Downregulation Of Tumor Suppressors Research Articles

HCMV detection in Asian gastric cancer RNA-seq data sets and clinical validation in Indian GC patients reveals the HCMV-GC specific gene signatures.

Gastric cancer (GC) prevalence is very high in the Asian population. Oncogenic viruses play a crucial role in the progression of different types of cancers. Through reanalysis of clinical RNA-seq data sets derived from Asian GC patients, this study identified the presence of human cytomegalovirus (HCMV) in Asian GC tumors, next to the well-studied association of EBV. Clinical recruitment of the Indian GC cohort and screening for HCMV presence identified a 14.28% occurrence, similar to that observed in the bioinformatics analysis. A combinatorial approach of rank-based meta-analysis and ranking of groups based on an expectation-maximization algorithm identified that the upregulated LINC02864 and MAGEA10 correlated with poor survival of GC patients and downregulated tumor suppressor genes enriching for gastric acid secretion pathway to be associated with HCMV-positive GC patients, revealing the progressive role of HCMV infection in GC. Genes that discriminate between different stages of GC were identified through feature selection implemented in a machine-learning approach. LTF and KLK10 expressions were found to be specifically dysregulated by HCMV and can also indicate the GC stages. The results of this study will guide future studies to identify the functional role of these genes in the HCMV-associated GC.IMPORTANCENearly 75% of gastric cancer (GC) cases reported globally are from the Asian population. Most existing public databases, such as TCGA, comprise only a fractional portion of data derived from Asian ancestry. This study identified EBV and human cytomegalovirus (HCMV)'s higher detection in GC patients. The presence and role of EBV associated with GC are well-known, and the observation of HCMV prompted us to validate the findings in a small cohort of 40 Indian GC patients. We observed a 14.28% occurrence of HCMV in the Indian cohort, similar to that observed from next-generation sequencing. A combinatorial approach of rank-based meta-analysis and ranking of groups based on an expectation-maximization algorithm identified that the upregulated LINC02864 and MAGEA10 correlated with poor survival of GC patients and downregulated tumor suppressor genes enriching for gastric acid secretion pathway to be associated with HCMV-positive GC patients, revealing the progressive role of HCMV infection in GC.

STAT1 mediated downregulation of the tumor suppressor gene PDCD4, is driven by the atypical cadherin FAT1, in glioblastoma

STAT1 (Signal Transducer and Activator of Transcription 1), belongs to the STAT protein family, essential for cytokine signaling. It has been reported to have either context dependent oncogenic or tumor suppressor roles in different tumors. Earlier, we demonstrated that Glioblastoma multiforme (GBMs) overexpressing FAT1, an atypical cadherin, had poorer outcomes. Overexpressed FAT1 promotes pro-tumorigenic inflammation, migration/invasion by downregulating tumor suppressor gene, PDCD4. Here, we demonstrate that STAT1 is a novel mediator downstream to FAT1, in downregulating PDCD4 in GBMs. In-silico analysis of GBM databases as well as q-PCR analysis in resected GBM tumors showed positive correlation between STAT1 and FAT1 mRNA levels. Kaplan-Meier analysis showed poorer survival of GBM patients having high FAT1 and STAT1 expression. SiRNA-mediated knockdown of FAT1 decreased STAT1 and increased PDCD4 expression in glioblastoma cells (LN229 and U87MG). Knockdown of STAT1 alone resulted in increased PDCD4 expression. In silico analysis of the PDCD4 promoter revealed four putative STAT1 binding sites (Site1-Site4). ChIP assay confirmed the binding of STAT1 to site1. ChIP-PCR revealed decrease in the binding of STAT1 on the PDCD4 promoter after FAT1 knockdown. Site directed mutagenesis of Site1 resulted in increased PDCD4 luciferase activity, substantiating STAT1 mediated PDCD4 inhibition. EMSA confirmed STAT1 binding to the Site 1 sequence. STAT1 knockdown led to decreased expression of pro-inflammatory cytokines and EMT markers, and reduced migration/invasion of GBM cells. This study therefore identifies STAT1 as a novel downstream mediator of FAT1, promoting pro-tumorigenic activity in GBM, by suppressing PDCD4 expression.

Survival-Associated Cellular Response Maintained in Pancreatic Ductal Adenocarcinoma (PDAC) Switched Between Soft and Stiff 3D Microgel Culture.

