CSIG-26. NF2/MERLIN DRIVES MENINGIOMA APOPTOSIS AND SUCEPTIBILITY TO CYTOTOXIC THERAPY

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi39-vi39
Author(s):  
Charlotte Eaton ◽  
Abrar Choudhury ◽  
Timothy Casey-Clyde ◽  
Danielle Swaney ◽  
Nevan Krogan ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tumor Suppressor ◽  
Rna Sequencing ◽  
Cell Biology ◽  
Target Genes ◽  
Copy Number Variant ◽  
Receptor Expression ◽  
Cytotoxic Therapy

Abstract BACKGROUND Alterations in NF2 underlie meningioma tumorigenesis, but tumor suppressor functions of the NF2 gene product, Merlin, are incompletely understood in meningiomas. Here we integrate proteomic proximity-labelling mass spectrometry with CRISPR interference (CRISPRi), RNA sequencing, and biochemical approaches to discover Merlin drives meningioma apoptosis and susceptibility to cytotoxic therapy. METHODS RNA sequencing was performed on triplicate M10G meningioma cells stably expressing CRISPRi machinery and either non-targeting control sgRNAs, sgRNAs suppressing NF2, or sgRNAs suppressing NF2 with Merlin rescue. QPCR in IOMM-Lee and MSC1 meningioma cells expressing non-targeting control shRNAs or shRNAs suppressing NF2 was used for orthogonal validation in vitro. RNA sequencing of euploid meningiomas (n=52) or meningiomas with loss of NF2 as the only copy number variant (n=28) was used for orthogonal validation in vivo. Merlin interactors in meningioma cells were identified using APEX proteomic proximity-labelling mass spectrometry. Mechanistic and functional studies were performed using biochemical, molecular, and cell biology approaches in meningioma cells and CH-157MN meningioma xenografts treated with cytotoxic chemotherapy or ionizing radiation. RESULTS Merlin suppression in meningioma cells and xenografts inhibited pro-apoptotic interferon regulatory factor (IRF) target genes and attenuated meningioma apoptosis. Merlin suppression did not alter IRF stability or subcellular localization in meningioma cells, and proteomic proximity-labelling mass spectrometry revealed a novel interaction between wildtype Merlin and ARHGAP35, a DNA binding factor that inhibits glucocorticoid receptor expression (NR3C1). NR3C1 inhibits IRF activity to prevent apoptosis, and Merlin suppression in meningioma cells induced NR3C1expression, which was inhibited by Merlin rescue. Further, NR3C1 suppression rescued meningioma cell apoptosis in the absence of Merlin, and NR3C1 expression was increased in human meningiomas with loss of NF2 compared to euploid meningiomas. CONCLUSIONS These data shed light on a novel pro-apoptotic tumor suppressor function of Merlin regulating glucocorticoid signalling and susceptibility to cytotoxic therapy in meningiomas.

The Pten/PI3K pathway governs the homeostasis of Vα14iNKT cells

Blood ◽  
2006 ◽  
Vol 109 (8) ◽  
pp. 3316-3324 ◽  
Author(s):  
Hiroyuki Kishimoto ◽  
Toshiaki Ohteki ◽  
Nobuyuki Yajima ◽  
Koichi Kawahara ◽  
Miyuki Natsui ◽  
...  
Keyword(s):  
Dendritic Cells ◽  
Tumor Suppressor ◽  
Pi3k Pathway ◽  
Melanoma Cells ◽  
Receptor Expression ◽  
Cytokine Secretion ◽  
Pten Mutation ◽  
Human Cancers

