Bioinformatics Analysis Of Data Research Articles

Comparison on the mechanism and potency of hepatotoxicity among hemp extract and its four major constituent cannabinoids

Cannabidiol (CBD) has been reported to induce hepatotoxicity in clinical trials and research studies; however, little is known about the safety of other nonintoxicating cannabinoids. New approach methodologies (NAMs) based on bioinformatic analysis of high-throughput transcriptomic data are gaining increasing importance in risk assessment and regulatory decision-making of data-poor chemicals. In the current study, we conducted a concentration response transcriptomic analysis of hemp extract and its four major constituent cannabinoids [CBD, cannabichromene (CBC), cannabigerol (CBG), and cannabinol (CBN)] in hepatocytes derived from human induced pluripotent stem cells (iPSCs). Each compound impacted a distinctive combination of biological functions and pathways. However, all the cannabinoids impaired liver metabolism and caused oxidative stress in the cells. Benchmark concentration (BMC) analysis showed potencies in transcriptional activity of the cannabinoids were in the order of CBN > CBD > CBC > CBG, consistent with the order of their cytotoxicity IC50 values. Patterns of transcriptomic changes induced by hemp extract and its median overall BMC were very similar to CBD but differed significantly from other cannabinoids, suggesting that potential adverse effects of hemp extract were largely due to its major constituent CBD. Lastly, transcriptomic point-of-departure (tPoD) values were determined for each of the compounds, with the value for CBD (0.106µM) being concordant with a previously reported one derived from apical endpoints of clinical and animal studies. Taken together, the current study demonstrates the potential utility of transcriptomic BMC analysis as a NAM for hazard assessment of data-poor chemicals, improves our understanding of the possible health effects of hemp extract and its constituent cannabinoids, and provides important tPoD data that could contribute to inform human safety assessment of these cannabinoid compounds.

The "Dry-Lab" Side of Food Authentication: Benchmark of Bioinformatic Pipelines for the Analysis of Metabarcoding Data.

Next Generation Sequencing Technologies (NGS), particularly metabarcoding, are valuable tools for authenticating foodstuffs and detecting eventual fraudulent practices such as species substitution. This technique, mostly used for the analysis of prokaryotes in several environments (including food), is in fact increasingly applied to identify eukaryotes (e.g., fish, mammals, avian, etc.) in multispecies food products. Besides the "wet-lab" procedures (e.g., DNA extraction, PCR, amplicon purification, etc.), the metabarcoding workflow includes a final "dry-lab" phase in which sequencing data are analyzed using a bioinformatic pipeline (BP). BPs play a crucial role in the accuracy, reliability, and interpretability of the metabarcoding results. Choosing the most suitable BP for the analysis of metabarcoding data could be challenging because it might require greater informatics skills than those needed in standard molecular analysis. To date, studies comparing BPs for metabarcoding data analysis in foodstuff authentication are scarce. In this study, we compared the data obtained from two previous studies in which fish burgers and insect-based products were authenticated using a customizable, ASV-based, and command-line interface BP (BP1) by analyzing the same data with a customizable but OTU-based and graphical user interface BP (BP2). The final sample compositions were compared statistically. No significant difference in sample compositions was highlighted by applying BP1 and BP2. However, BP1 was considered as more user-friendly than BP2 with respect to data analysis streamlining, cost of analysis, and computational time consumption. This study can provide useful information for researchers approaching the bioinformatic analysis of metabarcoding data for the first time. In the field of food authentication, an effective and efficient use of BPs could be especially useful in the context of official controls performed by the Competent Authorities and companies' self-control in order to detect species substitution and counterfeit frauds.

Nucleolin acute degradation reveals novel functions in cell cycle progression and division in TNBC.

Nucleoli are large nuclear sub-compartments where vital processes, such as ribosome assembly, take place. Technical obstacles still limit our understanding of the biological functions of nucleolar proteins in cell homeostasis and cancer pathogenesis. Since most nucleolar proteins are essential, their abrogation cannot be achieved through conventional approaches. Additionally, the biological activities of many nucleolar proteins are connected to their physiological concentration. Thus, artificial overexpression might not fully recapitulate their endogenous functions. Proteolysis-based approaches, such as the Auxin Inducible Degron (AID) system paired with CRISPR/Cas9 knock-in gene-editing, have the potential to overcome these limitations, providing unprecedented characterization of the biological activities of endogenous nucleolar proteins. We applied this system to endogenous nucleolin (NCL), one of the most abundant nucleolar proteins, and characterized the impact of its acute depletion on Triple-Negative Breast Cancer (TNBC) cell behavior. Abrogation of endogenous NCL reduced proliferation and caused defective cytokinesis, resulting in bi-nucleated tetraploid cells. Bioinformatic analysis of patient data, and quantitative proteomics using our experimental NCL-depleted model, indicated that NCL levels are correlated with the abundance of proteins involved in chromosomal segregation. In conjunction with its effects on sister chromatid dynamics, NCL abrogation enhanced the anti-proliferative effects of chemical inhibitors of mitotic modulators such as the Anaphase Promoting Complex. In summary, using the AID system in combination with CRISPR/Cas9 for endogenous gene editing, our findings indicate a novel role for NCL in supporting the completion of the cell division in TNBC models, and that its abrogation could enhance the therapeutic activity of mitotic-progression inhibitors.

