Low Basal Expression Research Articles

Differences in transcriptomic responses upon Phytophthora palmivora infection among cultivars reveal potential underlying resistant mechanisms in durian

BackgroundPhytophthora palmivora is a devastating oomycete pathogen in durian, one of the most economically important crops in Southeast Asia. The use of fungicides in Phytophthora management may not be a long-term solution because of emerging chemical resistance issues. It is crucial to develop Phytophthora-resistant durian cultivars, and information regarding the underlying resistance mechanisms is valuable for smart breeding programs.ResultsIn this study, we conducted RNA sequencing (RNA-seq) to investigate early gene expression responses (at 8, 24, and 48 h) after the P. palmivora infection in three durian cultivars, which included one resistant cultivar (Puangmanee; PM) and two susceptible cultivars (Monthong; MT and Kradumthong; KD). We performed co-expression and differential gene expression analyses to capture gene expression patterns and identify the differentially expressed genes. The results showed that genes encoding heat shock proteins (HSPs) were upregulated in all infected durians. The expression levels of genes encoding HSPs, such as ERdj3B, were high only in infected PM. A higher level of P. palmivora resistance in PM appeared to be associated with higher expression levels of various genes encoding defense and chitin response proteins, such as lysM domain receptor-like kinases. MT had a lower resistance level than PM, although it possessed more upregulated genes during P. palmivora infection. Many photosynthetic and defense genes were upregulated in the infected MT, although their expression levels were lower than those in the infected PM. KD, the least resistant cultivar, showed downregulation of genes involved in cell wall organization or biogenesis during P. palmivora infection.ConclusionsOur results showed that the three durian cultivars exhibited significantly different gene expression patterns in response to P. palmivora infection. The upregulation of genes encoding HSPs was common in all studied durians. The high expression of genes encoding chitin response proteins likely contributed to P. palmivora resistance in durians. Durian susceptibility was associated with low basal expression of defense genes and downregulation of several cell wall-related genes. These findings enhance our understanding of durian resistance to Phytophthora infection and could be useful for the development of elite durian cultivars.

Alternative splicing as a driver of natural variation in abscisic acid response.

Abscisic acid (ABA) is a crucial player in plant responses to the environment. It accumulates under stress, activating downstream signaling to implement molecular responses that restore homeostasis. Natural variance in ABA sensitivity remains barely understood, and the ABA pathway has been mainly studied at the transcriptional level, despite evidence that posttranscriptional regulation, namely, via alternative splicing, contributes to plant stress tolerance. Here, we identified the Arabidopsis accession Kn-0 as less sensitive to ABA than the reference Col-0, as shown by reduced effects of the hormone on seedling establishment, root branching, and stomatal closure, as well as by decreased induction of ABA marker genes. An in-depth comparative transcriptome analysis of the ABA response in the two variants revealed lower expression changes and fewer genes affected for the least ABA-sensitive ecotype. Notably, Kn-0 exhibited reduced levels of the ABA-signaling SnRK2 protein kinases and lower basal expression of ABA-reactivation genes, consistent with our finding that Kn-0 contains less endogenous ABA than Col-0. ABA also markedly affected alternative splicing, primarily intron retention, with Kn-0 being less responsive regarding both the number and magnitude of alternative splicing events, particularly exon skipping. We find that alternative splicing introduces a more ecotype-specific layer of ABA regulation and identify ABA-responsive splicing changes in key ABA pathway regulators that provide a functional and mechanistic link to the differential sensitivity of the two ecotypes. Our results offer new insight into the natural variation of ABA responses and corroborate a key role for alternative splicing in implementing ABA-mediated stress responses.

Abstract 307: Generation and characterization of a glioblastoma stem cell model with acquired resistance to LSD1 inhibition

