Tumor Suppressor Gene Research Articles

In silico screening and identifying phytoconstituents of Withania somnifera as potent inhibitors of BRCA1 mutants: A therapeutic against breast cancer

Breast CAncer gene 1 (BRCA1) is an anti-oncogene that helps the cell repair damaged DNA and preserve genetic material. BRCA1 also acts as a cell growth suppressor and produces tumor suppressor gene (TSG) proteins, i.e., BRCA1 protein. Remarkably, BRCA1 mutations account for 90 % of hereditary breast cancer and a majority of hereditary ovarian cancer. Hence, we have considered three mutants of BRCA1 (R1699W, R1699Q, T1700A) in this study and adopted an in-silico approach to find the best possible phytochemical to inhibit these mutated proteins, enabling early breast cancer diagnosis. Perceiving the importance, many natural molecules from ancient medicinal plants are considered for molecular docking. Our findings suggest that though many molecules bind actively with the receptor's active site, the top three phytoconstituents (27-Deoxy-14-hydroxywithaferin A, Withacoagulin, Somniferanolide) of Withania somnifera, commonly known as Ashwagandha, have high binding affinities and suitable pharmacokinetic properties, making these natural compounds potential drug candidates. Further, molecular dynamics (MD) simulation and the binding free energy calculation show stability and thermodynamically favourable. We can, therefore, draw the conclusion that these lead compounds act as potential inhibitors against BRCA1. However, wet lab experiments and clinical trials are recommended to ascertain its efficacy, hence the development of novel BRCA1 inhibitors.

Single-cell CRISPR screening characterizes transcriptional deregulation in T-cell acute lymphoblastic leukemia.

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive type of leukemia caused by accumulation of multiple genetic alterations in T-cell progenitors. However, for many genes it remains unknown how their mutations contribute to disease development. We therefore performed two single-cell CRISPR screens in primary pro-T cells ex vivo to study the transcriptional impact of loss-of-function alterations in T-ALL and correlate this with effects on cell fitness. The various perturbations were clustered based on their effects on E2F/MYC or STAT/NOTCH signatures, which play a defining role in driving T-cell proliferation. Many of the perturbations resulted in positive effects on the STAT and NOTCH signatures and were predicted to behave as haploinsufficient tumor suppressors in T-ALL. Additionally, Spi1 was identified as an essential gene for pro-T-cell survival, associated with deregulation of the MYC signature and epigenetic consequences. In contrast, Bcl11b was identified as a strong tumor suppressor gene in immature T lymphocytes, associated with deregulation of NF-kB and JAK/STAT signaling. We found a correlation between BCL11B expression level and JAK/STAT pathway mutations in T-ALL patients and demonstrated oncogenic cooperation between Bcl11b inactivation and JAK3 hyperactivation in pro-T cells. Altogether, these single-cell CRISPR screens in pro-T cells provide fundamental insights into the mechanisms of transcriptional deregulation caused by genetic alterations in T-ALL.

Molecular profiling of oral epithelial dysplasia and oral squamous cell carcinoma using next generation sequencing