Biochemical properties of chromatin domains define genome compartmentalization.

Chromatin three-dimensional (3D) organization inside the cell nucleus determines the separation of euchromatin and heterochromatin domains. Their segregation results in the definition of active and inactive chromatin compartments, whereby the local concentration of associated proteins, RNA and DNA results in the formation of distinct subnuclear structures. Thus, chromatin domains spatially confined in a specific 3D nuclear compartment are expected to share similar epigenetic features and biochemical properties, in terms of accessibility and solubility. Based on this rationale, we developed the 4f-SAMMY-seq to map euchromatin and heterochromatin based on their accessibility and solubility, starting from as little as 10000 cells. Adopting a tailored bioinformatic data analysis approach we reconstruct also their 3D segregation in active and inactive chromatin compartments and sub-compartments, thus recapitulating the characteristic properties of distinct chromatin states. A key novelty of the new method is the capability to map both the linear segmentation of open and closed chromatin domains, as well as their compartmentalization in one single experiment.

Discovery of Pathogenic Variants Associated with Idiopathic Recurrent Pregnancy Loss Using Whole-Exome Sequencing.

Idiopathic recurrent pregnancy loss (RPL) is defined as at least two pregnancy losses before 20 weeks of gestation. Approximately 5% of pregnant couples experience idiopathic RPL, which is a heterogeneous disease with various causes including hormonal, chromosomal, and intrauterine abnormalities. Although how pregnancy loss occurs is still unknown, numerous biological factors are associated with the incidence of pregnancy loss, including genetic variants. Whole-exome sequencing (WES) was conducted on blood samples from 56 Korean patients with RPL and 40 healthy controls. The WES data were aligned by means of bioinformatic analysis, and the detected variants were annotated using machine learning tools to predict the pathogenicity of protein alterations. Each indicated variant was confirmed using Sanger sequencing. A replication study was also conducted in 112 patients and 114 controls. The Variant Effect Scoring Tool, Combined Annotation Dependent Depletion tool, Sorting Intolerant from Tolerant annotation tool, and various databases detected 10 potential variants previously associated with spontaneous abortion genes in patients by means of a bioinformatic analysis of WES data. Several variants were detected in more than one patient. Interestingly, several of the detected genes were functionally clustered, including some with a secretory function (mucin 4; MUC4; rs200737893 G>A and hyaluronan-binding protein 2; HABP2; rs542838125 G>T), in which growth arrest-specific 2 Like 2 (GAS2L2; rs140842796 C>T) and dynamin 2 (DNM2; rs763894364 G>A) are functionally associated with cell protrusion and the cytoskeleton. ATP Binding Cassette Subfamily C Member 6 (ABCC6) was the only gene with two variants. HABP2 (rs542838125 G>T), MUC4 (rs200737893 G>A), and GAS2L2 (rs140842796 C>T) were detected in only the patient group in the replication study. The combination of WES and machine learning tools is a useful method to detect potential variants associated with RPL. Using bioinformatic tools, we found 10 potential variants in 9 genes. WES data from patients are needed to better understand the causes of RPL.

Abstract PO5-14-05: Circulating tumor DNA fraction correlates with residual cancer burden post-neoadjuvant chemotherapy in triple negative breast cancer patients

