillance mechanisms. However, relatively recent studies have suggested a dual role of IFNG, albeit there is no direct experimental evidence for its potential pro-tumor functions. Here we provide in vivo evidence that treatment of mouse melanoma cell lines with physiological levels of Ifng enhances their tumorigenicity and metastasis in lung colonization allograft assays performed in immunocompetent syngeneic host mice, but not in immunocompromised host mice. We also show that this enhancement is dependent on downstream signaling via Stat1 but not Stat3, providing evidence of an oncogenic function of Stat1 in melanoma. The experimental results suggest that melanoma cell-specific Ifng signaling modulates the tumor microenvironment and its pro-tumorigenic effects are dependent on the {gamma}{delta} T cells, as Ifng-enhanced tumorigenesis was inhibited in the TCR-{delta} knockout mice. Overall, these results show that Ifng signaling may have tumor-promoting effects in melanoma by modulating the immune cell composition of the tumor microenvironment.

cancer biology↗

bioRxiv2021

Ultraviolet radiation modulates DNA methylation in melanocytes

Ultraviolet radiation (UVR) is the principal causal factor for melanoma; albeit the underlying mechanisms remain unclear. While the mutagenic properties of UVR are irrefutable, the role of UVR-induced mutations in the initiation of melanoma is controversial which highlights the gap in our knowledge of the initial critical molecular mechanisms of UVR-induced melanomagenesis. To investigate the potential non-mutational mechanisms of UVR-induced melanomagenesis, we studied the role of UVR in modulating DNA methylation changes in melanocytes via next-generation sequencing-based methodologies. Here we show that UVR directly causes stable changes in the DNA methylome and transcriptome, one month after exposure. Genomic features associated with transcription were protected from 5mC alterations whereas CpG sites found in intergenic regions were more likely to be affected. Additionally, the long-term effects of UVR seem to perturb signaling pathways important for melanocyte biology. Interestingly, UVR-sensitive CpG sites were found to be prognostic of overall patient survival and highlighted a subset of CpG sites that may be relevant in melanomagenesis. SignificanceWe report a novel finding that ultraviolet radiation (UVR) induces DNA methylation changes along with stable alterations in gene expression in cultured melanocytes. Our results provide experimental evidence of UVR-induced epigenetic rewiring, which may be implicated in the susceptibility to melanomagenesis, independently of its mutational effects. These findings offer novel insight into the role of UVR in the initiation and pathogenesis of melanoma via a currently underappreciated mechanism.

cancer biology↗

bioRxiv2021

Interferon-gamma Induces Melanogenesis Via Post-Translational Modification of Tyrosinase

Melanogenesis (melanin pigment production) in melanocytes is canonically stimulated by the alpha-melanocyte stimulating hormone (MSH), which activates the cyclic-AMP-mediated expression of the melanocyte inducing transcription factor (MITF) and its downstream melanogenic genes, including the principal rate-limiting melanogenic enzyme tyrosinase (Tyr). Here we report that interferon-gamma (IFNG; type II interferon), but not IFN-alpha (a type I interferon), induces a noncanonical melanogenic pathway. Inhibition of IFNG pathway by the JAK inhibitor ruxolitinib or knocking out Stat1 abrogated the IFNG-induced melanogenesis. Interestingly, IFNG-induced melanogenesis was independent of MITF. IFNG markedly increased the Tyr protein expression but did not affect the mRNA expression, suggesting a post-translational regulatory mechanism. In contrast, IFNG had no effect on the expression of other melanogenesis-related proteins, e.g. tyrosinase-related protein 1 (Tyrp1) and dopachrome tautomerase (Dct). Glycosidase digestion assays revealed that IFNG treatment increased the mature glycosylated form of Tyr, but not its de novo synthesis. Moreover, cycloheximide chase assay showed that degradation of Tyr was decreased in IFNG-treated cells. These results suggest that the IFNG-STAT1 pathway regulates melanogenesis via modulation of the post-translational processing and protein stability of Tyr. SIGNIFICANCEThe canonical pathway that controls melanogenesis in melanocytes is activated by the alpha melanocyte stimulating hormone (MSH) via its receptor MC1R, which activates the cyclic-AMP-mediated expression of the melanocyte master regulator MITF and its downstream target genes involved in the melanogenic process. Here we report a novel non-canonical melanogenic pathway that is mediated via the Interferon-gamma cytokine signaling. We show that this non-canonical pathway is independent of MITF-mediated gene expression, but rather functions via post-translational modification of the principal melanogenic enzyme Tyrosinase.

molecular biology↗