title: Co-cultivation induces elicitation of unique Fungus-derived Natural products that leads to thiol stress mediated killing of Mycobacterium tuberculosis [F50]

city: Rockville

first: Helena

last: Boshoff

address: 12441 Parklawn Drive

department: LIG

institute: NIAID/ NIH

summary: Tuberculosis, caused by Mycobacterium tuberculosis has remained a leading cause of death worldwide even after decades of it being declared as global health emergency by the WHO. Newer drugs with novel modes of action are urgently needed to combat the threats imposed by the constantly emerging drug resistant strains. Natural products (NPs) derived anti-mycobacterials appear lucrative because of their complex structural features and unique cellular targets they bind to. Herein, we employed co-cultivation approach to identify cryptic biosynthetic gene clusters (BGCs) from fungal genomes eliciting the expression of genes that are silent or poorly transcribed in axenic cultures. Fungi were isolated from sphagnum peat bog samples collected from different regions of North-eastern USA because aspects of this ecological niche reflect the critical microenvironment of the human tuberculosis granuloma and are a natural habitat for slow growing mycobacterial species that compete for limited nutrients with other microbes. Bioactivity-guided assay led us to identify three unique fungal isolates that selectively produce growth inhibitory metabolites during co-cultivation with Mtb. Fungal mRNA sequencing from co-cultured isolates facilitated the identification of elicited Type I Polyketide Synthase BGCs that were silent/cryptic in monoculture conditions. Bioinformatic analyses followed by chemical validation identified these molecules to be patulin, citrinin and nidulalin A. Interestingly, these induced fungal metabolites led to a highly responsive redox-stress homeostasis within Mtb. Our study thus, illustrates a co-cultivation mediated elicitation of unique fungal NPs resulting in a thiol-burst oxidative stress mediated killing of Mtb. We believe that the identification of vulnerable drug targets may yield insights into further understanding of this essential thiol stress mediated killing of the mycobacteria

overall_design: In an effort to identify the intrinsic ability of microorganisms to produce prolific, highly specific and active small molecules against Mtb, we focused on utilizing the co-cultivation approach to identify cryptic BGCs from fungal genomes eliciting the expression of genes that are silent or poorly transcribed in axenic cultures. Fungi were isolated from sphagnum peat bog samples collected from different regions of North-eastern USA and were screened using co-cultivation based approach for their specific anti-Mtb activity induced upon co-cultivation with Mtb as assessed by performing growth inhibition of reprter strain of Mtb using cell free media from mono and co-cultures. Unique fungi obtained in our study F2, F50, F51, C7 and F31 were taken forward for RNA seq to identify the differentially expressed gene clusters responsible for producing anti-Mtb metabolites in cocultivation conditions. Fungal spores were grown in PDB media for 24h following which they were either treated with phosphate buffer or Mtb. The mono- and co-cultures were incubated for different day points at 32'C. Mycelia was then harvested, ground by mortar pestle in Liquid N2 and the ground mycelia was used for Total RNA extraction. mRNA was then extracted from Total RNA following rRNA depletion method

first: Neha

last: Malhotra

first: Clifton

middle: E

last: Barry 3rd


title: Co-cultivation induces elicitation of unique Fungus-derived Natural products that leads to thiol stress mediated killing of Mycobacterium tuberculosis [F22]

status: Public on Oct 15 2024

middle: I

state: MD

country: USA

type: Expression profiling by high throughput sequencing


title: Co-cultivation induces elicitation of unique Fungus-derived Natural products that leads to thiol stress mediated killing of Mycobacterium tuberculosis [Fun31]


title: Co-cultivation induces elicitation of unique Fungus-derived Natural products that leads to thiol stress mediated killing of Mycobacterium tuberculosis [C7]


title: Systematic phenotyping of the neomorphic Fgf9Y162C mutant mouse

status: Public on Dec 01 2024

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary: The novel neomorphic Fgf9Y162C mouse mutant was recently reported to cause small lenses and later on cataracts. Since Fgf9 is expressed also in other tissues and organs, we performed a systematic and comprehensive phenotyping of the heterozygous and homozygous mutants in the German Mouse Clinic. We did not observe any effect on dysmorphological parameters, on bone & cartilage, and no neurological effects (including pain). However, we observed an improved glucose tolerance in both sexes, but reduced lactate levels in homozygous males, and increased corticosterone levels in female mutants. Analysis of the blood count revealed more white blood cells, a higher frequency of T-cells in homozygous male mutants and an increased concentration of IgE in female mutants indicating that the immune system including the allergy state is affected at least in one sex. The Fgf9Y162C mutants showed also a significantly smaller total lung capacity, which might be due of non-significant changes in inspiratory capacity and functional residual capacity. Finally, we observed a decreased locomotion of the mutants combined with a decreased ability for social discrimination. These different phenotypes are interpreted as pleiotropic consequences of the mutation in those tissues where Fgf9 is expressed. In addition, transcriptome profiling of lenses from 18 week old homozygote mice revealed changes on molecular level associated with phototransduction and ophthalmic diseases.

overall_design: Total RNA obtained from lens of 3 homozygous Fgf9y162C and 3 wildtype mice

first: Johannes

last: Beckers

first: Marion

last: Horsch


title: Effect of Penicillium chrysogenum, Penicillium minioluteum, and Serendipita indica on gene expression in Solanum lycopersicum plants under control and drought stress conditions

status: Public on Oct 18 2024

city: Pozuelo de Alarcón

first: Stephan

last: Pollmann

state: Madrid

address: Campus de Montegancedo, Autovía M-40 (km 38)

department: Centro de Biotecnología y Genómica de Plantas

country: Spain

institute: Universidad Politécnica de Madrid

summary: Plants coexist in close proximity with numerous microorganisms in their rhizosphere. With certain microorganisms, plants establish mutualistic relationships that can confer physiological benefits to the interacting organisms, including enhanced nutrient assimilation or increased stress tolerance. The root-colonizing endophytic fungi Penicillium chrysogenum, Penicillium minioluteum, and Serendipita indica have been reported to enhance the drought stress tolerance of plants. However, to date, the molecular mechanisms triggered by these fungi in plants remain unexplored. This study presents a comparative analysis of the effects on mock- and fungus-infected tomato plants (var. Moneymaker) under drought stress conditions (40% field capacity) and control conditions (100% field capacity). The findings provide evidence for the induction of common response modules by the fungi.

overall_design: To investigate differential gene expression in tomato roots under drought stress (40FC) and control conditions (100FC) that were either mock-treated (Ctrl) or inoculated with Penicillium chrysogenum (Pchry), Penicillium miniolutem (Pmin), or Serendipita indica (Sind).


title: Early downmodulation of tumor glycolysis predicts response to fasting-mimicking diet in triple-negative breast cancer patients

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: In preclinical experiments, cyclic fasting-mimicking diets (FMDs) showed broad anticancer effects in combination with chemotherapy. Among different tumor types, triple-negative breast cancer (TNBC) is exquisitely sensitive to FMD. However, the antitumor activity and efficacy of cyclic FMD in TNBC patients remain unclear. Here, we show that a severely calorie-restricted, triweekly, 5-day FMD regimen results in excellent pathologic complete response (pCR) rates (primary endpoint) and long-term clinical outcomes (secondary endpoints) when combined with preoperative chemotherapy in 30 patients with early-stage TNBC enrolled in the phase II trial BREAKFAST. Bulk and single-cell RNA-sequencing analysis revealed that highly glycolytic cancer cells, myeloid cells and pericytes from tumors achieving pCR undergo a significant, early downmodulation of pathways related to glycolysis and pyruvate metabolism. Our findings pave the wave for conducting larger clinical trials to investigate the efficacy of cyclic FMD in early-stage TNBC patients, and to validate early changes of intratumor glycolysis as a predictor of clinical benefit from nutrient restriction. ClinicalTrials.gov Identifier: NCT04248998

overall_design: The BREAKFAST (clinicaltrial.gov registration code: NCT04248998) trial was a single center, open-label, two-arm, non-comparative, randomized phase II study that enrolled patients with treatment naïve, unilateral, localized (stage I-III, with clinical tumor diameter of at least 1 cm) invasive TNBC (negative HER2, ER, and PgR status according to American Society of Clinical Oncology/College of American Pathologists guidelines 52). The study was conducted at Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy. All TNBC pathological diagnoses were centrally reviewed by two expert pathologists. Eligible patients were women aged between 18 and 75 years with Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1, adequate hematological, renal, and hepatic function; a BMI equal to or higher than 20 kg/m2, and a LVEF of at least 50% at study enrollment. Patients were excluded if they had experienced significant, non-intentional weight loss during the 3 months before enrollment, if they had a diagnosis of type 1 or 2 diabetes mellitus requiring pharmacologic therapy, or if they had clinically relevant gastrointestinal diseases. Clinical T stage was defined by the longest tumor diameter measured by breast Magnetic Resonance Imaging (MRI) before the initiation of the neoadjuvant treatment. All patients enrolled in the BREAKFAST trial received preoperative chemotherapy, consisting of 4 triweekly cycles of intravenous doxorubicin (60 mg/m2) plus cyclophosphamide (600 mg/m2), followed by 12 cycles of weekly intravenous paclitaxel (80 mg/m2). For scRNA-seq analyses we collected fresh tumor samples at prespecified timepoints from 15 patients enrolled in the trial, finally obtaining scRNA-seq data from n=13 samples collected before treatment initiation (T0), n=11 samples collected after one treatment cycle (T1), and from n=5 samples collected at surgery (T2).

first: Francesca

last: Ligorio

first: Andrea

last: Vingiani

first: Tommaso

last: Torelli

first: Lucrezia

last: Zanenga

first: Caterina

last: Sposetti

first: Fabio

last: Iannelli

first: Lorenzo

last: Drufuca

first: Catherine

last: Depretto

first: Secondo

last: Folli

first: Gianfranco

last: Scaperrotta

first: Giuseppe

last: Capri

first: Giulia

middle: V

last: Bianchi

first: Cristina

last: Ferraris

first: Gabriele

last: Martelli

first: Ilaria

last: Maugeri

first: Leonardo

last: Provenzano

first: Federico

last: Nichetti

first: Riccardo

last: Lobefaro

first: Giovanni

last: Fucà

first: Luigi

last: Mariani

first: Daniele

last: Morelli

first: Maria

middle: C

last: De Santis

first: Laura

last: Lozza

first: Giovanna

last: Trecate

first: Antonino

last: Belfiore

first: Silvia

last: Brich

first: Alessia

last: Bertolotti

last: Lorenzini

first: Angela

last: Ficchì

first: Antonia

last: Martinetti

first: Elisa

last: Sottotetti

first: Alessio

last: Arata

first: Paola

last: Corsetto

last: Sorrentino

last: Salvadori

first: Saverio

last: Minucci

first: Marco

last: Foiani

last: Apolone

first: Massimiliano

last: Pagani

first: Giancarlo

last: Pruneri

first: Filippo

last: De Braud

first: Claudio

last: Vernieri


title: BMP suppresses Wnt signaling via the Bcl11b-regulated NuRD complex to maintain Lgr5+ intestinal stem cells