Abstract Background: Pathologic response after preoperative/neoadjuvant chemotherapy is a continuum that can range from no residual cancer to extensive disease. Viable cancers can shed tumor DNA into the blood and we hypothesized that plasma ctDNA levels can reflect pathologic response as continuum. Patients and methods: Post-neoadjuvant plasma samples were obtained after completion of chemotherapy but before surgery from patients with stage I to III TNBC who received treatment with durvalumab concurrent with weekly nab-paclitaxel followed by dose dense doxorubicin/cyclophosphamide in a single arm neoadjuvant clinical trial (NCT02489448). Up to 3 mL of blood was collected into EDTA- and heparin- containing vacutainer tubes, and plasma cfDNA was extracted and twice purified in the lab at Predicine Inc. Pathologic response was quantified on a continuous scale using the Residual Cancer Burden (RCB) score, and also categorized as RCB-0 (complete pathologic response, n=21), -I (minimal residual cancer, n=7), -II (moderate residual cancer, n=13), and -III (extensive residual cancer, n=3). Median follow-up was 35 months (range 25-70 months). Tumor whole exome sequencing (WES) data was previously generated using HiSeq 4000 at the Yale Center for Genome Analysis (dbGaP: PRJNA558949). A personalized MRD panel of up to 60 personalized variants per patient was designed based on the tumor WES data, and ultra-deep next-generation sequencing (100,000X) of plasma cfDNA was performed using the PredicineBEACON assay for MRD detection by Predicine. CtDNA positivity (MRD) was defined as a weighted score equivalent to 2 or more tumor variants detected in the plasma. cfDNA tumor fraction was measured based on mutant allele fraction of observed variants. Adjusted tumor fraction could be confidently measured for 37 out of 44 patients that had enough confidently called personalized ctDNA variants. We compared tumor fraction versus RCB score as continuous variables, and also compared tumor fraction between RCB categories as ordinal variables. Invasive disease-free survival was examined by Kaplan-Meier analysis. Bioinformatic data analysis was performed using Graphpad Prism and R. Results: 44 of 48 plasma samples yielded successful cfDNA generation and sequencing. Six patients (13.6%) were MRD positive. Among these 6 cases, 3 had RCB-0 response (14.3% of RCB 0 cases), 1 had RCB II response (7.7% of RCB II cases), and 2 had RCB III response (66.7% of RCB III cases). The median cfDNA tumor fraction of patients with pathological complete response to treatment (pCR) was significantly lower than patients with residual disease (RD) (0.06% vs. 0.3%, p=0.02). There was a positive correlation between RCB scores and tumor fraction (r= 0.45, Spearman). Tumor fraction was more strongly correlated with later recurrence than a binary ctDNA positivity call. Tumor fraction was significantly higher in patients that later experienced local or metastatic recurrence (n=8) compared to those with no evidence of disease (n=29) (Wilcoxon test, p=0.02). Both ctDNA positive RCB III cases had metastatic recurrence while the remaining 4 ctDNA positive cases currently remain recurrence-free. Mutational genomic landscape of both tumor WES and plasma ctDNA samples identified hotspot mutations in 19 cancer-associated genes. Novel hot-spot mutations were observed in the plasma of two patients following treatment. TP53 mutations were highly prevalent in tissue and plasma, however no significant association of mutation of any gene with treatment response was detected. Conclusions: PredicineBeacon MRD assay was successfully performed on 3 mL plasma samples collected using from EDTA and heparin-containing tubes. Tumor fraction correlated with residual disease, RCB score and disease recurrence. Citation Format: Naing Lin Shan, Billie Gould, Kim Blenman, Julia Foldi, Pan Du, Frank Zhang, Myles Walsh, Lajos Pusztai. Circulating tumor DNA fraction correlates with residual cancer burden post-neoadjuvant chemotherapy in triple negative breast cancer patients [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-14-05.

NANOG controls testicular germ cell tumour stemness through regulation of MIR9-2.

Testicular germ cell tumours (TGCTs) represent a clinical challenge; they are most prevalent in young individuals and are triggered by molecular mechanisms that are not fully understood. The origin of TGCTs can be traced back to primordial germ cells that fail to mature during embryonic development. These cells express high levels of pluripotency factors, including the transcription factor NANOG which is highly expressed in TGCTs. Gain or amplification of the NANOG locus is common in advanced tumours, suggesting a key role for this master regulator of pluripotency in TGCT stemness and malignancy. In this study, we analysed the expression of microRNAs (miRNAs) that are regulated by NANOG in TGCTs via integrated bioinformatic analyses of data from The Cancer Genome Atlas and NANOG chromatin immunoprecipitation in human embryonic stem cells. Through gain-of-function experiments, MIR9-2 was further investigated as a novel tumour suppressor regulated by NANOG. After transfection with MIR9-2 mimics, TGCT cells were analysed for cell proliferation, invasion, sensitivity to cisplatin, and gene expression signatures by RNA sequencing. For the first time, we identified 86 miRNAs regulated by NANOG in TGCTs. Among these, 37 miRNAs were differentially expressed in NANOG-high tumours, and they clustered TGCTs according to their subtypes. Binding of NANOG within 2kb upstream of the MIR9-2 locus was associated with a negative regulation. Low expression of MIR9-2 was associated with tumour progression and MIR9-2-5p was found to play a role in the control of tumour stemness. A gain of function of MIR9-2-5p was associated with reduced proliferation, invasion, and sensitivity to cisplatin in both embryonal carcinoma and seminoma tumours. MIR9-2-5p expression in TGCT cells significantly reduced the expression of genes regulating pluripotency and cell division, consistent with its functional effect on reducing cancer stemness. This study provides new molecular insights into the role of NANOG as a key determinant of pluripotency in TGCTs through the regulation of MIR9-2-5p, a novel epigenetic modulator of cancer stemness. Our data also highlight the potential negative feedback mediated by MIR9-2-5p on NANOG expression, which could be exploited as a therapeutic strategy for the treatment of TGCTs.

Bioinformatic Analysis of Metabolomic Data: From Raw Spectra to Biological Insight

Metabolites are at the end of the gene–transcript–protein–metabolism cascade. As such, metabolomics is the omics approach that offers the most direct correlation with phenotype. This allows, where genomics, transcriptomics and proteomics fail to explain a trait, metabolomics to possibly provide an answer. Complex phenotypes, which are determined by the influence of multiple small-effect alleles, are an example of these situations. Consequently, the interest in metabolomics has increased exponentially in recent years. As a newer discipline, metabolomic bioinformatic analysis pipelines are not as standardized as in the other omics approaches. In this review, we synthesized the different steps that need to be carried out to obtain biological insight from annotated metabolite abundance raw data. These steps were grouped into three different modules: preprocessing, statistical analysis, and metabolic pathway enrichment. We included within each one of them the different state-of-the-art procedures and tools that can be used depending on the characteristics of the study, providing details about each method’s characteristics and the issues the reader might encounter. Finally, we introduce genome-scale metabolic modeling as a tool for obtaining pseudo-metabolomic data in situations where their acquisition is difficult, enabling the analysis of the resulting data with the modules of the described workflow.

