Driver Pathways Research Articles

S170: DYNAMIC INTERPLAY BETWEEN TUMOR AND MICRO-ENVIRONMENT DURING MYELOMA DISEASE PROGRESSION

Background: Multiple Myeloma (MM) is an incurable plasma cell (PC) malignancy that evolves from two premalignant stages: Monoclonal Gammopathy of Undetermined Significance (MGUS) and Smoldering Multiple Myeloma (SMM). The disease progression has been characterized to be driven by intrinsic genomic events in the myeloma cells and by gradual dysregulation of the immune system. Aims: We investigated how the interplay between tumor cells with their microenvironment and the underlying complex and dynamic immune biology evolve during this process. Methods: Single cell multi-omics profiling, including RNA, B-cell receptor (BCR) and antibody barcode-tagged 10x sequencing, was conducted on human bone marrow (BM) aspirates collected at 6 Belgian centers from 4 cohorts: 31 healthy elderly and 28 MGUS, 32 SMM and 32 newly diagnosed MM. Mononuclear cell isolation, freezing and transport to central facilities was optimizedand data were integrated and filtered using Scanpy and Scirpy. The main immune cell types were identified from the RNA and antibody data using SingleR. Further functional subtyping was done using Leiden clustering. Differential pathway expression analysis was performed with Muscat and FGSEA. Results: From the tumor cell transcriptomes, our analyses confirmed the previously documented myeloma molecular hallmarks, such as MYC and IFN-a signaling, cell proliferation, energy metabolism and oxidative phosphorylation. Evidence was found for transcriptomic similarities and within-and between-patient malignant PC transcriptomic heterogeneity, as well as the existence of multiple transcriptomic clones in several patients. We observed a positive correlation between the antigen processing mechanism in the PCs with IFN response, suggesting that this mechanism associates with initiation of the immune recognition and activation against the tumor.The gradually increasing differential gene expression was also observed in the immune microenvironment: dysregulation of signaling pathways initiates early in MGUS and spreads throughout the various cell types surrounding the tumor cells. Cell population shifts were also found. In the CD1C+ DCs, that play a role in cancer immune control, a functional shift was observed that correlated with disease progression towards a more mature and antigen presenting phenotype with higher levels of CD83, HBEGF, MCL1 and CXCL16 as well as increased TNF-a pathway. Similarly, a shift was observed in the macrophage population, toward M1 state showing high IFN response along with expression of MS4A4A, STAT1, TNFSF13B and TRAIL in more severe disease. Interestingly, in the CD8+ T cells, we detected a pre-dysfunctional subpopulation with high expression of GZMK, activation markers CD69, CCL4, CXCR4 and genes associated with T cell pre-dysfunctionality NR4A2, RGS1, TOX and TIGIT, that was found to be associated with progression (Figure). In the CD4+ cytotoxic T cells, a proportion change was observed with more severe disease. Image:Summary/Conclusion: With the atlas of healthy, precursor and active MM patient BM samples, we generated a comprehensive and granular view of the various cell types involved in disease progression and provide evidence for early and gradually increasing immune dysregulation and activation of oncogenic driver pathways. Our data evidence the co-divergence and reciprocal stimulation of transcriptomes of tumor and microenvironment and support the postulation of microenvironment as a central modulator of cancer cell growth, survival and metastasis.

Abstract 3183: Targeting a myofibroblastic prostate cancer-associated fibroblast subtype through pharmacological inhibition of NADPH oxidase 4