BackgroundNext generation sequencing (NGS) is a massive, high-throughput sequencing technology used to analyze various mutations and genetic changes in cancer. Oral squamous cell carcinoma (OSCC) is the most common malignancy of the head and neck region. OSCC usually arises from oral potentially malignant disorders, like oral leukoplakia, oral submucous fibrosis and erythroplakia, and shows mutation of tumor suppressor genes, and several other critical genes involved in apoptotic pathways, cell migration, and cell growth. AimTo analyze the molecular profiles of oral epithelial dysplasia and different grades of oral squamous cell carcinoma using NGS in the Indian subpopulation. Methodology21 patients (5 patients each of well differentiated, moderately differentiated, poorly differentiated squamous cell carcinoma, severe epithelial dysplasia, and 1 normal appearing mucosal tissue from apparently healthy individuals) were included in the study. Next generation sequencing was carried out using 50 hotspot gene panel. Protein-protein analysis was carried out using STRING Consortium 2023 and the methylation profile of the expressed genes was evaluated using the UALCAN portal. ResultsSevere epithelial dysplasia showed TP53 (c.743G>A, p.R248Q) pathogenic mutations (SNV) in suboptimal QC parameters. Well differentiated squamous cell carcinoma showed TP53 (c.328delC, p.Arg110fs*13), APC (c.4135G>T, p.Glu1379*), and FBXW7 (c.832C>T, p.Arg278*) mutations. CTNNB1 (c.134C>T, p.Ser45PheS45F), TP53 (c.637C>T, Arg213TerR213*), NRAS (c.183A>C, p.Gln61HisQ61H) and PDGFRA (c.1672C>T, p.Arg558Cys) mutations were seen in moderately differentiated squamous cell carcinoma. No pathogenic mutations were evident in poorly differentiated squamous cell carcinoma. STRING analysis showed that all the expressed proteins in each group were interrelated to each other. No significant difference was evident in the methylation profile of all the expressed genes when compared to the normal controls. ConclusionThe results obtained in this study explain the diverse genetic mutations in various grades of oral squamous cell carcinoma. Identification of these mutations would help in providing better treatment, designing a proper treatment plan for the patients with OSCC and support minimal intervention medicine.

Loss of STING impairs lactogenic differentiation.

Heightened energetic and nutrient demand during lactogenic differentiation of the mammary gland elicits upregulation of various stress responses to support cellular homeostasis. Here, we identify the stimulator of interferon genes (STING) as an immune supporter of the functional development of mouse mammary epithelial cells (MECs). An in vitro model of MEC differentiation revealed that STING is activated in a cGAS-independent manner to produce both type I interferons and proinflammatory cytokines in response to the accumulation of mitochondrial reactive oxygen species. Induction of STING activity was found to be dependent on the breast tumor suppressor gene single-minded 2 (SIM2). Using mouse models of lactation, we discovered that loss of STING activity results in early involution of #3 mammary glands, severely impairing lactational performance. Our data suggest that STING is required for successful functional differentiation of the mammary gland and bestows a differential lactogenic phenotype between #3 mammary glands and the traditionally explored inguinal 4|9 pair. These findings affirm unique development of mammary gland pairs that is essential to consider in future investigations into normal development and breast cancer initiation.

Expression, DNA methylation pattern and transcription factor EPB41L3 in gastric cancer: a study of 262 cases

PurposeDNA methylation prominently inactivates tumor suppressor genes and facilitates oncogenesis. Previously, we delineated a chromosome 18 deletion encompassing the erythrocyte membrane protein band 4.1-like 3 (EPB41L3) gene, a progenitor for the tumor suppressor that is differentially expressed in adenocarcinoma of the lung-1 (DAL-1) in gastric cancer (GC).MethodsOur current investigation aimed to elucidate EPB41L3 expression and methylation in GC, identify regulatory transcription factors, and identify affected downstream pathways. Immunohistochemistry demonstrated that DAL-1 expression is markedly reduced in GC tissues, with its downregulation serving as an independent prognostic marker.ResultsHigh-throughput bisulfite sequencing of 70 GC patient tissue pairs revealed that higher methylation of non-CpGs in the EPB41L3 promoter was correlated with more malignant tumor progression and higher-grade tissue classification. Such hypermethylation was shown to diminish DAL-1 expression, thus contributing to the malignancy of GC phenotypes. The DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5-aza-CdR) was found to partially restore DAL-1 expression. Moreover, direct binding of the transcription factor CDC5L to the upstream region of the EPB41L3 promoter was identified via chromosome immunoprecipitation (ChIP)-qPCR and luciferase reporter assays. Immunohistochemistry confirmed the positive correlation between CDC5L and DAL-1 protein levels. Subsequent RNA-seq analysis revealed that DAL-1 significantly influences the extracellular matrix and space-related pathways. GC cell RNA-seq post-5-Aza-CdR treatment and single-cell RNA-seq data of GC tissues confirmed the upregulation of AREG and COL17A1, pivotal tumor suppressors, in response to EPB41L3 demethylation or overexpression in GC epithelial cells.ConclusionIn conclusion, this study elucidates the association between non-CpG methylation of EPB41L3 and GC progression and identifies the key transcription factors and downstream molecules involved. These findings enhance our understanding of the role of EPB41L3 in gastric cancer and provide a solid theoretical foundation for future research and potential clinical applications.