Abstract The tumor suppressor PTEN is mutated in many human cancers. We previously used the Cre-loxP system to generate mice (LckCrePten mice) with a Pten mutation in T-lineage cells. Here we describe the phenotype of Pten-deficient Vα14iNKT cells. A failure in the development of Vα14iNKT cells occurs in the LckCrePten thymus between stage 2 (CD44highNK1.1−) and stage 3 (CD44highNK1.1+), resulting in decreased numbers of peripheral Vα14iNKT cells. In vitro, Pten-deficient Vα14iNKT cells show reduced proliferation and cytokine secretion in response to αGalCer stimulation but enhanced inhibitory Ly49 receptor expression. Following interaction with dendritic cells (DCs) loaded with αGalCer, Pten-deficient Vα14iNKT cells demonstrate activation of PI3K. Indeed, the effects of the Pten mutation require intact function of the PI3K subunits p110γ and p110δ. In vivo, LckCrePten mice display reduced serum IFNγ after αGalCer administration. Importantly, Vα14iNKT cell–mediated protection against the metastasis of melanoma cells to the lung was impaired in the absence of Pten. Thus, the Pten/PI3K pathway is indispensable for the homeostasis and antitumor surveillance function of Vα14iNKT cells.

Retinoblastoma Protein and the Leukemia-Associated PLZF Transcription Factor Interact To Repress Target Gene Promoters.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 1240-1240
Author(s):  
Kevin R. Petrie ◽  
Fabien Guidez ◽  
Jun Zhu ◽  
Gareth Owen ◽  
Yat Peng Chew ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Stem Cell ◽  
Transcriptional Repression ◽  
Cell Biology ◽  
Target Genes ◽  
Retinoic Acid Receptor ◽  
Gene Promoters ◽  
Cell Commitment

Abstract Translocations of the retinoic acid receptor alpha (RARA) locus with the PLZF or PML genes lead to expression of oncogenic PLZF-RARα or PML-RARα fusion proteins, respectively. These fusion oncoproteins constitutively repress RARα target genes, in large part through aberrant recruitment of multiprotein co-repressor complexes. PML and PML-RARα have previously been shown to associate with the retinoblastoma (Rb) tumour suppressor protein in its hypophosphorylated state. Here we demonstrate that PLZF also interacts with Rb in vitro and in vivo. The interaction between PLZF and Rb is mediated through the Rb pocket and the region of PLZF that lies between its transcriptional repression (POZ) and DNA binding (zinc-finger) domains. Additionally, Rb can simultaneously interact with PLZF and the E2F1 S phase-inducing transcription factor, suggesting that these proteins can exist in the same multiprotein complex. In contrast to the interaction between PML or E2F1 with Rb, the PLZF-Rb interaction is not dependent on hypophosphorylation of Rb. The interaction between PLZF and Rb is further underlined by chromatin immunoprecipitation analysis of PLZF binding to genomic DNA, which shows that PLZF associates with genes controlling cell proliferation known to be regulated by Rb and E2F (for example cdc6). Co-expression of PLZF and Rb results in enhancement of transcriptional repression of PLZF and E2F target genes, indicating functional co-operation between the two proteins. Both PLZF and Rb have been shown to have roles in stem cell biology and, taken together, these data provide a plausible scenario in which interactions between PLZF and Rb function in stem cell commitment or maintenance and self-renewal. The oncogenic PLZF-RARα fusion also interacts with Rb, suggesting that deregulation of Rb function may be a factor in the molecular pathogenesis of PLZF-RARα associated acute promyelocytic leukemia.

MYC Regulation Via the LIN28B/Let-7 Axis in Multiple Myeloma

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1755-1755
Author(s):  
Salomon Manier ◽  
John Powers ◽  
Antonio Sacco ◽  
Siobhan Glavey ◽  
Daisy Huynh ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Rna Sequencing ◽  
Target Genes ◽  
Conflicts Of Interest ◽  
Scid Mice ◽  
Cellular Reprogramming ◽  
Western Blots

