Multisite Verification of a Targeted CFTR Polymerase Chain Reaction/Capillary Electrophoresis Assay That Evaluates Pathogenic Variants Across Diverse Ethnic and Ancestral Groups

CONTEXT.—

Existing targeted cystic fibrosis screening assays miss important pathogenic CFTR variants in the ethnically diverse US population.

OBJECTIVE.—

To evaluate the analytic performance of a multiplex polymerase chain reaction (PCR)/capillary electrophoresis (CE) CFTR assay panel that simultaneously interrogates primary pathogenic variants of different ethnic/ancestral groups.

DESIGN.—

Performance characteristic assessment and variant coverage comparison of the panel with a focus on ethnicity-specific CFTR variants were performed. Sample DNA was primarily from whole blood or cell lines. Detection of CFTR carriers was compared across several commercially available CFTR kits and recommended variant sets based on panel content.

RESULTS.—

The panel interrogated 65 pathogenic CFTR variants representing 92% coverage from a recent genomic sequencing survey of the US population, including 4 variants with top 5 frequency in African or Asian populations not reflected in other targeted panels. In simulation studies, the panel represented 95% of carriers across the global population, resulting in 6.9% to 19.0% higher carrier detection rate compared with 10 targeted panels or variant sets. Precision and sensitivity/specificity were 100% concordant. Multisite sample-level genotyping accuracy was 99.2%. Across PCR and CE instruments, sample-level genotyping accuracy was 97.1%, with greater than 99% agreement for all variant-level metrics.

CONCLUSIONS.—

The CFTR assay achieves 92% or higher coverage of CFTR variants in diverse populations and provides improved pan-ethnic coverage of minority subgroups of the US populace. The assay can be completed within 5 hours from DNA sample to genotype, and performance data exceed acceptance criteria for analytic metrics. This assay panel content may help address gaps in ancestry-specific CFTR genotypes while providing a streamlined procedure with rapidly generated results.

Phase 1 study of MRX34, a liposomal miR-34a mimic, in patients with advanced solid tumours

BACKGROUND

In this first-in-human, Phase 1 study of a microRNA-based cancer therapy, the recommended Phase 2 dose (RP2D) of MRX34, a liposomal mimic of microRNA-34a (miR-34a), was determined and evaluated in patients with advanced solid tumours.

METHODS

Adults with various solid tumours refractory to standard treatments were enrolled in 3 + 3 dose-escalation cohorts and, following RP2D determination, expansion cohorts. MRX34, with oral dexamethasone premedication, was given intravenously daily for 5 days in 3-week cycles.

RESULTS

Common all-cause adverse events observed in 85 patients enrolled included fever (% all grade/G3: 72/4), chills (53/14), fatigue (51/9), back/neck pain (36/5), nausea (36/1) and dyspnoea (25/4). The RP2D was 70 mg/m2 for hepatocellular carcinoma (HCC) and 93 mg/m2 for non-HCC cancers. Pharmacodynamic results showed delivery of miR-34a to tumours, and dose-dependent modulation of target gene expression in white blood cells. Three patients had PRs and 16 had SD lasting ≥4 cycles (median, 19 weeks, range, 11-55).

CONCLUSION

MRX34 treatment with dexamethasone premedication demonstrated a manageable toxicity profile in most patients and some clinical activity. Although the trial was closed early due to serious immune-mediated AEs that resulted in four patient deaths, dose-dependent modulation of relevant target genes provides proof-of-concept for miRNA-based cancer therapy.

CLINICAL TRIAL REGISTRATION

NCT01829971.

Synergy between next generation EGFR tyrosine kinase inhibitors and miR-34a in the inhibition of non-small cell lung cancer

OBJECTIVES

EGFR tyrosine kinase inhibitors (TKIs) are widely used to treat NSCLC, primarily patients with activating mutations, with more limited response in wild-type disease. However, even with EGFR-mutated disease, many patients fail to respond, most who initially respond fail to respond completely, and almost all develop resistance and inevitably progress. New therapeutic options that improve these outcomes could provide substantial clinical benefit. We previously demonstrated strong synergistic effects between erlotinib and the tumor suppressor microRNA miR-34a, sensitizing NSCLC cells with primary resistance (EGFR wild-type) and restoring sensitivity in cells with acquired resistance. Here, we report results of further research combining miR-34a with newer generation EGFR-TKIs in similar experiments.

