Additional Hits Research Articles

Natural volatiles preventing mosquito biting: An integrated screening platform for accelerated discovery of ORco antagonists

Insect olfactory receptors are heteromeric ligand-gated cation channels composed of an obligatory receptor subunit, ORco, and one of many variable subunits, ORx, in as yet undefined molar ratios. When expressed alone exvivo, ORco forms homotetrameric channels gated by ORco-specific ligands acting as channel agonists. Using an insect cell-based system as a functional platform for expressing mosquito odorant receptors exvivo, we identified small molecules of natural origin acting as specific ORco channel antagonists, orthosteric or allosteric relative to a postulated ORco agonist binding site, which cause severe inhibition of olfactory function in mosquitoes. In the present communication, we have compiled common structural features of such orthosteric antagonists and developed a ligand-based pharmacophore whose properties are deemed necessary for binding to the agonist binding site and causing inhibition of ORco's biological function. In silico screening of an available collection of natural volatile compounds with the pharmacophore resulted in identification of several ORco antagonist hits. Cell-based functional screening of the same compound collection resulted in the identification of several compounds acting as orthosteric and allosteric antagonists of ORco channel function exvivo and inducing anosmic behaviors to Aedes albopictus mosquitoes invivo. Comparison of the in silico screening results with those of the functional assays revealed that the pharmacophore predicted correctly seven out of the eight confirmed orthosteric antagonists and none of the allosteric ones. Because the pharmacophore screen produced additional hits that did not cause inhibition of the ORco channel function, we also generated a support vector machine (SVM) model based on two descriptors of all pharmacophore hits. Training of the SVM on the exvivo validated compound collection resulted in the selection of the confirmed orthosteric antagonists with a very low cross-validation out-of-sample misclassification rate. Employment of the combined pharmacophore-SVM platform for in silico screening of a larger collection of olfaction-relevant volatiles produced several new hits. Functional validation of randomly selected hits and rejected compounds from this screen confirmed the power of this virtual screening platform as a convenient tool for accelerating the pace of discovery of novel vector control agents. To the best of our knowledge, this study is the first one that combines a pharmacophore with a SVM model for identification of AgamORco antagonists and specifically orthosteric ones.

Molecular markers for pediatric low-grade glioma.

Over the past decade, our understanding of the molecular drivers of pediatric low-grade glioma (PLGG) has expanded dramatically. These tumors are predominantly driven by RAS/MAPK pathway activating alterations (fusions and point mutations), most frequently in BRAF, FGFR1, and NF1. Furthermore, additional second hits in tumor suppressor genes (TP53, ATRX, CDKN2A) can portend more aggressive behaviour. Accordingly, comprehensive molecular profiling-specifically genetic sequencing, often plus copy number profiling-has become critical for guiding the diagnosis and management of PLGG. In this review, we discuss the most important genetic alterations that inform on classification and prognosis of PLGG, highlighting their diagnostic and therapeutic relevance.

Tracking performances of the ePIC detector at the Electron-Ion Collider

The ePIC (electron–Proton/Ion Collider) experiment is a future facility at the Electron-Ion Collider (EIC) complex, located at the Brookhaven National Laboratory, USA. It will use ∼70% longitudinally polarized beam of electrons, protons, and light ions to study their collisions to understand the properties of the quarks, gluons, and the strong force responsible for the formation of the nucleus. The layout of the central detector of the ePIC experiment is not symmetric along the beams axis consisting of barrel, forward, and backward detectors to achieve a wide pseudorapidity (|η|< 3.5) coverage. There are further far-forward and far-backward tracking detectors to measure the luminosity and reconstruct the particles and fragments for the study of the exclusive deep-inelastic scattering (DIS) processes. The experiment has a challenging environment due to the presence of the background radiations (synchrotron radiation, beam-gas interactions, minimum-bias events, etc.) which will produce additional background hits on the tracker. The synchrotron radiation is suppressed to some extent by coating the beampipe with a 5μm gold layer. The experiment uses state-of-the-art bent wafer-scale silicon monolithic active pixel sensors (MAPS) with a ∼5μs acquisition window, micro-pattern gas detector (MPGD) with a good time resolution (∼20–30ns), and time-of-flight detectors based on AC-LGAD sensors (time resolution ∼30ps). The timing information of each detector will play a crucial role in track finding and rejecting the background hits utilizing the 4-dimensional tracking (space, time) to ensure the excellent performance of the experiment. The article presents the expected tracking performance of the ePIC detector using the modular ePIC software stack for simulation, reconstruction, and analysis. The Geant4 toolkit is employed for full detector simulations, alongside DD4hep (Detector Description for High Energy Physics) for geometry definition and exchange. The reconstruction incorporates the JANA2 framework, in addition to the tracking and vertexing algorithms inherited from A Common Tracking Software (ACTS).

In Vivo CRISPR Screening Platform for Studying Myeloid Inflammation and Clonal Dynamics

