Multiple Lines Research Articles

Serotonin and vasovagal syncope.

The goal of this manuscript was to review the biological and clinical evidence that serotonin neurotransmission might play an important role in the physiology and treatment of vasovagal syncope. The authors reviewed PubMed and handsearches of secondary sources for papers related to the Bezold-Jarisch reflex and serotonin, the plausible involvement of the Bezold-Jarisch reflex in vasovagal syncope, and three lines of clinical evidence involving serotonin and the syncope. The Bezold-Jarisch reflex was first described following the infusion of veratrum alkaloids into animals in the 19th century. The reflex is triggered by serotonin stimulation chemoreceptors and mechanoreceptors in the the left ventricle. The afferent component of the reflex is carried by unmyelinated type C vagal nerve fibers, which results in parasympathetic efferent stimulation that causes bradycardia. The similarity of the combination of hypotension and bradycardia in the Bezold-Jarisch reflex and in vasovagal syncope led to the suggestion that the reflex was the cause of the syndrome. Three lines of evidence implicate the serotonin 5HT3 receptors in the heart in the reflex. There is genetic and physiologic evidence for the serotonin 5HT1A and 5HT3 receptors and the serotonin reuptake transporter (SERT). Acute blockade of SERT induces vasovagal syncope in humans undergoing head-up tilt table testing, and SERT inhibition reduces hypotension and bradycardia during spinal anaesthesia. Finally, three randomized clinical trials of SERT inhibitors uniformly reported that they significantly reduce the likelihood of vasovagal syncope recurrences. Multiple lines of evidence implicate serotonin neurotransmission in the cause of vasovagal syncope.

Rapidly-manufactured CD276 CAR-T cells exhibit enhanced persistence and efficacy in pancreatic cancer.

Pancreatic cancer is one of the most lethal malignancies and the lack of treatment options makes it more deadly. Chimeric Antigen Receptor T-cell (CAR-T) immunotherapy has revolutionized cancer treatment and made great breakthroughs in treating hematological malignancies, however its success in treating solid cancers remains limited mainly due to the lack of tumor-specific antigens. On the other hand, the prolonged traditional manufacturing process poses challenges, taking 2 to 6weeks and impacting patient outcomes. CD276 has recently emerged as a potential therapeutic target for anti-solid cancer therapy. Here, we investigated the efficacy of CD276 CAR-T and rapidly-manufactured CAR-T against pancreatic cancer. In the present study, CD276 CAR-T was prepared by CAR structure carrying 376.96 scFv sequence, CD8 hinge and transmembrane domain, 4-1BB and CD3ζ intracellular domains. Additionally, CD276 rapidly-manufactured CAR-T (named CD276 Dash CAR-T) was innovatively developed by shortening the duration of ex vitro culture to reduce CAR-T manufacturing time. We evaluated the anti-tumor efficacy of CD276 CAR-T and further compared the functional assessment of Dash CAR-T and conventional CAR-T in vitro and in vivo by detecting the immunophenotypes, killing ability, expansion capacity and tumor-eradicatingeffect of CAR-T. We found that CD276 was strongly expressed in multiple solid cancer cell lines and that CD276 CAR-T could efficiently kill these solid cancer cells. Moreover, Dash CAR-T was successfully manufactured within 48-72h and the functional validation was carried out subsequently. In vitro, CD276 Dash CAR-T possessed a less-differentiated phenotype and robust proliferative ability compared to conventional CAR-T. In vivo xenograft mouse model, CD276 Dash CAR-T showed enhanced anti-pancreatic cancer efficacy and T cell expansion. Besides, except for the high-dose group, the body weight of mice was maintained stable, and the state of mice was normal. In this study, we proved CD276 CAR-T exhibited powerful activity against pancreatic cancer cells in vitro and in vivo. More importantly, we demonstrated the manufacturing feasibility, acceptable safety and superior anti-tumor efficacy of CD276 Dash CAR-T generated with reduced time. The results of the above studies indicated that CD276 Dash CAR-T immunotherapy might be a novel and promising strategy for pancreatic cancer treatment.

Similar genetic profile in early and late stage urothelial tract cancer.

