Oncogenic Interactions Research Articles

Abstract 7322: Polygenic adaptation and co-regulatory dynamics in Chernobyl wolves: Unveiling immune and oncogenic stress interactions with implications for human cancer resilience

Abstract Wolves living in the Chernobyl Exclusion Zone (CEZ) for at least six generations have adapted to high radiation exposure and are a unique model for studying genetic selection under extreme conditions of oncogenic stress. The objective of this study was to build off previously described signatures of adaptation in CEZ wolves, identify networks of genes associated with immune adaptation in CEZ wolves, and determine prognostic significance of these genes in human cancer datasets to provide insight into immune adaptation and cancer immunity. RNA from blood samples of wolves in CEZ, Belarus (BLR), and Yellowstone (YLS) were sequenced previously. Here we analyzed these data by mapping wolf transcripts to human orthologs. Radiation exposure (in CEZ and BLR) was quantified by intramuscular Cesium-137. Differential gene expression (DESeq2), network co-expression analysis (lmQCM), and gene set variation analysis (GSVA) assessed transcriptomic changes between populations. Germline single nucleotide polymorphism (SNP) for all three populations were inferred from RNA-seq data. Genes differentially regulated between populations, including gene modules showing signatures of polygenic selection through increased rates of genetic divergence (p< 0.05) in CEZ wolf populations, were deemed as outlier genes. Those n=3,180 CEZ outlier genes were then investigated in human cancer data from The Cancer Genome Atlas (TCGA) to determine prognostic impact in 10 tumor types highly conserved between human and canines. GSVA confirmed activation of neutrophil and macrophage signatures in CEZ wolves and suppression of several adaptive immune-related signatures (p < 0.05 vs BLR and YLS). A signature including immune checkpoint targets was also significantly differentially expressed in CEZ wolves. In TCGA, Cox PH analysis identified 23 genes over-expressed in CEZ wolves with significant positive prognostic impact in ≥ 2 human tumor types. PTPN6, previously identified to have positive prognostic value in bladder cancer1, was also prognostic in three additional tumor types. In human bladder cancer, genes identified as differentially regulated in CEZ wolves were disproportionately associated with improved survival. As predicted, gene signature variations in CEZ wolves reveal a distinct immune profile, likely shaped by prolonged radiation exposure. These findings, along with evidence of polygenic selection, suggest adaptation to multigenerational radiation exposure (an oncogenic stress). Notably, the enrichment of genes with positive prognosis in human cancer overexpressed in CEZ wolves present a valuable model to explore genetic underpinnings of cancer immunity and advance our understanding of cancer resilience in humans. Reference: 1Shen C. et al. The Analysis of PTPN6 for Bladder Cancer: An Exploratory Study Based on TCGA. Dis Markers. 2020. Citation Format: Christina Y. Yu, Cara N. Love, Merzu Belete, Hareesh Chandrupatla, Lauren K. Brady, Sriram Sridhar, Shane C. Campbell-Staton. Polygenic adaptation and co-regulatory dynamics in Chernobyl wolves: Unveiling immune and oncogenic stress interactions with implications for human cancer resilience [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7322.

Abstract 5978: Therapeutic targeting of MELK using a drug repurposing approach to combat TNBC cells