Pancreatic ductal adenocarcinoma (PDAC) accounts for about 90% of all pancreatic cancer cases. Five-year survival rates have remained below 12% since the 1970s, in part due to the difficulty in detection prior to metastasis (migration and invasion into neighboring organs and glands). Mechanical memory is a concept that has emerged over the past decade that may provide a path toward understanding how invading PDAC cells "remember" the mechanical properties of their diseased ("stiff", elastic modulus, E ≈ 10 kPa) microenvironment even while invading a healthy ("soft", E ≈ 1 kPa) microenvironment. Here, we investigated the role of mechanical priming by culturing a dilute suspension of PDAC (FG) cells within a 3D, rheologically tunable microgel platform from hydrogels with tunable mechanical properties. We conducted a suite of acute (short-term) priming studies where we cultured PDAC cells in either a soft (E ≈ 1 kPa) or stiff (E ≈ 10 kPa) environment for 6 h, then removed and placed them into a new soft or stiff 3D environment for another 18 h. Following these steps, we conducted RNA-seq analyses to quantify gene expression. Initial priming in the 3D culture showed persistent gene expression for the duration of the study, regardless of the subsequent environments (stiff or soft). Stiff 3D culture was associated with the downregulation of tumor suppressors (LATS1, BCAR3, CDKN2C), as well as the upregulation of cancer-associated genes (RAC3). Immunofluorescence staining (BCAR3, RAC3) further supported the persistence of this cellular response, with BCAR3 upregulated in soft culture and RAC3 upregulated in stiff-primed culture. Stiff-primed genes were stratified against patient data found in The Cancer Genome Atlas (TCGA). Upregulated genes in stiff-primed 3D culture were associated with decreased survival in patient data, suggesting a link between patient survival and mechanical priming.

DNA Methylation Landscape of Peripheral T-Cell Lymphomas Not Otherwise Specified

DNA methylation is an epigenetic modification catalyzed by DNA methyltransferases that regulate gene transcription in mammalian cells. DNA methylation in gene promoters is associated with repressive histone marks and contributes to gene repression. This process is involved in various physiological processes, including development, X chromosome inactivation, genomic imprinting, differentiation, and hematopoiesis. The global, genome-wide deregulation of methylation patterns contributes to the pathogenesis of immune disorders, hematologic malignancies, and cancer. Because aberrations in DNA methylation can deregulate spatiotemporal gene expression in a cell type-specific manner, genome-wide changes in this epigenetic modification may contribute to tumor development. Specifically, the downregulation of tumor suppressors through promoter hypermethylation is a widely accepted mechanism in cancer progression. Due to its distinct patterns in cancer, DNA methylation can be used as a diagnostic and predictive biomarker. Peripheral T-cell lymphomas, Not Otherwise Specified (PTCL-NOS), are a group of heterogeneous T-cell malignancies with diverse cytogenic, molecular, and morphological phenotypes. Despite large-scale gene expression profiling, the molecular features-and DNA methylation in particular-of these rare but aggressive malignancies remain poorly understood. To better understand the molecular landscape of PTCL-NOS, we performed global methylation profiling via Whole Genome Bisulfite Sequencing on 10 lymphomas and compared those to patterns seen in normal T-cells and Anaplastic Large Cell Lymphoma (ALCL). Our analysis revealed large-scale deregulation of methylation in all tumors at levels of both differentially methylated cytosines and regions. The dominant molecular change was hypomethylation, which was, on average, 7 times more frequent than hypermethylation. Hypomethylation was not limited to repetitive elements but was also seen in all genomic elements, including promoters, enhancers, gene bodies, and exons. Out of 1,286 genes whose promoters were consistently hypomethylated in Peripheral T-cell lymphomas (PTCL), 39 genes were associated with an increase in expression, suggesting that the loss of methylation may have contributed to their deregulation. This hypomethylated and overexpressed signature contained genes that might be involved in tumor progression or maintenance, such as Rac GTPase activating protein 1 ( RACGAP1), regulator of chromosome condensation 1 ( RCC1), anillin actin-binding protein ( ANLN), and others. Out of 578 genes whose promoters were consistently hypermethylated in PTCL, the expression of 56 genes was decreased. These included genes with tumor suppressor function, such as splicing factor 3b subunit 1 ( SF3B1) and lymphoid enhancer-binding factor 1 ( LEF1). Our analysis also identified differential methylation between PTCL-NOS and ALCL in various genomic features. For example, 71 hypo- and 59 hypermethylated promoters were found only in ALCL but not PTCL-NOS. Conversely, 326 hypo- and 254 hypermethylated promoters were observed only in PTCL-NOS. Analysis of gene expression also revealed specific changes in both PTCL subtypes, manifested by the activation of different signaling pathways as identified by Ingenuity Pathway Analysis. PTCL-NOS was characterized by the suppression of the SUMOylation pathway, PTEN, and EIF2 Signaling, and the activation of NF-κB and Notch signaling. ALCLs were characterized by the suppression of the Role of CHK Proteins in Cell Cycle Control, Erythropoietin, ERBB signaling, the Coronavirus Pathogenesis pathway, IGF-1 signaling, and the activation of Glutathione-mediated Detoxification and Triacylglycerol Biosynthesis. Altogether, we identified recurrent specific methylation and expression changes that could serve as the basis for the development of tools facilitating the diagnosis and prognosis of PTCL-NOS. In addition, our data may contribute to the identification of epigenetically-regulated drivers of tumor initiation, progression, and maintenance.

