Selective Effect Research Articles

Mapping QTL associated with resistance to Pseudomonas syringae pv. actinidiae in kiwifruit (Actinidia chinensis var. chinensis).

Pseudomonas syringae pv. actinidiae (Psa) is a bacterial pathogen of kiwifruit. This pathogen causes leaf-spotting, cane dieback, wilting, cankers (lesions), and in severe cases, plant death. Families of diploid A. chinensis seedlings grown in the field show a range of susceptibilities to the disease with up to 100% of seedlings in some families succumbing to Psa. But the effect of selection for field resistance to Psa on the alleles that remain in surviving seedlings has not been assessed. The objective of this work was to analyse, the effect of plant removal from Psa on the allele frequency of an incomplete-factorial-cross population. This population was founded using a range of genotypically distinct diploid A. chinensis var. chinensis parents to make 28 F1 families. However, because of the diversity of these families, low numbers of surviving individuals, and a lack of samples from dead individuals, standard QTL mapping approaches were unlikely to yield good results. Instead, a modified bulk segregant analysis (BSA) overcame these drawbacks while reducing the costs of sampling and sample processing, and the complexity of data analysis. Because the method was modified, part one of this work was used to determine the signal strength required for a QTL to be detected with BSA. Once QTL detection accuracy was known, part two of this work analysed the 28 families from the incomplete-factorial-cross population that had multiple individuals removed due to Psa infection. Each family was assigned to one of eight bulks based on a single parent that contributed to the families. DNA was extracted in bulk by grinding sampled leaf discs together before DNA extraction. Each sample bulk was compared against a bulk made up of WGS data from the parents contributing to the sample bulk. The deviation in allele frequency from the expected allele frequency within surviving populations using the modified BSA method was able to identify 11 QTLs for Psa that were present in at least two analyses. The identification of these Psa resistance QTL will enable marker development to selectively breed for resistance to Psa in future kiwifruit breeding programs.

A complementary learning systems model of how sleep moderates retrieval practice effects.

While many theories assume that sleep is critical in stabilizing and strengthening memories, our recent behavioral study (Liu & Ranganath, 2021, Psychonomic Bulletin & Review,28[6], 2035-2044) suggests that sleep does not simply stabilize memories. Instead, it plays a more complex role, integrating information across two temporally distinct learning episodes. In the current study, we simulated the results of Liu and Ranganath (2021) using our biologically plausible computational model, TEACH, developed based on the complementary learning systems (CLS) framework. Our model suggests that when memories are activated during sleep, the reduced influence of temporal context establishes connections across temporally separated events through mutual training between the hippocampus and neocortex. In addition to providing a compelling mechanistic explanation for the selective effect of sleep, this model offers new examples of the diverse ways in which the cortex and hippocampus can interact during learning.

Фізико-хімічні та біологічні властивості сахаридів та спирту після радіаційної обробки

The results of a complex study of the influence of nuclear radiation on the physical and chemical properties of distilled water, aqueous solutions of saccharides, ethyl alcohol, and their biological activity are presented. Irradiation was carried out on the M-30 microtron electron accelerator (12.5 MeV) and on isotope radiation stands based on 241Am, 137Cs, and 240Pu, which generate mixed nuclear radiation. The temporal evolution of chemical indicators and optical and frequency characteristics of electrical parameters of irradiated water environments are discussed. The selective biological effect of irradiated compounds on test microorganisms from different phylogenetic groups was established.

Assessing genetic diversity in critically endangered Chieniodendron hainanense populations within fragmented habitats in Hainan

Habitat fragmentation has led to a reduction in the geographic distribution of species, making small populations vulnerable to extinction due to environmental, demographic, and genetic factors. The wild plant Chieniodendron hainanense, a species with extremely small populations, is currently facing endangerment and thus requires urgent conservation efforts. Understanding its genetic diversity is essential for uncovering the underlying mechanisms of its vulnerability and for developing effective conservation strategies. In our study, we analyzed 35 specimens from six different populations of C. hainanense using genotyping-by-sequencing (GBS) and single nucleotide polymorphism (SNP) methodologies. Our findings indicate that C. hainanense has limited genetic diversity. The observed heterozygosity across the populations ranged from 10.79 to 14.55%, with an average of 13.15%. We categorized the six populations of C. hainanense into two distinct groups: (1) Diaoluoshan and Baishaling, and (2) Wuzhishan, Huishan, Bawangling, and Jianfengling. The genetic differentiation among these populations was found to be relatively weak. The observed loss of diversity is likely a result of the effects of natural selection.

