CRISPR Gene Editing Tool for MicroRNA Cluster Network Analysis

MicroRNAs (miRNAs) have emerged as important cellular regulators (tumor suppressors, pro-oncogenic factors) of cancer and metastasis. Most published studies focus on a single miRNA when characterizing the role of small RNAs in cancer. However, ~30% of human miRNA genes are organized in clustered units that are often co-expressed, indicating a complex and coordinated system of noncoding RNA regulation. A clearer understating of how clustered miRNA networks function cooperatively to regulate tumor growth, cancer aggressiveness, and drug resistance is required before translating noncoding small RNAs to the clinic. The use of a high-throughput clustered regularly interspaced short palindromic repeats (CRISPR)-mediated gene editing procedure has been employed to study the oncogenic role of a genomic cluster of seven miRNA genes located within a locus spanning ~35,000 bp in length in the context of prostate cancer. For this approach, human cancer cell lines were infected with a lentivirus vector for doxycycline (DOX)-inducible Cas9 nuclease grown in DOX-containing medium for 48 h. The cells were subsequently co-transfected with synthetic trans-activating CRISPR RNA (tracrRNA) complexed with genomic site-specific CRISPR RNA (crRNA) oligonucleotides to allow the rapid generation of cancer cell lines carrying the entire miRNA cluster deletion and individual or combination miRNA gene cluster deletions within a single experiment. The advantages of this high-throughput gene editing system are the ability to avoid time-consuming DNA vector subcloning, the flexibility in transfecting cells with unique guide RNA combinations in a 24-well format, and the lower-cost PCR genotyping using crude cell lysates. Studies using this streamlined approach promise to uncover functional redundancies and synergistic/antagonistic interactions between miRNA cluster members, which will aid in characterizing the complex small noncoding RNA networks involved in human disease and better inform future therapeutic design.

Plasmonic-Based Biosensor for the Early Diagnosis of Prostate Cancer

A tapered optical fiber (TOF) plasmonic biosensor was fabricated and used for the sensitive detection of a panel of microRNAs (miRNAs) in human serum obtained from noncancer and prostate cancer (PCa) patients. Oncogenic and tumor suppressor miRNAs let-7a, let-7c, miR-200b, miR-141, and miR-21 were tested as predictive cancer biomarkers since multianalyte detection minimizes false-positive and false-negative rates and establishes a strong foundation for early PCa diagnosis. The biosensing platform integrates metallic gold triangular nanoprisms (AuTNPs) laminated on the TOF to excite surface plasmon waves in the supporting metallic layer and enhance the evanescent mode of the fiber surface. This sensitive TOF plasmonic biosensor as a point-of-care (POC) cancer diagnostic tool enabled the detection of the panel of miRNAs in seven patient serums without any RNA extraction or sample amplification. The TOF plasmonic biosensor could detect miRNAs in human serum with a limit of detection between 179 and 580 aM and excellent selectivity. Statistical studies were obtained to differentiate cancerous from noncancerous samples with a p-value <0.0001. This high-throughput TOF plasmonic biosensor has the potential to expand and advance POC diagnostics for the early diagnosis of cancer.

Detection of rapidly accumulating stress-induced SUMO in prostate cancer cells by a fluorescent SUMO biosensor

SUMO conjugates and SUMO chains form when SUMO, a small ubiquitin-like modifier protein, is covalently linked to other cellular proteins or itself. During unperturbed growth, cells maintain balanced levels of SUMO conjugates. In contrast, eukaryotic cells that are exposed to proteotoxic and genotoxic insults mount a cytoprotective SUMO stress response (SSR). One hallmark of the SSR is a rapid and massive increase of SUMO conjugates in response to oxidative, thermal, and osmotic stress. Here, we use a recombinant fluorescent SUMO biosensor, KmUTAG-fl, to investigate differences in the SSR in a normal human prostate epithelial cell line immortalized with SV40 (PNT2) and two human prostate cancer cell lines that differ in aggressiveness and response to androgen (LNCaP and PC3). In cells that grow unperturbed, SUMO is enriched in the nuclei of all three cell lines. However, upon 30 min of exposure to ultraviolet radiation or oxidative stress, we detected significant cytosolic enrichment of SUMO as measured by KmUTAG-fl staining. This rapid enrichment in cytosolic SUMO levels was on average fivefold higher in the LNCaP and PC3 prostate cancer cell lines compared to normal immortalized PNT2 cells. Additionally, this enhanced enrichment of cytosolic SUMO was reversible as cells recovered from stress exposure. Our study validates the use of the fluorescent KmUTAG-fl SUMO biosensor to detect differences of SUMO levels and localization between normal and cancer cells and provides new evidence that cancer cells may exhibit an enhanced SSR.

