MicroRNA Biomarkers in Canine Diffuse Large B-Cell Lymphoma

Lymphoma is among the most common cancer in dogs. Diffuse large B-cell lymphoma (DLBCL) is the predominant type, accounting for up to half of all cases. Definitive diagnosis of DLBCL relies on cytologic evaluation with immunophenotyping, or histopathology and immunohistochemistry when needed. A rapid and specific molecular test aiding in the diagnosis could be beneficial. Noncoding microRNAs (miRNAs) are regulators of gene expression involved in a variety of cellular processes, including cell differentiation, cell cycle progression, and apoptosis. Not surprisingly, miRNA expression is aberrant in diseases such as cancers. Their high stability and abundance in tissues make them promising biomarkers for diagnosing and monitoring diseases. This study aimed to identify miRNA signatures of DLBCL to develop ancillary molecular diagnostic tools. miRNA was isolated from formalin-fixed, paraffin-embedded lymph node tissue from 22 DLBCL and 14 nonneoplastic controls. Relative gene expression of 8 tumor-regulating miRNAs was achieved by RT-qPCR (reverse transcriptase quantitative polymerase chain reaction). The results showed downregulation of the let-7 family of miRNAs and miR-155, whereas miR-34a was upregulated in DLBCL compared to the controls. We demonstrated that the combination of expression levels of miR-34a and let-7f or of let-7b and let-7f achieved 100% differentiation between DLBCL and controls. Furthermore, let-7f alone discriminated DLBCL from nonneoplastic tissue in 97% of cases. Our results represent one step forward in search of a rapid and accurate ancillary diagnostic test for DLBCL in dogs.

InVivo Cancer-Based Functional Genomics

Pinpointing the underlying mechanisms that drive tumorigenesis in human patients is a prerequisite for identifying suitable therapeutic targets for precision medicine. In contrast to cell culture systems, mouse models are highly favored for evaluating tumor progression and therapeutic response in a more realistic in vivo context. The past decade has witnessed a dramatic increase in the number of functional genomic studies using diverse mouse models, including in vivo clustered regularly interspaced short palindromic repeats (CRISPR) and RNA interference (RNAi) screens, and these have provided a wealth of knowledge addressing multiple essential questions in translational cancer research. We compare the multiple mouse systems and genomic tools that are commonly used for in vivo screens to illustrate their strengths and limitations. Crucial components of screen design and data analysis are also discussed.

Identification and validation of microRNAs that synergize with miR-34a - a basis for combinatorial microRNA therapeutics

Efforts to search for better treatment options for cancer have been a priority, and due to these efforts, new alternative therapies have emerged. For instance, clinically relevant tumor-suppressive microRNAs that target key oncogenic drivers have been identified as potential anti-cancer therapeutics. MicroRNAs are small non-coding RNAs that negatively regulate gene expression at the posttranscriptional level. Aberrant microRNA expression, through misexpression of microRNA target genes, can have profound cellular effects leading to a variety of diseases, including cancer. While altered microRNA expression contributes to a cancerous state, restoration of microRNA expression has therapeutic benefits. For example, ectopic expression of microRNA-34a (miR-34a), a tumor suppressor gene that is a direct transcriptional target of p53 and thus is reduced in p53 mutant tumors, has clear effects on cell proliferation and survival in murine models of cancer. MicroRNA replacement therapies have recently been tested in combination with other agents, including other microRNAs, to simultaneously target multiple pathways to improve the therapeutic response. Thus, we reasoned that other microRNA combinations could collaborate to further improve treatment. To test this hypothesis miR-34a was used in an unbiased cell-based approach to identify combinatorial microRNA pairs with enhanced efficacy over miR-34a alone. This approach identified a subset of microRNAs that was able to enhance the miR-34a antiproliferative activity. These microRNA combinatorial therapeutics could offer superior tumor-suppressive abilities to suppress oncogenic properties compared to a monotherapeutic approach. Collectively these studies aim to address an unmet need of identifying, characterizing, and therapeutically targeting microRNAs for the treatment of cancer.