Previous experimental approaches using CRISPR to study factors governing hematopoiesis in vivo have been hampered by heterogeneity in cellular expansion during hematopoietic reconstitution. To control for such ‘cellular jackpotting’, we developed an in vivo hematopoietic stem and progenitor (HSPC)-based CRISPR screening system with unique molecular identifiers (UMIs) and applied these techniques to study myeloid inflammation and clonal expansion of Tet2-mutated HSPCs. Transplantation of Cas9-expressing Lin -Sca1 +c-Kit + (LSK) cells transduced with high-diversity UMI-labeled guide-RNAs (gRNAs) enabled sufficient gRNA representation at a genome-wide level after lentiviral integration of one gRNA per cell and controlled for 10 log-fold differences in cellular expansion during hematopoietic reconstitution. Simultaneous comparison of barcoded CRISPR screening with non-barcoded screening revealed that barcoding decreases false-positive biological processes related to cell division while improving sensitivity for detecting biological processes related to transcriptional events and cellular differentiation. To study inflammatory mediators, we applied this CRISPR screening tool towards studying the recruitment of CD101 +Ly6G +CD11b + mature neutrophils during an inflammatory insult, which revealed the majority of genes involved in human congenital neutropenia (Figure A). To demonstrate the reproducibility of this screening system, we performed a targeted transcription factor (TF)-based CRISPR screen, which revealed concordance between the genome-wide screen and the targeted screen. Next, we also applied this screening system to studying dynamics of Tet2-mutated clonal hematopoiesis. To study master regulators of clonal expansion in Tet2 KO, we performed a UMI-based CRISPR screen using chromatic and transcription factors, which revealed Tet3 and Bcor, genes previously identified to cooperate with Tet2 KO to promote myeloproliferation (Figure B). Validation of additional novel genetic hits is currently ongoing. We hypothesize that this screening platform will be useful for dissecting many aspects of hematopoiesis including inflammatory mediators and clonal dynamics of HSPCs.

Malignant Peripheral Nerve Sheath Tumors Activate Distinct Immunosuppressive Pathways Following Radiotherapy and are Associated with Immune Depletion In Vivo

Patients with neurofibromatosis type I, caused by NF1 loss, develop benign plexiform neurofibromas (pNF) in their peripheral nervous system (PNS). Malignant transformation of pNFs into malignant peripheral nerve sheath tumors (MPNSTs) occurs following CDKN2A/B and SUZ12 loss, a process associated with radiotherapy (RT). However, the molecular mechanisms underlying RT responses by different PNS cell types remain unclear. We hypothesized normal peripheral nerve cells, pNFs, and MPNSTs harbor distinct RT responses. Patient derived NF1 WT immortalized peripheral nerve cells (iPNs), NF1 mutant pNF cells, and NF1/CDKN2AB/SUZ12 mutant MPNST cells were used to study RT responses in vitro. CRISPRi was used to assess the functional effects of candidate gene repression. In vitro viability was measured by cell counts. Transcriptomic signatures were measured by bulk RNA-sequencing and integrated with single-cell RNA sequencing (scRNA-seq) data from patient-derived pNF and MPNST resection specimens. Radiation dose response curves revealed pNF cells (IC50 0.61 Gy) were more radiosensitive than MPNST cells (4.15 Gy). WT iPNs, NF1 deficient iPNs, and pNFs cells displayed no difference in cell viability (p = 0.67; t-test) following initiation of 2 Gy x 5 fractions, while MPNST cells were significantly more viable (p = 0.02; t-test). Principal component analysis of bulk RNA-sequencing data at 5 or 14 days following 2 Gy x 5 fractions revealed cell line of origin accounted for the greatest inter-sample variation (64.9% variance), with additional components separating samples based on radiation presence and timing. Using the most variable genes in PCA space to identify markers of RT response, iPNs and pNFs upregulated pro-apoptotic pathways (BAD, DAPK3) at 5 days post-radiation while MPNST cells alone upregulated pro-survival growth factor signaling). At 14 days post radiation, MPNST cells uniquely upregulated TGFβ signaling and interferon response circuits. Incorporation of scRNA-seq data revealed enrichment of growth factor signaling and TGFβ signatures in MPNSTs compared to pNF. Moreover, MPNST harbored significantly fewer immune cells than pNFs (p = 0.008, t-test), suggesting cell-autonomous signaling and crosstalk with the microenvironment are both critical to MPNST radioresistance. Our data indicate additional genetic hits beyond NF1 loss may be required for RT-associated malignant transformation of pNFs and radioresistance in MPNSTs. Analysis of transcriptomic responses to RT suggests that upregulated growth factor signaling and TGFβ-associated immunosuppression are distinct features of MPNST. Future work will focus on CRISPRi screens to unbiasedly nominate functional modifiers of RT response in NF1/CDKN2AB deficient tumors, which may be broadly useful in cancer.

Structure-Based Discovery of Receptor Activator of Nuclear Factor-κB Ligand (RANKL)-Induced Osteoclastogenesis Inhibitors.

Receptor activator of nuclear factor-κB ligand (RANKL) has been actively pursued as a therapeutic target for osteoporosis, given that RANKL is the master mediator of bone resorption as it promotes osteoclast differentiation, activity and survival. We employed a structure-based virtual screening approach comprising two stages of experimental evaluation and identified 11 commercially available compounds that displayed dose-dependent inhibition of osteoclastogenesis. Their inhibitory effects were quantified through TRAP activity at the low micromolar range (IC50 < 5 μΜ), but more importantly, 3 compounds displayed very low toxicity (LC50 > 100 μΜ). We also assessed the potential of an N-(1-aryl-1H-indol-5-yl)aryl-sulfonamide scaffold that was based on the structure of a hit compound, through synthesis of 30 derivatives. Their evaluation revealed 4 additional hits that inhibited osteoclastogenesis at low micromolar concentrations; however, cellular toxicity concerns preclude their further development. Taken together with the structure-activity relationships provided by the hit compounds, our study revealed potent inhibitors of RANKL-induced osteoclastogenesis of high therapeutic index, which bear diverse scaffolds that can be employed in hit-to-lead optimization for the development of therapeutics against osteolytic diseases.

Discovery of PLpro and Mpro Inhibitors for SARS-CoV-2.

