Biology subjects

Shamay, M.

Publications and source records attributed to Shamay, M..

6 recordsLinked to original sources

bioRxiv2026

KSHV upregulates the long non-coding RNA PURPL via p73 to suppress p53

Long non-coding RNAs (lncRNAs) are a class of regulatory RNAs with lengths exceeding 200 nucleotides. The lncRNA PURPL (p53 upregulated regulator of p53 levels) is a p53-regulated gene. PURPL is an oncogenic lncRNA that represses p53 function; it is upregulated in many tumors and promotes cancer cell proliferation. Kaposi sarcoma-associated herpesvirus (KSHV) is the causative agent of all forms of Kaposi sarcoma (KS) and is tightly associated with primary effusion lymphoma (PEL). We found upregulation of PURPL in both de novo and chronically KSHV-infected cells. We found that p73 (a p53 homolog) associates with the PURPL promoter and upregulates PURPL expression. Previously, it has been shown that KSHV-encoded latency-associated nuclear antigen (LANA) stabilizes p73. We found that ectopic expression of LANA increased both p73 protein levels and PURPL expression. p73 knockdown abrogates PURPL upregulation following KSHV infection. Antisense oligonucleotides (ASO) targeting PURPL reduced PEL cell proliferation and increased acetylated p53 levels. In contrast to p53, p73 is not repressed by PURPL RNA. In summary, our study reveals how an oncogenic virus can utilize p73 to upregulate the oncogenic lncRNA PURPL as an additional way to repress p53. Moreover, we propose another mechanism by which p73 may promote tumor growth.

cancer biology↗

bioRxiv2026

LINE-1 transposable element is expressed in Kaposi's sarcoma and regulates gene expression in KSHV-infected cells

Long interspersed nuclear element-1 (LINE-1/L1) retrotransposons are expressed in various human cancers. Kaposis sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposis Sarcoma (KS) and Primary Effusion Lymphoma (PEL), which are characterized by global transcriptional reprogramming. Previously, we have found upregulation of L1 in PEL. Here, we show that knockdown of L1 in PEL cells significantly impaired their proliferation and induced broad transcriptional changes encompassing DNA replication, mitotic progression, and genome maintenance pathways. Analysis of KSHV-infected mouse and human mesenchymal stem cell models revealed that the KS-mimicking microenvironment robustly upregulates L1 expression, with sustained expression observed in KSHV-induced tumor cells even after the loss of the viral episome. Reanalysis of RNA-seq data from KS patient biopsies further showed elevated L1 expression in both endemic and AIDS-associated epidemic KS, with partial reduction following antiretroviral therapy. L1 ORF1p protein expression was confirmed by immunohistochemistry in KS tissues. Reanalysis of the enzymes that can modulate DNA methylation, a process that regulates L1 expression, revealed upregulation of DNMT3A and TET2 in both mouse KSHV tumor models and human KS. Altogether, our findings establish the L1 activation as a hallmark of KSHV-driven oncogenesis.

microbiology↗

bioRxiv2025

SMURF2/USP7-mediated ubiquitination of KAP1 controls its SUMO E3 ligase activity and chromatin regulation

KRAB-associated protein 1 (KAP1) is a critical nuclear protein that regulates chromatin architecture and gene expression, primarily through its SUMOylation activity. However, the mechanisms controlling KAP1 remain poorly understood. In a recent study, we identified the E3 ubiquitin ligase SMURF2 as a direct interactor and ubiquitin ligase for KAP1. Here, we show that SMURF2-mediated ubiquitination of KAP1 at lysines K254, K319, and K779 regulates its SUMOylation activity. We further demonstrate that SMURF2 collaborates with the deubiquitinase USP7/HAUSP, recruiting it to KAP1, to regulate a dynamic ubiquitination-deubiquitination cycle at these key residues. Cells expressing a KAP1 mutant, resistant to SMURF2-USP7 regulation, exhibit profound alterations in chromatin structure, gene expression, protein-protein interactions, and elevated LINE-1 retrotransposon activity. Notably, disrupting the SMURF2-USP7-KAP1-SUMOylation axis in cancer cells reduces their malignancy and tumor growth in vivo. Collectively, these findings uncover a novel regulatory mechanism for KAP1, highlighting its pivotal role in orchestrating critical cellular processes.

