Molecular Vulnerabilities Research Articles

In Vivo Crispr Screening Identifies Novel Vulnerabilities in ETO2/GLIS2-rearranged Leukemia

Background: CRISPR screening has allowed for massively parallel interrogation of the genome for vulnerabilities in a variety of cancer models. However, these experiments are largely performed in vitro due to the scale and conditions required to effectively conduct these screens. Furthermore, there still remain genetic subtypes of acute leukemia which are poorly represented among existing cell lines. We sought to determine the feasibility of conducting screens with focused libraries in patient-derived leukemia xenografts. Methods: We utilized a patient-derived acute megakaryoblastic leukemia (AMKL) bearing an ETO2/GLIS2 fusion, representing an aggressive subtype of pediatric acute leukemia with limited comparable cell lines (Gruber TA, et al. Cancer Cell 2012.) Based on its transplantability in NOD.scid.Il2Rγcnull-SGM3 (NSGS) mice vs culture in vitro, we performed all subsequent experiments in vivo. We first sought to establish stable Cas9 expression, which we successfully achieved by lentiviral transduction followed by FACS-enriched transplant, followed by a second round of FACS enrichment with limiting dilution transplant. As judged by mCherry flow cytometry, we achieved highly pure (>90%) Cas9-expressing populations, which we verified by western blotting. We further verified functionality of these cells by verifying cutting at the safe harbor locus AAVS1. In order to identify molecular vulnerabilities in this system, we identified the top 100 differentially expressed genes (DEG) between ETO2/GLIS2-rearranged leukemias versus other leukemia PDXs which we previously characterized. We included eight transcription factors with motifs enriched in our DEG analysis, as well as eight pan-essential positive controls (such as MYC, BRD4). Four guide RNAs (gRNA) per gene were selected from the Broad Brunello genome-wide library (Doench JG, et al. Nat Biotechnol 2016) as well as 50 "safe targeting" control guides (Morgens DW, et al. Nat Commun 2017) directed against non-essential genomic regions for a total of 518 guides. Guides were ordered as pooled oligonucleotides, cloned into a lentiviral gRNA backbone using standard techniques, then used to prepare lentivirus via transient transfection of 293T cells followed by titration to achieve an MOI of 0.3. With this MOI and an approximate engraftment frequency of 2% following intrafemoral injection, we transplanted 8.7e7 cells across eight NSGS mice to achieve adequate starting representation of our pooled library. Mice were sacrificed at humane endpoints, and spleens and bone marrow underwent PCR amplification for gRNA sequences followed by Illumina deep sequencing, and analysis with MAGeCK-VISPR (Wei L, et al. Genome Biol 2015). Results: One mouse per cohort was sacrificed at 24 hours post-transplant and sequenced for gRNA representation, which confirmed that library representation was largely preserved with our approach. At the time of sacrifice, spleen and bone marrow samples were independently sequenced, but no major bias in guide dropouts was observed between these compartments. Subsequent analyses were performed on the marrow alone. We observed the dropout of 38 genes with a false discovery rate < 0.25, including all positive control gRNAs as well as targets previously described to be essential through our own orthogonal experiments (BCL2) or previously published findings (GLIS2, GATA3) (Thirant C et al. Cancer Cell 2017). Among transcription factors found to be essential, we identified several which had not previously been strongly associated with acute leukemia (FOXD4L1, ZNF740). Conclusion: Patient-derived xenografts represent a unique platform for targeted functional genomic interrogation of acute leukemias. These screens can be performed with a tractable number of animals and modest sequencing requirements. Additional experiments are ongoing to identify the mechanistic implications of the vulnerabilities described here in ETO2/GLIS2-rearranged AMKL.

