Fluorescent Biosensor for Measuring Ras Activity in Living Cells

The small GTPase Ras is a critical regulator of cell growth and proliferation. Its activity is frequently dysregulated in cancers, prompting decades of work to pharmacologically target Ras. Understanding Ras biology and developing effective Ras therapeutics both require probing Ras activity in its native context, yet tools to measure its activities in cellulo are limited. Here, we developed a ratiometric Ras activity reporter (RasAR) that provides quantitative measurement of Ras activity in living cells with high spatiotemporal resolution. We demonstrated that RasAR can probe live-cell activities of all the primary isoforms of Ras. Given that the functional roles of different isoforms of Ras are intimately linked to their subcellular distribution and regulation, we interrogated the spatiotemporal regulation of Ras utilizing subcellularly targeted RasAR and uncovered the role of Src kinase as an upstream regulator to inhibit HRas. Furthermore, we showed that RasAR enables capture of KRasG12C inhibition dynamics in living cells upon treatment with KRasG12C covalent inhibitors, including ARS1620, Sotorasib, and Adagrasib. We found in living cells a residual Ras activity lingers for hours in the presence of these inhibitors. Together, RasAR represents a powerful molecular tool to enable live-cell interrogation of Ras activity and facilitate the development of Ras inhibitors.

Synthetic Lethal Interaction of SHOC2 Depletion with MEK Inhibition in RAS-Driven Cancers

The mitogen-activated protein kinase (MAPK) pathway is a critical effector of oncogenic RAS signaling, and MAPK pathway inhibition may be an effective combination treatment strategy. We performed genome-scale loss-of-function CRISPR-Cas9 screens in the presence of a MEK1/2 inhibitor (MEKi) in KRAS-mutant pancreatic and lung cancer cell lines and identified genes that cooperate with MEK inhibition. While we observed heterogeneity in genetic modifiers of MEKi sensitivity across cell lines, several recurrent classes of synthetic lethal vulnerabilities emerged at the pathway level. Multiple members of receptor tyrosine kinase (RTK)-RAS-MAPK pathways scored as sensitizers to MEKi. In particular, we demonstrate that knockout, suppression, or degradation of SHOC2, a positive regulator of MAPK signaling, specifically cooperated with MEK inhibition to impair proliferation in RAS-driven cancer cells. The depletion of SHOC2 disrupted survival pathways triggered by feedback RTK signaling in response to MEK inhibition. Thus, these findings nominate SHOC2 as a potential target for combination therapy.

Differential Effector Engagement by Oncogenic KRAS

KRAS can bind numerous effector proteins, which activate different downstream signaling events. The best known are RAF, phosphatidylinositide (PI)-3' kinase, and RalGDS families, but many additional direct and indirect effectors have been reported. We have assessed how these effectors contribute to several major phenotypes in a quantitative way, using an arrayed combinatorial siRNA screen in which we knocked down 41 KRAS effectors nodes in 92 cell lines. We show that every cell line has a unique combination of effector dependencies, but in spite of this heterogeneity, we were able to identify two major subtypes of KRAS mutant cancers of the lung, pancreas, and large intestine, which reflect different KRAS effector engagement and opportunities for therapeutic intervention.

[Genetic Polymorphisms of SNP Located in the 5' Region of VEGF Gene in Han Population in Guangdong]

OBJECTIVES

To investigate the genetic polymorphism of SNP located in the 5' region of the vascular endothelial growth factor （VEGF） gene in Han population in Guangdong and provide basic data for forensic application and population genetics research.

METHODS

The genetic polymorphisms of 4 SNP loci （rs699947, rs1570360, rs833061, rs2010963） within 5' region of VEGF gene of 184 unrelated individuals in Han population in Guangdong were analyzed by DNA micro sequencing technology SNaPshot. The statistical analysis was carried out by PowerMarker v3.25 software.