Urothelial tract cancer (UTC) ranks as the tenth most prevalent cancer and holds the seventh position in terms of mortality worldwide. Despite its prevalence and mortality ranking, there are still gaps in the knowledge of the mutational landscape in patients with advanced disease who have limited therapeutic options after multiple lines of prior treatment. This study compares the genomic and transcriptomic landscape, and targeted treatment options between metastatic UTC (mUTC) patients treated with multiple lines of therapy compared to newly diagnosed, untreated Muscle Invasive Bladder Cancer (MIBC). We compared genomic and clinical data from two cohorts: mUTC patients who received multiple lines of therapy and were referred to the Copenhagen Prospective Personalized Oncology (CoPPO) project at Rigshospitalet, University of Copenhagen. Data for MIBC UTC patients were acquired from the Cancer Genome Atlas Bladder Cancer (TCGA BLCA) cohort. Biopsies in CoPPO were performed at the time of enrollment. 523 highly important cancer-related genes (TrueSight Oncology-500 targeted sequencing panel) were used from both cohorts for comparative analysis. Analyses included RNA count data to compare predicted molecular subtypes in each cohort separately. Patients from the CoPPO cohort had a lower median age at first-line treatment than the TCGA BLCA cohort, with no significant gender disparity. The predominant histology was urothelial cell carcinoma in both cohorts. Genomic analysis revealed no significant difference between the top mutated genes in the two cohorts, specifically looking into DNA damage repair genes. Molecular subtyping indicated a higher frequency of neuroendocrine differentiation in the CoPPO cohort. 13% of patients in the CoPPO cohort received targeted therapy based on genomic findings, and 16% received non-targeted treatment, totaling 29% receiving CoPPO treatment (9 patients). The remaining 71% received best supportive care. Kaplan-Meier analysis showed a non-significant survival benefit for the intervention group in the CoPPO cohort. When focusing on 523 highly relevant cancer genes, the mutational profile of mUTC patients who have undergone numerous treatment lines resembles that of newly diagnosed MIBC. These alterations can be targeted, indicating the potential advantage of early genomic testing for personalized treatment within clinical trials.

HIF-1 Transcriptionally Regulates Basal Expression of STING to Maintain Cellular Innate Immunity.

Stimulator of IFN genes (STING) is a critical component of the innate immune system, playing an essential role in defending against DNA virus infections. However, the mechanisms governing basal STING regulation remain poorly understood. In this study, we demonstrate that the basal level of STING is critically maintained by hypoxia-inducible factor 1 (HIF-1)α through transcription. Under normal conditions, HIF-1α binds constitutively to the promoter region of STING, actively promoting its transcription. Knocking down HIF-1α results in a decrease in STING expression in multiple cell lines and zebrafish, which in turn reduces cellular responses to synthetic dsDNAs, including cell signaling and IFN production. Moreover, this decrease in STING levels leads to an increase in cellular susceptibility to DNA viruses HSV-1 and pseudorabies virus. These findings unveil a (to our knowledge) novel role of HIF-1α in maintaining basal STING levels and provide valuable insights into STING-mediated antiviral activities and associated diseases.

Oncogenic dependency on SWI/SNF chromatin remodeling factors in T-cell acute lymphoblastic leukemia.

T-cell acute lymphoblastic leukemia (T-ALL) is a hematological malignancy arising from immature thymocytes. Unlike well-known oncogenic transcription factors, such as NOTCH1 and MYC, the involvement of chromatin remodeling factors in T-ALL pathogenesis is poorly understood. Here, we provide compelling evidence on how SWI/SNF chromatin remodeling complex contributes to human T-ALL pathogenesis. Integrative analysis of transcriptomic and ATAC-Seq datasets revealed high expression of SMARCA4, one of the subunits of the SWI/SNF complex, in T-ALL patient samples and cell lines compared to normal T cells. Loss of SMARCA protein function resulted in apoptosis induction and growth inhibition in multiple T-ALL cell lines. ATAC-Seq analysis revealed a massive reduction in chromatin accessibility across the genome after the loss of SMARCA protein function. RUNX1 interacts with SMARCA4 protein and co-occupies the same genomic regions. Importantly, the NOTCH1-MYC pathway was primarily affected when SMARCA protein function was impaired, implicating SWI/SNF as a novel therapeutic target.

Xyloglucan side chains enable polysaccharide secretion to the plant cell wall.