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

country: China

institute: Tsinghua University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Lgr5+ intestinal stem cells (ISCs) play crucial roles in maintenance of the intestinal epithelium renewal and regeneration after injury. The mechanism underlying the interplay between Wnt and BMP signaling is not fully understood. Here we report that Bcl11b, which is downregulated by BMP signaling, enhances Wnt signaling to maintain Lgr5+ ISCs and promote the regeneration of the intestinal epithelium following damage. Conditional inactivation of the Bcl11b gene leads to a significant decrease of Lgr5+ ISCs in both mouse intestinal crypts and cultured organoids. Mechanistically, BMP suppresses the expression of Bcl11b, which can positively regulate Wnt target genes by inhibiting the function of the Nucleosome Remodeling and Deacetylase (NuRD) complex and facilitating the β-catenin-TCF4 interaction. Bcl11b can also promote intestinal epithelium repair after injuries elicited by both irradiation and DSS-induced inflammation. Furthermore, Bcl11b deletion prevents proliferation and tumorigenesis of colorectal cancer cells. Together, our findings suggest that BMP balances Wnt signaling via Bcl11b to delicately regulate the homeostasis and regeneration of the intestinal epithelium.

overall_design: Intestinal stem cells DNA profiles of WT and Bcl11b KO mice.

first: Yuan

last: Liu

first: Xiaodan

last: Wang

first: Meimei

last: Huang


title: The evolution of expression divergence in wild C. elegans

status: Public on Oct 14 2024

city: Atlanta

first: Avery

middle: Davis

last: Bell

state: GA

address: North Avenue

department: School of Biological Sciences

institute: Georgia Institute of Technology

summary: To examine the ways in which gene expression varies in natural populations and its relationship to genetic divergence, we estimated allele-specific expression in the offspring of multiple wild C. elegans strains crossed with the laboratory reference strain N2. Allele-specific expression analyses are uniquely sensitively able to identify cis regulatory changes, and coupled with analyses of differential expression between parental strains and parents and offspring can determine the regulatory pattern and inheritance mode of gene expression across the genome. We chose 7 strains that represented a range of divergence from N2 and spanned the species tree to cross with N2: EG4348; DL238; CB4856 (the classical ‘Hawaiian’ strain); ECA722; QX1211; and ECA701 and XZ1516 (two extremely diverged strains). This study sheds light on the relationship of genetic and expression divergence, the global patterns of inheritance and regulatory mode of genes in C. elegans, and the factors that differentiate genes with expression divergence from those with stabler expression.

overall_design: We performed RNA-sequencing on experimentally matched young (day 1) adult Caenorhabditis elegans from multiple natural genetic backgrounds (wild strains) and their hybrid offspring. Specifically, we RNA sequenced  three replicates each of 7 wild C. elegans strains (EG4348, DL238, CB4856, ECA722, QX1211, ECA701, XZ1516), the laboratory reference strain N2, and the F1 offspring of crosses between each of the wild strain and N2.

last: Davis Bell

first: Francisco

last: Valencia

first: Annalise

middle: B

last: Paaby


title: Co-cultivation induces elicitation of unique Fungus-derived Natural products that leads to thiol stress mediated killing of Mycobacterium tuberculosis

first: Helena

last: Boshoff

overall_design: In an effort to identify the intrinsic ability of microorganisms to produce prolific, highly specific and active small molecules against Mtb, we focused on utilizing the co-cultivation approach to identify cryptic BGCs from fungal genomes eliciting the expression of genes that are silent or poorly transcribed in axenic cultures. Fungi were isolated from sphagnum peat bog samples collected from different regions of North-eastern USA because aspects of this ecological niche reflect the critical microenvironment of the human tuberculosis granuloma like acidic pH, hypoxic and nutrient poor conditions. In addition, sphagnum peat bogs are a natural habitat for slow growing mycobacterial species that compete for limited nutrients with other microbes. A co-culture screen was utilized to identify metabolites specific for killing Mtb. Differential gene expression followed by bioinformatics analyses led us to identify unique biosynthetic gene clusters in these fungi expressed upon co-cultivation. Chemical approaches further facilitated the identification of Type I polyketide synthase derived nidulalin A and patulin responsible for specific anti-Mtb activity. Global transcriptomic profile of Mtb exposed to either of the induced fungal products at different concentrations and time was performed to understand the mechanism of action of killing. Total RNA from Mtb  was isolated from Control  (untreated) and Treatment (with Patulin and Nidulalin A containing fungal filtrates) groups in triplicates and utilized for mRNA sequencing. Differential gene expression analyses between either conditions would facilitate our understanding of the Mtb pathways influenced by these fungus derived anti-mycobacterials.

first: Neha

last: Malhotra

first: Tovah

last: Markowitz

first: Clifton

last: Earl Barry 3rd


title: TLR4 signaling of LPS chemotypes

city: Bonn

first: Felicitas

last: Lauber

address: Gerhard-Domagk-Str. 3

department: Pharmaceutical Institute

institute: University of Bonn

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Gene expression changes in mouse breast cancer cells (EMT6) after anti-PD-L1 treatment

city: Buffalo

first: John

last: Ebos

state: NY

address: Elm & Carlton Streets

department: Department of Cancer Genetics and Genomics

institute: Roswell Park Cancer Institute

summary: RNA sequencing analysis was used to identify changes in mouse breast cancer (EMT6) following prolonged anti-PD-L1 in vitro (PDRvitro).

overall_design: Mouse breast cancer cells (EMT6) were treated with anti-PD-L1 or isotype control for >4 weeks in vitro at 0.5μg/ml before cells were collected for sequencing analysis.

first: Yuhao

last: Shi

middle: M


title: TLR4 signaling of LPS chemotypes in THP-1 macrophages.

summary: The discovery of Toll-like receptors (TLRs) represented a significant breakthrough that paved the way for the study of host-pathogen interactions in innate immunity. However, there are still major gaps in understanding TLR function, especially the early dynamics of downstream TLR pathways remains less clear. We characterize a label-free optical biosensor-based assay as a powerful method to detect TLR activation in a native and label-free environment and to delineate the dynamics of TLR pathway activation. To gain a deeper insight into the biological processes underlying the ligand-specific signal traces of different LPS chemotypes in various cell types, RNA-seq analysis of transcriptional changes in THP-1 macropahges was performed. After 3 hours of stimulation with LPS E. coli or LPS S. minnesota, THP-1 macrophages showed significant changes in RNA expression compared to the unstimulated control.

overall_design:
THP-1 macrophages were stimulated with LPS E. coli or LPS S. minnesota for 3 hours. Unstimulated cells served as control.
Gene expression profiling analysis was performed using data obtained from RNA-seq of two independent experiments.

first: Holze

last: Janine

first: Lauber

last: Felicitas

first: Weindl

last: Günther


title: Gene expression changes in mouse breast tumor tissue (EMT6) after anti-PD-L1 resistance

summary: RNA sequencing analysis was used to identify changes in mouse breast tumor tissues (EMT6) resistant to anti-PD-L1 (PDR).

overall_design: EMT6 mouse breast tumor cells were implanted 5 x 10^5 in Balb/c mice mammary fat pads on day 0. Continuous treatment with anti-mouse-PD-L1 or isotype control began on day 1 every 3 days until tumors reached institutional endpoint where primary and metastatic tumor tissues were collected for sequencing analysis.


title: Impact of mitochondrial citrate carrier expression on metabolism in the developing heart

status: Public on Oct 11 2024

first: Jennifer

middle: Q.

last: Kwong

address: 1750 Haygood Dr. NE N423

institute: Emory University School of Medicine

summary: Slc25a1 encodes for the mitochondrial citrate carrier, a mitochondrial inner membrane transporter that mediates mitochondrial citrate export.  Systemic deletion of Slc25a1 (both homozygous and heterozygous loss) leads to cardiac structural defects and mitochondrial dysfunction. Transcriptomic profiles of metabolic gene expression in the the developing mouse heart at E17.5 reveal alterations in metabolic pathways including oxdiative phosphorylation, supporting mitochondrial structural and functional defects observed with loss of this transporter.

overall_design: In this study embryonic mouse hearts were collected from timed matings of Slc25a1 heterozgyous knockout mice at E17.5. Hearts were collected from wild type (WT), Slc25a1 heterozygous knockout (HET) and Slc25a1 homozygous knockout (KO) embryos. Total RNA was extracted from each heart and analysed using the NanoString nCounter platform to examine the expression of metabolic genes. 3 groups: WT, HET and KO. 4 samples per group.

first: J

middle: Q


title: eQTL in diseased colon tissue identifies novel target genes associated with IBD

status: Public on Oct 16 2024

city: Chapel Hill

first: Terrence

last: Furey

state: NC

address: 120 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

summary: Genome-wide association studies (GWAS) have identified over 300 loci associated with the inflammatory bowel diseases (IBD), but putative causal genes for most are unknown. We conducted the largest disease-focused expression quantitative trait loci (eQTL) analysis using colon tissue from 252 IBD patients to determine genetic effects on gene expression and potential contribution to IBD. Combined with two non-IBD colon eQTL studies, we identified 194 potential target genes for 108 GWAS loci. eQTL in IBD tissue were enriched for IBD GWAS loci colocalizations, provided novel evidence for IBD-associated genes such as ABO and TNFRSF14, and identified additional target genes compared to non-IBD tissue eQTL. IBD-associated eQTL unique to diseased tissue had distinct regulatory and functional characteristics with increased effect sizes. Together, these highlight the importance of eQTL studies in diseased tissue for understanding functional consequences of genetic variants, and elucidating molecular mechanisms and regulation of key genes involved in IBD.

overall_design:
RNA-seq of colon tissue from IBD patients for eQTL mapping

***************************************************************
Submitter states that missing raw data are being made available for controlled access in dbGaP.
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middle: S

first: Shehzad

middle: Z

last: Sheikh

first: Nina

last: Nishiyama


title: Plant BCL-DOMAIN HOMOLOG proteins play a conserved role in SWI/SNF complex stability

status: Public on Oct 10 2024

city: Valencia

first: Jaime

last: Pérez

address: Calle del Ingeniero Fausto Elio, s/n

institute: IBMCP

summary: The SWItch/Sucrose Non-Fermenting (SWI/SNF) complexes are evolutionarily conserved, ATP-dependent chromatin remodelers crucial for multiple nuclear functions in eukaryotes. Recently, plant BCL-Domain Homolog (BDH) proteins were identified as shared subunits of all plant SWI/SNF complexes, significantly impacting chromatin accessibility and various developmental processes in Arabidopsis. In this study, we performed a comprehensive characterization of bdh mutants, revealing a previously overlooked impact on hypocotyl cell elongation. Through detailed analysis of BDH domains, we identified a plant-specific N-terminal domain that facilitates the interaction between BDH and the rest of the complex. Additionally, we uncovered the critical role of the BDH β-hairpin domain, which is phylogenetically related to metazoan BCL7 SWI/SNF subunits. While phylogenetic analyses did not identify BDH/BCL7 orthologs in fungi, structure prediction modeling demonstrated strong similarities between the SWI/SNF catalytic modules of plants, animals, and fungi, and revealed the yeast Rtt102 protein as a structural homolog of BDH and BCL7. This finding is supported by the ability of Rtt102 to interact with the Arabidopsis catalytic module subunit ARP7 and partially rescue the bdh mutant phenotypes. Further experiments revealed that BDH promotes the stability of the ARP4-ARP7 heterodimer, leading to the partial destabilization of ARP4 in the SWI/SNF complexes. In summary, our study unveils the molecular function of BDH proteins in plant SWI/SNF complexes and suggests that β-hairpin-containing proteins are evolutionarily conserved subunits crucial for ARP heterodimer stability and SWI/SNF activity across eukaryotes.