Alternative polyadenylation reprogramming of MORC2 induced by NUDT21 loss promotes KIRC carcinogenesis.

Alternative polyadenylation (APA), a posttranscriptional mechanism of gene expression via determination of 3'UTR length, has an emerging role in carcinogenesis. Although abundant APA reprogramming is found in kidney renal clear cell carcinoma (KIRC), which is one of the major malignancies, whether APA functions in KIRC remains unknown. Herein, we found that chromatin modifier MORC2 gained oncogenic potential in KIRC among the genes with APA reprogramming, and moreover, its oncogenic potential was enhanced by 3'UTR shortening through stabilization of MORC2 mRNA. MORC2 was found to function in KIRC by downregulating tumor suppressor DAPK1 via DNA methylation. Mechanistically, MORC2 recruited DNMT3A to facilitate hypermethylation of the DAPK1 promoter, which was strengthened by 3'UTR shortening of MORC2. Furthermore, loss of APA regulator NUDT21, which was induced by DNMT3B-mediated promoter methylation, was identified as responsible for 3'UTR shortening of MORC2 in KIRC. Additionally, NUDT21 was confirmed to act as a tumor suppressor mainly depending on downregulation of MORC2. Finally, we designed an antisense oligonucleotide (ASO) to enhance NUDT21 expression and validated its antitumor effect in vivo and in vitro. This study uncovers the DNMT3B/NUDT21/APA/MORC2/DAPK1 regulatory axis in KIRC, disclosing the role of APA in KIRC and the crosstalk between DNA methylation and APA.

The Role of MicroRNAs in Development of Endometrial Cancer: A Literature Review.

Endometrial cancer (EC) ranks as the second most common gynaecological cancer worldwide. EC patients are diagnosed at an early clinical stage and generally have a good prognosis. Therefore, there is a dire need for development of a specific marker for early detection of endometrial adenocarcinoma. The development of EC is conditioned by a multistep process of oncogenic upregulation and tumor suppressor downregulation as shown by molecular genetic evidence. In this setting, microRNAs appear as significant regulators of gene expression and several variations in the expression of microRNAs have been implicated in normal endometrium, endometrial tissue, metrorrhagia, and endometrial cancer. Furthermore, microRNAs act as highly precise, sensitive, and robust molecules, making them potential markers for diagnosing specific cancers and their progression. With the rising incidence of EC, its management remains a vexing challenge and diagnostic methods for the disease are limited to invasive, expensive, and inaccurate tools. Therefore, the prospect of exploiting the utility of microRNAs as potential candidates for diagnosis and therapeutic use in EC seems promising.

Abstract 3775: Multi-omic spatial analysis with simultaneous detection of small RNAs, mRNAs and proteins using the novel RNAscope™ Plus technology

Abstract Regulatory RNA molecules such as microRNAs (miRNA) and long non-coding RNAs play critical roles in regulating translation of mRNA to protein. Several miRNAs have been implicated in disease initiation and progression, especially in cancer. The regulatory mechanisms of miRNAs and other small RNAs such as antisense oligos (ASOs) and silencing RNAs (siRNA) have been exploited to develop oligonucleotide therapies for 1. undruggable targets, 2. achieving longer-term effects 3. rapid production of therapeutics and 4. lower drug development costs. These therapeutics have the promise to treat debilitating neurodegenerative diseases, rare and inherited disorders. RNA therapies are typically delivered as a part of nanoparticles or a viral vector. Regardless of the delivery mechanism, methods to understand the biodistribution of the vector, transgene expression and cell type identification in a spatial context is crucial to study the safety and efficacy of these therapies. Built on the flagship RNAscope technology, the RNAscope Plus assay can detect 1 small RNA and 3 mRNA targets using TSA-based fluorescent readouts and is compatible with the new fluorescent Vivid™ dyes. Fixed, fresh frozen samples and formalin fixed paraffin embedded (FFPE) tissues are supported by manual and automated workflows using the Leica Bond Rx system. We have leveraged this technology to investigate spatial expression profile of miRNA and associated RNA targets across different tissue types and applications. We can also combine protein detection using a target antibody to visualize cell-type specific markers. This assay was used to demonstrate expression of miRNAs and target genes implicated in tumor initiation, progression, and angiogenesis. Expression of miR-205, associated tumor target genes such as PanCK, PTEN and tumor suppressor TP53 was visualized in head and neck cancer tumors. Downregulation of tumor-suppressor, TP53 resulted in upregulation of miR-205 which downregulates PTEN expression. Pan-CK stained the tumor region in the tissue. Similarly, miR-155 expression was observed in niche areas within breast cancer, head and neck cancer and cervical cancer tumors. Expression of miR-155 demonstrated correlation with high VEGF expression suggesting its role in angiogenesis. This novel platform will enable researchers to visualize regulatory RNA simultaneously with target RNAs, cell-type and morphology markers in intact cells/tissues with single cell resolution. This technology can provide meaningful insights into disease pathology driven by miRNAs as well as assess biodistribution and efficacy of oligonucleotide therapeutics. Citation Format: Anushka Dikshit, Sayantani Basak, Sonali Deshpande, Manvir Sambhi, Li-Chong Wang, Maithreyan Srinivasan. Multi-omic spatial analysis with simultaneous detection of small RNAs, mRNAs and proteins using the novel RNAscope™ Plus technology. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3775.