Selected Articles from This Issue

Mutant NRASG12V drives acute myeloid leukemia (AML) cell proliferation and self-renewal in a mutually exclusive manner. Previous studies demonstrated that AML cell proliferation and self-renewal are associated with differential NRASG12V transcript levels, but whether different NRASG12V protein levels dictate proliferative versus self-renewal phenotypes is not known. To address that knowledge gap, Kurata and colleagues engineered AML cell lines in which tetracycline-inducible NRASG12V expression levels are tunable using various doxycycline doses. The authors found that moderate NRASG12V protein expression promotes AML cell proliferation, whereas higher NRASG12V protein expression facilitates AML cell senescence and self-renewal. Using mass cytometry, the authors showed that abundances of several downstream NRASG12V effectors, including known stemness mediators such as β-catenin, increase in a dose-dependent fashion, whereas others, such as phosphorylated STAT1, are not dose-dependent. Overall, this study demonstrates that differential NRASG12V protein levels disparately drive AML cell proliferation and self-renewal and illuminates the downstream signaling dynamics underlying each phenotype.Tumor cell heterogeneity is a major impedance in eliminating cancer, as it promotes therapy-resistant clone selection in response to treatment. Identifying biomarkers indicative of tumor heterogeneity may help quantify it and uncover therapeutic vulnerabilities, but such biomarkers remain elusive. In their study, So and colleagues discovered that DNA methyltransferase 3B (DNMT3B) protein expression displays marked heterogeneity in primary tumors from triple-negative breast cancer (TNBC) patients and TNBC mouse models. By selecting DNMT3B-high and -low clones from 4T1 cells, labeling them with different fluorescent dyes, and quantifying them in circulation and lung metastases after orthotopic injection, the authors found that DNMT3B-high cells are more metastatic than DNMT3B-low cells. Mechanistically, prostaglandin E2 (PGE2) induces DNMT3B expression, and DNMT3B regulates expression of epithelial–mesenchymal transition effectors including vimentin, Twist2, and Snai1. Perioperative treatment with celecoxib, which lowers PGE2 expression, alongside DNMT inhibitor 5-azacytidine and other chemotherapeutic drugs decreases tumor recurrence and metastasis after primary tumor removal. Taken together, this study presents DNMT3B as a therapeutically targetable marker and effector of tumor heterogeneity.Therapeutic challenges and poor outcomes in pancreatic cancer make further elucidating its underlying molecular mechanisms and therapeutic vulnerabilities critical. While long non-coding RNA (lncRNA) α-2-macroglobulin-antisense 1 (A2M-AS1) expression positively correlates with overall survival in pancreatic cancer as well as ferroptosis-related genes, how A2M-AS1 might regulate ferroptosis and whether it does so in pancreatic cancer has not been solved. In their study, Qiu and colleagues found that pharmacologically inducing ferroptosis in pancreatic cell lines augments A2M-AS1 expression, and that modulating A2M-AS1 abundance using shRNA and overexpression inhibits and enhances ferroptosis, respectively. Accordingly, A2M-AS1 overexpression limits pancreatic cancer cell growth both in vitro and in vivo. An RNA pull-down and mass spectrometry revealed that A2M-AS1 interacts with PCBP3. Additional experiments demonstrated that the interaction between A2M-AS1 and PCBP3 abrogates mTOR and AKT activation, while increasing p38 activation and ferroptosis. In sum, this study unveils a novel molecular mechanism by which ferroptosis evasion occurs in pancreatic cancer.Acute myeloid leukemia (AML) cells are dependent on oxidative metabolism. However, electron transport chain complex II (CII) targeting agents and their potential effects on AML cell metabolism and viability have not been assessed. To evaluate CII therapeutic targeting in AML, Roma and colleagues abrogated expression of CII chaperone protein succinate dehydrogenase assembly factor 1 (SDHAF1) using shRNA in AML cell lines. Using an in silico screen and HPLC analysis, the authors also identified shikonin as a CII small molecule inhibitor. Both SDHAF1 ablation and shikonin promote AML cell death in vitro and in vivo, and stable isotope tracing demonstrated concurrent tricarboxylic acid (TCA) cycle truncation. The authors also showed that SDHAF1 ablation and shikonin increase glutamine flux into the TCA cycle via deamination to α-ketoglutarate as well as reductive flux to aspartate. Accordingly, supplementing α-ketoglutarate undermines shikonin effectiveness, and pharmacologically inhibiting glutaminase augments it. Altogether, this study reveals a novel therapeutic target and accompanying therapeutic agent in AML and identifies anaplerotic glutamine metabolism as a compensatory mechanism and therapeutic vulnerability in CII inhibition.

Sensitivities and Dependencies of BRAF Mutant Colorectal Cancer Cell Lines with or without PIK3CA Mutations for Discovery of Vulnerabilities with Therapeutic Potential.

Background: Colorectal cancer represents a common malignancy and remains incurable in the metastatic stage. Identification of molecular alterations that are present in colorectal cancer has led to the introduction of targeted therapies that improve outcomes. BRAF and PIK3CA mutations are observed in a subset of colorectal cancers. Colorectal cancers bearing BRAF mutations may be treated with specific BRAF inhibitors. These drugs benefit patients with BRAF mutant colorectal cancers but responses are rather brief, and progression is the rule. In contrast, no PI3K inhibitors have proven successful yet in the disease. Thus, new treatments to supplement the currently available drugs would be welcome to further improve survival. Methods: Profiled colorectal cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) were examined for BRAF and PIK3CA mutations and were interrogated for molecular characteristics and concomitant alterations that mirror clinical sample alterations. The Genomics of Drug Sensitivity in Cancer (GDSC) project was used for determination of drug sensitivities of BRAF mutated colorectal cell lines with or without concomitant PIK3CA mutations. The Cancer Dependency Map project served as the basis for identification of molecular dependencies and vulnerabilities in these cell lines. Results: CCLE includes 84 colorectal cancer cell lines, which recapitulate the molecular landscape of colorectal cancer. Of these, 23 and 24 cell lines possess BRAF and PIK3CA mutations, respectively. Seven BRAF mutant cell lines have V600E mutations and 14 PIK3CA mutant cell lines have hotspot helical or kinase domain mutations. V600E BRAF mutant cell lines with or without hotspot PIK3CA mutations are heterogeneous in their MSI status and mimic colorectal cancer tissues in other prevalent abnormalities including APC and TP53 mutations. Essential genes for survival include CTNNB1, WRN, and pyrimidine metabolism enzyme CAD. Besides BRAF mutations, BRAF inhibitor sensitivity in colorectal cancer cell lines is conferred by SACS mutations and PRKN locus loss. Conclusions: Colorectal cancer cell lines bearing the frequent BRAF and PIK3CA mutations present many alterations of the parental cancer tissue. Described vulnerabilities represent leads for therapeutic exploration in colorectal cancers with the corresponding alterations.