Synergistic Structural Inhibition of MMP-9 by Natural Flavonoids: A Natural Combinatorial Therapy against Cancer

Introduction: Cancer is the uncontrolled proliferation of cells leading to metastasis due to genetic alterations resulting in oncogenes activation and tumor suppressor genes deactivation. It is the 2nd leading cause of death across the world. MMP-9 or gelatinase B, plays an effective role in ECM degradation, normal tissue turnover, and tissue remodelling. Methods: Overexpression of MMP-9 has been studied in almost all types of cancers proving the effective role of MMP-9 in accelerating malignant conditions. Thus, targeting MMP-9 to treat cancer seems to be a potential strategy to deal with adverse pathologies of cancer. Methods: Chemotherapy and radiotherapy are frequently utilized for the treatment of cancer but are associated with diverse side effects. Flavonoids are natural compounds frequently found in plants and have been analyzed for the structural inhibition potential against MMP-9 by several researchers to develop natural treatments against cancer, but none of the flavonoids have landed into clinical use. In the present study, in-depth in-silico analysis to investigate the synergistic effects of flavonoids for structural inhibition of MMP-9 was done. The ADMET and bioactive properties analysis revealed effective drug-like properties of the considered flavonoids. Principal component analysis of ADMET and bioactive properties revealed high similarity in the chemical nature of luteolin and quercetin. Molecular docking analysis of MMP-9 with the considered flavonoids individually revealed the highest effective binding energy of luteolin. Results: Combination docking analysis of MMP-9 with different combinations of flavonoids led to the identification of two combinations including Quercetin with Genistein and Luteolin and Genistein revealing high negative binding energies of -15.48kcal/mol and -15.31kcal/mol which was significantly greater than the binding energies identified for respective ligands in individual dockings. Conclusion: Thus, the present study put forward synergistic natural flavonoid combinations against cancer via the MMP-9 inhibition approach that can be further evaluated to develop high-efficacy treatments.

Linking FOXM1 and PD-L1 to CDK4/6-MEK targeted therapy resistance in malignant peripheral nerve sheath tumors.

Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive, Ras-driven sarcomas characterized by loss of the NF1 tumor suppressor gene and hyperactivation of MEK and CDK4/6 kinases. MPNSTs lack effective therapies. We recently demonstrated remarkable efficacy of dual CDK4/6-MEK inhibition in mice with de novo MPNSTs, which was heightened by combined targeting of the immune checkpoint protein, PD-L1. The triple combination therapy targeting CDK4/6, MEK, and PD-L1 led to extended MPNST regression and improved survival, although most tumors eventually acquired drug resistance. Here, we consider the immune activation phenotype caused by CDK4/6-MEK inhibition in MPNSTs that uniquely involved intratumoral plasma cell accumulation. We discuss how PD-L1 and FOXM1, a tumor-promoting transcription factor, are functionally linked and may be key mediators of resistance to CDK4/6-MEK targeted therapies. Finally, the role of FOXM1 in suppressing anti-tumor immunity and potentially thwarting immune-based therapies is considered. We suggest that future therapeutic strategies targeting the oncogenic network of CDK4/6, MEK, PD-L1, and FOXM1 represent exciting future treatment options for MPNST patients.

Post-Transcriptional Modifications to miRNAs Undergo Widespread Alterations, Creating a Unique Lung Adenocarcinoma IsomiRome.