GDF11 induces kidney fibrosis, renal cell epithelial-to-mesenchymal transition, and kidney dysfunction and failure

BACKGROUND

GDF11 modulates embryonic patterning and kidney organogenesis. Herein, we sought to define GDF11 function in the adult kidney and in renal diseases.

METHODS

In vitro renal cell lines, genetic, and murine in vivo renal injury models were examined.

RESULTS

Among tissues tested, Gdf11 was highest in normal adult mouse kidney. Expression was increased acutely after 5/6 nephrectomy, ischemia-reperfusion injury, kanamycin toxicity, or unilateral ureteric obstruction. Systemic, high-dose GDF11 administration in adult mice led to renal failure, with accompanying kidney atrophy, interstitial fibrosis, epithelial-to-mesenchymal transition of renal tubular cells, and eventually death. These effects were associated with phosphorylation of SMAD2 and could be blocked by follistatin. In contrast, Gdf11 heterozygous mice showed reduced renal Gdf11 expression, renal fibrosis, and expression of fibrosis-associated genes both at baseline and after unilateral ureteric obstruction compared with wild-type littermates. The kidney-specific consequences of GDF11 dose modulation are direct effects on kidney cells. GDF11 induced proliferation and activation of NRK49f renal fibroblasts and also promoted epithelial-to-mesenchymal transition of IMCD-3 tubular epithelial cells in a SMAD3-dependent manner.

CONCLUSION

Taken together, these data suggest that GDF11 and its downstream signals are critical in vivo mediators of renal injury. These effects are through direct actions of GDF11 on renal tubular cells and fibroblasts. Thus, regulation of GDF11 presents a therapeutic target for diseases involving renal fibrosis and impaired tubular function.

Characterization and Evidence of the miR-888 Cluster as a Novel Cancer Network in Prostate

Prostate cancer afflicts 1 in 7 men and is the second leading cause of male cancer-related deaths in the United States. MicroRNAs (miRNAs), an extensive class of approximately 22 nucleotide noncoding RNAs, are often aberrantly expressed in tissues and fluids from prostate cancer patients, but the mechanisms of how specific miRNAs regulate prostate tumorigenesis and metastasis are poorly understood. Here, miR-888 was identified as a novel prostate factor that promotes proliferation and migration. miR-888 resides within a genomic cluster of 7 miRNA genes (mir-892c, mir-890, mir-888, mir-892a, mir-892b, mir-891b, mir-891a) on human chromosome Xq27.3. Moreover, as miR-888 maps within HPCX1, a locus associated with susceptibility and/or hereditary prostate cancer, it was hypothesized that additional miRNA cluster members also play functional roles in the prostate. Expression analysis determined that cluster members were similarly elevated in metastatic PC3-ML prostate cells and their secreted exosomes, as well as enriched in expressed prostatic secretions urine-derived exosomes obtained from clinical patients with high-grade prostate cancer. In vitro assays revealed that miR-888 cluster members selectively modulated PC3-derived and LNCaP cell proliferation, migration, invasion, and colony formation. Mouse xenograft studies verified miR-888 and miR-891a as pro-oncogenic factors that increased prostate tumor growth in vivo Further analysis validated RBL1, KLF5, SMAD4, and TIMP2 as direct miR-888 targets and that TIMP2 is also coregulated by miR-891a. This study provides the first comprehensive analysis of the entire miR-888 cluster and reveals biological insight.Implications: This work reveals a complex noncoding RNA network in the prostate that could be developed as effective diagnostic and therapeutic tools for advanced prostate cancer. Mol Cancer Res; 16(4); 669-81. ©2018 AACR.

