Downregulation Of Target Genes Research Articles

A protoplast-based transient gene expression assay for the identification of heat and oxidative stress-regulatory genes in perennial ryegrass

BackgroundWith the accumulating omics data, an efficient and time-saving transient assay to express target genes is desired. Mesophyll protoplasts, maintaining most stress-physiological responses and cellular activities as intact plants, offer an alternative transient assay to study target genes’ effects on heat and oxidative stress responses.ResultsIn this study, a perennial ryegrass (Loliumperenne L.) mesophyll protoplast-based assay was established to effectively over- or down-regulate target genes. The relative expression levels of the target genes could be quantified using RT-qPCR, and the effects of heat and H2O2-induced oxidative stress on protoplasts’ viability could be quantitatively measured. The practicality of the assay was demonstrated by identifying the potential thermos-sensor genes LpTT3.1/LpTT3.2 in ryegrass that over-expressing these genes significantly altered protoplasts’ viability rates after heat stress.ConclusionThis protoplast-based rapid stress regulatory gene identification assay was briefed as ‘PRIDA’ that will complement the stable genetic transformation studies to rapidly identify candidate stress-regulatory genes in perennial ryegrass and other grass species.

Abstract CT105: Early clinical experience with a novel first-in-class G-quadruplex experimental anti-cancer drug

Abstract The human genome contains G-rich regions that are over-represented in many cancer gene promoters. These can form higher-order G-quadruplex arrangements under the influence of an appropriate and selective small molecule compound. The resulting ligand-G-quadruplex complex may be resistant to polymerase read-through and thus results in transcriptional down-regulation of target genes. QN-302, based on a tetra-substituted naphthalene diimide chemotype, is a potent and selective G-quadruplex-binding compound that has been designed and initially developed at University College London. It displays single-digit cell growth inhibition in a panel of pancreatic ductal adenocarcinoma (PDAC) cell lines. RNA-seq analysis shows that it is a pan-quadruplex agent, down-regulating the expression of multiple G-quadruplex-promoter cancer genes and pathways in PDAC. It also shows in vivo anti-tumor activity in several animal models for PDAC, with low toxicity observed at therapeutic doses. QN-302 was licensed to Qualigen Therapeutics Inc in January 2022. It was granted Orphan Drug designation by the FDA in December 2022 for PDAC. This was followed by extensive regulatory toxicological and pharmacological studies together with successful scale-up synthesis, purification and formulation. QN-302 was granted IND clearance in August 2023 by the FDA for phase 1 clinical trials in advanced or metastatic solid tumors. This Phase 1a clinical trial is being conducted in two USA cancer centers (START Midwest, Grand Rapids, MI and Honor Health, Scottsdale, AZ) using a protocol based on 28-day once-weekly dose escalation and evaluation of three potential biomarkers, two of which have been suggested by transcriptomic analysis as being indicative of G-quadruplex-induced drug response and accompanying decrease of anti-tumor activity. So far 1 Cohort (3 patients) has been dosed at the lowest dose of 1.62 mg of QN-302 as part of this Phase 1a clinical trial. Patient #1, a male patient of metastatic pancreatic cancer, is currently in Cycle 4 of therapy showing Stable Disease and no AEs or SAEs reported. Patient #2, a female patient of metastatic colorectal cancer, completed Cycle 2 after which she showed progression upon CT Scan before entering Cycle 3 and was taken off study. Patient #3, a male patient of metastatic PDAC, is currently ending Cycle 2, about to enter Cycle 3, showing Stable Disease upon CT scan. All patients dosed showed no AEs, SAEs or side effects. They were also clinically observed to have improved QOL compared to prior SOC while on therapy with QN-302, This presentation will outline this unique approach and summarize safety, tolerability, PK/PD data and any early clinical data as described above including preliminary biomarker data now that clinical evaluation has commenced. The advantages and challenges of QN-302 will also be discussed. Citation Format: Tariq Arshad, Stephen Neidle, Sreenivasa Chandana, Erkut Borazanci. Early clinical experience with a novel first-in-class G-quadruplex experimental anti-cancer drug [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 CT105.

Abstract 3303: Paralogue selective p300 degraders induce synthetic lethality in pre-clinical models of CBP-deficient and p300-dependent malignancies