overall_design: We compared the expression profiles of wild type and bdh hypocotyls to investigate the molecular basis of the phenotypes that these mutants show when grown in darkness

first: Joan

last: Candela-Ferre

last: Pérez-Alemany

first: Borja

last: Diego-Martin

first: Vijaya

last: Pandey

first: James

last: Wohlschlegel

first: Jorge

last: Lozano-Juste

first: Javier

last: Gallego-Bartolomé


title: PTPN23-dependent ESCRT machinery functions as a cell death checkpoint in restraining multiple cell death pathways

city: Cold Spring Harbor

first: Nicholas

last: Tonks

state: New York

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

summary: Cell death plasticity is crucial for modulating tissue homeostasis and immune responses, but our understanding of the molecular components that regulate cell death pathways to determine cell fate remains limited. Here, a CRISPR screen of acute myeloid leukemia cells identifies protein tyrosine phosphatase non-receptor type 23 (PTPN23) as essential for survival. Loss of PTPN23 activates nuclear factor-kappa B, apoptotic, necroptotic, and pyroptotic pathways by causing the accumulation of death receptors and toll-like receptors (TLRs) in endosomes. These effects are recapitulated by depletion of PTPN23 co-dependent genes in the endosomal sorting complex required for transport (ESCRT) pathway. Through proximity-dependent biotin labeling, we show that NAK-associated protein 1 interacts with PTPN23 to facilitate endosomal sorting of tumor necrosis factor receptor 1 (TNFR1), sensitizing cells to TNF-alpha-induced cytotoxicity. Our findings reveal PTPN23-dependent ESCRT machinery as a cell death checkpoint that regulates the spatiotemporal distribution of death receptors and TLRs to restrain multiple cell death pathways.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NOMO-1 cells transfected with negative control sgRNA, or sgRNAs targeting PTPN23, UBAP1, HGS, USP8, TSG101, and CLTC.

first: Dongyan

last: Song

first: Xiaoli

last: Wu

first: Osama

last: Demerdash

middle: K


title: Progesterone increases metabolism via the pentose phosphate pathway in bovine uterine epithelial cells

status: Public on Oct 09 2024

city: Urbana

first: Camila

last: Braz

state: IL

address: 1207 W. Gregory Dr.

department: Animal Sciences

institute: University of Illinois Urbana-Champaign

summary: During early pregnancy, glucose is essential for the uterine epithelium and the developing embryo. In cows, studies have shown that progesterone increases the secretion of glucose into the uterine lumen. Nevertheless, how progesterone affects glucose metabolism in the uterine epithelium has been sparsely investigated. Therefore, our objective was to investigate how progesterone influences glucose metabolism in immortalized bovine uterine epithelial (BUTE) cells. Progesterone treatment (10 μM) increased glucose consumption. To gain a more global picture of the effects of progesterone, RNAseq was performed after BUTE cells were treated with vehicle (DMSO) or 10 μM for 24 hours. KEGG analysis indicated that progesterone altered genes associated with metabolic pathways and glutathione metabolism. Manually examining genes unique to specific glucose metabolic pathways identified an increase in the rate-limiting enzyme in the pentose phosphate pathway—glucose-6-phosphate dehydrogenase. Functionally, a major product of the pentose phosphate pathway is NADPH, and progesterone treatment increased NADPH concentrations in BUTE cells. In cows, immunohistochemistry confirmed that glucose-6-phosphate dehydrogenase levels were higher in the uterine epithelium in the luteal phase when progesterone concentrations are high. In conclusion, progesterone increased glucose-6-phosphate dehydrogenase expression and metabolism via the pentose phosphate pathway in the bovine uterine epithelium. This metabolism could provide substrates for cell proliferation, molecules to be secreted into the uterine lumen that supports embryonic development, or maintain reduction/oxidation balance in the uterine epithelium.

overall_design: We previously generated an immortalized bovine uterine epithelial (BUTE) cell line. Here BUTE cells were plated and allowed to grow until 80% confluent. Then the media was removed, rinsed twice with PBS, and the cells were serum and steroid starved in media without phenol red and treated with insulin-like growth factor 1 (IGF1) for 24 hours to stimulate glycogenesis. The media was removed and replaced with serum and steroid-free media containing 50 ng/ml of IGF1, vehicles (DMSO) or 10 μM progesterone for 24 hours.  Total RNA was extracted from BUTE cells using the Quick-RNA MiniPrep Plus Kit (Zymo Research) per the manufacturer’s instructions.

first: Malia

middle: D

last: Berg

first: Matthew

last: Dean


title: Co-cultivation induces elicitation of unique Fungus-derived Natural products that leads to thiol stress mediated killing of Mycobacterium tuberculosis [F51]

first: Helena

last: Boshoff

first: Neha

last: Malhotra

first: Clifton

last: Barry 3rd


title: mRNA ADENOSINE METHYLASE promotes drought tolerance through N6-methyladenosine-dependent and independent impacts on mRNA regulation in Arabidopsis

status: Public on Oct 07 2024

city: Philadelphia

first: Diep

middle: R

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

summary:
• Among many mRNA modifications, adenine methylation at the N6 position (N6-methyladenosine, m6A) is known to affect mRNA biology extensively. The influence of m6A has yet to be assessed under drought, one of the most impactful abiotic stresses.
• We show that Arabidopsis thaliana (L.) Heynh. (Arabidopsis) plants lacking mRNA ADENOSINE METHYLASE (MTA) are drought sensitive. Subsequently, we comprehensively assess the impacts of MTA-dependent m6A changes during drought on mRNA abundance, stability, and translation in Arabidopsis.
• During drought, there is a global trend towards hyper-methylation of many protein-coding transcripts that does not occur in mta. We also observe complex regulation of m6A at a transcript-specific level, possibly reflecting compensation by other m6A components. Importantly, a subset of transcripts that are hyper-methylated in an MTA-dependent manner exhibited reduced turnover and translation in mta, compared to wild-type plants, during drought. Additionally, MTA impacts transcript stability and translation independently of m6A. We also correlate drought-associated deposition of m6A with increased translation of modulators of drought response, such as RD29A, COR47, COR413, ALDH2B, ERD7, and ABF4 in WT, which is impaired in mta.
• m6A is dynamic during drought and, alongside MTA, promotes tolerance by regulating drought-responsive changes in transcript turnover and translation.

overall_design: Arabidopsis Col-0 (WT) and a line with embryo-specific expression of MTA (proABI3:MTA/mta) were exposed to a 12-day drought and leaf tissue was profiled with mRNA-seq, GMUCT, polysomal RNA-seq, and m6A-RIP-seq.

first: Yongfang

last: Li

first: Susheel

last: Bhat

first: Brian

last: Gregory

first: Ramanjulu

last: Sunkar


title: Inflammation Impacts Androgen Receptor Signaling in Basal Prostate Stem Cells Through Interleukin 1 Receptor Antagonist

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

summary: Chronic prostate inflammation in patients with benign prostate hyperplasia (BPH) correlates with the severity of symptoms. How inflammation contributes to prostate enlargement and/or BPH symptoms and the underlying mechanisms remain unclear. In this study, we utilized a unique transgenic mouse model that mimics chronic non-bacterial prostatitis in men and investigated the impact of inflammation on androgen receptor (AR) in basal prostate stem cells (bPSC) and their differentiation in vivo. We found that inflammation significantly enhanced AR levels and activity in bPSC. More importantly, we identified interleukin 1 receptor antagonist (IL-1RA) as a crucial regulator of AR in bPSC during inflammation. IL-1RA was one of the top genes upregulated by inflammation, and inhibiting IL-1RA reversed the enhanced AR activity in organoids derived from inflamed bPSC. Additionally, IL-1RA appeared to activate AR by counteracting IL-1's inhibitory effect. Furthermore, using a lineage tracing model, we observed that inflammation induced bPSC proliferation and differentiation into luminal cells even under castrate conditions, indicating that AR activation driven by inflammation is sufficient to promote bPSC proliferation and differentiation. Taken together, our study uncovered novel mechanisms through which inflammation modulates AR signaling in bPSC and induces bPSC luminal differentiation that may contribute to prostate hyperplasia.

overall_design: To compare the gene expression profiles between basal stem cells isolated from naïve or inflamed mouse prostates, cells were processed in batches and only batches 2 and 3 were used for this study.

first: Paula

middle: O

last: Cooper

first: Jiang

last: Yang

first: Hsing-Hui

last: Wang

first: Meaghan

last: Broman

first: Shyaman

last: Jayasundara

first: Subhransu

last: Sahoo

first: Bingyu

last: Yan

first: Gada

last: Awdalkreem

first: Gregory

last: Cresswell

first: Liang

first: Emery

last: Goossens

middle: A

last: Lanman

first: Rebecca

middle: W

last: Doerge

first: Faye

last: Zheng

last: Cheng

first: Saeed

last: Alqahtani

first: Scott

last: Crist

first: Robert

last: Braun

first: Majid

last: Kazemian

first: Travis

middle: J

last: Jerde

first: Timothy

middle: L

last: Ratliff


title: Single nuclei gene expression profile of brain cells from Pdgfbret/ret and Pdgfbret/wt mice

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: Brain calcification, the ectopic mineral deposits of calcium phosphate, is a common radiological finding in elderly and in various neurodegenerative disorders and a diagnostic criterion for primary familial brain calcification (PFBC). We made use of single nuclei RNA sequencing to understand the effect of calcification pathology in the  Pdgfb (ret/ret) model of PFBC. Calcifications are located in deep brain regions - hypothalamus, thalamus, mid brain, pons of Pdgfb (ret/ret) mice and absent in control Pdgfb (ret/wt) mice. Forebrain cortex and hippocampus regions in both genotypes are calcification free. Detailed descriptions of the mouse model can be found in the following publications:

overall_design: Nuclei were isolated from frozen brain tissue from cortical (calcification free) and deep brain (calcification prone) regions.