MATERIALS AND METHODS

Human NSCLC cell lines with varying degrees of primary and acquired resistance to erlotinib were assessed for sensitivity to a broad set of combined doses of miR-34a mimic and afatinib, rociletinib or osimertinib. Multiple analytical approaches were used to characterize effects on cancer cell proliferation as additive, antagonistic or synergistic.

RESULTS

Mimics of miR-34a synergized with afatinib, rociletinib or osimertinib in all EFGR-mutant cells tested. Best and consistently strong synergy was observed in cell models with acquired resistance. Synergy was also evident in most EGFR wild-type cells with miR-34a combined with rociletinib and osimertinib, but not with afatinib. The effects were observed across a broad range of dose levels and drug ratios, with maximal synergy at doses yielding high levels of inhibition beyond those possible to be induced by the single agents alone.

CONCLUSION

Combined miR-34a and EGFR-TKIs synergistically sensitize both EGFR wild-type and mutant NSCLC cells, supporting clinical investigation of these combinations as a strategy to overcome both primary and acquired resistance to EGFR-TKIs in NSCLC, possibly with an improved therapeutic index.

Abstract 4814: miRNA combination therapy: In vitro anticancer synergy between miR-34a mimic and next generation EGFR tyrosine kinase inhibitors (TKIs) in NSCLC

Background: miRNAs play a critical role in regulating key biological processes by modulating the expression of up to several hundred genes across multiple cellular pathways. miR-34a, one of the most widely studied miRNAs, is lost or expressed at reduced levels in many tumors, and normally functions as a natural tumor suppressor by down-regulating expression of >30 different oncogenes, as well as genes involved in tumor immune evasion, including PD-L1. MRX34 is a potential first-in-class liposome-encapsulated miR-34a mimic in Phase 1 study (NCT01829971) as monotherapy in patients with advanced malignancies. The ability of miR-34a to regulate the expression of key oncogenes across multiple oncogenic pathways makes MRX34 a rational candidate to combine with other anticancer therapies which are frequently subject to primary and acquired resistance in the clinic. Previous studies showed that miR-34a greatly sensitizes both EGFR wild-type and mutant NSCLC cell lines, as well as hepatocellular carcinoma cell lines, to the first generation EGFR TKI erlotinib. Here we report research combining miR-34a and the next generation EGFR TKIs afatinib (Gilotrif®) and rociletinib (CO-1686) in NSCLC cell lines.

Methods: Combination studies using single-drug ratios (∼IC50 ratio of miR-34a and TKI) and multiple ratios above and below were performed in a panel of EGFR wild-type (A549, H460, H1299, H226) and EGFR mutant (H1975, HCC827 parent and HCC827 erl res) NSCLC cell lines. Cells were transfected with miR-34a and incubated 24 hrs later with afatinib or rociletinib for 72 hrs, with cellular proliferation then determined by AlamarBlue. Synergistic, additive, or antagonistic effects were determined by combination index (CI) values (based on Loewe's concept of additivity), isobolograms, and curve-shift analyses.

Results: Strong synergy was observed between miR-34a and both TKIs in all EGFR-mutant cell lines tested (CI <0.5 at effect levels ≥50%). Synergy was also observed for miR-34a + rociletinib in most EGFR wild-type cell lines (CI <0.6 at effect levels of ∼50-80%), but not for miR-34a + afatinib. Best synergies overall were observed in EGFR-mutant cells with acquired erlotinib resistance. The effects were observed across a range of different dose levels and drug ratios, with maximal synergy providing a high level of inhibition (80%) at doses likely achievable in the clinic and well below those projected to be required for similar inhibition by the single agents alone.

Conclusions: Complementing previous results with miR-34a + erlotinib, the data demonstrate strongly synergistic anticancer effects between miR-34a and next generation EGFR TKIs in combination against a range of EGFR wild-type and mutant NSCLC cell lines. The results support clinical study of MRX34 + EGFR TKI combinations in patients with advanced NSCLC, including those with EGFR-mutant NSCLC that has progressed on EGFR TKI monotherapy.

