Human cytomegalovirus extensively re-organizes the human genome, diminishing TEAD1 transcription factor activity

Human cytomegalovirus (HCMV) infects up to 80% of the world's population. Here, we show that HCMV infection leads to widespread changes in human chromatin accessibility and chromatin looping, with hundreds of thousands of genomic regions affected 48 hours after infection. Integrative analyses reveal HCMV-induced perturbation of Hippo signaling through drastic reduction of TEAD1 transcription factor activity. We confirm extensive concordant loss of TEAD1 binding, active H3K27ac histone marks, and chromatin looping interactions upon infection. Our data position TEAD1 at the top of a hierarchy involving multiple altered important developmental pathways. HCMV infection reduces TEAD1 activity through four distinct mechanisms: closing of TEAD1-bound chromatin, reduction of YAP1 and phosphorylated YAP1 levels, reduction of TEAD1 transcript and protein levels, and alteration of TEAD1 exon-6 usage. Altered TEAD1-based mechanisms are highly enriched at genetic risk loci associated with eye and ear development, providing mechanistic insight into HCMV's established roles in these processes.

Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome

BACKGROUND

There are two major genetic types of Epstein-Barr Virus (EBV): type 1 (EBV-1) and type 2 (EBV-2). EBV functions by manipulating gene expression in host B cells, using virus-encoded gene regulatory proteins including Epstein-Barr Nuclear Antigen 2 (EBNA2). While type 1 EBNA2 is known to interact with human transcription factors (hTFs) such as RBPJ, EBF1, and SPI1 (PU.1), type 2 EBNA2 shares only ~ 50% amino acid identity with type 1 and thus may have distinct binding partners, human genome binding locations, and functions.

RESULTS

In this study, we examined genome-wide EBNA2 binding in EBV-1 and EBV-2 transformed human B cells to identify shared and unique EBNA2 interactions with the human genome, revealing thousands of type-specific EBNA2 ChIP-seq peaks. Computational predictions based on hTF motifs and subsequent ChIP-seq experiments revealed that both type 1 and 2 EBNA2 co-occupy the genome with SPI1 and AP-1 (BATF and JUNB) hTFs. However, type 1 EBNA2 showed preferential co-occupancy with EBF1, and type 2 EBNA2 preferred RBPJ. These differences in hTF co-occupancy revealed possible mechanisms underlying type-specific gene expression of known EBNA2 human target genes: MYC (shared), CXCR7 (type 1 specific), and CD21 (type 2 specific). Both type 1 and 2 EBNA2 binding events were enriched at systemic lupus erythematosus (SLE) and multiple sclerosis (MS) risk loci, while primary biliary cholangitis (PBC) risk loci were specifically enriched for type 2 peaks.

CONCLUSIONS

This study reveals extensive type-specific EBNA2 interactions with the human genome, possible differences in EBNA2 interaction partners, and a possible new role for type 2 EBNA2 in autoimmune disorders. Our results highlight the importance of considering EBV type in the control of human gene expression and disease-related investigations.

A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth

Epstein-Barr virus (EBV) immortalization of resting B lymphocytes (RBLs) to lymphoblastoid cell lines (LCLs) models human DNA tumor virus oncogenesis. RBL and LCL chromatin interaction maps are compared to identify the spatial and temporal genome architectural changes during EBV B cell transformation. EBV induces global genome reorganization where contact domains frequently merge or subdivide during transformation. Repressed B compartments in RBLs frequently switch to active A compartments in LCLs. LCLs gain 40% new contact domain boundaries. Newly gained LCL boundaries have strong CTCF binding at their borders while in RBLs, the same sites have much less CTCF binding. Some LCL CTCF sites also have EBV nuclear antigen (EBNA) leader protein EBNALP binding. LCLs have more local interactions than RBLs at LCL dependency factors and super-enhancer targets. RNA Pol II HiChIP and FISH of RBL and LCL further validate the Hi-C results. EBNA3A inactivation globally alters LCL genome interactions. EBNA3A inactivation reduces CTCF and RAD21 DNA binding. EBNA3C inactivation rewires the looping at the CDKN2A/B and AICDA loci. Disruption of a CTCF site at AICDA locus increases AICDA expression. These data suggest that EBV controls lymphocyte growth by globally reorganizing host genome architecture to facilitate the expression of key oncogenes.