Klotho exerts protection in chronic kidney disease associated with regulating inflammatory response and lipid metabolism.

The anti-aging protein Klotho plays a protective role in kidney disease, but its potential as a biomarker for chronic kidney disease (CKD) is controversial. Additionally, the main pathways through which Klotho exerts its effects on CKD remain unclear. Therefore, we used bioinformatics and clinical data analysis to determine its role in CKD. We analyzed the transcriptomic and clinical data from the Nephroseq v5 database and found that the Klotho gene was mainly expressed in the tubulointerstitium, and its expression was significantly positively correlated with estimated glomerular filtration rate (eGFR) and negatively correlated with blood urea nitrogen (BUN) in CKD. We further found that Klotho gene expression was mainly negatively associated with inflammatory response and positively associated with lipid metabolism in CKD tubulointerstitium by analyzing two large sample-size CKD tubulointerstitial transcriptome datasets. By analyzing 10-year clinical data from the National Health and Nutrition Examination Survey (NHANES) 2007-2016, we also found that Klotho negatively correlated with inflammatory biomarkers and triglyceride and positively correlated with eGFR in the CKD population. Mediation analysis showed that Klotho could improve renal function in the general population by modulating the inflammatory response and lipid metabolism, while in the CKD population, it primarily manifested by mediating the inflammatory response. Restricted cubic spline (RCS) analysis showed that the optimal concentration range for Klotho to exert its biological function was around 1000pg/ml. Kaplan-Meier curves showed that lower cumulative hazards of all-cause mortality in participants with higher levels of Klotho. We also demonstrated that Klotho could reduce cellular inflammatory response and improve cellular lipid metabolism by establishing an in vitro model similar to CKD. Our results suggest that Klotho exerts protection in CKD, which may be mainly related to the regulation of inflammatory response and lipid metabolism, and it can serve as a potential biomarker for CKD.

Long non‑coding RNA DANCR aggravates breast cancer through the miR‑34c/E2F1 feedback loop.

Emerging scientific evidence has suggested that the long non‑coding (lnc)RNA differentiation antagonizing non‑protein coding RNA (DANCR) serves a significant role in human tumorigenesis and cancer progression; however, the precise mechanism of its function in breast cancer remains to be fully understood. Therefore, the objective of the present study was to manipulate DANCR expression in MCF7 and MDA‑MB‑231 cells using lentiviral vectors to knock down or overexpress DANCR. This manipulation, alongside the analysis of bioinformatics data, was performed to investigate the potential mechanism underlying the role of DANCR in cancer. The mRNA and/or protein expression levels of DANCR, miR‑34c‑5p and E2F transcription factor 1 (E2F1) were assessed using reverse transcription‑quantitative PCR and western blotting, respectively. The interactions between these molecules were validated using chromatin immunoprecipitation and dual‑luciferase reporter assays. Additionally, fluorescence in situ hybridization was used to confirm the subcellular localization of DANCR. Cell proliferation, migration and invasion were determined using 5‑ethynyl‑2'‑deoxyuridine, wound healing and Transwell assays, respectively. The results of the present study demonstrated that DANCR had a regulatory role as a competing endogenous RNA and upregulated the expression of E2F1 by sequestering miR‑34c‑5p in breast cancer cells. Furthermore, E2F1 promoted DANCR transcription by binding to its promoter in breast cancer cells. Notably, the DANCR/miR‑34c‑5p/E2F1 feedback loop enhanced cell proliferation, migration and invasion in breast cancer cells. Thus, these findings suggested that targeting DANCR may potentially provide a promising future therapeutic strategy for breast cancer treatment.

Scientific figures interpreted by ChatGPT: strengths in plot recognition and limits in color perception

Emerging studies underscore the promising capabilities of large language model-based chatbots in conducting basic bioinformatics data analyses. The recent feature of accepting image inputs by ChatGPT, also known as GPT-4V(ision), motivated us to explore its efficacy in deciphering bioinformatics scientific figures. Our evaluation with examples in cancer research, including sequencing data analysis, multimodal network-based drug repositioning, and tumor clonal evolution, revealed that ChatGPT can proficiently explain different plot types and apply biological knowledge to enrich interpretations. However, it struggled to provide accurate interpretations when color perception and quantitative analysis of visual elements were involved. Furthermore, while the chatbot can draft figure legends and summarize findings from the figures, stringent proofreading is imperative to ensure the accuracy and reliability of the content.