RESULTS

The genotype distributions of the 4 SNP loci within 5' region of VEGF gene of 184 unrelated individuals in Han population in Guangdong were in accordance with Hardy-Weinberg equilibrium （P>0.05） and 3 kinds of genotypes were detected from each loci. There was high linkage disequilibrium between the rs833061 and rs699947 SNP loci. Six haplotypes were observed, while the frequency of C-G-T-C, C-G-T-G, A-A-C-G and A-G-C-G were more than 10%, which were the main haplotypes. The discrimination probabilities （DP） of rs699947, rs833061, and rs2010963 loci were between 0.583 and 0.634, with the power of exclusion （PE） between 0.133 and 0.144. The DP and PE of haplotypes of 4 SNP were 0.868 and 0.438, respectively.

CONCLUSIONS

There are great polymorphisms in the 5' region of VEGF gene in Han population in Guangdong, which could be used as genetic indexes for individual identification and paternity testing, as well as association analysis of the related diseases.

Developmental changes in polyamines and autophagic marker levels in normal and growth-restricted fetal pigs

Polyamines are essential for embryonic and fetal survival, growth, and development. Additionally, polyamines may induce autophagy in mammalian cells. However, little is known about the availability of polyamines or autophagy in the porcine conceptus with intrauterine growth restriction (IUGR). The present study was performed to evaluate the developmental changes of polyamine concentrations in IUGR and normal porcine fetuses as well as autophagic marker levels in the fetal intestinal mucosa during the second half of gestation when most fetal growth occurs. Allantoic fluid (ALF), amniotic fluid (AMF), umbilical vein, and the small-intestinal mucosa were obtained from both IUGR and normal fetal pigs at d 60, 90, and 110 of gestation. Concentrations of polyamines in fetal fluids as well as protein abundances of microtubule-associated protein light chain 3B (LC3B), an autophagic marker, in the fetal small-intestinal mucosa were determined. Concentrations of polyamines varied greatly in different fetal compartments and changed substantially with advancing gestation. Concentrations of polyamines in IUGR fetal fluids and the small-intestinal mucosa were markedly different from those in their normal counterparts at d 60 and 90 of gestation, whereas most of the differences were not detected by late (d 110) gestation. Specifically, polyamine levels were lower in the umbilical vein plasma but higher in ALF and AMF from IUGR fetuses. Furthermore, enhanced levels of an autophagic marker were observed in the small-intestinal mucosa of IUGR fetuses throughout mid and late gestation in association with abnormal spermidine levels in fetal plasma. These findings support the notion that enhanced autophagy may be an important survival mechanism in IUGR fetuses. Collectively, our findings provide a new framework for future studies to define the roles for polyamines in the prevention and treatment of IUGR in both human medicine and animal production.

SNP in Differentially Methylated Region Upstream of H19 Gene in Guangdong Han Population

OBJECTIVES

To investigate the single nucleotide polymorphism （SNP） and haplotypes in differentially methylated region （DMR） upstream of H19 gene in Guangdong Han population.

METHODS

The PIA typing and restriction enzyme McrBC and HpaⅡ were used to digest the genomic DNA and obtain the individual uniparental DNA template strand. The data of uniparental SNP alleles, genotypes and haplotypes in DMR upstream of H19 gene were obtained by sequencing.

RESULTS

A total of 13 SNPs （rs10840167, rs2525883, rs12417375, rs4930101, rs2525882, rs2735970, rs2735971, rs11042170, rs2735972, rs10732516, rs2071094, rs2107425, and rs4930098） and one mutation locus （g7351c） were found. All loci followed the Hardy-Weinberg equilibrium （P>0.05） by statistical analysis. Except for rs12417375 （DP=0.279） locus, the DP of remaining 12 SNPs were 0.446-0.614, and the g7351c mutation locus （DP=0.013） was the particular loci of the Southern Chinese Han population. Eight haplotypes （designated as haplotype 1-8） were detected, in which 3 haplotypes had not yet been reported and the DP, PIC, PE and H were 0.891, 0.714, 0.524 and 0.758, respectively.