Abstract Background. LIN28B regulates developmental processes and cellular reprogramming by suppressing let-7 microRNAs (miRNAs). A role for LIN28B has been reported in cancers, however the LIN28B/let-7 axis has not been studied in multiple myeloma (MM). Methods. LIN28B level expression in MM patients was studied using previously published gene expression profiling (GEP) datasets. Knockdown (KD) of LIN28B was performed on MM cell lines (U266, MOLP-8) using 2 shRNA and validated using 2 sgRNA by CRISPR knockout (KO). Downstream regulations were assessed by qRT-PCR and western blots, as well as RNA sequencing. For RNA sequencing, control and Lin28B CRISPR cells were used for library preparation (NEBNext kit) and sequencing on a HiSeq 2000. Proliferation of KD and KO cells were evaluated in vitro and in vivo in a xenograft mouse model. An LNA-GapmeR technology was used to develop a let-7 mimic in vivo in SCID mice. Findings. Two independent GEP datasets (GSE16558; GSE2658) were analyzed for LIN28B expression, showing a significantly higher level in MM patients compared to healthy controls. In addition, high LIN28B levels correlated with a shorter overall survival (p = 0.0226), along with an enrichment of let-7 target genes by Gene Set Enrichment Analyses (GSEA). LIN28B KD cells had a significantly increased expression level of let-7 family members and were associated with down-regulation of let-7 target genes Myc and Ras at the protein level. We further confirmed downstream regulation of MYC and RAS in a LIN28B CRISPR KO model in MM cells (MOPL-8). We next validated the role of LIN28B in MM in vivo by using a xenograft tumor model showing a decreased tumor burden in LIN28B KD mice compared to scramble control (p =0.0045). In addition, we performed a RNA sequencing from the CRISPR LIN28B KO and control cells and observed a central role by GSEA for both MYC and E2F cell cycle pathways in LIN28B-engineered cells. LIN28B activity in regulating MYC and cell proliferation was further defined to be dependent on let-7 by performing a rescue experiment in MM1S cells. Moreover, we explored the possibility to therapeutically regulate MYC expression through let-7 with an LNA-GapmeR containing a let-7b mimic, in vivo, and showed that high levels of let-7 expression represses tumor growth in SCID mice by regulating MYC expression compared to control GapmeR treated mice (p = 0.0026). Conclusions. These findings reveal the essential role of LIN28B/let-7 in regulating two essential oncogenic pathways in MM, MYC and RAS. Interference with this pathway may represent an efficient option for targeting MYC in cancer. Disclosures No relevant conflicts of interest to declare.

scholarly journals GNA14 stimulation of KLF7 promotes malignant growth of endometrial cancer through upregulation of HAS2

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jing Wang ◽  
Fei Teng ◽  
Hongxia Chai ◽  
Caixia Zhang ◽  
Xiaolei Liang ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Proliferation ◽  
Endometrial Cancer ◽  
Rna Sequencing ◽  
Colony Formation ◽  
Cell Biology ◽  
Cell Cycle Progression ◽  
Α Subunit

Abstract Background Endometrial cancer (UCEC) is one of the most common gynecological malignancies. We previously found that overexpression of G protein α subunit 14 (GNA14) promoted UCEC growth. Krüppel-like factor 7 (KLF7) acts as an oncogene in various cancer types, whereas the connection between GNA14 and KLF7 in UCEC is unclear. We herein explored the involvement of GNA14/KLF7 in UCEC development. Methods Clinical relevance of GNA14, KLF7 and HAS2 in UCEC was analyzed from TCGA and by immunohistochemical staining. Knockdown and overexpression of indicated genes were conducted by transfecting the cells with siRNAs and lentivirus, respectively. mRNA and protein expression was detected by qRT-PCR and Western blot. CCK8, colony formation, cell cycle, apoptosis, transwell and wound healing were performed to check cell biology function in vitro. Tumor growth in nude mice was conducted to check in vivo function. RNA sequencing was used to determine dys-regulated genes. Results We demonstrated that GNA14 stimulated the expression of KLF7 in UCEC cells. There was a positive correlation between GNA14 and KLF7 in normal and UCEC tissues. In vitro, KLF7 promoted cell proliferation, colony formation, cell cycle progression, and migration of UCEC cells. Apoptosis was inhibited by KLF7. Xenografted tumorigenesis of UCEC cells was suppressed by KLF7 knockdown. Furthermore, RNA sequencing results showed that KLF7 regulated the expression of a large amount of genes, among which hyaluronan synthase 2 (HAS2) was downregulated in KLF7 knockdown cells. Based on TCGA database and immunoblotting assays, KLF7 positively regulated HAS2 in UCEC cells and tissues. Lastly, knockdown of HAS2 reversed the oncogenic role of KLF7 on UCEC cell proliferation, migration, and xenografted tumor development. Conclusion Taken together, we reveal that GNA14/KLF7/HAS2 signaling cascade exerts tumor promoting function during UCEC development.