Abstract 1933: The miR-888 cluster: a new oncogenic cluster involved in aggressive prostate cancer

Prostate cancer (PCa) is the second leading cause of cancer-related death among men in the U.S. No accurate biomarkers exists that can discriminate for aggressive PCa and therapeutic options are limited for metastatic disease. MicroRNAs (MiRNAs) have emerged as promising clinical tools for cancers. These small non-coding RNAs negatively regulate gene expression post-transcriptionally. Widespread miRNA dysregulation has been noted in PCa. However, it is poorly understood how they function in the prostate to promote cancer progression and metastasis. Our lab recently identified miR-888 as a novel oncogenic miRNA up-regulated in specimens from patients with advanced PCa and acts to increase prostate cell proliferation, migration, & colony formation in vitro (Lewis et al, Cell Cycle 2014). MiR-888 belongs to a genomic cluster of seven miRNAs on human chromosome Xq27.3, an area linked to hereditary prostate cancer (HPCX1). We hypothesize additional members of miR-888 cluster (miR-892c, -890, -892a, -892b, -891b, -891a) function to promote PCa progression. Our studies employed paired syngenic human PCa cell lines differing in their metastatic status and response to androgen (i.e., androgen-sensitive, non-malignant RWPE-1 & aggressive WPE1-NB26; androgen-sensitive LNCaP & aggressive C4-2; hormone-refractory PC3-N & aggressive PC3-ML) to examine the miR-888 cluster's ability to modulate prostate cell proliferation (WST-1 assays), colony formation (Soft agar assays), migration, and invasion (Boyden chamber assays). Profiling miRNA expression in these cancer lines, we found that all miR-888 cluster members were preferentially elevated in highly aggressive PC3-ML and extensively down-regulated in non-aggressive PC3-N cells. Furthermore, we noted certain members of the miR-888 cluster, most notably miR-891a, acted in vitro to promote prostate cell proliferation, colony formation, migration & invasion activities. Interestingly, our results also suggested that other miR-888 cluster members act conversely to inhibit these activities - implying the miR-888 cluster functions as a unit to fine tune and coordinate prostate cancer pathways. Xenograft experiments are currently ongoing to evaluate in vivo effects of the miR-888 cluster during tumorigenesis. Preliminary data indicated that miR-888 could accelerate tumor formation of PC3-N cells subcutaneously implanted into flanks of NOD/SCID male mice. MiR-888 cluster members are now being evaluated for their non-cell autonomous effects in the prostate by exosomal transport. We have successfully isolated exosomes from human PCa cell lines and are working towards developing these secreted membrane-bound vesicles as novel miRNA delivery vehicles for PCa. Taken together, this study offers a more detailed understanding of PCa and insight into the complexity of miRNA networks involved in cancer progression.

Citation Format: Tsuyoshi Hasegawa, Mary Pahuski, Garrison Glavich, Holly B. Lewis, Aurora Esquela-Kerscher. The miR-888 cluster: a new oncogenic cluster involved in aggressive prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1933.

Abstract 3086: From profiling to function: A role for microRNA miR-888 in promoting prostate cancer progression

Prostate cancer remains the second leading cause of cancer-related deaths among men in the United States despite the widespread use of prostate specific antigen (PSA) as a diagnostic marker for prostate cancer and as a predictor of treatment outcome. MicroRNAs (MiRNAs) belong to a growing class of small non-coding RNAs that are often abnormally expressed in fluid and tissue specimens from prostate cancer patients compared to non-cancer individuals. These miRNAs are hypothesized to play a direct role in promoting disease progression and metastasis in the prostate and are intensely studied for both their diagnostic and therapeutic potential for human cancer. Our laboratory profiled candidate prostate-cancer associated miRNAs in an innovative prostatic fluid biomarker source called expressed prostatic secretions in urine (EPS urine) to determine their utility as discriminating biomarkers for advanced forms of prostate cancer. 10 out of 50 miRNA tested showed statistically significant differences in expression between cancer and non-cancer patient groups within the supernatant but not pellet fractions of whole EPS urine. We are investigating if differential miRNA expression in EPS supernatant is due to exosomal populations and how miRNA-loaded exosomes modulate prostate tumorigenesis in mice. Our profiling studies identified miR-888 as a novel factor that correlates with advanced prostate cancer in human prostate cancer cell lines, EPS urine, and primary tumors. Functional assays revealed that miR-888 promotes proliferation, migration, and colony formation of hormone-refractory and androgen-sensitive human prostate cancer cells. Our working model is that miR-888 overexpression in the diseased prostate suppresses SMAD4, RBL1, and TIMP2 targets leading to tumor progression and metastasis. Human miR-888 belongs to a genomic cluster of seven miRNAs on human chromosome Xq27.3. We are currently testing how this miR-888 cluster interacts within a growing network of coding and non-coding genes to regulate prostate tumor progression. This research will provide a better understanding how prostate tumor cells progress to a more metastatic, aggressive state and facilitate the development of more effective diagnostic and therapeutic strategies for this prevalent and deadly disease.