first: Sucheta

last: Sridhar

first: Yingyue

last: Zhou

first: Adiljan

last: Ibrahim

first: Sergio

last: Bertazzo

first: Amanda

last: Swain

first: Upasana

last: Maheshwari

first: Sheng-Fu

last: Huang

first: Marco

last: Colonna

first: Annika

last: Keller


title: SFRP2 modulates functional phenotype transition and energy metabolism of macrophages during diabetic wound healing [Skin wound]

status: Public on Oct 04 2024

city: 湛江

first: haili

last: huang

state: 广东

address: 广东省湛江市霞山区广东医科大学附属医院

institute: Guangdong medical university

summary: Diabetic foot ulcer (DFU) is a serious complication of diabetes mellitus, which causes great health damage and economic burden to patients. The pathogenesis of DFU is not fully understood.We screened wound healing-related genes using bioinformatics analysis, and full-thickness skin injury mice model and cellular assays were used to explore the role of target genes in diabetic wound healing. SFRP2 was identified as a wound healing-related gene, and the expression of SFRP2 is associated with immune cell infiltration in DFU. In vivo study showed that suppression of SFRP2 delayed the wound healing process of diabetic mice, impeded angiogenesis and matrix remodeling, and increased macrophage infiltration in wound tissues. In addition, suppression of SFRP2 enhanced M1 polarization in both the early and later stage of wound healing, and decreased M2 polarization in the later stage, which impeded the transition of M1 to M2 polarization of wound healing. Moreover, suppression of SFRP2 affected the transcriptome signatures-related to inflammatory response and energy metabolism at the early stage of wound healing. Extracellular flux analysis (EFA) showed that suppression of SFRP2 decreased mitochondrial energy metabolism and increased glycolysis in injury-related macrophages. Furthermore, suppression of SFRP2 inhibited transcriptome signaturesrelated to carbohydrate metabolism, lipid metabolism and amino acid metabolism, which consists the three main components of energy metabolism of macrophages. In conclusions, SFRP2 may function as a wound healing-related gene in DFU, and suppression of SFRP2 impaired diabetic wound healing by compromising the M1-to-M2 transition of macrophages and modulating the balance between mitochondrial energy metabolism and glycolysis.

overall_design: Dorsal full-thickness skin wounds of diabetic mice were created by 6-mm punch biopsies and were randomly treated with control siRNAs(NC) and siRNA stargeting SFRP2.

first: Jiaqi

last: Yang

first: Guorui

last: Xiong

first: Huijuan

last: He

first: Haili


title: Age-related DNA methylation in the hypothalamus versus the hippocampus and the olfactory bulb

status: Public on Oct 08 2024

city: Bronx

first: Dongsheng

last: Cai

address: 1300 Morris Park Avenue, 1300 MORRIS PARK AVENUE

institute: ALBERT EINSTEIN COLLEGE OF MEDICINE

type: Methylation profiling by high throughput sequencing

summary: This study aims to investigate the relationship between the hypothalamus and age-related DNA methylation in mouse model. The objective of this sequencing work is to compare the hypothalamus (HT) with two other components of the limbic system in mice, the hippocampus (HC) and the olfactory bulb (OB), to understand how DNA methylation levels in these regions are similarly versus differently altered as animals evolve from young age to middle age.

overall_design: DNA was isolated from the hypothalamus (HT), the hippocampus (HC), and the olfactory bulb (OB) of standard male C57BL/6 mice at a young age (2 months, 2M) vs. an old age (12 months, 12M). This experiment contained 3 mice per age group, which are named Young1-3 and Old1-3. DNA libraries were prepared and then processed through bisulfite oligonucleotide-captured sequencing (BOCS) procedure. Sequencing was done with an Illumina MiSeq PE75 for quality control and with NextSeq500 High PE75 for obtaining DNA methylation profiles.

first: Salman

last: Usmani


title: Fission yeast essential nuclear pore protein nup211 regulates the transcriptome

city: New York

first: Hualin

last: Zhong

address: 695 Park Ave

department: Department of Biological Sciences

institute: Hunter College, The City University of New York

summary:
While nuclear pore proteins mediate nucleo-cytoplasmic transport, they can have important roles in other activities such as transcription, chromatin organization, and cell cycle regulation. The fission yeast nuclear pore protein nup211 localizes to the nuclear basket and is essential for cell viability. Nup211 is important for RNA quality control and the nuclear export of polyadenylated RNAs. Interestingly, several nup211 orthologs have also been shown to regulate transcription at the chromatin level. Although nup211 preferentially associates with heterochromatin, it is unclear whether it modulates transcription.
To further investigate the functions of nup211, we constructed a strain in which nup211 expression can be reduced through the addition of thiamine to the growth medium (nup211-so) and examined how cells were affected when nup211 protein was reduced. Down-regulation of nup211 led to severe defects in cell cycle regulation, including septation and cytokinesis. Using RNA-Seq and RT-qPCR, we revealed that loss of nup211 significantly altered global gene expression. Our findings suggest a new role for nup211 in regulating the transcriptome.

overall_design: Comparative gene expression profiling analysis of RNA-seq data obtained from nup211-so cells grown in the absence (control) or presence of thiamine. Three biological replicates were prepared for both treatment conditions.

first: Ayisha

last: Sookdeo

first: Domenick

last: Kamel

first: Lia

last: Di

first: Wei-Gang

last: Qiu


title: Cellular and transcriptomic changes by the supplementation of aged rat serum in human pluripotent stem cell-derived myogenic progenitors

status: Public on Oct 03 2024

city: Madison

first: Ryan

middle: Scott

last: Anderson

state: WI

address: 2015 Linden Drive

department: Department of Surgical Sciences

institute: University of Wisconsin-Madison School of Veterinary Medicine

summary: Introduction: The changing composition of non-cell autonomous circulating factors in blood as humans age is believed to play a role in muscle mass and strength loss. The mechanisms through which these circulating factors act in age-related skeletal muscle changes is not fully understood. In this study, we used human myogenic progenitors derived from human pluripotent stem cells to study non-cell autonomous roles of circulating factors during the process of myogenic differentiation. Methods: Myogenic progenitors from human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) were supplemented with serum samples from aged or young Fischer 344 × Brown Norway F1-hybrid rats. The effect of aged or young serum supplementation on myogenic progenitor proliferation, myotube formation capacity, differentiation, and early transcriptomic profiles were analyzed. Results: We found that aged rat serum supplementation significantly reduced cell proliferation and increased cell death in both ESC- and iPSC-derived myogenic progenitors. Next, we found that the supplementation of aged rat serum inhibited myotube formation and maturation during terminal differentiation from progenitors to skeletal myocytes when compared to the cells treated with young adult rat serum. Lastly, we identified that gene expression profiles were affected following serum supplementation in culture. Discussion: Together, aged serum supplementation caused cellular and transcriptomic changes in human myogenic progenitors. The current data from our in vitro model possibly simulate non-cell autonomous contributions of blood composition to age-related processes in human skeletal muscle.

overall_design: Myogenic progenitors and myotubes were prepared from human embryonic stem cell line WA09 and human induced-pluipotent stem cell line IMR-90. To study the effects of aged versus young serum supplementation, the myogenic progenitors were exposed to serum from aged or young Fischer 344 × Brown Norway F1-hybrid rats. After the stem cell derived myogenic prognitors had been exposed to young serum, aged serum, or no serum for 48 hours, BRB-seq was conducted with 2 replicates in each from (aged, young, serum-free) for both iPSC and ESC-derived myogenic progenitors.

first: Sin-Ruow

last: Tey

first: Masatoshi

last: Suzuki


title: TLR4 signaling of LPS chemotypes in HEK Blue hTLR4 reporter cells.

first: Felicitas

last: Lauber

summary: The discovery of Toll-like receptors (TLRs) represented a significant breakthrough that paved the way for the study of host-pathogen interactions in innate immunity. However, there are still major gaps in understanding TLR function, especially the early dynamics of downstream TLR pathways remains less clear. We characterize a label-free optical biosensor-based assay as a powerful method to detect TLR activation in a native and label-free environment and to delineate the dynamics of TLR pathway activation. To gain a deeper insight into the biological processes underlying the ligand-specific signal traces of different LPS chemotypes in various cell types, RNA-seq analysis of transcriptional changes in HEK Blue hTLR4 reporter cells was performed. After 3 hours of stimulation with LPS E. coli or LPS S. minnesota, HEK Blue hTLR4 reporter cells showed significant changes in RNA expression compared to the unstimulated control.

overall_design:
HEK Blue hTLR4 reporter cells were stimulated with LPS E. coli or LPS S. minnesota for 3 hours. Unstimulated cells served as control.
Gene expression profiling analysis was performed using data obtained from RNA-seq of two independent experiments.

first: Holze

last: Janine

first: Lauber

last: Felicitas

first: Weindl

last: Günther


title: Gene expression changes in mouse kidney cancer cells (RENCA) after anti-PD-L1 resistance

first: John

last: Ebos

summary: RNA sequencing analysis was used to identify changes in mouse kidney cancer cells (RENCA) following resistance to anti-PD-L1 (PDR).

overall_design: Primary and metastatic mouse kidney cancer cells (RENCA) resistant to anti-PD-L1 were derived in vivo after continuous treatment with 250μg/mouse/every 3 day from primary orthotopic lesions. Resistant cells were maintained in vitro with 0.5μg/ml anti-PD-L1 for more than 2 month.

first: Yuhao

last: Shi


title: Multimodal single-cell profiling reveals neuronal vulnerability and pathological cell states in focal cortical dysplasia

city: Campinas

first: Diogo

middle: Fernando Troggian

last: Veiga

state: SP

address: Rua Vital Brasil, 80

department: Department of Translational Medicine

country: Brazil

institute: Universidade Estadual de Campinas

summary: Focal cortical dysplasia (FCD) is a neurodevelopmental condition characterized by malformations of the cerebral cortex that often cause drug-resistant epilepsy. In this study, we performed multi-omics single-nuclei profiling to map the chromatin accessibility and transcriptome landscapes of FCD type II, generating a comprehensive multimodal single-nuclei dataset comprising 61,525 cells from 11 clinical samples of lesions and controls. Our findings revealed profound chromatin, transcriptomic, and cellular alterations affecting neuronal and glial cells in FCD lesions, including the selective loss of upper-layer excitatory neurons, significant expansion of oligodendrocytes and immature astrocytic populations, and a distinct neuronal subpopulation harboring dysmorphic neurons. Furthermore, we uncovered activated microglia subsets, particularly in FCD IIb cases. This comprehensive study unveils neuronal and glial cell states driving FCD development and epileptogenicity, enhancing our understanding of FCD and offering directions for targeted therapy development.

overall_design: We conducted multi-omics single-cell sequencing on cortical brain tissue from focal cortical dysplasia (FCD) IIa (n=3) and IIb (n=6) lesions, as well as histologically normal tissue from FCD donors used as internal controls (n=2). Dissociated nuclei were profiled using the 10X Genomics Multiome ATAC + Gene Expression assay to simultaneously measure chromatin accessibility and gene expression in individual nuclei.