Plant cell walls are essential for growth. The cell wall hemicellulose xyloglucan (XyG) is produced in the Golgi apparatus before secretion. Loss of the Arabidopsis galactosyltransferase MURUS3 (MUR3) decreases XyG d-galactose side chains and causes intracellular aggregations and dwarfism. It is unknown how changing XyG synthesis can broadly impact organelle organization and growth. We show that intracellular aggregations are not unique to mur3 and are found in multiple mutant lines with reduced XyG D-galactose side chains. mur3 aggregations disrupt subcellular trafficking and induce formation of intracellular cell-wall-like fragments. Addition of d-galacturonic acid onto XyG can restore growth and prevent mur3 aggregations. These results indicate that the presence, but not the composition, of XyG side chains is essential, likely by ensuring XyG solubility. Our results suggest that XyG polysaccharides are synthesized in a highly substituted form for efficient secretion and then later modified by cell-wall-localized enzymes to fine-tune cell wall properties.

P-550 Monoallelic CCNB2 variants may cause oocyte maturation defects and embryo developmental arrest

Abstract Study question Have all the genes that may cause embryo development arrest and oocyte maturation defects been identified in female patients? Summary answer We identified a variant in CCNB2 in our patient. To our knowledge, this is first time that meiotic arrest can be caused by mutated-CCNB2. What is known already Successful reproduction involves the maturation of gametes, fertilization, and early development of the embryo. Oocyte maturation involves a sequence of both morphological and molecular transformations, progressing from germinal vesicle oocytes to metaphase I oocytes and ultimately to metaphase II oocytes. Any disruption in the process of oocyte maturation can result in infertility. With the widespread use of whole exome sequencing (WES), several genes that influence oocyte maturation at different stages have been recently identified. Study design, size, duration We here report the case of repeated ART failure due to oocyte maturation defect and embryo developmental arrest. Participants/materials, setting, methods A 30-year-old female and 38-year-old male applied to our clinic due to unexplained infertility for 4 years. The first ART attempt resulted in 2 of 13 oocytes with late MII. During ART performed in our center, germinal vesicle and meiotic arrest were observed in all oocytes. No mature oocytes were obtained. Her grandfather’s sister was also infertile. WES and Sanger analysis were performed to detect any mutation in known/candidate genes and show familial segregation Main results and the role of chance WES analysis revealed no mutation in genes that were previously reported as a cause of oocyte maturation defect or early embryo development in human. We do a further analysis of genes highly or specifically expressed in oocytes or expressed at low levels yet previous studies have suggested its role in embryo development. We identified a c.787C>T, p.Arg263* heterozygous nonsense variant in the CCNB2 gene that was extremely rare in both multiple databases and our in-house database. Multiple lines of computational evidence support the deleterious effect of the variant on the gene product. This variant was transmitted from her healthy father. CCNNB2 is not expressed in any cells other than oocytes in human. The activity of the M phase-promoting factor (MPF) is crucial for advancing through both mitosis and meiosis. CCNB2 plays a vital role by contributing to the activity of pre-MPF during prophase, necessary for generating enough MPF to proceed through maturation. Furthermore, CCNB2 is significantly involved in mouse oocyte meiosis, playing a key role in both the G2/M and MI/anaphase I transitions. Limitations, reasons for caution New disease-causing variants in this gene should be demonstrated in larger cohorts with female infertility. In addition, further functional studies should be carried out both in CCNB2-mutated human and animals. Wider implications of the findings This study may provide a better understanding background of female infertility and the failure of the ART process. CCNB2 may have a crucial role in the oocyte maturation process and can be utilized as a female infertility genetic marker. Trial registration number NA

The Next Generation Deep Extragalactic Exploratory Public Near-infrared Slitless Survey Epoch 1 (NGDEEP-NISS1): Extragalactic Star-formation and Active Galactic Nuclei at 0.5 < z < 3.6

