The Viral and Cellular MicroRNA Targetome in Lymphoblastoid Cell Lines

Skalsky, Rebecca L.; Corcoran, David L.; Gottwein, Eva; Frank, Christopher L.; Kang, Dong‐Wha; Hafner, Markus; Nusbaum, Jeffrey D.; Feederle, Regina; Delecluse, Henri Jacques; Luftig, Micah A.; Tuschl, Thomas; Ohler, Uwe; Cullen, Bryan R.

doi:10.1371/journal.ppat.1002484

Cited by 312 publications

(501 citation statements)

References 84 publications

(186 reference statements)

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“…Finally, we used 10 internally generated Ago-CLIP-seq samples (HPNE and MIA PaCa-2 cells and human brain tissue) and combined them with an additional 33 public datasets from HEK293 cells (46), LCLs (47), and human brain (48) (Dataset S1). Each mature miRNA candidate had to completely coincide with an Ago CLIP-seq site, be observed in at least 1 of the 43 CLIP-seq samples, and be supported by five or more unambiguously mapped CLIP-seq reads.…”

Section: Identification Of Significantly Expressed Sample-dependent Nmentioning

confidence: 99%

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs

Londin

Lohera

Telonis

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

377

365

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Two decades after the discovery of the first animal microRNA (miRNA), the number of miRNAs in animal genomes remains a vexing question. Here, we report findings from analyzing 1,323 short RNA sequencing samples (RNA-seq) from 13 different human tissue types. Using stringent thresholding criteria, we identified 3,707 statistically significant novel mature miRNAs at a false discovery rate of ≤0.05 arising from 3,494 novel precursors; 91.5% of these novel miRNAs were identified independently in 10 or more of the processed samples. Analysis of these novel miRNAs revealed tissue-specific dependencies and a commensurate low Jaccard similarity index in intertissue comparisons. Of these novel miRNAs, 1,657 (45%) were identified in 43 datasets that were generated by cross-linking followed by Argonaute immunoprecipitation and sequencing (Ago CLIP-seq) and represented 3 of the 13 tissues, indicating that these miRNAs are active in the RNA interference pathway. Moreover, experimental investigation through stemloop PCR of a random collection of newly discovered miRNAs in 12 cell lines representing 5 tissues confirmed their presence and tissue dependence. Among the newly identified miRNAs are many novel miRNA clusters, new members of known miRNA clusters, previously unreported products from uncharacterized arms of miRNA precursors, and previously unrecognized paralogues of functionally important miRNA families (e.g., miR-15/107). Examination of the sequence conservation across vertebrate and invertebrate organisms showed 56.7% of the newly discovered miRNAs to be human-specific whereas the majority (94.4%) are primate lineage-specific. Our findings suggest that the repertoire of human miRNAs is far more extensive than currently represented by public repositories and that there is a significant number of lineage-and/or tissue-specific miRNAs that are uncharacterized. SignificanceMicroRNAs (miRNAs) are small ∼22-nt RNAs that are important regulators of posttranscriptional gene expression. Since their initial discovery, they have been shown to be involved in many cellular processes, and their misexpression is associated with disease etiology. Currently, nearly 2,800 human miRNAs are annotated in public repositories. A key question in miRNA research is how many miRNAs are harbored by the human genome. To answer this question, we examined 1,323 short RNA sequence samples and identified 3,707 novel miRNAs, many of which are human-specific and tissue-specific. Our findings suggest that the human genome expresses a greater number of miRNAs than has previously been appreciated and that many more miRNA molecules may play key roles in disease etiology.