There are very few small-molecule antivirals for SARS-CoV-2 that are either currently approved (or emergency authorized) in the US or globally, including remdesivir, molnupiravir, and paxlovid. The increasing number of SARS-CoV-2 variants that have appeared since the outbreak began over three years ago raises the need for continual development of updated vaccines and orally available antivirals in order to fully protect or treat the population. The viral main protease (Mpro) and the papain-like protease (PLpro) are key for viral replication; therefore, they represent valuable targets for antiviral therapy. We herein describe an in vitro screen performed using the 2560 compounds from the Microsource Spectrum library against Mpro and PLpro in an attempt to identify additional small-molecule hits that could be repurposed for SARS-CoV-2. We subsequently identified 2 hits for Mpro and 8 hits for PLpro. One of these hits was the quaternary ammonium compound cetylpyridinium chloride with dual activity (IC50 = 2.72 ± 0.09 μM for PLpro and IC50 = 7.25 ± 0.15 μM for Mpro). A second inhibitor of PLpro was the selective estrogen receptor modulator raloxifene (IC50 = 3.28 ± 0.29 μM for PLpro and IC50 = 42.8 ± 6.7 μM for Mpro). We additionally tested several kinase inhibitors and identified olmutinib (IC50 = 0.54 ± 0.04 μM), bosutinib (IC50 = 4.23 ± 0.28 μM), crizotinib (IC50 = 3.81 ± 0.04 μM), and dacominitinib (IC50 = IC50 3.33 ± 0.06 μM) as PLpro inhibitors for the first time. In some cases, these molecules have also been tested by others for antiviral activity for this virus, or we have used Calu-3 cells infected with SARS-CoV-2. The results suggest that approved drugs can be identified with promising activity against these proteases, and in several cases we or others have validated their antiviral activity. The additional identification of known kinase inhibitors as molecules targeting PLpro may provide new repurposing opportunities or starting points for chemical optimization.

TET2 Loss Conspires with MYC to Foster Lymphomagenesis

Programmed DNA methylation patterning serves the generation and maintenance of cell identity, and represents a major barrier against transformation. TET dioxygenases (TET1-3) facilitate DNA demethylation at enhancers, promoting chromatin accessibility and cell type-specific gene expression patterns. Work from our and other labs had shown that TET enzymes settle B lymphocyte identity and warrant antibody-mediated immunity. Due to the prevalence of TET2 mutations in hematological and immune cell tumors, often identified as loss-of-function (LOF) versions, TET2 LOF is considered a cancer driver. Intriguingly, although showing a predisposition for blood cancer, healthy humans carrying TET2 mutations in hematopoietic stem cells can remain cancer-free for decades despite increasing clonal dominance of the affected cells and their offspring, a condition termed clonal hematopoiesis. Furthermore, mice deficient for TET2 only rarely develop tumors. This scenario suggests roles for TET2 LOF as cancer facilitator, rather than driver. In B lymphocytes, the MYC oncoprotein is a potent driver of malignancy. However, therapeutic targeting of MYC is far from reaching the clinic. Thus, establishing functional links between MYC and dependencies imposed by TET2 LOF should provide information on the molecular mechanisms of predisposition, and guide clinical practice and targeted therapy in the future. To address whether TET2 LOF conspires with MYC, we employed the prototypic EμMYC transgenic mouse model, where enforced MYC overexpression early in the B lymphocyte lineage drives lymphomas, but additional hits are required for full transformation. Confirming a tumor suppressor role for TET2, partial or complete loss of the protein accelerated lymphomagenesis, and facilitated specifically the outgrowth of IgM+ lymphomas. The premalignant IgM+ population contained a higher fraction of cells with double strand breaks (EμMYC 2,5% vs. EμMYCTet2+/- or EμMYCTet2-/- 6%) and in the S/G2/M cell cycle phases (EμMYC 15% vs. EμMYCTet2+/- or EμMYCTet2-/- 25%), along with higher spontaneous apoptosis rates (EμMYC 4% vs. EμMYCTet2+/- or EμMYCTet2-/- 7%). Mechanistically, in the context of MYC overexpression, TET2 LOF associates with enhanced JAK/STAT signaling and selective upregulation of the pro-survival BCL2 family protein BCLX. To recapitulate alternative scenarios of TET2 LOF in diffuse large B cell lymphoma (DLBCL), a tumor that originates from germinal center B lymphocytes, we established two preclinical mouse models, (1) either with TET2 LOF in the germline to mimic the scenario of clonal hematopoiesis along with ectopic MYC expression restricted to germinal center B lymphocytes, or (2) using a fully conditional approach where we synchronize ectopic MYC expression and TET2 LOF specifically in germinal center B lymphocytes. In line with the results from the EμMYC model, germline heterozygous Tet2 loss (scenario (1)) sufficed to boost MYC-driven lymphomagenesis, a phenotype that is strongly enhanced by the absence of both Tet2 alleles. Germinal center-specific elimination of Tet2 in scenario (2) also produced lymphomas, however, heterozygous Tet2 loss in germinal center B lymphocytes was not sufficient to unleash MYC-driven lymphomagenesis. Our data from three powerful MYC-driven mouse models suggest (i) that TET2 loss in B lymphocytes nudges MYC-mediated transformation, (ii) that TET2 loss, early on in hematopoietic stem cells, potentiates the transformative potential later on in B lymphocytes, and (iii) that TET2 loss dampens apoptosis during transformation and in established lymphomas, potentially via JAK/STAT signaling and BCLX. Altogether, we provide novel in vivo evidence that TET2 prevents MYC-mediated transformation in B lymphocytes, and our results produced testable dependencies. Beyond MYC-driven blood cancer, TET2 LOF in hematopoietic stem cells predisposes to all-cause mortality in humans. Thus, identifying targetable vulnerabilities of TET2 LOF will serve healthy aging.