Abstract EP300 (or p300) acts as histone acetyltransferase (HAT) and transcriptional adapter or co-activator regulating transcription via chromatin remodeling. Both histone and non-histone proteins are acetylated by p300. In addition to HAT function, p300 has crotonyl-transferase activities, and that p300-catalyzed histone crotonylation directly stimulates transcription to a greater degree. p300 functions by scaffolding or as co-activator and enhancer of different transcription factors like HIF1a, BRCA-1, p53, NFκB, c-Myc, estrogen receptor (ER) and androgen receptor (AR) and other proteins such as PD-L1 and FOXP3. Selective targeting of p300 is expected to lead to therapeutic efficacy in CBP-mutant and p300-dependent malignancies with high degree of tolerability because of sparing of the other paralog CBP in normal cells. CBP mutant cancers comprise of several solid and hematological malignancies including 10% to 15% of non-small cell and small cell lung cancers harboring loss-of-function (LOF) aberrations. p300-dependent malignancies include prostate cancer, in which p300 plays a major role for androgen-dependent and -independent transactivation of the AR, MYCN-amplified neuroblastoma and ER+ breast cancers. Since the conventional CBP/p300 inhibitors do not discriminate between CBP and p300 proteins due to high sequence homology, we adopted a degrader approach, which has the potential to lead to paralog selectivity due to differentiated ternary complex formation. Herein we report best-in-class novel, potent and paralog selective p300 degraders with excellent selectivity over CBP and and other bromodomain containing proteins such as BRD4 by implementing molecular modeling, iterative medicinal chemistry and SAR based approaches. Synthetic lethality has been demonstrated while selectively degrading p300 in the cell lines having LOF mutation of another paralogue, CBP. Identified selective p300 degraders displayed excellent selectivity towards p300 degradation across tested cell lines and are orally bioavailable. Selective antiproliferative activity was observed in a panel of cell lines with CBP mutations or p300 dependency including AR+/ER+ cell lines along with the downregulation of target genes. In summary, we have identified highly selective degraders of p300 with desirable profile. Efforts are underway to advance them further towards nominating a development candidate. Citation Format: Saravanan Thiyagarajan, Chandrasekhar Abbineni, Krishna Chaitanya T, Achala Apte, Iram Khan Iqbal, Naveen Kumar R, Aravind A B, Avinash Kumar, Dabbeeru Madhu Babu, Shwetha Shwetha, Ankita Manna, Monalisha Mandal, Rituparna Panigrahi, Sivapriya Marappan, Suraj T Gore, Mohamad Fairus, Lim Yang Jin, Subhendu Mukherjee, Girish Daginakatte, Shekar Chelur, Kavitha Nellore, Murali Ramachandra, Susanta Samajdar. Paralogue selective p300 degraders induce synthetic lethality in pre-clinical models of CBP-deficient and p300-dependent malignancies [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 3303.

Abstract 469: PIWI-interacting RNA 50485 (piRNA-50485) is a novel lung tumor suppressor

Abstract Introduction: It is crucial to identify new driver genes and associated downstream pathways to facilitate the development of targeted therapies to effectively treat late-stage and metastatic lung cancer. One pathway involves the Ras association domain family 1 (RASSF1) gene which encodes multiple isoforms. Our laboratory has discovered that the RASSF1C isoform exhibits functional characteristics of an oncogene. We discovered that RASSF1C modulates the expression of PIWI-(Drosophila)-like 1 (PIWIL1, a stem cell renewal gene), as well as novel PIWI-interacting RNAs (piRNAs), which are regulators of the stem cell phenotype and have been linked to oncogenesis. While studying this pathway, we have identified novel piRNAs that are modulated by RASSF1C in non-small cell lung cancer (NSCLC) cells that appear to act as oncogenes or tumor suppressors. Methods: We conducted a global microarray screen to identify RASSF1C PIWI-interacting RNA (piRNA) gene targets. Several piRNA genes that are up- and down-regulated by RASSF1C were identified and the expression of selected up-regulated and down-regulated target genes were confirmed by RT-PCR. We evaluated the impact of selected piRNAs on lung cancer cell proliferation and migration in vitro. We also assessed the expression of the validated piRNA target genes in lung tumor and matched normal tissues. Host and target genes for specific piRNAs were identified using a piRNA database (piRNAdb.org). Results: Among the down-regulated piRNAs, we found that restoring piR-50485 expression drastically decreased lung cancer cell proliferation and invasion, suggesting that piR-50485 could be a potent inhibitor of lung cancer cell growth and progression. Consistent with this, we found that piR-50485 expression is significantly down-regulated in about 60% of human lung cancers. We also identified that the ZHX3 gene (a transcription repressor), which is down-regulated in human lung cancers, is the host gene for piR-50485. In addition, we identified the ZNF618 gene (a transcription co-regulator) that is up-regulated in lung tumor tissue, is a piR-50485 target gene. Consistent with this, treatment of lung cancer cells with piR-50485 mimics resulted in a significant decrease of ZNF618 protein levels, cell proliferation, and migration. Further, increased expression levels of ZHX3 are associated with higher lung cancer patient survival, while increased ZNF618 levels are associated with lower survival. Our novel findings suggest the hypothesis that the piR-50485-ZHX3-ZNF618 gene axis could negatively impact lung cancer cell growth and progression. Conclusion: Exploring the impact of the piR-50485-ZHX3-ZNF618 gene axis on lung cancer growth is a novel concept about which nothing is currently known. We are studying piR-50485 to determine if it can be an effective therapy for lung cancer metastasis, and whether it provides important prognostic information about lung cancer outcomes. Citation Format: Mark E. Reeves, Yousef G. Amaar. PIWI-interacting RNA 50485 (piRNA-50485) is a novel lung tumor suppressor [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 469.