first: Isabella

middle: C

last: Galvão

first: Manuela

last: Lemoine

first: Lauana

last: Messias

first: Patrícia

last: Araújo

first: Jaqueline

last: Geraldis

first: Clarissa

last: Yasuda

first: Marina

last: Alvim

first: Enrico

last: Ghizoni

first: Helder

last: Tedeschi

first: Fernando

last: Cendes

first: Fabio

last: Rogerio

first: Iscia

last: Lopes-Cendes

middle: F


title: Identification of  LncRNAs/circRNAs  associated with testicular development and spermatogenesis in black goat

status: Public on Oct 01 2024

city: Nanning

first: Zhiqiang

last: Wang

address: No. 6 TaoYuan Rd.

institute: Guangxi Academy of Medical Sciences and the People’s Hospital of Guangxi Zhuang Autonomous Region

summary: Establishment and maintenance of spermatogenesis need a complex process and vast regulatory network. There is growing evidence reveals that long noncoding RNAs (lncRNA) plays important role in regulating testicular development and spermatogenesis in a stage-specific way. We here report the identification of lncRNA LOC108635509 as key lncRNA regulator in black goat spermatogenesis. In the current study, we screened the transcriptomes (lncRNA and mRNA) of testicular from Guangxi black goats before puberty (3 days old, D3; 30 days old, D30), puberty (90 days old, D90) and postpuberty (180 days old, D180), and found there were 1211, 12180, 834 differential lncRNAs and 1196, 8838,269 differential mRNAs at the ages of D30 vs D3, D90 vs D30, and D180 vs D90. The expression pattern of differentially expressed (DE) lncRNAs indicated that D90 was a key node of lncRNAs participated in the regulation of testicular development and spermatogenesis in black goat. The of GO and KEGG analyses identified that DE lncRNAs and their target genes regulated spermatogenesis through MAPK, Ras, and PI3K-Akt signal pathways. Using cis- and trans-acting, 39 DE lncRNA-targeted genes were found to be enriched for male reproduction. Of these, LOC108635509, which specific expressed in testis and upregulated the expression levels at D90, was found participated in the regulation of testicular development through promoting the proliferation of SCs. Overall, this study provides new insight into the regulatory mechanisms that support spermatogenesis and testicular development in black goats.

overall_design: To investigate the roles of mRNAs, lncRNAs andcircRNAs in the regulation of black goat testicular development, twelve cDNA libraries of neonatal (D3-1, D3-2, D3-3), prepuberty (D30-1, D30-2, D30-3), puberty (D90-1, D90-2, D90-3) and postpuberty (D180-1, D180-2, D180-3) testes were constructed. Then performed comparative gene expression profiling analysis of RNA-seq data and identified key DE lncRNAs. Finally,  the location and function of  key lncRNAs in Sertoli cells  were confirmed.

first: Chan

last: Luo

first: Deshun

first: Qinyang

last: Jiang


title: Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling [CUT&RUN]

status: Public on Oct 13 2024

first: Neville

last: Sanjana

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: MultiPerturb-seq is a high-throughput CRISPR screening platform with joint single nucleus chromatin accessibility, transcriptome, and guide RNA capture. It uses combinatorial indexing combined with droplet microfluidics to scale throughput and integrate all three modalities. We apply MultiPerturb-seq to identify key genes whose loss can trigger differentiation in a rare pediatric cancer, atypical teratoid/rhabdoid tumor (AT/RT), which is driven by loss of the SWI/SNF chromatin remodeling subunit SMARCB1.

overall_design: MultiPerturb-seq data consists of single-cell ATAC-seq, RNA-seq, and CRISPR guide RNA capture for BT16 cells transduced with a CRISPR library to knock-down epigenomic remodelers and a 20% spike-in of NIH3T3 cells transduced with non-targeting guide RNAs. In addition, CUT&RUN data (H2A.Z and H3K4me3) is from BT16 cells that received either non-targeting (NT) or ZNHIT1-targeting guide RNAs.

first: Yan

middle: E

last: Rachel

first: Corman

last: Alba

first: Katgara

last: Lyla

first: Wang

last: Xiao

first: Xue

last: Xinhe

first: Gajic

last: Zoran

first: Sam

last: Richard

first: Farid

last: Michael

first: Friedman

last: Samuel M

first: Choo

last: Jungwook

first: Raimondi

last: Ivan

first: Ganesan

last: Shridar

first: Katsevich

last: Eugene

first: Greenfield

middle: P

last: Jeffrey

first: Dahmane

last: Nadia

first: Sanjana

last: Neville


first: Jaime

last: Pérez

overall_design: We profiled the genomic binding of BDH1 proteins on inflorescences by performing ChIP-seq on transgenic lines expressing BDH1-FLAG on bdh1 background

first: Joan

last: Candela-Ferre

last: Pérez-Alemany

first: Borja

last: Diego-Martin

first: Vijaya

last: Pandey

first: James

last: Wohlschlegel

first: Jorge

last: Lozano-Juste

first: Javier

last: Gallego-Bartolomé


title: Loss of aryl hydrocarbon receptor and long-term, but not short-term treatment with BAY2416964 alters gene expression profiles and reduces proliferation and migration of PyMT mammary cancer cells

city: Oslo

first: Jason

last: Matthews

address: Sognsvannsveien 9

department: Nutrition

country: Norway

institute: University of Oslo

summary: The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor that drives pro-survival processes that facilitate tumorigenesis, malignant cell migration, invasion, and metastasis. Much of AHR’s pro-tumorigenic action is due to its activation by the oncometabolite, kynurenine. Because of this AHR antagonists are being actively investigated as new anti-tumor therapy. In this study we compared the effects of treatment with the AHR antagonists, BAY2416964 and GNF351, to that of AHR knockout in PyMT murine mammary cancer cells. BAY2146964 and GNF351 effectively inhibited kynurenine-dependent increases in Cyp1a1 and Cyp1b1 mRNA levels. However, single doses of 10 mM BAY2416964, but not 10 mM GNF351, exhibited agonist activity reflected by weak increases Cyp1a1 and Cyp1b1 mRNA levels. CRISPR/Cas9-generated PyMT AhrKO cells exhibited reduced cell proliferation compared with controls, but treatment with 1 mM BAY2416964 for 96 h had no effect on the proliferation of wildtype cells. To examine the differences between AHR knockout and short term BAY2416964 further, we generated long-term BAY2416964 (LT-BAY) by exposing wildtype cells to 1 mM BAY2416964 for at least 6 weeks. Similar to AhrKO cells, LT-BAY cells exhibited reduced cell proliferation and migration compared with wildtype cells; although not to the same extent as that observed with AhrKO cells. RNA sequencing studies identified 714 differentially expressed genes (DEGs) that overlapped between LT-BAY and AhrKO cells, but none after 24 h exposure with 1 mM BAY2416964. Our data reveal BAY2416964 exhibits weak AHR agonist activity in PyMT cells and that long-term pharmacological inhibition of AHR more closely mimicked AHR loss.

overall_design: PyMT WT, AhrKO and LT-BAY cells were plated in a 12-well plate at a density of 1×10^5 cells/well in quadruplicates. Total RNA was isolated with the Aurum™ Total RNA isolation kit (BioRad), following manufacturer’s protocol and were subjected to RNA sequencing

first: Ninni

last: Olafsen

first: Siddhartha

last: Das

first: Chiara

last: Gorrini

middle: B


title: Single-nucleus Multiome ATAC and Gene Expression analysis of the liver tissues from matrin-3 floxed and liver-specific knockout mice

city: Lincoln

first: Xinghui

last: Sun

state: NE

address: 1901 Vine Street

department: Biochemistry

institute: University of Nebraska - Lincoln

summary: Matrin-3 is an RNA-binding protein involved in the pathogenesis of human diseases. Here we examined the hepatic transcriptome and chromatin accessibility of high-fat-diet (Research Diets, Inc; D12492) fed mice. After quality control filtering and removal of putative doublets, single-nucleus RNA-seq clusters were assigned to five different cell types, including hepatocytes (Hep), Kupffer cells (KC), endothelial cells (EC), hepatic stellate cells (HSC), and leukocytes (Leuk). The total number of cells is 1,543.  Differential analysis of single-nucleus RNA-seq data identified 492 DEGs (FDR < 0.05 & fold change > 1.5) in the hepatocyte cluster between matrin-3 floxed and liver-specific knockout (LKO) mice. GSEA revealed that KEGG terms such as “Drug metabolism cytochrome P450” and “Metabolism of xenobiotics by cytochrome P450” were enriched in hepatocytes

overall_design: Mice were fed a high-fat diet for 16 weeks. The livers were snap-freezed and stored at -80 °C freezer. Nuclei were isolated from the pooled liver tissues of six mice (20 mg liver per mouse). Two libraries were constructed from floxed mice and LKO mice, respectively.

first: Xiao

last: Cheng


title: Single-cell transcriptomics reveals evolutionary reconfiguration of embryonic cell fate specification in the sea urchin Heliocidaris erythrogramma

status: Public on Oct 05 2024

city: DURHAM

first: Alejandro

last: Berrio

address: 124 Science Dr

department: Biology

institute: Duke University

summary: Altered regulatory interactions during development likely underlie a large fraction of phenotypic diversity within and between species, yet identifying specific evolutionary changes remains challenging. Analysis of single-cell developmental transcriptomes from multiple species provides a powerful framework for unbiased identification of evolutionary changes in developmental mechanisms. Here, we leverage a “natural experiment” in developmental evolution in sea urchins, where a major life history switch recently evolved in the lineage leading to Heliocidaris erythrogramma, precipitating extensive changes in early development. Comparative analyses of scRNA-seq developmental time courses from H. erythrogramma and Lytechinus variegatus (representing the derived and ancestral states respectively) reveals numerous evolutionary changes in embryonic patterning. The earliest cell fate specification events, and the primary signaling center are co-localized in the ancestral dGRN but remarkably, in H. erythrogramma they are spatially and temporally separate. Fate specification and differentiation are delayed in most embryonic cell lineages, although in some cases, these processes are conserved or even accelerated. Comparative analysis of regulator-target gene co-expression is consistent with many specific interactions being preserved but delayed in H. erythrogramma, while some otherwise widely conserved interactions have likely been lost. Finally, specific patterning events are directly correlated with evolutionary changes in larval morphology, suggesting that they are directly tied to the life history shift. Together, these findings demonstrate that comparative scRNA-seq developmental time courses can reveal a diverse set of evolutionary changes in embryonic patterning and provide an efficient way to identify likely candidate regulatory interactions for subsequent experimental validation.