Pioglitazone enhances cisplatin’s impact on triple-negative breast cancer: Role of PPARγ in cell apoptosis

Peroxisome proliferator-activated receptor-gamma (PPARγ) has been recently shown to play a role in many cancers. The breast tissue of triple-negative breast cancer (TNBC) patients were found to have a significantly lower expression of PPARγ than the other subtypes. Furthermore, PPARγ activation was found to exert anti-tumor effects by inhibiting cell proliferation, differentiation, cell growth, cell cycle, and inducing apoptosis. To start with, we performed a bioinformatic analysis of data from OncoDB, which showed a lower expression pattern of PPARγ in different cancer types. In addition, high expression of PPARγ was associated with better breast cancer patient survival. Therefore, we tested the impact of pioglitazone, a PPARγ ligand, on the cytotoxic activity of cisplatin in the TNBC cell line. MDA-MB-231 cells were treated with either cisplatin (40 μM) with or without pioglitazone (30 or 60 μM) for 72 h. The MTT results showed a significant dose-dependent decrease in cell viability as a result of using cisplatin and pioglitazone combination compared with cisplatin alone. In addition, the protein expression of Bcl-2, a known antiapoptotic marker, decreased in the cells treated with cisplatin and pioglitazone combination at doses of 40 and 30 μM, respectively. On the other hand, cleaved- poly-ADP ribose polymerase (PARP) and -caspase-9, which are known as pro-apoptotic markers, were upregulated in the combination group compared with the solo treatments. Taken together, the addition of pioglitazone to cisplatin further reduced the viability of MDA-MB-231 cells and enhanced apoptosis compared with chemotherapy alone.

Construction and analysis of a network of exercise-induced mitochondria-related non-coding RNA in the regulation of diabetic cardiomyopathy.

Diabetic cardiomyopathy (DCM) is a major factor in the development of heart failure. Mitochondria play a crucial role in regulating insulin resistance, oxidative stress, and inflammation, which affect the progression of DCM. Regular exercise can induce altered non-coding RNA (ncRNA) expression, which subsequently affects gene expression and protein function. The mechanism of exercise-induced mitochondrial-related non-coding RNA network in the regulation of DCM remains unclear. This study seeks to construct an innovative exercise-induced mitochondrial-related ncRNA network. Bioinformatic analysis of RNA sequencing data from an exercise rat model identified 144 differentially expressed long non-coding RNA (lncRNA) with cutoff criteria of p< 0.05 and fold change ≥1.0. GSE6880 and GSE4745 were the differentially expressed mRNAs from the left ventricle of DCM rat that downloaded from the GEO database. Combined with the differentially expressed mRNA and MitoCarta 3.0 dataset, the mitochondrial located gene Pdk4 was identified as a target gene. The miRNA prediction analysis using miRanda and TargetScan confirmed that 5 miRNAs have potential to interact with the 144 lncRNA. The novel lncRNA-miRNA-Pdk4 network was constructed for the first time. According to the functional protein association network, the newly created exercise-induced ncRNA network may serve as a promising diagnostic marker and therapeutic target, providing a fresh perspective to understand the molecular mechanism of different exercise types for the prevention and treatment of diabetic cardiomyopathy.

Abstract 2026: Single-cell RNA-sequencing analysis of tumor endothelial cells reveals suppression of specific endothelial subtypes by the combination treatment of Wnt/β-catenin signaling modulator E7386 plus lenvatinib

Abstract Background: Aberrant activation of Wnt/β-catenin signaling plays an important role in both carcinogenesis and modulation of the tumor microenvironment. E7386, a novel orally active antitumor agent, inhibits the interaction between β-catenin and CREB-binding protein (CBP) and thereby modulates Wnt/β-catenin signaling. We previously reported that E7386 in combination with lenvatinib (LEN), a multiple receptor tyrosine kinase inhibitor mainly targeting VEGFRs and FGFRs, showed a greater antitumor activity and reduction of tumor microvessels than each treatment alone in preclinical tumor models. Multiple clinical studies are in progress including the combination of E7386 plus LEN (NCT04008797). Here, we further tried to elucidate the mechanism underlying the antitumor and antiangiogenic effect of the combination of E7386 plus LEN by using single-cell RNA sequencing (scRNA-seq) of tumor endothelial cells (ECs). Methods: Mice bearing subcutaneous RAG (mouse renal cell carcinoma cell line) tumors were treated with E7386 at 25 mg/kg and/or with LEN at 10 mg/kg by daily oral gavage for 8 days. Tumor ECs (CD31+/CD45−) were isolated by magnetic cell separation and flow cytometry and were subjected to scRNA-seq using 10x Genomics pipeline. Bioinformatics data analysis was conducted by Clarivate Analytics. After quality control and filtering, ECs were gated by their expression of pan-EC markers and were further classified into 9 subtypes (tip, capillary, arterial, venous, proliferating, immature, interferon, activated artery, and lymphatic) according to previously reported markers for each subtype. Results: Among classified subtypes, proliferating and immature subtypes showed clear reduction in the percentage of total ECs with combination of E7386 plus LEN versus LEN monotherapy. In both proliferating and immature subtypes, a subset of Wnt/β-catenin downstream genes showed increased expression with LEN monotreatment. Conversely, these Wnt/β-catenin downstream genes were downregulated with the combination of E7386 plus LEN, suggesting that Wnt/β-catenin signaling may be associated with a drug resistance mechanism against LEN in these subtypes. Pathway analysis indicated that genes involved in cell proliferation and survival were downregulated by the E7386 plus LEN combination versus LEN monotreatment in both proliferating and immature subtypes. Conclusion: Taken together, these results suggest a role for E7386 in suppressing the activation of Wnt/β-catenin signaling induced by LEN monotreatment in specific EC subtypes; this activity leads to enhanced antiangiogenic and antitumor activity with E7386 plus LEN combination therapy in a preclinical tumor model. Citation Format: Masahiko Kume, Ryoga Ishida, Yoichi Ozawa, Jialing Shen, Hiroto Konishi, Megumi Kuronishi, Takayuki Kimura, Yusuke Adachi, Yu Kato. Single-cell RNA-sequencing analysis of tumor endothelial cells reveals suppression of specific endothelial subtypes by the combination treatment of Wnt/β-catenin signaling modulator E7386 plus lenvatinib [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2026.