MicroRNAs (miRNAs) modulate the expression of oncogenes and tumor suppressor genes, functioning as significant epigenetic regulators in cancer. IsomiRs are miRNA molecules that have undergone small modifications during miRNA processing. These modifications can alter an isomiR's binding stability with mRNA targets, and certain isomiRs have been implicated in the development of specific cancers. Still, the isomiRomes of many tissues, including the lung, have not been characterized; Methods: In this study, we analyzed small RNA sequencing data for three cohorts of lung adenocarcinoma (LUAD) and adult non-malignant lung (ANL) samples. We quantified isomiR expression and found 16 A-to-I edited isomiRs expressed in multiple cohorts, as well as 213 5' isomiRs, 128 3' adenylated isomiRs, and 100 3' uridylated isomiRs. Rates of A-to-I editing at editing hotspots correlated with mRNA expression of the editing enzymes ADAR and ADARB1, which were both observed to be deregulated in LUAD. LUAD samples displayed lower overall rates of A-to-I editing and 3' adenylation than ANL samples. Support vector machines and random forest models were trained on one cohort to distinguish ANL and stage I/II LUAD samples using reads per million (RPM) and frequency data for different types of isomiRs. Models trained on A-to-I editing rates at editing hotspots displayed high accuracy when tested on the other two cohorts and compared favorably to classifiers trained on miRNA expression alone; Conclusions: We have identified isomiRs in the human lung and found that their expression differs between non-malignant and tumor tissues, suggesting they hold potential as cancer biomarkers.

Prevalence Estimation of the PALB2 Germline Variant in East Asians and Koreans through Population Database Analysis.

PALB2 is a tumor suppressor gene. Heterozygous germline pathogenic variants of PALB2 significantly increase the lifetime risk of breast cancer and moderately increase the risk of ovarian and pancreatic cancers. This study analyzed the estimated prevalence of PALB2 variants globally, focusing on East Asian and Korean populations, where limited data were previously available. We examined 125,748 exomes from the Genome Aggregation Database (gnomAD), including 9197 East Asians, and additional data from 5305 individuals in the Korean Variant Archive and 1722 in the Korean Reference Genome Database. All PALB2 variants were interpreted according to guidelines from the American College of Medical Genetics and Genomics and the Clinical Genome Resource. The global prevalence of PALB2 variants was 0.18%, with the highest prevalence in Finnish populations (0.41%) and the lowest in Ashkenazi Jewish populations (0.04%). East Asians had a prevalence of 0.09%. By combining data from Korean genome databases and gnomAD totaling 8936 individuals, the overall prevalence of PALB2 variants in the Korean population was determined to be 0.13%. This study is the first comprehensive investigation of PALB2 variant prevalence in East Asians and Koreans using gnomAD and Korean genome databases. These findings provide essential reference data for future research and highlight the importance of region-specific genetic studies that will inform genetic counseling and hereditary cancer risk management.

Spatial transcriptomics reveal tumor microenvironment and SLCO2A1 correlated with tumor suppression in hypopharyngeal squamous cell carcinoma