CONCLUSIONS

Obtained by PIA typing, the SNP in DMR upstream of H19 gene and its haplotypes genetic marker system have a high determination power and show a good practical value in forensic identification.

Abstract 4690: Next-generation screen for integrative subtyping and target discovery for KRAS-mutant cancer

Mutations in the small GTPase, KRAS, are found in ∼140,000 new cases of cancer every year in the United States. This heterogeneous class of cancers manifests primarily as adenocarcinomas of the lung, colon and pancreas. These cancers display a wide spectrum of KRAS-dependency and differentially activate downstream effector signaling. The tumors further diverge in their array of co-occurring secondary mutations, expression signatures and KRAS mutant allele. Ultimately, the sole trait these cancers share in common is an obstinate resistance to chemo- and targeted-therapies, making identification of effective treatments an urgent need. To identify treatments for such a heterogeneous class of cancers, we developed a strategy to stratify KRAS-mutant cell lines into subtypes by integrating next-generation RNAi screening and “Omics” database mining. Each subtype is characterized by unique biomarkers and distinct patterns of effector dependency, both of which represent potential targets for personalized therapeutic strategies.

Our RNAi screen systematically evaluates sensitivity to siRNA-mediated knockdown of 40 KRAS effector nodes in a panel of 135 lung, colorectal and pancreatic cancer cell lines. Data is analyzed on the single cell level, through the simultaneous measurement of 5 functional parameters. This single-cell, multi-dimensional approach allows for a comprehensive assessment of cellular homeostasis, with unprecedented depth and dynamic range that allows robust classification of cell lines by similarity. We identify subtypes of KRAS-mutant cell lines that rely on particular effector pathways such as the RAL, RSK, MTOR and autophagy pathways, which are not engaged by all KRAS-mutant cell lines, and thus may represent targets for personalized treatment. We further identify widely shared dependencies such as on the RAF, glycolytic and cell cycle pathways. Through integrative data mining of exome, transcriptome and drug/siRNA sensitivity databases for each KRAS-mutant subtype, we can identify unique biomarkers that will serve to stratify patients in the clinic and recommend personalized treatment strategies.

Citation Format: Tina L. Yuan, Rachel Bagni, Ming Yi, Arnaud Amzallag, Shervin Afghani, Katie Beam, William Burgan, Nicole Fer, Leslie Garvey, Brian Smith, Andrew Waters, Robert Stephens, Cyril Benes, Frank McCormick. Next-generation screen for integrative subtyping and target discovery for KRAS-mutant cancer. [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 4690. doi:10.1158/1538-7445.AM2015-4690

Abstract LB-247: Querying the RAS genomic network with siRNAs and and flow cytometry: Automatic, multidimensional phenotyping of 135 cancer cell lines by Gaussian mixture fitting and expectation maximization

To discover novel therapeutic modalities and genomic predictors of response, large screen utilizing small molecules or sh/siRNA are performed on increasingly large collections of cancer cell lines. However these screens suffer from two main limitations: 1) the off-target effects of the probes 2) the coarse measurement of the cellular response that cannot distinguish between different outcomes such as proliferation block and apoptosis.

Here we profile 50 lung cancer cell lines using highly specific combinations of siRNAs against effector nodes of KRAS, and measured several characteristics of phenotypic response by flow cytometry including viability, level of reactive oxygen species and cell membrane integrity.

For each assay [node-cell line], typically 25,000 events were measured. We often observed multi modal distributions following node silencing. We used the expectation maximization algorithm to fit the different cell populations induced by the gene silencing. This allows us to automatically extract the proportion of dying cells, and also provides estimates of the cell growth impairment. Assessment of replicates shows that our results are highly reproducible, provide an accurate estimate of the proportion of dying cells, and reveal the complexity of multi-modal response of KRAS cancer cell lines to perturbation of key signaling nodes. Using the genomic profiling and pharmaceutical screen of the same cell lines, we reveal the association of specific node silencing with 1) the basal genomic state of the cell lines 2) the activity of a panel of drugs with the goal of identifying new targeting modalities and patient selection strategies for KRAS mutant cancers.