Abstract Epigenetic modifications play an important role in the initiation of various cancer types, including glioblastoma (GBM), and in the development of therapeutic resistance. Patients with GBM, a common malignant brain tumor, have an average survival of 12-15 months after first-line therapy. Lysine-specific demethylase 1 (LSD1) is a histone demethylase that is overexpressed in glioblastoma stem cells (GSCs) and functions to promote proliferation, inhibit differentiation, and enhance motility. Previous work from our group has investigated LSD1 as a therapeutic target in glioblastoma and identified genes that may predict resistance to pharmacological LSD1 inhibitors using RNA-seq. Five upregulated genes, HKDC1, RAB3IL1, RAB39B, FTH1, and FAM213A, were associated with LSD1 inhibitor (LSD1i) resistance and were validated in brain tissue of a GBM model treated with GSK-LSD1 after succumbing to tumor burden. In order to determine whether selection pressure from LSD1 inhibitor treatment caused upregulation of these genes, we created a model of acquired resistance in GSC lines in vitro. Isogenic resistant lines were generated by treating MDA-GSC17 cells with increasing concentrations of LSD1i or diluent (DMSO), as tolerated starting at 50 uM (which was five fold below the IC50 for these lines). In parallel, MDA-GSC17 controls were exposed to DMSO. The resistant line was created over 4 weeks and monitored by cell number and viability to reach 90%. To assess the change in gene expression, we conducted quantitative PCR for the five genes in the parental and resistant MDA-GSC17 line and saw upregulation in 3 of the 5 genes. Two genes, HKDC1 and RAB3IL1, were unable to be assessed due to low basal expression. However, 3 genes were upregulated which are RAB39B, FTH1, and FAM213A. RAB39B is a Ras-analog in brain (RAB) small GTPase and a member of the RAS oncogene family, involved in vesicular trafficking. High expression of ferritin heavy chain 1 (FTH1) is correlated with high-grade gliomas and poor prognosis in glioblastoma. Lastly, the redox regulatory protein, FAM213A, can activate antioxidant proteins and elevated expression is associated with worse outcomes for AML patients. This suggests that modulating the RAS signaling pathways and specific redox pathways may overcome LSD1 resistance. Understanding the changes in gene expression as the cells acquire resistance to LSD1 inhibitors will help us understand the mechanism of resistance to LSD1 inhibitors in glioblastoma and to design new treatment strategies. Citation Format: Kareena H. Patel, Lea Stitzlein, Deokhwa Nam, Frederick Lang, Joy Gumin, Joya Chandra. Generation and characterization of a glioblastoma stem cell model with acquired resistance to LSD1 inhibition [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 307.

CEACAM6 and IFITM3 as potential biomarkers for pelareorep in pancreatic adenocarcinoma (PDAC).

684 Background: Pelareorep (P) is a proprietary formulation of live, replication-competent, naturally occurring Reovirus Type 3 Dearing strain. We previously performed a phase II trial of P with carboplatin (C) and paclitaxel (Pxl) vs C and Pxl alone in metastatic PDAC (NCT01280058). Although P did not improve progression-free survival compared to C and Pxl alone, some exceptional durable responses were seen in the P arm. Low levels of carcinoembryonic antigen cell adhesion molecule 6 (CEACAM6) mRNA expression were associated with prolonged PFS in P-treated pts (p=0.05) and there was a 3.3 times higher fold change in Interferon-inducible transmembrane protein 3 (IFITM3) expression in the pts doing poorly versus responders (nominal p<0.05) in P arm. Here we investigate mechanisms of resistance to P infection mediated through CEACAM6 and IFITM3 in a panel of pancreatic ductal adenocarcinoma cell lines. Methods: Prior studies noted CEACAM6 and IFITM3 may restrict cell entry of certain enveloped viruses. CEACAM6 and IFITM3 protein levels were measured in PDAC cell lines using Western blot. Flow cytometry was used to assess P infectivity. We have generated multiple knockdowns of CEACAM6 and IFITM3 in PDAC cell lines to determine changes in P infectivity and other inflammatory signalling pathways. Live cell imaging was used to assess cell viability. Results: Basal expression of CEACAM6 was measured in a panel of 4 PDAC cells (PANC10.5, HPAFII, BxPC3, CFPAC1). Panc10.05 had low basal expression nor could expression be induced by 24hr P infection. All other cell lines showed moderate to high basal expression that was inducible. P infectivity at 24hrs was significantly higher in Panc10.05 cells compared to high CEACAM6 expressing cell lines. There was varying basal expression of IFITM3, however all cell lines showed IFITM3 induction when exposed to P. Of the 3 cell lines that also expressed high levels of CEACAM6 (HPAFII, CFPAC1, BxPC3), low basal expression of IFITM3 was strongly associated with increased sensitivity to P infection and decreased viability at 72hrs, which could be induced by knockdown of IFITM3 in high expressing cell lines. Neither C or Pxl altered levels of CEACAM6 or IFITM3 in any of the four cell lines. Conclusions: High CEACAM6 and IFITM3 play a role in P viral infectivity across multiple pancreatic cell lines, confirming results obtained in translational datasets. Further analysis is ongoing to elucidate mechanism and identify pathways to alter expression of CEACAM6 and IFITM3 and enhance P infectivity in future trials.

A tightly controlled gene induction system that contributes to the study of lethal gene function in Streptococcus mutans

ABSTRACT Effective control of gene expression is crucial for understanding gene function in both eukaryotic and prokaryotic cells. While several inducible gene expression systems have been reported in Streptococcus mutans, a conditional pathogen that causes dental caries, the significant non-inducible basal expression in these systems seriously limits their utility, especially when studying lethal gene functions and molecular mechanisms. We introduce a tightly controlled xylose-inducible gene expression system, TC-Xyl, for Streptococcus mutans. Western blot results and fluorescence microscopy analysis indicate that TC-Xyl exhibits an extremely low non-inducible basal expression level and a sufficiently high expression level post-induction. Further, by constructing a mutation in which the only source FtsZ is under the control of TC-Xyl, we preliminarily explored the function of the ftsz gene. We found that FtsZ depletion is lethal to Streptococcus mutans, resulting in abnormal round cell shape and mini cell formation, suggesting FtsZ’s role in maintaining cell shape stability.