Targeting Mitochondria for Cancer Photodynamic Therapy

Cancer remains a health-related concern globally from the ancient times till to date. The application of light to be used as therapeutic potential/agent has been used for several thousands of years. Photodynamic therapy (PDT) is a modern, non-invasive therapeutic modality for the treatment of various infections by bacteria, fungi, and viruses. Mitochondria are subcellular, double-membrane organelles that have the role in cancer and anticancer therapy. Mitochondria play a key role in regulation of apoptosis and these organelles produce most of the cell's energy which enhance its targeting objective. The role of mitochondria in anticancer approach is achieved by targeting its metabolism (glycolysis and TCA cycle) and apoptotic and ROS homeostasis. The role of mitochondria-targeted cancer therapies in photodynamic therapy have proven to be more effective than other similar non-targeting techniques. Particularly in PDT, mitochondria-targeting sensitizers are important as they have a crucial role in overcoming the hypoxia factor, resulting in high efficacy. IR-730 and IR-Pyr are the indocyine derivatives photosensitizers that play a crucial role in targeting mitochondria because of their better photostability during laser irradiation. Clinical and pre-clinical trials are going on this approach to target different solid tumors using mitochondrial targeted photodynamic therapy.

The Impact of Epstein-Barr Virus Infection on Epigenetic Regulation of Host Cell Gene Expression in Epithelial and Lymphocytic Malignancies

Epstein-Barr virus (EBV) infection is associated with a variety of malignancies including Burkitt's lymphoma (BL), Hodgkin's disease, T cell lymphoma, nasopharyngeal carcinoma (NPC), and ∼10% of cases of gastric cancer (EBVaGC). Disruption of epigenetic regulation in the expression of tumor suppressor genes or oncogenes has been considered as one of the important mechanisms for carcinogenesis. Global hypermethylation is a distinct feature in NPC and EBVaGC, whereas global reduction of H3K27me3 is more prevalent in EBVaGC and EBV-transformed lymphoblastoid cells. In BL, EBV may even usurp the host factors to epigenetically regulate its own viral gene expression to restrict latency and lytic switch, resulting in evasion of immunosurveillance. Furthermore, in BL and EBVaGC, the interaction between the EBV episome and the host genome is evident with respectively unique epigenetic features. While the interaction is associated with suppression of gene expression in BL, the corresponding activity in EBVaGC is linked to activation of gene expression. As EBV establishes a unique latency program in these cancer types, it is possible that EBV utilizes different latency proteins to hijack the epigenetic modulators in the host cells for pathogenesis. Since epigenetic regulation of gene expression is reversible, understanding the precise mechanisms about how EBV dysregulates the epigenetic mechanisms enables us to identify the potential targets for epigenetic therapies. This review summarizes the currently available epigenetic profiles of several well-studied EBV-associated cancers and the relevant distinct mechanisms leading to aberrant epigenetic signatures due to EBV.

Photodynamic therapy on prostate cancer cells involve mitochondria membrane proteins

OBJECTIVE

Photodynamic therapy for prostate cancer has emerged, however the evaluation of its mechanism of action has not yet been clarified. This study aims to explore the mechanism and significance of photodynamic therapy on prostate cancer in vitro.

METHODS

Cultured prostate cancer cells were divided into two groups: untreated and photodynamic therapy treatment. The protein of each group was extracted and analyzed by MALDI-TOF/MSMS method. The significantly expressed proteins were identified in the NCBI human protein database. The change of mitochondrial membrane permeability after photodynamic treatment was examined by transmission electron microscopy.

RESULTS

The total protein content and band distribution of photodynamic treatment group were similar to the control group. Two mitochondrial membrane proteins were down-regulated significantly. They are mitochondrial heat shock protein (HSP60) (Entrez Gene ID: 31542947, PI 5.7, MW: 61016.4, Protein Score: 354, Protein Score C.I.%:100), and voltage-dependent anion channel (VDAC) (Entrez Gene ID: 340201, PI 7.49, MW: 31574.6, Protein Score: 178, Protein Score C.I.%:100). Transmission electron microscopy showed the loss of integrity of mitochondrial membranes.

CONCLUSIONS

Photodynamic therapy changes mitochondrial membrane permeability, leading to the eventual death of cancer cells. The regulation of proteins related to mitochondrial membrane permeability may become an indicator of the efficacy of photodynamic therapy.

Abstract 5192: EBV-associated histone modifications regulate DNA damage repair pathway and associate with cisplatin resistance in nasopharyngeal epithelial malignancy

Introduction: Epstein-Barr virus (EBV) infection is associated with various cancers. Some studies have confirmed EBV can induce hypermethylation to suppress the expression of several key cancer-related genes in gastric cancer. Previously, we showed that nasopharyngeal carcinoma (NPC), an EBV-associated malignancy, is characterized by low mutation rate, but harbors extensive hypermethylation compared with other cancer types. Also, the de novo methylated regions in NPC extensively overlap with the histone bivalent marks (H3K4me3 and H3K27me3) derived from human embryonic stem cells . This suggests an important role of EBV in regulating histone modifications in NPC development. Hence, further studies focusing on the EBV-associated histone modifications are necessary.