Non-Coding RNA Investigations in Cutaneous Melanoma: A Step forward in Discovering Novel Biomarkers

Non-Coding RNA Investigations in Cutaneous Melanoma: A Step forward in Discovering Novel Biomarkers

Dissecting novel mechanisms of hepatitis B virus related hepatocellular carcinoma using meta-analysis of public data.

BACKGROUNDHepatitis B virus (HBV) is a cause of hepatocellular carcinoma (HCC). Interestingly, this process is not necessarily mediated through cirrhosis and may in fact involve oncogenic processes. Prior studies have suggested specific oncogenic gene expression pathways were affected by viral regulatory proteins. Thus, identifying these genes and associated pathways could highlight predictive factors for HCC transformation and has implications in early diagnosis and treatment.AIMTo elucidate HBV oncogenesis in HCC and identify potential therapeutic targets.METHODSWe employed our Search, Tag, Analyze, Resource platform to conduct a meta-analysis of public data from National Center for Biotechnology Information’s Gene Expression Omnibus. We performed meta-analysis consisting of 155 tumor samples compared against 185 adjacent non-tumor samples and analyzed results with ingenuity pathway analysis.RESULTSOur analysis revealed liver X receptors/retinoid X receptor (RXR) activation and farnesoid X receptor/RXR activation as top canonical pathways amongst others. Top upstream regulators identified included the Ras family gene rab-like protein 6 (RABL6). The role of RABL6 in oncogenesis is beginning to unfold but its specific role in HBV-related HCC remains undefined. Our causal analysis suggests RABL6 mediates pathogenesis of HBV-related HCC through promotion of genes related to cell division, epigenetic regulation, and Akt signaling. We conducted survival analysis that demonstrated increased mortality with higher RABL6 expression. Additionally, homeobox A10 (HOXA10) was a top upstream regulator and was strongly upregulated in our analysis. HOXA10 has recently been demonstrated to contribute to HCC pathogenesis in vitro. Our causal analysis suggests an in vivo role through downregulation of tumor suppressors and other mechanisms.CONCLUSIONThis meta-analysis describes possible roles of RABL6 and HOXA10 in the pathogenesis of HBV-related HCC. RABL6 and HOXA10 represent potential therapeutic targets and warrant further investigation.

Genome-wide CRISPR knockout screening identified G protein pathway suppressor 2 as a novel tumor suppressor for uveal melanoma metastasis.

Uveal melanoma (UM) is the most common intraocular malignant tumor in adults. Due to the lack of effective treatments for metastatic UM, the survival of UM has not changed over the past 3 decades. Therefore, it is important to identify essential genes regulating the metastasis of UM. In this study, a genome-wide CRISPR knockout screen in an orthotopic mouse model of UM was performed to identify the regulatory genes conferring the metastatic phenotype. Loss-of-function analyses were performed to explore the function of G protein pathway suppressor 2 (GPS2) in UM metastasis in vitro and in vivo. RNA sequencing was performed to investigate the molecular mechanism underlying the function of GPS2 as a tumor suppressor in UM. Among the highest-ranking genes, we found several validated tumor suppressors, such asSHPRH, GPS2, PRPH2, and hsa-mir-1229; GPS2 was chosen as the candidate gene for further studies. GPS2 was lower expressed in the tumor tissues of UM patients. Furthermore, knocking-down GPS2 promoted the proliferation and metastatic abilities of UM cells both in vivo and in vitro. Finally, analysis of the transcriptome data revealed that silencing GPS2 upregulates oncogenic signaling pathways MAPK and PI3K-Akt, and in the meantime downregulates tumor suppressor signaling pathway Slit/Robo in UM cells. Altogether, our study proved that the GPS2 gene functions as a tumor suppressor and might be a novel potential therapeutic target for UM treatment.