Upregulation of Somatostatin Receptor Type 2 Improves 177Lu-DOTATATE Therapy in Receptor-Deficient Pancreatic Neuroendocrine Tumor Model.

Pancreatic neuroendocrine tumors (PNET) express high levels of somatostatin receptor type 2 (SSTR2), a unique target for both tumor imaging and therapy. This surface expression is lost in metastatic high-grade PNETs, making patients ineligible for SSTR2-targeted 177 Lutetium (Lu)-DOTATATE peptide receptor radionuclide therapy (PRRT), and represents an unmet clinical need. Here, we aimed to restore SSTR2 expression through the reversal of inhibitory epigenetic gene silencing to improve tumor responsiveness to PRRT. We first assessed human SSTR2 promoter methylation and expression levels in 96 patient samples. We then used three NET cell lines (QGP-1, BON-1, GOT-1) with variable SSTR2 expression profiles for functional in vitro studies using histone deacetylase inhibitors (HDACi). Finally, the QGP-1 xenograft mouse model, with low basal SSTR2 expression, was used to assess the therapeutic efficacy of combined HDACi and 177Lu-DOTATATE therapies. We confirm that SSTR expression is decreased and correlates with SSTR2 promoter methylation in patients with high-grade NETs. When exposed to HDACis, SSTR2 surface expression is increased in three NET cell lines in vitro. In an in vivo PNET xenograft model with low basal SSTR2 expression, our studies demonstrate significantly higher tumor uptake of SSTR2-targeted 177Lu-DOTATATE in animals pretreated with HDACis compared with controls. For the first time, we show that this higher tumor uptake results in significant antitumor response when compared with standard PRRT alone. These preclinical results provide a rationale for utilizing HDACi pretreatment to improve targeted radionuclide therapy in patients with SSTR2-negative, metastatic PNETs.

An engineered Trop2/CD3 bispecific antibody for treatment of gastric, pancreatic, and colorectal cancers.

e14521 Background: Given its over-expression and poor prognosis in a variety of solid tumors, trophoblast cell surface antigen 2 (Trop2) is regarded as a potential therapeutic target. Trop2-directed antibody-drug conjugates have been developed for treatment of solid tumors; however, their clinical benefits can be limited by the associated undesirable effects which is likely attributed to the on-target off-tumor effect arising from the low basal Trop2 expression on the surface of multiple normal epithelial tissues. The present study aims to develop a humanized Trop2/CD3 bispecific T-cell engager antibody that can promote immunological synapse formation with tumor cells overexpressing Trop2, redirecting T cell-mediated killing specifically to cancers with reduced risk of on-target off-tumor effects. Methods: A Trop2/CD3 bispecific antibody was generated by linking a humanized anti-Trop2 monoclonal antibody with a CD3-binding scFv. To tune the affinity of the bispecific antibody for tumor target, in silico paratope prediction was firstly done using ProABC-2 (Ambrosetti F et al., 2020), following by alanine substitution of the identified paratope residues individually. A total of 6 CDR variants were generated with their binding to Trop2 examined using biolayer interferometry. Selected candidates were further characterized for their binding to Trop2-positive cancer cells and activation of T cells upon target engagement. Redirection of T cell-mediated killing on cancer cells expressing high Trop2 level was also studied in vitro. Results: Substitution of a complementarity-determining residue (CDR) on the heavy chain of anti-Trop2 antibody with an alanine significantly reduced binding affinity to Trop2. This CDR variant was selected for further functional characterization. Apart from weaker binding to Trop2-positive tumor cells, the variant also demonstrated a slower cytokine induction, a less acute T-cell activation, and a cytotoxic effect which was more restricted to Trop2-high cancer cells. Conclusions: Our new Trop2/CD3 bispecific antibody demonstrates potent anti-tumor activity, while at the same time shows a reduced risk of on-target off-tumor toxicity. The drug candidate warrants further investigations including toxicity study in monkeys. [Table: see text]

Liver-specific overexpression of HKDC1 increases hepatocyte size and proliferative capacity

A primary role of the liver is to regulate whole body glucose homeostasis. Glucokinase (GCK) is the main hexokinase (HK) expressed in hepatocytes and functions to phosphorylate the glucose that enters via GLUT transporters to become glucose-6-phosphate (G6P), which subsequently commits glucose to enter downstream anabolic and catabolic pathways. In the recent years, hexokinase domain-containing-1 (HKDC1), a novel 5th HK, has been characterized by our group and others. Its expression profile varies but has been identified to have low basal expression in normal liver but increases during states of stress including pregnancy, nonalcoholic fatty liver disease (NAFLD), and liver cancer. Here, we have developed a stable overexpression model of hepatic HKDC1 in mice to examine its effect on metabolic regulation. We found that HKDC1 overexpression, over time, causes impaired glucose homeostasis in male mice and shifts glucose metabolism towards anabolic pathways with an increase in nucleotide synthesis. Furthermore, we observed these mice to have larger liver sizes due to greater hepatocyte proliferative potential and cell size, which in part, is mediated via yes-associated protein (YAP) signaling.