BackgroundHypopharyngeal squamous cell carcinoma (HSCC) is a type of head and neck tumor with malignant behavior and poor prognosis. Spatial transcriptomics is a method that spatially analyzes gene expression patterns in tissues and has been used to discover tumor microenvironment and molecular markers in various tumors. However, there are no published reports on spatial transcriptomic analysis of HSCC. MethodsIn this study, spatial transcriptomic analysis was performed on tumor tissues in situ, peritumoral tissues, and lymphatic metastatic tissues of four patients with HSCC. Morphological markers, including panCK, SMA, and CD45, were used to identify epithelial, fibroblast, and immune cells, respectively. By analyzing the expression of more than 18, 000 genes within the transcriptome of all ROIs, differentially expressed genes of three cell types in different tissues were identified, and differentially expressed signaling pathways and immune infiltration were analyzed. ResultsThe spatial distribution of cells suggests that fibroblast cells in tumor tissues may be involved in the genesis and development of tumors, and the immune infiltration of lymphatic tumor metastasis is lower than that of tumors in situ. For epithelial cells, SLCO2A1, which is a favorable prognosis marker in head and neck squamous cell carcinoma (HNSCC), was significantly down-regulated in tumor tissues and lymphatic metastatic tissues compared with adjacent normal tissues. For immune cells, KANK3, which is a favorable prognosis markers in HNSCC, was significantly down-regulated in lymphatic metastatic tissues compared with adjacent normal tissues. For fibroblast cells, AQP1, CLEC3B and SLCO2A1, which are favorable prognosis markers in HNSCC, were significantly down-regulated in tumor tissues compared with adjacent normal tissues. ITGA8, which is a favorable prognosis markers in HNSCC, was significantly down-regulated in lymphatic metastatic tissues compared with normal lymphatic tissues. CSRP1, DES, and SLCO2A1 positively correlate with immune infiltration in HNSCC. Moreover, SLCO2A1 overexpression suppressed Fadu cells proliferation and metastasis and significantly correlated with favorable survival overcome in HSCC. ConclusionsWe investigated tumor and fibroblast heterogeneity, as well as the immune microenvironment in HSCC by using spatial transcriptomics. SLCO2A1 may be a tumor suppressor gene and correlates with immune infiltration for HSCC and could serve as a potential target for its diagnosis and treatment.

High-glucose impact on UVB responses in human epidermal keratinocytes: Insights on diabetic skin's resistance to photocarcinogenesis

Ultraviolet (UV) B-induced damage in human epidermal keratinocytes (HEKs) initiates photocarcinogenesis. However, how diabetes influences photocarcinogenesis is not well understood. To investigate the impact of high-glucose environments on responses to UVB, we cultured HEKs in normal-glucose (NG) or high-glucose (HG) conditions (G6 and G26), followed by UVB irradiation at 25 mJ/cm2 (G6UVB and G26UVB). We performed next-generation sequencing and analyzed HEKs' expression profiles bioinformatically to identify candidate genes and cellular responses involved. We found UVB induced consistent responses in both NG- and HG-cultivated HEKs, but it also triggered certain distinct processes and pathways specifically in the HG groups. The 459 differentially expressed (DE) genes in the HG groups revealed their roles in chromatin remodeling, nucleosome assembly, and interferon signaling activation. Moreover, the 29 DE genes identified in G26UVB/G6UVB comparison, including the potent tumor suppressor gene TFPI2, were considered key genes contributing to HEKs' altered response to UVB in HG environments. UVB irradiation induced significantly higher TFPI2 expression in HG-cultivated HEKs than their NG-cultivated counterpart. Finally, HG-cultivation significantly increased oxidative stress, cyclobutane pyrimidine dimer formation, and apoptosis, while reducing HEKs' viability after UVB irradiation. These changes under HG conditions probably mediate cell fate toward death and tumor regression. Overall, our findings provide evidence and associated molecular basis on how HG conditions reduce keratinocytes' photocarcinogenic potential following UVB exposure.

Prohibitin 2 orchestrates long noncoding RNA and gene transcription to accelerate tumorigenesis

The spatial co-presence of aberrant long non-coding RNAs (lncRNAs) and abnormal coding genes contributes to malignancy development in various tumors. However, precise coordinated mechanisms underlying this phenomenon in tumorigenesis remains incompletely understood. Here, we show that Prohibitin 2 (PHB2) orchestrates the transcription of an oncogenic CASC15-New-Isoform 2 (CANT2) lncRNA and the coding tumor-suppressor gene CCBE1, thereby accelerating melanoma tumorigenesis. In melanoma cells, PHB2 initially accesses the open chromatin sites at the CANT2 promoter, recruiting MLL2 to augment H3K4 trimethylation and activate CANT2 transcription. Intriguingly, PHB2 further binds the activated CANT2 transcript, targeting the promoter of the tumor-suppressor gene CCBE1. This interaction recruits histone deacetylase HDAC1 to decrease H3K27 acetylation at the CCBE1 promoter and inhibit its transcription, significantly promoting tumor cell growth and metastasis both in vitro and in vivo. Our study elucidates a PHB2-mediated mechanism that orchestrates the aberrant transcription of lncRNAs and coding genes, providing an intriguing epigenetic regulatory model in tumorigenesis.