Finding Common Ground on the Site of Onset of Amyotrophic Lateral Sclerosis.

The fundamental origin of amyotrophic lateral sclerosis (ALS) has remained an enigma since its earliest description as a relentlessly progressive degeneration with prominent neuromuscular manifestations that are associated with upper and lower motor neuron dysfunction. Although this remains the hallmark of ALS, a significant proportion of patients will also demonstrate one or more features of frontotemporal dysfunction, including a frontotemporal dementia (FTD). Understanding whether these 2 seemingly disparate syndromes are simply reflective of the co-occurrence of 2 distinct pathologic processes or the clinical manifestations of a common pathophysiologic derangement involving the brain more widely has gripped contemporary ALS researchers. Supporting a commonality of causation, both ALS and FTD show an alteration in the metabolism of TAR DNA-binding protein 43, marked by a shift in nucleocytoplasmic localization alongside a broad range of neuronal cytoplasmic inclusions consisting of pathologic aggregates of RNA-binding proteins. Similarly, several disease-associated or disease-modifying genetic variants that are shared between the 2 disorders suggest shared underlying mechanisms. In both, a prominent glial response has been postulated to contribute to non-cell-autonomous spread. A more contemporary hypothesis, however, suggests that syndromes of cortical and subcortical dysfunction are driven by impairments in discrete neural networks. This postulates that such networks, including networks subserving motor or cognitive function, possess unique and selective vulnerabilities to either single molecular toxicities or combinations thereof. The co-occurrence of one or more network dysfunctions in ALS and FTD is thus a reflection not of unique neuroanatomic correlates but rather of shared molecular vulnerabilities. The basis of such shared vulnerabilities becomes the fulcrum around which the next advances in our understanding of ALS and its possible therapy will develop.

Dissecting the Immunological Profiles in NSD3-Amplified LUSC through Integrative Multi-Scale Analyses.

Simple SummaryAlthough cancer immunotherapy has become a “game changer” in treating LUSC patients, challenges still prevail due to the heterogeneous response and insufficient predictive biomarkers. Recently, NSD3, a neighbor gene of FGFR1, was identified as a key genetic driver of LUSC tumorigenesis. While previous studies have reported the relevance of NSD3 in innate antiviral immunity, the association of NSD3 with the TIME remains an open question requiring further investigation. We first show that NSD3 gene amplification is associated with an immune-desert phenotype and correlated with a worse immunotherapy outcome. Further molecular characterizations pinpoint that the high activity of UPR signaling might be a pivotal mediator for the non-inflamed TME phenotype of NSD3-amplified LUSC. Concordantly, the pharmaco-transcriptomic correlation analysis indicated that the intervention of UPR signaling could be a promising synthetic lethality target for NSD3-amplified LUSC. Our findings reveal a previously unappreciated immunological role for NSD3 in LUSC pathobiology and provide therapeutic rationales for this daunting disease.The histone H3 lysine 36 (H3K36) methyltransferase NSD3, a neighboring gene of FGFR1, has been identified as a critical genetic driver of lung squamous cell carcinoma (LUSC). However, the molecular characteristics, especially the immunological roles of NSD3 in driving carcinogenesis, are poorly understood. In this study, we systematically integrated multi-omics data (e.g., genome, transcriptome, proteome, and TMA array) to dissect the immunological profiles in NSD3-amplified LUSC. Next, pharmaco-transcriptomic correlation analysis was implemented to identify the molecular underpinnings and therapeutic vulnerabilities in LUSC. We revealed that NSD3-amplified LUSC presents a non-inflamed tumor immune microenvironment (TIME) state in multiple independent LUSC patient cohorts. Predictably, elevated NSD3 expression was correlated with a worse immunotherapy outcome. Further molecular characterizations revealed that the high activity of unfolded protein response (UPR) signaling might be a pivotal mediator for the non-immunogenic phenotype of NSD3-amplified LUSC. Concordantly, we showed that NSD3-amplified LUSCs exhibited a more sensitive phenotype to compounds targeting UPR branches than the wild-type group. In brief, our multi-level analyses point to a previously unappreciated immunological role for NSD3 and provide therapeutic rationales for NSD3-amplified squamous lung cancer.