Voltage-Gated Sodium Channel NaV1.7 Inhibitors with Potent Anticancer Activities in Medullary Thyroid Cancer Cells.

Our results from quantitative RT-PCR, Western blotting, immunohistochemistry, and the tissue microarray of medullary thyroid cancer (MTC) cell lines and patient specimens confirm that VGSC subtype NaV1.7 is uniquely expressed in aggressive MTC and not expressed in normal thyroid cells and tissues. We establish the druggability of NaV1.7 in MTC by identifying a novel inhibitor (SV188) and investigate its mode of binding and ability to inhibit INa current in NaV1.7. The whole-cell patch-clamp studies of the SV188 in the NaV1.7 channels expressed in HEK-293 cells show that SV188 inhibited the INa current in NaV1.7 with an IC50 value of 3.6 µM by a voltage- and use-dependent blockade mechanism, and the maximum inhibitory effect is observed when the channel is open. SV188 inhibited the viability of MTC cell lines, MZ-CRC-1 and TT, with IC50 values of 8.47 μM and 9.32 μM, respectively, and significantly inhibited the invasion of MZ-CRC-1 cells by 35% and 52% at 3 μM and 6 μM, respectively. In contrast, SV188 had no effect on the invasion of TT cells derived from primary tumor, which have lower basal expression of NaV1.7. In addition, SV188 at 3 μM significantly inhibited the migration of MZ-CRC-1 and TT cells by 27% and 57%, respectively.

PD-L1 and PD-L2 immune checkpoint protein induction by type III interferon in non-small cell lung cancer cells

IntroductionDespite the clinical success of PD-1/PD-1-ligand immunotherapy in non-small cell lung cancer (NSCLC), the appearance of primary and acquired therapy resistance is a major challenge reflecting that the mechanisms regulating the expression of the PD-1-ligands PD-L1 and PD-L2 are not fully explored. Type I and II interferons (IFNs) induce PD-L1 and PD-L2 expression. Here, we examined if PD-L1 and PD-L2 expression also can be induced by type III IFN, IFN-λ, which is peculiarly important for airway epithelial surfaces. MethodsIn silico mRNA expression analysis of PD-L1 (CD274), PD-L2 (PDCD1LG2), and IFN- λ signaling signature genes in NSCLC tumors and cell lines was performed using RNA sequencing expression data from TCGA, OncoSG, and DepMap portals. IFN-λ-mediated induction of PD-L1 and PD-L2 expression in NSCLC cell lines was examined by real-time quantitative polymerase chain reaction and flow cytometry. ResultsIFNL genes encoding IFN- λ variants are expressed in the majority of NSCLC tumors and cell lines along with the IFNLR1 and IL10R2 genes encoding the IFN-λ receptor subunits. The expression of PD-L1 and PD-L2 mRNA is higher in NSCLC tumors with IFNL mRNA expression compared to tumors without IFNL expression. In the NSCLC cell line HCC827, stimulation with IFN-λ induced both an increase in PD-L1 and PD-L2 mRNA expression and cell surface abundance of the corresponding proteins. In the NSCLC cell line A427, displaying a low basal expression of PD-L1 and PD-L2 mRNA and corresponding proteins, stimulation with IFN-λ resulted in an induction of the former. ConclusionThe type III IFN, IFN- λ, is capable of inducing PD-L1 and PD-L2 expression, at least in some NSCLC cells, and this regulation will need acknowledgment in the development of new diagnostic procedures, such as gene expression signature profiles, to improve PD-1/PD-1-ligand immunotherapy in NSCLC.

Small-Molecule Aptamer for Regulating RNA Functions in Mammalian Cells and Animals.

Synthetic riboswitches that can regulate gene expression by a small molecule recognized by an RNA aptamer in mammalian cells have various potential applications in biotechnology and medicine. However, the variety of small molecules and their cognate aptamers that have been demonstrated to function in mammalian cells is limited. The currently available aptamer-ligand pairs also require high small molecule concentrations to enable gene regulation, making them less desirable for industrial and biomedical applications. We conducted in vitro selection of RNA aptamers against a small molecule ASP7967 whose structure is closely related to ASP2905, a known inhibitor of potassium voltage-gated channel sub-family H member 3 (KCNH3). One of the aptamers selected (AC17-4) was found to be functional in HEK293 cells, and it was used to design aptazyme-based riboswitches that can activate gene expression (>10-fold) in the presence of ASP2905 or ASP7967 at as low as 5 μM in the culture medium. An aptazyme-based riboswitch was successfully used to regulate human erythropoietin expression in mice injected with an adeno-associated virus (AAV8) vector using orally administered ASP7967. Furthermore, by combining aptazyme-based and exon-skipping riboswitch mechanisms, an ON/OFF ratio approaching 300 was achieved with a low basal expression level in cultured cells.