Abstract Background: Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer linked to high chemo-resistant metastatic cases and limited therapeutic options due to the absence of conventional bioreceptors. Therefore, to treat TNBC, it is imperative to identify promising druggable biological targets. Experimental Procedures: An integrated bioinformatic analysis of microarray datasets was performed to identify significantly differentially expressed genes (DEGs) in TNBC. For selecting a potent therapeutic target, the function and significance of the upregulated DEGs in TNBC was investigated by an in silico study employing the UALCAN portal, String database, KM plotter, and Enrichr tools. This analysis included gene expression validation, insights into protein-protein interactions, survival analysis, and pathway mapping of the genes. To obtain potent drugs binding to the selected target MELK (maternal embryonic leucine zipper kinase), a drug repurposing approach was employed starting with virtual screening followed by molecular dynamic simulation (MDS) using GROMACS. Further, the anti-cancer activity of the top two drugs was validated by live-dead imaging, gene expression analyses, MTT-based cell viability and ROS detection assays. Results: Based on a stringent criterion for significant DEG identification (log2|FC|>1 & adjust P-value < 0.05), 25 overlapping upregulated genes were obtained from three selected datasets. Further, in silico analysis revealed that MELK is significantly upregulated across the four stages and subtypes of breast cancer, including TNBC. Higher MELK expression and its oncogenic interactions correlated with poor overall survival of TNBC patients. Evidence suggests that the existing inhibitor for MELK (OTSSP167) has shown poor specificity. Therefore, to block its activity, a library of 1293 FDA-approved drugs was screened against the kinase domain of MELK. MDS study and analysis using parameters like RMSD, RMSF and pair distance revealed that the top 10 drugs were strongly stabilized by H-bonds in the binding pocket of MELK, with minimal deviation and reduced fluctuations of MELK upon drug binding. Binding free energy calculation of drug-MELK interaction using the MM-PBSA method revealed that nine drugs possessed higher binding energy than the inhibitor. The top two drugs obtained from the study (originally kinase and reductase inhibitors respectively) were further validated for their in vitro anti-cancer efficacy in MDA-MB-231 and MDA-MB-468 cells. Treatment with these drugs exhibited (a) a dose-dependent decrease in proliferation, (b) significant cell death, (c) a marked increase in the cellular ROS levels, and (d) a decrease in the expression of MELK and its downstream targets in TNBC cell lines. Conclusion: The present study opens the avenue for using repurposed drugs as potential therapeutic molecules against MELK activity to combat TNBC progression. Citation Format: Arisha Arora, Shilpi Sarkar, Siddhartha S. Ghosh. Therapeutic targeting of MELK using a drug repurposing approach to combat TNBC cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5978.

NOVA1 acts as an oncogenic RNA-binding protein to regulate cholesterol homeostasis in human glioblastoma cells

NOVA1 is a neuronal RNA-binding protein identified as the target antigen of a rare autoimmune disorder associated with cancer and neurological symptoms, termed paraneoplastic opsoclonus-myoclonus ataxia. Despite the strong association between NOVA1 and cancer, it has been unclear how NOVA1 function might contribute to cancer biology. In this study, we find that NOVA1 acts as an oncogenic factor in a GBM (glioblastoma multiforme) cell line established from a patient. Interestingly, NOVA1 and Argonaute (AGO) CLIP identified common 3' untranslated region (UTR) targets, which were down-regulated in NOVA1 knockdown GBM cells, indicating a transcriptome-wide intersection of NOVA1 and AGO-microRNA (miRNA) targets regulation. NOVA1 binding to 3'UTR targets stabilized transcripts including those encoding cholesterol homeostasis related proteins. Selective inhibition of NOVA1-RNA interactions with antisense oligonucleotides disrupted GBM cancer cell fitness. The precision of our GBM CLIP studies point to both mechanism and precise RNA sequence sites to selectively inhibit oncogenic NOVA1-RNA interactions. Taken together, we find that NOVA1 is commonly overexpressed in GBM, where it can antagonize AGO2-miRNA actions and consequently up-regulates cholesterol synthesis, promoting cell viability.

Abstract A112: A semi-supervised approach to classify atypical BRAF mutations to identify effective targeted therapies in colorectal cancer