MicroRNA-223 Suppresses the Canonical NF-κB Pathway in Basal Keratinocytes to Dampen Neutrophilic Inflammation

MicroRNA-223 is known as a myeloid-enriched anti-inflammatory microRNA that is dysregulated in numerous inflammatory conditions. Here, we report that neutrophilic inflammation (wound response) is augmented in miR-223-deficient zebrafish, due primarily to elevated activation of the canonical nuclear factor κB (NF-κB) pathway. NF-κB over-activation is restricted to the basal layer of the surface epithelium, although miR-223 is detected throughout the epithelium and in phagocytes. Not only phagocytes but also epithelial cells are involved in miR-223-mediated regulation of neutrophils' wound response and NF-κB activation. Cul1a/b, Traf6, and Tab1 are identified as direct targets of miR-223, and their levels rise in injured epithelium lacking miR-223. In addition, miR-223 is expressed in cultured human bronchial epithelial cells, where it also downregulates NF-κB signaling. Together, this direct connection between miR-223 and the canonical NF-κB pathway provides a mechanistic understanding of the multifaceted role of miR-223 and highlights the relevance of epithelial cells in dampening neutrophil activation.

Enhancing MicroRNA Activity through Increased Endosomal Release Mediated by Nigericin

The therapeutic promise of small-RNA therapeutics is limited, not only by the lack of delivery vehicles, but also by the inability of the small RNAs to reach intracellular compartments where they can be biologically active. We previously reported successful delivery of functionally active miRNAs via receptor-mediated endocytosis. This type of targeted therapy still faces a major challenge in the delivery field: endosomal sequestration. Here, a new method has been developed to promote endosomal escape of delivered miRNA. The strategy relies on the difference in solute contents between nascent endosomes and the cytoplasm; early endosomes are rich in sodium ions, whereas the intracellular fluid is rich is potassium ions. Exploiting this difference through favoring the influx of potassium into the endosomes without the exchange of osmotically active sodium, results in an osmotic differential leading to the endosomes swelling and bursting. One molecule that is able to exchange potassium for an osmotically inactive hydrogen ion is the ionophore nigericin. Through generating an intramolecular miRNA delivery vehicle, containing a ligand, in this case folate and nigericin, we enabled the escape of folate-RNA conjugates from their entrapping endosomes into the cytoplasm where they bound the RNA-induced silencing complex and activated the RNAi response.

Abstract 2349: Identifying genes and microRNAs that when lost, can drive neoplastic transformation of non-cancerous lung cells

Despite the fact that the death rate continues to drop over the last decades, lung cancer is still by far the leading cause of cancer mortalities due to lack of highly accurate prediction method and effective targeted therapeutics. Thus, this calls for identification of novel biomarkers and therapeutic targets, particularly those targeting critical genes that drive lung cancer development and malignancy. KRAS and TP53 are two of the most commonly mutated genes in non-small cell lung cancer (NSCLC) which represents 85% of all cases in lung cancer. However, aberrant expressions of many other genes that act as drivers of lung cancer are yet unidentified. Particularly, microRNAs which are genome-encoded small RNA molecules are globally downregulated in many cancers, and disrupting microRNA biogenesis has been shown to promote tumor formation. We utilize the power of the CRISPR-Cas9 gene knockout system to screen for critical tumor suppressor genes and microRNAs in the human and mouse genomes that when lost, can drive neoplastic transformation of lung cells. Two non-cancerous mammalian lung model systems are used for this study. (1) The human bronchial epithelial cells that stably express KRAS G12V and TP53-targeting shRNA (HBEC-KP) are used as the baseline in the first approach. Importantly, the HBEC-KP cells are anchorage dependent and incapable of forming tumor in in vivo. We have transiently transfected HBEC-KP tdTomato-expressing cells with Cas9 and transduced the cells with lenti-sgRNA human library (A). Cells were either passaged in two-dimensions for over two-months or were selected for growth in soft agar assays. Resulting cells were harvested to identify sgRNAs enriched in each of the individual condition. Several known tumor suppressor genes and microRNAs (such as BRCA2, let-7a-3, miR-34a) are present among top hits, while MYC and TP53 are highly depleted, which suggests the validity of this data. Top hits will be selected and validated. (2) The second model being used is the KrasLSL-G12D mouse model. Genetic recombination induces lung hyperplasia in these mice, which will serve as the baseline to identify gene and microRNA knockouts that drive advanced tumor progression. The KrasLSL-G12D; RosaLSL-Cas9/LSL-Cas9 (KC) mice have been generated, and will be validated for Cre-induced Cas9 stable expression. KC mice will be intratracheally injected with the mixture of adeno-Cre and lenti-sgRNAs, and eventually sgRNAs that are highly enriched in individual tumors that develop will be identified through deep sequencing and bioinformatic analysis, and targeted genes and microRNAs downregulated in the tumors will be validated in functional assays and for loss in human NSCLC tumor samples.