Single-Cell Transcriptome Analysis Reveals Stem Cell-like Subsets in the Progression of Waldenström's Macroglobulinemia

Waldenström's macroglobulinemia (WM) is an uncommon lymphoproliferative disorder characterized by monoclonal immunoglobulin M protein production and bone marrow infiltration by lymphoplasmacytoid cells. It remains an incurable disease. IgM monoclonal gammopathy of undetermined significance (MGUS) is the premalignant condition and is associated with the risk of developing WM. MYD88L265P is a recurrent mutation found in more than 90% of WM patients, and this genetic event is detectable in at least half of IgM MGUS patients. However, the precise cellular landscape and the mechanisms of progression from IgM MGUS to WM remain unclear. Single-cell RNA sequencing (scRNA-seq) provides us a powerful approach to explore tumor heterogeneity and identify rare malignant cells. Anti-CD38 monoclonal antibodies have been introduced into the therapeutic arsenal for plasma cell diseases. Therefore, we analyzed CD38+ immune microenvironment together with B cells and plasma cells to illustrate the first cellular landscape of IgM MGUS and WM in single cell resolution. We isolated bone marrow CD19+ and CD19-CD38+ cells from WM patients(n=3), IgM MGUS patients(n=3) and healthy donors(n=3) and employed the 10x Genomics platform to perform single-cell transcriptomic sequencing. After quality control, our dataset contained a total of 73024 cells. We used UMAP to visualize the cell superclusters and identified clusters including B cells, plasma cells, CD3+CD20+ (CD19+) cells, T cells and NK cells based on the expression of canonical lineage markers and cluster-specific markers. We found that healthy donors had the highest percentage of B cells (72.7% in healthy donors, 19.0% in IgM MGUS patients, 60.5% in WM patients; p<0.001) and that IgM MGUS and WM patients had more NK and T cells than healthy controls (0.06% and 17.7%, respectively, in healthy donors; 24.1% and 20.5% in IgM MGUS patients; 8.5% and 24.0% in WM patients; p<0.001). We also noticed that CD3+CD20+(CD19+) cells were present in both IgM MGUS and WM patients. First, we investigated the cell clusters correlated with WM pathology including B cells and plasma cells. We compared the B-cell gene expression profiles after removing the early B cells. Compared with those of IgM MGUS patients, mature B cells of WM patients showed upregulation of PIM1, DUSP22, HES1, NEAT1, RGS1, RGS16, and GADD45B. Light chain restriction and higher CNV levels were found in B cells of WM patients. SCENIC analysis showed that FOS, FOSB, EGR1 and JUNB were downregulated in B cells from WM and IgM MGUS patients. REL, a proto-oncogene promoting the survival and proliferation of B lymphocytes, was upregulated in B cells of WM patients, and IRF8 and ELF1 were upregulated in B cells of IgM MGUS patients. Nevertheless, plasma cells of WM patients, IgM MGUS patients and healthy donors were colocalized in one cluster, which might indicate their similar gene expression patterns. Next, we further determined the characteristics of B-cell subpopulation with aberrant T-cell antigen expression. Trajectory analysis revealed that CD3+CD20+(CD19+) cells and pro-B cells were located at the same end of the branched structure and were then directed toward mature B cell and plasma cell fates, respectively (Figure. 1A). This inferred developmental trajectory suggested that CD3+CD20+(CD19+) cells may be tumor stem cell-like subset. Using flow cytometry, we validated that CD3 was expressed in a fraction of CD19+ cells (mean: 3.69%, range: 0.28%-15.10%) of bone marrow samples from 8 WM patients. In addition, targeted gene sequencing was performed on CD3+CD19+ and CD3-CD19+ cells from 6 WM patients. MYD88 were proved to be the most frequently mutated gene in this cell subset. And we inferred that MYD88 mutation might be the early events in tumorigenesis by VAF analysis (Figure. 1B). Additional subclonal hits, such as CXCR4 and MAP2K1 mutations, could be acquired during tumor progression. In conclusion, our study provides comprehensive insights into mechanisms of progression from IgM MGUS to WM. We identified the rare CD19+ cell subpopulation with T-cell antigen expression in WM patients. It will be interesting to explore novel therapeutic strategies targeting rare potential cancer-initiating cells in future. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

EXTH-41. COMBINED PHARMACOLOGICAL AND GENETIC SCREENING TO IDENTIFY DEPENDENCIES AND COMBINATIONS IN ACVR1-MUTANT DIFFUSE MIDLINE GLIOMA

Abstract Somatic mutations in ACVR1, which encodes the serine/threonine kinase ALK2, are found in 20-25% of DMG-H3K27 patients. Treatment of ACVR1-mutant patient-derived models with multiple chemotypes of ALK2 inhibitors (ALK2i) results in reduced cell viability in vitro and extended survival in orthotopic xenografts in vivo but, as single agents, these inhibitors were unable to achieve a complete anti-tumour response. Recently we reported that combinatorial treatment of ACVR1-mutant DIPG cells with vandetanib (RTK inhibitor) and everolimus (mTOR/ABC transporter inhibitor) was synergistic both in vitro and in vivo and was shown to be a feasible combination to trial clinically in this setting. To identify specific dependencies in ACVR1-mutant cells which may be translatable with novel synergistic drug combinations alongside ALK2i, we have implemented both candidate and unbiased drug and genetic screening approaches. Using a panel of 13 patient-derived ACVR1-mutant models (and 6 wild-type controls), we identified synergy between multiple chemotypes of ALK2i (M4K2009/LDN-214117) and PI3K/mTOR (AZD8055/everolimus) and MEK inhibitors (trametinib), reflecting the common co-segregation of PIK3CA/PIK3R1 alterations in these tumours. Whole-genome CRISPR/Cas9 screening of ACVR1-mutant SU-DIPG-IV cells in combination with two ALK2i (M4K2009/LDN-193189), confirmed a specific MTOR genetic dependency, as well as for the protein phosphatase regulatory subunit PPP2R1A, known to play a role in MAPK pathway activation. Additional hits include the serine/threonine kinase PKMYT1, a negative regulator of the G2/M checkpoint via a functionally redundant phosphorylation of CDK1/CCNB1 alongside WEE1; confirmatory drug assays with the WEE1 inhibitor AZD1775 resulted in a synergistic interaction with ALK2i in ACVR1-mutant cells. Hits were integrated with DepMap using ‘gene effect’ scores (Chronos) enabling filtering of common essential genes. Preliminary pathway enrichment analysis (MAGeCKFlute) identified ALK2i-specific vulnerabilities involving TGFB1/SMAD signalling and histone deacetylation. These data highlight functionally rational and novel combinatorial possibilities for children with ACVR1-mutant DMG, with systematic preclinical assessment required for prioritisation for the clinic.