Development of a First-in-Class DNMT1/HDAC Inhibitor with Improved Therapeutic Potential and Potentiated Antitumor Immunity.

Epigenetic therapies have emerged as a key paradigm for treating malignancies. In this study, a series of DNMT1/HDAC dual inhibitors were obtained by fusing the key pharmacophores from DNMT1 inhibitors (DNMT1i) and HDAC inhibitors (HDACi). Among them, compound (R)-23a demonstrated significant DNMT1 and HDAC inhibition both in vitro and in cells and largely phenocopied the synergistic effects of combined DNMT1i and HDACi in reactivating epigenetically silenced tumor suppressor genes (TSGs). This translated into a profound tumor growth inhibition (TGI = 98%) of (R)-23a in an MV-4-11 xenograft model, while displaying improved tolerability compared with single agent combination. Moreover, in a syngeneic MC38 mouse colorectal tumor model, (R)-23a outperformed the combinatory treatment in reshaping the tumor immune microenvironment and inducing tumor regression. Collectively, the novel DNMT1/HDAC dual inhibitor (R)-23a effectively reverses the cancer-specific epigenetic abnormalities and holds great potential for further development into cancer therapeutic agents.

Rodent models of tumours of the central nervous system.

Modelling of human diseases is an essential component of biomedical research, to understand their pathogenesis and ultimately, develop therapeutic approaches. Here, we will describe models of tumours of the central nervous system, with focus on intrinsic CNS tumours. Model systems for brain tumours were established as early as the 1920s, using chemical carcinogenesis, and a systematic analysis of different carcinogens, with a more refined histological analysis followed in the 1950s and 1960s. Alternative approaches at the time used retroviral carcinogenesis, allowing a more topical, organ-centred delivery. Most of the neoplasms arising from this approach were high-grade gliomas. Whilst these experimental approaches did not directly demonstrate a cell of origin, the localisation and growth pattern of the tumours already pointed to an origin in the neurogenic zones of the brain. In the 1980s, expression of oncogenes in transgenic models allowed a more targeted approach by expressing the transgene under tissue-specific promoters, whilst the constitutive inactivation of tumour suppressor genes ('knock out')-often resulted in embryonic lethality. This limitation was elegantly solved by engineering the Cre-lox system, allowing for a promoter-specific, and often also time-controlled gene inactivation. More recently, the use of the CRISPR Cas9 technology has significantly increased experimental flexibility of gene expression or gene inactivation and thus added increased value of rodent models for the study of pathogenesis and establishing preclinical models.

Exploring Novel Therapeutic Breakthroughs for Cancers: Potential Roles of miRNAs

MicroRNAs (miRNAs) are small non-coding RNAs, 19–25 nucleotides in length, that regulate gene expression. miRNAs are involved in various cellular, biological, and pathological activities, including the development and progression of malignant tumors. Numerous studies have highlighted the significant roles of miRNA deregulation in various cancer types, involving critical pathways such as gene deletions and amplifications, abnormal epigenetic changes, and dysfunctional miRNA regulatory systems. miRNAs can function both as oncogenes and tumor suppressor genes in different contexts. Several cancer hallmarks are associated with deregulated miRNAs, including resistance to cell death, metastasis, sustained proliferative signaling, promotion of angiogenesis, and the suppression of growth factors. Recent research has demonstrated that miRNAs contribute to drug resistance in tumor cells by targeting genes linked to drug resistance or by influencing genes that regulate the cell cycle, apoptosis, and proliferation. A single miRNA often has tissue-specific regulatory functions and can affect multiple genes. Various miRNA types have been identified as potential biomarkers for tumor diagnosis and critical targets for novel therapeutic approaches. This review aims to explore the role of miRNAs in cancer progression, metastasis, and potential therapeutic interventions.