overall_design: 7 scRNA-seq samples capturing 7 time points over 24 hours of a lecithotrophic sea urchin development

first: Abdull

last: Massri

first: Anton

last: Afanassiev

first: Laura

last: Greenstreet

first: Krista

last: Pipho

first: Maria

last: Byrne

first: Geoffrey

last: Schiebinger

first: David

last: McClay

first: Gregory

last: Wray


title: HIV-1 m6A methylome investigation by m6A-SAC-seq

city: Chicago

first: Chuan

last: He

address: 929 E 57th St

department: Chemistry Department

institute: University of Chicago

summary: Despite effective antiretroviral therapy at reducing HIV-1 viral loads to undetectable levels, the presence of latently infected CD4+ T cells poses a major barrier to HIV-1 cure. N6-methyladenosine (m6A) modification of viral and cellular RNA has a functional role in regulating HIV-1 infection. m6A modification of HIV-1 RNA can affect its stability, translation, and splicing in cells and suppresses type-I interferon induction in macrophages. However, the function of m6A modification in regulating HIV-1 latency reactivation remains unknown. We used the Jurkat T cell line-derived HIV-1 latency model (J-Lat cells) to investigate changes in m6A levels of cellular RNA in response to latency reversal. We observed a significant increase in m6A levels of total cellular RNA upon reactivation of latent HIV-1 in J-Lat cells. This increase in m6A levels was transient and returned to steady-state levels despite continued high levels of viral gene expression in reactivated cells compared to control cells. Upregulation of m6A levels occurred without significant changes in the protein expression of m6A writers or erasers that add or remove m6A, respectively. Knockdown of m6A writers in J-Lat cells significantly reduced HIV-1 reactivation. Treatment of a m6A writer inhibitor reduced cellular RNA m6A levels along with reduction in HIV-1 reactivation. Furthermore, using m6A-specific sequencing, we identified cellular RNAs that are differentially m6A-modified during HIV-1 reactivation in J-Lat cells. Knockdown of identified m6A-modified RNA validate these results with established primary CD4+ T-cell models of HIV-1 latency. These results showed the importance of m6A RNA modification in HIV-1 latency reversal.

overall_design: J-Lat 10.6 cells were treated either with DMSO or PMA+Ionomycin (P+I) for 6 hours and total RNA was isolated from three independent samples. Poly-A RNA was enriched using oligodT beads and used for m6A-SAC-seq and RNA-sequencing.

first: Yutao

last: Zhao

first: Tarun

last: Mishra

first: Li

last: Wu


title: Liver-specific matrin-3 knockout alters the hepatic transcriptome of chow diet-fed mice [RNA-seq]

summary: Matrin-3 is an RNA-binding protein involved in the pathogenesis of human diseases. Here we examined the hepatic transcriptome of chow-diet fed mice. Bulk RNA-seq and bioinformatics analysis identified 646 and 145 differentially expressed genes (Padj < 0.05), respectively in the livers of female and male matrin-3 LKO mice. Enrichr analysis of these DEGs revealed several common Hallmark terms including cholesterol homeostasis, fatty acid metabolism, xenobiotic metabolism, and epithelial mesenchymal transition between female and male mice. Our data demonstrated that liver-specific matrin-3 deficiency re-programs the hepatic transcriptome in the liver of chow diet-fed mice.

overall_design: Matrin-3 floxed mice were bred with Albumin-Cre mice (The Jackson Laboratory, #003574) to produce liver-specific matrin-3 knockout mice (LKO). Mice were housed on a normal 12/12 light-dark cycle. Mice had ad libitum access to a normal chow diet (Envigo, cat# 2016) and water. At 16 weeks of age, mice were euthanized for tissue collection. Total RNAs were extracted from mouse tissues after homogenization using TRIzol Reagent (Thermo Fisher, 15596026) according to the manufacturer’s instructions. For RNA sequencing by Novogene, total RNA quality was examined using Agilent 2100 Bioanalyzer. The RNA Integrity Number of each RNA sample is above 8.5. A total amount of 1 µg RNA per sample was used for library construction. Total eight libraries were constructed; one library was produced from two liver tissues; and each group of mice has two library replicates.

first: Cheng

last: Xiao

first: Sun

last: Xinghui


title: SFRP2 modulates functional phenotype transition and energy metabolism of macrophages during diabetic wound healing [RAW264.7 cells]

first: haili

last: huang

address: 广东省湛江市霞山区广东医科大学附属医院

overall_design: RAW264.7 cells were transfected with SFRP2 siRNAs and polarized to M1 phenotype using LPS stimulation.

first: Jiaqi

last: Yang

first: Guorui

last: Xiong

first: Huijuan

first: Haili

last: Huang


title: Identification of lipid senolytics targeting senescent cells through ferroptosis induction

city: Minneapolis

first: Lei

middle: Justan

last: Zhang

state: MN

address: 312 Church Street SE

department: Department of Biochemistry, Molecular Biology, and Biophysics

institute: University of Minnesota

summary: Through phenotypic drug screening, we identified a novel class of lipid senolytics that selectively eliminated a broad range of senescent cells, reduced tissue senescence, and extended healthspan in mice. Extensive mechanistic studies reveal that these lipids induce ferroptotic cell death by exploiting the iron-rich and ROS-prone characteristics of senescent cells, offering a new therapeutic strategy to target senescence in aging and age-related diseases.

overall_design: Primary mouse embryonic fibroblasts (MEFs) cells were used. WT MEFs non-senescent (proliferative control) and WT MEFs induced to senescence by oxidative stress (H2O2) and genotoxic stress (etoposide). Cells were treated with α-ESA  and its derivative α-ESA-me for 12 hours. 3 biological replicates per group.

first: Carolina

last: Soto-Palma

first: Paul

last: Robbins


title: Effect of regorafenib, anti-PD1, and anti-CD40 agonist in Head and Neck Squamous Cell Carcinoma

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptomics Profiling of the Non-Small Cell Lung Cancer (NSCLC) Microenvironment Reveals Dual Immune Cell-Type Behaviors

city: Toulouse

first: Leila

last: Khajavi

address: TOULOUSE

country: France

institute: INSERM

summary: Lung cancer is the leading cause of cancer death worldwide, with a poor survival rate despite recent therapeutic. A better understanding of the tumor and microenvironnement complexity is needed to improve patients outcome.

overall_design: We applied a computational immunology approach (involving immune cell proportion estimation by deconvolution, transcription factor inference and immune score estimation) in order to better characterize bulk transcriptomics of primary lung adenocarcinoma (LUAD) samples from patients across disease stages. We validated our findings using an independent LUAD cohort with bulk and scRNAseq data.

last: KHAJAVI

first: Marcelo

last: HURTADO

first: Abdelmounim

last: ESSABBAR

first: Michael

last: KAMMER

first: Julien

last: Mazieres

first: Vera

last: Pancaldi


title: Liver-specific matrin-3 knockout regulates hepatic transcriptome and chromatin accessibility in mice

first: Xinghui

last: Sun


title: Refractory testicular germ cell tumors are highly sensitive to the targeting of polycomb pathway demethylases KDM6A and KDM6B

city: Urbana

first: Doha

last: Shokry

state: Illinois

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois Urbana-Champaign

summary: Testicular germ cell tumors (TGCTs) can be treated with cisplatin-based therapy. However, a clinically significant number of cisplatin-resistant patients die from progressive disease as no effective alternatives exist. Curative cisplatin therapy results in acute and life-long toxicities in the young TGCT patient population providing a rationale to decrease cisplatin exposure. In contrast to genetic alterations, recent evidence suggests that epigenetics is a major driving factor for TGCT formation, progression, and response to chemotherapy. Hence, targeting epigenetic pathways with “epidrugs” is one potential relatively unexplored strategy to advance TGCT treatment beyond cisplatin. In this report, we demonstrate for the first time that targeting polycomb demethylases KDM6A and KDM6B with epidrug GSK-J4 can treat both cisplatin-sensitive and -resistant TGCTs. While GSK-J4 had minimal effects alone on TGCT tumor growth in vivo, it dramatically sensitized cisplatin-sensitive and -resistant TGCTs to cisplatin. We validated KDM6A/KDM6B as the target of GSK-J4 since KDM6A/KDM6B genetic depletion had a similar effect to GSK-J4 on cisplatin-mediated anti-tumor activity and transcriptome alterations. Pharmacologic and genetic targeting of KDM6A/KDM6B potentiated or primed the p53-dominant transcriptional response to cisplatin, with also evidence for basal activation of p53. Further, several chromatin modifier genes, including BRD4, lysine demethylases, chromodomain helicase DNA binding proteins, and lysine methyltransferases, were repressed with cisplatin only in KDM6A/KDM6B-targeted cells, implying that KDM6A/KDM6B inhibition sets the stage for extensive chromatin remodeling of TGCT cells upon cisplatin treatment. Our findings demonstrate that targeting polycomb demethylases is a new potent pharmacologic strategy for treating cisplatin resistant TGCTs that warrants clinical development.

overall_design: gene expression of treated and untreated cisplatin resistant cells (vc or KDM6A6B knockdown) with either GSK-J4, Cisplatin or combination of both in biological triplicate were analysed

last: Spinella


title: Cytokine polymorphism in HBV infected patients in Ghanaian population

city: Cape Coast

first: Nicholas

middle: Ekow

last: Thomford

state: Central

address: PMB, University of Cape Coast School of Medical Sciences, Coast Coast, Ghana

department: Dept. of Med. Biochem.,SMS, CoHAS,

country: Ghana

institute: University of Cape Coast, Ghana

summary: Genetic variations in drug metabolising enzymes play a role in how individuals respond to drugs. Pharmacogene variation data in the Ghanaian population is limited and this study looks at exploring common variations that exist in our population for commonly used drugs. In addition, the study also looks at the how variations in cytokines and HLA play a role in HBV pathogenesis.  Samples were validated with PCR-RFLP for accuracy

overall_design:
166 samples were genotyped for variations in 5 cytokines using the MassArrayiPLEX genotyping assay using the iPLEX Gold genotyping kit from Agena Bioscience. This requires an input of 40ng of DNA per sample. Samples are dispensed onto a SpectroCHIP Array and data acquired using MassARRAY analyzer. Data is automatically analyzed and acquired using Typer software version 3.99.105 for each sample.
Please note that there are total 185 sample records because some of the samples have been repeated and validated randomly.

first: Faustina

last: Adu


title: Topoisomerase I (TOP1) is a functional mitotic interactor of the bookmarking factor HNF1B [RNAseq_KEC]

city: Paris

first: Marco

last: PONTOGLIO

state: Choisir votre état

address: Inserm U1016, 24 rue du Faubourg Saint-Jacques

department: Growth and Signalling

institute: Inserm

summary: HNF1B (Hepatocyte Nuclear Factor 1-Beta) is a POU-homeobox transcription factor expressed in kidney and frequently mutated in patients suffering from Congenital Anomalies of the Kidney and the Urinary Tract (CAKUT). HNF1B is a bookmarking factor, able to bind mitotic chromatin and necessary for the post-mitotic reactivation of gene expression. In order to characterize the molecular functions of HNF1B as a bookmarking factor, we performed ChIPseq on asynchronous and mitotic renal cells. We developed a novel ChIP method with a non-aqueous crosslinking (NAQC) to circumvent the well-known artefactual effects of formaldehyde crosslinking of mitotic chromosomes. NAQC-ChIP allowed the retention of the mitotic signal that was lost with a regular ChIP. With this novel methodology, we show that the vast majority HNF1B binding sites detected in asynchronous cells are also bound in mitosis.

overall_design: In order to assess the transcriptional biological impact of the loss of HNF1B we performed RNAseq on WT and CRISPR/Cas9 HNF1B-KO KEC cells.

