Multiple Target Genes Research Articles

Mechanism of oxymatrine in the treatment of cryptosporidiosis through TNF/NF-κB signaling pathway based on network pharmacology and experimental validation

Cryptosporidiosis is a worldwide zoonotic disease. Oxymatrine, an alkaloid extracted and isolated from the plant bitter ginseng, has been reported to have therapeutic effects on cryptosporidiosis. However, the underlying mechanism of its action remains unclear. In this study, we utilized network pharmacology and experimental validation to investigate the mechanism of oxymatrine in the treatment of cryptosporidiosis. First, the potential targets of drugs and diseases were predicted by TCMSP, Gene Cards, and other databases. Following the intersection of drug-disease targets, the DAVID database was used to implement the enrichment analysis of GO functions and KEGG pathways, and then the network diagram of "intersected target-KEGG" relationship was constructed. Autodock 4.2.6 software was used to carry out the molecular docking of core targets to drug components. Based on the establishment of a mouse model of cryptosporidiosis, the validity of the targets in the TNF/NF-κB signaling pathway was confirmed using Western blot analysis and Quantitative Rea-ltime-PCR. A total of 41 intersectional targets of oxymatrine and Cryptosporidium were generated from the results, and five core targets were screened out by network analysis, including RELA, AKT1, ESR1, TNF, and CASP3. The enrichment analysis showed that oxymatrine could regulate multiple gene targets, mediate TNF, Apoptpsis, IL-17, NF-κB and other signaling pathways. Molecular docking experiments revealed that oxymatrine was tightly bound to core targets with stable conformation. Furthermore, we found through animal experiments that oxymatrine could regulate the mRNA and protein expression of IL-6, NF-κB, and TNF-α in the intestinal tissues of post-infected mice through the TNF/NF-κB signaling pathway. Therefore, it can be concluded that oxymatrine can regulate the inflammatory factors TNF-α, NF-κB, and IL-6 through the TNF/NF-κB signaling pathway for the treatment of cryptosporidiosis. This prediction has also been validated by network pharmacology and animal experiments.

Targeting mutant p53 with arsenic trioxide: A preclinical study focusing on triple negative breast cancer

New treatments are urgently required for triple-negative breast cancer (TNBC). As TP53 is mutated in approximately 80% of TNBC, it is theoretically an attractive target for new drugs for this disease. Arsenic trioxide (ATO), which is used to treat promyelocytic leukaemia, was recently shown to reactivate mutant p53 and restore wild-type functionality. The aim of this study was to evaluate ATO as a potential new treatment for TNBC. Using a panel of 20 cell lines, we found that TNBC cell lines were more sensitive to ATO than non-TNBC cell lines (P = 0.045). Consistent with its ability to reactivate mutant p53, ATO was a more potent inhibitor of proliferation in cell lines with mutant TP53 than the wildtype TP53 (P = 0.027). Direct evidence of mutant p53 reactivation was the induction of multiple wild-type p53 canonical target genes such as CDKN1A, SLC7A11, BBC3, PMAIP1, SESN2, SRXN1 and TXNRD1. Our findings support the activation of mutant p53 by ATO and, furthermore, the possible repurposing of ATO to treat TP53-mutated TNBC.

A phase 1 study evaluating the safety, pharmacokinetics, and efficacy of fadraciclib, an oral CDK2/9 inhibitor, in patients with advanced solid tumors and lymphoma.

3125 Background: Fadraciclib (formerly CYC065)is a highly selective inhibitor of CDK2 (IC50= 5 nM) and CDK9 (IC50=26 nM) causing mitotic catastrophe and apoptotic death of cancer cells at sub-micromolar concentrations. In a previous Phase 1 study of intravenous fadraciclib monotherapy, a heavily pretreated endometrial cancer patient with CDNK2A, CDKN2B and PRMT5 loss achieved confirmed CR. This is the first study to evaluate oral fadraciclib monotherapy. Methods: A global Phase 1/2, open-label, dose-escalation study in subjects with advanced solid tumors or lymphoma (NCT04983810). The Phase 1 portion is exploring both schedule and dose of oral fadraciclib monotherapy in 28-day cycles to identify MTD and/or RP2D using a standard 3+3 design. Results: As of January 31, 2024, 45 subjects have received fadraciclib at 8 dose levels (DL1-6a: 50-150 mg, bid given 3-5 days per week for 3-4 out of 4 weeks or DL6b: 125 mg, daily for 4/4 weeks). Heavily pretreated patients with breast, colorectal, gynecological cancers, and T cell lymphoma with ECOG PS 0:1 (9:36) were enrolled. Fadraciclib was well tolerated at dose levels 1 to 5 (up to 100 mg bid). Adverse events reported were nausea (n=31), vomiting (n=23), thrombocytopenia (n=6). Grade 3 DLT of hyperglycemia (1/2 DL6 and 2/6 DL6a) and nausea (1/2 DL6) was observed at doses above 125mg bid M-F, 4/4 weeks. Hyperglycemia was controlled after dose interruption and blood glucose levels returned to normal range after treatment. Preliminary PK analysis suggests dose dependent exposure. At DL5 and above, plasma concentration was above target concentration from CDK2 and CDK9 target engagement studies. Preliminary PD analysis of treated patient samples showed suppression of expression in multiple target genes, including MYC, MCL1, CCNE/cyclin E, CDKN2A, CDKN2B, and PRMT5. Preliminary efficacy data are available for 31 evaluable patients. Two PRs after the first cycle were observed in one patient with CTCL and one with angioimmunoblastic T-Cell Lymphoma (AITL). Twenty patients showed SD. Tumor size reduction was observed in 10 patients. A squamous NSCLC patient harboring a CDK2NB loss of function mutation and prior chemo- and immunotherapy achieved reduction of 22% in the sum of all target lesions after 1 cycle of treatment. Conclusions: Based on data from the CYC065-101 study, fadraciclib appears well tolerated from DL1 to 5. The MTD for the bid dosing schedule is 100mg bid, M-F, 4/4 weeks. The trial is ongoing with evaluation of a daily dosing schedule. Clinical trial information: NCT04983810 .