scholarly journals Inactivation of the PBRM1 tumor suppressor gene amplifies the HIF-response in VHL−/−clear cell renal carcinoma

2017 ◽  
Vol 114 (5) ◽  
pp. 1027-1032 ◽  
Author(s):  
Wenhua Gao ◽  
Wei Li ◽  
Tengfei Xiao ◽  
Xiaole Shirley Liu ◽  
William G. Kaelin
Keyword(s):  
Tumor Suppressor ◽  
Tumor Suppressor Gene ◽  
Target Genes ◽  
Clear Cell ◽  
Suppressor Gene ◽  
Loss Of Function ◽  
Renal Carcinogenesis ◽  
Transcriptional Signature

Most clear cell renal carcinomas (ccRCCs) are initiated by somatic inactivation of theVHLtumor suppressor gene. TheVHLgene product, pVHL, is the substrate recognition unit of an ubiquitin ligase that targets the HIF transcription factor for proteasomal degradation; inappropriate expression of HIF target genes drives renal carcinogenesis. Loss of pVHL is not sufficient, however, to cause ccRCC. Additional cooperating genetic events, including intragenic mutations and copy number alterations, are required. Common examples of the former are loss-of-function mutations of thePBRM1andBAP1tumor suppressor genes, which occur in a mutually exclusive manner in ccRCC and define biologically distinct subsets of ccRCC.PBRM1encodes the Polybromo- and BRG1-associated factors-containing complex (PBAF) chromatin remodeling complex component BRG1-associated factor 180 (BAF180). Here we identified ccRCC lines whose ability to proliferate in vitro and in vivo is sensitive to wild-type BAF180, but not a tumor-associated BAF180 mutant. Biochemical and functional studies linked growth suppression by BAF180 to its ability to form a canonical PBAF complex containing BRG1 that dampens the HIF transcriptional signature.

scholarly journals RNA sequencing reveals an additional Crz1-binding motif in promoters of its target genes in the human fungal pathogen Candida albicans

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Huihui Xu ◽  
Tianshu Fang ◽  
Raha Parvizi Omran ◽  
Malcolm Whiteway ◽  
Linghuo Jiang
Keyword(s):  
Candida Albicans ◽  
Rna Sequencing ◽  
Microarray Analysis ◽  
Target Genes ◽  
Binding Motif ◽  
Cellular Transport ◽  
Gene Promoters ◽  
Calcium Stress

Abstract Background The calcium/calcineurin signaling pathway is mediated by the transcription factors NFAT (nuclear factor of activated T cells) in mammals and Crz1 (calcineurin-responsive zinc finger 1) in yeasts and other lower eukaryotes. A previous microarray analysis identified a putative Crz1-binding motif in promoters of its target genes in Candida albicans, but it has not been experimentally demonstrated. Methods An inactivation mutant for CaCRZ1 was generated through CRISPR/Cas9 approach. Transcript profiling was carried out by RNA sequencing of the wild type and the inactivation mutant for CaCRZ1 in response to 0.2 M CaCl2. Gene promoters were scanned by the online MEME (Multiple Em for Motif Elicitation) software. Gel electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) analysis were used for in vitro and in vivo CaCrz1-binding experiments, respectively. Results RNA sequencing reveals that expression of 219 genes is positively, and expression of 59 genes is negatively, controlled by CaCrz1 in response to calcium stress. These genes function in metabolism, cell cycling, protein fate, cellular transport, signal transduction, transcription, and cell wall biogenesis. Forty of these positively regulated 219 genes have previously been identified by DNA microarray analysis. Promoter analysis of these common 40 genes reveals a consensus motif [5′-GGAGGC(G/A)C(T/A)G-3′], which is different from the putative CaCrz1-binding motif [5′-G(C/T)GGT-3′] identified in the previous study, but similar to Saccharomyces cerevisiae ScCrz1-binding motif [5′-GNGGC(G/T)CA-3′]. EMSA and ChIP assays indicate that CaCrz1 binds in vitro and in vivo to both motifs in the promoter of its target gene CaUTR2. Promoter mutagenesis demonstrates that these two CaCrz1-binding motifs play additive roles in the regulation of CaUTR2 expression. In addition, the CaCRZ1 gene is positively regulated by CaCrz1. CaCrz1 can bind in vitro and in vivo to its own promoter, suggesting an autoregulatory mechanism for CaCRZ1 expression. Conclusions CaCrz1 differentially binds to promoters of its target genes to regulate their expression in response to calcium stress. CaCrz1 also regulates its own expression through the 5′-TGAGGGACTG-3′ site in its promoter.