Citation Format: Arnaud Amzallag, Tina L. Yuan, Rachel Bagni, Ming Yi, Robert Stephens, Sridhar Ramawamy, Frank McCormick, Cyril H. Benes. Querying the RAS genomic network with siRNAs and and flow cytometry: Automatic, multidimensional phenotyping of 135 cancer cell lines by Gaussian mixture fitting and expectation maximization. [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 LB-247. doi:10.1158/1538-7445.AM2015-LB-247

Development of siRNA payloads to target KRAS-mutant cancer

RNAi is a powerful tool for target identification and can lead to novel therapies for pharmacologically intractable targets such as KRAS. RNAi therapy must combine potent siRNA payloads with reliable in vivo delivery for efficient target inhibition. We used a functional "Sensor" assay to establish a library of potent siRNAs against RAS pathway genes and to show that they efficiently suppress their targets at low dose. This reduces off-target effects and enables combination gene knockdown. We administered Sensor siRNAs in vitro and in vivo and validated the delivery of KRAS siRNA alone and siRNA targeting the complete RAF effector node (A/B/CRAF) as promising strategies to treat KRAS-mutant colorectal cancer. We further demonstrate that improved therapeutic efficacy is achieved by formulating siRNA payloads that combine both single-gene siRNA and node-targeted siRNAs (KRAS + PIK3CA/B). The customizable nature of Sensor siRNA payloads offers a universal platform for the combination target identification and development of RNAi therapeutics.

SIGNIFICANCE

To advance RNAi therapy for KRAS-mutant cancer, we developed a validated siRNA library against RAS pathway genes that enables combination gene silencing. Using an in vivo model for real-time siRNA delivery tracking, we show that siRNA-mediated inhibition of KRAS as well as RAF or PI3K combinations can impair KRAS-mutant colorectal cancer in xenograft models.

Killing tumors by keeping ras and PI3' kinase apart

Ras proteins mediate PI3K activation through direct binding to p110 catalytic subunits. However, it is unclear when and where this interaction occurs. In this issue of Cancer Cell, Castellano and colleagues report that KRAS-driven lung cancers require the Ras-p110α interaction for full activation of PI3K and tumor maintenance.

Abstract LB-94: Nanoparticle-based RNAi therapy for the delivery of personalized siRNA payloads to KRAS-driven tumors

The current landscape of druggable disease targets represents only ~10% of the human genome. Among those targets that are frequently mutated in cancer yet remain undruggable by conventional small molecules are the Ras family of GTPases. Somatic mutations in KRAS occur in 35% of colorectal cancers, 16% of lung cancers and 61% of pancreatic cancers. Common KRAS mutations lock the enzyme in the active GTP-bound state, which leads to constitutive activation of downstream effector modules such as MAPK, PI3K, Ral, Rac and Rho, which promote tumor growth, proliferation and survival.

RNAi interference allows for the ablation of any gene product through the engagement of the endogenous microRNA machinery. The successful delivery of siRNA against KRAS or downstream effectors to tumors would represent a novel alternative treatment for KRASmut cancers, which currently lack strong clinical options. We have thus developed an RNAi therapy that employs 1) a cyclodextrin-based nanoparticle with high siRNA carrying capacity and tumor-targeting modules; and 2) highly potent “Sensor” siRNAs that can be used at low dose to efficiently ablate gene targets while avoiding off-target effects.