Identification and Characterization of microRNAs in Morphological Color Change of Polychromatic Midas Cichlids (Amphilophus citrinellus)

As a representative genetic and economic trait, pigmentation has a strong impact on speciation and adaptation. However, information and reports on microRNAs (miRNAs) associated with pigmentation remain limited. The Midas cichlid fish, with three typical distinct stages of body color pattern, “black-gray-gold”, is an ideal model system for investigating pigmentation traits. In this study, miRNA libraries from scale tissues with the attached epidermis of Midas cichlids at three distinct stages of color transformation, black (B), transition (T), and gold (G), were sequenced using Illumina sequencing technology. In total, 53 (B vs. G), 88 (B vs. T), and 57 (T vs. G) miRNAs were differentially expressed between the respective groups. Target genes of the identified miRNAs were predicted, and the results showed that multiple target genes were related to pigmentation and pigment–cell differentiation. The miRNA–mRNA regulatory network suggests that miR-183-x and miR-133-x were predicted to be involved in regulating morphological color changes in Midas cichlids. The results advance our understanding of potential functions of miRNAs in skin pigment differentiation and early skin color fading of fishes.

#1948 Transcriptome analysis of the effect of roxadustat on osteoclasts

Abstract Background and Aims In recent years, hypoxia-inducing factor prolyl hydroxylase inhibitors (HIF-PHIs) have been widely used in the treatment of renal anemia, bringing a revolutionary breakthrough in the treatment of anemia in CKD patients. However, HIF-PHIs acts on a variety of cells and regulates the expression of multiple target genes. Some studies have reported that HIF-PHIs plays an important role in regulating bone metabolism and promoting the differentiation and calcification of osteoblasts, but its influence on osteoclasts remains controversial. This study intends to explore the effect of roxadustat, a representative drug of HIF-PHIs, on osteoclasts. Method Bone marrow mononuclear cells (BMMCs) from 6-8 weeks old male C57BL/6 wild mice were extracted and induced to differentiate into osteoclasts using macrophage colony-stimulating factor (M-CSF) and receptor activator of nuclear factor-κB ligand (RANKL). Meanwhile, lipopolysaccharide (LPS) was used to simulate the inflammatory environment in CKD patients. According to the experimental group, different concentrations of roxadustat (0 μM, 2.5 μM, 5 μM, 10μM) were added simultaneously. When osteoclast induction reached day 6, mRNA was extracted for transcriptome sequencing and bioinformatics analysis. Results As shown in Table 1, different concentrations of roxadustat were given to primary bone marrow monocytes under both conditions, and there were 3 biological replicates for each sample. The reproducibility scatter plot showed that the data in each group had good repeatability (Fig. 1), and the heat map for basic difference analysis of each sample was shown in Fig. 2. The trend analysis results of the two groups were shown in Fig. 3. BMMCs group and LPS stimulated group showed two upward trends, respectively. KEGG enrichment analysis of these two upward trends showed that HIF-1, MAPK, PI3K-Akt, NF-κB and osteoclast differentiation pathways were significantly enriched in both groups. It is suggested that roxadustat can promote osteoclast differentiation and increase inflammatory response with the increase of roxadustat concentration. The enrichment analysis of the two groups showed that there was no significant enrichment pathway. Conclusion We explored the differentiation of osteoclasts under normal conditions and osteoclast differentiation under simulated inflammation in CKD patients respectively. Transcriptomic analysis results showed that HIF-1, MAPK, PI3K-Akt, NF-κB and osteoclast differentiation pathways were significantly enriched with the increase of roxadustat concentration. It is suggested that the use of roxadustat may promote bone destruction and increase the risk of inflammatory response.