scholarly journals LINC00473 promotes the Taxol resistance via miR-15a in colorectal cancer

2018 ◽  
Vol 38 (5) ◽  
Author(s):  
Lin Wang ◽  
Xufeng Zhang ◽  
Li Sheng ◽  
Chun Qiu ◽  
Rongcheng Luo
Keyword(s):  
Colorectal Cancer ◽  
Tumor Suppressor ◽  
Target Genes ◽  
Tumor Regression ◽  
Large Tumor ◽  
Apoptosis Pathway ◽  
Normal Tissues ◽  
Taxol Resistance

Dysregulation of long non-coding RNAs (LncRNAs) participated into the initiation and progression of different diseases via direct regulation of proteins or indirect regulation of microRNA (miRNA)-target genes. LINC00473 is a novel carcinoma-related LncRNA and up-regulated in many cancers for tumor growth and metastasis, but its role in chemotherapy resistance is unclear. We here investigated the function of LINC00473 in colorectal cancer (CRC) in vitro and in vivo. The CRC tissues (n=20) and relative normal tissues were collected and found that LINC00473 was overexpressed in CRC tissues when compared with which in normal tissues. Highly expressed LINC00473 predicted large tumor size, high TNM stage of CRC patients. Interestingly, the tumor suppressor miR-15a was down-regulated and negatively correlated with LINC00473 levels in CRC. LINC00473 harbored the binding sites for miR-15a and reduced its availability in CRC cell line HCT116. Knockdown of LINC00473 elevated the expression of miR-15a. Moreover, in the Taxol-resistant HCT116, the LINC00473 level was further increased than that in HCT116. Knockdown of LINC00473 restored the Taxol-induced cytotoxicity, inhibited the cell vitality, colony formation and induced apoptosis, impaired the ability of migration or invasion, but these effects could be abrogated by the inhibition of miR-15a. Mechanistically, the BCL-2-related anti-apoptosis pathway was activated and the multidrug-resistant (MDR) genes LRP, MDR1 were up-regulated by LINC00473. Furthermore, inhibition of LINC00473 in vivo could overcome the Taxol resistance of CRC cells, could recover the expression of tumor suppressor miR-15a and chemotherapy-induced tumor regression, indicating that LINC00473 functioned as oncogene in CRC via miR-15a.

Targeting of Casein Kinase II (CK2) Enhances Ikaros-Mediated Control of the Cell Cycle Progression in Pre-Clinical Model of Pre-B-ALL.