first: Alessia

last: Bagattin

first: Salvina

last: Tammaccaro

first: Magali

last: Chiral

first: Munevver

last: Makinistoglu

first: Jonathan

last: Lerner

first: Serge

last: Garbay

first: Nicolas

last: Kuperwasser

last: Pontoglio


title: Genomic reconstruction of Galápagos dog history reveals strategies for management of an invasive species

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: Free-breeding dogs have occupied the Galápagos islands at least since the 1830s, however, it was not until the 1900s that dog populations grew substantially, endangering wildlife and spreading disease. In 1981, authorities sanctioned the culling of free-roaming dogs. Yet there are currently large free-roaming dog populations of unknown ancestry on the islands of Isabela and Santa Cruz, whose ancestry has never been assessed on a genome-wide scale. Thus, we performed a complete genomic analysis of the current Galápagos dog population as well as historical Galápagos dogs sampled between 1969 and 2003, testing for population structure, admixture, and shared ancestry. Our dataset included samples from 187 modern and six historical Galápagos dogs, together with whole genome sequence from over 2,000 modern purebred and village dogs. Our results indicate that modern Galápagos dogs are recently admixed with purebred dogs but show no evidence of a population bottleneck related to the culling. Additionally, IBD analyses reveal evidence of shared shepherd-dog ancestry in the historical Galápagos dogs. Overall, our results demonstrate that the 1980s culling of dogs was ineffective in controlling population size and did little to reduce genetic diversity, instead producing a stable and expanding population with genomic signatures of historical dogs remaining today. The insights from this study can be used to improve population control strategies for the Galápagos Islands and other endangered endemic communities worldwide.

overall_design: 187 samples of free-roaming dogs collected from Santa Cruz and Isabela Islands in the Galápagos

first: G

last: Spatola

first: T

last: Feuerborn

first: J

last: Betz

first: R

middle: M

last: Buckley

middle: K

last: Ostrander

first: E

middle: V

last: Dutrow

first: A

last: Velez

first: M

last: Pinto

last: Hale

first: B

middle: D

last: Barnett

last: Mousseau


title: Topoisomerase I (TOP1) is a functional mitotic interactor of the bookmarking factor HNF1B [RNAseq_786O]

first: Marco

last: PONTOGLIO

overall_design: In order to assess the transcriptional biological impact of the loss of HNF1B we performed RNAseq on HNF1B-depleted 786-O (HNF1B siRNA).

last: Bagattin

last: Tammaccaro

last: Chiral

last: Makinistoglu


title: Single nucleus multiome (RNAseq and ATACseq) of female mouse pituitary

first: Elena

last: Zaslavsky

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

summary: We report the single nucleus multiome (RNAseq+ATACseq) of a female mouse pituitary sample. This dataset was generated for supporting the development of a data-driven batch inference method and transforms often heterogeneous data matrices obtained from different samples into a uniformly cell-type annotated and integrated dataset.

overall_design: Multiomic (RNAseq+ATACseq) sequencing of pituitary tissue from 14 female samples.

first: Frederique

last: Ruf-Zamojski


title: Topoisomerase I (TOP1) is a functional mitotic interactor of the bookmarking factor HNF1B

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: MAD2-dependent insulin receptor endocytosis regulates metabolic homeostasis

first: Eunhee

last: Choi

address: 630 West 168th Street

institute: Columbia University

summary: We determined transcriptomic profile in the liver and epididymal white adipose tissue (eWAT) from wild-type (WT) and MAD2 binding deficient IR 4A mice after 6 hour fasting using RNA sequencing.

overall_design: RNA-seq of livers and epididymal white adipose tissues (eWAT) from 2 month old male mice (WT, liver, n=5; WT, eWAT, n=5; IR 4A, liver, n=5; IR 4A, eWAT, n=5)

first: Junhee

last: Park

first: Fang

last: Li

first: Hanrui

last: Zhang


title: Multi-omics analysis using antibody-based in situ biotinylation technique reveals the mechanism of Cajal body formation

city: Yokohama

first: Hidefumi

last: Suzuki

address: Fukuura 3-9

country: Japan

institute: Yokohama City University

summary: Membrane-less subcellular compartments such as cytoplasmic bodies, nuclear bodies, and paraspeckles play important roles in a variety of cellular functions. Although many of the techniques for identifying the components of cellular bodies were developed to address their function, no technique to comprehensively identify the components of these bodies in both static and dynamic states has been established. Here, we developed an antibody-based in situ biotinylation proximity-labeling technique and succeeded in identifying the components of both static and dynamic nuclear bodies, nucleolus and γH2AX foci, respectively. Using this technique, we comprehensively identified the components of Cajal bodies (CBs), including DNAs, RNAs, and proteins, and clarified their interactome in CBs. Furthermore, we captured the dynamic change of CBs by inhibiting transcription. Our analysis revealed that nascent snRNAs transcribed in CBs play a role in CB nucleation through assembling RNA binding proteins, including FTD-related proteins, RBMs and HNRNPs.

overall_design: Experiment 1:  Coilin antibody-based in situ biotinylation DNA-seq with control or Coilin siRNA-transfected HeLa cells. D. melanogastor S2 genomic DNA was used as spike-in control.   Experiment 2: Coilin antibody-based in situ biotinylation RNA-seq in HeLa cells. D. melanogastor S2 RNA was used as spike-in control. Experiment 3: Coilin ChIP-seq in HEK293T cells.

first: Keisuke

last: Noguchi

first: Ryota

last: Abe

first: Atsushi

last: Toyoda

first: Yutaka

first: Hidehisa

last: Takahashi


title: Topoisomerase I (TOP1) is a functional mitotic interactor of the bookmarking factor HNF1B [ChIPseq_KEC]

overall_design: ChIPseq was performed with HNF1b or TOP1 antibodies in asynchronous and mitotic WT and HNF1b-KO KEC cells fixed with NAQC (non-aqueous crosslinking) or AQC (aqueous crosslinking) methods.

first: Alessia

first: Salvina

first: Magali

first: Munevver

first: Jonathan

last: Lerner

first: Serge

last: Garbay

first: Nicolas

last: Kuperwasser

last: Pontoglio


title: Liver-specific matrin-3 knockout alters the hepatic transcriptome of high-fat diet-fed mice [RNA-seq]

first: Xinghui

last: Sun

summary: Matrin-3 is an RNA-binding protein involved in the pathogenesis of human diseases. Here we examined its previously uncharacterized role in limiting hepatic steatosis and stress response via the constitutive androstane receptor. Matrin-3 expression was induced in the steatotic livers of mice and humans. Liver-specific matrin-3 knockout (LKO) exacerbated high-fat diet (HFD)-induced steatosis, acute phase response, and inflammation in the liver of mice. Bulk RNA-seq and bioinformatics analysis identified 1,333 and 239 differentially expressed genes (fold change > 1.5 & Padj < 0.05), respectively in the livers of female and male matrin-3 LKO mice. Gene Set Enrichment Analysis revealed that the top most enriched Gene Ontology Biological Process was the “Xenobiotic metabolic process” in female matrin-3 floxed mice that is downregulated. The top two enriched biological processes are “Acute inflammatory response” and “Acute phase response” in the liver of female LKO mice that are upregulated. Several GO terms related to lipid metabolism and xenobiotic metabolism were enriched in the livers of male mice. Real-time qPCR revealed that the expression of many genes involved in xenobiotic metabolism was reduced in the liver of female LKO mice and to a lesser extent in the liver of male LKO mice, while the expression of acute-phase response genes was induced in the liver of female but not male LKO mice. Our data demonstrated that liver-specific matrin-3 deficiency re-programs the hepatic transcriptome enriched for xenobiotic metabolism pathway, acute-phase and inflammatory response signaling in the liver of HFD-fed mice.

overall_design: Matrin-3 floxed mice were bred with Albumin-Cre mice (The Jackson Laboratory, #003574) to produce liver-specific matrin-3 knockout mice (LKO).  Mice were housed on a normal 12/12 light-dark cycle. Mice had ad libitum access to a normal chow diet (Envigo, cat# 2016) and water, or a HFD with 60 kcal% fat (Research Diets, D12492) and water. Male and female matrin-3 floxed mice and littermate LKO  mice were fed a HFD at 7 weeks of age for 16 weeks. Sixteen weeks post-HFD, mice were fasted for 12 hours for euthanasia and tissue collection. Total RNAs were extracted from mouse tissues after homogenization using TRIzol Reagent (Thermo Fisher, 15596026) according to the manufacturer’s instructions. For RNA sequencing by Novogene, total RNA quality was examined using Agilent 2100 Bioanalyzer. The RNA Integrity Number of each RNA sample is above 8.5. A total amount of 1 µg RNA per sample was used for library construction.

first: Xiao

last: Cheng


title: The function of the ZFP189 transcription factor in the nucleus accumbens facilitates cocaine-specific transcriptional and behavioral adaptations

city: Richmond

first: Joseph

middle: Anthony

last: Picone

state: Virginia

address: 1217 E Marshall St,

department: Anatomy and Neurobiology

institute: Virginia Commonwealth University

summary: Here, we explore the function of a drug-associated repressive transcription factor (TF), ZFP189, whose expression in the nucleus accumbens (NAc) facilitates cocaine-induced molecular and behavioral adaptations. To uncover the molecular action of ZFP189, we created synthetic ZFP189 TFs of distinct transcriptional function, including ZFP189VPR, which activates the expression of target genes and exerts opposite transcriptional control to the endogenously repressive ZFP189. By virally delivering synthetic ZFP189 TFs to the NAc of mice, we discover that the molecular control exerted by synthetic or endogenous ZFP189 solely alters behavioral response to cocaine but not morphine or palatable food. Transcriptional adaptation occurred in response to cocaine, but not morphine. We demonstrate that NAc ZFP189 function drives the cocaine self-administration behaviors, whereas NAc ZFP189VPR impedes this worsening of cocaine taking behaviors. Collectively, this research illuminates the mechanisms through which a drug-associated TF specifically coordinates the brain adaptations necessary for the increasing of cocaine self-administration behaviors.

overall_design: To investigate the function of ZFP189 TF in driving drug-response, we surgically delivered HSV-ZFP189 TFs within mouse NAc tissue and perform drug-induced locomotor testing, followed by NAc tissue extraction and RNA seqencing.