Abstract 5752: Enhanced cancer therapy strategies utilizing gelatin-lipidoid hybrid nanoparticles for RNA delivery

Abstract Nanoparticle delivery platforms have provided impetus for the emergence of novel RNA-based cancer therapeutics due to their ability to circumvent the physiological and cellular barriers in the delivery. The clinical success of these strategies hinges primarily on the safety and efficacy of the delivery vehicle. Here, we have developed a gelatin-lipidoid hybrid nanoparticle (GLNP) that utilizes gelatin's biocompatibility, biodegradability, and lipidoids' high transfection efficiency. With GLNP, we have demonstrated the efficacy of delivering siRNA and silencing AXL, a receptor tyrosine kinase commonly associated with cancer progression, metastasis, and drug resistance. siRNA is attached to the surface of GLNP through covalent conjugation with gelatin, while the lipidoid on the system's interior electrostatically complexes with the siRNA. siRNAs are well protected by the GLNP when exposed to serum for at least 48 hours. The GLNP's bivalency significantly enhanced the downregulation of target genes in vitro and in vivo. Furthermore, the bivalent GLNP can simultaneously target and downregulate two oncogenes. Apart from siRNA, GLNP was also able to encapsulate and deliver mRNA, thereby suggesting the potential to simultaneously deliver RNA therapeutics to effect knockdown and expression of target proteins and maximize therapeutic effect. The length of the carbon chain of the lipidoid can be manipulated to influence the physico-chemical properties of the GLNP and its efficiency in encapsulating and delivering RNA drugs. Importantly, gelatin was found to effectively shield the cationic lipidoid and negate its toxicity. Toxicity studies indicate that high doses of GLNPs (up to 48 mg/kg BW) are well-tolerated with no significant changes in body weight, hematology, or serum chemistry. The co-administration of GLNP-siAXL and TKI in PDX models has shown notable control of tumor growth. It is important to note that immune checkpoint blockade (ICB) therapy has shown significant survival benefits in NSCLC patients. However, the therapeutic effect is limited to only 20% of patients due to several resistance mechanisms, such as increased expression of oncogenic proteins. Therefore, our future study will explore GLNP's ability to sensitize NSCLC tumors to immune therapy. Citation Format: Abilash Gangula, Dhananjay Suresh, Agasthya Suresh Babu, Zhaohui Li, Anandhi Upendran, Raghuraman Kannan. Enhanced cancer therapy strategies utilizing gelatin-lipidoid hybrid nanoparticles for RNA delivery [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 5752.

Abstract 6068: Discovery of BTX-9341, a bifunctional degrader of CDK4 and CDK6 for HR+/HER2- breast cancer

Abstract CDK4/6 inhibitors (CDK4/6i) such as palbociclib, abemaciclib and ribociclib are used to treat HR+/HER2- breast cancer, but patients can develop resistance via many mechanisms, several of which converge on the upregulation of the cyclin D-CDK4/6 signaling node. This has been shown to limit the effectiveness of CDK4/6i in ER+ breast cancer with up to 20% patients exhibiting innate resistance and up to 70% patients developing acquired resistance after 3 years on therapy (Scheidemann, 2021). To address acquired resistance, we sought a degrader approach. We utilized our PRODEGY platform of Cereblon (CRBN) binders to synthesize CRBN mediated CDK4/6 bifunctional degraders and identified BTX-9341 as a development candidate. Breast cancer cell lines treated with BTX-9341 showed up to 85% degradation of CDK4 and CDK6 with DC50s <1nM. CDK4/6 phosphorylates the protein RB which releases the transcription factor E2F, inducing the expression of genes which promote cell cycle progression. We examined RB phosphorylation by in-cell western, E2F target gene expression by qPCR and cell cycle progression by propidium iodide staining followed by flow cytometry. BTX-9341 was potent in all downstream assays, with phospho-RB IC50s <30nM, E2F target gene downregulation and G0/G1 cell cycle arrest at concentrations as low as 10nM. These downstream effects were sustained throughout 72 hours with BTX-9341 treatment but recovered more rapidly with Palbociclib treatment. We used a 2D colony formation assay (CFA) to assess inhibition of proliferation by cell cycle arrest. BTX-9341 potently inhibited cell proliferation with CFA IC50s of 20-50nM while CDK4/6i had CFA IC50s of 50-1000nM. This increased activity was due to CRBN mediated target degradation, as demonstrated by a shift in CFA IC50 values in a CRBN knockout cell line towards the values seen with the inhibitors. In palbociclib-resistant HR+/HER2- cell line models BTX-9341 maintained a low CFA IC50 (<150nM) while CDK4/6i displayed micromolar CFA IC50s. BTX-9341 displays excellent pharmacokinetic properties which allowed for oral dosing in xenograft studies. In several breast cancer xenograft models, BTX-9341 showed dose-dependent tumor growth inhibition, tumor regression at higher dose levels, and was effective with multiple alternate dosing regimens. These results show that BTX-9341 displays excellent single agent activity in vitro and in vivo and that this activity is maintained in CDK4/6i resistant models. This indicates that a degrader approach to targeting this pathway may be more effective than current therapies, and that using this modality in a post CDK4/6i setting may be more effective than switching CDK4/6 inhibitors. Reference: Scheidemann, Erin R, and Ayesha N Shajahan-Haq. “Resistance to CDK4/6 Inhibitors in Estrogen Receptor-Positive Breast Cancer.” International journal of molecular sciences vol. 22,22 12292. 14 Nov. 2021, doi:10.3390/ijms222212292 Citation Format: Hannah Majeski, Akinori Okano, Kirti Chahal, Angela Pasis, Casey Carlson, Arvind Shakya, Qiao Liu, Shenlin Huang, Aparajita Hoskote Chourasia, Leah Fung. Discovery of BTX-9341, a bifunctional degrader of CDK4 and CDK6 for HR+/HER2- 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 6068.