Abstract A031: Interplay of YAP1, β-catenin and the SS18-SSX fusion protein in synovial sarcoma

Abstract Introduction: Synovial sarcoma (SySa) is a rare soft-tissue malignancy characterized by a specific chromosomal translocation t(X;18). The resulting chimeric SS18-SSX fusion protein drives SySa pathogenesis by dysregulating gene transcription. As therapeutic targeting of SS18-SSX is notoriously difficult, the identification of SS18-SSX-dependent pathomechanisms may uncover novel molecular vulnerabilities. Since previous functional analyses revealed a connection between SS18-SSX and the activity of the transcriptional co-regulators YAP1/TAZ and β-catenin, this study examined a potential crosstalk between these effectors in SySa. Experimental Procedures: Nuclear abundance of YAP1/TAZ and β-catenin was analyzed by immunohistochemistry in a large cohort of SySa tissue specimens. Two SySa cell lines were employed to modulate YAP1/TAZ/β-catenin transcriptional activity by RNAi-mediated knockdown, small molecule inhibitors, and overexpression vectors in vitro. Changes in transcriptional activity were determined via luciferase reporter assays. As YAP1 and β-catenin showed highest interdependence, co-immunoprecipitation experiments were performed to investigate their interplay with the SS18-SSX fusion protein in SySa cells. Results: Immunohistochemically, a substantial subset of SySa tissue specimens showed concurrent nuclear accumulation of YAP1/TAZ and β-catenin. In vitro, SS18-SSX was found to promote YAP1/TAZ and β-catenin transcriptional activity. RNAi-mediated knockdown of YAP1, TAZ or β-catenin and small molecule inhibitor treatment mutually downregulated TEAD and TCF luciferase reporter activity, while expression of hyperactive variants led to a reciprocal luciferase reporter induction. Finally, co-immunoprecipitation assays demonstrated nuclear co-localization of SS18-SSX with YAP1 and β-catenin in SySa cell lines. Conclusions: This study reveals an interdependency between YAP1 and β-catenin activation and a complex interplay with the SySa-specific SS18-SSX fusion protein. Citation Format: Ilka Isfort, Ruth Berthold, Lorena Heinst, Eva Wardelmann, Marcel Trautmann, Wolfgang Hartmann. Interplay of YAP1, β-catenin and the SS18-SSX fusion protein in synovial sarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A031.

APE1 redox function is required for activation of Yes-associated protein 1 under reflux conditions in Barrett’s-associated esophageal adenocarcinomas

BackgroundEsophageal adenocarcinoma (EAC) is characterized by poor prognosis and low survival rate. Chronic gastroesophageal reflux disease (GERD) is the main risk factor for the development of Barrett’s esophagus (BE), a preneoplastic metaplastic condition, and its progression to EAC. Yes-associated protein 1 (YAP1) activation mediates stem-like properties under cellular stress. The role of acidic bile salts (ABS) in promoting YAP1 activation under reflux conditions remains unexplored.MethodsA combination of EAC cell lines, transgenic mice, and patient-derived xenografts were utilized in this study. mRNA expression and protein levels of APE1 and YAP1 were evaluated by qRT-PCR, western blot, and immunohistochemistry. YAP1 activation was confirmed by immunofluorescence staining and luciferase transcriptional activity reporter assay. The functional role and mechanism of regulation of YAP1 by APE1 was determined by sphere formation assay, siRNA mediated knockdown, redox-specific inhibition, and co-immunoprecipitation assays.ResultsWe showed that YAP1 signaling is activated in BE and EAC cells following exposure to ABS, the mimicry of reflux conditions in patients with GERD. This induction was consistent with APE1 upregulation in response to ABS. YAP1 activation was confirmed by its nuclear accumulation with corresponding up-regulation of YAP1 target genes. APE1 silencing inhibited YAP1 protein induction and reduced its nuclear expression and transcriptional activity, following ABS treatment. Further investigation revealed that APE1-redox-specific inhibition (E3330) or APE1 redox-deficient mutant (C65A) abrogated ABS-mediated YAP1 activation, indicating an APE1 redox-dependent mechanism. APE1 silencing or E3330 treatment reduced YAP1 protein levels and diminished the number and size of EAC spheroids. Mechanistically, we demonstrated that APE1 regulated YAP1 stability through interaction with β-TrCP ubiquitinase, whereas APE1-redox-specific inhibition induced YAP1 poly-ubiquitination promoting its degradation.ConclusionOur findings established a novel function of APE1 in EAC progression elucidating druggable molecular vulnerabilities via targeting APE1 or YAP1 for the treatment of EAC.

Local molecular and global connectomic contributions to cross-disorder cortical abnormalities

Numerous brain disorders demonstrate structural brain abnormalities, which are thought to arise from molecular perturbations or connectome miswiring. The unique and shared contributions of these molecular and connectomic vulnerabilities to brain disorders remain unknown, and has yet to be studied in a single multi-disorder framework. Using MRI morphometry from the ENIGMA consortium, we construct maps of cortical abnormalities for thirteen neurodevelopmental, neurological, and psychiatric disorders from N = 21,000 participants and N = 26,000 controls, collected using a harmonised processing protocol. We systematically compare cortical maps to multiple micro-architectural measures, including gene expression, neurotransmitter density, metabolism, and myelination (molecular vulnerability), as well as global connectomic measures including number of connections, centrality, and connection diversity (connectomic vulnerability). We find a relationship between molecular vulnerability and white-matter architecture that drives cortical disorder profiles. Local attributes, particularly neurotransmitter receptor profiles, constitute the best predictors of both disorder-specific cortical morphology and cross-disorder similarity. Finally, we find that cross-disorder abnormalities are consistently subtended by a small subset of network epicentres in bilateral sensory-motor, inferior temporal lobe, precuneus, and superior parietal cortex. Collectively, our results highlight how local molecular attributes and global connectivity jointly shape cross-disorder cortical abnormalities.