Abstract Recent developments in single cell sequencing have revealed significant heterogeneity in the stromal tumor microenvironment. It is now widely accepted that there are different cancer-associated fibroblast (CAF) subtypes with different functions and effects on tumor progression. Since CAFs are generally considered an emerging therapeutic target, it is crucial to identify those subtypes that are tumor-promoting and to characterize their driver pathways. In this study we describe a population of CAFs in prostate cancer (PCa) that express elevated levels of NADPH oxidase 4 (Nox4) and localize adjacent to tumor foci. We previously showed that Nox4 is essential for TGFβ-mediated differentiation to a myofibroblastic CAF phenotype and that its increased expression is associated with biochemical relapse and reduced survival. Thus, this study aims to investigate whether pharmacological Nox4 inhibition can be used as an adjuvant therapeutic approach in PCa and which molecular pathways are regulated by Nox4 in the tumor microenvironment. Experiments using GKT831, a small molecule Nox1/Nox4 inhibitor with promising effects in clinical trials for fibrotic diseases, so far support its use as a therapeutic target. Most importantly, Nox4 inhibition reduced CAF marker expression in primary prostate CAFs and attenuated the expression of PSA, the key clinical biomarker of PCa progression, in ex vivo cultured human PCa tissue. The translational application of Nox4 inhibition is currently under investigation in vivo using CAF-PCa cell xenografts. To elucidate the molecular mechanisms regulated by Nox4 we performed integrative bioinformatics and functional assays, which revealed that Nox4 regulates CAF adhesion and migration. In addition, we found that Nox4 regulated genes were associated with a YAP signature and the transcription factor TEAD1, a major cofactor of YAP. Ongoing experiments suggest that during adhesion Nox4 signals via oxidation of SHP2, a redox-sensitive phosphatase that has previously been implicated in regulating YAP transcriptional activity. Previous studies have shown that adhesion and mechanotransduction pathways are commonly altered in myofibroblastic CAFs and that they support the formation of a tumor-promoting microenvironment. Our data suggest that Nox4 acts as a central regulator of these key oncogenic pathways and thus represents a promising therapeutic target. Citation Format: Elena Brunner, Lucy Neumann, Elisabeth Damisch, Martin Puhr, Georg Schäfer, Cédric Szyndralewiez, Helmut Klocker, Natalie Sampson. Targeting a myofibroblastic prostate cancer-associated fibroblast subtype through pharmacological inhibition of NADPH oxidase 4 [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 3183.

Abstract 3107: Identifying therapeutic vulnerabilities in HR-positive, HER2-negative advanced breast cancer patient-derived xenograft models refractory to CDK4/6 inhibition

Abstract Background: Clinically, the addition of CDK4/6 inhibitors (e.g. palbociclib) to endocrine therapy (ET) significantly delays progression of advanced hormone receptor-positive (HR+), HER2-negative (HER2-) breast cancer patients. However, most patients develop resistance and progress following long-term treatment. Thus, an ongoing clinical challenge has been the identification of biomarkers that predict response to CDK4/6 inhibitors. There is also an unmet need to identify actionable targets for patients who have progressed. Currently, there are no clinically useful biomarkers to predict response and/or resistance to anti-CDK4/6 therapy. Hence, the goal of our study was to identify the therapeutic vulnerabilities of CDK4/6 inhibitor resistant patient derived xenograft (PDX) models and identify key markers that longitudinally correlate with development of resistance and inform new treatment directions. Methods: We obtained 4 different PDX models, two from patients who progressed after 2-4 months on treatment with palbociclib plus ET (i.e. intrinsic resistance) and the other two who developed resistance over time (i.e. acquired resistance) with disease progression between 12-18 months while on palbociclib plus ET. To elucidate mechanisms of resistance, we performed genome-wide expression analysis via RNA-sequencing. Results: The molecular assessment of the PDX models revealed different transcriptomic signatures for intrinsic resistance compared to acquired resistance. We identified 3,386 upregulated and 2,829 downregulated significant differentially expressed genes (DEGs) in the acquired compared to intrinsic resistant PDX models. Further, gene set enrichment analysis (GSEA) revealed enrichment of distinct driver pathways in the acquired-compared to the intrinsic resistant models. Conclusions: Collectively, these results have identified potential unique targets for intrinsic and acquired resistance to guide treatment strategies. Thus, our ongoing studies are geared towards identifying and targeting distinct therapeutic vulnerabilities of intrinsic and acquired resistance to palbociclib. Citation Format: Nicole M. Kettner, Juliana Navarro-Yepes, Tuyen N. Bui, Xiayu Rao, Jing Wang, Funda Meric-Bernstam, Kelly K. Hunt, Debu Tripathy, Khandan Keyomarsi. Identifying therapeutic vulnerabilities in HR-positive, HER2-negative advanced breast cancer patient-derived xenograft models refractory to CDK4/6 inhibition [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 3107.