Citation Format: Jane Zhao, Adriana Guerrero, Kevin Kelnar, Heidi J. Peltier, Andreas G. Bader. miRNA combination therapy: In vitro anticancer synergy between miR-34a mimic and next generation EGFR tyrosine kinase inhibitors (TKIs) in NSCLC. [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 4814.

Abstract B43: Quantitative PCR and in-situ-hybridization analysis to determine tissue concentration and localization of MRX34

MRX34, a liposomal microRNA (miRNA)-based therapy for cancer, has recently entered clinical trials as a potential first clinical candidate in its class. MRX34 is a mimic of naturally occurring microRNA-34 (miR-34) encapsulated in a liposomal nanoparticle formulation. Preclinical animal studies have shown that intravenous delivery of MRX34 can increase miR-34 levels in liver tumor cells more than 100-fold when analyzing whole-tissue RNA extracts by quantitative PCR (qPCR). MRX34-induced tumor regression has enhanced the survival of mice by inhibiting the growth of both hepatic and non-hepatic tumors. We have established a chromogenic in situ hybridization (CISH) method to track the cellular location of the miR-34 mimic in tissues after systemic MRX34 administration. In contrast to conventional biodistribution approaches that cannot distinguish between spatial differences in tissue accumulation, CISH in conjunction with microscopy allows the detection of the miRNA mimic on a cellular level and may provide new insights into cell-type specific accumulation. Here, we evaluated the localization and tissue concentrations of systemically delivered MRX34 in mice bearing orthotopic Huh7 tumors by CISH followed by image correlation to a formalin-fixed and paraffin-embedded tissue equivalent, and isolation-free qPCR analysis. Our results show that the CISH procedure is a reproducible and robust assay capable of over 2 logs of miR-34 detection when correlated to qPCR data from matching micro-dissected samples. Systemic MRX34 delivery leads to accumulation of miR-34 mimics in tumor cells with Cmax reached approximately 2 hrs post dosing. In addition, the CISH data reveal how biodistribution data generated from whole-tissue extracts can be biased due to minute impurities and suggests that these methods should be used in combination with CISH for an accurate assessment of tissue concentrations.

Citation Format: Desiree Martin, Kevin Kelnar, Andreas G. Bader. Quantitative PCR and in-situ-hybridization analysis to determine tissue concentration and localization of MRX34. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr B43.

PDL1 Regulation by p53 via miR-34

BACKGROUND

Although clinical studies have shown promise for targeting PD1/PDL1 signaling in non-small cell lung cancer (NSCLC), the regulation of PDL1 expression is poorly understood. Here, we show that PDL1 is regulated by p53 via miR-34.

METHODS

p53 wild-type and p53-deficient cell lines (p53(-/-) and p53(+/+) HCT116, p53-inducible H1299, and p53-knockdown H460) were used to determine if p53 regulates PDL1 via miR-34. PDL1 and miR-34a expression were analyzed in samples from patients with NSCLC and mutated p53 vs wild-type p53 tumors from The Cancer Genome Atlas for Lung Adenocarcinoma (TCGA LUAD). We confirmed that PDL1 is a direct target of miR-34 with western blotting and luciferase assays and used a p53(R172HΔ)g/+K-ras(LA1/+) syngeneic mouse model (n = 12) to deliver miR-34a-loaded liposomes (MRX34) plus radiotherapy (XRT) and assessed PDL1 expression and tumor-infiltrating lymphocytes (TILs). A two-sided t test was applied to compare the mean between different treatments.

RESULTS

We found that p53 regulates PDL1 via miR-34, which directly binds to the PDL1 3' untranslated region in models of NSCLC (fold-change luciferase activity to control group, mean for miR-34a = 0.50, SD = 0.2, P < .001; mean for miR-34b = 0.52, SD = 0.2, P = .006; and mean for miR-34c = 0.59, SD = 0.14, and P = .006). Therapeutic delivery of MRX34, currently the subject of a phase I clinical trial, promoted TILs (mean of CD8 expression percentage of control group = 22.5%, SD = 1.9%; mean of CD8 expression percentage of MRX34 = 30.1%, SD = 3.7%, P = .016, n = 4) and reduced CD8(+)PD1(+) cells in vivo (mean of CD8/PD1 expression percentage of control group = 40.2%, SD = 6.2%; mean of CD8/PD1 expression percentage of MRX34 = 20.3%, SD = 5.1%, P = .001, n = 4). Further, MRX34 plus XRT increased CD8(+) cell numbers more than either therapy alone (mean of CD8 expression percentage of MRX34 plus XRT to control group = 44.2%, SD = 8.7%, P = .004, n = 4). Finally, miR-34a delivery reduced the numbers of radiation-induced macrophages (mean of F4-80 expression percentage of control group = 52.4%, SD = 1.7%; mean of F4-80 expression percentage of MRX34 = 40.1%, SD = 3.5%, P = .008, n = 4) and T-regulatory cells.