Citation Format: Chennan Li, Sagar M. Utturkar, Andrea L. Kasinski. Identifying genes and microRNAs that when lost, can drive neoplastic transformation of non-cancerous lung cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2349.

Abstract 4656: Development of an RNA-based cancer therapeutic targeting the let-7-LIN28 interaction

Based on the knowledge that microRNAs (miRNAs) are dysregulated in diseases such as cancer, various attempts have been explored to develop miRNA-based cancer therapeutics. Although many strategies have been used to restore the levels of therapeutically relevant microRNAs, clinical delivery of the processed or mature miRNA to cancer cells still remains a challenge. To overcome this challenge, innovative methods are being explored to increase the pools of tumor-suppressive miRNAs, such as enhancing miRNA biogenesis. This is especially true for the let-7 family of tumor-suppressive miRNAs, which has an additional layer of regulation over the canonical miRNA biogenesis pathway. In particular, the DROSHA and DICER cleavage steps are blocked when unprocessed let-7 is bound by the RNA-binding protein LIN28. LIN28 interacts specifically with unprocessed let-7 via a sequence-specific motif, GGAG, contained in most let-7 family members. Because previous attempts to restore mature let-7 levels through increasing let-7 pools have been quite successful at reducing tumor burden, identifying novel and clinically relevant ways to increase the level of this tumor-suppressive miRNA represents a critical need. In this study, we hypothesize that small-molecule inhibitors that disrupt the LIN28-let-7 interaction will lead to enhanced processing and increased levels of mature, tumor-suppressive let-7. Thus, an in vitro high-throughput fluorescence polarization screen has been conducted using His-tagged LIN28 and a Cy5 fluorophore-tagged let-7 RNA probe. The nine-nucleotide RNA probe was designed through in silico modeling to include the GGAG motif, which associates with LIN28 through the zinc knuckle domain of LIN28. Due to the size difference between unbound let-7 probe and LIN28-bound let-7 probe, a wide window of polarization values was achieved, resulting in a Z′ score of 0.61, indicating that the assay was robust to proceed with the screen. The screen was performed against 23,680 compounds, which consist of FDA-approved LOPAC and blood-brain barrier-permeable CNS library compounds. Eight compounds were identified as positive hits from the screen. These compounds are currently being characterized in secondary assays both in vitro and in cell culture. The significance of this research is that small-molecule inhibitors may provide novel therapeutic strategies to increase the pool of mature, tumor-suppressive let-7 in tumors with elevated LIN28.

Citation Format: Sunghyun Myoung, Sergey Savinov, Lan Chen, Gaurav Chopra, Larisa Avramova, James Welch, Bradley Loren, David Thompson, Andrea L. Kasinski. Development of an RNA-based cancer therapeutic targeting the let-7-LIN28 interaction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4656.

Abstract 3545: Identifying the effects of lung cancer exosomes on non-tumorigenic human bronchial epithelial cells

