Ivan Martinez

Human papillomavirus type 16 reduces the expression of microRNA-218 in cervical carcinoma cells

Human papillomaviruses (HPVs) are involved in the pathogenesis of cancer of the cervix (CaCx). MicroRNA (miRNA) expression analysis using Ambion (Austin, TX, USA) arrays showed that three miRNAs were overexpressed and 24 underexpressed in cervical cell lines containing integrated HPV-16 DNA compared to the normal cervix. Furthermore, nine miRNAs were overexpressed and one underexpressed in integrated HPV-16 cell lines compared to the HPV-negative CaCx cell line C-33A. Based on microarray and/or quantitative real-time PCR and northern blot analyses, microRNA-218 (miR-218) was specifically underexpressed in HPV-positive cell lines, cervical lesions and cancer tissues containing HPV-16 DNA compared to both C-33A and the normal cervix. Expression of the E6 oncogene of high-risk HPV-16, but not that of low-risk HPV-6, reduced miR-218 expression, and conversely, RNA interference of E6/E7 oncogenes in an HPV-16-positive cell line increased miR-218 expression. We also demonstrate that the epithelial cell-specific marker LAMB3 is a target of miR-218. We also show that LAMB3 expression is increased in the presence of the HPV-16 E6 oncogene and this effect is mediated through miR-218. These findings may contribute to a better understanding of the molecular mechanisms involved in cervical carcinogenesis.

miR-29 and miR-30 regulate B-Myb expression during cellular senescence

Cellular senescence is a form of irreversible growth arrest and a major tumor suppressor mechanism. We show here that the miR-29 and miR-30 microRNA families are up-regulated during induced and replicative senescence and that up-regulation requires activation of the Rb pathway. Expression of a reporter construct containing the 3′UTR of the B-Myb oncogene is repressed during senescence, and repression is blocked by mutations in conserved miR-29 and miR-30 binding sites in the B-Myb 3′UTR. In proliferating cells, transfection of miR-29 and miR-30 represses a reporter construct containing the wild-type but not the mutant B-Myb 3′UTR, and repression of the mutant 3′UTR is reinstituted by compensatory mutations in miR-29 and miR-30 that restore binding to the mutant sites. miR-29 and miR-30 introduction also represses expression of endogenous B-Myb and inhibits cellular DNA synthesis. Finally, interference with miR-29 and miR-30 expression inhibits senescence. These findings demonstrate that miR-29 and miR-30 regulate B-Myb expression by binding to its 3′UTR and suggest that these microRNAs play an important role in Rb-driven cellular senescence.

B-Myb, cancer, senescence, and microRNAs.

The transcription factor B-Myb plays a critical role in regulating gene expression and is implicated in controlling carcinogenesis and cellular senescence. Transcription of the B-Myb gene is regulated by retinoblastoma proteins acting directly on the B-Myb promoter. Recently, we found that microRNAs also control the abundance of B-Myb mRNA during senescence, adding another level of complexity to B-Myb regulation. This review focuses on the importance of B-Myb in cancer and senescence, with an emphasis on the regulation of B-Myb expression and activity.

Translational Regulation of the Mitochondrial Genome Following Redistribution of Mitochondrial MicroRNA in the Diabetic Heart

Background—Cardiomyocytes are rich in mitochondria which are situated in spatially distinct subcellular regions, including those under the plasma membrane, subsarcolemmal mitochondria, and those between the myofibrils, interfibrillar mitochondria. We previously observed subpopulation-specific differences in mitochondrial proteomes following diabetic insult. The objective of this study was to determine whether mitochondrial genome–encoded proteins are regulated by microRNAs inside the mitochondrion and whether subcellular spatial location or diabetes mellitus influences the dynamics. Methods and Results—Using microarray technology coupled with cross-linking immunoprecipitation and next generation sequencing, we identified a pool of mitochondrial microRNAs, termed mitomiRs, that are redistributed in spatially distinct mitochondrial subpopulations in an inverse manner following diabetic insult. Redistributed mitomiRs displayed distinct interactions with the mitochondrial genome requiring specific stoichiometric associations with RNA-induced silencing complex constituents argonaute-2 (Ago2) and fragile X mental retardation–related protein 1 (FXR1) for translational regulation. In the presence of Ago2 and FXR1, redistribution of mitomiR-378 to the interfibrillar mitochondria following diabetic insult led to downregulation of mitochondrially encoded F0 component ATP6. Next generation sequencing analyses identified specific transcriptome and mitomiR sequences associated with ATP6 regulation. Overexpression of mitomiR-378 in HL-1 cells resulted in its accumulation in the mitochondrion and downregulation of functional ATP6 protein, whereas antagomir blockade restored functional ATP6 protein and cardiac pump function. Conclusions—We propose mitomiRs can translationally regulate mitochondrially encoded proteins in spatially distinct mitochondrial subpopulations during diabetes mellitus. The results reveal the requirement of RNA-induced silencing complex constituents in the mitochondrion for functional mitomiR translational regulation and provide a connecting link between diabetic insult and ATP synthase function.