Abstract 940: Loss of Pkd1 limits colorectal cancer by increasing colon barrier function

Abstract Colorectal cancer (CRC) is one of the most common cancers, with an annual incidence of ~135,000 in the US, associated with ~ 50,000 deaths. CRC typically arises from mutations that inactivate the tumor suppressor APC, which activates the WNT/CTNNB1 pathway to drive cell transformation and tumor growth. Identifying factors that reduce incidence of CRC is of high interest. Intriguingly, a large population study has found a decreased incidence of CRC in patients with autosomal dominant polycystic kidney disease (ADPKD), an inherited disease affecting approximately 1 in 1,000 individuals. ADPKD typically arises from germline mutations in the PKD1 gene, which encodes a transmembrane signaling protein that is ubiquitously expressed. Puzzlingly, activated WNT/CTNNB1 signaling is also found in ADPKD, which would be expected to enhance rather than reduce likelihood of CRC. To investigate the role of PKD1 in modulating CRC tumorigenesis, we established a mouse model with tamoxifen-inducible loss of Apc with or without parallel loss of Pkd1 in the colon. Pkd1 loss vey significantly reduced tumor incidence (~80%) and rate of growth. In addition, growth of Pkd1-/-;Apc-/- organoids was reduced relative to Apc-/-organoids, indicating a cancer cell-intrinsic activity. Analysis of signaling pathway activation by RNA-seq indicated that Pkd1-deficient CRC organoids had enhanced WNT/CTNNB1 signaling, excluding reduced activation of this core driver pathway as a mechanism of action. Considering alternative mechanisms, a prominent feature of ADPKD is reprogramming barrier function in renal cells to reduce permeability, supporting cyst development; notably, compromised integrity of the epithelial barrier is associated with CRC. We tested the hypothesis that loss of Pkd1 increased colon barrier integrity. As a first approach, we compared susceptibility of wt versus Pkd1-/- mice to dextran-sodium sulfate (DSS), which induces colitis by damaging epithelial barriers. Histopathological assessment confirmed significantly less DSS-induced damage of colon tissue in Pkd1-/- mice. Further, treatment of DSS-treated mice with orally gavaged FITC-dextran led to elevated FITC-dextran in the serum of wt versus Pkd1-/- mice, indicating greater passage through a functionally impaired barrier. In ADPKD, decreased barrier permeability is mediated by upregulation of specific claudins (CLDN4, 7); in CRC, these claudins are typically reduced during and promote tumor formation. We detected strong elevation of CLDN4 and CLDN7 in the colonic epithelium of Pkd1-/- versus wt mice, with the expressed proteins having consistently greater localization to cell junctions. Based on these and other data, we identify PKD1 control of barrier function as an important regulatory mechanism in CRC tumorigenesis, which may suggest novel therapeutic strategies based on targeting PKD1-associated effector pathways. Citation Format: Anna S. Nikonova, Alexander Y. Deneka, Flaviane Silva, Rosella Tricarico, Anna Kiseleva, Sergey Grivennikov, Erica A. Golemis. Loss of Pkd1 limits colorectal cancer by increasing colon barrier function [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 940.

Direct and Indirect Determinants of Body Mass Index in Both Major Ethnic Groups Experiencing the Nutritional Transition in Cameroon.

In the context of rapid nutritional transitions in Africa, few studies have analyzed the etiology of obesity by considering the driver pathways that predict body mass index (BMI). The aim of this study is to innovatively identify these driver pathways, including the main sociodemographic and socioecological drivers of BMI. We conducted a rural–urban quantitative study in Cameroon (n = 1106; balanced sex ratio) to explore this issue. We recruited participants and reported several sociodemographic characteristics (e.g., marital status, socioeconomic status (SES), and ethnicity). We then assessed three main socioecological drivers of BMI (body weight perception, dietary intake, and physical activity) and conducted bioanthropometric measurements. We identified several driver pathways predicting BMI. In Cameroon, Bamiléké ethnicity, higher SES, being married, and older age had positive effects on BMI through overweight valorization and/or dietary intake. Accordingly, we found that being Bamiléké, married, and middle-aged, as well as having a higher SES, were factors that constituted at-risk subgroups overexposed to drivers of obesity. As such, this study highlights the necessity of investigating the complex driver pathways that lead to obesity. Therefore, better identification of the subgroups at risk for obesity will help in developing more targeted population health policies in countries where this burden is a major public health issue.

OMEN: network-based driver gene identification using mutual exclusivity.