Abstract Due to a minority of atypical BRAF alleles being classified as either activating and RAS-independent (class 2) or kinase-impaired and RAS-dependent (class 3), few pre-clinical models of these atypical BRAF mutations exist, limiting efforts to discover effective targeted therapies for these tumors. Here we evaluated the activity of 100 different mutant BRAF alleles (6 Class 2, 10 Class 3, 84 unclassified) using Reverse Phase Protein Array (RPPA) profiles and then used principal component analysis (PCA) and semi-supervised clustering learning methods to classify the 84 unclassified mutations. To identify the protein features that best defined each class of BRAF mutation (Class 1,2,3 and non-activating) pairwise t-tests were performed on the RPPA profiles identifying a total of 43 proteomic features. PCA with K-means clustering was performed; known Class 2 and Class 3 samples separated from each other and non-activating controls. Within the same cluster, previously unclassified mutations were assigned to the same class as mutations with known classification; 8 mutations were classified as Class 1, 42 Class 2, 28 Class 3, and 6 non-activating.Analyzing RPPA profiles across each BRAF class with several markers utilized by Yao and colleagues showed similar patterns in protein expression levels between the putative and Yao classification systems (MAPK_pT202_Y204: p = 0.57, n = 13 for Class 2 and p = 0.62, n = 21 for Class 3; Cyclin-D1: p = 0.83, n = 8 for Class 2 and p = 0.26, n = 17 for Class 3). Cell viability analysis of BRAF-mutant Ba/F3 cells using Student’s t-test yielded no significant differences in mean AUC values between new and old classification systems (class 2: p = 0.53, n = 63, Cohen’s d = 0.22; class 3: p = 0.93, n = 40, Cohen’s d = 0.03), further validating that the newly established classification system is consistent with the Yao classes.Network analysis was also performed to uncover essential oncogenic interactions for each BRAF class. KRAS, NRAS, and PIK3CA were found to have higher CERES scores for class-2 and -3 cells, while atypical BRAF yielded lower CERES scores. This suggests that in cells carrying atypical BRAF mutations, BRAF is less independently important for cell survival and it must partner with other oncogenes to drive tumor growth. Several key genes, including PIK3CA, EGFR, and MEK, were identified as potential drug targets for CRC cell lines with class-3 atypical BRAF mutations. In the cell lines, NCIH508 (Yao class 3) and HT55 (putative class 3), Trametinib (MEK inhibitor) and Afatinib (EGFR inhibitor) yielded IC 50 values below 3 µM (0.1 µM for HT55 with Afatinib and for NCIH508 with Trametinib), while Dactolisib (PIK3CA inhibitor) yielded an IC50 value of 0.1 µM.In conclusion, we extended the previous BRAF-mutant Yao classification system to establish the Yao Classification System Plus, which includes 84 more atypical BRAF mutations. This allows for the development of greater therapeutic options to target tumors carrying these newly characterized mutations and expand care options for many CRC patients. Citation Format: Abhinav B Madduri, Yang Liu, Bela G Nelson, Darren J Wang, Kaitlin E Sanders, Naadir H Jamal, Nidhi Sahni, John Paul Shen. A semi-supervised approach to classify atypical BRAF mutations to identify effective targeted therapies in colorectal cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A112.

Targeting Oncogenic Enhancers in ASXL1-Mutant Chronic Myelomonocytic Leukemia

Introduction: Chronic myelomonocytic leukemia (CMML) is a myeloid neoplasm with limited therapeutic options and dismal outcomes. Truncating mutations in the epigenetic modifier ASXL1 are common and lead to a proliferative disease phenotype, resistance to epigenetic therapies, and higher rates of AML transformation. ASXL1-mutant CMML is characterized by widespread epigenetic remodeling and up-regulation of key leukemogenic driver genes (e.g. HOXA9 and its co-factor MEIS1). There is a genotype-specific activation of enhancers in ASXL1-mutant CMML that is associated with up-regulation of these leukemogenic driver genes. Here, we test the hypothesis that disrupting the oncogenic interactions at these genotype-specific enhancers can be exploited for therapeutic benefit. Methods: We identified activated enhancers specific to ASXL1-mutant CMML as previously described ( Binder et al. Nat Commun 2022;13(1):1434). To disrupt the E2542605 enhancer, we created unique mapped single guide RNAs (confirmed by BLAT). We generated a ribonucleoprotein complex using the Alt-R CRISPR-Cas9 system (IDT Technologies, Coralville IA). We combined the RNP along with Electroporation Enhancer to 3x10^5 cells of the monocytic cell line U937 in 20uL strip-wells provided by the SF Cell Line 4D-Nucleofector X Kit (Lonza, Basel, Switzerland). To deliver the RNP, U937 cells were electroporated via listed cell line specific protocol by the Amaxa 4D-Nucleofector (Lonza). Forty-eight hours post-electroporation, cells were split and sequenced for E2542605 genomic structure disruption. In parallel, RNA was harvested, converted to cDNA and qPCR for HOXA9 and MEIS1 expression was performed using PrimeTime qPCR FAM labeled probe assays (IDT). Gene expression was determined using delta-delta Ct method. For assessment of selective sensitivity of ASXL1 / enhancer interactions, we performed progenitor colony forming assays using primary bone marrow mononuclear cells from CMML patients with or without ASXL1 mutations and healthy normal controls (n=2 in each category), exposed to increasing concentrations of the dual p300/CBP and BET bromodomain inhibitor EP31670. Briefly, we plated cells in methocellulose fortified with recombinant human cytokines supporting hematopoietic growth in duplicate, in a range of EP31670 concentrations. After 10 days, visible hematopoietic colonies were quantified and characterized. IC 50 values were generated using non-linear regression log(EP31670) vs. normalized response. Results: We computationally identified candidate transcriptional regulators enriched at the activated enhancers specific to ASXL1-mutant CMML, including BRD4 (FDR<2.57x10 -370), CBP (FDR=2.56x10 -217), and p300 (FDR=6.36x10 -93). We selected the ASXL1-mutant-specific enhancer E2542605 (predicted to drive HOXA9 expression), given the up-regulation of HOXA9 in ASXL1-mutant CMML (log 2-fold change +2.05, FDR=0.006, n=14). We disrupted E2542605 using two different CRISPR guides, leading to a PCR trace detection of a 14bp deletion and a 26bp indel in the E2542605 enhancer region, respectively. Both enhancer disruptions led to a down-regulation of its putative target gene HOXA9: Mean relative fold-change 0.36 (p=0.001, n=3) and 0.65 (p=0.046, n=3), respectively ( Fig. 1a). We then used a pharmacologic approach (EP31670) to target the candidate transcriptional regulators involved in the oncogenic interaction at these ASXL1-mutant-specific enhancers. We observed selective sensitivity to growth of CMML colonies (particularly ASXL1-mutant colonies) compared to ASXL1-wild type cases and normal bone marrow controls ( Fig. 1b). Conclusions: In CMML patients, truncating ASXL1 mutations are associated with the activation of genotype-specific enhancers and the recruitment of an extended repertoire of transcriptional regulators including BRD4, CBP, and p300. In a model system, the disruption of an enhancer predicted to govern the expression of the leukemogenic driver HOXA9, led to a significant down-regulation of HOXA9 expression. Pharmacologically disrupting the oncogenic interaction at such enhancers with EP31670 in primary patient samples led to significant therapeutic effects at nanomolar drug concentrations in a genotype-specific manner. Oncogenic interactions at activated enhancers are viable therapeutic targets in ASXL1-mutant CMML and warrant further clinical investigation.