Naxitamab Activity in Neuroblastoma Cells Is Enhanced by Nanofenretinide and Nanospermidine

Neuroblastoma cells highly express the disialoganglioside GD2, a tumor-associated carbohydrate antigen, which is also expressed in neurons, skin melanocytes, and peripheral nerve fibers. Immunotherapy with monoclonal anti-GD2 antibodies has a proven efficacy in clinical trials and is included in the standard treatment for children with high-risk neuroblastoma. However, the strong neuro-toxicity associated with anti-GD2 antibodies administration has hindered, until now, the possibility for dose-escalation and protracted use, thus restraining their therapeutic potential. Strategies to increase the efficacy of anti-GD2 antibodies are actively sought, with the aim to enable chronic treatments that could eradicate minimal residual disease and subsequent relapses, often occurring after treatment. Here, we report that Nanofenretinide and Nanospermidine improved the expression of GD2 in neuroblastoma cells (CHP-134) and provided different effects in combination with the anti-GD2 antibody naxitamab. In particular, Nanofenretinide significantly increased the cytotoxic effect of naxitamab while Nanospermidine inhibited cell motility at extents proportional to naxitamab concentration. In neuroblastoma cells characterized by a low and heterogeneous basal expression of GD2, such as SH-SY5Y, which may represent the cell heterogeneity in tumors after chemotherapy, both Nanofenretinide and Nanospermidine increased GD2 expression in approximately 50% of cells, thus shifting the tumor population towards improved sensitivity to anti-GD2 antibodies.

A20 functions as a negative regulator of the lipopolysaccharide-induced inflammation in corneal epithelial cells

A20, also called TNFAIP3, is a crucial regulator of inflammation in various diseases but has not evidenced its function in the cornea. We aimed to evaluate the existence and the functions of A20 in human corneal epithelial (HCE-T) cells. After being treated with lipopolysaccharide (LPS) in different concentrations or at separate times, cells were collected to analyze A20 expressions. We then constructed the A20 knockdown system by siRNA and the A20 overexpressing system by lentivirus transduction. Systems were further exposed to medium with or without LPS for indicated times. Next, we evaluated the production of inflammatory cytokines (IL-6 and IL-8) by qRT-PCR and ELISA. Also, the translocation of P65 and the phosphorylation of P65, P38 and JNK were observed in two systems. In addition, we used the nuclear factor kappa-B (NF-κB) antagonist TPCA-1 for the pretreatment in cells and then detected the A20 expressions. We found a low basal expression of A20 in HCE-T cells, and the expressions could be dose-dependently induced by LPS, peaking at 4 h in protein level after stimulation. Both the A20 knockdown and A20 overexpressing systems were confirmed to be effective. After the LPS treatment, productions of IL-6 and IL-8 were enhanced in the A20 knockdown system and reduced in the A20 overexpressing system. A20 reduced the translocation of P65 into the nucleus and the phosphorylation of P65, P38 and JNK. Furthermore, TPCA-1 pretreatment reduced the expression of A20 in cells. We concluded that A20 is a potent regulator for corneal epithelium's reaction to inflammation, and it thus is expected to be a potential therapy target for ocular surface diseases.

Expanding the Therapeutic Window of EGFR-Targeted PE24 Immunotoxin for EGFR-Overexpressing Cancers by Tailoring the EGFR Binding Affinity.

Immunotoxins (ITs), which are toxin-fused tumor antigen-specific antibody chimeric proteins, have been developed to selectively kill targeted cancer cells. The epidermal growth factor receptor (EGFR) is an attractive target for the development of anti-EGFR ITs against solid tumors due to its overexpression on the cell surface of various solid tumors. However, the low basal level expression of EGFR in normal tissue cells can cause undesirable on-target/off-tumor toxicity and reduce the therapeutic window of anti-EGFR ITs. Here, based on an anti-EGFR monobody with cross-reactivity to both human and murine EGFR, we developed a strategy to tailor the anti-EGFR affinity of the monobody-based ITs carrying a 24-kDa fragment of Pseudomonas exotoxin A (PE24), termed ER-PE24, to distinguish tumors that overexpress EGFR from normal tissues. Five variants of ER-PE24 were generated with different EGFR affinities (KD ≈ 0.24 nM to 104 nM), showing comparable binding activity for both human and murine EGFR. ER/0.2-PE24 with the highest affinity (KD ≈ 0.24 nM) exhibited a narrow therapeutic window of 19 pM to 93 pM, whereas ER/21-PE24 with an intermediate affinity (KD ≈ 21 nM) showed a much broader therapeutic window of 73 pM to 1.5 nM in in vitro cytotoxic assays using tumor model cell lines. In EGFR-overexpressing tumor xenograft mouse models, the maximum tolerated dose (MTD) of intravenous injection of ER/21-PE24 was found to be 0.4 mg/kg, which was fourfold higher than the MTD (0.1 mg/kg) of ER/0.2-PE24. Our study provides a strategy for the development of IT targeting tumor overexpressed antigens with basal expression in broad normal tissues by tailoring tumor antigen affinities.