Network-based driver identification methods that can exploit mutual exclusivity typically fail to detect rare drivers because of their statistical rigor. Propagation-based methods in contrast allow recovering rare driver genes, but the interplay between network topology and high-scoring nodes often results in spurious predictions. The specificity of driver gene detection can be improved by taking into account both gene-specific and gene-set properties. Combining these requires a formalism that can adjust gene-set properties depending on the exact network context within which a gene is analyzed. We developed OMEN: a logic programming framework based on random walk semantics. OMEN presents a number of novel concepts. In particular, its design is unique in that it presents an effective approach to combine both gene-specific driver properties and gene-set properties, and includes a novel method to avoid restrictive, a priori filtering of genes by exploiting the gene-set property of mutual exclusivity, expressed in terms of the functional impact scores of mutations, rather than in terms of simple binary mutation calls. Applying OMEN to a benchmark dataset derived from TCGA illustrates how OMEN is able to robustly identify driver genes and modules of driver genes as proxies of driver pathways. The source code is freely available for download at www.github.com/DriesVanDaele/OMEN. The dataset is archived at https://doi.org/10.5281/zenodo.6419097 and the code at https://doi.org/10.5281/zenodo.6419764. Supplementary data are available at Bioinformatics online.

Unique molecular characteristics of NAFLD-associated liver cancer accentuate β-catenin/TNFRSF19-mediated immune evasion

The hepatic manifestation of the metabolic syndrome, non-alcoholic fatty liver disease (NAFLD), can lead to the development of hepatocellular carcinoma (HCC). Despite a strong causative link, NAFLD-HCC is often underrepresented in systematic genome explorations. Herein, tumor-normal pairs from 100 patients diagnosed with NAFLD-HCC were subject to next-generation sequencing. Bioinformatic analyses were performed to identify key genomic, epigenomic and transcriptomic events associated with the pathogenesis of NAFLD-HCC. Establishment of primary patient-derived NAFLD-HCC culture was used as a representative human model for downstream invitro investigations of the underlying CTNNB1 S45P driver mutation. A syngeneic immunocompetent mouse model was used to further test the involvement of CTNNB1mutand TNFRSF19 in reshaping the tumor microenvironment. Mutational processes operative in the livers of patients with NAFLD inferred susceptibility to tumor formation through defective DNA repair pathways. Dense promoter mutations and dysregulated transcription factors accentuated activated transcriptional regulation in NAFLD-HCC, in particular the enrichment of MAZ-MYC activities. Somatic events common in HCCs arising from NAFLD and viral hepatitis B infection underscore similar driver pathways, although an incidence shift highlights CTNNB1mut dominance in NAFLD-HCC (33%). Immune exclusioncorrelated evidently with CTNNB1mut. Chromatin immunoprecipitation-sequencing integrated with transcriptome and immune profiling revealed a unique transcriptional axis, wherein CTNNB1mut leads to an upregulation of TNFRSF19 whichsubsequently represses senescence-associated secretory phenotype-like cytokines (including IL6 and CXCL8). This phenomenon could be reverted by the Wnt-modulator ICG001. The unique mutational processes in the livers of patients with NAFLD and NAFLD-HCC allude to a "field effect" involving a gain-of-function role of CTNNB1 mutations in immune exclusion. The increasing prevalence of metabolic syndrome in adult populations means that NAFLD is poised to be the major cause of liver cancer in the 21st century. We showed a strong "field effect" in the livers of patients with NAFLD, wherein activated β-catenin was involved in reshaping the tumor-immune microenvironment.

Identification of Potential Driver Genes and Pathways Based on Transcriptomics Data in Alzheimer's Disease.

Alzheimer's disease (AD) is one of the most common neurodegenerative diseases. To identify AD-related genes from transcriptomics and help to develop new drugs to treat AD. In this study, firstly, we obtained differentially expressed genes (DEG)-enriched coexpression networks between AD and normal samples in multiple transcriptomics datasets by weighted gene co-expression network analysis (WGCNA). Then, a convergent genomic approach (CFG) integrating multiple AD-related evidence was used to prioritize potential genes from DEG-enriched modules. Subsequently, we identified candidate genes in the potential genes list. Lastly, we combined deepDTnet and SAveRUNNER to predict interaction among candidate genes, drug and AD. Experiments on five datasets show that the CFG score of GJA1 is the highest among all potential driver genes of AD. Moreover, we found GJA1 interacts with AD from target-drugs-diseases network prediction. Therefore, candidate gene GJA1 is the most likely to be target of AD. In summary, identification of AD-related genes contributes to the understanding of AD pathophysiology and the development of new drugs.

Combinatorial Inactivation of Tumor Suppressors Efficiently Initiates Lung Adenocarcinoma with Therapeutic Vulnerabilities.