EPCO-45. CELLULAR HIERARCHIES OF ETMR ARE SHAPED BY ONCOGENIC MICRORNAS AND RECEPTOR-LIGAND INTERACTIONS

Abstract Embryonal tumor with multilayered rosettes (ETMR) is a highly aggressive brain tumor that predominantly occurs in children under the age of four years. Most children succumb within 10 months of diagnosis, typically due to invasive tumor growth and therapy-refractory behavior. 95% of ETMR harbor activating genetic alterations of the chromosome 19 microRNA cluster (C19MC). Despite the identification of this presumed oncogenic driving event, its biological consequences remain understudied and targeted therapy options are lacking. Here, we set out to further explore the intracellular heterogeneity of ETMR and shed light onto its oncogenic mechanisms with the goal to identify novel therapeutic targets for this dismal disease. We have compiled and analyzed a cohort of 11 ETMR tumors using single-cell RNA sequencing and multiplexed spatial imaging. We reveal a common, spatially distinct cellular hierarchy, closely resembling physiological brain development. This hierarchy spans a highly proliferative neural stem cell-like population that gives rise to more differentiated neuron-like cells. C19MC, predominantly expressed in the malignant stem-like population, controls a transcriptional network governing stemness and lineage commitment, as resolved by genome-wide analysis of microRNA-mRNA interactions. Targeting specific C19MC members by antisense oligonucleotides results in reduced cell proliferation, suggesting potent new avenues for future therapeutic approaches. Seeking more immediate therapeutic targets, we performed comprehensive cell-cell interaction analyses and reveal that FGF-FGFR and Delta-Notch interactions are important to maintain oncogenic signaling across malignant cell populations. These interactions were successfully targeted using small molecule inhibitors in preclinical models and in one ETMR patient. Taken together, we identify different malignant ETMR cell populations that follow a common developmental hierarchy, explore the regulatory reach of C19MC activation, and identify an oncogenic receptor-ligand interaction network. Targeting this interaction network opens a powerful new rationale for more effective ETMR therapies.