Citation Format: Holly Lewis, Tsuyoshi Hasegawa, Garrison Glavich, Raymond Lance, O. John Semmes, Hind Beydoun, Richard Drake, Aurora Esquela-Kerscher. From profiling to function: A role for microRNA miR-888 in promoting prostate cancer progression. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3086. doi:10.1158/1538-7445.AM2015-3086

miR-888 is an expressed prostatic secretions-derived microRNA that promotes prostate cell growth and migration

MicroRNAs (MiRNAs) are a growing class of small non-coding RNAs that exhibit widespread dysregulation in prostate cancer. We profiled miRNA expression in syngeneic human prostate cancer cell lines that differed in their metastatic potential in order to determine their role in aggressive prostate cancer. miR-888 was the most differentially expressed miRNA observed in human metastatic PC3-ML cells relative to non-invasive PC3-N cells, and its levels were higher in primary prostate tumors from cancer patients, particularly those with seminal vesicle invasion. We also examined a novel miRNA-based biomarker source called expressed prostatic secretions in urine (EPS urine) for miR-888 expression and found that its levels were preferentially elevated in prostate cancer patients with high-grade disease. These expression studies indicated a correlation for miR-888 in disease progression. We next tested how miR-888 regulated cancer-related pathways in vitro using human prostate cancer cell lines. Overexpression of miR-888 increased proliferation and migration, and conversely inhibition of miR-888 activity blocked these processes. miR-888 also increased colony formation in PC3-N and LNCaP cells, supporting an oncogenic role for this miRNA in the prostate. Our data indicates that miR-888 functions to promote prostate cancer progression and can suppress protein levels of the tumor suppressor genes RBL1 and SMAD4. This miRNA holds promise as a diagnostic tool using an innovative prostatic fluid source as well as a therapeutic target for aggressive prostate cancer.

Gongylonema pulchrum infection in a resident of Williamsburg, Virginia, verified by genetic analysis

We describe the thirteenth reported case of human infection with Gongylonema spp. in the United States and the first to be confirmed as Gongylonema pulchrum. The parasite described was isolated from the oral cavity of a resident of Williamsburg, Virginia. The identity of the parasite was verified through morphological and genetic approaches, and provided the first genetic confirmation of a Gongylonema sp. in humans.

A growing molecular toolbox for the functional analysis of microRNAs in Caenorhabditis elegans

With the growing number of microRNAs (miRNAs) being identified each year, more innovative molecular tools are required to efficiently characterize these small RNAs in living animal systems. Caenorhabditis elegans is a powerful model to study how miRNAs regulate gene expression and control diverse biological processes during development and in the adult. Genetic strategies such as large-scale miRNA deletion studies in nematodes have been used with limited success since the majority of miRNA genes do not exhibit phenotypes when individually mutated. Recent work has indicated that miRNAs function in complex regulatory networks with other small RNAs and protein-coding genes, and therefore the challenge will be to uncover these functional redundancies. The use of miRNA inhibitors such as synthetic antisense 2'-O-methyl oligoribonucleotides is emerging as a promising in vivo approach to dissect out the intricacies of miRNA regulation.

The complexities of microRNA regulation: mirandering around the rules

MicroRNAs (miRNAs) are an important class of non-coding small RNAs that possess a large range of biological activities in a variety of organisms and are linked to human diseases such as cancer. Initially, miRNAs were thought to act solely as negative regulators of gene expression and exert their effects by binding to regions within the 3'UTR of their target protein-coding messenger RNAs (mRNAs) in a sequence dependent manner. However, recent data reveals that miRNA regulation entails a far more complex system of post-transcriptional control than initially appreciated. An evolving consensus has emerged of how miRNAs can repress as well as activate gene expression by interacting with complementary regions found in the promoter, coding region, as well as the 3'UTR of their mRNA targets. Furthermore, miRNAs are extensively regulated at the levels of miRNA promoter transcription, methylation, miRNA processing, RNA editing, and miRNA-target interactions. This review will discuss new insights into miRNA-based mechanisms and the role specific DNA- and RNA-binding factors play in fine-tuning gene expression in both negative and positive ways by directing miRNA biogenesis and activity. We will also discuss the influence that cellular context and environmental cues have on miRNA function. In the future, a clear understanding of miRNA regulation will be essential when understanding the role miRNAs play during animal development and in maintaining adult homeostasis as well as exploring the use of small RNAs for diagnostic and therapeutic purposes.