CONCLUSIONS

We identified a novel mechanism by which tumor immune evasion is regulated by p53/miR-34/PDL1 axis. Our results suggest that delivery of miRNAs with standard therapies, such as XRT, may represent a novel therapeutic approach for lung cancer.

Abstract B57: miR-34 mimics synergize with small molecule inhibitors targeting the EGFR and Raf kinase pathways

Sorafenib (Nexavar®) and erlotinib (Tarceva®) are FDA-approved therapies for patients with hepatocellular carcinoma (HCC) and non-small cell lung cancer (NSCLC), respectively. Sorafenib is a multi-kinase inhibitor targeting the Raf/Mek/Erk pathway, and erlotinib is a tyrosine kinase inhibitor antagonizing epidermal growth factor receptor (EGFR). Due to their selective inhibitory action and observed toxicities, current treatment options for liver and lung cancer are limited and many cancers develop resistance. Naturally occurring tumor suppressor microRNAs inhibit tumor growth by regulating multiple oncogenes at once and, therefore, microRNA mimics, which are copies of the naturally occurring microRNAs, may be used in combination with the respective standard of care drugs to bring this tumor suppressor activity back into tumor cells and thereby augment drug sensitivity. Here, we investigated the relationship of a mimic of the tumor suppressor microRNA miR-34 in combination with erlotinib or sorafenib and determined the therapeutic activity of the combination in lung and liver cancer cells. Data derived from isobolograms, combination index plots and curve shift analyses indicate synergy in all cancer cell lines tested. Synergy was observed at multiple microRNA and drug ratios and at drug concentrations that induce 50% or greater cancer cell inhibition. Data from cell and animal studies will be presented.

Citation Format: Jane Zhao, Kevin Kelnar, Chris Daige, Jason Wiggins, Leslie Priddy, Terri Muenzer, Julie Tran, David Brown, Andreas G. Bader. miR-34 mimics synergize with small molecule inhibitors targeting the EGFR and Raf kinase pathways. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B57.

In-depth analysis shows synergy between erlotinib and miR-34a

Tyrosine kinase inhibitors directed against epidermal growth factor receptor (EGFR-TKI), such as erlotinib, are effective in a limited fraction of non-small cell lung cancer (NSCLC). However, the majority of NSCLC and other cancer types remain resistant. Therapeutic miRNA mimics modeled after endogenous tumor suppressor miRNAs inhibit tumor growth by repressing multiple oncogenes at once and, therefore, may be used to augment drug sensitivity. Here, we investigated the relationship of miR-34a and erlotinib and determined the therapeutic activity of the combination in NSCLC cells with primary and acquired erlotinib resistance. The drug combination was also tested in a panel of hepatocellular carcinoma cells (HCC), a cancer type known to be refractory to erlotinib. Using multiple analytical approaches, drug-induced inhibition of cancer cell proliferation was determined to reveal additive, antagonistic or synergistic effects. Our data show a strong synergistic interaction between erlotinib and miR-34a mimics in all cancer cells tested. Synergy was observed across a range of different dose levels and drug ratios, reducing IC50 dose requirements for erlotinib and miR-34a by up to 46-fold and 13-fold, respectively. Maximal synergy was detected at dosages that provide a high level of cancer cell inhibition beyond the one that is induced by the single agents alone and, thus, is of clinical relevance. The data suggest that a majority of NSCLC and other cancers previously not suited for erlotinib may prove sensitive to the drug when used in combination with a miR-34a-based therapy.