The ABCISIC ACID INSENSITIVE (ABI) 4 Transcription Factor Is Stabilized by Stress, ABA and Phosphorylation.

The Arabidopsis transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4) is a key player in the plant hormone abscisic acid (ABA) signaling pathway and is involved in plant response to abiotic stress and development. Expression of the ABI4 gene is tightly regulated, with low basal expression. Maximal transcript levels occur during the seed maturation and early seed germination stages. Moreover, ABI4 is an unstable, lowly expressed protein. Here, we studied factors affecting the stability of the ABI4 protein using transgenic Arabidopsis plants expressing 35S::HA-FLAG-ABI4-eGFP. Despite the expression of eGFP-tagged ABI4 being driven by the highly active 35S CaMV promoter, low steady-state levels of ABI4 were detected in the roots of seedlings grown under optimal conditions. These levels were markedly enhanced upon exposure of the seedlings to abiotic stress and ABA. ABI4 is degraded rapidly by the 26S proteasome, and we report on the role of phosphorylation of ABI4-serine 114 in regulating ABI4 stability. Our results indicate that ABI4 is tightly regulated both post-transcriptionally and post-translationally. Moreover, abiotic factors and plant hormones have similar effects on ABI4 transcripts and ABI4 protein levels. This double-check mechanism for controlling ABI4 reflects its central role in plant development and cellular metabolism.

P597: HIGH DOSE IRON IMPAIRS MALIGNANT B-CELL VIABILITY IN CHRONIC LYMPHOCYTIC LEUKEMIA

Background: Identification of new strategies to improve Chronic Lymphocytic Leukemia (CLL) outcome is fundamental since the disease remains incurable. Malignant B-cells show high levels of reactive oxygen species (ROS), which favors adaptation and survival but also enhances sensitivity to pro-oxidant therapeutics. Redox homeostasis is affected by iron balance since iron excess works as pro-oxidant, and cancer cells rearrange iron trafficking proteins to promote iron uptake. This adaptation might be exploited by exposing malignant cells to iron excess to cause ROS generation, lipid peroxidation, and eventually ferroptosis. We previously demonstrated the feasibility of this strategy in multiple myeloma and prostate cancer pre-clinical models. Aims: We aim at exploiting high dose iron to negatively affect malignant cell survival and increase therapeutic efficacy of current target therapies (BTK and BCL2 inhibitors). We aim at dissecting the molecular mechanisms underlying iron toxicity and at testing whether iron can improve immune dysfunctions. Methods: CLL cell lines (MEC-1, MEC-2 and PCL-12), patients peripheral blood and bone marrow mononuclear cells (PBMC and BMMC) and B lymphocytes purified from patients PB were treated with 300 µM ferric ammonium citrate (FeAC) alone or in combination with the BTK inhibitor ibrutinib (IBR, 5-10 µM) or the BCL2 inhibitor venetoclax (VNTX, 1.25-2.5 nM). We evaluated cell viability by annexin PI staining, lipid peroxidation and ferroptosis by measuring malondialdehyde (MDA) levels and antioxidant gene expression levels by qRT-PCR. We additionally evaluated T cell activation by measuring CD25 expression. MEC-1 xenografts generated in immunodeficient RAG2-/-yc-/- mice were treated with 20 mg/Kg ferric carboximaltose. Results:In vitro, iron treatment impaired cell proliferation in all CLL cell lines analyzed, inducing accumulation of MDA and cell death (p<0.01). In vivo, iron supplementation reduced the amount of MEC-1 cells in bone marrow and spleen of xenograft mice as compared to control saline-treated mice. In patients primary samples, iron induced cell death of leukemic lymphocytes (CD19+CD5+) either as purified cells or within bulk PBMC (p<0.01). Moreover, combination of iron with IBR or VNTX induced cell death at a higher extent compared to each single drug or to iron alone (p<0.01). Leukemic cells in BMMC samples were also iron sensitive and the effect became more evident upon combination with IBR or VNTX (p<0.05). Neither iron nor iron-drug combinations induced cell death in non-malignant cells. Iron also increased CD25 expression in CD8+ T cells and we are currently exploring whether this might indicate that iron can also improve cytotoxic mediated immune response against leukemic cells. As single patient analysis revealed heterogeneity of response, we investigated whether we might predict iron sensitivity by analyzing the antioxidant gene expression profile. All CLL cell lines analyzed showed a lower basal expression of NFE2L2, HMOX1, and GPX4 antioxidant genes than typical iron-resistant cell lines, such as prostate cancer PC-3 cells, suggesting that differences in antioxidant gene expression levels may mediate iron response and that this association is worth to be explored in CLL primary samples to explain heterogeneous iron response. Summary/Conclusion: Our pre-clinical studies suggests that exploiting iron toxicity might be a valuable strategy to improve current target therapies in CLL. Additional studies aimed at distinguishing iron sensitive patients from poor responders will improve the translational potential of this therapeutic approach.