molecular biology↗

bioRxiv2024

KSHV genome harbors both constitutive and lytically induced enhancers

Kaposis sarcoma-associated herpesvirus (KSHV) belongs to the gamma-herpesvirus family and is a well-known human oncogenic virus. In infected cells, the viral genome of 165 kbp is circular DNA wrapped in chromatin. The tight control of gene expression is critical for latency, the transition into the lytic phase, and the development of viral-associated malignancies. Distal cis-regulatory elements (CRE), such as enhancers and silencers, can regulate gene expression in a position and orientation-independent manner. Open chromatin is another characteristic feature of enhancers. To systematically search for enhancers, we cloned all the open chromatin regions in the KSHV genome downstream to the luciferase gene and tested their enhancer activity in infected and uninfected cells. A silencer was detected upstream of the latency promoter (LANAp). Two constitutive enhancers were identified in the K12p-OriLyt-R and ORF29 Intron region, where ORF29 Intron is a tissue-specific enhancer. The following promoters: OriLyt-L, PANp, ALTp, and the Terminal Repeats (TRs) acted as lytically induced enhancers. Expression of the Replication and Transcription Activator (RTA), the master regulator of the lytic cycle, was sufficient to induce the activity of lytic enhancers in uninfected cells. We propose that the TRs that span about 24 kbp region serve as a "viral super-enhancer" that integrates the repressive effect of the latency protein LANA with the activating effect of RTA. Utilizing CRISPR activation and interference techniques, we determined the connections between these enhancers and their regulated genes. The silencer and enhancers described here provide an additional layer to the complex gene regulation of herpesviruses. ImportanceIn this study, we performed a systematic functional assay to identify cis-regulatory elements within the genome of the oncogenic herpesvirus, Kaposi sarcoma-associated herpesvirus (KSHV). Similar to other herpesviruses, KSHV presents both latent and lytic phases. Therefore, our assays were performed in uninfected cells, during latent infection, and under lytic conditions. We identified two constitutive enhancers, where one seems to be a tissue- specific enhancer. In addition, four lytically induced enhancers, which are all responsive to the Replication and Transcription Activator (RTA), were identified. Furthermore, a silencer was identified between the major latency promoter and lytic genes locus. Utilizing CRISPR activation and interference techniques, we determined the connections between these enhancers with their regulated genes. The terminal repeats spanning a region of about 24 kbp, seem like a "viral super-enhancer" that integrates the repressive effect of the latency protein LANA with the activating effect of RTA to regulate latency to lytic transition.

microbiology↗

bioRxiv2021

Unidirectional recruitment relations between proteins can be determined by a CRISPR/dCas9 recruitment assay

Kaposis sarcoma associated herpesvirus (KSHV, HHV-8) is associated with several human malignancies. During latency the viral genomes reside in the nucleus of infected cells as large non-integrated plasmids, known as episomes. All KSHV infected cells express LANA, and LANA is essential for viral latency. LANA binding to the viral episomes is critical for both replication of the viral genomes during latency, and for tethering the viral episomes to the cell chromosomes during cell division. Directional recruitment of protein complexes are critical for proper function of many nuclear processes. To test for recruitment directionality between LANA and cellular proteins we directed LANA via catalytically inactive Cas9 (dCas9) to a repeat sequence to obtain easily detectable dots. Then, recruitment of nuclear proteins to these dots can be evaluated. We found that LANA recruited its known interactors ORC2 and SIN3A. Interestingly, LANA was unable to recruit MeCP2, but MeCP2 recruited LANA. Both LANA and histone deacetylase 1 (HDAC1) interact with the transcriptional-repression domain (TRD) of MeCP2. Similar to LANA, HDAC1 was unable to recruit MeCP2. While heterochromatin protein 1 (HP1) which interacts with the N-terminal of MeCP2, was able to recruit MeCP2. Forcing MeCP2 dimerization via the tandem epitopes of SunTag, allows LANA to recruit MeCP2 in infected cells. We propose that available interacting domains force this recruitment directionality. Knock-down of MeCP2 by shRNA, as well as cells derived from Rett syndrome and express a mutant MeCP2 (T158M), dramatically reduced the ability of LANA to support viral latency. Therefore, this unidirectional recruitment of LANA by MeCP2 identified MeCP2 as a critical factor for KSHV viral maintenance. Significance StatementUsing a CRISPR/Cas9 recruitment assay, we show that some interacting proteins have a unidirectional recruitment property, where only one of the proteins can recruit its partner. We found unidirectional recruitment relations between the methylated DNA binding protein MeCP2 and KSHV encoded LANA. Where MeCP2 recruits LANA, but LANA is unable to recruit MeCP2. We were able to break this unidirectional recruitment by forcing MeCP2 dimerization. We propose that this unidirectional recruitment is the result of available interacting domains. Furthermore, this unidirectional recruitment seems to be critical for viral latency since LANA fails to maintain the viral genomes in MeCP2 mutant cells. Therefore, in this case unidirectional recruitment is a matter of survival or extinction.