The Next Generation Deep Extragalactic Exploratory Public (NGDEEP) survey program was designed specifically to include Near Infrared Slitless Spectroscopic observations (NGDEEP-NISS) to detect multiple emission lines in as many galaxies as possible and across a wide redshift range using the Near Infrared Imager and Slitless Spectrograph. We present early results obtained from the first set of observations (Epoch 1, 50% of the allocated orbits) of this program (NGDEEP-NISS1). Using a set of independently developed calibration files designed to deal with a complex combination of overlapping spectra, multiple position angles, and multiple cross filters and grisms, in conjunction with a robust and proven algorithm for quantifying contamination from overlapping dispersed spectra, NGDEEP-NISS1 has achieved a 3σ sensitivity limit of 2 × 10−18 erg s−1 cm−2. We demonstrate the power of deep wide field slitless spectroscopy (WFSS) to characterize the star formation rates, and metallicity ([O iii]/Hβ), and dust content, of galaxies at 1 < z < 3.5. The latter showing intriguing initial results on the applicability and assumptions made regarding the use of Case B recombination. Further, we identify the presence of active galactic nuclei and infer the mass of their supermassive black holes using broadened restframe Mg ii and Hβ emission lines. The spectroscopic results are then compared with the physical properties of galaxies extrapolated from fitting spectral energy distribution models to photometry alone. The results clearly demonstrate the unique power and efficiency of WFSS at near-infrared wavelengths over other methods to determine the properties of galaxies across a broad range of redshifts.

Feeder-free culture of human pluripotent stem cells drives MDM4-mediated gain of chromosome 1q.

Culture-acquired variants in human pluripotent stem cells (hPSCs) hinder their applications in research and clinic. However, the mechanisms that underpin selection of variants remain unclear. Here, through analysis of comprehensive karyotyping datasets from over 23,000 hPSC cultures of more than 1,500 lines, we explored how culture conditions shape variant selection. Strikingly, we identified an association of chromosome 1q gains with feeder-free cultures and noted a rise in its prevalence in recent years, coinciding with increased usage of feeder-free regimens. Competition experiments of multiple isogenic lines with and without a chromosome 1q gain confirmed that 1q variants have an advantage in feeder-free (E8/vitronectin), but not feeder-based, culture. Mechanistically, we show that overexpression of MDM4, located on chromosome 1q, drives variants' advantage in E8/vitronectin by alleviating genome damage-induced apoptosis, which is lower in feeder-based conditions. Our study explains condition-dependent patterns of hPSC aberrations and offers insights into the mechanisms of variant selection.

Episodic-like memory in wild free-living blue tits and great tits.

Episodic-like memory in non-human animals represents the behavioral characteristics of human episodic memory-the ability to mentally travel backward in time to "re-live" past experiences. A focus on traditional model species of episodic-like memory may overlook taxa possessing this cognitive ability and consequently its evolution across species. Experiments conducted in the wild have the potential to broaden the scope of episodic-like memory research under the natural conditions in which they evolved. We combine two distinct yet complementary episodic-like memory tasks (the what-where-when memory and incidental encoding paradigms), each targeting a different aspect of human episodic memory, namely the content (what-where-when) and process (incidental encoding), to comprehensively test the memory abilities of wild, free-living, non-caching blue tits (Cyanistes caeruleus) and great tits (Parus major). Automated feeders with custom-built programs allowed for experimental manipulation of spatiotemporal experiences on an individual-level basis. In the what-where-when memory experiment, after learning individualized temporal feeder rules, the birds demonstrated their ability to recall the "what" (food type), "where" (feeder location), and "when" (time since their initial visit of the day) of previous foraging experiences. In the incidental encoding experiment, the birds showed that they were able to encode and recall incidental spatial information regarding previous foraging experiences ("where" test), and juveniles, but not adults, were also able to recall incidentally encoded visual information ("which" test). Consequently, this study presents multiple lines of converging evidence for episodic-like memory in a wild population of generalist foragers, suggesting that episodic-like memory may be more taxonomically widespread than previously assumed.