Exploring the mitochondrial microRNA import pathway through Polynucleotide Phosphorylase (PNPase)

Cardiovascular disease is the primary cause of mortality for individuals with type 2 diabetes mellitus. During the diabetic condition, cardiovascular dysfunction can be partially attributed to molecular changes in the tissue, including alterations in microRNA (miRNA) interactions. MiRNAs have been reported in the mitochondrion and their presence may influence cellular bioenergetics, creating decrements in functional capacity. In this study, we examined the roles of Argonaute 2 (Ago2), a protein associated with cytosolic and mitochondrial miRNAs, and Polynucleotide Phosphorylase (PNPase), a protein found in the inner membrane space of the mitochondrion, to determine their role in mitochondrial miRNA import. In cardiac tissue from human and mouse models of type 2 diabetes mellitus, Ago2 protein levels were unchanged while PNPase protein expression levels were increased; also, there was an increase in the association between both proteins in the diabetic state. MiRNA-378 was found to be significantly increased in db/db mice, leading to decrements in ATP6 levels and ATP synthase activity, which was also exhibited when overexpressing PNPase in HL-1 cardiomyocytes and in HL-1 cells with stable miRNA-378 overexpression (HL-1-378). To assess potential therapeutic interventions, flow cytometry evaluated the capacity for targeting miRNA-378 species in mitochondria through antimiR treatment, revealing miRNA-378 level-dependent inhibition. Our study establishes PNPase as a contributor to mitochondrial miRNA import through the transport of miRNA-378, which may regulate bioenergetics during type 2 diabetes mellitus. Further, our data provide evidence that manipulation of PNPase levels may enhance the delivery of antimiR therapeutics to mitochondria in physiological and pathological conditions.

An Exportin-1–dependent microRNA biogenesis pathway during human cell quiescence

Significance Quiescence is a growth-arrested cellular state; genes involved in this process are finely regulated by several factors, including miRNAs. During miRNA biogenesis, Exportin-5 transports miRNA precursors from the nucleus to the cytoplasm. In this study, we demonstrated the existence of an alternative miRNA biogenesis pathway in quiescent primary human cells. This pathway involves the repression of Exportin-5 expression by autophagy and miRNAs and the 2,2,7-trimethylguanosine-cap modification of specific primary miRNAs (pri-miRNAs), which signal their export to the cytoplasm by Exportin-1. We further showed that these pri-miRNAs are processed rapidly in the cytoplasm by a small isoform of Drosha. Collectively, these results reveal an alternative mechanism of miRNA biogenesis that will expand our understanding of miRNA regulation in normal or disease-related cells. The reversible state of proliferative arrest known as “cellular quiescence” plays an important role in tissue homeostasis and stem cell biology. By analyzing the expression of miRNAs and miRNA-processing factors during quiescence in primary human fibroblasts, we identified a group of miRNAs that are induced during quiescence despite markedly reduced expression of Exportin-5, a protein required for canonical miRNA biogenesis. The biogenesis of these quiescence-induced miRNAs is independent of Exportin-5 and depends instead on Exportin-1. Moreover, these quiescence-induced primary miRNAs (pri-miRNAs) are modified with a 2,2,7-trimethylguanosine (TMG)-cap, which is known to bind Exportin-1, and knockdown of Exportin-1 or trimethylguanosine synthase 1, responsible for (TMG)-capping, inhibits their biogenesis. Surprisingly, in quiescent cells Exportin-1–dependent pri-miR-34a is present in the cytoplasm together with a small isoform of Drosha, implying the existence of a different miRNA processing pathway in these cells. Our findings suggest that during quiescence the canonical miRNA biogenesis pathway is down-regulated and specific miRNAs are generated by an alternative pathway to regulate genes involved in cellular growth arrest.