Quantification of therapeutic miRNA mimics in whole blood from nonhuman primates

MRX34, a microRNA (miRNA)-based therapy for cancer, has recently entered clinical trials as the first clinical candidate in its class. It is a liposomal nanoparticle loaded with a synthetic mimic of the tumor suppressor miRNA miR-34a as the active pharmaceutical ingredient. To understand the pharmacokinetic properties of the drug and to rationalize an optimal dosing regimen in the clinic, a method is needed to quantitatively detect the miRNA mimic. Here, we report the development and qualification of a quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay in support of pharmacokinetic and toxicokinetic assessments in the nonhuman primate. Detection and quantification were performed on total ribonucleic acid (RNA) isolated from whole blood. The qualified range of the standard curve spans 6 orders of magnitude from 2.5 × 10(-7) to 2.5 × 10(-1) ng per reverse transcription (RT) reaction, corresponding to an estimated blood concentration from 6.2 × 10(-5) to 6.2 × 10(1) ng/mL. Our results demonstrate that endogenous as well as the exogenous miR-34a can be accurately and precisely quantified. The assay was used to establish the pharmacokinetic profile of MRX34, showing a favorable residence time and exposure of the miRNA mimic in whole blood from nonhuman primates.

Abstract LB-250: Development of a miR34-based cancer therapy

miR-34 is a tumor suppressor miRNA that functions within the p53 pathway and regulates the expression of more than twenty oncogenes, including MET, MYC, WNT, and MYB. We have created a mimic of miR-34 called miR-Rx34 that induces cell cycle arrest, senescence, and apoptosis in cancer cells. Transient transfection of miR-Rx34 significantly reduces the proliferation of cancer cells derived from patients with liver, lung, breast, colon, and pancreatic cancers as well as melanoma, lymphoma, and multiple myeloma. miR-Rx34 has been encapsulated in an anionic liposome to produce a particle called MRX34 that has a diameter of ~120 nm. Intravenous injections of MRX34 causes dose-dependent increases in miR-34 levels in liver tumor, lung tumor, liver, lung, spleen, and other highly vascularized tissues in mice without inducing an immune response. Systemic delivery of MRX34 causes complete tumor regression in two orthotopic models of liver cancer. The exceptional potency of MRX34 likely results from its capacity to stimulate the p53 pathway and down-regulate genes in the wnt/B-catenin, MET, MAPK, and VegF pathways in liver tumors. The no adverse effects level observed for MRX34 in IND-enabling toxicology studies in monkeys and rats are 10-100-fold higher than the doses that produce complete tumor regression in mice, suggesting that the drug candidate will have a broad therapeutic window in cancer patients. Clinical studies with MRX34 that are expected to begin in early 2013 will provide the first measure of the therapeutic potential of a tumor suppressor miRNA.

Citation Format: Chris Daige, Jason Wiggins, Leslie Priddy, Kevin Kelnar, Jane Zhao, Andreas Bader, David Brown. Development of a miR34-based cancer therapy. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-250. doi:10.1158/1538-7445.AM2013-LB-250

Distinct microRNA expression profiles in prostate cancer stem/progenitor cells and tumor-suppressive functions of let-7

MiRNAs regulate cancer cells, but their potential effects on cancer stem/progenitor cells are still being explored. In this study, we used quantitative real-time-PCR to define miRNA expression patterns in various stem/progenitor cell populations in prostate cancer, including CD44+, CD133+, integrin α2β1+, and side population cells. We identified distinct and common patterns in these different tumorigenic cell subsets. Multiple tumor-suppressive miRNAs were downregulated coordinately in several prostate cancer stem/progenitor cell populations, namely, miR-34a, let-7b, miR-106a, and miR-141, whereas miR-301 and miR-452 were commonly overexpressed. The let-7 overexpression inhibited prostate cancer cell proliferation and clonal expansion in vitro and tumor regeneration in vivo. In addition, let-7 and miR-34a exerted differential inhibitory effects in prostate cancer cells, with miR-34a inducing G1 phase cell-cycle arrest accompanied by cell senescence and let-7 inducing G2-M phase cell-cycle arrest without senescence. Taken together, our findings define distinct miRNA expression patterns that coordinately regulate the tumorigenicity of prostate cancer cells.