The transposable element-derived transcript of LIN28B has a placental origin and is not specific to tumours

Transposable elements (TEs) are genetic elements that have evolved as crucial regulators of human development and cancer, functioning as both genes and regulatory elements. When TEs become dysregulated in cancer cells, they can serve as alternate promoters to activate oncogenes, a process known as onco-exaptation. This study aimed to explore the expression and epigenetic regulation of onco-exaptation events in early human developmental tissues. We discovered co-expression of some TEs and oncogenes in human embryonic stem cells and first trimester and term placental tissues. Previous studies identified onco-exaptation events in various cancer types, including an AluJb SINE element–LIN28B interaction in lung cancer cells, and showed that the TE-derived LIN28B transcript is associated with poor patient prognosis in hepatocellular carcinoma. This study further characterized the AluJb–LIN28B transcript and confirmed that its expression is restricted to the placenta. Targeted DNA methylation analysis revealed differential methylation of the two LIN28B promoters between placenta and healthy somatic tissues, indicating that some TE–oncogene interactions are not cancer-specific but arise from the epigenetic reactivation of developmental TE-derived regulatory events. In conclusion, our findings provide evidence that some TE–oncogene interactions are not limited to cancer and may originate from the epigenetic reactivation of TE-derived regulatory events that are involved in early development. These insights broaden our understanding of the role of TEs in gene regulation and suggest the potential importance of targeting TEs in cancer therapy beyond their conventional use as cancer-specific markers.

α4-α5 Helices on Surface of KRAS Can Accommodate Small Compounds That Increase KRAS Signaling While Inducing CRC Cell Death

KRAS is the most frequently mutated oncogene associated with the genesis and progress of pancreatic, lung and colorectal (CRC) tumors. KRAS has always been considered as a therapeutic target in cancer but until now only two compounds that inhibit one specific KRAS mutation have been approved for clinical use. In this work, by molecular dynamics and a docking process, we describe a new compound (P14B) that stably binds to a druggable pocket near the α4-α5 helices of the allosteric domain of KRAS. This region had previously been identified as the binding site for calmodulin (CaM). Using surface plasmon resonance and pulldown analyses, we prove that P14B binds directly to oncogenic KRAS thus competing with CaM. Interestingly, P14B favors oncogenic KRAS interaction with BRAF and phosphorylated C-RAF, and increases downstream Ras signaling in CRC cells expressing oncogenic KRAS. The viability of these cells, but not that of the normal cells, is impaired by P14B treatment. These data support the significance of the α4-α5 helices region of KRAS in the regulation of oncogenic KRAS signaling, and demonstrate that drugs interacting with this site may destine CRC cells to death by increasing oncogenic KRAS downstream signaling.

Integrating Genomic Information with Tumor-Immune Microenvironment in Triple-Negative Breast Cancer.

the development and progression of triple-negative breast cancer (TNBC) is driven by somatic driver mutations and the tumor-immune microenvironment. To date, data on somatic mutations has not been leveraged and integrated with information on the immune microenvironment to elucidate the possible oncogenic interactions and their potential effects on clinical outcomes. Here, we investigated possible oncogenic interactions between somatic mutations and the tumor-immune microenvironment, and their correlation with patient survival in TNBC. We performed analysis combining data on 7,875 somatic mutated genes with information on 1,751 immune-modulated genes, using gene-expression data as the intermediate phenotype, and correlated the resulting information with survival. We conducted functional analysis to identify immune-modulated molecular networks and signaling pathways enriched for somatic mutations likely to drive clinical outcomes. We discovered differences in somatic mutation profiles between patients who died and those who survived, and a signature of somatic mutated immune-modulated genes transcriptionally associated with TNBC, predictive of survival. In addition, we discovered immune-modulated molecular networks and signaling pathways enriched for somatic mutations. The investigation revealed possible oncogenic interactions between somatic mutations and the tumor-immune microenvironment in TNBC, likely to affect clinical outcomes.

The Importance of Mg2+ -Free State in Nucleotide Exchange of Oncogenic K-Ras Mutants.

For efficient targeting of oncogenic K-Ras interaction sites, a mechanistic picture of the Ras-cycle is necessary. Herein, we used NMR relaxation techniques and molecular dynamics simulations to decipher the role of slow dynamics in wild-type and three oncogenic P-loop mutants of K-Ras. Our measurements reveal a dominant two-state conformational exchange on the ms timescale in both GDP- and GTP-bound K-Ras. The identified low-populated higher energy state in GDP-loaded K-Ras has a conformation reminiscent of a nucleotide-bound/Mg2+ -free state characterized by shortened β2/β3-strands and a partially released switch-I region preparing K-Ras for the interaction with the incoming nucleotide exchange factor and subsequent reactivation. By providing insight into mutation-specific differences in K-Ras structural dynamics, our systematic analysis improves our understanding of prolonged K-Ras signaling and may aid the development of allosteric inhibitors targeting nucleotide exchange in K-Ras.