Long Non-coding RNAs Sponging MicroRNAs With Efficacy in Preclinical In Vivo Models of Esophageal Squamous Cell Cancer.

Esophageal cancer is of two subtypes: Esophageal adenocarcinoma and esophageal squamous cell carcinoma (ESCC). Both are associated with a dismal prognosis. Therefore, the identification of new targets and treatment modalities is an issue of paramount importance. In this review, we focus on long non-coding RNAs (lncRNAs) which have been shown to mediate efficacy in preclinical in vivo models of ESCC by sponging microRNAs. Searching the literature, we identified four lncRNAs which were down-regulated and 23 which were up-regulated in comparison to corresponding normal tissues. The down-regulated lncRNAs lead to up-regulation of oncogenic pathways and down-regulation of tumor suppressors. The up-regulated lncRNAs target transcription factors, transmembrane receptors, cell-cycle related proteins, actin-binding proteins, signaling pathways, enzymes including epigenetic modification factors, cellular transport proteins and other categories. We describe reconstitution and inhibition of function of the corresponding lncRNAs and comment on validation and druggability of the identified targets.

Evaluation of Circulating MicroRNA-221 and Il-10 Levels as Potential Diagnostic Markers for Colorectal Cancer in Correlation with Prognosis

Background: Because of the capacity of MicroRNAs to down-regulate tumor suppressor expression and enhance tumorigenesis, they are of great importance in the knowledge of cancer. Aim of the study: To study the performance of miR-221 and IL-10 in colorectal carcinoma. Patients and methods: In the present study, venous blood specimens were taken from (55) patient suffering from colorectal cancer who were attending the Medical City, Baghdad (Teaching laboratories), during the period from 1st Jun. 2018 to 30th Sep. 2019. For detection of miRNA-221 expression in patient’s sera, the Real-time polymerase chain reaction (PCR) was used. Results: Descriptive analysis of miRNA-221 expression according to pathological grading and gender showed no significant difference (p > 0.05), however, variations of miRNA-221 expression among patient and controls revealed significant differences (p < 0.05). There was a highly significant difference in the mean serum IL-10 levels among patients with CRC when compared with the control group (p > 0.04). While the highest disease risk was correlated to higher mi-RNA-221 with IL-10 levels related with poor prognosis. Conclusion: The high expressions of mi-RNA-221 can act as prognostic markers in patients with colorectal cancer. Besides, the higher levels of miRNA-221 and IL-10 were correlated with worse prognosis.

Abstract 769: Genomic and transcriptomic characterization of benign and malignant struma ovarii

Abstract Background: Struma Ovarii (SO) is a rare ovarian teratoma characterized by the presence of thyroid tissue in >50% of the tumor. The majority of SO are benign; however, malignant transformation occurs in up to 5% of the cases. The molecular foundations of benign and malignant SO are grossly unknown. Therefore, the goal of this study was to perform the first comprehensive genomic and transcriptomic analysis of the benign and malignant SO. Material and Method: We performed whole-exome sequencing (WES) and targeted RNA-sequencing (seq) on the DNA and RNA extracted from formalin-fixed paraffin-embedded SO tumor tissue samples. WES library was prepared using Agilent’s SureSelect XT HS2 kit, with 4 samples failing the quality assessment (QA). Variants were called from GATK processed WES data and annotated using VEP (with ClinVar and COSMIC databases). The targeted RNA-Seq library was prepared using the TruSight RNA Pan-Cancer Panel kit covering 1385 cancer genes, with all samples passing QA. The clinical characteristics of the study cohort were summarized by percentages for categorical variables and medians with 25-75% interquartile ranges for continuous variables. Results: The study included 31 tissue samples - 21 benign and 10 malignant, including 6 cases of papillary thyroid cancer (PTC), 3 of follicular variant of PTC, and 1 of follicular thyroid cancer. Patients with benign SO were characterized by the median age at diagnosis of 39 years [33-54], tumor size of 3.1 cm [2.5-5.8], while the patients with malignant SO presented at age of 45 [28-54], tumor size of 6 cm [0.85-14] and metastatic disease in 30% (3/10) - 2 patients with peritoneal metastases and 1 patient with pelvic lymph node metastases. The E1A Binding Protein P300, EP300 (6/27), and Isocitrate dehydrogenase, IDH2 (5/27) were the topmost mutated genes in the SO samples. Malignant SO samples were characterized with the presence of pathogenic variants of KRAS (pQ61L and pG12V), NRAS (pQ61R), TP53 (splice site) mutations, and Nuclear Receptor Binding SET Domain Protein 1 (NSD1) fusion as the most common molecular drivers. Among benign SO samples, the most common driver was Thyroglobulin (TG) fusion with either Guanine Nucleotide binding protein (GNAS) or Rac Family Small GTPase 1 (RAC1). Differential expression analysis showed that the member of tumor suppressor family - tumor protein 63 (TP63) was the most downregulated (Log2FC = -3), while Double-sex and Mab-3 Related Transcription Factor 1 (DMRT1), implicated in the development of germ cell tumors, was the most upregulated gene in malignant SO samples over benign (Log2FC = 2.1; padj<0.05). Conclusions: In contrast to cancer arising from the thyroid gland, characterized by BRAFV600E as the most common mutation, malignant SO belongs to RAS-like tumors. The downregulation of tumor suppressors and upregulation of DMRT1 might be implicated in the malignant transformation of SO. Citation Format: Shilpa Thakur, Darryl Nousome, Kshama Aswath, Stephanie Cardenas, Sonam Kumari, Ruth Adewale, Maria Merino, Esra Dikoglu, Padmasree Veeraraghavan, Sriram Gubbi, Joanna Klubo-Gwiezdzinska. Genomic and transcriptomic characterization of benign and malignant struma ovarii [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 769.