Lung cancer is the leading cause of death from cancer in most industrialized countries and many lung cancer patients remain undiagnosed until the development of locally advanced or metastatic lung cancer. Despite extensive research, universal biomarkers for the early diagnosis of lung cancer remain elusive, and therapies for treating lung cancer patients remain ineffective and unfocused. This makes the identification of new diagnostic biomarkers and therapeutic targets for the treatment of lung cancer a critical need for patients. Exosomes, nanovesicles secreted by a variety of cell types, are known to transfer bioactive molecules such as proteins and nucleic acids that induce physiological changes in recipient cells. Exosomes secreted by cancer cells have been shown to promote tumor initiation, progression, and metastasis in various cancer types, but have been understudied in lung cancer. Our study aims to identify the effects lung cancer secreted exosomes may have on non-cancerous cells of the tumor microenvironment by assessing their tumorigenic effects on normal lung epithelial cells. To that end, we treated normal lung epithelial cells with exosomes derived from a panel of human non-small lung cancer cell lines. Treated cells acquired the ability to invade and migrate. As a proxy for metastasis, cancer exosomes are also being assayed for their ability to permeabilize a monolayer of normal lung epithelial cells. Further assessing the molecules within cancer exosomes critical for promoting these oncogenic behaviors in non-tumorigenic cells could lead to the discovery of potential diagnostic biomarkers and therapeutic targets for inhibiting tumor growth in affected patients.

Citation Format: Hana Kubo, Sean E. Humphrey, Sarunya Kitdumrongthum, Feng Tian, Sarah Allen, Andrea L. Kasinski. Identifying the effects of lung cancer exosomes on non-tumorigenic human bronchial epithelial cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3545.

Abstract 2477: Exosomal RNA mediates transformation of nontumorigenic human bronchial lung epithelial cells

Exosomes are nanovesicles with a diameter between 30-150 nm. Exosomes are produced and released by all cell types into body fluids and, thus, play a major role in cell-cell communication through the transfer of proteins, lipids, and nucleic acids into recipient cells. Uptake of bioactive cargo into recipient cells can impart physiologic and biologic changes in the recipient cell. Especially in cancer, exosome released from cancer cells can reprogram cells, driving various hallmarks of cancer, such as proliferation, migration, invasion, and angiogenesis. In this study we evaluated the effects of exosomes, isolated from non-small cell lung cancer (NSCLC) cells, on nontumorigenic human bronchial epithelial cells (HBECs). Firstly, we determined that cancer cells generate more exosomes than nontumorigenic cells and that cancer cell-derived exosomes are readily taken up by nontumorigenic cells. The nontumorigenic cells exposed to NSCLC-derived exosomes gained the ability to migration and invade. In parallel, we observed that NSCLC-derived exosomes promoted changes in epithelial-to-mesenchymal gene profiles, supporting the conclusion that HBECs were becoming transformed. Exosomes were also capable of permeablizing a monolayer of human endothelial cells, suggesting that NSCLC-derived exosomes may disrupt the vasculature enhancing metastatic capabilities. Importantly, the transformative effects of the exosomes were mediated mostly by exosomal RNA. Comparing the RNA profile from a panel of cancerous exosomes to RNAs contained inside of exosomes isolated from nontumorigenic, one long noncoding RNA (lncRNA) was highly elevated. Knockout of this lncRNA greatly diminished the capability of the cancerous exosomes to promote the observed hallmarks of cancer, suggesting that a single lncRNA is responsible for the majority of the tumorigenic capacity of the exosomes. In vivo mouse modeling and patient-based evidence are currently under way to support these cell-based findings.

Citation Format: Sarunya Kitdumrongthum, Sean Humphrey, Hana Kubo, Feng Tian, Sarah Allen, Nadia Atallah, Humna Hasan, Andrea L. Kasinski. Exosomal RNA mediates transformation of nontumorigenic human bronchial lung epithelial cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2477.

FolamiRs: Ligand-targeted, vehicle-free delivery of microRNAs for the treatment of cancer

MicroRNAs are small RNAs that negatively regulate gene expression posttranscriptionally. Because changes in microRNA expression can promote or maintain disease states, microRNA-based therapeutics are being evaluated extensively. Unfortunately, the therapeutic potential of microRNA replacement is limited by deficient delivery vehicles. In this work, microRNAs are delivered in the absence of a protective vehicle. The method relies on direct attachment of microRNAs to folate (FolamiR), which mediates delivery of the conjugated microRNA into cells that overexpress the folate receptor. We show that the tumor-suppressive FolamiR, FolamiR-34a, is quickly taken up both by triple-negative breast cancer cells in vitro and in vivo and by tumors in an autochthonous model of lung cancer and slows their progression. This method delivers microRNAs directly to tumors in vivo without the use of toxic vehicles, representing an advance in the development of nontoxic, cancer-targeted therapeutics.