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 2431-2431
Author(s):  
Sinsa Dovat ◽  
Chunhua Song ◽  
Kimberly J Payne ◽  
Chandrika S. Gowda
Keyword(s):  
Cell Cycle ◽  
Tumor Suppressor ◽  
Cell Cycle Progression ◽  
Target Genes ◽  
Signal Transduction Pathway ◽  
Preclinical Model ◽  
Suppressor Activity ◽  
Cycle Progression

Abstract Abstract 2431 The Ikaros (IKZF1) gene encodes a DNA-binding zinc finger protein that functions as a tumor suppressor in leukemia. Defects in the Ikaros gene that lead to its decreased activity are associated with the development of B-cell precursor acute lymphoblastic leukemia (pre-B-ALL). However, the mechanisms by which Ikaros exerts its tumor suppressor activity, as well as the mechanisms that control the tumor suppressor function of Ikaros are poorly understood. Here, we report the identification of two novel Ikaros target genes, as well as a signal transduction pathway that regulates the Ikaros-mediated transcriptional control of these genes in pre-B ALL. We also present evidence that targeting the signal transduction pathway which regulates Ikaros transcriptional control is a potent therapeutic tool for treating pre-B ALL. Analysis of the promoter sequences of the CDC7 and the CDK6 genes revealed multiple evolutionarily-conserved Ikaros consensus binding sites. Using qChIP (quantitative chromatin immunoprecipitation assay) we found that Ikaros binds in vivo to the promoters of the CDC7 and CDK6 genes in the human Nalm6 pre-B ALL cell line, and in primary human pre-B ALL cells. This led to the hypothesis that Ikaros regulates transcription of CDC7 and CDK6 - genes whose expression is essential for cell cycle progression and cellular proliferation. The effect of Ikaros on CDC7 and CDK6 expression was studied using a transient co-transfection assay. Luciferase reporter plasmids containing the CDC7 or CDK6 promoter regions were co-transfected with or without Ikaros into 293T cells. Co-transfection of Ikaros led to decreased luciferase activity, suggesting that Ikaros acts as a repressor of the CDC7 and CDK6 upstream regulatory elements. Increased expression of Ikaros via retroviral transduction in Nalm6 cells resulted in decreased transcription of CDC7 and CDK6. Decreased transcription of these genes was associated with increased binding of Ikaros to their promoter regions as measured by qChIP. These results suggest that Ikaros negatively regulates transcription of CDC7 and CDK6, and thus negatively regulates cell cycle progression in pre-B cell leukemia. We have shown previously that phosphorylation of Ikaros by casein kinase II (CK2) inhibits Ikaros' ability to bind DNA and to regulate transcription of its target genes. CK2 activity is elevated in human leukemia. We tested whether the inhibition of CK2 affects the transcription of CDC7 and CDK6 in pre-B ALL in vitro and in vivo. In vitro treatment of Nalm6 pre-B ALL with TBB, a specific CK2 inhibitor, decreased transcription of CDC7 and CDK6 and was associated with increased binding of Ikaros to the promoters of these genes. Using an in vivo preclinical model of pre-B ALL we tested whether targeting of CK2 would affect transcription of CDC7 and CDK6. In vivo treatment of a human-mouse xenograft model of pre-B ALL with a CK2 inhibitor resulted in decreased transcription of CDC7 and CDK6 and strongly increased Ikaros binding to the promoters of these genes. The in vivo targeting of CK2 provided a strong anti-leukemia effect that resulted in the prolonged survival of treated mice as compared to controls. In summary, our results suggest that Ikaros exerts its tumor suppressor activity in pre-B ALL by repressing transcription of cell cycle-promoting genes. Targeting CK2 in vivo enhances Ikaros-mediated repression of cell cycle progression resulting in an anti-leukemia effect. These data demonstrate the efficacy of CK2 targeting as a treatment for pre-B ALL in a preclinical model. These results provide a mechanistic rationale and support for the use of CK2 inhibitors as a targeted treatment of pre-B ALL in early-stage clinical trials. Supported by National Institutes of Health R01 HL095120 and a St. Baldrick's Foundation Career Development Award (to S.D.). Disclosures: No relevant conflicts of interest to declare.