Abstract 3717: KMT2D loss cooperates with PTCH loss for medulloblastoma genesis

Abstract We have previously reported that the histone H3 lysine 4 methyltransferase KMT2D (also called MLL4, MLL2, and ALR; a transcriptional coactivator) is required for neuronal differentiation of human neuron-committed NT2/D1 embryonal carcinoma stem cells. Notably, we have shown that brain-specific knockout of Kmt2d alone induces spontaneous medulloblastoma (MB) in mice and that Kmt2d loss in the brain highly upregulates several oncogenic signaling programs and downregulates tumor suppressor genes. Consistent with this, our analysis of several publicly available databases indicates that Kmt2d is the most frequently mutated epigenetic modifier (8%‒10%) in MB. In this study, we sought to assess whether Kmt2d loss cooperates with another oncogenic event in MB genesis. Particularly, PTCH (also known as PTCH1), a potent MB-signaling suppressor, is one of the most frequently mutated genes in MB, and KMT2D mutations co-occur with PTCH mutations more than with many other mutations in MB. Therefore, we determined the effect of Kmt2d loss on of Ptch+/--driven MB genesis by generating and analyzing Nestin-Cre Kmt2dfl/+ Ptch+/- mice. Our results showed that heterozygous loss of Kmt2d strongly increased the genesis and incidence of Ptch+/--driven MB. Supporting this, immunohistochemistry staining of Ki-67 (a proliferation marker) showed that heterozygous loss of Kmt2d in Ptch+/--driven MB highly increased the proliferation of MB cells. Our transcriptomic analysis showed that heterozygous Kmt2d loss upregulated tumor-promoting programs, including G-protein-coupled receptor signaling and oxidation-reduction process. In line with this, heterozygous Kmt2d loss upregulated oncogenic kinases (e.g., phospho-AKT1 and phospho-ERK) that may be downstream of G-protein-coupled receptor signaling. Mechanistically, our results indicate that these tumor-promoting programs are repressed, at least in part, by the transcription-repressive and tumor-suppressive factor (s) NCOR2, whose expression is activated by KMT2D. Our results would be the first to provide molecular insights into how co-losses of an epigenetic modifier and an MB-signaling suppressor cooperate for MB genesis. Our new mouse model would be helpful in future preclinical therapeutic experiments for MB treatment. Our findings suggest that targeting oncogenic effectors downstream of KMT2D loss can be considered a potential therapeutic strategy for MB treatment. Citation Format: Shilpa S. Dhar, Calena J. Brown, Ali S. Rizvi, Janak R. Abraham, Roy V. Sillitoe, Kaifu Chen, Min Gyu Lee. KMT2D loss cooperates with PTCH loss for medulloblastoma genesis [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 3717.