Abstract 3697: Exploiting patient-derived xenografts and organoids to tackle apoptotic dependencies in EGFR-inhibited colorectal tumours

Abstract Treatment with EGFR-targeted therapies, such as the EGFR monoclonal antibody cetuximab, has improved the outcome of patients with metastatic colorectal cancer (mCRC). However, EGFR inhibition is mainly cytostatic and does not lead to tumor eradication: subsets of drug-tolerant cancer cells often persist even after maximal response to therapy and foster residual disease, leading to relapse. Importantly, drug-tolerant cells are less prone to undergo apoptosis, and thus constitute a reservoir of treatment-refractory persisters that are difficult to extinguish. Here we aimed to investigate the mechanisms by which apoptosis escape mediates survival of cetuximab-tolerant mCRC cells as a means to find new therapeutic strategies for limiting residual disease and delaying disease recurrence. By performing an innovative functional assay named Dynamic BH3 Profiling in cetuximab-sensitive patient-derived organoids (PDOs), we found that antibody treatment increased the “apoptotic priming”, i.e. decreased the distance of cells from the apoptotic threshold without eliciting overt cell death. To start investigating the mechanisms of this increased apoptotic priming, protein levels of the major anti-apoptotic molecules (BCL2, BCL-XL, MCL1) and the pro-apoptotic molecule BIM were evaluated by Western blot in cetuximab-treated PDOs. BIM was consistently upregulated by cetuximab in all tested models. Increased BIM was sequestered by the anti-apoptotic BCL-XL, suggesting that EGFR blockade may render mCRC residual cells dependent on BCL-XL to elude cell death and, consequently, more susceptible to its inhibition. We therefore challenged a panel of 14 PDOs with different BH3 mimetics currently in preclinical or clinical development and found that only the combination of cetuximab with BH3 mimetics against BCL-XL strongly reduced cell viability and induced apoptosis. BCL-XL blockade enhanced cetuximab efficacy also in mCRC patient-derived xenografts, which displayed more durable tumor regression that was maintained also after treatment discontinuation. Notably, the combination of cetuximab with BCL-XL inhibitors was effective in vivo in all tested models except for one, which was characterized by low basal expression of BIM. Mechanistically, unleashed apoptosis by combination therapy was due to cetuximab-induced BIM upregulation concomitantly with its displacement from BCL-XL by the BH3 mimetic. Overall, this study offers new insights into the molecular mechanisms assisting residual disease after cetuximab treatment in mCRC, providing hints to design rational strategies that may convert the cytostatic effect of cetuximab into a cytotoxic, fully apoptotic outcome. Basal expression of BIM could be exploited as a predictive biomarker to enrich for potential responders to the combination of cetuximab and BH3 mimetics. Citation Format: Simonetta Maria Leto, Irene Catalano, Martina Ferri, Valentina Vurchio, Francesca Cottino, Eugenia Rosalinda Zanella, Francesco Sassi, Giorgia Migliardi, Andrea Bertotti, Livio Trusolino. Exploiting patient-derived xenografts and organoids to tackle apoptotic dependencies in EGFR-inhibited colorectal tumours [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3697.

Engineering of a TrpR-Based Biosensor for Altered Dynamic Range and Ligand Preference.

Transcriptional factors play a crucial role in regulating cellular functions. Understanding and altering the dynamic behavior of the transcriptional factor-based biosensors will expand our knowledge in investigating biomolecular interactions and facilitating biosynthetic applications. In this study, we characterized and engineered a TrpR-based tryptophan repressor system in Escherichia coli. We found that the reconstructed TrpR1-PtrpO1 biosensor system exhibited low basal expression and narrow dynamic range in the presence of tryptophan or its analogue 5-hydroxytryptophan (5-HTP). Given the application potential of the biosensor, we introduced engineering approaches in multiple levels to optimize its dynamic behavior. First, the I57 and V58 residues in the ligand-binding pocket were rationally mutated in search of variants with altered ligand specificity. Two TrpR1 variants, V58E and V58K, successfully acquired ligand preference toward tryptophan and 5-HTP, respectively. The biosensor-induced expression levels were increased up to 10-fold with those variants. Furthermore, to pursue broader operational range, we tuned the regulator-operator binding affinity by mutating the binding box of TrpR1. Collectively, we demonstrated that the biosynthesis-significant biosensor TrpR1-PtrpO1 can be engineered to acquire extended dynamic ranges and improved ligand preference. The engineered biosensor variants with remarkable dynamic behavior can serve as key genetic elements in high-throughput screening and dynamic regulation in biosynthetic scenarios.