New Mechanism for Release of Endosomal Contents: Osmotic Lysis via Nigericin-Mediated K+/H+ Exchange

Although peptides, antibodies/antibody fragments, siRNAs, antisense DNAs, enzymes, and aptamers are all under development as possible therapeutic agents, the breadth of their applications has been severely compromised by their inability to reach intracellular targets. Thus, while macromolecules can often enter cells by receptor-mediated endocytosis, their missions frequently fail due to an inability to escape their entrapping endosomes. In this paper, we describe a general method for promoting release of any biologic material from any entrapping endosome. The strategy relies on the fact that all nascent endosomes contain extracellular (Na⁺-enriched) medium, but are surrounded by intracellular (K⁺-enriched) fluid in the cytoplasm. Osmotic swelling and rupture of endosomes will therefore be facilitated if the flow of K⁺ down its concentration gradient from the cytosol into the endosome can be facilitated without allowing downhill flow of Na⁺ from the endosome into the cytosol. While any K⁺ selective ionophore can promote the K⁺ specific influx, the ideal K⁺ ionophore will also exchange influxed K⁺ for an osmotically inactive proton (H⁺) in order to prevent buildup of an electrical potential that would rapidly halt K⁺ influx. The only ionophore that catalyzes this exchange of K⁺ for H⁺ efficiently is nigericin. We demonstrate here that ligand-targeted delivery of nigericin into endosomes that contain an otherwise impermeable fluorescent dye can augment release of the dye into the cell cytosol via swelling/bursting of the entrapping endosomes. We further show that nigericin-facilitated escape of a folate-targeted luciferase siRNA conjugate from its entrapping endosomes promotes rapid suppression of the intended luciferase reporter gene. Taken together, we propose that ionophore-catalyzed entry of K⁺ into endosomal compartments can promote the release of otherwise impermeable contents from their encapsulating endosomes.

Animal Models to Study MicroRNA Function

The discovery of the microRNAs, lin-4 and let-7 as critical mediators of normal development in Caenorhabditis elegans and their conservation throughout evolution has spearheaded research toward identifying novel roles of microRNAs in other cellular processes. To accurately elucidate these fundamental functions, especially in the context of an intact organism, various microRNA transgenic models have been generated and evaluated. Transgenic C. elegans (worms), Drosophila melanogaster (flies), Danio rerio (zebrafish), and Mus musculus (mouse) have contributed immensely toward uncovering the roles of multiple microRNAs in cellular processes such as proliferation, differentiation, and apoptosis, pathways that are severely altered in human diseases such as cancer. The simple model organisms, C. elegans, D. melanogaster, and D. rerio, do not develop cancers but have proved to be convenient systesm in microRNA research, especially in characterizing the microRNA biogenesis machinery which is often dysregulated during human tumorigenesis. The microRNA-dependent events delineated via these simple in vivo systems have been further verified in vitro, and in more complex models of cancers, such as M. musculus. The focus of this review is to provide an overview of the important contributions made in the microRNA field using model organisms. The simple model systems provided the basis for the importance of microRNAs in normal cellular physiology, while the more complex animal systems provided evidence for the role of microRNAs dysregulation in cancers. Highlights include an overview of the various strategies used to generate transgenic organisms and a review of the use of transgenic mice for evaluating preclinical efficacy of microRNA-based cancer therapeutics.

Abstract 3142: Aberrantly expressed microRNAs drive the development of acquired Erlotinib resistance in non-small cell lung cancer

Lung cancer is the leading cause of cancer-related deaths in the world. Non-small cell lung cancer (NSCLC) accounts for ~85% of the cases. NSCLC patients frequently harbor causal gene mutations. Epidermal Growth Factor Receptor (EGFR), an NSCLC causal gene, is mutated in 10-35% of NSCLC patients. Patients with EGFR activating mutation are treated with a tyrosine-kinase inhibitor, Erlotinib, specifically targeting EGFR. However, most patients develop Erlotinib resistance within a year. Although multiple mechanisms are involved in the development of Erlotinib resistance, the role of microRNAs in mediating Erlotinib resistance is largely unexplored. MicroRNAs (miRNAs) are small non-coding RNAs that regulate normal cellular physiology. In cancers, miRNAs are severely dysregulated, contributing to multiple cancer processes, including drug response. Despite the involvement of miRNAs in cancer, their direct role as drivers of drug resistance remain understudied, therefore, there is a critical need to understand the role of miRNAs in inducing Erlotinib resistance.