Selective adsorption of soluble starch on the cassiterite surface for effective flotation separation of scheelite from cassiterite

Tungsten and tin are important strategic resources. Scheelite and cassiterite have similar physical and chemical properties and face the challenge of flotation separation. This study proposes soluble starch (SS) as an effective depressant for the flotation separation of scheelite from cassiterite. The depression mechanism of SS was investigated using micro-flotation, zeta potential, total organic carbon, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and time-of-flight secondary ion mass spectroscopy. SS exhibited a good selective depressive effect on cassiterite and was able to efficiently separate scheelite from cassiterite. The results of artificial mixed mineral test showed that the recovery of scheelite and cassiterite were 79.35 % and 9.48 %, respectively and the grade were 70.15 % and 8.11 %, respectively at pH 10. The macromolecular organic depressant SS has abundant hydrophilic groups, such as hydroxyl groups, which cause the material to stably adsorb on Sn active sites on the surface of cassiterite and hinder the adsorption of the collector sodium oleate (NaOL, C17H33CO2Na). The selective adsorption of SS on the surface of cassiterite results in efficient flotation separation of the two minerals.

Abstract 2067: QUANTROseq, a transcriptomic based drug discovery platform using time-resolved gene expression profiling: Identification of inhibitors and degraders of transcription factors and cell signaling regulators

Abstract Integrative analyses of CRISPR/Cas9 screening datasets from different sources revealed - besides known oncogenes - a series of transcriptional master regulators as most prominent context-specific dependencies in cancer that remained largely inaccessible to conventional drug discovery approaches. New chemical entities (NCEs) that specifically interfere with a transcription factor (TF) at any level should induce and be detectable based on selective effects on their primary biochemical activity - i.e., the transcriptional activation of specific target genes. However, the definition of direct targets of a TF and, more generally, the unbiased detection of direct transcriptional effects has remained challenging due to the limited time resolution of conventional techniques for gene perturbation and transcriptional profiling. To overcome this limitation, QUANTRO Therapeutics relies on SLAMseq technology that, by metabolic labeling de novo-synthesized RNA immediately after intervention and conserving the information for later readout, provides unprecedent time-resolution in transcriptomic analysis. Aiming to target previously undruggable targets, we set out to first build definitive knowledge around their direct effect on transcription, inducing their quick protein degradation through the auxin-inducible degron (AID) technology followed by immediate transcriptional readout though SLAMseq -before any secondary, confounding effect could appear in the cell. The targets´ mRNA fingerprints produced are then used as a reference and cross-compared with existing and new chemical entities to: (i) benchmark the real mode of action of existing drugs; (ii) identify new drug candidates that specifically interfere with disease-causing transcriptional programs in cancer; (iii) interrogate the efficiency, selectivity, and potency of drug candidates during Hit-validation and Hit-to-Lead activities. Proof of concept data demonstrated that time-resolved transcriptional profiling can reveal drugs´ mode of action with unprecedent precision and sensitivity, when drugs act on Targets that have a direct effect on transcriptional regulation - such as TFs and signaling pathways. Building on this knowledge, QUANTRO Therapeutics unleashed the unique potential of mRNA fingerprinting technology for HTS-compatible drug discovery by (1) establishing scalable and automated workflows for metabolic RNA labeling, treatment of cells, and RNA extraction; (2) developing algorithms for combinatorial mRNA fingerprint-readout that allow for the simultaneous assessment of TF signatures by multiplexed targeted RNA sequencing (QUANTROseq), thus transforming the precision and scope of cell-based compound screens. Citation Format: Arianna Sabò, Nina Fasching Griesmayr, Tobias Neumann, Raphael Manzenreither, Maja Ivankovic, Rodrigo Pacheco Valamatos Costa, Sarah Rieser, Sara Scinicariello, Petr Triska, Anna Stingeder, Astrid Gruss, Ryan Cubero, Olga Frank, Ivica Sowemimo, Paul Kirchgatterer, Adriana Cantoran, Stefan Ameres, Johannes Zuber, Michael Bauer. QUANTROseq, a transcriptomic based drug discovery platform using time-resolved gene expression profiling: Identification of inhibitors and degraders of transcription factors and cell signaling regulators [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 2067.