The let-7 microRNA reduces tumor growth in mouse models of lung cancer

MicroRNAs have been increasingly implicated in human cancer and interest has grown about the potential to use microRNAs to combat cancer. Lung cancer is the most prevalent form of cancer worldwide and lacks effective therapies. Here we have used both in vitro and in vivo approaches to show that the let-7 microRNA directly represses cancer growth in the lung. We find that let-7 inhibits the growth of multiple human lung cancer cell lines in culture, as well as the growth of lung cancer cell xenografts in immunodeficient mice. Using an established orthotopic mouse lung cancer model, we show that intranasal let-7 administration reduces tumor formation in vivo in the lungs of animals expressing a G12D activating mutation for the K-ras oncogene. These findings provide direct evidence that let-7 acts as a tumor suppressor gene in the lung and indicate that this miRNA may be useful as a novel therapeutic agent in lung cancer.

The let-7 microRNA represses cell proliferation pathways in human cells

MicroRNAs play important roles in animal development, cell differentiation, and metabolism and have been implicated in human cancer. The let-7 microRNA controls the timing of cell cycle exit and terminal differentiation in Caenorhabditis elegans and is poorly expressed or deleted in human lung tumors. Here, we show that let-7 is highly expressed in normal lung tissue, and that inhibiting let-7 function leads to increased cell division in A549 lung cancer cells. Overexpression of let-7 in cancer cell lines alters cell cycle progression and reduces cell division, providing evidence that let-7 functions as a tumor suppressor in lung cells. let-7 was previously shown to regulate the expression of the RAS lung cancer oncogenes, and our work now shows that multiple genes involved in cell cycle and cell division functions are also directly or indirectly repressed by let-7. This work reveals the let-7 microRNA to be a master regulator of cell proliferation pathways.

Reciprocal expression of lin-41 and the microRNAs let-7 and mir-125 during mouse embryogenesis

In C. elegans, heterochronic genes control the timing of cell fate determination during development. Two heterochronic genes, let-7 and lin-4, encode microRNAs (miRNAs) that down-regulate a third heterochronic gene lin-41 by binding to complementary sites in its 3'UTR. let-7 and lin-4 are conserved in mammals. Here we report the cloning and sequencing of mammalian lin-41 orthologs. We find that mouse and human lin-41 genes contain predicted conserved complementary sites for let-7 and the lin-4 ortholog, mir-125, in their 3'UTRs. Mouse lin-41 (Mlin-41) is temporally expressed in developing mouse embryos, most dramatically in the limb buds. Mlin-41 is down-regulated during mid-embryogenesis at the time when mouse let-7c and mir-125 RNA levels are up-regulated. Our results suggest that mammalian lin-41 is temporally regulated by miRNAs in order to direct key developmental events such as limb formation.

Post-embryonic expression of C. elegans microRNAs belonging to the lin-4 and let-7 families in the hypodermis and the reproductive system

MicroRNAs (miRNAs) are regulatory molecules that negatively control gene expression by binding to complementary sequences on target mRNAs. The most thoroughly characterized miRNAs, lin-4 and let-7, direct cell fate determination during the larval transitions in C. elegans and act as key regulators of temporal gene expression. lin-4 and let-7 are founding members of two distinct families of miRNA genes sharing strong sequence homology primarily in the 5' end of the mature miRNAs. In this report, we characterize the temporal and spatial expression patterns of lin-4 and let-7 family members using northern blot analysis and mir::gfp fusion studies. Our results show that lin-4 and let-7 homologues possess distinct temporal and spatial expression patterns during nematode development and that known heterochronic genes regulate their expression. We find that certain lin-4 and let-7 family members display overlapping expression patterns in the hypodermis and the reproductive system, suggesting that combinations of miRNAs from across families may control common developmental events.

Oncomirs - microRNAs with a role in cancer

MicroRNAs (miRNAs) are an abundant class of small non-protein-coding RNAs that function as negative gene regulators. They regulate diverse biological processes, and bioinformatic data indicates that each miRNA can control hundreds of gene targets, underscoring the potential influence of miRNAs on almost every genetic pathway. Recent evidence has shown that miRNA mutations or mis-expression correlate with various human cancers and indicates that miRNAs can function as tumour suppressors and oncogenes. miRNAs have been shown to repress the expression of important cancer-related genes and might prove useful in the diagnosis and treatment of cancer.