Roles of Mutant TP53 Gene in Cancer Development and Progression

TP53 is a tumor suppressor gene that is mutated in most cancer types and has been extensively studied in cancer research. p53 plays a critical role in regulating the expression of target genes and is involved in key processes such as apoptosis, cell cycle regulation, and genomic stability, earning it the title “guardian of the genome.” Numerous studies have demonstrated p53’s influence on and regulation of autophagy, ferroptosis, the tumor microenvironment, and cell metabolism, all of which contribute to tumor suppression. Alterations in p53, specifically mutant p53 (mutp53), not only impair its tumor-suppressing functions but also enhance oncogenic characteristics. Recent data indicate that mutp53 is strongly associated with poor prognosis and advanced cancers, making it an ideal target for the development of novel cancer therapies. This review summarizes the post-translational modifications of p53, the mechanisms of mutp53 accumulation, and its gain-of-function, based on previous findings. Additionally, this review discusses its impact on metabolic homeostasis, ferroptosis, genomic instability, the tumor microenvironment, and cancer stem cells, and highlights recent advancements in mutp53 research.

P53motifDB: integration of genomic information and tumor suppressor p53 binding motifs.

The tumor suppressor gene TP53 encodes the DNA binding transcription factor p53 and is one of the most commonly mutated genes in human cancer. Tumor suppressor activity requires binding of p53 to its DNA response elements and subsequent transcriptional activation of a diverse set of target genes. Despite decades of close study, the logic underlying p53 interactions with its numerous potential genomic binding sites and target genes is not yet fully understood. Here, we present a database of DNA and chromatin-based information focused on putative p53 binding sites in the human genome to allow users to generate and test new hypotheses related to p53 activity in the genome. Users can query genomic locations based on experimentally observed p53 binding, regulatory element activity, genetic variation, evolutionary conservation, chromatin modification state, and chromatin structure. We present multiple use cases demonstrating the utility of this database for generating novel biological hypotheses, such as chromatin-based determinants of p53 binding and potential cell type-specific p53 activity. All database information is also available as a precompiled sqlite database for use in local analysis or as a Shiny web application.

ARHGAP26 deficiency drives the oocyte aneuploidy and early embryonic development failure.

Aneuploidy, the presence of a chromosomal anomaly, is a major cause of spontaneous abortions and recurrent pregnancy loss in humans. However, the underlying molecular mechanisms still remain poorly understood. Here, we report that ARHGAP26, a putative tumor suppressor gene, is a newly identified regulator of oocyte quality to maintain mitochondrial integrity and chromosome euploidy, thus ensuring normal embryonic development and fertility. Taking advantage of knockout mouse model, we revealed that genetic ablation of Arhgap26 caused the oocyte death at GV stage due to the mitochondrial dysfunction-induced ROS accumulation. Lack of Arhgap26 also impaired both in vitro and in vivo maturation of survived oocytes which results in maturation arrest and aneuploidy, and consequently leading to early embryonic development defects and subfertility. These observations were further verified by transcriptome analysis. Mechanistically, we discovered that Arhgap26 interacted with Cofilin1 to maintain the mitochondrial integrity by regulating Drp1 dynamics, and restoration of Arhgap26 protein level recovered the quality of Arhgap26-null oocytes. Importantly, we found an ARHGAP26 mutation in a patient with history of recurrent miscarriage by chromosomal microarray analysis. Altogether, our findings uncover a novel function of ARHGAP26 in the oocyte quality control and prevention of aneuploidy and provide a potential treatment strategy for infertile women caused by ARHGAP26 mutation.