To this end, we propose an unbiased two-prong approach to identify the miRNAs that drive the development of Erlotinib resistance. Therefore, miRNAs are either being (i) overexpressed, or (ii) silenced in Erlotinib sensitive cells with the hypothesis that perturbed miRNA levels will drive Erlotinib resistance. Erlotinib sensitive NSCLC cell lines, EKVX and H322M were identified from the NCI-60 Developmental Therapeutics Project and their Erlotinib dose response curves were established. To perform the miRNA overexpression screen, EKVX and H322M cells stably expressing renilla and firefly luciferase genes were generated, which will be used to monitor cell number and transfection efficiency, respectively. The luciferase-expressing cells will be transfected with a library of 2,019 individually arrayed human miRNAs and cell growth in the presence of Erlotinib will be monitored. The second prong of the study will identify miRNAs, that when lost, confer Erlotinib resistance. 400-fold coverage of small guide RNA (sgRNA) library of the CRISPR-Cas9 system was transduced in Cas9 overexpressing EKVX cells, to knockout ~21,000 human encoded genes (~1800 miRNA genes). Cells are being cultured in the presence of 75% or 90% growth inhibitory concentrations (GI75 or GI90) of Erlotinib so that only cells with sgRNAs against genes critical for Erlotinib response, survive and grow due to acquired resistance. DNA from these cells will be harvested, the sgRNAs sequenced, and compared to the sgRNAs present in Erlotinib-untreated cells.

Successful completion of this project will identify miRNAs that drive Erlotinib resistance and may contribute towards development of miRNA therapeutics to enhance Erlotinib sensitivity of NSCLC tumors.

Citation Format: Arpita S. Pal, Alejandra Agredo, Andrea L. Kasinski. Aberrantly expressed microRNAs drive the development of acquired Erlotinib resistance in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3142. doi:10.1158/1538-7445.AM2017-3142

Targeting adhesion signaling in KRAS, LKB1 mutant lung adenocarcinoma

Loss of LKB1 activity is prevalent in KRAS mutant lung adenocarcinoma and promotes aggressive and treatment-resistant tumors. Previous studies have shown that LKB1 is a negative regulator of the focal adhesion kinase (FAK), but in vivo studies testing the efficacy of FAK inhibition in LKB1 mutant cancers are lacking. Here, we took a pharmacologic approach to show that FAK inhibition is an effective early-treatment strategy for this high-risk molecular subtype. We established a lenti-Cre-induced Kras and Lkb1 mutant genetically engineered mouse model (KL_Lenti) that develops 100% lung adenocarcinoma and showed that high spatiotemporal FAK activation occurs in collective invasive cells that are surrounded by high levels of collagen. Modeling invasion in 3D, loss of Lkb1, but not p53, was sufficient to drive collective invasion and collagen alignment that was highly sensitive to FAK inhibition. Treatment of early, stage-matched KL_Lenti tumors with FAK inhibitor monotherapy resulted in a striking effect on tumor progression, invasion, and tumor-associated collagen. Chronic treatment extended survival and impeded local lymph node spread. Lastly, we identified focally upregulated FAK and collagen-associated collective invasion in KRAS and LKB1 comutated human lung adenocarcinoma patients. Our results suggest that patients with LKB1 mutant tumors should be stratified for early treatment with FAK inhibitors.

Sulforhodamine B (SRB) Assay in Cell Culture to Investigate Cell Proliferation

The SRB assay has been used since its development in 1990 (Skehan et al., 1990) to inexpensively conduct various screening assays to investigate cytotoxicity in cell based studies (Vichai and Kirtikara, 2006). This method relies on the property of SRB, which binds stoichiometrically to proteins under mild acidic conditions and then can be extracted using basic conditions; thus, the amount of bound dye can be used as a proxy for cell mass, which can then be extrapolated to measure cell proliferation. The protocol can be divided into four main steps: preparation of treatment, incubation of cells with treatment of choice, cell fixation and SRB staining, and absorbance measurement. This assay is limited to manual or semiautomatic screening, and can be used in an efficient and sensitive manner to test chemotherapeutic drugs or small molecules in adherent cells. It also has applications in evaluating the effects of gene expression modulation (knockdown, gene expression upregulation), as well as to study the effects of miRNA replacement on cell proliferation (Kasinski et al., 2015).