Abstract 1691: p300 catalytic inhibition selectively targets IRF4 oncogenic activity in multiple myeloma

Abstract Multiple myeloma (MM), an incurable plasma cell malignancy, is addicted to oncogenic transcription factor (TF) IRF4 signaling. Lineage TFs like IRF4 are difficult to drug but represent high value oncology targets owing to the depth and context selectivity of their genetic dependency. Using a transcription regulatory network (TRN) based approach to integrate a high dimensional multi-platform dataset, we defined the key regulatory activity of IRF4 and its druggable co-factors. This unbiased analysis identified p300 lysine acetyl transferase (KAT) function as the nearest selective neighbor for therapeutic intervention, with more potent and selective effects than historically observed with p300/CBP bromodomain inhibitors. To further probe this biology, we developed a highly selective inhibitor of the KAT domain of p300 and its close homolog CBP. p300 KAT inhibition led to selective downregulation of IRF4 at the mRNA and protein level as well as reduction in acetylation at highly specific sites co-localized with IRF4, in contrast to more general agents like BET inhibitors. Gene expression reduction was most pronounced at IRF4/p300 co-bound genes, in particular IRF4 itself and MYC. IRF4 and p300 also directly bind to each other and other key MM nodes regulating them at the chromatin, mRNA, and protein levels. p300 KAT inhibition exhibits strong antiproliferative activity across in vitro MM models regardless of cytogenetics or resistance to other therapies. Moreover, this relationship is mediated by the KAT domain and not its acetyl-lysine recognizing bromodomain. Comparative pharmacology studies found that a p300 KAT inhibitor downregulated the IRF4 TRN and induced apoptosis in MM cells more effectively than existing standard of care agents, including IMiDs and glucocorticoid receptor agonists, or p300/CBP bromodomain inhibitors. Combinations of a p300 KAT inhibitor with clinically active molecules such as IMiDs and glucocorticoid agonists showed synergistic impacts on reducing key MM TFs and cell line viability. Ex vivo treatment of primary patient samples demonstrated broad anti-proliferative activity with loss of IRF4 and induction of apoptosis in relapsed-refractory MM patient samples, independent of prior lines of therapy. Importantly, the induction of MM cell apoptosis occurs in the milieu of CD138 negative bone marrow stromal cells while also sparing them from toxicity, supporting a potential therapeutic index. Finally, p300 KAT inhibition demonstrated activity in in vivo MM models with robust tumor growth inhibition at tolerated doses and exposures correlated to reduced p300-dependent substrate acetylation. IRF4 dependency is a hallmark of MM that has been challenging to target with existing therapies, motivating further development of p300 KAT targeting therapeutics. Citation Format: Michael R. McKeown, Giulia Giorgetti, Walter F. Lenoir, Marek J. Kobylarz, Tamara D. Hopkins, Wayne L. Glore, Michelle G. Shum, Yare Calderon, Kameron R. Mori, Hua Gao, Luis A. Carvajal, Nikolaus D. Obholzer, Benjamin W. Trotter, Christopher D. Dinsmore, Nikhil C. Munshi, Peter B. Rahl, Mariateresa Fulciniti, Charles Y. Lin. p300 catalytic inhibition selectively targets IRF4 oncogenic activity in multiple myeloma [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 1691.

Abstract 3227: Developing brain-penetrating MAT2A inhibitors for MTAP-deleted brain metastatic cancer and GBM

Abstract Background: Homozygous deletion of MTAP is one of the most frequent genetic alterations in various solid tumors including glioblastoma (GBM), mesothelioma, pancreatic cancer and lung cancer. While MTAP-deleted cancers are associated with a poor prognosis, there are no approved drugs for the treatment of patients with MTAP deficiency. MAT2A has emerged as a potential target for selective anticancer effects in MTAP-deleted cancers. However, development of brain-penetrating MAT2A inhibitors are yet to be reported in preclinical or clinical stages despite of high MTAP deletion fraction in GBM and brain metastatic cancers. Here, we present highly potent and selective MAT2A inhibitors capable of brain penetration for MTAP deleted cancer therapy. Methods: A MAT2A biochemical enzyme assay was performed with phosphonate colorimetric kit. To evaluate in vitro and in vivo activities of compounds, S-adenosylmethionine (SAM) and symmetrical dimethyl arginine (SDMA) levels were measured using LC-MS/MS and high-content screening systems. Cell growth inhibition assay was evaluated to confirm the selectivity in isogenic pairs of HCT116 WT and MTAP-deleted cells. In vivo efficacy was conducted using the MTAP-deleted HCT116 xenograft. Results: To develop novel brain penetrating scaffolds, we focused on interaction of hydrogen bond acceptor in the scaffolds with arginine residue Arg313 in MAT2A protein and the improvement of physicochemical properties, including logP and logBB. A series of MAT2A inhibitors significantly inhibited MAT2A enzymatic activity, resulting in the reduction of intracellular SAM level, the direct product of MAT2A. These compounds showed highly potent inhibition of SDMA and cell proliferation in MTAP-deleted cells, while displaying minimal effect on MTAP-WT cells, showing >100-fold selectivity towards MTAP-deletion over MTAP-WT. Furthermore, anti-proliferative activity of MAT2A inhibitors were observed in MTAP-deleted cancer cells across various cancer types, including GBM, breast cancer, and non-small cell lung cancer. Remarkably, mouse pharmacokinetic study revealed high level of plasma and brain exposure with outstanding brain-to-plasma ratio (> 0.75). Robust tumor growth inhibition as well as reduction in tumor SAM levels were observed as monotherapy in an MTAP-deleted HCT116 xenograft model. Conclusion: We have identified novel brain-penetrating MAT2A inhibitors displaying encouraging in vitro and in vivo pharmacological profiles, indicating the potential use of these compounds as therapeutic agents for MTAP deleted brain metastatic cancer and GBM. Citation Format: Soyoung Ki, Jinhee Kim, Jungtae Na, Ilkyoo Koh, Hyunho Cho, Ho Yeon Lee, Hoiyun Jung, Gyeonghi Cho, Mijin Moon, Yongje Shin, Sook-Kyung Park. Developing brain-penetrating MAT2A inhibitors for MTAP-deleted brain metastatic cancer and GBM [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 3227.