Abstract 2022: E7386, a Wnt/β-catenin signaling modulator, suppresses the differentiation of regulatory T cells in combination with lenvatinib plus anti-PD-1 antibody

Abstract Background: E7386, a selective inhibitor of the interaction between β-catenin and CREB binding protein (CBP), showed antitumor activity in preclinical tumor models with aberrant activation of the Wnt/β-catenin signaling pathway. Previously, we reported the enhanced antitumor activity of a triple combination (E7386 in combination with Lenvatinib [LEN, a multiple receptor tyrosine kinase inhibitor mainly targeting VEGFRs and FGFRs] plus anti-PD-1 antibody) versus a 2-drug combination (LEN plus anti-PD-1 antibody). In this study, we further investigated the immunomodulatory functions of E7386 as a triple combination by single-cell RNA-sequencing (scRNA-Seq) analysis and subsequent functional assays. Methods: Mice bearing subcutaneous RAG (mouse renal cell carcinoma) tumors were randomized into 4 groups (n=6 in each group), including ⑴ Nontreatment, ⑵ E7386 at 25 mg/kg (PO, QD), ⑶ LEN at 10 mg/kg (PO, QD) plus anti-PD-1 antibody at 10 mg/kg (IP, BIW), and ⑷ triple combination. Tumor tissues were collected after a 2-week treatment period. CD45+ immune cells were isolated from the tumors by magnetic cell separation (MACS) and subjected to scRNA-Seq using 10x Genomics pipelines. Bioinformatics data analysis was conducted with Clarivate Analytics. To evaluate the effects of E7386 on Treg differentiation, an in vitro-induced regulatory T cells (Tregs) differentiation assay was conducted. Naïve CD4+ T cells were isolated by MACS and plated under iTreg differentiation conditions (stimulation of TGF-β and IL-2) with or without treatment of E7386. Induced Tregs and conditional culture medium were collected for evaluation of Treg differentiation, including gene expression and protein analysis. Results: CD45+ immune cells were clustered into 14 cell-type groups. Increased proportion of monocytes, NK cells, Tregs, CD4+ T cells, CD8+ T cells, eosinophils, and neutrophils were observed after LEN plus anti-PD-1 treatment. Among these subpopulations, Treg were most significantly suppressed by E7386 plus LEN plus anti-PD-1. Gene expression analysis revealed that the triple combination suppressed the activated gene expression of the Stat5/Foxp3 axis in CD4+ T cells, particularly Tregs, induced by LEN plus anti-PD-1 treatment. Consistently, the iTreg differentiation assay confirmed the suppressive function of E7386 on the Treg differentiation rate. Multiple subsequent in vitro assays also demonstrated the inhibitory effects of E7386 on TGF-β secretion and the expression levels of TGF-β downstream target genes. Conclusion: In summary, these data suggest a suppressive role of E7386 on Treg differentiation, which leads to antitumor activity of E7386 in combination with lenvatinib and anti-PD-1 antibody in a preclinical tumor model. Citation Format: Jialing Shen, Ryoga Ishida, Masahiko Kume, Takayuki Kimura, Yusuke Adachi, Yu Kato. E7386, a Wnt/β-catenin signaling modulator, suppresses the differentiation of regulatory T cells in combination with lenvatinib plus anti-PD-1 antibody [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2022.

Abstract 1274: Investigating PLOD2 as a therapeutic target to overcome metastasis in radiorecurrent prostate cancer