New synthetic phenylquinazoline derivatives induce apoptosis by targeting the pro-survival members of the BCL-2 family

Chemo-resistant cancer cells acquire robust growth potential through cell signaling mechanisms such as the down-regulation of tumor suppressors and the up-regulation of pro-survival proteins, respectively. To overcome chemo-resistance of cancer, small molecule drugs that interact with the cell signaling proteins to enhance sensitization of cancer cells toward cancer therapies are likely to be effective for the treatment of chemo-drug resistant cancer. To identify high potency small molecules, a series of ten novel phenylquinazoline derivatives were synthesized to determine their cellular effects in MCF-7 and MCF-7- cisplatin-resistant (CR) human breast cancer cells which led to the identification of two bioactive compounds, SMS-IV-20 and SMS-IV-40, that exhibited an elevated level of cytotoxicity against the human breast cancer cells and spheroid cells. In addition, both compounds enhanced chemo-sensitization of the human breast cancer cells that were genetically engineered to express the tumor suppressor and pro-apoptotic proteins, MOAP-1, Bax, and RASSF1a (MBR), suggesting that the compounds interact with the MBR signaling pathway. Furthermore, when MCF-7-CR cells were treated with SMS-IV-20 and SMS-IV-40 in the presence of ABT-737, a BCL-XL and BCL-2 inhibitor, enhanced chemo-sensitization was observed, suggesting SMS-IV-20 and SMS-IV-40 exert antagonistic activity to regulate the functional activity of BCL-2 and BCL-XL. Western blot analysis showed that both SMS-IV-20 and SMS-IV-40 induced down-regulation of BCL-2 or both BCl-2 and BCL-XL expression, respectively while promoting the release of mitochondrial Cytochrome C. Taken together, the data showed that SMS-IV-20 and SMS-IV-40 are potent activators of apoptosis that enhance chemo-sensitization through their antagonistic actions on the pro-survival activity of the BCl-2 family in human cancer cells.

In silico Study of Natural inhibitors for Human papillomavirus-18 E6 protein

Globally, the leading cause of death from cancer in women is infection with the human papillomavirus (HPV). This calls for imperative actions to explore anticancer drugs against this threatening viral infection, in which case, natural ingredients are presumed to be a promising source. Several studies show that plant-origin compounds such as allicin, apigenin, capsaicin, cyanidin, fisetin, genistein, laricitrin, naringenin, piperine, and syringetin have demonstrated therapeutic effects against several cancer types. In this study, the interaction mechanism of these compounds with HPV-18 E6 oncoprotein, that is known to downregulate tumor suppressor p53, was predicted using an in silico approach. Molecular docking simulations of natural ligands and E6 protein were performe, followed by chemical interaction analysis and 3D molecular visualization. Results indicated that fisetin is the best natural inhibitor as it has the lowest binding energy. It is highly recommended that the results of this study be used as a reference in designing anticancer drugs in vitro and in vivo.

Proteolysis-Targeting Chimera (PROTAC): Is the Technology Looking at the Treatment of Brain Tumors?

Post-translational modifications, such as ubiquitylation, need to be tightly controlled to guarantee the accurate localization and activity of proteins. Ubiquitylation is a dynamic process primarily responsible for proteasome-mediated degradation of substrate proteins and crucial for both normal homeostasis and disease. Alterations in ubiquitylation lead to the upregulation of oncoproteins and/or downregulation of tumor suppressors, thus concurring in tumorigenesis. PROteolysis-TArgeting Chimera (PROTAC) is an innovative strategy that takes advantage by the cell’s own Ubiquitin-Proteasome System (UPS). Each PROTAC molecule is composed by a ligand that recruits the target protein of interest (POI), a ligand specific for an E3 ubiquitin ligase enzyme, and a linker that connects these units. Upon binding to the POI, the PROTAC recruits the E3 inducing ubiquitylation-dependent proteasome degradation of the POI. To date, PROTAC technology has entered in clinical trials for several human cancers. Here, we will discuss the advantages and limitations of PROTACs development and safety considerations for their clinical application. Furthermore, we will review the potential of PROTAC strategy as therapeutic option in brain tumor, focusing on glioblastoma.

Processing body (P-body) and its mediators in cancer.

In recent years, processing bodies (P-bodies) formed by liquid-liquid phase separation, have attracted growing scientific attention due to their involvement in numerous cellular activities, including the regulation of mRNAs decay or storage. These cytoplasmic dynamic membraneless granules contain mRNA storage and decay components such as deadenylase and decapping factors. In addition, different mRNA metabolic regulators, including m6A readers and gene-mediated miRNA-silencing, are also associated with such P-bodies. Cancerous cells may profit from these mRNA decay shredders by up-regulating the expression level of oncogenes and down-regulating tumor suppressor genes. The main challenges of cancer treatment are drug resistance, metastasis, and cancer relapse likely associated with cancer stem cells, heterogeneity, and plasticity features of different tumors. The mRNA metabolic regulators based on P-bodies play a great role in cancer development and progression. The dysregulation of P-bodies mediators affects mRNA metabolism. However, less is known about the relationship between P-bodies mediators and cancerous behavior. The current review summarizes the recent studies on P-bodies mediators, their contribution to tumor development, and their potential in the clinical setting, particularly highlighting the P-bodies as potential drug-carriers such as exosomes to anticancer in the future.