Abstract 5705: Discovery of a selective slow-off CDK2 inhibitor NKT3447 with distinct features of suppressing pCDK2, downregulating cyclin E, and achieving prolonged pathway inhibition

Abstract CDK2 is a cell cycle kinase that plays a critical role in controlling the G1 to S-phase transition and its abnormal activation through cyclin E1(CCNE1) amplification has been indicated as the primary oncogenic driver in advanced cancers including ovarian, endometrial, and gastric cancers. In addition, cyclin E1 overexpression has emerged as a key resistance mechanism to CDK4/6 inhibitors in hormone receptor-positive breast cancer patients. Therefore, CDK2 represents a promising novel oncology target. However, development of a potent and selective CDK2 inhibitor has been challenging due to the high homology of CDK2 with other CDKs, particularly CDK1, which is essential in normal cell cycle progression. NKT3447 is a novel, orally bioavailable small molecule CDK2 inhibitor with slow-off kinetics and is highly selective against CDK1 and other CDKs. In addition, NKT3447 exhibits a distinct mechanism of action, including suppression of the Thr160 activating phosphorylation on CDK2 and downregulation of cyclin E1. In biochemical assays, NKT3447 drives a concentration dependent disruption of the CDK2/cyclin E1 and CDK2/cyclin A2 complexes, but not the CDK1/cyclin B1 complex. Consequently, NKT3447 potently inhibits the phosphorylation of Rb (pRb) and induces G1 cell cycle arrest in CCNE1 amplified OVCAR3 cells, while showing minimal or no effect on G2/M phase distribution in all the cell lines tested, including OVCAR3 and KYSE520 (CDK1-dependent) cells. Importantly, NKT3447 has a slow-off kinetics, as demonstrated by NanoBRET target engagement assay, which leads to sustained pRb inhibition after treatment withdrawal. In addition, NKT3447 treatment reduces cyclin E1 protein levels and suppresses phospho-CDK2 (Thr160), which further represses CDK2 activity and prolongs the inhibition of CDK2 signaling. NKT3447 also demonstrates a selective anti-proliferation effect in a panel of human cancer cell lines with elevated cyclin E1 expression and/or dependency on CDK2 or cyclin E1 (DepMap). In line with cellular studies, pharmacodynamic study of NKT3447 in mouse tumor models recapitulates a significant repression of pRb, pCDK2 and cyclin E1. Furthermore, NKT3447 treatment results in a dose-dependent tumor growth inhibition or tumor regression in CCNE1 amplified OVCAR3 and MKN1 tumor models. In addition, the combination of NKT3447 with carboplatin exhibits enhanced anticancer effects in OVCAR3 and MFE-280 models. These results demonstrate that NKT3447 is a potent, selective CDK2 inhibitor with distinct properties and mechanism of action, which holds great potential to effectively treat patients with aberrant CDK2/Cyclin E activation in a variety of cancer types. NKT3447 is currently being investigated in a Phase 1 clinical trial in patients with advanced solid tumors. Citation Format: Jianlin Geng, Ke Liu, Zhiyong Yu, Wenfeng Sun, Hairong Wei, Wenjun Li, Jing Lu, Juan Deng, Liqing Geng, Zhihong Liu, Zhenhai Gao, Yan Lou. Discovery of a selective slow-off CDK2 inhibitor NKT3447 with distinct features of suppressing pCDK2, downregulating cyclin E, and achieving prolonged pathway 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 5705.