Central role of the mTORC1 pathway in glucocorticoid activity against B-ALL cells

AbstractGlucocorticoids (GCs), such as dexamethasone and prednisone, are crucial components of B-cell precursor acute lymphoblastic leukemia (B-ALL) therapies. However, the molecular basis of GC-induced cell death remains elusive. Here, we show that GC suppresses mechanistic target of rapamycin complex 1 (mTORC1) signaling and that, conversely, oncogenic activation of mTORC1 confers resistance to GCs. Our genome-wide CRISPR/CRISPR-associated protein 9 (CRISPR/Cas9) dropout screens reveal that depletion of components of either the gap activity toward Rags 1 or tuberous sclerosis complexes, both negative regulators of mTORC1 signaling, significantly attenuates B-ALL cell sensitivity to dexamethasone. Dexamethasone primarily induces B-ALL cell death by downregulating mTORC1 activity, thus promoting autophagy and impairing protein synthesis. Dexamethasone treatment failed to suppress mTORC1 activity in B-ALL cells expressing mutant GC receptors lacking DNA-binding capacity, suggesting that dexamethasone transcriptionally represses mTORC1 activity. RNA-sequencing analysis identified multiple dexamethasone target genes that negatively regulate mTORC1 activity. Our findings suggest that GC sensitivity is significantly influenced by oncogenic stimuli and/or growth factors that activate the PI3K-AKT-mTORC1 pathway. This is consistent with the frequent GC resistance found in Ph and Ph-like ALLs.

Stemness and Cell Cycle Regulators and Their Modulation by Retinoic Acid in Ewing Sarcoma.

Retinoic acid (RA) regulates stemness and differentiation in human embryonic stem cells (ESCs). Ewing sarcoma (ES) is a pediatric tumor that may arise from the abnormal development of ESCs. Here we show that RA impairs the viability of SK-ES-1 ES cells and affects the cell cycle. Cells treated with RA showed increased levels of p21 and its encoding gene, CDKN1A. RA reduced mRNA and protein levels of SRY-box transcription factor 2 (SOX2) as well as mRNA levels of beta III Tubulin (TUBB3), whereas the levels of CD99 increased. Exposure to RA reduced the capability of SK-ES-1 to form tumorspheres with high expression of SOX2 and Nestin. Gene expression of CD99 and CDKN1A was reduced in ES tumors compared to non-tumoral tissue, whereas transcript levels of SOX2 were significantly higher in tumors. For NES and TUBB3, differences between tumors and control tissue did not reach statistical significance. Low expression of CD99 and NES, and high expression of SOX2, were significantly associated with a poorer patient prognosis indicated by shorter overall survival (OS). Our results indicate that RA may display rather complex modulatory effects on multiple target genes associated with the maintenance of stem cell's features versus their differentiation, cell cycle regulation, and patient prognosis in ES.

Evaluation of histological and ultrastructural changes provoked by prenatal tramadol on postnatal cortical cerebellar neuronal development in rats: possible implication of Ki67, GFAP and MicroRNA-7/P53 signalling trajectories

Tramadol is a novel centrally acting analgesic. Despite, its implementation during pregnancy may impair neuronal survival and synaptic development in neonatal cerebella. The current investigation assessed the histological and ultrastructural alterations in postnatal cortical cerebellar neuronal development induced by prenatal tramadol. 30 offsprings were divided to control group I: fifteen pups born to mothers given saline from D10 till D21 of gestation. Tramadol-treated group II: fifteen pups born to mothers received tramadol HCL (50 mg/kg/day) from D10 till D21 of gestation. Pups were categorized into three subgroups (a, b, and c) and offered for sacrifice on the seventh, fourteenth and twenty-first post-natal days. Light microscopic examination revealed the overcrowding and signs of red degeneration affecting purkinje cell layer. Neurodegenerative signs of both purkinje and granule cell neurons were also confirmed by TEM in form of chromatin condensation, dilated Golgi channels, disrupted endoplasmic reticulum, marked infolding of the nuclear envelope and decrease in granule cell precursors. In addition, the astrocytic processes and terminal nerve axons appeared with different degrees of demyelination and decreased number of oligodendrocytes and degenerated mitochondria. Furthermore, group II exhibited an increase in P53 immune expression. The area percentage of apoptotic cells detected by TUNEL assay was significantly increased. Besides to the significant decrease of Ki67 immunoreactivity in the stem neuronal cell progenitors. Quantitative PCR results showed a significant decline in micro RNA7 gene expression in tramadol treated groups resulting in affection of multiple target genes in P53 signaling pathways, improper cortical size and defect in neuronal development.

Cross-kingdom RNA interference mediated by insect salivary microRNAs may suppress plant immunity

Communication between insects and plants relies on the exchange of bioactive molecules that traverse the species interface. Although proteinic effectors have been extensively studied, our knowledge of other molecules involved in this process remains limited. In this study, we investigate the role of salivary microRNAs (miRNAs) from the rice planthopper Nilaparvata lugens in suppressing plant immunity. A total of three miRNAs were confirmed to be secreted into host plants during insect feeding. Notably, the sequence-conserved miR-7-5P is specifically expressed in the salivary glands of N. lugens and is secreted into saliva, distinguishing it significantly from homologues found in other insects. Silencing miR-7-5P negatively affects N. lugens feeding on rice plants, but not on artificial diets. The impaired feeding performance of miR-7-5P-silenced insects can be rescued by transgenic plants overexpressing miR-7-5P. Through target prediction and experimental testing, we demonstrate that miR-7-5P targets multiple plant genes, including the immune-associated bZIP transcription factor 43 (OsbZIP43). Infestation of rice plants by miR-7-5P-silenced insects leads to the increased expression of OsbZIP43, while the presence of miR-7-5P counteracts this upregulation effect. Furthermore, overexpressing OsbZIP43 confers plant resistance against insects which can be subverted by miR-7-5P. Our findings suggest a mechanism by which herbivorous insects have evolved salivary miRNAs to suppress plant immunity, expanding our understanding of cross-kingdom RNA interference between interacting organisms.