To address the large fraction of lung adenocarcinomas lacking mutations in proto-oncogenes for which targeted therapies are unavailable, this work uncovers driver pathways of oncogene-negative lung adenocarcinomas and demonstrates their therapeutic vulnerabilities.

The Labour Market for Uber Drivers in Australia

AbstractWe describe the labour market for Uber drivers, the first detailed study of a gig economy market in Australia. Uber drivers' characteristics, reasons for driving with Uber, hours of work and driving schedules, earnings and job satisfaction are analysed, using both administrative and survey data. Uber drivers have diverse pathways to the job, with the objective to earn supplemental income most important in Australia. Total hours and timing of work differ substantially between drivers. Drivers express high satisfaction regarding job flexibility but lower satisfaction about pay. Hours worked and job satisfaction depend importantly on a driver's pathway to the job.

Transcriptomic profiling to identify subsets of immune hot locally advanced rectal adenocarcinomas with favorable outcomes after neoadjuvant treatment.

155 Background: Understanding the role of the tumor microenvironment in the response to chemotherapy and radiation in patients with locally advanced rectal cancer (LARC, stage II-III) can lead to the identification of novel immunologic biomarkers to preselect patients who can avoid surgery and benefit from watch-and-wait strategies. Methods: We performed DNA and RNA sequencing of pre-treatment biopsies from 89 LARC patients who received neoadjuvant therapy, including 5 microsatellite unstable (MSI) and 84 microsatellite stable (MSS) patients. We computed single-sample gene set enrichment analysis (ssGSEA) scores for immune infiltrates and signaling pathways implicated in tumor progression. Immunofluorescence and hematoxylin-eosin staining of tumor slides was performed to confirm significant correlations with RNA-Seq estimates of immune markers. Other genomic variables were also included in the analysis, such as tumor mutational burden (TMB), fraction of genome altered by copy number changes, whole genome duplication events and somatic mutations in rectal cancer driver genes and pathways. Results were largely replicated using an independent cohort of 42 LARC samples with publicly available data from The Cancer Genome Atlas (TCGA). Results: Since MSI tumors are known to have a distinct immunologic profile, we separated them into their own group and performed unsupervised hierarchical clustering on the MSS tumors. We identified a set of immune hot MSS tumors (n = 7) with extensive immune infiltration. These tumors had low TMB and were predominantly classified as CMS4 (5/7). None of the 12 patients in the combined MSI and immune hot MSS groups recurred during the length of our study and they had response rates > 50% (vs. < 25% in the rest of MSS patients). MSI and immune hot MSS tumors had lower frequency of TP53 and APC mutations, and they exhibited increased levels of T cell infiltration. In particular, we observed overexpression of markers for Th1 cells, which produce inflammatory cytokines (e.g., IFN-gamma) and are associated with antitumor immunity. Genes encoding protein targets of immune checkpoint blockade, such as PDCD1 (PD-1), CD274 (PD-L1), CTLA4, HAVCR2 (TIM3) and LAG3, were also overexpressed in the immune hot MSS and - to a lesser extent – the MSI tumors, suggesting that these patients might benefit from the use of immune checkpoint inhibitors. Conclusions: Our results uncover a unique LARC tumor immune profile evident in the pre-treatment setting that could be used to better prognosticate rectal cancer patients and develop novel therapeutic strategies.

Highlights from Recent Cancer Literature

Highlights from Recent Cancer Literature

PHOENIX rises: Genomic-based therapies for diffuse large B cell lymphoma.

The molecular classification of diffuse large B cell lymphoma has paved the way for precision medicine that targets oncogenic driver pathways and actionable mutations. In this issue of Cancer Cell, Wilson etal. execute a massive genomic analysis in order to identify putative molecular signatures linked to a differential response to ibrutinib plus R-CHOP.

Variant profiling of colorectal adenomas from three patients of two families with MSH3-related adenomatous polyposis.