Neutrino oscillation parameter determination at INO-ICAL using track and hit information from GEANT

We study the capability of INO-ICAL to determine the neutrino oscillation parameters |ΔM 2 31| and sin2 θ 23. We do not use any generator level information. Instead, we process the generated atmospheric neutrino events through GEANT4 simulation of the detector and the event reconstruction framework. Among the outputs of this framework, only the momentum and direction of the longest track were used in a previous study by other authors. In this study, in addition to these two variables, we consider a third variable based on additional hits, which arise due to hadrons in the event. We show that the inclusion of this variable leads to a 30% reduction in the uncertainty of |ΔM 2 31| for a 5-year run of ICAL. We find that doubling the exposure time leads to an additional 30% reduction in the uncertainties of both |ΔM 2 31| and sin2 θ 23.

Abstract 5325: Image-based functional precision medicine for repurposing neuroactive drugs in glioblastoma

Abstract Treatment of glioblastoma multiforme (GBM), the most aggressive form of primary brain cancer, has essentially not advanced over the past few decades. Numerous challenges hinder the successful development of new therapies, including drug delivery across the blood-brain barrier (BBB), the complexity of the tumor microenvironment (TME), and the lack of clinically predictive cancer models. Here, we present the results of an image-based ex vivo drug-testing platform that addresses these therapeutic roadblocks. To demonstrate the clinical utility of our platform, in a retrospective cohort of 14 GBM patients, we show that ex vivo sensitivity to Temozolomide (TMZ, 1st-line GBM chemotherapy), is associated with longer progression free survival (PFS) and overall survival (OS). Next, by screening 150 clinically approved drugs across 27 GBM surgical patient samples, we identify a set of BBB-permeable neuroactive drugs with anti-glioma activity. These neurological drugs display remarkably consistent on-target killing of cancer cells with minimal toxicity to non-malignant TME cells across both primary and recurrent GBM samples. Single-cell transcriptional profiling of GBM patient samples and functional genetics reveals novel glioma-dependencies on neurological drug-target expression. Furthermore, a drug-target network enrichment analysis uncovers an AP1/BTG/TP53 gene signature associated with the anti-glioma activity of neurological drugs. In silico screening of over 1 million compounds for this common gene signature identified additional drug hits that could be validated in patient samples with 90% accuracy. Multiplexed transcriptomics revealed AP-1 transcription factor family activation to be the common underlying feature of neurological drugs with anti-glioma activity. Among the most promising candidate drugs, we identify the atypical antidepressant Vortioxetine as the strongest inducer of this gene signature, and confirm its efficacy in vivo across multiple mouse models. Vortioxetine in combination with Temozolomide or Lomustine further increased median survival in vivo compared to single agents alone. This study thus provides a clinically predictive and personalized drug-testing platform that identifies new treatment opportunities for GBM, warranting further investigation. Citation Format: Sohyon Lee, Tobias Weiss, Marcel Bühler, Rebekka Wegmann, Julien Mena, Michel Bihl, Sandra Goetze, Audrey van Drogen, Elisabeth J. Rushing, Bernd Wollscheid, Michael Weller, Berend Snijder. Image-based functional precision medicine for repurposing neuroactive drugs in glioblastoma [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 5325.

DIPG-40. Combined pharmacological and genetic screening to identify dependencies and combinations in ACVR1-mutant diffuse midline glioma

Somatic mutations in ACVR1, which encodes the serine/threonine kinase ALK2, are found in 20-25% of DMG-H3K27 patients. Treatment of ACVR1-mutant patient-derived models with multiple chemotypes of ALK2 inhibitors (ALK2i) results in reduced cell viability in vitro and extended survival in orthotopic xenografts in vivo but, as single agents, these inhibitors were unable to achieve a complete anti-tumour response. Recently we reported that combinatorial treatment of ACVR1-mutant DIPG cells with vandetanib (RTK inhibitor) and everolimus (mTOR/ABC transporter inhibitor) was synergistic both in vitro and in vivo and was shown to be a feasible combination to trial clinically in this setting. To identify specific dependencies in ACVR1-mutant cells which may be translatable with novel synergistic drug combinations alongside ALK2i, we have implemented both candidate and unbiased drug and genetic screening approaches. Using a panel of patient-derived ACVR1-mutant and wild-type models, we identified synergy between multiple chemotypes of ALK2i (M4K2009/LDN-214117) and PI3K/mTOR (AZD8055/everolimus) and MEK inhibitors (trametinib), reflecting the common co-segregation of PIK3CA/PIK3R1 alterations in these tumours. Whole-genome CRISPR/Cas9 screening of ACVR1-mutant SU-DIPG-IV cells in combination with two ALK2i (M4K2009/LDN-193189), confirmed a specific MTOR genetic dependency, as well as for the protein phosphatase regulatory subunit PPP2R1A, known to play a role in MAPK pathway activation. Additional hits include the serine/threonine kinase PKMYT1, a negative regulator of the G2/M checkpoint via a functionally redundant phosphorylation of CDK1/CCNB1 alongside WEE1; confirmatory drug assays with the WEE1 inhibitor AZD1775 resulted in a synergistic interaction with ALK2i in ACVR1-mutant cells. Hits were integrated with DepMap using ‘gene-effect’ scores (Chronos) enabling filtering of common essential genes. Preliminary pathway enrichment analysis (MAGeCKFlute) identified ALK2i-specific vulnerabilities involving TGFB1/SMAD signalling and histone deacetylation. These data highlight functionally rational and novel combinatorial possibilities for children with ACVR1-mutant DMG, with systematic preclinical assessment required for prioritisation for the clinic.