Integrative Transcriptome Analysis of mRNA and miRNA in Pepper's Response to Phytophthora capsici Infection.

Phytophthora blight of pepper is a notorious disease caused by the oomycete pathogen Phytophthora capsici, which poses a great threat to global pepper production. MicroRNA (miRNA) is a class of non-coding small RNAs that regulate gene expressions by altering the translation efficiency or stability of targeted mRNAs, which play important roles in the regulation of a plant's response to pathogens. Herein, time-series mRNA-seq libraries and small RNA-seq libraries were constructed using pepper roots from the resistant line CM334 and the susceptible line EC01 inoculated with P. capsici at 0, 6, 24, and 48 h post-inoculation, respectively. For mRNA-seq analysis, a total of 2159 and 2971 differentially expressed genes (DEGs) were identified in CM334 and EC01, respectively. For miRNA-seq analysis, 491 pepper miRNAs were identified, including 330 known miRNAs and 161 novel miRNAs. Among them, 69 and 88 differentially expressed miRNAs (DEMs) were identified in CM334 and EC01, respectively. Examination of DEMs and their targets revealed 22 regulatory networks, predominantly featuring up-regulated miRNAs corresponding to down-regulated target genes. Notably, these DEM-DEG regulatory networks exhibited significant overlap between CM334 and EC01, suggesting that they might contribute to pepper's basal defense against P. capsici. Furthermore, five selected DEMs (miR166, miR1171, miR395, miR530 and miRN2) and their target genes underwent qRT-PCR validation, confirming a consistent negative correlation in the expression patterns of miRNAs and their targets. This comprehensive analysis provides novel insights into the regulatory networks of miRNAs and their targets, offering valuable contributions to our understanding of pepper's defense mechanisms against P. capsici.

Micro-transcriptome analysis reveals miRNA-mediated survival strategies between megalocytivirus RBIV-C1 and Scophthalmus maximus

A successful viral infection is primarily dependent on interactions between the viral pathogenesis and the host's antiviral immunity. MicroRNAs (miRNAs) are non-coding regulatory RNAs that play significant roles in modulating the host's antiviral immune responses. To elucidate the functional mechanism of miRNAs during megalocytivirus infection, in this study, micro-transcriptome analysis was performed on the head-kidney of turbot (Scophthalmus maximus) infected with RBIV-C1 or not at 3, 6 and 9 days after infection. A total of 247 differentially expressed miRNAs (DEmiRs) were identified, among which 125 were known miRNA and 122 were newly identified. Based on an integrated negative correlation analysis of miRNA-mRNA, a total of 1173 up-regulated and 644 down-regulated target genes (DEmRs) were identified. These DEmRs were found to be enriched in different KEGG pathways associated with signal transduction, endocrine system, immune system, cancer, and infectious diseases. Moreover, networks of immune-related DEmiRs-DEmRs were constructed and analyzed, revealing significant associations between RBIV-C1 infection and immune-related pathways, such as pattern recognition receptor, apoptosis, phagolysosome, autophagy, TNF signaling, adaptive immunity, cytotoxicity, and NF-kappa B signaling. Additionally, the negative correlation network analysis unveiled numerous known and novel DEmiRs that directly target RBIV-C1 genes. This study presents, for the first time, a comprehensive micro-transcriptome dataset of turbot following RBIV-C1 infection, offering valuable insights into the underlying survival mechanisms that involve immune evasion and antiviral immunity.

An RNAi screen for conserved kinases that enhance microRNA activity after dauer in Caenorhabditis elegans.

Gene regulation in changing environments is critical for maintaining homeostasis. Some animals undergo a stress-resistant diapause stage to withstand harsh environmental conditions encountered during development. MicroRNAs are one mechanism for regulating gene expression during and after diapause. MicroRNAs downregulate target genes posttranscriptionally through the activity of the microRNA-induced silencing complex. Argonaute is the core microRNA-induced silencing complex protein that binds to both the microRNA and to other microRNA-induced silencing complex proteins. The 2 major microRNA Argonautes in the Caenorhabditis elegans soma are ALG-1 and ALG-2, which function partially redundantly. Loss of alg-1 [alg-1(0)] causes penetrant developmental phenotypes including vulval defects and the reiteration of larval cell programs in hypodermal cells. However, these phenotypes are essentially absent if alg-1(0) animals undergo a diapause stage called dauer. Levels of the relevant microRNAs are not higher during or after dauer, suggesting that activity of the microRNA-induced silencing complex may be enhanced in this context. To identify genes that are required for alg-1(0) mutants to develop without vulval defects after dauer, we performed an RNAi screen of genes encoding conserved kinases. We focused on kinases because of their known role in modulating microRNA-induced silencing complex activity. We found RNAi knockdown of 4 kinase-encoding genes, air-2, bub-1, chk-1, and nekl-3, caused vulval defects and reiterative phenotypes in alg-1(0) mutants after dauer, and that these defects were more penetrant in an alg-1(0) background than in wild type. Our results implicate these kinases as potential regulators of microRNA-induced silencing complex activity during postdauer development in C. elegans.