Abstract CT231: Identification of a novel agnostic predictive multiomic signature via Elastic Net/Machine Learning in TALAPRO-2 (TP-2), a phase 3 study of talazoparib (TALA) + enzalutamide (ENZA) vs placebo (PBO) + ENZA as first-line (1L) treatment in patients (pts) with metastatic castration-resistant prostate cancer (mCRPC)

Abstract Background: TP-2 (NCT03395197) demonstrated significantly improved radiologic progression-free survival (rPFS) regardless of homologous recombination repair (HRR) gene alteration status for pts with mCRPC who received 1L TALA + ENZA (n=402) vs PBO + ENZA (n=403; Agarwal et al. Lancet. 2023. PMID: 37285865). We explore potential associations of ctDNA genomics and tumor gene expression with efficacy in TP-2. Methods: The analysis was based on the safety population (n=799). Two data sets were used: a FoundationOne®Liquid CDx data set (Azad et al. ASCO 2023, #5056) of prospectively collected/retrospectively analyzed plasma samples (n=681); and a tumor transcriptomic data set generated via HTG’s Oncology Biomarker Panel (with 10 additional genes implicated in PARP inhibitor sensitivity; n=304). Correlations between baseline molecular biomarkers and rPFS were assessed via a Cox proportional hazards model. Multivariate elastic net regression analysis incorporated 151 pts in the TALA + ENZA arm with 2,868 molecular features (ctDNA: 309 genes [only short variant alterations incorporated]; HTG: 2,559 tumor transcripts). Results: Positively predictive candidate tumor biomarkers for TALA + ENZA included androgen response signature and individual androgen receptor (AR) target genes such as PSA, ALDH1A3, and CAMKK2. These expression signatures/transcripts had no/minimal predictive value for PBO + ENZA. A 33-feature (3 genes, 30 transcripts) elastic net signature was identified that was predictive of rPFS with TALA + ENZA: TP53 and AR short variant alteration status were each prognostic and associated with worse rPFS. Expression of multiple AR target genes, including ALDH1A3 (top selected feature) and CAMKK2, was positively associated with rPFS. For TALA + ENZA, this multiomic signature was predictive of rPFS in pts regardless of HRR gene alteration status, and to a lesser extent for PBO + ENZA. None of the 12 HRR genes used for stratification in TP-2 were included in the signature. Conclusions: Our exploratory analysis identified candidate gene expression signatures, including AR pathway elements, potentially associated with differential benefit from TALA + ENZA, reinforcing the potential for exploitable crosstalk between AR and DNA repair pathways. Though validation is necessary, a predictive multiomic signature for benefit from TALA + ENZA regardless of HRR alteration status was identified that included alterations in genes previously implicated in prognosis and expression of multiple AR target transcripts. Strikingly, it did not include any of the 12 HRR genes used in prospective stratification for TP-2, reinforcing the potential benefit for TALA + ENZA beyond HRR-deficient tumors. Citation Format: Glenn Liu, Xinmeng Jasmine Mu, Karim Fizazi, A. Douglas Laird, Nobuaki Matsubara, Steven M. Yip, Jie Pu, Joan Carles, Andre P. Fay, Robert J. Jones, Stefanie Zschäbitz, Josep M. Piulats, Jae Young Joung, Whijae Roh, Jijumon Chelliserry, Nicola Di Santo, Michelle Saul, Arun A. Azad, Neeraj Agarwal. Identification of a novel agnostic predictive multiomic signature via Elastic Net/Machine Learning in TALAPRO-2 (TP-2), a phase 3 study of talazoparib (TALA) + enzalutamide (ENZA) vs placebo (PBO) + ENZA as first-line (1L) treatment in patients (pts) with metastatic castration-resistant prostate cancer (mCRPC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr CT231.