Assessing the diagnostic utility of tRNA-derived fragments as biomarkers of head and neck cancer

Roughly 54,000 individuals are diagnosed with head and neck cancers in the United States yearly. Transfer RNA-derived fragments (tRF) are the products of enzymatic cleavage of precursor tRNAs, and have been proposed for use as biomarkers of head and neck cancer. In this study, we aim to further analyze the utility that tRFs might provide as biomarkers of head and neck cancer. tRF read counts were obtained for 453 tumor and 44 adjacent normal tissue samples and used to construct a gradient boosting diagnostic model. Although we identified 129 tRFs that were significantly dysregulated between these samples, the model achieved a sensitivity of only 69 % and a specificity of 59 %. tRFs are thought to induce the degradation of mRNA transcripts containing a complementary “seed” region. Despite the above performances, we chose to explore this concept of translational regulation by analyzing these tRFs for inverse correlation to the expression of select oncogenes and tumor suppressor genes implicated in head and neck cancer. Among others, CysGCA 5′-half and LysCTT 3′-tRF were upregulated in the tumor samples, and corresponded to decreased expression of PIK3R1, AKT1, and CPEB3. These transcripts were further found to contain numerous significantly complementary sites at which tRF-mediated mRNA degradation might occur. Although these tRFs did appear to correlate to many of the oncogenic metrics analyzed, we believe that additional research is needed before they might be used to improve the diagnosis, treatment, and survival of patients with this disease.

Abstract C119: Exploring the functional role of LRIG1 and WWOX tumor suppressors in breast cancer disparities

Abstract Breast cancer is the most commonly diagnosed cancer among women in the US. Despite a lower rate of breast cancer incidence, Black women in the US suffer higher rates of mortality compared to White women. This disparity poses a major clinical issue for Black women in the US, and we are particularly interested in understanding how molecular and environmental mechanisms may be contributing to these disproportionate outcomes. Our previous study found that in a cohort of women from Baltimore, Maryland (110 Black, 75 White), higher neighborhood deprivation was associated with decreased gene body methylation and gene expression of two tumor suppressor genes, LRIG1 and WWOX. These findings were unique to the tumor, which potentially points to ancestry-specific somatic mutations that may impact gene and protein expression for LRIG1 and WWOX. The goal of this project is to determine gene and protein differences in LRIG1 and WWOX by population group in women with and without breast cancer as it relates to neighborhood-level socioeconomic deprivation. We hypothesize that LRIG1 and WWOX exhibit decreased gene and protein expression in Black women compared to White women. Using the same diverse cohort from Baltimore, Maryland, we identified and conducted DNA genotyping on clinically relevant mutations of LRIG1 and WWOX using amplification by PCR and detection by fluorescent reporters. We found that the genotype frequencies in two single nucleotide polymorphisms (SNPs) for LRIG1, rs1403626 (P=6.3e-1) and rs2306272 (P=0.005967), differ significantly between population groups in these breast tissue samples, an interesting finding that matches our previous predictions. We also identified a dose-dependent relationship between LRIG1 gene expression and rs1403626 SNP genotypes. Additional patient genotyping will be conducted to determine relationships between LRIG1 and WWOX SNPs, differences in DNA methylation, and correlations with neighborhood deprivation measures. To interrogate the impact on protein expression, we will construct LRIG1 and WWOX knockdown mutants in estrogen receptor (ER)-positive and ER-negative commercially available breast cancer cell lines derived from Black and White patients, and determine the functional consequences of LRIG1 and WWOX loss by immunofluorescence and western blot, including how this may differ by population group. These studies will give us a better understanding of how the expression of tumor suppressor genes may contribute to the higher susceptibility of Black women developing more aggressive breast tumors. Citation Format: Angel H. Pajimola, Brittany Jenkins-Lord. Exploring the functional role of LRIG1 and WWOX tumor suppressors in breast cancer disparities [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C119.