Global CpG DNA Methylation Footprint in Kaposi's Sarcoma

An atlas of chromatin landscape in KSHV-infected cells during de novo infection and reactivation

Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic γ-herpesvirus with a double-stranded DNA capable of establishing latent infection in the host cell. During latency, only a limited number of viral genes are expressed in infected host cells, and that helps the virus to evade host immune cell response. During primary infection, the KSHV genome is chromatinized and maintained as an episome, which is tethered to the host chromosome via Latency Associated Nuclear Antigen (LANA). The KSHV episome undergoes the same chromatin modification with the host cell chromosome and, therefore, is regulated by various epigenetic modifications, such as DNA methylation, histone methylation, and histone acetylation. The KSHV genome is also organized in a spatiotemporal manner by forming genomic loops, which enable simultaneous and coordinated control of dynamic gene transcription, particularly during the lytic replication phase. The genome-wide approaches and advancing bioinformatic tools have increased the resolution of studies on the dynamic transcriptional control and our understanding of KSHV latency-lytic switch regulation. We will summarize our current understanding of the epigenetic gene regulation on the KSHV chromatin.

Insight into the Epigenetics of Kaposi's Sarcoma-Associated Herpesvirus

Epigenetic reprogramming represents a series of essential events during many cellular processes including oncogenesis. The genome of Kaposi's sarcoma-associated herpesvirus (KSHV), an oncogenic herpesvirus, is predetermined for a well-orchestrated epigenetic reprogramming once it enters into the host cell. The initial epigenetic reprogramming of the KSHV genome allows restricted expression of encoded genes and helps to hide from host immune recognition. Infection with KSHV is associated with Kaposi's sarcoma, multicentric Castleman's disease, KSHV inflammatory cytokine syndrome, and primary effusion lymphoma. The major epigenetic modifications associated with KSHV can be labeled under three broad categories: DNA methylation, histone modifications, and the role of noncoding RNAs. These epigenetic modifications significantly contribute toward the latent-lytic switch of the KSHV lifecycle. This review gives a brief account of the major epigenetic modifications affiliated with the KSHV genome in infected cells and their impact on pathogenesis.

Diagnostic and Prognostic Value of DACH1 Methylation in the Sensitivity of Esophageal Cancer to Radiotherapy

To detect the methylation status of the cell fate determinant (DACH1) gene in esophageal cancer tissues and to explore the predictive value of methylation of DACH1 on the sensitivity to radiotherapy for esophageal cancer. Cancer tissues, corresponding paracancerous tissues, and 30 specimens of normal esophageal mucosal tissues from 70 patients admitted to the hospital after radical esophageal cancer radiotherapy from January 2016 to April 2017 were collected. The methylation status of DACH1 was detected by a methylation-specific polymerase chain reaction (MSP). The 70 esophageal cancer patients were divided into radiotherapy-sensitive and radiotherapy-insensitive groups according to the efficacy of radiotherapy, and the methylation status of DACH1 was compared between the two groups. The χ 2 test was used to analyze the relationship between the methylation status of DACH1 and the clinicopathological characteristics of esophageal cancer patients. The Kaplan-Meier survival curve was used to analyze the relationship between the methylation status of DACH1 and radiotherapy sensitivity and survival of esophageal cancer patients, and the Cox proportional risk model was used to analyze the independent influencing factors affecting the radiotherapy sensitivity of esophageal cancer patients. The methylation rate of DACH1 in esophageal cancer tissues was higher than that in paracancerous tissues and normal tissues, and the differences were statistically significant (P < 0.05). 70 patients with esophageal cancer completed radiotherapy, including 46 patients with radiotherapy sensitivity and 24 patients with radiotherapy insensitivity. The DACH1 methylation rate of esophageal cancer patients in the radiotherapy-sensitive group was lower than that in the radiotherapy-insensitive group, and the difference was statistically significant (P < 0.05). The DACH1 methylation rate of esophageal cancer patients with TNM stage (III-IV), tumor differentiation degree (hypofractionation), and lymph node metastasis was higher, and the difference was statistically significant (P < 0.05). The Kaplan-Meier curve showed that the median survival time of patients with DACH1 methylation before radiotherapy was 23 months, which was shorter than that of patients with DACH1 unmethylation before radiotherapy (36 months), and the difference between the survival curves of the two groups was statistically significant (χ 2 = 7.425, P < 0.05); the median survival time of patients in the radiotherapy-sensitive group was 39 months, which was longer than that of patients in the radiotherapy-insensitive group (25 months), and the difference between the two groups was statistically significant (P < 0.05). The median survival time of patients in the radiotherapy-sensitive group was 39 months, which was longer than that of patients in the radiotherapy-insensitive group (25 months), and the difference in survival curves between the two groups was statistically significant (χ 2 = 7.011, P < 0.05). The results of the multifactorial Cox regression model showed that TNM stage (stage III-IV) (HR = 1.961, 95% CI: 1.125-2.768), tumor hypofractionation (HR = 1.453, 95% CI: 1.034-2.857), presence of lymph node metastasis (HR = 1.499, 95% CI: 1.025-2.851), and DACH1 methylation (HR = 1.718, 95% CI: 1.067-2.596) may increase the risk of insensitivity to radiotherapy in patients with esophageal cancer (P < 0.05). The rate of DACH1 methylation in esophageal cancer tissues was increased, and the methylation status of DACH1 was related to radiotherapy sensitivity and survival of esophageal cancer patients, which is expected to be a new target for diagnosis and treatment of esophageal cancer patients.