The TELOMERE REPEAT BINDING proteins TRB4 and TRB5 function as transcriptional activators of PRC2-controlled genes to regulate plant development

Plant-specific transcriptional regulators called TELOMERE REPEAT BINDING proteins (TRBs) combine two DNA-binding domains, the GH1 domain, which binds to linker DNA and is shared with H1 histones, and the Myb/SANT domain, which specifically recognizes the telobox DNA-binding site motif. TRB1, TRB2, and TRB3 proteins recruit Polycomb group complex 2 (PRC2) to deposit H3K27me3 and JMJ14 to remove H3K4me3 at gene promoters containing telobox motifs to repress transcription. Here, we demonstrate that TRB4 and TRB5, two related paralogs belonging to a separate TRB clade conserved in spermatophytes, regulate the transcription of several hundred genes involved in developmental responses to environmental cues. TRB4 binds to several thousand sites in the genome, mainly at transcription start sites and promoter regions of transcriptionally active and H3K4me3-marked genes, but, unlike TRB1, it is not enriched at H3K27me3-marked gene bodies. However, TRB4 can physically interact with the catalytic components of PRC2, SWINGER, and CURLY LEAF (CLF). Unexpectedly, we show that TRB4 and TRB5 are required for distinctive phenotypic traits observed in clf mutant plants and thus function as transcriptional activators of several hundred CLF-controlled genes, including key flowering genes. We further demonstrate that TRB4 shares multiple target genes with TRB1 and physically and genetically interacts with members of both TRB clades. Collectively, these results reveal that TRB proteins engage in both positive and negative interactions with other members of the family to regulate plant development through both PRC2-dependent and -independent mechanisms.

An Emerging Role for Enhancer RNAs in Brain Disorders.

Noncoding DNA undergoes widespread context-dependent transcription to produce noncoding RNAs. In recent decades, tremendous advances in genomics and transcriptomics have revealed important regulatory roles for noncoding DNA elements and the RNAs that they produce. Enhancers are one such element that are well-established drivers of gene expression changes in response to a variety of factors such as external stimuli, cellular responses, developmental cues, and disease states. They are known to act at long distances, interact with multiple target gene loci simultaneously, synergize with other enhancers, and associate with dynamic chromatin architectures to form a complex regulatory network. Recent advances in enhancer biology have revealed that upon activation, enhancers transcribe long noncoding RNAs, known as enhancer RNAs (eRNAs), that have been shown to play important roles in enhancer-mediated gene regulation and chromatin-modifying activities. In the brain, enhancer dysregulation and eRNA transcription has been reported in numerous disorders from acute injuries to chronic neurodegeneration. Because this is an emerging area, a comprehensive understanding of eRNA function has not yet been achieved in brain disorders; however, the findings to date have illuminated a role for eRNAs in activity-driven gene expression and phenotypic outcomes. In this review, we highlight the breadth of the current literature on eRNA biology in brain health and disease and discuss the challenges as well as focus areas and strategies for future in-depth research on eRNAs in brain health and disease.

Abstract 6589: Discovery of potent and selective pan-TEAD autopalmitoylation inhibitors for the treatment of Hippo-pathway altered cancers

Abstract TEAD1-4 are DNA bound transcription factors regulated by the Hippo tumor suppressor pathway that bind the coactivators YAP/TAZ to activate oncogenic gene expression programs involved in cell survival, proliferation, and drug resistance. TEAD-dependent transcription is activated in many tumor types through a variety of mechanisms including LOF Hippo pathway mutations (e.g. NF2, LATS) and YAP/TAZ amplification, and also as an adaptive resistance mechanism, for example in response to EGFR TKI and KRAS inhibition. Here, we report the initial characterization of a novel pan-TEAD inhibitor, AZ4331, which was identified following a structure-guided drug design campaign. AZ4331 disrupts the post-translational palmitoylation of TEAD proteins through covalent binding to a conserved cysteine residue resulting in inhibition of TEAD-dependent transcriptional output. AZ4331 inhibited the proliferation of NF2m NCI-H226 cells (GI50: 92 nM) while having no effect on Hippo-wild type NCI-H2452 (GI50: undetermined). Cell-based metabolic labeling studies demonstrated the ability of AZ4331 to inhibit palmitoylation of all four TEAD paralogs and led to disruption of the YAP/TEAD complex assessed by immunoprecipitation resulting in reduced TEAD transcriptional output as assessed by qPCR. Furthermore, in vivo profiling showed AZ4331 achieved sufficient exposures (plasma free Cmax: 2.7 µM) and robust target engagement as measured through reduction of multiple canonical TEAD target genes (CTGF [IC50: 0.127 µM], ANKRD1, AMOTL2 and CYR61) in Hippo-altered mesothelioma xenograft tumors. This target engagement in turn drove inhibition of tumor proliferation in xenograft models representing common Hippo-alterations. AZ4331 treatment of NF2m NCI-H226 and LATS1/2 loss MSTO-211H mesothelioma xenografts drove 50% and 93% regression of tumors, respectively. While treatment of head and neck squamous cell carcinoma FAT1m FaDu and YAP1amp Detroit562 xenografts lead to 58% tumor growth inhibition and 35% tumor regression, respectively. These findings identify AZ4331 as a potent inhibitor of the TEAD transcription factor family and further validate the inhibition of TEAD in Hippo-altered cancers as a potential therapeutic strategy. Citation Format: Jacob A. Gordon, Jolanta Dubauskaite, Michelle DuPont, Nin Guan, Geoff Holdgate, Scott Mlynarski, Neil Umbreit, Danielle Sanchez, Abhishek Srivastava, Janek Suski, Nancy Su, Ryan Richards, Sabina Cosulich, Corinne Reimer, James Brownell. Discovery of potent and selective pan-TEAD autopalmitoylation inhibitors for the treatment of Hippo-pathway altered cancers [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 6589.