Abstract 2967: The mammalian 8-oxo-dGTPase, MTH1, as a novel targetable vulnerability in pancreatic ductal adenocarcinoma

Abstract Pancreatic ductal adenocarcinoma (PDAC) is an aggressive KRAS-driven cancer that remains one of the most lethal of all human malignancies. Oncogenic KRAS relies on elevated reactive oxygen species (ROS) to support pro-tumorigenic signaling. However, these elevated ROS levels can also evoke tumor suppressive oxidative stress; thus KRAS-driven cancers must evolve protective redox adaptations to mitigate ROS-induced anti-tumor consequences. Here we report a unique adaptation centered on redox maintenance of nucleotide pool integrity, that supports aggressive PDAC tumorigenesis. MTH1 is the main mammalian 8-oxodGTPase that is known to be elevated in various RAS-driven cancers including PDAC. We have previously shown MTH1 is critical for ROS-mediated oncogenic signaling, and promotes escape from oncogene-induced senescence. We therefore hypothesized that MTH1 provides important redox support for aggressive PDAC tumor growth. Consistent with this, we found that elevated MTH1 expression was strongly correlated with poor disease-free survival in PDAC patients. These findings extended to KRAS-driven PDAC cell lines: highly proliferative human PDAC cells strongly expressed MTH1 (MTH1high), and MTH1 deletion was selectively anti-tumorigenic against MTH1high cells. Furthermore, introduction of MTH1-null backgrounds into gold standard genetically engineered PDAC mouse models selectively decreased 8-oxodGTPase activity levels and slowed PDAC growth in aggressive, short latency Ptf1acre/+;LSL-KrasG12D/+;Tgfbr2flox/flox (PKT) mice, but with no effect in longer latency Pdx1Cre; LSL- KrasG12D/+; LSL-Trp53R172H/+ (KPC) mice. These selective anti-tumorigenic effects were accompanied by a reduction in circulating immunosuppressive cytokines in PKT mice, further suggesting that MTH1 potentially supports aggressive tumorigenesis through induction of systemic immunosuppression. Consistent with this, pancreatic-restricted MTH1 conditional deletion fully rescued PDAC growth in PKT mice. Our findings here thus suggest that MTH1-dependent redox protection of the nucleotide pool represents a unique TME adaptation that supports aggressive PDAC tumorigenesis. Further studies will investigate whether this adaptation is maintained through symbiotic tumor/stroma or tumor/immune cell crosstalk, as observed for other KRAS-driven traits. Ultimately, interventions designed to target MTH1-dependent protection of the nucleotide pool could hold promise as novel therapeutic strategies for this untreatable disease. Citation Format: Beatriz Mateo-Victoriano, Ling Zhang, Jaya Samaranayake, Z McGaughey, Cassie Due, Clara Troccoli, Michael G. Mohsen, Nagaraj Nagathihalli, Oliver G. McDonald, Michael VanSaun, Eric T. Kool, Priyamvada Rai. The mammalian 8-oxo-dGTPase, MTH1, as a novel targetable vulnerability in pancreatic ductal adenocarcinoma [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 2967.

Abstract 4583: Development of selective HDAC6 inhibitors to improve cancer immunotherapy

Abstract Histone Deacetylases (HDACs) are enzymes that modify histones and non-histone proteins. Our group has previously demonstrated that HDAC6 inhibitors (HDAC6is) modulate multiple immune pathways, including those that suppress the antitumoral M2 phenotype, leading to improved antitumor immunity. Despite the potential of HDAC6is, current inhibitors have poor selectivity and off-target effects and only work at micromolar concentrations. In this work, we designed a screening pipeline of HDAC6i, considering selectivity, potency, capacity to prevent the protumoral phenotype of macrophages, and low cytotoxicity on macrophages and other immune cells. This approach has not been tested before, as the standard screening method for antitumoral HDACis has focused on its cytotoxic effect on cancer cells. We initially designed in silico 980 compound derivatives from previously reported HDAC6i, such as SS208, Nexturastat A, and Suprastat. Twenty-four compounds with a high capacity to bind HDAC6 and chemical stability were screened by their ability to inhibit HDAC6 in cell-free conditions. Sixteen compounds demonstrated high potency and were further evaluated in murine macrophages by their cytotoxic effect using CellTox. The capacity to impede tubulin deacetylation was assessed by western blot and deacetylase activity by HDAC-Glo. The top six candidates were then evaluated by their selectivity compared to other HDAC members and by their effect on repressing the expression of protumoral M2 macrophages Arginase 1 and Fizz1, and activation of antitumoral markers TNFa and iNOS by western blot and qRT-PCR. The best three candidates were then evaluated at nanomolar concentrations to explore their immunomodulatory potential of M1 against M2 by performing antigen presentation (SIINFEKL presentation) and phagocytic capacity using microscopy. Two of these compounds, SM-06-09 and SM-05-947, will be further tested in syngeneic murine melanoma models for their ability in tumor regression and antitumor immunity. This study has yielded important insights into developing new and improved HDAC6is with minimal cytotoxicity, and we believe our work will help advance cancer research and ultimately lead to better patient outcomes. Citation Format: Nithya Gajendran, Manasa Suresh, David Quiceno, Xintang Li, Marie Durr, Karen Tan, Satish Kumar Reddy Noonepalle, Alejandro Villagra. Development of selective HDAC6 inhibitors to improve cancer immunotherapy [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 4583.

