All Publications

  • Click Quantitative Mass Spectrometry Identifies PIWIL3 as a Mechanistic Target of RNA Interference Activator Enoxacin in Cancer Cells JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Abell, N. S., Mercado, M., Caneque, T., Rodriguez, R., Xhemalce, B. 2017; 139 (4): 1400-1403


    Enoxacin is a small molecule that stimulates RNA interference (RNAi) and acts as a growth inhibitor selectively in cancer but not in untransformed cells. Here, we used alkenox, a clickable enoxacin surrogate, coupled with quantitative mass spectrometry, to identify PIWIL3 as a mechanistic target of enoxacin. PIWIL3 is an Argonaute protein of the PIWI subfamily that is mainly expressed in the germline and that mediates RNAi through piRNAs. Our results suggest that cancer cells re-express PIWIL3 to repress RNAi through miRNAs and thus open a new opportunity for cancer-specific targeting.

    View details for DOI 10.1021/jacs.6b11751

    View details for Web of Science ID 000393355600013

    View details for PubMedID 28094937

  • Chromatin Regulates Genome Targeting with Cisplatin. Angewandte Chemie (International ed. in English) Zacharioudakis, E., Agarwal, P., Bartoli, A., Abell, N., Kunalingam, L., Bergoglio, V., Xhemalce, B., Miller, K. M., Rodriguez, R. 2017; 56 (23): 6483–87


    Cisplatin derivatives can form various types of DNA lesions (DNA-Pt) and trigger pleiotropic DNA damage responses. Here, we report a strategy to visualize DNA-Pt with high resolution, taking advantage of a novel azide-containing derivative of cisplatin we named APPA, a cellular pre-extraction protocol and the labeling of DNA-Pt by means of click chemistry in cells. Our investigation revealed that pretreating cells with the histone deacetylase (HDAC) inhibitor SAHA led to detectable clusters of DNA-Pt that colocalized with the ubiquitin ligase RAD18 and the replication protein PCNA. Consistent with activation of translesion synthesis (TLS) under these conditions, SAHA and cisplatin cotreatment promoted focal accumulation of the low-fidelity polymerase Polη that also colocalized with PCNA. Remarkably, these cotreatments synergistically triggered mono-ubiquitination of PCNA and apoptosis in a RAD18-dependent manner. Our data provide evidence for a role of chromatin in regulating genome targeting with cisplatin derivatives and associated cellular responses.

    View details for DOI 10.1002/anie.201701144

    View details for PubMedID 28474855

  • Small RNA Sequencing in Cells and Exosomes Identifies eQTLs and 14q32 as a Region of Active Export G3-GENES GENOMES GENETICS Tsang, E. K., Abell, N. S., Li, X., Anaya, V., Karczewski, K. J., Knowles, D. A., Sierra, R. G., Smith, K. S., Montgomery, S. B. 2017; 7 (1): 31-39
  • MiR-191 Regulates Primary Human Fibroblast Proliferation and Directly Targets Multiple Oncogenes PLOS ONE Polioudakis, D., Abell, N. S., Iyer, V. R. 2015; 10 (5)


    miRNAs play a central role in numerous pathologies including multiple cancer types. miR-191 has predominantly been studied as an oncogene, but the role of miR-191 in the proliferation of primary cells is not well characterized, and the miR-191 targetome has not been experimentally profiled. Here we utilized RNA induced silencing complex immunoprecipitations as well as gene expression profiling to construct a genome wide miR-191 target profile. We show that miR-191 represses proliferation in primary human fibroblasts, identify multiple proto-oncogenes as novel miR-191 targets, including CDK9, NOTCH2, and RPS6KA3, and present evidence that miR-191 extensively mediates target expression through coding sequence (CDS) pairing. Our results provide a comprehensive genome wide miR-191 target profile, and demonstrate miR-191's regulation of primary human fibroblast proliferation.

    View details for DOI 10.1371/journal.pone.0126535

    View details for Web of Science ID 000354921400066

    View details for PubMedID 25992613

    View details for PubMedCentralID PMC4439112

  • miR-503 represses human cell proliferation and directly targets the oncogene DDHD2 by non-canonical target pairing BMC GENOMICS Polioudakis, D., Abell, N. S., Iyer, V. R. 2015; 16


    The pathways regulating the transition of mammalian cells from quiescence to proliferation are mediated by multiple miRNAs. Despite significant improvements in our understanding of miRNA targeting, the majority of miRNA regulatory networks are still largely unknown and require experimental validation.Here we identified miR-503, miR-103, and miR-494 as negative regulators of proliferation in primary human cells. We experimentally determined their genome wide target profiles using RNA-induced silencing complex (RISC) immunoprecipitations and gene expression profiling. Analysis of the genome wide target profiles revealed evidence of extensive regulation of gene expression through non-canonical target pairing by miR-503. We identified the proto-oncogene DDHD2 as a target of miR-503 that requires pairing outside of the canonical 5' seed region of miR-503, representing a novel mode of miRNA-target pairing. Further bioinformatics analysis implicated miR-503 and DDHD2 in breast cancer tumorigenesis.Our results provide an extensive genome wide set of targets for miR-503, miR-103, and miR-494, and suggest that miR-503 may act as a tumor suppressor in breast cancer by its direct non-canonical targeting of DDHD2.

    View details for DOI 10.1186/s12864-015-1279-9

    View details for Web of Science ID 000349254600001

    View details for PubMedID 25653011

    View details for PubMedCentralID PMC4326481

  • A Myc-microRNA network promotes exit from quiescence by suppressing the interferon response and cell-cycle arrest genes NUCLEIC ACIDS RESEARCH Polioudakis, D., Bhinge, A. A., Killion, P. J., Lee, B., Abell, N. S., Iyer, V. R. 2013; 41 (4): 2239-2254


    The transition of mammalian cells from quiescence to proliferation is accompanied by the differential expression of several microRNAs (miRNAs) and transcription factors. However, the interplay between transcription factors and miRNAs in modulating gene regulatory networks involved in human cell proliferation is largely unknown. Here we show that the miRNA miR-22 promotes proliferation in primary human cells, and through a combination of Argonaute-2 immunoprecipitation and reporter assays, we identified multiple novel targets of miR-22, including several cell-cycle arrest genes that mediate the effects of the tumor-suppressor p53. In addition, we found that miR-22 suppresses interferon gene expression by directly targeting high mobility group box-1 and interferon regulatory factor (IRF)-5, preventing activation of IRF3 and NF-κB, which are activators of interferon genes. The expression of interferon genes is elevated in quiescent cells and their expression is inhibitory for cell proliferation. In addition, we find that miR-22 is activated by the transcription factor Myc when quiescent cells enter proliferation and that miR-22 inhibits the Myc transcriptional repressor MXD4, mediating a feed-forward loop to elevate Myc expression levels. Our results implicate miR-22 in downregulating the anti-proliferative p53 and interferon pathways and reveal a new transcription factor-miRNA network that regulates the transition of primary human cells from quiescence to proliferation.

    View details for DOI 10.1093/nar/gks1452

    View details for Web of Science ID 000318062000021

    View details for PubMedID 23303785

    View details for PubMedCentralID PMC3575845