FC033: Genome-Wide Association Meta-Analysis Identifies Novel Loci for Kidney Failure

Abstract BACKGROUND AND AIMS The genetics of kidney function has been extensively studied, but since these analyses have been done mostly in populations with normal or mildly impaired kidney function, it is still unknown whether variants linked to kidney function also translate into genetic susceptibility for kidney failure. The primary aim of this study was to investigate the genetic background of kidney failure. METHOD We performed a meta-analysis of kidney failure genome-wide association studies, using kidney transplant recipients as cases (n = 6942) and donors as controls (n = 4788). Secondary disease-specific analyses were performed for kidney failure due to diabetes, IgA nephropathy, glomerulonephritis or polycystic kidney disease. Subsequently, we investigated genetic overlap with eGFR and urinary albumin-creatinine ratio (UACR) variability, based on publicly available CKDgen consortium meta-analysis data. RESULTS In the primary analysis, we found two suggestive hits for kidney failure: rs17046239 in GRM7 (P = 8.9 × 10−8), and rs9273431 in HLA-DQB1 (P = 5.3 × 10−8). In disease-specific analyses, we found three genome-wide (P &amp;lt; 5 × 10−8) significant hits for kidney failure due to diabetes: rs9273431 in HLA-DQB1 (P = 5.0 × 10−50), rs2476601 in PTPN22 (P = 2.9 × 10−13) and rs7110099 in INS-IGF2 (P = 4.4 × 10−9). Furthermore, we found suggestive hits for kidney failure due to glomerulonephritis (rs6531751, nearest gene: PDS5a, P = 9.3 × 10−8) or polycystic kidney disease (rs111857047 in PTPRD, P = 9.6 × 10−8). As follow-up analysis, we performed lookups for the identified SNPs in prior kidney function GWAS results of the CKDGen consortium. Our top hits for kidney failure due to diabetes were nominally significant (P &amp;lt; 0.05) in the creatinine-based estimated glomerular filtration rate (eGFRcrea) and/or the UACR results. The other hits were not significantly associated with either phenotype. Linkage disequilibrium score regression (LDSC) analysis did not reveal a significant genetic correlation (rG) between kidney failure and eGFRcrea or UACR. There was significant genetic overlap of type 2 diabetes with both kidney failure due to any cause (rG = 0.27; P = 0.0027) and kidney failure due to diabetes (rG = 0.57; P = 0.0002). In silico sequencing revealed that our diabetes-induced kidney failure hits had previously been associated with auto-immunity and type 1 diabetes; the other hits yielded no results. A UK Biobank phenome-wide association scan confirmed the associations of the three diabetes-specific kidney failure genetic hits with auto-immunity and diabetes phenotypes, and additionally linked them to thyroid function and blood cell counts. CONCLUSION We identified three genome-wide significant variants associated with kidney failure due to diabetes and four additional suggestive hits associated with cause-specific or overall kidney failure. The lack of strong genetic overlap with eGFR and UACR suggests that there is a separate genetic component that drives the risk of progression to kidney failure, independent of normal kidney function.

One-Hit Wonders versus Hit Makers: Sustaining Success in Creative Industries

Creative industries produce many one-hit wonders who struggle to repeat their initial success and fewer hit makers who sustain success over time. To develop theory on the role of creativity in driving sustained market success, I propose a path dependence theory of creators’ careers that considers creators’ whole portfolios of products over time and how their early portfolios shape their later capacity to sustain success. The main idea is that a creator’s path to sustained success depends on the creativity in their portfolio at the time of their initial hit—relatively creative portfolios give creators more options for leveraging their past portfolios while adapting to market changes, increasing their odds of additional hits. I tested the proposed theory using an archival study of the U.S. music industry from 1959–2010, including data on over 3 million songs by 69,050 artists, and the results largely support the hypotheses. Artists who reached their initial hits with relatively creative (novel or varied) portfolios were more likely to generate additional hits, but a novel portfolio was less likely to yield an initial hit than was a typical portfolio. These findings suggest that new creators face a tradeoff between their likelihood of initial versus sustained success, such that building a relatively creative early portfolio is a risky bet that can make or break a creator’s career.

Structure-Activity Studies of Novel Di-substituted [1,2,5]oxadiazolo [3,4-b]pyrazine Analogs Targeting the A-loop Regulatory Site of p38 MAP Kinase.