Conserved plant transcriptional responses to microgravity from two consecutive spaceflight experiments.

Understanding how plants adapt to the space environment is essential, as plants will be a valuable component of long duration space missions. Several spaceflight experiments have focused on transcriptional profiling as a means of understanding plant adaptation to microgravity. However, there is limited overlap between results from different experiments. Differences in experimental conditions and hardware make it difficult to find a consistent response across experiments and to distinguish the primary effects of microgravity from other spaceflight effects. Plant Signaling (PS) and Plant RNA Regulation (PRR) were two separate spaceflight experiments conducted on the International Space Station utilizing the European Modular Cultivation System (EMCS). The EMCS provided a lighted environment for plant growth with centrifugal capabilities providing an onboard 1 g control. An RNA-Seq analysis of shoot samples from PS and PRR revealed a significant overlap of genes differentially expressed in microgravity between the two experiments. Relative to onboard 1 g controls, genes involved in transcriptional regulation, shoot development, and response to auxin and light were upregulated in microgravity in both experiments. Conversely, genes involved in defense response, abiotic stress, Ca++ signaling, and cell wall modification were commonly downregulated in both datasets. The downregulation of stress responses in microgravity in these two experiments is interesting as these pathways have been previously observed as upregulated in spaceflight compared to ground controls. Similarly, we have observed many stress response genes to be upregulated in the 1 g onboard control compared to ground reference controls; however these genes were specifically downregulated in microgravity. In addition, we analyzed the sRNA landscape of the 1 g and microgravity (μ g) shoot samples from PRR. We identified three miRNAs (miR319c, miR398b, and miR8683) which were upregulated in microgravity, while several of their corresponding target genes were found to be downregulated in microgravity. Interestingly, the downregulated target genes are enriched in those encoding chloroplast-localized enzymes and proteins. These results uncover microgravity unique transcriptional changes and highlight the validity and importance of an onboard 1 g control.

Structure-guided design of a selective inhibitor of the methyltransferase KMT9 with cellular activity.

Inhibition of epigenetic regulators by small molecules is an attractive strategy for cancer treatment. Recently, we characterised the role of lysine methyltransferase 9 (KMT9) in prostate, lung, and colon cancer. Our observation that the enzymatic activity was required for tumour cell proliferation identified KMT9 as a potential therapeutic target. Here, we report the development of a potent and selective KMT9 inhibitor (compound 4, KMI169) with cellular activity through structure-based drug design. KMI169 functions as a bi-substrate inhibitor targeting the SAM and substrate binding pockets of KMT9 and exhibits high potency, selectivity, and cellular target engagement. KMT9 inhibition selectively downregulates target genes involved incell cycle regulation and impairs proliferation of tumours cells including castration- and enzalutamide-resistant prostate cancer cells. KMI169 represents a valuable tool to probe cellular KMT9 functions and paves the way for the development of clinical candidate inhibitors as therapeutic options to treat malignancies such as therapy-resistant prostate cancer.

Upregulation of apoptotic genes and downregulation of target genes of Sonic Hedgehog signaling pathway in DAOY medulloblastoma cell line treated with arsenic trioxide

Sonic hedgehog (SHH) medulloblastoma etiology is associated with the SHH molecular pathway activation at different levels. We investigated the effect of arsenic trioxide as a downstream-level inhibitor of the SHH signaling pathway on morphology, cytotoxicity, migration, and SHH-related and apoptotic gene expression of DAOY cells. Cells were treated at various arsenic trioxide (ATO)concentrations (1, 2, 3, 5, and 10 μM) for different times (24 and 48 hr). Following treatments, the morphology of the cells was investigated at ×20 and ×40 magnification by an inverted microscope. Then, cytotoxicity was investigated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and trypan blue assays. Cell migration was analyzed through the wound-healing assay. Furthermore, the expression of SHH-related (GLI1, GLI2, SMO, and MYCN) and apoptotic genes (BAX, BCL2, and TP53) was assessed by real-time quantitative polymerase chain reaction (qPCR). Finally, GLI1, SMO, and MYCN markers were analyzed through immunocytochemistry. Data were analyzed by SPSS (version 16) and P≤0.05 was considered significant. Morphological changes were seen at 3 and 2 μM in 24 and 48 hr of treatment, respectively. The MTT assay showed a dose-dependent cytotoxicity indicating an IC50 value of 3.39±0.35 and 2.05±0.64 μM in 24 and 48hr treatment, respectively. In addition, the trypan blue assay showed higher IC50 values of 4.29±0.25 and 3.92±0.22 μM in 24 and 48 hr treatment, respectively. The wound-healing assay indicated a dose-dependent reduction of cell migration speed showing a 50% reduction at 2.89±0.26 μM. Significant downregulation of GLI1 and GLI2, as well as the upregulation of BAX, BAX/BCL2 ratio, and TP53 were evident. Significant increases in GLI1 and MYCN markers were also evident in immunocytochemistry. ATO, as a downstream effective inhibitor of the SHH pathway, substantially leads to cell death, cell migration inhibition, apoptosis upregulation, and downregulation of SHH target genes in DAOY medulloblastoma. Since ATO is a toxic chemotherapeutic agent, it must be used at low concentrations (2 μM) in order not to damage healthy cells.