MicroRNAs in Cancer: A Historical Perspective on the Path from Discovery to Therapy

Recent progress in microRNA (miRNA) therapeutics has been strongly dependent on multiple seminal discoveries in the area of miRNA biology during the past two decades. In this review, we focus on the historical discoveries that collectively led to transitioning miRNAs into the clinic. We highlight the pivotal studies that identified the first miRNAs in Caenorhabditis elegans to the more recent reports that have fueled the quest to understand the use of miRNAs as markers for cancer diagnosis and prognosis. In addition, we provide insights as to how unraveling basic miRNA biology has provided a solid foundation for advancing miRNAs, such as miR-34a, therapeutically. We conclude with a brief examination of the current challenges that still need to be addressed to accelerate the path of miRNAs to the clinic: including delivery vehicles, miRNA- and delivery-associated toxicity, dosage, and off target effects.

RNA-guided CRISPR-Cas technologies for genome-scale investigation of disease processes

From its discovery as an adaptive bacterial and archaea immune system, the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system has quickly been developed into a powerful and groundbreaking programmable nuclease technology for the global and precise editing of the genome in cells. This system allows for comprehensive unbiased functional studies and is already advancing the field by revealing genes that have previously unknown roles in disease processes. In this review, we examine and compare recently developed CRISPR-Cas platforms for global genome editing and examine the advancements these platforms have made in guide RNA design, guide RNA/Cas9 interaction, on-target specificity, and target sequence selection. We also explore some of the exciting therapeutic potentials of the CRISPR-Cas technology as well as some of the innovative new uses of this technology beyond genome editing.

Opportunities to integrate new approaches in genetic toxicology: an ILSI-HESI workshop report

Genetic toxicity tests currently used to identify and characterize potential human mutagens and carcinogens rely on measurements of primary DNA damage, gene mutation, and chromosome damage in vitro and in rodents. The International Life Sciences Institute Health and Environmental Sciences Institute (ILSI-HESI) Committee on the Relevance and Follow-up of Positive Results in In Vitro Genetic Toxicity Testing held an April 2012 Workshop in Washington, DC, to consider the impact of new understanding of biology and new technologies on the identification and characterization of genotoxic substances, and to identify new approaches to inform more accurate human risk assessment for genetic and carcinogenic effects. Workshop organizers and speakers were from industry, academe, and government. The Workshop focused on biological effects and technologies that would potentially yield the most useful information for evaluating human risk of genetic damage. Also addressed was the impact that improved understanding of biology and availability of new techniques might have on genetic toxicology practices. Workshop topics included (1) alternative experimental models to improve genetic toxicity testing, (2) Biomarkers of epigenetic changes and their applicability to genetic toxicology, and (3) new technologies and approaches. The ability of these new tests and technologies to be developed into tests to identify and characterize genotoxic agents; to serve as a bridge between in vitro and in vivo rodent, or preferably human, data; or to be used to provide dose response information for quantitative risk assessment was also addressed. A summary of the workshop and links to the scientific presentations are provided.

Generation of Mouse Lung Epithelial Cells

Although in vivo models are excellent for assessing various facets of whole organism physiology, pathology, and overall response to treatments, evaluating basic cellular functions, and molecular events in mammalian model systems is challenging. It is therefore advantageous to perform these studies in a refined and less costly setting. One approach involves utilizing cells derived from the model under evaluation. The approach to generate such cells varies based on the cell of origin and often the genetics of the cell. Here we describe the steps involved in generating epithelial cells from the lungs of Kras^LSL-G12D/+; p53^LSL-R172/+ mice (Kasinski and Slack, 2012). These mice develop aggressive lung adenocarcinoma following cre-recombinase dependent removal of a stop cassette in the transgenes and subsequent expression of Kra^-G12D and p53^R172 . While this protocol may be useful for the generation of epithelial lines from other genetic backgrounds, it should be noted that the Kras; p53 cell line generated here is capable of proliferating in culture without any additional genetic manipulation that is often needed for less aggressive backgrounds.