Abstract 6154: Targeted CRISPRi screen identifies functional variants and novel target genes at multiple renal cell carcinoma (RCC) susceptibility loci

Abstract Genome-wide association studies (GWAS) have identified 13 renal cell carcinoma (RCC) risk regions, as well as 7 regions with nominal significance, but detailed investigation of how these regions function is required to reveal the underlying biological bases of disease susceptibility. While detailed study of four loci have implicated critical pathways in RCC, causal genes and pathways for most loci remain unidentified. To identify such causative variants and target genes, we evaluated a set of variants based on Massively Parallel Reporter Assays (MPRA), eQTL analysis, capture Hi-C, and an arrayed CRISPR inhibition (CRISPRi) screen. The MPRA identified 196 variants across 19 regions with significant allele-specific effects, indicating cis-regulatory activity. Of these, 39 variants across 10 RCC loci displayed chromatin loops allowing physical interaction with the promoter of 24 nearby putative gene targets, as well as a significant cis-eQTL with the same gene. To confirm the presence of a cis-regulatory relationship between these 39 candidate variants and 24 putative target genes, we performed an arrayed CRISPRi screen in ACHN (RCC) and HEK293T (embryonic renal) cells covering each of the 10 nominated regions. Cells were stably transduced with inactive Cas9 fused to the ZIM3 transcriptional repressor domain and cis-regulatory relationships were assessed by TaqMan qPCR for the target genes. The screen identified multiple novel relevant target genes of RCC predisposition variants, including UCK2 at 1q24, ABL2 and TDRD5 at 1q25, GTDC1 at 2q22, GPR37 at 7q31, AGBL3 and CALD1 at 7q33, and MAP2K1 at 15q22. At some regions, evidence indicates cis-regulatory relationships occur between a target gene and all variants predicted to be ‘causative’ at the region (e.g., UCK2 at 1q24 and ABL2 at 1q25). For other regions, cis-regulatory relationships occur between a gene and only one variant tested (e.g., GPR37 at 7q31 and TDRD5 at 1q25).Previously, target genes of only four RCC susceptibility regions had been identified and published. This study identifies eight novel target genes across six additional RCC susceptibility regions, representing a significant advance in understanding of the underlying biology of RCC susceptibility variants. Furthermore, ongoing screening using the orthologous method, CRISPR activation (CRISPRa), and integration of both normoxic and hypoxic conditions continues to provide further insight into the underlying biology at these regions. Citation Format: Timothy Winter, Timothy Myers, Leandro Colli, Lea Jessop, Jiyeon Choi, Mitchell J. Machiela, Mark P. Purdue, Kevin Brown, Stephen Chanock. Targeted CRISPRi screen identifies functional variants and novel target genes at multiple renal cell carcinoma (RCC) susceptibility loci [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 6154.

Abstract 4131: Combination therapeutic strategy to fight against triple-negative breast cancer

Abstract Triple-negative breast cancers (TNBCs) lack estrogen-and progesteron receptors and human epidermal growth factor receptor-2 (HER2) which limits the therapeutic approaches. The high metastasizing capability of TNBCs is in correlation with the poor oxygenation of the cancerous breast tissue. This leads to the activation of the hypoxia-inducible-factor 1 (HIF-1), which induces multiple target genes that are involved in tumor progression and metastasis formation. This makes HIF-1 an attractive drug target, however, HIF-1 inhibitors failed if applied in monotherapy. Therefore, our aim is to investigate the combined therapeutic effect of HIF-1 inhibitor acriflavine and paclitaxel, a commonly used taxane in TNBC treatment. The synergy assessment of the two drugs was carried out by utilizing Sulforhodamine B assay on TNBC cell lines. The in vivo toxicity and efficacy of the drug combination was tested on NOD SCID mice with orthotopically inoculated MDA-MB-231 cell line. Quantitative and qualitative analysis of multiple genes involved in tumor progression was performed by mRNA and protein expression level assessment with qPCR, western blot and immunohistochemistry methods. HIF-1 stimulation was achieved by either incubating the cells at 1% oxygen level or through CoCl2 treatment. The in vitro mRNA expression studies demonstrated that acriflavin possesses a hypoxic-effect-mitigating property on the expression of metastasis-involved- and HIF-1 target genes. Acriflavine alleviated the epithelial-mesenchymal transition of TNBC cells by increasing the expression of the epithelial marker, E-cadherin. At protein level, we detected decrease in HIF-1alpha and Phospho-Protein kinase B (Akt) and increase in p53 tumor suppressor gene expression in response to acriflavine treatment. We further established MDA-MB-231 xenograft model in mice for investigating in vivo toxicity and efficacy. The drug combination efficiently reduced the tumor size and the macrometastasis formation compared to the control groups. The protein analysis of frozen tumor tissue samples indicated that the combination therapy decreased the HIF-1alpha expression and the amount of Phospho-Akt and Phospho-Mitogen-activated protein kinases (pMAPK/pERK) in CoCl2treated mice. Additionally, expression of epithelial markers increased and that of mesenchymal markers decreased. The combination therapy led to a decrease in the platelet-derived growth factor receptor beta (PDGFRB) as well. To conclude, we identified a novel drug combination which can efficiently combat TNBC by inhibiting HIF-1 signaling, mitigating cell migration and metastasis formation and suppressing the activation of the Phosphoinositide 3-kinase (PI3K) and MAPK pathways. This work was supported by the Hungarian Thematic Excellence Program (TKP2021-EGA-44) and the National Laboratories Program - National Laboratory for Tumor Biology (NLP-17). Citation Format: Laura Svajda, Ivan Ranđelović, Sára Eszter Surguta, Marcell Baranyi, István Kenessey, Mihály Cserepes, József Tóvári. Combination therapeutic strategy to fight against triple-negative breast 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 4131.