Abstract Prostate cancer (PCa) is the second most common cancer in males, with 1 in 8 men developing the disease in their lifetime. For PCa, a common treatment strategy is external beam radiation therapy to the prostate. However, when cancer recurs (radiorecurrent PCa), it often behaves aggressively by invading into surrounding organs or spreading distantly. Radiorecurrent PCa metastasis is therefore a significant cause of morbidity and mortality that must be overcome to improve survival of advanced PCa patients. Proteomic analysis revealed the procollagen enzyme Lysyl Hydroxylase 2 (PLOD2) to be upregulated in our radiorecurrent, and highly aggressive, conventionally fractionated DU145 (DU145-CF) PCa cell line. Given its established function as a mediator of invasion in various other cancers, we sought to characterize the role of PLOD2 in the aggressive phenotype of our radiorecurrent PCa cells. Bioinformatic analysis of clinical data revealed PLOD2 genomic amplification to be significantly associated with biochemical recurrence in PCa patients. Upon further examination in vitro, it was revealed that PLOD2 knockdown significantly reduces matrigel invasion and migration in our radiorecurrent DU145-CF cell line, in addition to numerous other PCa cell lines, including primary cells we derived directly from PCa patients. Using the in vivo chick Chorioallantoic Membrane (CAM) model, we confirmed that PLOD2 knockdown significantly reduces the ability of DU145-CF cells to extravasate from the CAM vasculature into the surrounding stroma, a critical step of the metastatic cascade. To explore mechanisms of metastatic cellular reprogramming downstream of PLOD2, RNA sequencing of DU145-CF cells was conducted; a total of 681 genes were discovered to be dysregulated by PLOD2 knockdown, with their functional analysis suggesting changes in cellular metabolism and respiration. Finally, since PLOD2 is known to be regulated by hypoxia-induced protein HIF1α, we explored whether PLOD2 expression could be inhibited by the HIF1α inhibitor, PX-478. Treatment with PX-478 reduced both HIF1α and PLOD2 protein expression, and significantly reduced invasion, migration, and in vivo extravasation in DU145-CF cells, thereby indicating its potential as a pharmacological inhibitor of HIF1α-associated PLOD2 in radiorecurrent PCa. Together, our results demonstrate for the first time the role of PLOD2 in radiorecurrent PCa invasiveness, and point towards its potential as a therapeutic target to reduce metastasis and improve survival outcomes in PCa patients. Citation Format: Gavin Frame, Hon Leong, Roni Haas, Xiaoyong Huang, Jessica Wright, Paul C. Boutros, Thomas Kislinger, Stanley K. Liu. Investigating PLOD2 as a therapeutic target to overcome metastasis in radiorecurrent prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1274.

Abstract 5668: Long non-coding RNA LINC01614 knockdown decreases carcinogenic behavior of papillary thyroid cancer in vitro

Abstract Papillary thyroid cancer (PTC) accounts for the vast majority of thyroid cancer cases with increasing incidence over the past few decades. PTC has a significantly higher prevalence in females in their childbearing years. Despite high survival rates, disease recurrence and metastasis remain prominent issues, thus highlighting the critical need for molecular biomarker detection. A newer class of molecular regulators, known as long non-coding RNAs (lncRNAs), have demonstrated differential expression patterns in a multitude of cancers. The largest subclass of these RNA molecules in the human genome consists of long intergenic non-coding RNAs (lincRNAs) with many of their functions yet to be identified. Known functional roles of lncRNAs center on their ability to modulate gene expression and drive carcinogenic behavior, deeming them attractive biomarkers and/or therapeutic targets for study. Bioinformatic analysis of RNA sequencing data from our patient sample biobank identified LINC01614 as being significantly upregulated (~12 fold increase) in PTC, when compared to normal, matched thyroid tissue. Further, it was also upregulated ~30-fold in male PTC compared to ~5.5 fold increase in female PTC, highlighting a potential sex correlation for study. Thus, we are studying LINC01614 as a potential PTC biomarker. Gene expression analysis of LINC01614 in vitro was found to be upregulated in various thyroid cancer cell lines, specifically two PTC cell lines: TPC1 (~5 fold; RET/PTC rearrangement; female) and K1 (~2 fold; BRAFV600E; male) when compared to the immortalized “normal” thyroid cell line (Nthy-ori-3-1). For phenotypic evaluation, we utilized the CRISPRi technique to employ transcriptional repression of LINC01614 in both TPC1 and K1. LINC01614 knockdown in TPC1 and K1 resulted in decreased healing capacity (~20%), clonogenicity (~50% and ~34%, respectively), and proliferation (~55% and ~45%, respectively). Studies are currently underway to further assess invasion, morphology, and RNA localization within the cell in vitro, as well as the identification of potential protein interactions and mechanisms of action of LINC01614 in PTC. Studying lncRNAs and their regulatory roles in cancer cell function is critical in the identification of various diagnostic and prognostic biomarkers for therapeutic intervention. Our data support the potential biological role of LINC01614 in driving PTC growth and metastatic potential. Further elucidation of how LINC01614 impacts PTC development and progression is a promising avenue of exploration. Citation Format: Danielle Quaranto, Michelle Carnazza, Nicole R. DeSouza, Sina Dadafarin, Augustine Moscatello, Humayun K. Islam, Raj K. Tiwari, Jan Geliebter. Long non-coding RNA LINC01614 knockdown decreases carcinogenic behavior of papillary thyroid cancer in vitro [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5668.