We have assembled a library of potent Sensor siRNAs, which are identified using a massively parallel biological assay. These siRNA sequences are screened in high-throughput in KRASmut cell lines for negative effects on viability and disruption of cellular signaling pathways (ViBE, Bioscale). To subsequently assess the ability of these personalized nanoparticle-siRNA treatments to inhibit the growth of KRASmut tumors, we have developed an in vivo screening platform to monitor nanoparticle-siRNA delivery and payload efficacy at varying siRNA doses. Successful delivery of siRNAs to solid tumors has been one of the major hurdles to the advancement of RNAi therapy. Our fluorescent reporter system thus allows for the careful tracking of nanoparticle delivery and siRNA payload activity in real time using optical imaging. Additionally, the effect of different nanoparticle-siRNA treatments on transduced tumor cells can be measured non-invasively in real time.

We demonstrate that delivery of low dose Sensor siRNAs targeting KRAS and other effector genes to KRASmut xenograft tumors significantly impedes tumor growth by inhibition of MAPK signaling and induction of apoptosis. The highly customizable nature of the siRNA payload offers a promising and universal platform to access previously intractable targets such as KRAS and personalize treatment for various oncogene-addicted tumors.

Citation Format: Tina L. Yuan, Chih-Shia Lee, Christof Fellmann, Cayde Ritchie, Changwoo Lee, Colin Merrifield, Thomas Schluep, Scott W. Lowe, Ji Luo, Frank McCormick. Nanoparticle-based RNAi therapy for the delivery of personalized siRNA payloads to KRAS-driven tumors. [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-94. doi:10.1158/1538-7445.AM2013-LB-94

Disruption of calvarial ossification in E2f4 mutant embryos correlates with increased proliferation and progenitor cell populations

The E2F family of transcription factors, in association with pocket protein family members, are important for regulating genes required for cellular proliferation. The most abundant E2F, E2F4, is implicated in maintaining the G(0)/G(1) cell cycle state via transcriptional repression of genes that encode proteins required for S-phase progression. Here, we investigate E2F4's role in bone development using E2f4 germline mutant mice. We find that mutation of E2f4 impairs the formation of several bones that arise through intramembranous or endochondral ossification. The most severe defect occurred in the calvarial bones of the skull where we observed a striking delay in their ossification. In vivo and in vitro analyses established that E2F4 loss did not block the intrinsic differentiation potential of calvarial osteoblast progenitors. However, our data showed that E2f4 mutation elevated proliferation in the developing calvaria in vivo and it increased the endogenous pool of undifferentiated progenitor cells. These data suggest that E2F4 plays an important role in enabling osteoblast progenitors to exit the cell cycle and subsequently differentiate thereby contributing to the commitment of these cells to the bone lineage.

Introduction

The phosphoinositide-3-kinase (PI3K) family of lipid kinases has been well conserved from yeast to mammals. In this evolutionary perspective on the PI3K family, we discuss the prototypical properties of PI3Ks: 1) the utilization of sparse but specifically localized lipid substrates; 2) the nucleation signaling complexes at membrane-targeted sites; and 3) the integration of intracellular signaling with extracellular cues. Together, these three core properties serve to establish order within the entropic environment of the cell. Many human diseases, including cancer and diabetes, are the direct result of loss or defects in one or more of these core properties, putting much hope in the clinical use of PI3K inhibitors singly and in combination to restore order within diseased tissues.

E2F4 cooperates with pRB in the development of extra-embryonic tissues

The retinoblastoma gene, RB-1, was the first identified tumor suppressor. Rb(-/-) mice die in mid-gestation with defects in proliferation, differentiation and apoptosis. The activating E2F transcription factors, E2F1-3, contribute to these embryonic defects, indicating that they are key downstream targets of the retinoblastoma protein, pRB. E2F4 is the major pRB-associated E2F in vivo, yet its role in Rb(-/-) embryos is unknown. Here we establish that E2f4 deficiency reduced the lifespan of Rb(-/-) embryos by exacerbating the Rb mutant placental defect. We further show that this reflects the accumulation of trophectoderm-like cells in both Rb and Rb;E2f4 mutant placentas. Thus, Rb and E2f4 play cooperative roles in placental development. We used a conditional mouse model to allow Rb(-/-);E2f4(-/-) embryos to develop in the presence of Rb wild-type placentas. Under these conditions, Rb(-/-);E2f4(-/-) mutants survived to birth. These Rb(-/-);E2f4(-/-) embryos exhibited all of the defects characteristic of the Rb and E2f4 single mutants and had no novel defects. Taken together, our data show that pRB and E2F4 cooperate in placental development, but play largely non-overlapping roles in the development of many embryonic tissues.