The spectrum of somatic genetic variation in colorectal adenomas caused by biallelic pathogenic germline variants in the MSH3 gene, was comprehensively analysed to characterise mutational signatures and identify potential driver genes and pathways of MSH3-related tumourigenesis. Three patients from two families with MSH3-associated polyposis were included. Whole exome sequencing of nine adenomas and matched normal tissue was performed. The amount of somatic variants in the MSH3-deficient adenomas and the pattern of single nucleotide variants (SNVs) was similar to sporadic adenomas, whereas the fraction of small insertions/deletions (indels) (21–42% of all small variants) was significantly higher. Interestingly, pathogenic somatic APC variants were found in all but one adenoma. The vast majority (12/13) of these were di-, tetra-, or penta-base pair (bp) deletions. The fraction of APC indels was significantly higher than that reported in patients with familial adenomatous polyposis (FAP) (p < 0.01) or in sporadic adenomas (p < 0.0001). In MSH3-deficient adenomas, the occurrence of APC indels in a repetitive sequence context was significantly higher than in FAP patients (p < 0.01). In addition, the MSH3-deficient adenomas harboured one to five (recurrent) somatic variants in 13 established or candidate driver genes for early colorectal carcinogenesis, including ACVR2A and ARID genes. Our data suggest that MSH3-related colorectal carcinogenesis seems to follow the classical APC-driven pathway. In line with the specific function of MSH3 in the mismatch repair (MMR) system, we identified a characteristic APC mutational pattern in MSH3-deficient adenomas, and confirmed further driver genes for colorectal tumourigenesis.

HER2\u2009+\u2009breast cancers evade anti-HER2 therapy via a switch in driver pathway

Inhibition of HER2 in HER2-amplified breast cancer has been remarkably successful clinically, as demonstrated by the efficacy of HER-kinase inhibitors and HER2-antibody treatments. Whilst resistance to HER2 inhibition is common in the metastatic setting, the specific programs downstream of HER2 driving resistance are not established. Through genomic profiling of 733 HER2-amplified breast cancers, we identify enrichment of somatic alterations that promote MEK/ERK signaling in metastatic tumors with shortened progression-free survival on anti-HER2 therapy. These mutations, including NF1 loss and ERBB2 activating mutations, are sufficient to mediate resistance to FDA-approved HER2 kinase inhibitors including tucatinib and neratinib. Moreover, resistant tumors lose AKT dependence while undergoing a dramatic sensitization to MEK/ERK inhibition. Mechanistically, this driver pathway switch is a result of MEK-dependent activation of CDK2 kinase. These results establish genetic activation of MAPK as a recurrent mechanism of anti-HER2 therapy resistance that may be effectively combated with MEK/ERK inhibitors.

CBIO-13. THOC1 DRIVES GBM AGGRESSION THROUGH MODULATION OF R-LOOPS AND GENOMIC STABILITY

Abstract Glioblastoma (GBM) is the most aggressive and common type of adult malignant brain tumor, with a median survival of only 21 months. To identify which genes drive its highly aggressive phenotype, we performed a genome-wide CRISPR-Cas9 knockout screen. Results showed substantial enrichment of ~160 novel essential oncogenic driver genes and pathways, including a previously unstudied gene THOC1—involved in RNA processing—that showed significant elevations in expression at RNA and protein levels (p&amp;lt; 0.05) in GBM, as well as a significant survival benefit in patient datasets when downregulated (p&amp;lt; 0.05). Knocking out THOC1 resulted in cell death in multiple GBM patient-derived xenograft (PDX) lines and extended survival compared to the controls (p&amp;lt; 0.01) in vivo. Overexpression of THOC1 in neural stem cells resulted in transformation to a cancerous phenotype, as evidenced by sphere formation in a soft agar assay (p&amp;lt; 0.01) and in vivo tumor engraftment assays. Further investigation of THOC1 through immunoprecipitation in neural stem cells and multiple GBM lines showed significant interaction in GBM with histone deacetylase complex SIN3A, involved in recruiting major histone deacetylases in order to close the DNA and prevent the accumulation of R-loops, RNA:DNA hybrids that pose a threat to genomic stability. Additional investigation revealed that THOC1-knockdowns in vitro induced R-loop formation and DNA damage, while THOC1-overexpression in vitro resulted in an untenable decrease in R-loops and DNA damage, suggesting that the THOC1-SIN3A axis is elevated in GBM in order to prevent the accumulation of genotoxic R-loops. Additionally, histone deacetylase activity was shown to be elevated in THOC1-overexpression conditions and reduced in THOC1-knockdown conditions, confirming that the THOC1-SIN3A axis functions to prevent R-loop accumulation through the epigenetic regulation. In summary, our whole-genome CRISPR-Cas9 knockout screen has identified a promising therapeutic target for GBM—a disease desperately in need of therapeutic innovations.

MAD2L1 Functions As a Novel Diagnostic and Predictive Biomarker in Cholangiocarcinoma.