Properties of Leukemic Stem Cells in Regulating Drug Resistance in Acute and Chronic Myeloid Leukemias.

Notoriously known for their capacity to reconstitute hematological malignancies in vivo, leukemic stem cells (LSCs) represent key drivers of therapeutic resistance and disease relapse, posing as a major medical dilemma. Despite having low abundance in the bulk leukemic population, LSCs have developed unique molecular dependencies and intricate signaling networks to enable self-renewal, quiescence, and drug resistance. To illustrate the multi-dimensional landscape of LSC-mediated leukemogenesis, in this review, we present phenotypical characteristics of LSCs, address the LSC-associated leukemic stromal microenvironment, highlight molecular aberrations that occur in the transcriptome, epigenome, proteome, and metabolome of LSCs, and showcase promising novel therapeutic strategies that potentially target the molecular vulnerabilities of LSCs.

Aberrant expansion of spontaneous splenic germinal centers induced by hallmark genetic lesions of aggressive lymphoma

AbstractUnique molecular vulnerabilities have been identified in the aggressive MCD/C5 genetic subclass of diffuse large B-cell lymphoma (DLBCL). However, the premalignant cell-of-origin exhibiting MCD-like dependencies remains elusive. In this study, we examined animals carrying up to 4 hallmark genetic lesions found in MCD consisting of gain-of-function mutations in Myd88 and Cd79b, loss of Prdm1, and overexpression of BCL2. We discovered that expression of combinations of these alleles in vivo promoted a cell-intrinsic accumulation of B cells in spontaneous splenic germinal centers (GCs). As with MCD, these premalignant B cells were enriched for B-cell receptors (BCRs) with evidence of self-reactivity, displayed a de novo dependence on Tlr9, and were more sensitive to inhibition of Bruton's tyrosine kinase. Mutant spontaneous splenic GC B cells (GCB) showed increased proliferation and IRF4 expression. Mice carrying all 4 genetic lesions showed a >50-fold expansion of spontaneous splenic GCs exhibiting aberrant histologic features with a dark zone immunophenotype and went on to develop DLBCL in the spleen with age. Thus, by combining multiple hallmark genetic alterations associated with MCD, our study identifies aberrant spontaneous splenic GCBs as a likely cell-of-origin for this aggressive genetic subtype of lymphoma.

Abstract LB188: Identification of intrinsic molecular vulnerabilities in inherited and treatment-related hypermutant patient-derived glioma cell line models

Abstract Background: Hypermutant gliomas in children are caused by inherited or therapy related replication repair deficiency (RRD), the latter typically following treatment with the alkylating agent temozolomide (TMZ). Recently, immune checkpoint inhibitors (ICIs) revealed clinical responses and prolonged survival in 30% of pediatric-inherited hypermutant gliomas but none of the treatment-related adult hypermutant gliomas. We hypothesized that high-throughput screening of hypermutant and RRD patient derived glioma cell lines from both glioma types (PDGCL) would reveal specific molecular vulnerabilities immediately translatable as targeted therapies to be used in combination with ICIs. Methods: We screened two pediatric hypermutant and RRD PDGCLs (1806, 1260); one pediatric non-hypermutant non-RRD PDGCL (477); an adult non-hypermutant non-RRD PDGCL (189EW); matched recurrent post-TMZ treatment hypermutant RRD PDGCL (248z, 248xy) from patient 189 against a library of 3336 bioactive compounds, including 1500 FDA approved drugs supplemented with 16 additional compounds (BET, PLK1, EZH2, PARP1 inhibitors) at 100nM.Each plate screened contained negative (0.2% DMSO) and positive controls (50nM bortezomib). Cell viability was calculated at 96hr by ATP measurement. Raw values from negative and positive control wells were aggregated and used to calculate Z’-factors for each assay plate, as a measure of assay performance and data quality, with a Z’-factor &amp;gt;0.5 representing high quality data. Only drugs scoring Normalized Percentage of Inhibition (NPI) &amp;gt;50% and z-score&amp;gt;3 were considered potential hits for follow-up evaluation, focusing on those enriched in the pediatric and adult hypermutant PDGCLs. Results: We identified 45 drugs active in all three of the pediatric PDGCLs and 23 common hits in the adult cell lines. Broad target classes were identified such as microtubule associated inhibitors, heat shock protein inhibitors for PDGCLs and proteasome inhibitors for adult cell lines. Unique targets were also identified. Importantly, the inherited and treatment related mismatch repair deficient glioma cells (MMR1260,248z, 248xy) and the hypermutant pediatric cell line (1806) exhibited significant response to PI3K/mTOR inhibitors. Ultrahypermutant RRD cell line and the treatment-related hypermutant cell lines (1806 248z 248xy ) displayed sensitivity to topoisomerase I inhibitors. Preliminary in vitro data confirm sensitivity to topotecan of hypermutant pediatric and adult cell lines. Conclusion: We have identified both mechanism specific and common intrinsic vulnerabilities in hypermutant PDGCLs that can be tested as adjuvant therapies for ICI. Functional validation of the lead candidates is ongoing and will be reported. Citation Format: Laura Scolaro, Nuno Miguel Nunes, Michelle Kushida, David C. Schultz, Sara Cherry, Kanupriya Whig, Peter Dirks, Uri Tabori, John M. Maris. Identification of intrinsic molecular vulnerabilities in inherited and treatment-related hypermutant patient-derived glioma cell line models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB188.