Abstract 7569: Characterizing pathways for metastasis of retinoblastoma in forebrain organoids

Abstract Retinoblastoma (Rb) is a childhood cancer of the eye, which usually presents in children under the age of five. When detected early, Rb has favorable prognosis in developed countries, but metastasis into the central nervous system (CNS) through the optic nerve correlate with a high mortality rate. Even if detected early, the available harsh and unspecific treatments can cause serious side effects, and enucleations are still performed frequently. There is still uncertainty regarding the mechanism for metastasis into the central nervous system. We performed bioinformatic analysis of single cell sequencing data for retinoblastoma, retinal tissues, optic nerve, and brain, to identify potential pathways and cell-cell communications fostering Rb invasion into the optic nerve and brain. Our analysis revealed several potential metastatic drivers, including immune modulation involving MIF, secreted by the Rb cells, as well as cell-adhesion pathways promoting a change in cellular phenotype. Given that animal models do not faithfully recapitulate human Rb initiation and progression, we developed a novel human iPSC-derived forebrain organoid model to investigate mechanisms of Rb CNS metastasis. Microinjections of GFP-labelled Rb cells allow to track growth and spread. In this fully human model including microglial cells, we can, for the first time, study the Rb forebrain interactions and pathways involved. RNA-seq analysis of Rb cells growing in forebrain organoids shows increased activity in neuron projection development and neuron migration, overlapping with the observed phenotype switch of invading Rb. Together, we present a novel iPSC-derived human forebrain model to monitor growth and spread of metastatic Rb, and describe new pathways involved in invading and metastasizing Rb. Citation Format: Yulia Shtanko, Sara Rodriguez, Benjamin Schachner, Emily Adis, Samantha McLaughlin, Sebastian Borges, James Dollar, Ashley Zuniga, Gabriela Quintana, Sofia Lopez, Dawn Owens, Chloe Moulin, Steffanie Braun, Gulum Yenisehirli, Daniel Pelaez, J. William Harbour, Stefan Kurtenbach. Characterizing pathways for metastasis of retinoblastoma in forebrain organoids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7569.

Abstract 6257: Genome wide, high-throughput, high-resolution structural variation detection at low variant allele fraction for oncology samples

Abstract Structural variation detection remains an elusive undertaking. For decades, G-banded karyotyping has remained the standard practice for nearly all hematological malignancy samples. Cancers are diseases of the genome and structural variants (SVs) are a hallmark of nearly all cancers, are often drivers of oncogenicity, and can sometimes be targeted for treatment, as highlighted by the discovery of the Philadelphia chromosome and later the development of targeted kinase inhibitors. One of the most important limitations of karyotyping, its requirement for cells to divide in culture, has prevented its application for most solid tumors and therefore, there is considerably less understanding of the impact of SVs in solid tumors. Optical genome mapping is a technique that is revolutionizing cytogenomics and unlocking the understanding of SVs in the genome at a level never seen before. It not only can detect nearly all variants that a karyotype can, but it can provide 10,000x higher resolution and does not require cell culture. Because of this, it is being adopted for oncology studies across hematological malignancies and solid tumors. This study demonstrates the performance of a new high throughput Stratys instrument for generation of optical genome map data at extraordinarily high coverage depth. With this instrument, 12 samples can be loaded at once, each loaded onto its own cartridge and the instrument can collect 400x genome coverage for each of these samples in 24 hours. The instrument has random access to the cartridges so that completed samples can be swapped out to facilitate optimal instrument run efficiency. To date, this system has been demonstrated to run 60 samples in a week, each at 400x coverage. Data from the instrument can be processed by Bionano Access™ and VIA™ software to call SVs, copy number variants (CNVs), regions of loss of heterozygosity (LOH), on a genome wide basis, and to classify those variants automatically according to guidelines such as the National Comprehensive Cancer Network (NCCN), World Health Organization (WHO), and National Health Services (NHS, United Kingdom). This new high throughput system with advanced bioinformatic data analysis has the potential to further transform structural variation analysis in cancer research. Citation Format: Alex R. Hastie, Pat Lynch. Genome wide, high-throughput, high-resolution structural variation detection at low variant allele fraction for oncology samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6257.

Barley AGO4 proteins show overlapping functionality with distinct small RNA-binding properties in heterologous complementation

Key messageBarley AGO4 proteins complement expressional changes of epigenetically regulated genes in Arabidopsis ago4-3 mutant and show a distinct affinity for the 5′ terminal nucleotide of small RNAs, demonstrating functional conservation and divergence.The function of Argonaute 4 (AGO4) in Arabidopsis thaliana has been extensively characterized; however, its role in monocots, which have large genomes abundantly supplemented with transposable elements (TEs), remains elusive. The study of barley AGO4 proteins can provide insights into the conserved aspects of RNA-directed DNA methylation (RdDM) and could also have further applications in the field of epigenetics or crop improvement. Bioinformatic analysis of RNA sequencing data identified two active AGO4 genes in barley, HvAGO4a and HvAGO4b. These genes function similar to AtAGO4 in an Arabidopsis heterologous complementation system, primarily binding to 24-nucleotide long small RNAs (sRNAs) and triggering methylation at specific target loci. Like AtAGO4, HvAGO4B exhibits a preference for binding sRNAs with 5′ adenine residue, while also accepting 5′ guanine, uracil, and cytosine residues. In contrast, HvAGO4A selectively binds only sRNAs with a 5′ adenine residue. The diverse binding capacity of barley AGO4 proteins is reflected in TE-derived sRNAs and in their varying abundance. Both barley AGO4 proteins effectively restore the levels of extrachromosomal DNA and transcript abundancy of the heat-activated ONSEN retrotransposon to those observed in wild-type Arabidopsis plants. Our study provides insight into the distinct binding specificities and involvement in TE regulation of barley AGO4 proteins in Arabidopsis by heterologous complementation.