miRNA-34 prevents cancer initiation and progression in a therapeutically resistant K-ras and p53-induced mouse model of lung adenocarcinoma

Lung cancer is the leading cause of cancer deaths worldwide, and current therapies fail to treat this disease in the vast majority of cases. The RAS and p53 pathways are two of the most frequently altered pathways in lung cancers, with such alterations resulting in loss of responsiveness to current therapies and decreased patient survival. The microRNA-34 (mir-34) gene family members are downstream transcriptional targets of p53, and miR-34 expression is reduced in p53 mutant tumors; thus, we hypothesized that treating mutant Kras;p53 tumors with miR-34 would represent a powerful new therapeutic to suppress lung tumorigenesis. To this end we examined the therapeutically resistant Kras(LSL-G12D)(/+);Trp53(LSL-R172H)(/+) mouse lung cancer model. We characterized tumor progression in these mice following lung-specific transgene activation and found tumors as early as 10 weeks postactivation, and severe lung inflammation by 22 weeks. Tumors harvested from these lungs have elevated levels of oncogenic miRNAs, miR-21 and miR-155; are deficient for p53-regulated miRNAs; and have heightened expression of miR-34 target genes, such as Met and Bcl-2. In the presence of exogenous miR-34, epithelial cells derived from these tumors show reduced proliferation and invasion. In vivo treatment with miR-34a prevented tumor formation and progression in Kras(LSL-G12D)(/+);Trp53(LSL-R172H)(/+) mice. Animals infected with mir-34a-expressing lentivirus at the same time as transgene activation had little to no evidence of tumorigenesis, and lentivirus-induced miR-34a also prevented further progression of preformed tumors. These data support the use of miR-34 as a lung tumor-preventative and tumor-static agent.

Abstract 2950: miR-34 prevents in vivo lung tumor initiation and progression in the therapeutically resistant Kras;p53 mouse model

Lung cancer represents the leading cause of cancers deaths in men and women worldwide, and current therapies fail to treat this disease in the overwhelming majority of cases. The RAS and p53 pathways are two of the most frequently genetically modified pathways in lung cancers. Alterations in both result in loss of responsiveness to current therapies leading to decreased overall patient survival. Because the microRNA, mir-34 is a downstream transcriptional target of p53, which is reduced in its expression in p53 null tumors, we hypothesized that targeting Kras;p53 tumors with miR-34 would represent a novel yet powerful therapeutic to suppress lung tumorigenesis. To this end we have made use of the therapeutically resistant KrasLSL-G12D/+;p53LSL-R172H/+ mouse model of lung cancer. In this work we characterized the tumor progression in these mice following transgene activation specifically in the lung through intratracheal administration of adenoviral particles expressing cre recombinase. We note that adenocarcinomas are evident as early as 10 weeks following cre-recombination with severe lung inflammation presenting at 22 weeks. Epithelial cells from these tumors were harvested and cultured in vitro where they remain propagating, currently at passage 45. All three lines generated support growth in soft agar assays and are invasive based on transwell migration assays. Because of the pro-apoptotic effects of miR-34, we transduced the cells with miR-34-expressing lentivirus. Transduced cells responded with reduced proliferation and decreased migration. Based on these promising results we began two series of in vivo experiments. We first assessed the contribution of miR-34 to prevent tumor formation in KrasLSL-G12D/+;p53LSL-R172H/+ mice. Animals that were treated with miR-34 at the same time as cre-induced recombination of transgenes show little to no evidence of tumorigenesis at 19 weeks, while control animals had multiple nodules that represented ∼8% of the total lung area. The second series of in vivo experiments evaluated the ability of miR-34 to act as a treatment in pre-formed tumors. While miR-34 was unable to reduce the preformed tumors in these animals it was able to prevent further tumor growth. These data support the use of miR-34 as a tumor preventive mechanism and suggest that miR-34 may be useful in sensitizing tumors to other conventional therapeutics.

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 2950. doi:1538-7445.AM2012-2950