Abstract A174: Antitumor activity of lipid nanoparticle-delivered anti-miR-21

Abstract Background: MicroRNAs (miRNAs) are small non-coding RNA molecules that play crucial roles in various biological processes, such as growth, development, aging, and apoptosis. Several studies have shown that miRNAs, including miR-21, can function as either oncogenes or tumor suppressor genes, influencing tumor initiation and progression. Aberrant expression of miR-21 has been observed in different cancer cells, indicating its significant involvement as an oncogenic miRNA in the development of various types of tumors. Antisense oligonucleotides (ASOs) have been identified as effective tools for downregulating target genes by either triggering RNase H endonuclease activity to cleave the ASO-target gene heteroduplex or by interfering with splicing and translation regulation of the target RNA sequence. ASOs have the potential to target not only mRNA but also oligonucleotides like miRNAs or small interfering RNAs (siRNAs), making them a promising approach for miRNA inhibition. However, the efficient delivery of freely circulating ASOs to the tumor microenvironment poses a challenge due to their high density of negative charges, impeding cell uptake. To address this issue, a novel lipid nanoparticle (LNP) platform called QTsome has been developed, which combines quaternary amine cationic lipids and tertiary amine ionizable lipids to enhance drug delivery. The utilization of a mixture of cationic and ionizable lipids in QTsome allows for optimal pH-dependent drug loading and release characteristics. In this study, our objective was to employ the QTsome system to deliver an ASO targeting miR-21 (AM-21) for potential tumor therapy. Methods: A total of 8E6 A549 cells were inoculated into mice, and when the tumor volume reached 100mm3, the mice were randomly divided into seven groups based on tumor volume, with each group consisting of five mice.On the day of grouping, drug administration was initiated with the following doses: 1mg/kg, every 3 days (Q3D); 2mg/kg, Q3D; 3mg/kg, Q3D; 4mg/kg, Q3D; 4mg/kg, every 4 days (Q4D); 4mg/kg, every 5 days (Q5D); 4mg/kg, every 7 days (Q7D). The drugs were administered a total of 5 times. Additionally, the A549/MC38 model was constructed using the same method. The antitumor activity of the drug and its therapeutic effect in combination with Erlotinib were evaluated in both the A549 CDX and MC38 syngeneic mouse models through intravenous injection, with a dose of 4mg/kg, Q3D. Results: The study revealed that the optimal dose for achieving the maximum antitumor effect was 4mg/kg, administered 3 times per day. In the A549 model, the tumor growth inhibition rates were 71.91%, 60.93%, and 80.44% for the AM-21/QTsome group, Erlotinib group, and the combination of AM-21/QTsome and Erlotinib group, respectively. In the MC38 mouse model, the tumor inhibition rate of AM-21/QTsome was 33.29%. Conclusion: These results emphasize the potential of miR-21 as a therapeutic target for cancer treatment, demonstrating that AM-21/QTsome holds great promise as a groundbreaking drug in this field. Citation Format: Jing Li, Qiaofang Ma, Xinyue Zhang, Xiaojie Chen, Jialiang Lin, Jun Bai, Fei Su, Xiaobin Zhao, Robert J. Lee, Yongsheng Yang. Antitumor activity of lipid nanoparticle-delivered anti-miR-21 [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A174.