MO420: Effects of Indoxyl Sulfate and Apixaban in Liver Gene Expression

Abstract BACKGROUND AND AIMS Uraemic toxins accumulate in the blood and tissues of patients with chronic kidney disease (CKD). Previous animal studies have shown that chronic kidney disease (CKD) not only alters the elimination of drugs excreted by the kidneys, but it also impacts the metabolism of drugs subject to non-renal clearance, which involves mainly the liver and the gut. The use of apixaban, an oral anticoagulant, has been approved in the USA for dialysis patients. However, the coexistence of thrombotic and haemorrhagic risk in patients with CKD makes dose adjustment difficult. The liver has a major role in drug metabolization. Hepatocytes express high levels of AhR, a ligand-inducible transcription factor that mediates the induction of various liver cytochrome P450 enzymes by xeno and endobiotic. Tryptophan-derived uraemic toxins (TDUT) are AhR agonists. Indoxyl sulfate (IS) is the main TDUT involved in uraemic syndrome. IS increases the expression and activity of P-glycoprotein (P-gp) in the liver. Apixaban metabolism is mediated by P-gp and Cyp3a4 (Cyp3a11 in mice). We aim to study the effect of apixaban and IS in the expression of drug metabolism genes. Our hypothesis is that AhR activation by IS could severely modify drug metabolism during CKD. METHOD C57BL/6J Wild-type mice purchased from The Jackson Laboratory were fed ad libitum with a standard diet. At 10 weeks of age, mice drinking water was substituted with a 5% sucrose water solution with either 0.1% indoxyl sulphate or KCl (control) added at equivalent concentrations. 48-h before sacrifice some mice were gavaged with an apixaban solution (0.6 mg/mL) twice a day with the last dose given 4 h prior to sacrifice. All mice were sacrificed at 11 weeks of age. Liver samples were stored in an RNA-later solution at −20°C. Samples were thawed and lysed in Trizol using the Tissue-Ruptor system (Qiagen). RNA was extracted and purified with chloroform and precipitated with isopropanol. RNA concentration was estimated by spectrophotometry. Gene expression was analysed by q-RT-PCR using Gusb as a housekeeping gene. Apixaban levels were quantified by LC-MS. Kruskal–Wallis followed by a two-stage linear step-up procedure of Benjamini, Krieger and Yekutieli (q &amp;lt; 0.05) was performed using GraphPad Prism 9.2.1. RESULTS Four groups of mice per sex were thus created: WT-KCl, WT-IS, WT-KCl Apix, WT-IS Apix. In the IS/KCl model we observe higher mRNA basal expression of Abcb1a (q = 0.008) and Sult1a1 (q = 0.006) and lower basal expression of Abcg2 (q = 0.0005) in females compared to males when treated with KCl. IS treatment increases Cyp1a2 expression in females (q = 0.0139) and Cyp1a1 in both males (q = 0.0145) and females (q = 0.026). In the IS/KCl-Apix model the same sex-related differences are maintained for Abcb1a (q = 0.0031), Sult1a1 (q = 0.0316) and Abcg2 (q &amp;lt; 0.0001). In males, CYP2e1 expression is increased by apixaban in KCl (q = 0.067) and IS (q = 0.0278) treated mice. Moreover, apixaban counteracts the increased expression of Cyp1a1 induced by IS (q = 0.0177). The expression of Cyp3a11 is augmented in males treated with KCl-apixaban (q = 0.0143), an effect that seems to be reversed by IS (q = 0.0066). In females, apixaban has no effect in gene expression. Apixaban serum concentration is higher in KCl (q = 0.0350) and IS (q = 0.0019) treated females when compared to males. CONCLUSION The effect of IS as an agonist of AhR in the liver is confirmed by the increased expression of Cyp1a1. Apixaban provokes a remarkable increase of Cyp3a11 in male mice, which could lead to higher degradation rates decreasing its activity. IS seems to reverse this effect. This could lead to increased activity of apixaban during CKD which could derive in an increased risk of bleeding. Higher BCRP rates could explain lower rates of apixaban in male serum. Apixaban did not alter gene expression in females. Clinical trials in CKD are generally biased regarding sex (fewer women represented) possibly masking important sex-dependent drug adverse effects. Our results show great differences in basal expression of various genes, confirming the importance to study men and women separately with respect to drug metabolism.

Transgenic mice encoding modern imaging probes: Properties and applications.

SUMMARYModern biology is increasingly reliant on optical technologies, including visualization and longitudinal monitoring of cellular processes. The major limitation here is the availability of animal models to track the molecules and cells in their natural environment in vivo. Owing to the integrity of the studied tissue and the high stability of transgene expression throughout life, transgenic mice encoding fluorescent proteins and biosensors represent unique tools for in vivo studies in norm and pathology. We review the strategies for targeting probe expression in specific tissues, cell subtypes, or cellular compartments. We describe the application of transgenic mice expressing fluorescent proteins for tracking protein expression patterns, apoptotic events, tissue differentiation and regeneration, neurogenesis, tumorigenesis, and cell fate mapping. We overview the possibilities of functional imaging of secondary messengers, neurotransmitters, and ion fluxes. Finally, we provide the rationale and perspectives for the use of transgenic imaging probes in translational research and drug discovery.