Oncogenic gene expression and epigenetic remodeling of cis-regulatory elements in ASXL1-mutant chronic myelomonocytic leukemia

Myeloid neoplasms are clonal hematopoietic stem cell disorders driven by the sequential acquisition of recurrent genetic lesions. Truncating mutations in the chromatin remodeler ASXL1 (ASXL1MT) are associated with a high-risk disease phenotype with increased proliferation, epigenetic therapeutic resistance, and poor survival outcomes. We performed a multi-omics interrogation to define gene expression and chromatin remodeling associated with ASXL1MT in chronic myelomonocytic leukemia (CMML). ASXL1MT are associated with a loss of repressive histone methylation and increase in permissive histone methylation and acetylation in promoter regions. ASXL1MT are further associated with de novo accessibility of distal enhancers binding ETS transcription factors, targeting important leukemogenic driver genes. Chromatin remodeling of promoters and enhancers is strongly associated with gene expression and heterogenous among overexpressed genes. These results provide a comprehensive map of the transcriptome and chromatin landscape of ASXL1MT CMML, forming an important framework for the development of novel therapeutic strategies targeting oncogenic cis interactions.

Mapping oncogenic protein interactions for precision medicine.

Normal protein‐protein interactions (normPPIs) occur with high fidelity to regulate almost every physiological process. In cancer, this highly organised and precisely regulated network is disrupted, hijacked or reprogrammed resulting in oncogenic protein‐protein interactions (oncoPPIs). OncoPPIs, which can result from genomic alterations, are a hallmark of many types of cancers. Recent technological advances in the field of mass spectrometry (MS)‐based interactomics, structural biology and drug discovery have prompted scientists to identify and characterise oncoPPIs. Disruption of oncoPPI interfaces has become a major focus of drug discovery programs and has resulted in the use of PPI‐specific drugs clinically. However, due to several technical hurdles, studies to build a reference oncoPPI map for various cancer types have not been undertaken. Therefore, there is an urgent need for experimental workflows to overcome the existing challenges in studying oncoPPIs in various cancers and to build comprehensive reference maps. Here, we discuss the important hurdles for characterising oncoPPIs and propose a three‐phase multidisciplinary workflow to identify and characterise oncoPPIs. Systematic identification of cancer‐type‐specific oncogenic interactions will spur new opportunities for PPI‐focused drug discovery projects and precision medicine.

Mechanistic Translation of Melanoma Genetic Landscape in Enriched Pathways and Oncogenic Protein-Protein Interactions.

Malignant melanoma is a skin cancer originating from the oncogenic transformation of melanocytes located in the epidermal layers. Usually, the patient's prognosis depends on timing of disease detection and molecular and genetic profiling, which may all significantly influence mortality rates. Genetic analyses often detect somatic BRAF, NRAS and cKIT mutations, germline substitutions in CDKN2A, and alterations of the PI3K-AKT-PTEN pathway. A peculiar molecular future of melanoma is its high immunogenicity, making this tumor targetable by programmed cell death protein 1-specific antibodies. Ten formalin-fixed paraffin embedded samples derived from melanoma patients were subjected to next-generation sequencing (NGS) analysis using the FDA-approved FoundationOne CDx™ test. The molecular features of each case were then analyzed employing several in silico prediction tools. We analyzed the mutational landscape of patients with metastatic or relapsed cutaneous melanoma to define enriched pathways and protein-protein interactions. The analysis showed that both known genetic alterations and variants of unknown significance rely on redundant signaling converging on similar gene ontology biological processes. Complex informatics analyses of NGS-based genetic results identified pivotal signaling pathways that could provide additional targets for cancer treatment. Our data suggest an additional role for NGS in melanoma, as analysis of comprehensive genetic findings using innovative informatic tools may lengthen the list of druggable molecular targets that impact patient outcome.

Identification of a peptide that disrupts hADA3-E6 interaction with implications in HPV induced cancer therapy