High prevalence of RET tyrosine kinase activation in Mexican patients with papillary thyroid carcinomas.

RET/PTC oncogene expression is restricted to papillary thyroid carcinomas (PTC). At least three forms of this oncogene have been described. These are generated by the rearrangement of the 5′-terminal region of different expressed genes with the tyrosine-kinase (TK) domain of the ret proto-oncogene. Several studies showing the correlation between the expression of this oncogene, clinical outcome, and histological subtypes have been published. Thirty-five paraffin-embedded PTC samples from patients without a history of radiation exposure were studied. Immunohistochemistry (IHC) and in situ hybridization (ISH) were used to determine a possible correlation between RET activation, clinical outcome, and tumor subtype. Almost half of the studied cases presented with tumoral extension or metastases. Ret gene transcripts and protein were found in all PTC variants as well as in their corresponding metastases. In contrast, none of the follicular adenomas, goiters, or normal follicular cells from the thyroid gland showed evidence of ret activation. We observed a high frequency of ret expression in PTCs, suggesting that ret activation is a common event in nonradiation-related PTC from Mexican patients.

Bone Marrow Microenvironment Niche Regulates miR-221/222 in Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) has many features in common with normal B-cell progenitors, including their ability to respond to diverse signals from the bone marrow microenvironment (BMM) resulting in regulation of cell-cycle progression and survival. Bone marrow–derived cues influence many elements of both steady state hematopoiesis and hematopoietic tumor cell phenotypes through modulation of gene expression. miRNAs are one regulatory class of small noncoding RNAs that have been shown to be increasingly important in diverse settings of malignancy. In the current study, miRNA profiles were globally altered in ALL cells following exposure to primary human bone marrow niche cells, including bone marrow stromal cells (BMSC) and primary human osteoblasts (HOB). Specifically, mature miR-221 and miR-222 transcripts were decreased in ALL cells cocultured with BMSC or HOB, coincident with increased p27 (CDKN1B), a previously validated target. Increased p27 protein in ALL cells exposed to BMSC or HOB is consistent with accumulation of tumor cells in the G0 phase of the cell cycle and resistance to chemotherapy-induced death. Overexpression of miR-221 in ALL cells during BMSC or HOB coculture prompted cell-cycle progression and sensitization of ALL cells to cytotoxic agents, blunting the protective influence of the BMM. These novel observations indicate that BMM regulation of miR-221/222 contributes to marrow niche-supported tumor cell quiescence and survival of residual cells. Implications: Niche-influenced miR-221/222 may define a novel therapeutic target in ALL to be combined with existing cytotoxic agents to more effectively eradicate refractory disease that contributes to relapse. Mol Cancer Res; 14(10); 909–19. ©2016 AACR.

Abstract A26: Importance of long noncoding RNAs in human papillomavirus-related cancers