Abstract 132: MicroRNA expression profiling in tumorigenic prostate cancer cells and tumor suppressive functions of let-7

Most human tumors contain a small population of cells with stem cell properties, called cancer stem cells (CSCs), which are believed to be responsible for tumor initiation, metastasis, resistance to clinical therapy and relapse. It's crucial to understand the regulatory mechanisms unique to CSCs, so that we may design CSC-specific therapeutics. Recent discoveries of microRNA (miRNA) have provided a new avenue in understanding the regulatory mechanisms of cancer. In our previous studies, we have showed miR-34a under-expression in prostate CSC populations, and its critical role in negatively regulating prostate tumor development and metastasis. However, detailed profiling process was not presented due to space limit. Here, we presented the detailed miRNA expression profiling process and results, together with functional studies of let-7. By quantitative RT-PCR, we dicovered miRNA expressions profiles specific to the prostate cancer (PCa) stem/progenitor populations, i.e., CD44, CD133, α2β1 and side population from thee prostate xenograft models (LAPC9, LAPC4, and Du145). Functional annotation of let-7, one of the commonly under-expressed miRNAs in PCa stem/progenitor populations, showed that over-expression of let-7 inhibited proliferation and clonal expansion of prostate cancer cells in vitro. In addition, over-expression of let-7 by a lentiviral vector suppressed tumor development in mice. To further understand how these miRNAs are differentially expressed in the stem/progenitor population of PCa cells, we took miR-34a as an example, and explored p53 and c-Myc regulation in the CD44+ and CD44- populations, but failed to draw a connection.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 132. doi:1538-7445.AM2012-132

Abstract 5636: Preclinical data of a microRNA-based therapy for hepatocellular carcinoma

MicroRNA (miRNA) mimics have emerged as a novel class of therapeutics with promising anti-oncogenic activity. These mimics are modeled after naturally occurring tumor suppressor miRNAs that are ubiquitously expressed in normal cells but frequently show a loss-of-function in human malignancies. The premise for the strong inhibitory activity is based on the observation these endogenous miRNAs control multiple oncogenic pathways commonly deregulated in cancer. Therefore, “miRNA replacement therapy” acts in accordance with our current understanding of cancer as a pathway disease that can only be successfully treated when intervening with multiple cancer pathways. We have identified a series of key tumor suppressor miRNAs, including miR-34, and validated the therapeutic potential in cultured cancer cells and mouse models of cancer. The translation of this potential into future medicines, however, was hampered by the lack of a robust clinically relevant delivery system. To facilitate a rapid route to the clinic, we have screened a panel of external delivery systems that are in pre-clinical development or have already reached the clinic featuring another oligonucleotide. Here, we present the pharmacologic and pharmacodynamic parameters of miRNA mimics complexed in ionizable NOV340 liposomes (SMARTICLEs, Marina Biotech, Bothell, WA) in an orthotopic tumor model of hepatocellular carcinoma. Treatment of mice carrying existing tumors mimics led to significant tumor regression, prolonged survival and lacked notable drug-related side effects. Some of the mice appeared to be tumor-free. The data demonstrate the therapeutic utility of the NOV340/miRNA formulation and support the initiation of IND-enabling studies.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5636. doi:1538-7445.AM2012-5636

Abstract C142: The development of a miRNA-based therapeutic candidate for hepatocellular carcinoma

Tumor suppressor miRNAs function by regulating multiple cancer-related genes and pathways. The tumor suppressor miRNAs miR-34, let-7, miR-16, miR-26, and miR-145 have proven to be effective in inhibiting tumor growth in mouse models of cancer. Based upon the availability of systemic delivery technologies that provide significant accumulation of siRNAs in liver tumors, we chose to identify tumor suppressor miRNAs that might be used as therapies for hepatocellular carcinoma (HCC). Cell culture studies with mimics of eight tumor suppressor miRNAs revealed five with the capacity to significantly inhibit the proliferation of multiple HCC cell lines. The five miRNA mimics were complexed with several lipid formulations and injected into NOD/SCID mice with orthotopically grown Hep3B liver cancer xenografts. All five miRNAs significantly inhibited the growth of the liver tumors compared to animals treated with formulated negative control miRNAs. Intriguingly, mimics of three of the tumor suppressor miRNAs eliminated detectable tumors. Preliminary studies indicate that the formulated miRNAs are neither toxic nor immunostimulatory. The formulated miRNAs are currently being evaluated for therapeutic activity in mouse models of other cancers and a development program has been initiated in anticipation of creating candidates for cancer therapy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr C142.