OR11-01 A New Model for Estrogen Receptor-alpha Antagonist Mechanism of Action

Abstract Disclosure: J.C. Nwachukwu: None. J.W. Njeri: None. T. Venables: None. C. Seath: None. M.E. Pipkin: None. Y. Hou: None. B.S. Katzenellenbogen: None. J.A. Katzenellenbogen: None. K.W. Nettles: None. We recently developed Dual Mechanism Estrogen Receptor-α (ERα) Inhibitors (DMERI) with more antagonist efficacy than selective ERα modulators (SERMs) such as tamoxifen, and selective ERα degraders (SERDs) such as fulvestrant in certain breast cancer models. Current models of anti-estrogen action are largely based on genomics studies in growth arrested cells, where the effects primarily reversed estradiol-mediated gene expression. In that context, most ER antagonists, especially the SERDs, show very little gene activation. We were interested in understanding antagonist mechanism of action in asynchronous cells that were growing in intact medium that had not been charcoal-stripped to remove estradiol and growth factors. RNA-seq of asynchronous MCF-7 cells treated with 4-hydroxytamoxifen, fulvestrant, a SERM-like DMERI, and a SERD-like DMERI showed that all four classes of ligands equally up-regulated and down-regulated differentially expressed genes (DEGs), which included a core set of regulatory networks, as well as ligand-selective gene networks. The number of DEGs predicted efficacy, with tamoxifen regulating few genes, and the SERD-like DMERI regulating the most genes. The SERD-like DMERI also inhibited expression of many more genes that encode cell cycle regulators and key cancer drivers, such as ERα, AKT1, HRAS, and several growth factor receptors. Landscape in silico analysis based on chromatin immunoprecipitation (ChIP)-seq data suggests that recruitment of the ERα MegaTrans complex in collaboration with the oxysterol receptor, LXRα, predicts up-regulation, while cooperation with the retinoblastoma-associated proteins, RB1 and RBL1, predicts down-regulation of target genes. APEX2-mediated proximity labeling in asynchronous cells revealed that fulvestrant and the SERD-like DMERI labeled both coactivators and corepressors. Both compounds also increase labeling of STAG1 and other cohesin subunits that coordinate chromatin looping, while also associating with the nuclear matrix protein Lamin B1 and heterochromatin-associated proteins. These data suggest that antagonists have dual roles in genome organization. An shRNAmiR screen targeting over 300 chromatin regulatory factors revealed networks of shared and exclusive coregulators used by antiestrogens, including the heterochromatin protein, CBX1, which was exclusively required for growth inhibition by fulvestrant, and subunits of histone acetylase and methylase complexes such as KMT2A (the catalytic subunit of the MLL1 complex), which were broadly required. Thus, antiestrogen-driven growth suppression involves both common and ligand-selective transcriptional regulatory networks through utilization of both coactivators and corepressors. Supported by NIH R01CA220284 and BCRF-083 and BCRF-084 grants. Presentation Date: Friday, June 16, 2023

GiRAFR improves gRNA detection and annotation in single-cell CRISPR screens

Novel methods that combine single cell RNA-seq with CRISPR screens enable high-throughput characterization of transcriptional changes caused by genetic perturbations. Dedicated software is however lacking to annotate CRISPR guide RNA (gRNA) libraries and associate them with single cell transcriptomes. Here, we describe a CRISPR droplet sequencing (CROP-seq) dataset. During analysis, we observed that the most commonly used method fails to detect mutant gRNAs. We therefore developed a python tool to identify and characterize intact and mutant gRNAs, called GiRAFR. We show that mutant gRNAs are dysfunctional, and failure to detect and annotate them leads to an inflated estimate of the number of untransformed cells, attenuated downregulation of target genes, as well as an underestimated multiplet frequency. These findings are mirrored in publicly available datasets, where we find that up to 35% of cells are transduced with a mutant gRNA. Applying GiRAFR hence stands to improve the annotation and quality of single cell CRISPR screens.

Long non-coding RNAs influence aging process of sciatic nerves in SD rats.

To investigate the long non-coding RNAs (lncRNAs) changes in the sciatic nerve (SN) in Sprague Dawley (SD) rats during aging. Eighteen healthy SD rats were selected at the age of 1 month (1M) and 24 months (24M) and SNs were collected. High-throughput transcriptome sequencing and bioinformatics analysis were performed. Protein-protein interaction (PPI) networks and competing endogenous RNA (ceRNA) networks were established according to differentially expressed genes (DEGs). As the length of lncRNAs increased, its proportion to the total number of lncRNAs decreased. A total of 4079 DElncRNAs were identified in Con vs. 24M. GO analysis was primarily clustered in nerve and lipid metabolism, extracellular matrix, and vascularization-related fields. There were 17 nodes in the PPI network of the target genes of up-regulating genes including Itgb2, Lox, Col11a1, Wnt5a, Kras, etc. Using quantitative RT-PCR, microarray sequencing accuracy was validated. There were 169 nodes constructing the PPI network of down-regulated target genes, mainly including Col1a1, Hmgcs1, Hmgcr. CeRNA interaction networks were constructed. Lipid metabolism, angiogenesis, and ECM fields might play an important role in the senescence process in SNs. Col3a1, Serpinh1, Hmgcr, and Fdps could be candidates for nerve aging research.

Cascade dynamic assembly/disassembly of DNA nanoframework enabling the controlled delivery of CRISPR-Cas9 system.

CRISPR-Cas9 has been explored as a therapeutic agent for down-regulating target genes; the controlled delivery of Cas9 ribonucleoprotein (RNP) is essential for therapeutic efficacy and remains a challenge. Here, we report cascade dynamic assembly/disassembly of DNA nanoframework (NF) that enables the controlled delivery of Cas9 RNP. NF was prepared with acrylamide-modified DNA that initiated cascade hybridization chain reaction (HCR). Through an HCR, single-guide RNA was incorporated to NF; simultaneously, the internal space of NF was expanded, facilitating the loading of Cas9 protein. NF was designed with hydrophilic acylamino and hydrophobic isopropyl, allowing dynamic swelling and aggregation. The responsive release of Cas9 RNP was realized by introducing disulfide bond-containing N,N-bis(acryloyl)cystamine that was specifically in response to glutathione of cancer cells, triggering the complete disassembly of NF. In vitro and in vivo investigations demonstrated the high gene editing efficiency in cancer cells, the hypotoxicity in normal cells, and notable antitumor efficacy in a breast cancer mouse model.

Exogenous dsRNA trigger RNAi in Venturia inaequalis resulting in down regulation of target genes and growth reduction.