The objective of this study is to identify the importance of long non-coding RNAs (lncRNAs) in the induction of carcinogenesis by high-risk human papillomavirus (HPV)-16 oncoprotein E6 in HPV-related cancers. Dysregulation of long non-coding RNAs (lncRNAs) occurs in most human cancers, however, there are only a few studies showing dysregulation of specific lncRNAs in human papillomavirus (HPV)-related cancers. High-risk HPV infection (e.g. HPV-16 and HPV-18) is one the most common causes of cervical cancer, as well as a subset of head and neck squamous cell carcinoma (HNSCC). It is well known that one of the main factors contributing to HPV-related carcinogenesis is the expression of high-risk HPV E6 viral oncoprotein and its interaction with several human proteins, such as the tumor suppressor p53 and the anti-apoptotic protein Bak. It is hypothesized that HPV-16 E6 changes the expression of host lncRNAs to regulate downstream processes important in the induction of carcinogenesis. To test this hypothesis, we stably express high-risk HPV-16 E6 in primary human keratinocytes and conducted high-throughput RNA sequencing analysis to identify HPV-16 E6-mediated changes in lncRNAs expression. Our preliminary data shows over 500 lncRNAs up- or down- regulated by greater than 2-fold with the expression of HPV-16 E6 compared to control. We validated the expression changes of many individual lncRNAs after the expression of HPV-16E6, via q-RT-PCR and Northern blots. In addition we observe similar expression patterns when comparing normal cells to HPV+ cervical cancer cell lines. Currently, we are characterizing specific lncRNAs of interest that are altered with expression of HPV-16 E6 by using 59 and 39 rapid amplification of cDNA ends (RACE) experiments as well as determining certain lncRNA9s mechanism of action contributing to cancer by conducting knockdown and rescue experiments followed by behavior assays (e.g. invasion, angiogenesis, and proliferation). To aid in the determination of the function of the lncRNAs, we plan to use Fluorescence in situ Hybridization (FISH) assays to identify their localization. We believe this project will be significant in that it will identify and show the importance of lncRNAs in HPV-related cancers as well as give us new information about a novel mechanism by which high-risk HPV infection contributes to cervical and HNSCC carcinogenesis. Citation Format: Jamie A. Barr, Karen E. Hayes, Ivan Martinez. Importance of long noncoding RNAs in human papillomavirus-related cancers. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A26.

Abstract A34: The discovery of novel noncoding circular RNAs generated by high-risk human papillomavirus type 16

Recently, two independent research teams discovered thousands of conserved non-coding human circular RNAs (circRNAs), however, there are no studies suggesting the existence of circRNAs produced by human viruses. The objective of this study is to explore our hypothesis that human papillomavirus (HPV)-16 creates viral circRNAs that may alter host activity in order to promote viral replication and induction of carcinogenesis. CircRNAs are non-coding RNAs generated by the alternative splicing of a 59 acceptor and 29 or 39 donor sites, creating a “head” to “tail” covalent junction of exonic and/or intronic regions. Although the role of circRNAs is largely unknown, studies have demonstrated several functions for circRNAs including sequestering microRNAs (miRNAs) and regulation of transcription. Recently, circRNAs have also been associated with several cancers such as colorectal, breast, and gastric cancers. Infections with high-risk HPVs, such as types 16 and 18, are responsible for the majority of cervical cancers and a subset of head and neck squamous cell carcinomas (HNSCC). HPV is a small double-stranded circular DNA encoding six early proteins (E-1, -2, -4, -5, -6, and -7) and two late proteins (L-1, -2). HPV DNA is tightly regulated and undergoes extensive and complex splicing to achieve the expression of these proteins. Our preliminary data suggest that HPV-16 extensive splicing generates at least two viral circRNAs (hpv-circRNAs) that could potentially regulate host cellular processes promoting tumorigenesis. We demonstrated the existence of the “head” to “tail” junctions of hpv-circRNAs in HPV-16 viral RNA with reverse transcription polymerase chain reaction (RT-PCR) amplification using divergent primers in RNA extracted from cervical tumor cell lines. Quantitative RT-PCR (qRT-PCR) analysis showed the retention of the hpv-circRNAs in RNase R treated samples suggesting the absence of free RNA ends in these hpv-circRNAs. Moreover, these viral circRNAs persisted even after the cervical tumor cells were exposed to Actinomycin D for 48 hrs (to inhibit RNA synthesis), confirming the stability of these hpv-circRNAs in comparison to the short-lived lariat structures that also can occur during splicing. Together, our data suggest the existence of viral circRNAs produced in HPV-16. To the best of our knowledge, these are the first described human viral generated circRNAs. Currently, we are characterizing these hpv-circRNAs by conducting knockdown and rescue experiments followed by behavior assays (e.g. invasion, angiogenesis, and proliferation). We believe this project will be significant in that it will identify and show the importance of viral circRNAs in HPV-related cancers as well as give us new information about a novel mechanism by which high-risk HPV infection contributes to cervical and HNSCC carcinogenesis. Citation Format: Karen E. Hayes, Jamie A. Barr, Jeremy E. Wilusz, Ivan Martinez. The discovery of novel noncoding circular RNAs generated by high-risk human papillomavirus type 16. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A34.