AimHigh risk Human Papillomavirus (HPV) is an infectious pathogen implicated in a variety of cancers with poor clinical outcome. The mechanism of HPV induced cellular transformation and its intervention remains to be elucidated. Human ADA3 (hADA3), a cellular target of HPV16 E6, is an essential and conserved component of the ADA transcriptional coactivator complex. High risk HPV-E6 binds and functionally inactivates hADA3 to initiate oncogenesis. The aim of this study was to identify the interaction interface between hADA3 and HPV16E6 for designing inhibitory peptides that can potentially disrupt the hADA3-E6 interaction. Material methodsThe present investigation employed structure-based in silico tools supported by biochemical validation, in vivo interaction studies and analysis of posttranslational modifications. Key findingsFirst 3D-model of hADA3 was proposed and domains involved in the oncogenic interaction between hADA3 and HPV16E6 were delineated. Rationally designed peptide disrupted hADA3-E6 interaction and impeded malignant properties of cervical cancer cells. SignificanceIntervention of hADA3-E6 interaction thus promises to be a potential strategy to combat HPV induced oncogenic conditions like cervical cancer. The investigation provides mechanistic insights into HPV pathogenesis and shows promise in developing novel therapeutics to treat HPV induced cancers.

Understanding the Role of Flavonoid Based Small Molecules in Modulating the Oncogenic Protein-Protein Interactions: A Quest for Therapeutic Arsenal

We explored the anticancer activity of two synthetic flavonoid-based small molecules, HMDC and HMDF, with bioactive methylenedioxy functionality. HMDF inhibited the proliferation of the p53 wild-type (NCIH460 and A549), and p53 null (NCIH1299) non-small cell lung cancer and breast cancer (MCF-7) cells more potently than HMDC without significant cytotoxic effects on the normal lung-epithelial (L132) and macrophage (Raw 264.7) cells. HMDF mediated reduction of the cell proliferation occurred due to its attachment at the p53-binding domain of MDM2 (also evident from molecular docking analysis), which induced the disruption of the p53-MDM2 interactions. Ultimately, a higher expression of p53 in the NCIH460 cells was observed. The up-regulated p53 level instigated apoptosis of cancer cells. However, MDM2 expression level remained unaltered. The docking studies further indicate that HMDF can suppress the anti-apoptotic activity of Bcl-2 protein by blocking its BH3 domain.

Treatment of malignant melanoma - a review of the literature

Melanoma is caused by genetic mutations in melanocytes, pigment-producing cells found in the skin, eye, inner ear, and soft meninges. Sun exposure, atypical nevi, previous history of melanoma, and the presence of multiple (≥40) common nevi were found to be associated with an increased risk of melanoma detection (OR: 1. 3; 95% CI: 1. 1-1. 6). Its prevalence is highest among light-skinned populations and in regions of lower latitudes. Significance of family history of melanoma and presence of congenital nevi were excluded. For localized primary melanoma, the dominant prognostic factors for survival are lesion thickness, ulceration, and lymph node involvement Understanding the pathogenesis of melanoma has been crucial in developing new therapeutic approaches. The characterization of oncogenic signaling pathways and interactions has made it possible to identify new targets for clinically effective therapies, such as pathway inhibitors and antibodies to immune checkpoints or the use of phototherapy. In this article we describe the main signaling pathways which are deregulated in melanoma. We also mention how it has become a viable and crucial strategy for melanoma therapy and then thoroughly review the safety, clinical efficacy and progress regarding PDT- promising alternative therapy and the immunotherapies of melanoma in especially advanced metastatic stage basing on published clinical data and registered clinical trials, most of which are in phase III.

Radiation-Induced Phosphorylation of a Prion-Like Domain Regulates Transformation by FUS-CHOP.

Chromosomal translocations generate oncogenic fusion proteins in approximately one-third of sarcomas, but how these proteins promote tumorigenesis is not well understood. Interestingly, some translocation-driven cancers exhibit dramatic clinical responses to therapy, such as radiotherapy, although the precise mechanism has not been elucidated. Here we reveal a molecular mechanism by which the fusion oncoprotein FUS-CHOP promotes tumor maintenance that also explains the remarkable sensitivity of myxoid liposarcomas to radiation therapy. FUS-CHOP interacted with chromatin remodeling complexes to regulate sarcoma cell proliferation. One of these chromatin remodelers, SNF2H, colocalized with FUS-CHOP genome-wide at active enhancers. Following ionizing radiation, DNA damage response kinases phosphorylated the prion-like domain of FUS-CHOP to impede these protein-protein interactions, which are required for transformation. Therefore, the DNA damage response after irradiation disrupted oncogenic targeting of chromatin remodelers required for FUS-CHOP-driven sarcomagenesis. This mechanism of disruption links phosphorylation of the prion-like domain of an oncogenic fusion protein to DNA damage after ionizing radiation and reveals that a dependence on oncogenic chromatin remodeling underlies sensitivity to radiation therapy in myxoid liposarcoma. SIGNIFICANCE: Prion-like domains, which are frequently translocated in cancers as oncogenic fusion proteins that drive global epigenetic changes, confer sensitivity to radiation via disruption of oncogenic interactions.