Abstract 5775: Structure and dynamics of the major PDGFR-β oncogene promoter G-quadruplex and insights into its cellular regulation

Abstract Overexpression of the receptor tyrosine kinase PDGFR-β promotes cancer growth and metastasis. PDGFR-β is a validated cancer target but PDGFR-β kinase inhibitors suffer from lack of selectivity and side effects. G-quadruplexes are an exciting class of non-B DNA secondary structures with functional importance. The G-quadruplex formed in the PDGFR-β promoter is a transcription repressor and targetable by small molecules. Therefore, the PDGFR-β promoter G-quadruplex is an attractive molecular target for anticancer drugs. Structural information of the PDGFR-β promoter G-quadruplex is crucial for understanding its cellular function and rational drug design. Herein, we used nuclear magnetic resonance (NMR) spectroscopy and biophysical methods to determine the structure and dynamics of the major G-quadruplex formed in the human PDGFR-β promoter. Unlike canonical G-quadruplexes formed by four runs of three continuous guanines (G), the major PDGFR-β G-quadruplex adopts a novel broken-strand structure where a two-G segment is continued by a non-adjacent guanine. The broken-strand G-quadruplex has a vacancy-G-tetrad (vG4) which is filled-in intramolecularly by a distal guanine. Interestingly, we discovered that the major PDGFR-β G-quadruplex is a novel mixture of two equilibrating broken-strand G-quadruplexes. Both structures adopt overall parallel-stranded folding with all 1-nt chain-reversal loops. However, a different 3’-filled-in guanine is delivered by a lateral loop, which forms structurally similar hairpin with a unique capping G-G base-pair. The formation of the equilibrating broken-strand G-quadruplexes and unique capping structures are both specific to the PDGFR-β promoter sequence. Intriguingly, the observed dynamic equilibrium between the two co-existing structures with different intramolecular fill-in guanines indicates a novel vG4 intermediate, which could be filled-in by cellular guanine metabolites such as cGMP. Therefore, our study provides critical insights into how the dynamics of the major PDGFR-β G-quadruplex lead to vG4 formation and potential regulation of gene transcription by cellular guanine metabolites. The determined molecular structures of the novel broken-strand G-quadruplexes provide a structural basis for rational design of small molecules to specifically target the major PDGFR-β promoter G-quadruplex for cancer therapeutics. Citation Format: Yichen Han, Jonathan Dickerhoff, Danzhou Yang. Structure and dynamics of the major PDGFR-β oncogene promoter G-quadruplex and insights into its cellular regulation [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 5775.

Abstract 138: UCHL5 and PAX3-FOXO1 resolve replication stress in rhabdomyosarcoma

Abstract PAX3-FOXO1 positive rhabdomyosarcoma (RMS) is an aggressive pediatric sarcoma with a terrible prognosis. The resultant fusion acts as a chimeric transcription factor, in part remodeling chromatin to inhibit terminal differentiation and maintain cancer cell proliferation. As this oncoprotein is not directly druggable, we have used genetic screens to identify dependencies downstream of PAX3-FOXO1 to improve our understanding of pathogenesis and develop new therapeutic targets. We performed pooled CRISPRi screening in an isogenic system of a patient-derived RMS cell line with or without knockdown of PAX3-FOXO1. Loss of the ubiquitin hydroxylase UCHL5 led to selective depletion of PAX3-FOXO1 positive Rh30 cells compared to PAX3-FOXO1 knockdown cells, suggesting that the fusion creates UCHL5 dependence. We validated this finding in competition growth assays in additional fusion positive (FP) and fusion negative (FN) RMS cell lines, and observed UCHL5 dependency only in the former. By contrast, UCHL5 was dispensable for cell growth and survival in FN RMS cell lines. These data were recapitulated in the large DepMap dataset, which also identified the top genetic co-dependencies of UCHL5 as INO80-complex (INO80c) members. We therefore investigated whether the fusion selective effects of UCHL5 were mediated by the INO80c, of which UCHL5 is an N-terminal member. We observed that knockdown of another N-terminal component of INO80c, NFRKB, phenocopies the fusion-selective effects of UCHL5 loss. Conversely, the catalytic ATPase INO80 was pan-essential, suggesting that only N-terminal subunits of INO80c regulate PAX3-FOXO1 specific functions. INO80c plays an essential role in mitigating DNA replication stress. Indeed, loss of UCHL5 led to DNA damage as measured by γH2AX and slowing of replication forks as measured by fiber assays in FP, but not FN RMS. Unexpectedly, acute degradation of PAX3-FOXO1 also slowed DNA replication fork speed, suggesting a genetic model in which UCHL5 and PAX3-FOXO1 cooperate to resolve replication stress in FP RMS. Finally, in vivo experiments using cell line xenografts confirms that loss of UCHL5 slows the growth of FP RMS, but not FN RMS. These findings suggest that loss of UCHL5 induces replication stress in a fusion-specific manner, and offers both an opportunity to study the mechanisms by which the PAX3-FOXO1 oncoprotein mitigates replication stress, and to develop UCHL5 inhibitors as precision therapies for FP RMS patients. Citation Format: Amit J. Sabnis, Pushpendra K. Sahu, Yue Pan. UCHL5 and PAX3-FOXO1 resolve replication stress in rhabdomyosarcoma [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 138.