Abstract 1166: Inhibition of tumor growth in mouse models of cancer by systemic delivery of tumor suppressor miRNAs

Tumor suppressor miRNAs represent an intriguing new class of biomolecules that might be developed into therapeutic candidates for cancer. Based upon its involvement in the p53 pathway and its capacity to regulate cell cycle and apoptosis via multiple oncogenic pathways, miR-34 might be the most intriguing of the tumor suppressor miRNAs. We have developed mimics of the miR-34 tumor suppressor that have been tested for efficacy using xenograft and transgenic mouse models of cancer. When complexed with an effective delivery agent, tail-vein injected miR-34 mimics have proven capable of inhibiting the growth and metastasis of mature tumors. When delivered systemically to BalbC mice, the same complexed miR-34 mimics fail to incease the serum levels of liver, kidney, and heart toxicity markers. Systemically delivered miR-34 mimics also failed to induce cytokines in mice. The development of miR-34 mimics with enhanced pharmacokinetic profiles and a systemic delivery formulation that can be manufactured under cGMP conditions are underway. Preclinical efficacy, PK/PD, and rodent safety data will be presented.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1166. doi:10.1158/1538-7445.AM2011-1166

Development of a lung cancer therapeutic based on the tumor suppressor microRNA-34

Tumor suppressor microRNAs (miRNA) provide a new opportunity to treat cancer. This approach, "miRNA replacement therapy," is based on the concept that the reintroduction of miRNAs depleted in cancer cells reactivates cellular pathways that drive a therapeutic response. Here, we describe the development of a therapeutic formulation using chemically synthesized miR-34a and a lipid-based delivery vehicle that blocks tumor growth in mouse models of non-small-cell lung cancer. This formulation is effective when administered locally or systemically. The antioncogenic effects are accompanied by an accumulation of miR-34a in the tumor tissue and downregulation of direct miR-34a targets. Intravenous delivery of formulated miR-34a does not induce an elevation of cytokines or liver and kidney enzymes in serum, suggesting that the formulation is well tolerated and does not induce an immune response. The data provide proof of concept for the systemic delivery of a synthetic tumor suppressor mimic, obviating obstacles associated with viral-based miRNA delivery and facilitating a rapid route for miRNA replacement therapy into the clinic.

Identification of miRNA changes in Alzheimer's disease brain and CSF yields putative biomarkers and insights into disease pathways

MicroRNAs have essential functional roles in brain development and neuronal specification but their roles in neurodegenerative diseases such as Alzheimer's disease (AD) is unknown. Using a sensitive qRT-PCR platform we identified regional and stage-specific deregulation of miRNA expression in AD patient brains. We used experimental validation in addition to literature to reveal how the deregulated brain microRNAs are biomarkers for known and novel pathways in AD pathogenesis related to amyloid processing, neurogenesis, insulin resistance, and innate immunity. We additionally recovered miRNAs from cerebrospinal fluid and discovered AD-specific miRNA changes consistent with their role as potential biomarkers of disease.

Genome-scale microRNA and small interfering RNA screens identify small RNA modulators of TRAIL-induced apoptosis pathway

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) binds to death receptors 4/5 and selectively induces caspase-dependent apoptosis. The RNA interference screening approach has led to the discovery and characterization of several TRAIL pathway components in human cells. Here, libraries of synthetic small interfering RNA (siRNA) and microRNAs (miRNA) were used to probe the TRAIL pathway. In addition to known genes, siRNAs targeting CDK4, PTGS1, ALG2, CLCN3, IRAK4, and MAP3K8 altered TRAIL-induced caspase-3 activation responses. Introduction of the miRNAs let-7c, mir-10a, mir-144, mir-150, mir-155, and mir-193 also affected the activation of the caspase cascade. Putative targets of these endogenous miRNAs included genes encoding death receptors, caspases, and other apoptosis-related genes. Among the novel genes revealed in the screen, CDK4 was selected for further characterization. CDK4 was the only member of the cyclin-dependent kinase gene family that bore a unique function in apoptotic signal transduction.