Integrative oncogene-dependency mapping identifies RIT1 vulnerabilities and synergies in lung cancer

CRISPR-based cancer dependency maps are accelerating advances in cancer precision medicine, but adequate functional maps are limited to the most common oncogenes. To identify opportunities for therapeutic intervention in other rarer subsets of cancer, we investigate the oncogene-specific dependencies conferred by the lung cancer oncogene, RIT1. Here, genome-wide CRISPR screening in KRAS, EGFR, and RIT1-mutant isogenic lung cancer cells identifies shared and unique vulnerabilities of each oncogene. Combining this genetic data with small-molecule sensitivity profiling, we identify a unique vulnerability of RIT1-mutant cells to loss of spindle assembly checkpoint regulators. Oncogenic RIT1M90I weakens the spindle assembly checkpoint and perturbs mitotic timing, resulting in sensitivity to Aurora A inhibition. In addition, we observe synergy between mutant RIT1 and activation of YAP1 in multiple models and frequent nuclear overexpression of YAP1 in human primary RIT1-mutant lung tumors. These results provide a genome-wide atlas of oncogenic RIT1 functional interactions and identify components of the RAS pathway, spindle assembly checkpoint, and Hippo/YAP1 network as candidate therapeutic targets in RIT1-mutant lung cancer.

STUDY OF VARIABILITY IN THE ACTIVITY OF RIBOSOMAL CISTRONES IN COLORECTAL CANCER

According to the World Health Organization, colon cancer is one of the most common cancers. By 2020, approximately 1,900,000 cases of CRC were detected worldwide (a total of 10%). In 2020, American Cancer Society 104,610 new cases of CRC were identified and 53,200 patients died. Similar to other tumors colon cancer (CRC) is a genetically inherited multifactorial disease. It is established that genetic, immunologic, as well as environmental factors, all play significant role in CRC development and metastasis. As mentioned, carcinogenesis is associated with the whole number of genetic phenomena ongoing in certain groups of the genes; it is of staged nature and includes interactions of gene suppressors and oncogenes. Many genes responsible for CRC development were identified, family forms were described as well. In particular, high risk of CRC development in case of family history of adenomatous polyposis was demonstrated. As mentioned, neoplastic variability of the tumors is associated with changed morphogenesis of the nucleus, in turn, playing certain role in regulation of the suppressor genes p53, APC and pro-carcinogenesis KRAS.

Elucidation of the Genomic-Epigenomic Interaction Landscape of Aggressive Prostate Cancer.

Background Majority of prostate cancer (PCa) deaths are attributed to localized high-grade aggressive tumours which progress rapidly to metastatic disease. A critical unmet need in clinical management of PCa is discovery and characterization of the molecular drivers of aggressive tumours. The development and progression of aggressive PCa involve genetic and epigenetic alterations occurring in the germline, somatic (tumour), and epigenomes. To date, interactions between genes containing germline, somatic, and epigenetic mutations in aggressive PCa have not been characterized. The objective of this investigation was to elucidate the genomic-epigenomic interaction landscape in aggressive PCa to identify potential drivers aggressive PCa and the pathways they control. We hypothesized that aggressive PCa originates from a complex interplay between genomic (both germline and somatic mutations) and epigenomic alterations. We further hypothesized that these complex arrays of interacting genomic and epigenomic factors affect gene expression, molecular networks, and signaling pathways which in turn drive aggressive PCa. Methods We addressed these hypotheses by performing integrative data analysis combining information on germline mutations from genome-wide association studies with somatic and epigenetic mutations from The Cancer Genome Atlas using gene expression as the intermediate phenotype. Results The investigation revealed signatures of genes containing germline, somatic, and epigenetic mutations associated with aggressive PCa. Aberrant DNA methylation had effect on gene expression. In addition, the investigation revealed molecular networks and signalling pathways enriched for germline, somatic, and epigenetic mutations including the STAT3, PTEN, PCa, ATM, AR, and P53 signalling pathways implicated in aggressive PCa. Conclusions The study demonstrated that integrative analysis combining diverse omics data is a powerful approach for the discovery of potential clinically actionable biomarkers, therapeutic targets, and elucidation of oncogenic interactions between genomic and epigenomic alterations in aggressive PCa.