Background: Most cholangiocarcinoma (CCA) patients are diagnosed at an advanced stage of disease, and the postoperational recurrence rates are high in those undergoing resection. The lack of satisfying biomarkers for early diagnoses and effective targeting of driver pathways is the leading reason for therapeutic failures. The goal of this study was to find a biomarker for making improved diagnoses with enhanced prognostic capabilities for CCA. Materials and Methods: Our study used bioinformatic analyses of microarray data from the Gene Expression Omnibus (GEO) database and investigated mitotic arrest deficient 2-like protein 1 (MAD2L1) expression in tumor and adjacent non-neoplastic biliary ducts through immunocytochemistry in 42 surgically removed primary CCAs from a single institute. In vitro and in vivo models were used to explore the function of MAD2L1. Results: In total, 297 high probability differentially expressed genes (DEGs) were obtained from overlapping the DEGs from the three individual data sets. Through enrichment assays and protein-protein interaction networks analyses, seven hub genes were identified. MAD2L1 was picked up as a novel biomarker based on hierarchical cluster analyses and Kaplan-Meier survival analyses. MAD2L1 was expressed in cancer tissues but not in the surrounding normal tissue, with 31 (73.81%) of 42 CCAs MAD2L1 positive by immunohistochemistry (IHC). MAD2L1 expression levels were significantly correlated with tumor size, pathological grade, and clinical stage. A Kaplan-Meier survival analysis demonstrated an inverse correlation with MAD2L1 expression. Real-time polymerase chain reaction and immunoblotting results further confirmed the results of IHC and bioinformatic analyses. In vitro and in vivo models demonstrated decreasing MAD2L1 could significantly suppress tumor growth, whereas increasing MAD2L1 could promote tumor growth. Conclusion: MAD2L1 could be used as a biomarker to predict prognosis and potential therapeutic target in CCA. Clinical Trial Registration Number: [2020]KY157-01.

Single-cell transcriptional and epigenomic dissection of human heart in health and coronary artery disease reveals cell-type-specific driver genes and pathways

Background and Aims: Genome-wide association studies have uncovered over 200 genetic loci underlying coronary artery disease (CAD), providing great hope for a deeper understanding of the causal mechanisms leading to this disease. However, in order to understand CAD at the molecular level, we need to uncover cell-type-specific circuits and to use these circuits to dissect driver variants, genes, pathways, and cell types, in normal and diseased tissues.

Combination targeted treatment may enhance antitumor activity in ERBB3 amplified high-grade serous endometrial cancer cells resistant to single agent targeted therapy