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.

Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification

The RNA-dependent protein kinase (PKR) is activated by binding to double-stranded RNA (dsRNA). Activation of PKR by short-interfering RNAs (siRNAs) and stimulation of the innate immune response has been suggested to explain certain off-target effects in some RNA interference experiments. Here we show that PKR's kinase activity is stimulated in vitro 3- to 5-fold by siRNA duplexes with 19 bp and 2 nt 3′-overhangs, whereas the maximum activation observed for poly(I)•poly(C) was 17-fold over background under the same conditions. Directed hydroxyl radical cleavage experiments indicated that siRNA duplexes have at least four different binding sites for PKR's dsRNA binding motifs (dsRBMs). The location of these binding sites suggested specific nucleotide positions in the siRNA sense strand that could be modified with a corresponding loss of PKR binding. Modification at these sites with N²-benzyl-2′-deoxyguanosine (BndG) blocked interaction with PKR's dsRBMs and inhibited activation of PKR by the siRNA. Importantly, modification of an siRNA duplex that greatly reduced PKR activation did not prevent the duplex from lowering mRNA levels of a targeted message by RNA interference in HeLa cells. Thus, these studies demonstrate that specific positions in an siRNA can be rationally modified to prevent interaction with components of cellular dsRNA-regulated pathways.

High-throughput RNAi screening in vitro: from cell lines to primary cells

Small interfering RNAs (siRNAs) are being used to induce sequence-specific gene silencing in cultured cells to study mammalian gene function. Libraries of siRNAs targeting entire human gene classes can be used to identify genes with specific cellular functions. Here we describe high-throughput siRNA delivery methods to facilitate siRNA library screening experiments with both immortalized and primary cells. We adapted chemical reverse transfection for immortalized adherent cell lines in a 96-well format. The method is fast, robust, and exceptionally effective for many cell types. For primary cells and immortalized cells that are recalcitrant to lipofection-based methods, we developed electropermeabilization (electroporation) conditions that facilitate siRNA delivery to a broad range of cell types, including primary human T-cells, hMSC, NHA, NDHF-Neo, HUVEC, DI TNC1, RPTEC, PC12, and K562 cells. To enable high-throughput electropermeabilization of primary cells, we developed a novel 96-well electroporation device that provides highly efficient and reproducible delivery of siRNAs. The combination of high-throughput chemical reverse transfection and electroporation makes it possible to deliver libraries of siRNAs to virtually any cell type, enabling gene function analysis and discovery on a genome scale.

A microsatellite genetic linkage map for Xiphophorus

Interspecies hybrids between distinct species of the genus Xiphophorus are often used in varied research investigations to identify genomic regions associated with the inheritance of complex traits. There are 24 described Xiphophorus species and a greater number of pedigreed strains; thus, the number of potential interspecies hybrid cross combinations is quite large. Previously, select Xiphophorus experimental crosses have been shown to exhibit differing characteristics between parental species and among the hybrid fishes derived from crossing them, such as widely differing susceptibilities to chemical or physical agents. For instance, genomic regions harboring tumor suppressor and oncogenes have been identified via linkage association of these loci with a small set of established genetic markers. The power of this experimental strategy is related to the number of genetic markers available in the Xiphophorus interspecies cross of interest. Thus, we have undertaken the task of expanding the suite of easily scored markers by characterization of Xiphophorus microsatellite sequences. Using a cross between Xiphophorus maculatus and X. andersi, we report a linkage map predominantly composed of microsatellite markers. All 24 acrocentric chromosome sets of Xiphophorus are represented in the assembled linkage map with an average intergenomic distance of 7.5 cM. Since both male and female F1 hybrids were used to produce backcross progeny, these recombination rates were compared between "male" and "female" maps. Although several genomic regions exhibit differences in map length, male- and female-derived maps are similar. Thus Xiphophorus, in contrast to zebrafish, Danio rerio, and several other vertebrate species, does not show sex-specific differences in recombination. The microsatellite markers we report can be easily adapted to any Xiphophorus interspecies and some intraspecies crosses, and thus provide a means to directly compare results derived from independent experiments.