Synthesis, biological evaluation, and molecular docking of novel 1,3,4-substituted-thiadiazole derivatives as potential anticancer agent

In an attempt to develop potent anti-cancer agents, a new 1,3,4-substituted-thiadiazole derivatives (8b-g), starting from 4-substituted-thiazol-2-chloroacetamides (4b-g), were synthesized and evaluated for their cytotoxic effects on multiple human cancer cell lines, including the hepatocellular carcinoma (HEPG-2), human lung carcinoma (A549), human breast carcinoma (MCF-7) and pseudo-normal human embryonic liver (L02) cancer cell lines by an MTT assay. Among all synthesized compounds, compound 8d showed the potent anti-cancer activities with GI50 values of 2.98, 2.85 and 2.53 μM against MCF-7, A549 and HepG-2 cell lines respectively as compared to standard drug Doxorubicin. Furthermore, molecular modelling studies have spotlighted the anchoring role of 1,3,4-substituted-thiadiazole moiety in bonding and hydrophobic interaction with the key amino acid residues. Therefore, these results can provide promising starting points for further development of best anti-cancer agents.Graphical

BatFix: Repairing language model-based transpilation

To keep up with changes in requirements, frameworks, and coding practices, software organizations might need to migrate code from one language to another. Source-to-source migration, or transpilation, is often a complex, manual process. Transpilation requires expertise both in the source and target language, making it highly laborious and costly. Languages models for code generation and transpilation are becoming increasingly popular. However, despite capturing code-structure well, code generated by language models is often spurious and contains subtle problems. We propose BatFix , a novel approach that augments language models for transpilation by leveraging program repair and synthesis to fix the code generated by these models. BatFix takes as input both the original program, the target program generated by the machine translation model, and a set of test cases and outputs a repaired program that passes all test cases. Experimental results show that our approach is agnostic to language models and programming languages. BatFix can locate bugs spawning multiple lines and synthesize patches for syntax and semantic bugs for programs migrated from Java to C++ and Python to C++ from multiple language models, including, OpenAI’s Codex .

A comparative analysis of several multivariate zero-inflated and zero-modified models with applications in insurance

. Given that insurance companies often operate across multiple lines of insurance business, where claim frequencies on different lines are often correlated, it often becomes advantageous to employ multivariate count modeling where dependence between lines of business can be included in the modeling. Due to the operation of bonus-malus systems where there is a reward to the insurance policyholder for not claiming, claims data in automobile insurance often exhibits an excess of common zeros, a characteristic known as multivariate zero-inflation. In this article, we propose two approaches to address this feature. The first approach involves utilizing a multivariate zero-inflated model, where we artificially enhance the probability of common zeros based on standard multivariate count distributions. The second approach applies a multivariate zero-modified model, which separately handles the common zeros and the number of claims incurred in each line given that at least one claim occurs. We present several models under these frameworks, along with detailed inference procedures. In the applications section, we conduct a comprehensive comparative analysis of these models using data from an automobile insurance portfolio.

Treatment Outcomes in Advanced Biliary Tract Cancers: Single Institution Retrospective Analysis

Abstract Purpose Biliary tract cancers (BTCs), particularly gallbladder cancers (GBCs), are prevalent in India. Yet there are limited data on treatment outcomes. To bridge this gap, we performed an analysis of advanced BTC treatment outcomes at our institute, seeking to offer insights into real-world scenario. Materials and Methods This is a retrospective study comprising advanced BTC patients treated at our institute from January 2015 to March 2023. We assessed demographics, treatment approaches, progression-free survival (PFS), overall survival (OS), and associated toxicities. Results Of the 411 patients analyzed, the majority were GBC (67.3%, n = 277), while the rest were cholangiocarcinoma (CCA) (32.6%, n = 134). The median age of study population was 56 years. Palliative chemotherapy was administered in 85% (n = 349) of all patients. Gemcitabine–cisplatin doublet was the most commonly used chemotherapy regimen (80.2%, n = 280). Platinum doublets yielded higher response rates compared with single-agent/nonplatinum chemotherapy (60 vs. 30%, n = 133). The median PFS was 4 months. The median OS was 8 months with platinum doublets and 5 months with single-agent/nonplatinum chemotherapy (hazard ratio [HR]: 0.60, 95% confidence interval: [CI] 0.43–0.84, p = 0.0001). OS was no different based on the type of platinum agent used. Patients receiving multiple lines of treatment lived longer compared with those who received single line only (14 vs. 6 months, respectively, HR: 0.36, 95% CI: 0.28–0.45, p &lt; 0.0001). Significant prognostic factors for OS were treatment with chemotherapy, platinum doublets, platinum exposure in first line, and treatment beyond first line. Grade 3 or 4 adverse effects seen were anemia (13.9%, n = 36), vomiting (4.2%, n = 11), diarrhea (3.4%, n = 9), thrombocytopenia (3.4%, n = 9), and febrile neutropenia (3.1%, n = 8). Conclusion This analysis confirms that chemotherapy is beneficial for advanced BTC. Platinum-based doublets are more effective than single agents. There is no significant difference between cisplatin and oxaliplatin. Patients who received multiple lines of treatment had better OS.