Patterns of genetic variation and local adaptation of a native herbivore to a lethal invasive plant.

Understanding the evolutionary processes that influence fitness is critical to predicting species' responses to selection. Interactions among evolutionary processes including gene flow, drift and the strength of selection can lead to either local adaptation or maladaptation, especially in heterogenous landscapes. Populations experiencing novel environments or resources are ideal for understanding the mechanisms underlying adaptation or maladaptation, specifically in locally co-evolved interactions. We used the interaction between a native herbivore that oviposits on a patchily distributed introduced plant that in turn causes significant mortality to the larvae to test for signatures of local adaptation in areas where the two co-occurred. We used whole-genome sequencing to explore population structure, patterns of gene flow and signatures of local adaptation. We found signatures of local adaptation in response to the introduced plant in the absence of strong population structure with no genetic differentiation and low genetic variation. Additionally, we found localized allele frequency differences within a single population between habitats with and without the lethal plant, highlighting the effects of strong selection. Finally, we identified that selection was acting on larval ability to feed on the plant rather than on females' ability to avoid oviposition, thus uncovering the specific ontogenetic target of selection. Our work highlights the potential for adaptation to occur in a fine-grained landscape in the presence of gene flow and low genetic variation.

Importance of Probiotics in Fish Aquaculture: Towards the Identification and Design of Novel Probiotics.

Aquaculture is a growing industry worldwide, but it faces challenges related to animal health. These challenges include infections by parasites, bacteria, and viral pathogens. These harmful pathogens have devastating effects on the industry, despite efforts to control them through vaccination and antimicrobial treatments. Unfortunately, these measures have proven insufficient to address the sanitary problems, resulting in greater environmental impact due to the excessive use of antimicrobials. In recent years, probiotics have emerged as a promising solution to enhance the performance of the immune system against parasitic, bacterial, and viral pathogens in various species, including mammals, birds, and fish. Some probiotics have been genetically engineered to express and deliver immunomodulatory molecules. These promote selective therapeutic effects and specific immunization against specific pathogens. This review aims to summarize recent research on the use of probiotics in fish aquaculture, with a particular emphasis on genetically modified probiotics. In particular, we focus on the advantages of using these microorganisms and highlight the main barriers hindering their widespread application in the aquaculture industry.

Diversity of CFTR variants across ancestries characterized using 454,727 UK biobank whole exome sequences