In the quest for novel allosteric inhibitors of the p38 MAP kinase, we recently described the A-loop regulatory site, identified by means of molecular modeling studies together with the disclosure of a small molecule hit with a moderate inhibitory profile. Starting from this structure, we subsequently identified two additional hits with simpler molecular structures from an in silico screening study, using a substructure search in the SciFinder database. After corroboration of their inhibitory profile, analysis of their structures permitted to conclude about the suitability of the [1,2,5]oxadiazolo[3,4-b]pyrazine (furazano[ 3,4-b]pyrazine) scaffold for the development of potent A-loop regulatory site p38 MAP kinase inhibitors. Accordingly, we report the synthesis and pharmacological evaluation of a series of di-substituted analogs with a potent inhibitory profile of p38 MAP kinase, as shown by in vitro assays of their capability to inhibit IL-1β secretion in human monocyte-derived macrophages. To find small molecule potent inhibitors of the p38 MAP kinase A-loop regulatory site. Starting from this structure, we subsequently identified two additional hits with simpler molecular structures from an in silico screening study, using a substructure search in the SciFinder database. After corroboration of their inhibitory profile, we carried out a hit-tolead optimization process guided by molecular modeling using a [1,2,5]oxadiazolo[3,4- b]pyrazine (furazano[3,4-b]pyrazine) scaffold. We report the synthesis and pharmacological evaluation of a series of di-substituted analogs with a potent inhibitory profile of p38 MAP kinase, as shown by in vitro assays of their capability to inhibit IL-1β secretion in human monocyte-derived macrophages. We describe in the present work a series of [1,2,5]oxadiazolo[3,4-b]pyrazine (furazano[3,4-b]pyrazine), which are potent inhibitors of IL-1β secretion in human monocytederived macrophages allosteric modulators of the p38 MAP kinase A-loop regulatory site.

Effects of early life adversity on immediate early gene expression: Systematic review and 3-level meta-analysis of rodent studies.

Early-life adversity (ELA) causes long-lasting structural and functional changes to the brain, rendering affected individuals vulnerable to the development of psychopathologies later in life. Immediate-early genes (IEGs) provide a potential marker for the observed alterations, bridging the gap between activity-regulated transcription and long-lasting effects on brain structure and function. Several heterogeneous studies have used IEGs to identify differences in cellular activity after ELA; systematically investigating the literature is therefore crucial for comprehensive conclusions. Here, we performed a systematic review on 39 pre-clinical studies in rodents to study the effects of ELA (alteration of maternal care) on IEG expression. Females and IEGs other than cFos were investigated in only a handful of publications. We meta-analyzed publications investigating specifically cFos expression. ELA increased cFos expression after an acute stressor only if the animals (control and ELA) had experienced additional hits. At rest, ELA increased cFos expression irrespective of other life events, suggesting that ELA creates a phenotype similar to naïve, acutely stressed animals. We present a conceptual theoretical framework to interpret the unexpected results. Overall, ELA likely alters IEG expression across the brain, especially in interaction with other negative life events. The present review highlights current knowledge gaps and provides guidance to aid the design of future studies.

Functional Multi-Omics Reveals Genetic and Pharmacologic Regulation of Surface CD38 in Multiple Myeloma

Background: CD38 is a surface ectoenzyme expressed at high levels on myeloma plasma cells and is the target for the monoclonal antibodies (mAbs) daratumumab and isatuximab. These antibodies have multiple mechanisms of action, primarily involving recruiting and modulating components of the immune system, but they may also carry direct anti-tumor effects. CD38 density on tumor cells is an important determinant of mAb efficacy while CD38 is lost after mAb treatment. Several small molecules have been found to increase tumor surface CD38, with the goal of boosting mAb efficacy in a co-treatment strategy. However, we do not yet have a broad global sense of the transcriptional or post-transcriptional networks that most strongly impact CD38 expression. There may be alternate strategies to even more potently increase CD38 expression that have not yet been identified. Furthermore, prior clinical studies showed that CD38 downregulation after daratumumab treatment was accompanied by increases in the complement inhibitors CD55 and CD59. Are there other features of myeloma surface remodeling driven by CD38 downregulation? Here we sought to extend our currently limited insight into CD38 surface expression by using a multi-omics approach.Methods: Genome-wide CRISPR interference screening was performed in RPMI-8226 cells stably expressing the dCas9-KRAB fusion protein. Cells were grown for 14 days after library transduction, flow-sorted on the top and bottom 25% of CD38 surface expression, and sgRNA's deep sequenced. Antibody-dependent cellular cytoxicity assays were performed with NK92-CD16 cells. Cell surface proteomics was performed using N-glycoprotein cell surface capture in triplicate. Phosphoproteomics was performed used immobilized metal affinity chromatography in triplicate. Murine studies were performed in NSG mice under approved IACUC-approved institutional protocols.Results: A genome-wide CRISPR-interference screen in RPMI-8226 cells demonstrated that transcriptional and epigenetic factors played the most prominent role in surface CD38 regulation (Fig. 1A). One of the genes that when knocked down led to greatest surface CD38 increase was RARA. This finding supports the promise of all-trans retinoic acid (ATRA), which leads to RARA degradation, as a potent agent to induce CD38 upregulation. Validation of additional screen hits TLE3 and HEXIM1 also illustrated that these negative regulatory transcription factors suppress CD38 expression at baseline (not shown). We found the transcription factor SPI1 to be a prominent positive regulator of CD38. SPI1 knockdown led to daratumumab resistance both in vitro and in vivo, similar to the resistance observed after CD38 knockdown (not shown). Analysis of myeloma patient ATAC-seq data, assessing transcription factor motifs present at the CD38 locus, combined with a predictive machine learning model, further identified XBP1 as one of the most potent transcriptional regulators of CD38 (Fig. 1B). We next used “antigen escape profiling” - knockdown of CD38 followed by unbiased cell surface proteomics - to mimic surface alterations in the context of CD38 loss. We found minimal changes in other cell surface proteins beyond CD38 (Fig. 1C), indicating the CD38 loss alone is not sufficient to remodel the myeloma surfaceome. This finding also supports the hypothesis that complement or other immune system interactions are necessary to lead to other myeloma surface protein alterations. In a parallel analysis of pharmacologic regulation, we also used cell surface proteomics integrated with RNA-seq to demonstrate that ATRA leads to few other surface protein changes beyond CD38 (not shown). In contrast, other molecules, such as azacytidine and panobinostat, led to broader changes across many more surface proteins, showing a lack of specificity when driving CD38 upregulation. Finally, unbiased phosphoproteomics revealed partial inhibition of the MAP kinase pathway after daratumumab binding (Fig. 1D). This result may comprise a direct anti-proliferative effect of anti-CD38 therapeutic antibody engagement in myeloma.Conclusions: Our work provides a resource to design strategies to enhance efficacy of CD38-targeting immunotherapies in myeloma. Our approach also outlines a broad multi-omic strategy to evaluate surface and transcriptional regulation of other key immunotherapeutic targets in hematologic malignancies. [Display omitted] DisclosuresChoudhry: Genentech: Current Employment, Current equity holder in publicly-traded company. Ramkumar: Senti Biosciences: Current Employment, Current holder of individual stocks in a privately-held company.