Multiline study of the radial extent of SiO, CS, and SiS in asymptotic giant branch envelopes

Circumstellar envelopes around asymptotic giant branch (AGB) stars contain a rich diversity of molecules, whose spatial distribution is regulated by different chemical and physical processes. In the outer circumstellar layers, all molecules are efficiently destroyed due to interactions with interstellar ultraviolet photons. Here we aim to carry out a coherent and uniform characterization of the radial extent of three molecules (SiO, CS, and SiS) in envelopes around O- and C-rich AGB stars, and to study their dependence on mass-loss rate. To this end, we observed a reduced sample of seven M-type and seven C-type AGB envelopes in multiple lines of SiO, CS, and SiS with the Yebes\,40m and IRAM\,30m telescopes. The selected sources cover a wide range of mass-loss rates, from sim $ $M_ odot $ yr$^ $ to a few times 10$^ $ $M_ odot $ yr$^ $, and the observed lines cover a wide range of upper-level energies, from 2 K to 130 K. We carried out excitation and radiative transfer calculations over a wide parameter space in order to characterize the abundance and radial extent of each molecule. A $ analysis indicates that the abundance is usually well constrained while the radial extent is in some cases more difficult to constrain. Our results indicate that the radial extent of the molecules considered here increases with increasing envelope density, in agreement with previous observational findings. At high envelope densities of $ M /v_ infty $ $M_ odot $ yr$^ $ km$^ $ s, SiO, CS, and SiS show a similar radial extent, while at low envelope densities of $ M /v_ infty $ $M_ odot $ yr$^ $ km$^ $ s, differences in radial extent appear among the three molecules, in agreement with theoretical expectations based on destruction due to photodissociation. At low envelope densities, we find a sequence of increasing radial extent, SiS\,rightarrow \,CS\,rightarrow \,SiO. We also find a tentative dependence of the radial extent on the chemical type (O- or C-rich) of the star for SiO and CS. Interferometric observations and further investigation of the photodissociation of SiO, CS, and SiS should provide clarification of the situation in regards to the relative photodissociation radii of SiO, CS, and SiS in AGB envelopes and their dependence on envelope density and C/O ratio.

Autologous CD19- targeting CAR T cells in refractory juvenile dermatomyositis.

To report safety and efficacy of CD19-targeting CAR T cells in a child with refractory juvenile dermatomyositis (JDM). We describe the case of a 12-year-old Caucasian boy with severe, chronically active JDM, refractory to multiple immunosuppressive treatment lines, including B-cell depletion with rituximab. The patient received a single infusion of fresh, autologous, second-generation anti-CD19 CAR T-cell product (lentiviral vector) manufactured on the Prodigy device (1x106 CAR T cells/kg), after lymphodepletion with cyclophosphamide (1000 mg/m2 over 2 days) and fludarabine (90 mg/m2 over 3 days). Immunosuppressive and glucocorticoid treatment were withdrawn before leukapheresis and CAR T-cell infusion. Before anti-CD19 CAR T-cell therapy, the patient had persistent severe skin and muscular disease activity. CAR T cells expanded significantly (peak at day 7, 32.69 cells/μL). Complete B-cell depletion was documented on day 5 in blood and at week 2 in bone marrow. The patient presented fever as part of mild cytokine release syndrome (G1), transient anemia (G2) and neutropenia (G4). Neither infection nor neurotoxicity were observed. Laboratory tests, MRI imaging, Physician's Global Assessment of disease activity (PGA), Childhood Myositis Assessment Scale (CMAS) and Cutaneous Assessment Tool for myositis (CAT) were performed at baseline and follow-up to assess treatment response, showing remarkable progressive improvement that persists over time, even after B-cell recovery. This JDM patient with severe chronic disease, refractory to multiple treatments, achieved sustained B-cell depletion and ongoing immunosuppressive drug-free clinical and radiological improvement eight months after a single infusion of anti-CD19 CAR T cells.