Abstract 1668: Development and characterization of a c-Myc-driven preclinical mouse model of osteosarcoma to investigate the tumor immune microenvironment

Abstract Osteosarcoma (OS) is the most common bone tumor in pediatric patients, particularly in adolescents and young adults. Currently, no effective molecular targeted therapies are available for the OS, however, many OS patients possess genetically defined somatic DNA copy number alterations, including amplification of chromosome 8q24, which harbors the oncogene Myc, and correlates with a worse prognosis. To better understand the molecular pathogenesis, and identify targeted therapy for OS, a robust and reliable preclinical model is needed both for the primary and metastatic disease. We have developed a novel conditional, osteoblast-specific Myc knock-in murine model to understand the mechanisms that underlie the ability of Myc to drive the development and progression of OS and utilize it for the identification of Myc-dependent intrinsic and extrinsic molecular vulnerabilities. A tissue-specific Myc-in genetically engineered murine model was generated by crossing Col2.3-Cre; TP53Flox/+ mice with LSL-MycT58A mice and characterized integrating RNA-seq and Mass Spectrometry. Syngeneic murine OS cell lines were also generated and characterized. The molecular characterization of the GEMM model was compared with high and low Myc expressing human tumors using the OS-TARGET dataset. Differential gene expression in Myc-driven and non-driven-tumor tissue samples were quantified by RNA sequencing. The immune landscape of OS was evaluated using SymphonyFACS and IHC staining. Murine OS tumor type was confirmed by H&amp;E staining. OS tumor was highly aggressive and metastatic in more than 60% of the mice. Myc expression was significantly higher both at the transcriptional and protein levels in the Myc-in tissue/cells compared to the non-Myc-driven model. Expression of 1479 genes (out of 13781 genes) were significantly altered in which 543 were upregulated and 936 were downregulated at transcriptional levels in Myc-in tumor tissue samples as compared to the low-Myc-driven OS tumor model analyzed by RNA sequencing. Myc-target-genes, splicing factor-related genes, E2F, G2M check-point, and DNA repair associated genes were significantly upregulated whereas the immune-related genes, oxidative phosphorylation, adipogenesis, and E2M transition genes were significantly downregulated when compared between two groups, which correlates to differential gene ontologies noted in high Myc human tumors. The total immune cell population, specifically the myeloid and macrophage populations were significantly diminished in the Myc-in tumor models, which could contribute to the poor prognosis in OS.Our murine model closely resembles human OS and will provide new opportunities for dissecting the molecular pathogenesis, identification of novel therapeutic strategies, and pre-clinical modeling for direct translational applications and targeting of Myc-driven OS. Citation Format: Bikesh K. Nirala, Lyazat Kurenbekova, Ryan L. Shuck, Tajhal Patel, Kimal Rajapakshe, Jason T. Yustein. Development and characterization of a c-Myc-driven preclinical mouse model of osteosarcoma to investigate the tumor immune microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1668.

Abstract 1795: Molecular vulnerabilities of the polyaneuploid cancer cell state

Abstract Once cancer has metastasized it remains incurable owing to resistance to nearly all systemic therapies. Classical views of therapeutic resistance include tumor heterogeneity and genetic instability, but our group and others have identified an unappreciated cancer cell phenotype, the polyaneuploid cancer cell (PACC) state, that provides an alternative model. The PACC state is induced upon exposure to a variety of applied stressors, including multiple different classes of chemotherapy, and is characterized by an enlarged cell size, polyploidy of the typically aneuploid cancer genome, and the ability to repopulate tissue through depolyploidization. We have demonstrated that PACCs are present in a variety of cell lines, arise in response to a multitude of stressors in vitro, and are resistant to cisplatin, docetaxel and Ipatasertib treatment. Thus, we hypothesize that the PACC state is driving cancer’s therapeutic resistance to nearly all available treatment regimens and enabling cancer relapse. Elimination of the PACC state is essential to prevent cancer recurrence, and ultimately enable a cure for cancer.To identify candidate drug targets specific to the PACC state, we performed RNA sequencing, NanoString mRNA panels, bulk proteomics and cell surface proteomics of PACCs versus their parental cell line. PACCs were induced from prostate cancer lines PC3 and LNCaP, and breast cancer line MDAMB231 with both cisplatin and docetaxel treatment. Initial datasets with PC3 cells found that 1013 genes are enriched (greater than 1.5 Log2 Fold Change) in cisplatin induced PACCs while 88 genes are enriched in docetaxel induced PACCs. 22 genes were enriched with both chemotherapy treatments implying that there are genes common to the PACC state. NanoString mRNA and proteomic analysis further validated a subset of the overlapping genes, including ATF3, BIRC3, IL6, and NOX5.Our existing data reveals that there are molecular vulnerabilities of the PACC state that can be manipulated for therapeutic elimination. We will further validate candidate genes across numerous stressors and cell lines and then assess the PACC state’s dependence on these pathways through inhibition and engineered cell lines. Information from these studies will directly lead to development of a therapeutic strategy specifically targeting the PACC state, with the intention of eliminating cancer resistance. Citation Format: Luke Loftus. Molecular vulnerabilities of the polyaneuploid cancer cell state [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1795.