The retinoblastoma protein tumor suppressor is important for appropriate osteoblast differentiation and bone development

Mutation of the retinoblastoma (RB) tumor suppressor gene is strongly linked to osteosarcoma formation. This observation and the documented interaction between the retinoblastoma protein (pRb) and Runx2 suggests that pRb is important in bone development. To assess this hypothesis, we used a conditional knockout strategy to generate pRb-deficient embryos that survive to birth. Analysis of these embryos shows that Rb inactivation causes the abnormal development and impaired ossification of several bones, correlating with an impairment in osteoblast differentiation. We further show that Rb inactivation acts to promote osteoblast differentiation in vitro and, through conditional analysis, establish that this occurs in a cell-intrinsic manner. Although these in vivo and in vitro differentiation phenotypes seem paradoxical, we find that Rb-deficient osteoblasts have an impaired ability to exit the cell cycle both in vivo and in vitro that can explain the observed differentiation defects. Consistent with this observation, we show that the cell cycle and the bone defects in Rb-deficient embryos can be suppressed by deletion of E2f1, a known proliferation inducer that acts downstream of Rb. Thus, we conclude that pRb plays a key role in regulating osteoblast differentiation by mediating the inhibition of E2F and consequently promoting cell cycle exit.

Selective requirements for E2f3 in the development and tumorigenicity of Rb-deficient chimeric tissues

The tumor suppressor function of the retinoblastoma protein pRB is largely dependent upon its capacity to inhibit the E2F transcription factors and thereby cell proliferation. Attempts to study the interplay between pRB and the E2Fs have been hampered by the prenatal death of Rb; E2f nullizygous mice. In this study, we isolated Rb; E2f3 mutant embryonic stem cells and generated Rb(-/-); E2f3(-/-) chimeric mice, thus bypassing the lethality of the Rb(-/-); E2f3(-/-) germ line mutant mice. We show that loss of E2F3 has opposing effects on two of the known developmental defects arising in Rb(-/-) chimeras; it suppresses the formation of cataracts while aggravating the retinal dysplasia. This model system also allows us to assess how E2f3 status influences tumor formation in Rb(-/-) tissues. We find that E2f3 is dispensable for the development of pRB-deficient pituitary and thyroid tumors. In contrast, E2f3 inactivation completely suppresses the pulmonary neuroendocrine hyperplasia arising in Rb(-/-) chimeric mice. This hyperproliferative state is thought to represent the preneoplastic lesion of small-cell lung carcinoma. Therefore, our observation highlights a potential role for E2F3 in the early stages of this tumor type.

The role of E2F4 in adipogenesis is independent of its cell cycle regulatory activity

The E2F and pocket protein families are known to play an important role in the regulation of both cellular proliferation and terminal differentiation. In this study, we have used compound E2F and pocket protein mutant mouse embryonic fibroblasts to dissect the role of these proteins in adipogenesis. This analysis shows that loss of E2F4 allows cells to undergo spontaneous differentiation. The ability of E2F4 to prevent adipogenesis seems to be quite distinct from the known properties of E2F. First, it can be separated from any change in either E2F-responsive gene expression or cell cycle regulation. Second, it is a specific property of E2F4, and not other E2Fs, and it occurs independently of E2F4's ability to interact with pocket proteins. In addition, E2F4 loss does not override the differentiation defect resulting from pRB loss even though it completely suppresses the proliferation defect of Rb(-/-) mouse embryonic fibroblasts. This finding definitively separates the known, positive role of pRB in adipogenesis from its cell cycle function and shows that this pocket protein is required to act downstream of E2F4 in the differentiation process.