Hsa-miR-21-3p associates with breast cancer patient survival and targets genes in tumor suppressive pathways.

Breast cancer is the cancer most often diagnosed in women. MicroRNAs (MIRs) are short RNA molecules that bind mRNA resulting in their downregulation. MIR21 has been shown to be an oncomiR in most cancer types, including breast cancer. Most of the effects of miR-21 have been attributed to hsa-miR-21-5p that is transcribed from the leading strand of MIR21, but hsa-miR-21-3p (miR-21-3p), transcribed from the lagging strand, is much less studied. The aim of the study is to analyze whether expression of miR-21-3p is prognostic for breast cancer. MiR-21-3p association with survival, clinical and pathological characteristics was analyzed in a large breast cancer cohort and validated in three separate cohorts, including TCGA and METABRIC. Analytical tools were also used to infer miR-21-3p function and to identify potential target genes and functional pathways. The results showed that in the exploration cohort, high miR-21-3p levels associated with shorter survival and lymph node positivity. In the three validation cohorts, high miR-21-3p levels associated with pathological characteristics that predict worse prognosis. Specifically, in the largest validation cohort, METABRIC (n = 1174), high miR-21-3p levels associated with large tumors, a high grade, lymph node and HER2 positivity, and shorter breast-cancer-specific survival (HR = 1.38, CI 1.13–1.68). This association remained significant after adjusting for confounding factors. The genes with expression levels that correlated with miR-21-3p were enriched in particular pathways, including the epithelial-to-mesenchymal transition and proliferation. Among the most significantly downregulated targets were MAT2A and the tumor suppressive genes STARD13 and ZNF132. The results from this study emphasize that both 3p- and 5p-arms from a MIR warrant independent study. The data show that miR-21-3p overexpression in breast tumors is a marker of worse breast cancer progression and it affects genes in pathways that drive breast cancer by down-regulating tumor suppressor genes. The results suggest miR-21-3p as a potential biomarker.

40P MALAT-1/miR-30a-5p competing endogenous (ceRNA) network releases the brakes of immune surveillance in breast cancer through its quadruple targets: PD-L1, MIF, IL-10 and TNF-α

The tumor immune escape phenomenon is a vicious cycle of smart tactics orchestrated by cancer cells to evade immune recognition. Induction of co-inhibitor molecules such as macrophage migration inhibitory factor (MIF), immune checkpoints such as PD-L1and immunoinhibitory cytokines such as IL-10 and TNF-α in the tumor microenvironment are the most effective strategies cancer cells follow to holds the brakes of the immune surveillance phenomena. Immune evasion tactics in breast cancer (BC) patients are still poorly understood. Yet, strong evidence supports the involvement of immune inhibitory cytokines and upregulation of PD-L1 and MIF in BC patients. Non-coding RNAs (ncRNAs) are endogenous molecules that have the ability to form a signaling network modulating multiple targets simultaneously. Our group has recently reported the involvement of MALAT-1 in tuning the immuno-oncogenic profile of BC. Yet, microRNA-30a-5p is a novel miRNA in terms of immunoncology and its involvement in MALAT-1 modulatory network is yet to be explored. The aim of this study was to investigate the involvement of miR-30a-5p in MALAT-1circuit and its impact of PD-L1, MIF, IL-10 and TNF-α in BC. BC patients (n=24) were recruited. Bioinformatics analysis was performed. MDA-MB-231 cells were cultured transfected by miR-30a-5p oligonucleotides and MALAT-1 siRNAs using Hiperfect Transfection protocol. RNA was extracted using biazol, reverse transcribed and quantified using q-RTPCR. MALAT-1 and miR-30a-5p are paradoxically acting ncRNAs in BC patients. MALAT-1 is an upregulated oncogenic lncRNA while miR-30a-5p is a downregulated tumor suppressor miRNA in BC patients. In-silico analysis showed a strong binding of miR-30a-5p to MALAT-1. Experimentally, ectopic expression of miR-30a-5p represses MALAT-1 levels while MALAT-1 siRNAs induced miR-30a-5p levels in MDA-MB-231 cells. miR-30a-5p mimics and/or MALAT-1 siRNAs resulted in a marked repression of PD-L1, MIF, IL-10 and TNF-α. MALAT-1/miR-30a-5p are vital players releasing the immune surveillance brakes supported by BC cells. Dual targeting of MALAT-1 and miR-30a-5p is novel immune-oncological therapeutic approach in BC.