Abstract 4643: A novel epigenomic profiling assay reveals disease biology and therapeutic targets in gastro-esophageal cancer from 1 ml of plasma

Abstract INTRODUCTION: Gastro-esophageal adenocarcinoma (GEA) is an aggressive and heterogeneous disease with a poor prognosis. Targeted therapies have failed largely due to challenges associated with biopsy collection, tumor antigen heterogeneity, and accurately distinguishing transcriptionally distinct esophageal, GE junction or gastric tumor types. We developed a novel, multimodal liquid biopsy assay that profiles genome-wide transcriptional activation. Here, we deploy this assay to define clinically relevant insights in a cohort of GEA patients. METHODS: 1 ml of plasma from whole blood samples was used to assess genome-wide enhancer, promoter and DNA methylation loci in 11 GEA patients (Stage III: 1, Stage IV: 10) and 7 healthy volunteers. 6 patients were confirmed as HER2+ based on standard tissue IHC/ISH methods. ctDNA estimation was performed using the ichorCNA algorithm on low pass whole genome sequencing data. A multimodal HER2 classifier developed previously using genome-wide features including HER2 was used to predict HER2 status of the GEA samples. RESULTS: Epigenomic profiling and comparison of GEA and healthy volunteer plasma samples revealed distinct genome-wide transcriptional activation patterns associated with gastroesophageal adenocarcinoma, including (i) the characteristic upregulation of HER2, FGFR2 and VEGF (ii) SOX2, KLF4, GATA6 transcription factor circuitry, and (iii) DNA methylation at the CHFR and MGMT promoters. We then explored if epigenomic profiling of liquid biopsies could infer the activation status of antibody-drug conjugate (ADC) targets currently under investigation in GEA cancers. Simultaneous examination of multiple target genes including HER2, HER3, TROP2, CLDN18, CEACAM5 and MET demonstrated patient-specific differences and dynamic range in transcriptional activation of a subset of these target genes. Finally, we investigated if HER2 status could be assigned accurately and quantitatively from a liquid biopsy using the multimodal HER2 classifier. HER2 positivity by IHC was predicted accurately in 8/11 samples corresponding to an area under the ROC curve (AUC) greater than 0.85. Discordance between plasma and tissue HER2 calls could be partially attributed to variability associated with tumor site/section used for tissue collection, IHC staining, and time between biopsy collection and blood draw. CONCLUSIONS: We demonstrate the feasibility of comprehensive epigenomic profiling from low input volume of 1ml of plasma to provide a snapshot of the tumor’s transcriptional state to derive clinically actionable insights. The HER2 classifier overcomes several of the challenges with IHC profiling by providing a uniform and quantitative measurement of HER2 activation. This non-invasive assay provides an accurate reflection of tumor transcriptional biology that can inform optimal patient selection strategies. Citation Format: Jonathan Beagan, Aparna Gorthi, Anthony D'Ippolito, Travis Clark, Michael Coyne, Tyrone Tamakloe, Amy Donahue, Baovy Tran, Hyun-Hwan Jeong, Kristian Cibulskis, Hathairat Sawaengsri, Corrie A. Painter, Juliann Chmielecki, J Carl Barrett, Mosammat Faria Afreen, Aditya Pandey, Ilexa Ashley Schechter, Martin S. Taylor, Matthew R. Strickland, Matthew Eaton, Samuel J. Klempner. A novel epigenomic profiling assay reveals disease biology and therapeutic targets in gastro-esophageal cancer from 1 ml of plasma [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 4643.

MicroRNA-33 controls hunger signaling in hypothalamic AgRP neurons

AgRP neurons drive hunger, and excessive nutrient intake is the primary driver of obesity and associated metabolic disorders. While many factors impacting central regulation of feeding behavior have been established, the role of microRNAs in this process is poorly understood. Utilizing unique mouse models, we demonstrate that miR-33 plays a critical role in the regulation of AgRP neurons, and that loss of miR-33 leads to increased feeding, obesity, and metabolic dysfunction in mice. These effects include the regulation of multiple miR-33 target genes involved in mitochondrial biogenesis and fatty acid metabolism. Our findings elucidate a key regulatory pathway regulated by a non-coding RNA that impacts hunger by controlling multiple bioenergetic processes associated with the activation of AgRP neurons, providing alternative therapeutic approaches to modulate feeding behavior and associated metabolic diseases.