LGG-45. Genetic dependencies inMYB/MYBL1-driven pediatric low-grade glioma models

AIM: Pediatric low-grade gliomas (pLGGs) are a heterogenous group of tumors, diverse in their localization, histology, mutational landscape, clinical behavior, and treatment response. Genomic alterations impacting the MYB family of transcription factors were identified in two distinct pLGG subtypes: Angiocentric Gliomas (AG) and Diffuse Astrocytomas (DA). The molecular profiles and therapeutic vulnerabilities associated with these genomic alterations remain unexplored. In this study we highlight the use of genome-wide CRISPR/Cas9 knock-out screens for an unbiased identification of translatable therapeutic targets. METHODOLOGY: Given the lack of patient-derived pLGG cell lines, we engineered in vitro pLGG mouse and human neural stem cell (NSC) models to harbor pLGG-relevant genomic alterations. We performed single cell RNA sequencing to investigate the transcriptional profiles driven by these mutations and to dissect the central regulatory networks enabling tumorigenesis. Specific genetic dependencies associated with MYB/MYBL1 mutations were screened using the Brie genome-wide mouse CRISPR lentiviral knock-out pooled library, consisting of 78,637 single guide RNAs (sgRNAs) targeting 19,674 mouse genes. RESULTS: We have successfully generated in vitro NSC-based pLGG models crucial to deepening our knowledge on pLGG biology and the identification of translatable therapeutic targets. Genome-scale CRISPR/Cas9 knock-out screens in isogenic NSCs models, expressing distinct MYB/MYBL1 alterations or a control transgene, revealed several differential genetic dependencies. Among the top identified dependencies are regulators of cell-stress response, cell-cycle progression, and modulators of the ubiquitin-proteasome degradation pathway. CONCLUSION: Genome-wide CRISPR knock-out screens are a powerful tool for the unbiased identification of mutation-specific genetic dependencies that can be explored as candidates for precision medicine approaches.

Early growth response 1 transcription factor is essential for the pathogenic properties of human endometriotic epithelial cells.

Although a non-malignant gynecological disorder, endometriosis displays some pathogenic features of malignancy, such as cell proliferation, migration, invasion and adaptation to hypoxia. Current treatments of endometriosis include pharmacotherapy and/or surgery, which are of limited efficacy and often associated with adverse side effects. Therefore, to develop more effective therapies to treat this disease, a broader understanding of the underlying molecular mechanisms that underpin endometriosis needs to be attained. Using immortalized human endometriotic epithelial and stromal cell lines, we demonstrate that the early growth response 1 (EGR1) transcription factor is essential for cell proliferation, migration and invasion, which represent some of the pathogenic properties of endometriotic cells. Genome-wide transcriptomics identified an EGR1-dependent transcriptome in human endometriotic epithelial cells that potentially encodes a diverse spectrum of proteins that are known to be involved in tissue pathologies. To underscore the utility of this transcriptomic data set, we demonstrate that carbonic anhydrase 9 (CA9), a homeostatic regulator of intracellular pH, is not only a molecular target of EGR1 but is also important for maintaining many of the cellular properties of human endometriotic epithelial cells that are also ascribed to EGR1. Considering therapeutic intervention strategies are actively being developed for EGR1 and CAIX in the treatment of other pathologies, we believe EGR1 and its transcriptome (which includes CA9) will offer not only a new conceptual framework to advance our understanding of endometriosis but will also furnish new molecular vulnerabilities to be leveraged as potential therapeutic options in the future treatment of endometriosis.

Role of EMT in the DNA damage response, double-strand break repair pathway choice and its implications in cancer treatment.

Numerous epithelial–mesenchymal transition (EMT) characteristics have now been demonstrated to participate in tumor development. Indeed, EMT is involved in invasion, acquisition of stem cell properties, and therapy‐associated resistance of cancer cells. Together, these mechanisms offer advantages in adapting to changes in the tumor microenvironment. However, recent findings have shown that EMT‐associated transcription factors (EMT‐TFs) may also be involved in DNA repair. A better understanding of the coordination between the DNA repair pathways and the role played by some EMT‐TFs in the DNA damage response (DDR) should pave the way for new treatments targeting tumor‐specific molecular vulnerabilities, which result in selective destruction of cancer cells. Here we review recent advances, providing novel insights into the role of EMT in the DDR and repair pathways, with a particular focus on the influence of EMT on cellular sensitivity to damage, as well as the implications of these relationships for improving the efficacy of cancer treatments.