EPCO-05. GENOME-WIDE ANALYSIS OF TEAD1 OCCUPANCY IN BIOLOGICALLY DISTINCT GLIOBLASTOMA SAMPLES

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi2-vi2
Author(s):  
Tanvi Joshi ◽  
German Nudelman ◽  
Elena Zaslavsky ◽  
Nadejda Tsankova
Keyword(s):  
Cell Biology ◽  
Target Genes ◽  
Specific Binding ◽  
Treatment Options ◽  
Critical Role ◽  
Negative Control ◽  
Functional Enrichment ◽  
Rapid Progression

Abstract The diffusely infiltrative nature of glioblastoma (GBM) cells is a major contributor to the disease’s aggressive behavior, including its rapid progression and therapeutic resistance. Moreover, current treatment options do not target the invasive nature of GBM. Recent chromatin accessibility studies prioritized enrichment of the TEAD1 transcription factor motif in glioblastoma stem cell biology and subsequent knockout and overexpression studies confirmed a critical role for TEAD1 in GBM migration, in vitro and in vivo. However, the downstream mechanisms through which TEAD1 regulates GBM cell migration remain poorly understood. In this study, we performed chromatin immunoprecipitation (ChIP-seq) using TEAD1-specific antibody and IgG as non-specific binding control, to characterize TEAD1 occupancy across GBM samples with unique genomic alterations. ChIP-seq peaks were called using MACS2, filtered for duplicates and blacklisted regions, and normalized per sample to their respective genomic input. Initial functional enrichment analyses were performed on three GBM samples with the highest number of TEAD1 occupancy peaks using CistromeGO, which ranked genes based on their TEAD1-specific regulatory potential (RP) score, as a function of peak number and distance from the transcription start site. Analyses of the top 1000 genes with highest TEAD1 RP scores identified 132 common targets across all samples, including known TEAD target genes ETV1 and Cyr61, which related to angiogenesis, cadherin and integrin signaling, cell adhesion, and chromatin regulation gene ontology terms, among others. Interestingly, KEGG pathway analysis also revealed Hippo pathway enrichment across all GBM samples, suggesting a possible TEAD1 regulatory feedback loop in GBM. Analysis of TEAD1 ChIP-seq peaks in non-GBM negative control tissue did not show functional enrichment for any of the terms seen in the GBM samples. Ongoing analyses are focused on characterizing TEAD1 occupancy at active cis-regulatory regions using parallel H3K27ac ChIP-seq data, in order to prioritize the most salient TEAD1-regulatory targets in GBM.

iTSP-PseAAC: Identify Tumor Suppressor Proteins by Using Fully Connected Neural Network and PseAAC

2021 ◽  
Vol 15 ◽  
Author(s):  
Muhammad Awais ◽  
Waqar Hussain ◽  
Nouman Rasool ◽  
Yaser Daanial Khan
Keyword(s):  
Tumor Suppressor ◽  
Cross Validation ◽  
Control Cell ◽  
Normal Function ◽  
In Vivo Studies ◽  
Tumor Suppressor Proteins ◽  
Proposed Model ◽  
Self Consistency

Background: The uncontrolled growth due to accumulation of genetic and epigenetic changes as a result of loss or reduction in the normal function of Tumor Suppressor Genes (TSGs) and Pro-oncogenes is known as cancer. TSGs control cell division and growth by repairing of DNA mistakes during replication and restrict the unwanted proliferation of a cell or activities, those are the part of tumor production. Objectives: This study aims to propose a novel, accurate, user-friendly model to predict tumor suppressor proteins, which would be freely available to experimental molecular biologists to assist them using in vitro and in vivo studies. Methods: The predictor model has used the input feature vector (IFV) calculated from the physicochemical properties of proteins based on FCNN to compute the accuracy, sensitivity, specificity, and MCC. The proposed model was validated against different exhaustive validation techniques i.e. self-consistency and cross-validation. Results: Using self-consistency, the accuracy is 99%, for cross-validation and independent testing has 99.80% and 100% accuracy respectively. The overall accuracy of the proposed model is 99%, sensitivity value 98% and specificity 99% and F1-score was 0.99. Conclusion: It concludes, the proposed model for prediction of the tumor suppressor proteins can predict the tumor suppressor proteins efficiently, but it still has space for improvements in computational ways as the protein sequences may rapidly increase, day by day.

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