Aim: This study aims to elucidate the role of EBV in regulating a transcription-activation histone mark (H3K4me3) and a suppressive mark (H3K27me3) in nasopharyngeal epithelial (NPE) cells.

Methodologies: Two pairs of EBV+/- NPE cell lines were used for chromatin immunoprecipitation sequencing (ChIP-Seq) to identify the genes regulated by EBV-associated histone modifications. ChIP-QPCR and RT-QPCR were utilized to validate the ChIP-Seq results. The candidate genes and pathways identified from the ChIP-Seq results were validated by in vitro and in vivo functional studies.

Results: A panel of 16 DNA damage repair family members were identified with significant reduction of H3K4me3 in the EBV+ NPE cells. One of the candidate genes, MLH1, was validated with down-regulation in the EBV+ NPC cell lines and NPC specimens, and the expression level was demonstrated to associate with cisplatin resistance. Also, the base excision repair (BER) pathway was significantly enriched with reduction of H3K4me3 after EBV infection. Down-regulation of the 7 members from BER was validated in the EBV+ NPE cell lines and NPC specimens. The defective DNA damage repair in the EBV+ NPE cell lines was further validated by the comet assay. Furthermore, after EBV infection, gain of H3K27me3 in MLH1 and the 7 members from BER pathway was identified by ChIP-QPCR. Interestingly, our results from bisulfite sequencing reveals that the promoter regions of the candidate genes are hypomethylated in both EBV +/- NPE cells.

Conclusion: EBV modulates histone bivalent marks independent of the promoter DNA methylation status to regulate DNA damage repair in the host cells.

Acknowledgements: This work was supported by the Research Grants Council of the Hong Kong Special Administrative Region, People’s Republic of China: Grant number AoE/M-06/08 to MLL and Seed Funding Programme for Basic Research of HKU 201308159003 to AKLC.

Citation Format: Merrin Man Long Leong, Arthur Kwok Leung Cheung, Wei Dai, Sai Wah Tsao, Maria Li Lung. EBV-associated histone modifications regulate DNA damage repair pathway and associate with cisplatin resistance in nasopharyngeal epithelial malignancy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5192.

Proteomic analysis reveals that pheophorbide a-mediated photodynamic treatment inhibits prostate cancer growth by hampering GDP-GTP exchange of ras-family proteins

BACKGROUND

We previously reported that pheophorbide a (PhA), excited by 630 nm light, significantly inhibited the growth of prostate cancer cells. In this study, we employed whole-cell proteomics to investigate photodynamic treatment (PDT)-related proteins.

METHODS

Two-dimensional gel electrophoresis (2-DE) coupled with tandem mass spectrometry was employed to reveal the proteins involved in PhA-mediated PDT in LNCaP and PC-3 prostate cancer cells.

RESULTS

After PhA-PDT treatment, decreased expression of translationally-controlled tumor protein (TCTP) was found in both PC-3 and LNCaP whole-cell proteomes. In contrast, human rab GDP dissociation inhibitor (GDI) in LNCaP cells and ras-related homologs GDI in PC-3 cells were up-regulated.

CONCLUSIONS

GDP-GTP exchange is an underlying target of photodynamic treatment in prostate cancer cells.

PTPRG suppresses tumor growth and invasion via inhibition of Akt signaling in nasopharyngeal carcinoma

Protein Tyrosine Phosphatase, Receptor Type G (PTPRG) was identified as a candidate tumor suppressor gene in nasopharyngeal carcinoma (NPC). PTPRG induces significant in vivo tumor suppression in NPC. We identified EGFR as a PTPRG potential interacting partner and examined this interaction. Dephosphorylation of EGFR at EGFR-Y1068 and -Y1086 sites inactivated the PI3K/Akt signaling cascade and subsequent down-regulation of downstream pro-angiogenic and -invasive proteins (VEGF, IL6, and IL8) and suppressed tumor cell proliferation, angiogenesis, and invasion. The effect of Akt inhibition in NPC cells was further validated by Akt knockdown experiments in the PTPRG-down-regulated NPC cell lines. Our results suggested that inhibition of Akt in NPC cells induces tumor suppression at both the in vitro and in vivo levels, and also importantly, in vivo metastasis. In conclusion, we confirmed the vital role of PTPRG in inhibiting Akt signaling with the resultant suppression of in vivo tumorigenesis and metastasis.