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Section: Identification Of Significantly Expressed Sample-dependent Nmentioning

confidence: 99%

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs

Londin

Lohera

Telonis

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

377

365

View full text Add to dashboard Cite

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“…The roles of these BHRF1 miRNAs were unclear until recent in vitro studies using viral knockouts in lymphoblastoid cell lines (LCLs), a widely used cellular model of latency III EBV infection, revealed that the BHRF1 miRNAs cooperate to enhance B cell expansion, reduce levels of latent gene expression, and possibly also inhibit apoptosis (10-12). Additionally, as circumstantial evidence for the roles of these miRNAs, studies that comprehensively examined the targets of EBV miRNAs have shown that BHRF1 miRNAs bind a number of targets involved in proliferation, latent gene expression, and regulation of apoptosis (13,14).…”

Section: Over 90% Of the Adult Human Population Is Chronically Infectmentioning

confidence: 99%

A Cluster of Virus-Encoded MicroRNAs Accelerates Acute Systemic Epstein-Barr Virus Infection but Does Not Significantly Enhance Virus-Induced Oncogenesis In Vivo

Wahl

Linnstaedt

Esoda

et al. 2013

J Virol

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Over 90% of the adult human population is chronically infected with the Epstein-Barr virus (EBV), an oncogenic herpesvirus. EBV primarily infects naive human B cells and persists latently in memory B cells. Most individuals experience an asymptomaticinfection that is effectively controlled by the adaptive immune response. However, EBV-associated lymphomas can develop in immunocompromised individuals. These tumors typically express all nine EBV latent proteins (latency III). Latency III is also associated with the expression of three precursor microRNAs (miRNAs) located within the EBV BHRF1 gene locus. The role of these BHRF1 miRNAs was unclear until recent in vitro studies demonstrated that they cooperate to enhance virus-induced B cell transformation and decrease the antigenic load of virus-infected cells, indicating that the BHRF1 miRNA cluster may serve as a novel therapeutic target for the treatment of latency III EBV-associated malignancies. However, to date, it is not known if BHRF1 miRNAs enhance virus-induced oncogenesis and/or immune evasion of EBV in vivo. To understand the in vivo contribution of the BHRF1 miRNA cluster to EBV infection and EBV-associated tumorigenesis, we monitored EBV infection and assessed tumor formation in humanized mice exposed to wild-type virus and a viral mutant (⌬123) that lacks all three BHRF1 miRNAs. Our results demonstrate that while the BHRF1 miRNAs facilitate the development of acute systemic EBV infection, they do not enhance the overall oncogenic potential of EBV in vivo.E pstein-Barr Virus (EBV), a human gamma herpesvirus, is widespread in all populations; more than 90% of adults worldwide have antibodies to EBV, and infection with EBV persists for the life of its host (1). In healthy individuals, EBV is effectively controlled by the immune system and typically remains asymptomatic. Upon primary infection, virus-targeted B cells undergo a period of rapid proliferation until either CD8 ϩ T cells mount an efficient antiviral response (2) or infected B cells differentiate into a pool of latently infected memory-like B cells (3). When the immune system is suppressed, EBV can induce the development of certain lymphomas (4-6).EBV-associated malignancies that arise in immunodeficient individuals (i.e., posttransplant and AIDS patients) typically express all nine EBV latent proteins (latency III): six Epstein-Barr virus nuclear antigens (EBNA) and three latent membrane proteins (LMP) (1, 3). Although most EBV-associated malignancies respond poorly to chemotherapy, immunotherapy approaches that boost or supplement the patient's EBV-specific T cell response have been successful in treating some latency III tumors due to their high antigenic load (4). However, these strategies, which typically involve the adoptive transfer of autologous or allogeneic EBV-specific T cells stimulated in vitro, are often laborious and technically challenging (4). Therefore, new therapeutic targets and approaches are urgently needed for the treatment of EBV-associated malignancies.In addition to th...

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“…There are an increasing number of viral miRNAs that contain seed sequences identical to known cellular miRNAs. For example, the EBV miRNAs miR-BART1 and miR-BART3, which have seed sequences either identical to miR-B4 and miR-29 (miR-BART1) or offset by one nucleotide from the miR-B4 and miR-29 seed (miR-BART3), have recently been shown to share a number of mRNA targets with miR-29 (17). EBV is also an established transforming virus in human B cells, so the importance of viral mimics of cellular miRNAs in viral tumorigenesis in general, and of viral analogs of miR-29 in B-cell lymphoma in particular, certainly merits additional investigation.…”

mentioning

confidence: 99%