Venturia inaequalis is an apple scab causing fungal pathogen. It is a highly contagious and destructive pathogen which rapidly spreads infection in the surrounding orchards if not managed. The management and control of disease require multiple fungicides to be sprayed at different development stages of the apple. Persistent applications of fungicides also raises environmental concerns. Here, we demonstrate the potential of using spray induced gene silencing (SIGS) by developing target specific gene constructs for the synthesis of corresponding double-stranded RNA (dsRNA). The exogenous application of dsRNAs was found to reduce mycelial growth and spore formation of V. inaequalis on culture plates. Four genes of V. inaequalis viz. CIN1, CE5, VICE12 and VICE16 which get upregulated during infection, were selected as targets for the development of gene construct expressing the corresponding dsRNA. The effect of exogenously supplied in vitro synthesized dsRNA on V. inaequalis was assessed in culture bioassay experiments with respect to growth, and spore formation. The expression level of the target genes in treated and control fungus was evaluated using quantitative PCR. Fungus treated with VICE12 targeted dsRNA showed maximum reduction in colony size (~ 55%), conidia formation (~ 93%) and expression level of the corresponding gene (2.2 fold), which was followed by CIN1-dsRNA. VICE16-dsRNA treatment was least effective with 32% reduction in growth, the non-significant effect of conidial spore formation and 1.13 fold down regulation of corresponding target gene expression level. The result of this investigation validates the hypothesis that RNAi is evoked in V. inaequalis by exogenously supplied dsRNA and spray induced gene silencing (SIGS) based solutions may reduce burden of fungicide usage on apple crop against apple scab disease in future.

Exosomal miR-184 in the aqueous humor of patients with central serous chorioretinopathy: a potential diagnostic and prognostic biomarker

BackgroundCentral serous chorioretinopathy (CSC) is the fourth most prevalent retinal disease leading to age-related macular degeneration (AMD) and retinal atrophy. However, CSC's pathogenesis and therapeutic target need to be better understood.ResultsWe investigated exosomal microRNA in the aqueous humor of CSC patients using next-generation sequencing (NGS) to identify potential biomarkers associated with CSC pathogenesis. Bioinformatic evaluations and NGS were performed on exosomal miRNAs obtained from AH samples of 62 eyes (42 CSC and 20 controls). For subgroup analysis, patients were divided into treatment responders (CSC-R, 17 eyes) and non-responders (CSC-NR, 25 eyes). To validate the functions of miRNA in CECs, primary cultured-human choroidal endothelial cells (hCEC) of the donor eyes were utilized for in vitro assays. NGS detected 376 miRNAs. Our results showed that patients with CSC had 12 significantly upregulated and 17 downregulated miRNAs compared to controls. miR-184 was significantly upregulated in CSC-R and CSC-NR patients compared to controls and higher in CSC-NR than CSC-R. In vitro assays using primary cultured-human choroidal endothelial cells (hCEC) demonstrated that miR-184 suppressed the proliferation and migration of hCECs. STC2 was identified as a strong candidate for the posttranscriptional down-regulated target gene of miR-184.ConclusionOur findings suggest that exosomal miR-184 may serve as a biomarker reflecting the angiostatic capacity of CEC in patients with CSC.

A vector-free gene interference system using delaminated Mg–Al-lactate layered double hydroxide nanosheets as molecular carriers to intact plant cells

BackgroundThe Mg–Al-lactate layered double hydroxide nanosheet (LDH-NS) has shown great potential as an optimal nanocarrier for extensive use in plants. However, previous studies in plant sciences have not provided a clear description of the application for the LDH-NSs-based double-stranded RNA (dsRNA) delivery (LDH-dsRNA) system in different tissues of both model and non-model species.ResultsLDH-NSs were synthesized by using the co-precipitation method, while the dsRNAs targeting genes of interest were prepared in vitro using T7 RNA polymerase. The LDH-dsRNA bioconjugates with a neutral charge were produced by incubating with the mass ratio of LDH-NSs to dsRNA at 3:1, which were then introduced into intact plant cells using three different approaches, including injection, spray, and soak. The LDH-dsRNA delivery method was optimized by inhibiting the expression of the Arabidopsis thaliana ACTIN2 gene. As a result, soaking A. thaliana seedlings in a medium containing LDH-dsRNA for 30 min led to the silencing of 80% of the target genes. The stability and effectiveness of the LDH-dsRNA system were further confirmed by the high-efficiency knockdown of plant tissue-specific genes, including that encoding phytoene desaturase (PDS), WUSCHEL (WUS), WUSCHEL-related homeobox 5 (WOX5), and ROOT HAIR DEFECTIVE 6 (RHD6). In addition, the LDH-dsRNA system was employed in cassava, where it was found that the expression of the gene encoding nucleotide-binding site and leucine-rich repeat (NBS-LRR) was significantly reduced. As a result, the resistance of cassava leaves to pathogens was weakened. Noteworthy, the injection of LDH-dsRNA into leaves resulted in a significant downregulation of target genes in both stems and flowers, indicating the successful transport of LDH-dsRNA from leaves to other parts of plants.ConclusionsLDH-NSs have proven to be a highly effective molecular tool for delivering dsRNA into intact plant cells, enabling accurate control of target gene expression.