Brain Exosomes: Friend or Foe in Alzheimer's Disease?

Alzheimer's disease (AD) is the most common neurodegenerative disease. It is known to be a multifactorial disease and several causes are associated with its occurrence as well as progression. However, the accumulation of amyloid beta (Aβ) is widely considered its major pathogenic hallmark. Additionally, neurofibrillary tangles (NFT), mitochondrial dysfunction, oxidative stress, and aging (cellular senescence) are considered as additional hits affecting the disease pathology. Several studies are now suggesting important role of inflammation in AD, which shifts our thought towards the brain's resident immune cells, microglia, and astrocytes; how they interact with neurons; and how these interactions are affected by intra and extracellular stressful factors. These interactions can be modulated by different mechanisms and pathways, in which exosomes could play an important role. Exosomes are multivesicular bodies secreted by nearly all types of cells. The exosomes secreted by glial cells or neurons affect the interactions and thus the physiology of these cells by transmitting miRNAs, proteins, and lipids. Exosomes can serve as a friend or foe to the neuron function, depending upon the carried signals. Exosomes, from the healthy microenvironment, may assist neuron function and health, whereas, from the stressed microenvironment, they carry oxidative and inflammatory signals to the neurons and thus prove detrimental to the neuronal function. Furthermore, exosomes can cross the blood-brain barrier (BBB), and from the blood plasma they can enter the brain cells and activate microglia and astrocytes. Exosomes can transport Aβ or Tau, cytokines, miRNAs between the cells, and alter the physiology of recipient cells. They can also assist in Aβ clearance and regulation of synaptic activity. The exosomes derived from different cells play different roles, and this field is still in its infancy stage. This review advocates exosomes' role as a friend or foe in neurodegenerative diseases, especially in the case of Alzheimer's disease.

Abstract 309: Development of a multi-omic, pooled cancer cell screen for nanoparticle delivery

Abstract Background: Nanoparticles (NPs) hold enormous promise for the targeted delivery of therapeutics for cancer, but clinical translation is lacking largely due to limited tumor accumulation. Tumor heterogeneity and NP complexity make it challenging to deconvolute individual factors that contribute to NP-cell interactions. To address this, we developed a competition assay leveraging 500 stably DNA-barcoded adherent cancer cell lines annotated with multi-omic data from the Broad Institute (PRISM cells) to investigate cell association patterns across a library of NPs. We hypothesize that simultaneous screening of hundreds of cancer cell lines will identify factors underlying differential NP-cancer cell interactions. Methods: We synthesized a library of 40 fluorescently-labeled NPs comprising clinical and experimental formulations. Clinical formulations included liposomal doxorubicin and irinotecan analogs and liposomal or poly(lactide-co-glycolide, PLGA) NPs with and without polyethylene glycol (PEG); these are either FDA-approved or in clinical trials. Experimental formulations included liposomal and PLGA cores electrostatically coated with a range of native and synthetic polymers as well as polystyrene NPs of varying sizes and surface chemistries. Fluorescent antibodies -in free form or NP-conjugated—were included as validation compounds. PRISM cells were pooled and incubated with NPs prior to fluorescence-activated cell sorting (FACS) to bin cells based on strength of NP association. After cell lysis, DNA barcodes were amplified and sequenced. Using appropriate controls to adjust for baseline barcode abundance, we generated an association score for each NP-cell line pair. Next, we performed multi-omic univariate analyses and applied a random forest algorithm to identify factors predictive of NP-cancer cell association. Results: After pooled screening of PRISM cells, we consistently identified cancer cell lines based on strength of NP-association across technical and biologic replicates. Using antibodies and antibody-conjugated NPs targeting epidermal growth factor receptor (EGFR), we identified EGFR gene and protein expression as highly significant hits, validating our ability to robustly identify relevant biomarkers. Additional hits were evaluated based on strength and direction of association to identify predictive biomarkers by formulation. We also employed k-means clustering to investigate hits across NP formulations, identifying highly interconnected protein association networks that elucidate likely mechanisms of NP-cancer cell association. Conclusions: We report a new pooled screening platform to investigate factors influencing NP-cancer cell interactions. We validated the screen by identifying known biomarkers, and also identified new predictive biomarkers that may pave the way for more effective nanotherapeutics. Citation Format: Joelle P. Straehla, Natalie Boehnke, Mustafa Kocak, Melissa Ronan, Hannah Safford, Matthew G. Rees, Jennifer A. Roth, Angela N. Koehler, Paula T. Hammond. Development of a multi-omic, pooled cancer cell screen for nanoparticle delivery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 309.