Asiatic acid prevents glucocorticoid-induced femoral head osteonecrosis via PI3K/AKT pathway

Glucocorticoid-induced osteonecrosis of the femoral head (GIONFH) represents a predominant etiology of non-traumatic osteonecrosis, imposing substantial pain, restricting hip mobility, and diminishing overall quality of life for affected individuals. Centella asiatica (L.) Urb. (CA), an herbal remedy deeply rooted in traditional oriental medicine, has exhibited noteworthy therapeutic efficacy in addressing inflammation and facilitating wound healing. Drawing from CA's historical applications, its anti-inflammatory, anti-apoptotic, and antioxidant attributes may hold promise for managing GIONFH. Asiatic acid (AA), a primary constituent of CA, has been substantiated as a key contributor to its anti-apoptotic, antioxidant, and anti-inflammatory capabilities, showcasing a close association with orthopedic conditions.For the investigation of whether AA could alleviate GIONFH through suppressing oxidative stress, apoptosis, and to delve into its potential cellular and molecular mechanisms, the connection between AA and disease was analyzed through network pharmacology. DEX-induced apoptosis in rat osteoblasts and GIONFH in rat models, got utilized for the verification in vitro/vivo, on underlying mechanism of AA in GIONFH. Network pharmacology analysis reveals a robust correlation between AA and GIONFH in multiple target genes. AA has demonstrated the inhibition of DEX-induced osteoblast apoptosis by modulating apoptotic factors like BAX, BCL-2, Cleaved-caspase3, and cleaved-caspase9. Furthermore, it effectively diminishes the ROS overexpression and regulates oxidative stress through mitochondrial pathway. Mechanistic insights suggest that AA's therapeutic effects involve phosphatidylinositol 3-kinase/Protein kinase B (PI3K/AKT) pathway activation. Additionally, AA has exhibited its potential to ameliorate GIONFH progression in rat models. Our findings revealed that AA mitigated DEX-induced osteoblast apoptosis and oxidative stress through triggering PI3K/AKT pathway. Also, AA can effectively thwart GIONFH occurrence and development in rats.

Use of microRNAs as Diagnostic, Prognostic, and Therapeutic Tools for Glioblastoma.

Glioblastoma (GB) is the most aggressive and common type of cancer within the central nervous system (CNS). Despite the vast knowledge of its physiopathology and histology, its etiology at the molecular level has not been completely understood. Thus, attaining a cure has not been possible yet and it remains one of the deadliest types of cancer. Usually, GB is diagnosed when some symptoms have already been presented by the patient. This diagnosis is commonly based on a physical exam and imaging studies, such as computed tomography (CT) and magnetic resonance imaging (MRI), together with or followed by a surgical biopsy. As these diagnostic procedures are very invasive and often result only in the confirmation of GB presence, it is necessary to develop less invasive diagnostic and prognostic tools that lead to earlier treatment to increase GB patients' quality of life. Therefore, blood-based biomarkers (BBBs) represent excellent candidates in this context. microRNAs (miRNAs) are small, non-coding RNAs that have been demonstrated to be very stable in almost all body fluids, including saliva, serum, plasma, urine, cerebrospinal fluid (CFS), semen, and breast milk. In addition, serum-circulating and exosome-contained miRNAs have been successfully used to better classify subtypes of cancer at the molecular level and make better choices regarding the best treatment for specific cases. Moreover, as miRNAs regulate multiple target genes and can also act as tumor suppressors and oncogenes, they are involved in the appearance, progression, and even chemoresistance of most tumors. Thus, in this review, we discuss how dysregulated miRNAs in GB can be used as early diagnosis and prognosis biomarkers as well as molecular markers to subclassify GB cases and provide more personalized treatments, which may have a better response against GB. In addition, we discuss the therapeutic potential of miRNAs, the current challenges to their clinical application, and future directions in the field.

Cas-mCfLAMP: A multiplex rapid visualization assay for sugarcane pathogens based on labeled LAMP and CRISPR/Cas12a

Sugarcane diseases are caused by various pathogens, and rapid and accurate identification of these diseases has many challenges. Detection of sugarcane diseases using conventional assays are often handicapped by their low-throughput, high-cost, and low-sensitivity nature. Here, we report a novel method for the multiplexed and visual detection of sugarcane pathogens using CRISPR/Cas12a coupled with labeled loop-mediated isothermal amplification (Cas-mCfLAMP). This method labels the product during LAMP amplification, relieving the high dependence of CRISPR/Cas12a on specific CrRNAs and enabling the detection of multiple target genes in a single reaction. In addition, we have developed a field detection system that allows visual detection of sugarcane diseases in the field without the need for specialized technicians or expensive equipment. This method is simple, efficient, specific, and cost-effective for sugarcane disease detection, and holds potential to be modified for the field detection of other plant diseases.