A novel analysis of contamination in Lyman-break galaxy samples at z ∼ 6-8: spatial correlation with intermediate-redshift galaxies at z ∼ 1.3-2

ABSTRACT Potential contamination from low/intermediate-redshift galaxies, such as objects with a prominent Balmer break, affects the photometric selection of high-redshift galaxies through identification of a Lyman break. Traditionally, contamination is estimated from spectroscopic follow-up and/or simulations. Here, we introduce a novel approach to estimating contamination for Lyman-break galaxy (LBG) samples based on measuring spatial correlation with the parent population of lower redshift interlopers. We propose two conceptual approaches applicable to different survey strategies: a single large contiguous field and a survey consisting of multiple independent lines of sight. For a large single field, we compute the cross-correlation function between galaxies at redshift $z \sim 6$ and intermediate-redshift galaxies at $z \sim 1.3$. We apply the method to the CANDELS GOODS-S and XDF surveys and compare the measurement with simulated mock observations, finding that the contamination level in both cases is not measurable and lies below 5.5 per cent (at 90 per cent confidence). For random-pointing multiple field surveys, we measure instead the number count correlation between high-redshift galaxies and interlopers, as a two-point correlation analysis is not generally feasible. We show an application to the LBG samples at redshift $z \sim 8$ and the possible interloper population at $z \sim 2$ in the Brightest of Reionizing Galaxies (BoRG) survey. By comparing the Pearson correlation coefficient with the result from Monte Carlo simulations, we estimate a contamination fraction of $62^{+13}_{-39} \, \mathrm{ per}\, \mathrm{ cent}$, consistent with previous estimates in the literature. These results validate the proposed approach and demonstrate its utility as an independent check of contamination in photometrically selected samples of high-redshift galaxies.

Identify Regulatory eQTLs by Multiome Sequencing in Prostate Single Cells.

While genome-wide association studies and expression quantitative trait loci (eQTL) analysis have made significant progress in identifying noncoding variants associated with prostate cancer risk and bulk tissue transcriptome changes, the regulatory effect of these genetic elements on gene expression remains largely unknown. Recent developments in single-cell sequencing have made it possible to perform ATAC-seq and RNA-seq profiling simultaneously to capture functional associations between chromatin accessibility and gene expression. In this study, we tested our hypothesis that this multiome single-cell approach allows for mapping regulatory elements and their target genes at prostate cancer risk loci. We applied a 10X Multiome ATAC + Gene Expression platform to encapsulate Tn5 transposase-tagged nuclei from multiple prostate cell lines for a total of 65,501 high quality single cells from RWPE1, RWPE2, PrEC, BPH1, DU145, PC3, 22Rv1 and LNCaP cell lines. To address data sparsity commonly seen in the single-cell sequencing, we performed targeted sequencing to enrich sequencing data at prostate cancer risk loci involving 2,730 candidate germline variants and 273 associated genes. Although not increasing the number of captured cells, the targeted multiome data did improve eQTL gene expression abundance by about 20% and chromatin accessibility abundance by about 5%. Based on this multiomic profiling, we further associated RNA expression alterations with chromatin accessibility of germline variants at single cell levels. Cross validation analysis showed high overlaps between the multiome associations and the bulk eQTL findings from GTEx prostate cohort. We found that about 20% of GTEx eQTLs were covered within the significant multiome associations (p-value ≤ 0.05, gene abundance percentage ≥ 5%), and roughly 10% of the multiome associations could be identified by significant GTEx eQTLs. We also analyzed accessible regions with available heterozygous SNP reads and observed more frequent association in genomic regions with allelically accessible variants (p = 0.0055). Among these findings were previously reported regulatory variants including rs60464856-RUVBL1 (multiome p-value = 0.0099 in BPH1) and rs7247241-SPINT2 (multiome p-value = 0.0002- 0.0004 in 22Rv1). We also functionally validated a new regulatory SNP and its target gene rs2474694-VPS53 (multiome p-value = 0.00956 in BPH1 and 0.00625 in DU145) by reporter assay and SILAC proteomics sequencing. Taken together, our data demonstrated the feasibility of the multiome single-cell approach for identifying regulatory SNPs and their regulated genes.