microbiology↗

bioRxiv2019

RNA-sequencing analysis of a multistep and hit-and-run cell and animal model of KSHV tumorigenesis reveal the roles of mutations, CpG methylation, and viral-infection footprints in oncogenesis.

Human viral oncogenesis is the consequence of cell transformation mediated by virally encoded oncogenes in combination with host oncogenic alterations. Kaposis sarcoma (KS), caused by the Kaposis sarcoma-associated herpes virus (KSHV), is an AIDS-associated cancer characterized by angiogenesis and spindle-cells proliferation. KSHV-infected KS lesions are composed of latently-infected cells, as well as cells expressing lytic genes that have been implicated in the development of the KS angioproliferative phenotype. The existence of KS lesions with varying levels of KSHV-infected cells suggests also the existence of virus-independent \"hit-and-run\" mechanisms of sarcomagenesis, whereby viral infection irreversibly induce genetic or epigenetic oncogenic alterations in host cells. We have integrated genetic mutations, changes in expression signatures and methylation analysis to dissect genetic and epigenetic signaling pathways in an unbiased manner in the mECK36 mouse model of KSHV tumorigenesis. Pathway analysis of differential expressed genes (DEGs) showed KSHV lytic switch, DNA methylation and Epigenetic as the most regulated pathways during KSHV-dependent in vivo tumorigenesis. Methylation analysis data indicates that during the development of KSHV-infected tumors the most changes were towards hypo-methylation of tissues specific genes and oncogenic signature pathways, on the other hand during viral loss and development of KSHV-negative tumors changes are towards hyper-methylation. Mutational analysis of KSHV-infected cells and tumors revealed a set of mutations, including mutations in three inflammasome-related IFN response genes, that were absent in KSHV-infected cells but present in all KSHV-infected tumors in the same loci pointing to clonal selection \"in vivo\". This result suggests that in the context of in vivo tumorigenesis both these mutations and the virus may determine tumor growth. On the other hand, clustering analysis of mutations driving KSHV-negative tumors reveal a network comprising PDGFRA D842V, Pak1 and Nucleolin mutations implicated in cell proliferation. Our results have uncovered novel specific aspects of the interplay between host oncogenic alterations and virus-induced transcriptional effects as well as the epigenetic changes induced by KSHV infection and tumorigenesis. The existence virally-induced irreversible genetic and epigenetic oncogenic alterations support the possibility for hit-and-run KSHV sarcomagenesis which is consistent with pathological and clinical findings.\n\nAUTHOR SUMMARYWe performed whole genome RNA sequencing and CpG DNA methylation analysis in a mouse bone-marrow endothelial-lineage cells (mEC) transfected with the KSHVBac36 (mECK36 cells), that are able to form KSHV-infected tumors in nude mice, which were thoroughly characterized as KS-like tumors. This unique model allowed us to dissect genetic and epigenetic mechanisms of KSHV dependent and hit-and-run sarcomagenesis. We found that during KSHV in vivo lytic switch and KSHV-dependent tumorigenesis DNA methylation and Epigenetic regulation are among the most host-regulated pathways. CpG DNA methylation analysis during transformation supports the notion that loss of methylation (hypo-methylation) is the major epigenetic change during this process. Sequence analysis of KSHV-positive tumors revealed that KSHV tumorigenesis not only selects for the presence of the virus but also pre-existing host mutations that allow the KSHV oncovirus to express the oncogenic lytic program and creates a permissive environment of inflammation and viral tumorigenesis providing a selective advantage in vivo.

cancer biology↗