Fusion protein-driven IGF-IR/PI3K/AKT signals deregulate Hippo pathway promoting oncogenic cooperation of YAP1 and FUS-DDIT3 in myxoid liposarcoma

Myxoid liposarcoma (MLS) represents a common subtype of liposarcoma molecularly characterized by a recurrent chromosomal translocation that generates a chimeric FUS-DDIT3 fusion gene. The FUS-DDIT3 oncoprotein has been shown to be crucial in MLS pathogenesis. Acting as a transcriptional dysregulator, FUS-DDIT3 stimulates proliferation and interferes with adipogenic differentiation. As the fusion protein represents a therapeutically challenging target, a profound understanding of MLS biology is elementary to uncover FUS-DDIT3-dependent molecular vulnerabilities. Recently, a specific reliance on the Hippo pathway effector and transcriptional co-regulator YAP1 was detected in MLS; however, details on the molecular mechanism of FUS-DDIT3-dependent YAP1 activation, and YAP1´s precise mode of action remain unclear. In elaborate in vitro studies, employing RNA interference-based approaches, small-molecule inhibitors, and stimulation experiments with IGF-II, we show that FUS-DDIT3-driven IGF-IR/PI3K/AKT signaling promotes stability and nuclear accumulation of YAP1 via deregulation of the Hippo pathway. Co-immunoprecipitation and proximity ligation assays revealed nuclear co-localization of FUS-DDIT3 and YAP1/TEAD in FUS-DDIT3-expressing mesenchymal stem cells and MLS cell lines. Transcriptome sequencing of MLS cells demonstrated that FUS-DDIT3 and YAP1 co-regulate oncogenic gene signatures related to proliferation, cell cycle progression, apoptosis, and adipogenesis. In adipogenic differentiation assays, we show that YAP1 critically contributes to FUS-DDIT3-mediated adipogenic differentiation arrest. Taken together, our study provides mechanistic insights into a complex FUS-DDIT3-driven network involving IGF-IR/PI3K/AKT signals acting on Hippo/YAP1, and uncovers substantial cooperative effects of YAP1 and FUS-DDIT3 in the pathogenesis of MLS.

Concurrent Activation of Kras and Canonical Wnt Signaling Induces Premalignant Lesions That Progress to Extrahepatic Biliary Cancer in Mice.

This work shows how dysregulation of canonical cell growth pathways drives precursors to biliary cancers and identifies several molecular vulnerabilities as potential therapeutic targets in these precursors to prevent oncogenic progression.

SOX17 and PAX8 constitute an actionable lineage-survival transcriptional complex in ovarian cancer.

Müllerian tissue-specific oncogenes, prototyped by PAX8, underlie ovarian tumorigenesis and represent unique molecular vulnerabilities. Further delineating such lineage-dependency factors and associated therapeutic implications would provide valuable insights into ovarian cancer biology and treatment. In this study, we identified SOX17 as a new lineage-survival master transcription factor, which shared co-expression pattern with PAX8 in epithelial ovarian carcinoma. Genetic disruption of SOX17 or PAX8 analogously inhibited neoplastic cell viability and downregulated a spectrum of lineage-related transcripts. Mechanistically, we showed that SOX17 physically interacted with PAX8 in cultured cell lines and clinical tumor specimens. The two nuclear proteins bound to overlapping genomic regions and regulated a common set of downstream genes, including those involved in cell cycle and tissue morphogenesis. In addition, we revealed that small-molecule inhibitors of transcriptional cyclin-dependent kinases (CDKs) effectively reduced SOX17 and PAX8 expression. ZSQ1722, a novel orally bioavailable CDK12/13 covalent antagonist, exerted potent anti-tumor activity in xenograft models. These findings shed light on an actionable lineage-survival transcriptional complex in ovarian cancer, and facilitated drug discovery by generating a serial of candidate compounds to pharmacologically target this difficult-to-treat malignancy.

Molecular vulnerabilities and therapeutic resistance in hormone receptor positive and HER2 dependent breast cancer tumours.

Over the past two decades, high sensitivity to HER2-amplified primary breast cancers has been achieved with HER2-targeted therapies. CDK4/6 inhibitors have long been identified as a potential treatment option for advanced breast cancer patients. However, acquired HER2 heterogeneity leading to resistance during the treatment has been identified as a bottleneck. This review focuses on the recent resistance mechanisms identified and potential therapeutic targets for conventional and combination endocrine therapies with CDK4/6 inhibitors by various breast cancer clinical trials and research groups in HER amplified and/or mutated breast cancer tumour. Activating HER2 alterations, JNK pathway, hyperactivated TORC1, co-mutations in HER2 and HER3, phenotypic changes of HER2, and few other advanced findings are identified as potential therapeutic targets in treating current HER2 endocrine therapy-resistant tumour. Along with the HER2-focused resistance mechanisms, we also describe how the microbiome may play a role in breast cancer therapy and its potential for new therapeutic strategies to overcome drug resistance in breast cancers.