DIPG-85. MALT1 IN H3K27-ALTERED DIFFUSE MIDLINE GLIOMA

Abstract BACKGROUND H3K27-altered diffuse midline glioma (DMG) is a devastating pediatric brainstem tumor that affects 200-300 individuals in the US per year. Median survival is 9-11 months, and there are virtually no long-term survivors. Despite decades of clinical trials, radiation therapy remains standard of care, extending survival by 2-3 months. Elucidating the mechanisms that drive H3K27-altered DMG pathogenesis in order to uncover therapeutic vulnerabilities is of critical importance. Recent studies implicate MALT1 as a potential therapeutic target in gliomas. MALT1 is the effector molecule of the CARMA-BCL10-MALT1 (CBM) signalosome, a cytoplasmic protein complex that drives downstream pro-survival transcriptional activity. MALT1, which possesses scaffolding and protease functions, promotes cell viability, proliferation, and migration/invasion in multiple cancer types. We aim to evaluate the hypotheses that MALT1 promotes DMG cancer cell proliferation and migration and that MALT1 inhibition will abrogate tumor progression. METHODS/RESULTS We screened a panel of cells including astrocytes, neural stem cells, and DMG cell lines by Western blot and found that CBM complex members BCL10 and MALT1 are present in all cells tested. We next demonstrated that MALT1 is proteolytically active in DMG cell lines SF8628 and HSJD-DIPG-007. Specifically, we showed cleavage of the MALT1 protease substrate HOIL, which was abrogated by treatment with the MALT1 protease inhibitor MLT-748. We next generated multiple dox-inducible MALT1 shRNA DMG cell lines to assess the impact of MALT1 deficiency on DMG biology. Thus far, we find that shRNA knockdown of MALT1 does not impact SF8628 cell proliferation. CONCLUSIONS MALT1 is expressed and proteolytically active in DMG cells. Initial studies show that MALT1 knockdown does not affect proliferation of SF8628 cells. We will next evaluate the effect of MALT1 knockdown on proliferation of additional DMG cell lines, as well as the impact on other malignant features of DMG cells including migration/invasion.

ATG10S promotes IFNL1 expression and autophagic degradation of multiple viral proteins mediated by IFNL1

ABSTRACT ATG10S is a newly discovered subtype of the autophagy protein ATG10. It promotes complete macroautophagy/autophagy, degrades multiple viral proteins, and increases the expression of type III interferons. Here, we aimed to investigate the mechanism of ATG10S cooperation with IFNL1 to degrade viral proteins from different viruses. Using western blot, immunoprecipitation (IP), tandem sensor RFP-GFP-LC3B and in situ proximity ligation assays, we showed that exogenous recombinant ATG10S protein (rHsATG10S) could enter into cells through clathrin, and ATG10S combined with ATG7 with IFNL1 assistance to facilitate ATG12–ATG5 conjugation, thereby contributing to the autophagosome formation in multiple cell lines containing different virions or viral proteins. The results of DNA IP and luciferase assays also showed that ATG10S was able to directly bind to a core motif (CAAGGG) within a binding site of transcription factor ZNF460 on the IFNL1 promoter, by which IFNL1 transcription was activated. These results clarified that ATG10S promoted autophagosome formation with the assistance of IFNL1 to ensure autophagy flux and autophagic degradation of multiple viral proteins and that ATG10S could also act as a novel transcription factor to promote IFNL1 gene expression. Importantly, this study further explored the antiviral mechanism of ATG10S interaction with type III interferon and provided a theoretical basis for the development of ATG10S into a new broad-spectrum antiviral protein drug. Abbreviation: ATG: autophagy related; ATG10S: the shorter isoform of autophagy-related 10; CC50: half cytotoxicity concentration; CCV: clathrin-coated transport vesicle; CLTC: clathrin heavy chain; CM: core motif; co-IP: co-immunoprecipitation; CPZ: chlorpromazine; ER: endoplasmic reticulum; HCV: hepatitis C virus; HBV: hepatitis B virus; HsCoV-OC43: Human coronavirus OC43; IFN: interferon; PLA: proximity ligation assay; rHsATG10S: recombinant human ATG10S protein; RLU: relative light unit; SQSTM1: sequestosome 1; ZNF: zinc finger protein