BackgroundLimited understanding of the diversity of variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene across ancestries hampers efforts to advance molecular diagnosis of cystic fibrosis (CF). The consequences pose a risk of delayed diagnoses and subsequently worsened health outcomes for patients. Therefore, characterizing the spectrum of CFTR variants across ancestries is critical for revolutionizing molecular diagnoses of CF.MethodsWe analyzed 454,727 UK Biobank (UKBB) whole-exome sequences to characterize the diversity of CFTR variants across ancestries. Using the PanUKBB classification, the participants were assigned into six major groups: African (AFR), American/American Admixed (AMR), Central South Asia (CSA), East Asian (EAS), European (EUR), and Middle East (MID). We segregated ancestry-specific CFTR variants, including those that are CF-causing or clinically relevant. The ages of certain CF-causing variants were determined and analyzed for selective pressure effects, and curated phenotype analysis was performed for participants with clinically relevant CFTR genotypes.ResultsWe detected over 4000 CFTR variants, including novel ancestry-specific variants, across six ancestries. Europeans had the most unique CFTR variants [n = 2212], while the American group had the least unique variants [n = 23]. F508del was the most prevalent CF-causing variant found in all ancestries, except in EAS, where V520F was the most prevalent. Common EAS variants such as 3600G > A, V456A, and V520, which appeared approximately 270, 215, and 338 generations ago, respectively, did not show evidence of selective pressure. Sixteen participants had two CF-causing variants, with two being diagnosed with CF. We found 154 participants harboring a CF-causing and varying clinical consequences (VCC) variant. Phenotype analysis performed for participants with multiple clinically relevant variants returned significant associations with CF and its pulmonary phenotypes [Bonferroni-adjusted p < 0.05].ConclusionsWe leveraged the UKBB database to comprehensively characterize the broad spectrum of CFTR variants across ancestries. The detection of over 4000 CFTR variants, including several ancestry-specific and uncharacterized CFTR variants, warrants the need for further characterization of their functional and clinical relevance. Overall, the presentation of classical CF phenotypes seen in non-CF diagnosed participants with more than one CF-causing variant indicates that they may benefit from current CFTR modulator therapies.

Hybrid mesoporous electrodes evidence CISS effect on water oxidation.

Controlling product selectivity is essential for improving the efficiency of multi-product reactions. Electrochemical water oxidation is a reaction of main importance in different applications, e.g., renewable energy schemes and environmental protection, where H2O2 and O2 are the two principal products. In this Communication, the product selectivity of electrochemical water oxidation was controlled by making use of the chiral induced spin selectivity (CISS) effect at mesoporous-TiO2 on the molecule-modified Au substrate. Our results show a decrease in H2O2 formation when using chiral hetero-helicene molecules adsorbed on the Au substrate. We propose a mechanism for this kinetic effect based on the onset of CISS-induced spin polarization on the Au-helicene chiral interface. We also present a new tunable substrate to investigate the CISS mechanism.

Improved ant colony optimization for safe path planning of AUV

In order to address the autonomous underwater vehicle navigation challenge for dam inspections, with the goal of enabling safe inspections and reliable obstacle avoidance, an improved smooth Ant Colony Optimization algorithm is proposed for path planning. This improved algorithm would optimize the smoothness of the path besides the robustness, avoidance of local optima, and fast computation speed. To achieve the goal of reducing turning time and improving the directional effect of path selection, a corner-turning heuristic function is introduced. Experimental simulation results show that the improved algorithm performs best than other algorithms in terms of path smoothness and iteration stability in path planning.

LSFSR: Local label correlation-based sparse multilabel feature selection with feature redundancy

In recent studies, existing multilabel feature selection models have focused on either considering the relationship between labels or the redundancy between features. Furthermore, they only use simple sparsity constraints to process high-dimensional data without the intrinsic relationships between features and labels. These issues can have a great impact on the classification effectiveness of feature selection. To address these limitations, this article describes a new local label correlation-based sparse multilabel feature selection approach with feature redundancy. First, a new loss function is established among the matrices of samples, label coefficients, and labels. Then, the Frobenius norm is imposed to investigate the potential relationships between features and labels. The weight matrix is sparsified by the l2,1 norm to ensure that the new loss function has high interpretability. Second, a manifold constraint is employed to capture the local geometric structure between labels and to delve deeper into the latent information among the local labels. Then manifold constraints and Laplacian scores are combined for embedding feature selection to guide the exploration of hidden latent label. Finally, by considering the differences between the feature scores and the redundancy between the samples, feature redundancy is analyzed via the modified cosine similarity, and a candidate feature subset with low redundancy is generated. The l2 norm is used to select features with low redundancy while preserving sparsity, and a novel objective function is developed to optimize this solution. Thus, a sparse feature selection algorithm via local label correlation and feature redundancy is designed, and has demonstrated remarkable classification effectiveness in comparative experiments conducted on 21 multilabel datasets.

Biocatalysis for Green Synthesis: Exploring the Use of Enzymes and Microorganisms as Catalysts for Organic Synthesis, Highlighting Their Advantages over Traditional Chemical Catalysts in Terms of Selectivity, Efficiency, and Environmental Impact

This study explores the use of microorganisms and enzymes as catalysts for organic synthesis, highlighting the advantages of these catalysts over conventional chemical catalysts in terms of selectivity, efficiency, and environmental effect. This study explains the major advantages of biocatalysis, such as its high selectivity, mild reaction conditions, efficiency, low environmental impact, and compatibility with renewable feedstocks, by looking at several case studies and experimental results. The importance of biocatalysis in advancing environmentally friendly and sustainable manufacturing processes is emphasized.