Role of Epitranscriptomic and Epigenetic Modifications during the Lytic and Latent Phases of Herpesvirus Infections

Herpesviruses are double-stranded DNA viruses occurring at a high prevalence in the human population and are responsible for a wide array of clinical manifestations and diseases, from mild to severe. These viruses are classified in three subfamilies (Alpha-, Beta- and Gammaherpesvirinae), with eight members currently known to infect humans. Importantly, all herpesviruses can establish lifelong latent infections with symptomatic or asymptomatic lytic reactivations. Accumulating evidence suggest that chemical modifications of viral RNA and DNA during the lytic and latent phases of the infections caused by these viruses, are likely to play relevant roles in key aspects of the life cycle of these viruses by modulating and regulating their replication, establishment of latency and evasion of the host antiviral response. Here, we review and discuss current evidence regarding epitranscriptomic and epigenetic modifications of herpesviruses and how these can influence their life cycles. While epitranscriptomic modifications such as m⁶A are the most studied to date and relate to positive effects over the replication of herpesviruses, epigenetic modifications of the viral genome are generally associated with defense mechanisms of the host cells to suppress viral gene transcription. However, herpesviruses can modulate these modifications to their own benefit to persist in the host, undergo latency and sporadically reactivate.

PRC1-independent binding and activity of RYBP on the KSHV genome during de novo infection

Kaposi’s sarcoma-associated herpesvirus (KSHV) is an oncogenic virus that causes lifelong infection in humans by establishing latency after primary infection. Latent infection is a prerequisite for both persistent infection and the development of KSHV-associated cancers. While viral lytic genes are transiently expressed after primary infection, their expression is significantly restricted and concomitant with the binding of host epigenetic repressors Polycomb Repressive Complex 1 and 2 (PRC1 and PRC2) to lytic genes. PRC1 and PRC2 mediate the repressive histone marks H2AK119ub and H3K27me3, respectively, and maintain heterochromatin structure on KSHV lytic genes to inhibit their expression. In contrast to PRC2, little is known about the recruitment and role of PRC1 factors on the KSHV genome following de novo infection. Thus, the goal of this study was to examine the function of PRC1 factors in the establishment of KSHV latency. To address this question, we performed an shRNA screen targeting 7 different components of the canonical and non-canonical PRC1 complexes during primary KSHV infection. We found that RYBP, a main subunit of the non-canonical PRC1 complexes, is a potent repressor of KSHV lytic genes that can bind to the viral genome and inhibit lytic genes as early as 4 hours post infection. Surprisingly, our ChIP analyses showed that RYBP binds to lytic viral gene promoters in a PRC1-independent manner, does not affect PRC1 activity on the KSHV genome, and can reduce the level of histone marks associated with transcription elongation. Our data also suggest that RYBP can repress the viral lytic cycle after primary infection by inhibiting the transcription elongation of the lytic cycle inducer KSHV gene RTA. Based on our results we propose that RYBP uses a PRC1-independent mechanism to block KSHV RTA expression thereby promoting the establishment of KSHV latency following de novo infection.