Objectives: Up-regulation of ERBB pathways represent targetable alterations in many high grade endometrial cancers (EC); ERBB3 amplifications in particular may contribute to ineffective pathway targeting due to persistent co-activation of other ERBB binding partners, leading to tumor growth and survival. The efficacy of downstream dual-inhibition of MEK+AKT or MEK+PI3K in an ERBB3 amplified EC primary tumor was studied using a microcancer 3D ex-vivo tumor cell viability assay. Methods: Tumor was prospectively collected from a patient with stage II, FIGO grade 3, serous EC and genomic characterization was performed using multiple sequencing methods: whole exome, RNA, and MatePair analysis. Somatic mutations, structural variance, with transcriptomic profiling was used to identify potential driver pathways for subsequent pharmacologic inhibition. Primary tumor cells were grown in a three-dimensional environment and the formed microcancers were subjected to drug treatment. Cell viability was determined by the CellTiter-Glow Luminescent Assay. Data transformation and dose-response curves were generated using GraphPad PRISM using four parameter logistic regression. CompuSyn software with the Chou-Talalay method was used to analyze drug interactions and synergy. The Fractional response-Combination index (Fa-CI) plot was generated with Microsoft Excel. Capivasertib, GDC-0084, and cobimetinib were used to inhibit AKT, PI3K/mTOR, and MEK, respectively. Inhibitory effect was defined as percent reduction in ATP at clinically-defined predicted plasma maximum concentration (Cmax) values. Results: Genomic sequencing revealed overexpression of a mutated ERBB3 (c.889G>T; p.Asp297Tyr) transcript within a 6N focal amplification. Additional pertinent alterations included a MYC mid-level gain, and TP53 double hit (loss and exonic splicing silencer (ESS)). Inhibition of cell viability was moderate by single agents: capivasertib, cobimetanib, or GDC-0084, as shown by inhibitory effect values of 33.9%, 35.9% and 49.9%, respectively. Two combinations with cobimetinib demonstrated increasing inhibitory effect values of 76.2% for cobimetanib/capivasertib at the Cmax of capivasertib and 79.7% for cobimetanib/GDC-0084 at the Cmax of cobimetanib. Synergy was evidenced by a combination index <1 at all points with Fa>0.8 (Figure 1). Conclusions: Combined inhibition of MEK and PI3K-AKT-mTOR pathways synergistically suppress viability in a patient-derived high-grade serous EC harboring a ERBB3 amplification. Further ex-vivo testing should be performed in endometrial tumors with other ERBB3 aberrations to allow generalization of results. Up-regulation of ERBB pathways represent targetable alterations in many high grade endometrial cancers (EC); ERBB3 amplifications in particular may contribute to ineffective pathway targeting due to persistent co-activation of other ERBB binding partners, leading to tumor growth and survival. The efficacy of downstream dual-inhibition of MEK+AKT or MEK+PI3K in an ERBB3 amplified EC primary tumor was studied using a microcancer 3D ex-vivo tumor cell viability assay. Tumor was prospectively collected from a patient with stage II, FIGO grade 3, serous EC and genomic characterization was performed using multiple sequencing methods: whole exome, RNA, and MatePair analysis. Somatic mutations, structural variance, with transcriptomic profiling was used to identify potential driver pathways for subsequent pharmacologic inhibition. Primary tumor cells were grown in a three-dimensional environment and the formed microcancers were subjected to drug treatment. Cell viability was determined by the CellTiter-Glow Luminescent Assay. Data transformation and dose-response curves were generated using GraphPad PRISM using four parameter logistic regression. CompuSyn software with the Chou-Talalay method was used to analyze drug interactions and synergy. The Fractional response-Combination index (Fa-CI) plot was generated with Microsoft Excel. Capivasertib, GDC-0084, and cobimetinib were used to inhibit AKT, PI3K/mTOR, and MEK, respectively. Inhibitory effect was defined as percent reduction in ATP at clinically-defined predicted plasma maximum concentration (Cmax) values. Genomic sequencing revealed overexpression of a mutated ERBB3 (c.889G>T; p.Asp297Tyr) transcript within a 6N focal amplification. Additional pertinent alterations included a MYC mid-level gain, and TP53 double hit (loss and exonic splicing silencer (ESS)). Inhibition of cell viability was moderate by single agents: capivasertib, cobimetanib, or GDC-0084, as shown by inhibitory effect values of 33.9%, 35.9% and 49.9%, respectively. Two combinations with cobimetinib demonstrated increasing inhibitory effect values of 76.2% for cobimetanib/capivasertib at the Cmax of capivasertib and 79.7% for cobimetanib/GDC-0084 at the Cmax of cobimetanib. Synergy was evidenced by a combination index <1 at all points with Fa>0.8 (Figure 1). Combined inhibition of MEK and PI3K-AKT-mTOR pathways synergistically suppress viability in a patient-derived high-grade serous EC harboring a ERBB3 amplification. Further ex-vivo testing should be performed in endometrial tumors with other ERBB3 aberrations to allow generalization of results.

The BTK/PI3K/BRD4 axis inhibitor SRX3262 overcomes Ibrutinib resistance in mantle cell lymphoma

SummaryMantle cell lymphoma (MCL) is an aggressive subtype of non-Hodgkin's lymphoma and one of the most challenging blood cancers to combat due to frequent relapse after treatment. Here, we developed the first-in-class BTK/PI3K/BRD4 axis inhibitor SRX3262, which simultaneously blocks three interrelated MCL driver pathways – BTK, PI3K-AKT-mTOR and MYC. SRX3262 concomitantly binds to BTK, PI3K, and BRD4, exhibits potent in vitro and in vivo activity against MCL, and overcomes the Ibrutinib resistance resulting from the BTK-C481S mutation. Our results reveal that SRX3262 inhibits IgM-induced BTK and AKT phosphorylation and abrogates binding of BRD4 to MYC loci. SRX3262 promotes c-MYC destabilization, induces cell cycle arrest and apoptosis, and shows antitumor activity in in vivo xenograft models. Together, our study provides mechanistic insights and rationale for the use of the triple BTK/PI3K/BRD4 activity inhibitors as a new approach to treat MCL.