middle: A

first: Annalise

last: Hassan

first: R

last: Kim

first: Diego

last: Lira

first: Gabriella

last: Silva

first: Natalie

last: Truby

first: Hadessah

last: Johnson

first: Collin

last: Teague

first: Rachael

last: Neve

first: Matthew

last: Banks

first: Xiaohong

last: Cui

first: Peter

last: Hamilton


title: YAP overcomes restriction of translation induced by nutrient deprivation through restoration of mTORC1 activity [Ribo-seq]

city: Daejeon

first: Daehee

last: Hwang

address: Yuseong-gu, Daehak-ro 291 Basic Science Bldg. (E6-6) #413

department: Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: The Hippo pathway downstream effectors YAP and TAZ display oncogenic potential via their transcriptional co-activator function, mediated primarily by binding to TEAD transcription factors. Many studies have focused on identifying YAP/TAZ-TEAD target genes, but their role in the regulation of protein synthesis has remained largely unexplored. Here we show that YAP activation is sufficient to overcome the global translation restriction of 5TOP-containing mRNAs, which is induced by serum deprivation and dependent on the inactivation of mTORC1. We found that YAP/TAZ repressed the expression of DDIT4, a negative regulator of mTORC1 whose expression is otherwise upregulated by serum deprivation. Forced expression of DDIT4 was sufficient to suppress translation and transformative potential of serum-unresponsive uveal melanoma cells, which harbor G protein mutations. Our findings highlight crosstalk between Hippo-YAP/TAZ and mTORC1 pathways in the regulation of translation and offer a new perspective towards understanding YAP/TAZ-driven malignancies.

overall_design: Ribo-seq data of 293AD cells expressing vector control or FLAG-YAP 5SA, subjected to (or not) overnight (14 h) serum deprivation

first: DaeHee

first: Jeeyoon

last: Chang

first: Hongseok

last: Ha

first: Dae-Sik

last: Lim


title: YAP overcomes restriction of translation induced by nutrient deprivation through restoration of mTORC1 activity [293AD]

overall_design: RNA-seq data of 293AD cells expressing vector control or FLAG-YAP 5SA, subjected to (or not) overnight (14 h) serum deprivation


title: Paclitaxel resistance in isogenic PDX

first: Eivind Valen

last: Egeland

address: Ullernchausseen 70

department: Department of Tumor Biology, Institute for Cancer Research

institute: Oslo University Hospital

summary: Tumor heterogeneity and resistance to chemotherapy represents a significant challenge in the clinical management of triple negative breast cancer (TNBC). By dissecting molecular pathways associated with treatment resistance, we sought to define patient sub-groups and define actionable targets for next-line treatment. Bulk RNA sequencing were performed on isogenic patient-derived xenografts (PDX) representing paclitaxel-sensitive and -resistant tumors. Pathways identified as upregulated in the resistant model were further explored as targets in downstream approcaches, and their clinical relevance evaluated in publicly available clincial data.

overall_design: Resistance to paclitaxel were generated in mice by continous treatment of triple negative breast cancer patient-derived xenograft. The isogenic pair of the parental MAS98.12 and resistance derived MAS98.12PR were subjected to RNAseq.

first: Eivind

first: Gunhild

last: Mælandsmo

first: Lina

last: Prasmickaite


title: YAP overcomes restriction of translation induced by nutrient deprivation through restoration of mTORC1 activity [MCF10A]

overall_design: RNA-seq data of MCF10A cells expressing vector control or FLAG-YAP 5SA, subjected to (or not) overnight (14 h) serum deprivation


title: Comparison of gene expression by activated T-cells that express NKG2D-based CARs

city: London

first: John

last: Maher

address: Great Maze Pond

country: United Kingdom

institute: King's College London

summary: NKG2D ligands are broadly expressed in cancer. To exploit this, we engineered an adaptor chimeric antigen receptor (CAR) termed NKG2D / Dap10-12 in which NKG2D is co-expressed with a fusion of Dap10 and the Dap12 endodomain. Dap10 was deployed to provide co-stimulation while Dap12 delivers an activation signal via a single immunoreceptor tyrosine-based activation motif (ITAM). NKG2D / Dap10-12 T-cells elicited compelling anti-tumor activity in several solid tumor xenograft models. Disease eradication was accompanied by sustained functional persistence, indicated by reproducible protection from secondary tumor re-challenge. Anti-cancer activity was consistently superior to an analog of a clinical stage linear CAR comprising an NKG2D-CD3 fusion. Mechanistically, functionality of NKG2D / Dap10-12 CAR T-cells was underpinned by transcriptomic re-programming to increase oxidative phosphorylation and ribosome biosynthesis..

overall_design: To compare gene expression by ligand-activated NKG2D-based CAR T-cells of the indicated design, retrovirus-engineered CAR T-cells were activated for 24 hours on immobilised MICA

first: Jana

last: Obajdin

first: Daniel

last: Larcombe-Young

first: Maya

last: Glover

first: Fahima

last: Kausar

first: Caroline

last: Hull

first: Katie

middle: R

last: Flaherty

first: Richard

last: Beatson

first: Domenico

last: Cozzetto

first: Ge

last: Tan

first: Phoebe

last: Dunbar

first: Alessandra

last: Vigilante

first: Anna

last: Schurich

first: David

last: Davies


title: Activation of STAT3-mediated ciliated cell survival protects against severe infection by respiratory syncytial virus

status: Public on Sep 30 2024

city: Boston

first: Caiqi

last: Zhao

address: 55 Fruit St

institute: MGH

summary: Respiratory syncytial virus (RSV) selectively targets ciliated cells in human bronchial epithelium and can cause bronchiolitis and pneumonia mostly in infants. To identify molecular targets of intervention during RSV infection in infants, we investigate how age regulates RSV interaction with the bronchial epithelium barrier. Employing precision-cut lung slices and air-liquid interface cultures generated from infant and adult human donors, we found robust RSV virus spread and extensive apoptotic cell death only in infant bronchial epithelium. In contrast, adult bronchial epithelium showed insignificant barrier damage and limited RSV infection. Single nuclear RNA-sequencing revealed age-related insufficiency of an anti-apoptotic STAT3 activation response to RSV infection in infant ciliated cells, which was exploited to facilitate virus spread via the extruded apoptotic ciliated cells carrying RSV. Activation of STAT3 and blockade of apoptosis rendered protection against severe RSV infection in infant bronchial epithelium. Lastly, apoptotic inhibitor treatment of a neonatal mouse model of RSV infection ameliorated infection and inflammation in the lung. Taken together, our findings identify a STAT3-mediated anti-apoptosis pathway as a target to battle severe RSV disease in infants.

overall_design: Single nuclei of neonatal and adult air-liquid-interface (ALI) cultures  were dissociated and isolated at 1 day post RSV infection and analyzed using single-nuclei RNA sequencing

first: Xingbin

last: Ai


title: A deep phenotyping study in mouse and iPSC models to understand the role of oligodendroglia in optic neuropathy in Wolfram syndrome

city: Leuven

first: Yoke Chin

last: Chai

state: Leuven

address: Herestraat 49, ON5

department: Development & Regeneration

country: Belgium

institute: KU Leuven

summary: Oligodendrocyte progenitor cells (OPCs) derived from two WS patient lines (c2002_mutant and 2010_Mutant) and their respective isogenic line (Cl7_Ctrl and 2g6_Ctrl) were sequenced to determine transcriptomic differences

overall_design: 6 replicates of each Patient and Isogenic iPSC derived OPCs were sequenced

first: Karan

last: Ahuja

first: Catherine

last: Verfaillie

first: Fatemeharefeh

last: Nami

first: Yoke-Chin

first: Lies

last: De Groef


title: Functional heterogeneity of meniscal fibrochondrocytes and microtissue models is dependent on modality of fibrochondrocyte isolation

city: Edmonton

first: Zhiyao

last: Ma

state: Alberta

country: Canada

institute: University of Alberta

summary: Collagenase digestion (d) and cellular outgrowth (og) are the current modalities of meniscus fibrochondrocytes (MFC) isolation for bioengineering and mechanobiology related studies. However, how these modalities may impact study outcomes are unknown. Here, we show og- and d-isolated MFC have distinct proliferative capacity, transcriptomic profiles via RNA sequencing (RNAseq), extracellular matrix (ECM)-forming and migratory capacities. Our data show that microtissue models developed from og-isolated MFC display a contractile phenotype with higher expressions of α-smooth muscle actin (ACTA2) and transgelin (TAGLN) and are mechanically stiffer than their counterparts from d-MFC. Moreover, we introduce a novel method of MFC designated digestion-after-outgrowth (dog). The transcriptomic prolife of dog-MFC are distinct from d-and og-MFC including a higher expression of mechanosensing caveolae-associated caveolin-1 (CAV1). Additionally, dog-MFC were superior chondrogenically and generated larger-size microtissue models containing a higher frequency of smaller collagen fiber diameters. Thus, we demonstrate that the modalities of MFC isolation influences the downstream outcomes of bioengineering and mechanobiology-related studies.

overall_design: In details the current study aimed to deduce the differences in the phenotype of cell population isolated using different isolation methods digestion (d), outgrowth (og) and digestion-after-outgrowth (dog). Further, using the pellet based microtissue model we evaluated how different cell isolation methods effect morphology and chondrogenic differentiation capacities as measured by ECM synthesis, expression of chondrogenic markers, microtissue mechanical properties, expression of contractile markers alpha-smooth muscle actin (alpha-SMA) and Transgelin (TAGLN) and migration of the cells and detailed transcriptomics analysis of cells cultured under chondrogenic induction cultured under hypoxia (5% O2) as optimised in our previous study to promote MFC proliferation and upregulation of the expression of collagen type II and aggrecan in the expanded cells

first: Shikha

last: Chawla

first: Xiaoyi

last: Lan

first: Eva

last: Zhou

first: Aillette

last: Mulet-Sierra

first: Melanie

last: Kunze

first: Adetola

last: Adesida


title: RNA-seq of RET-aberrant cancer cell lines treated with RET-TKI selpercatinib

city: Kyoto

first: Yuki

last: Katayama

address: 465, Kajii-cho, Kamigyo-ku

institute: Kyoto prefectural university of medicine

summary: RET-aberrant cancer discovered as a relevant targetable oncogene in several types of tumors, whose inhibitors have marked efficacy. However, some of patients with RET-aberrant cancer are insensitive to RET- tyrosine kinase inhibitors (TKIs) and are clinically non-responders. Recently, drug-tolerant mechanisms have been gaining attention as targets for initial therapies aimed at overcoming drug resistance. However, the underlying mechanisms of drug-tolerant cells emergence treated with RET-TKIs derived from RET-aberrant cancer cells remains unknown. In this study, HER3 signal activity through YAP1 was led to maintaining cell survival and inducing the emergence of cells tolerant to RET-TKIs selpercatinib and pralsetinib in high YAP1 expressed RET- rearranged cancer cells.  These results suggested that YAP1-HER3 axis plays pivotal roles for cell survival under an exposure with RET-TKIs in the intrinsic resistance to RET-TKIs and the emergence of tolerant cells by RET-TKIs in YAP1 expressed RET-aberrant cancer, suggesting that YAP1/HER3 inhibition and RET-TKIs is a highly potent combination for initial treatment.

overall_design: LC-2/ad and TPC-1 cells were treated with selpercatinib for 48 hours. Total RNA was collected and performed gene expression profiling analysis using data obtained from RNA-seq of parent cells and cells treated with selpercatinib.

first: Tadaaki

last: Yamada


title: Transcriptomic Landscape of Treatment - Naïve Erosive Esophagitis

city: Shanghai

first: Ye

address: 197 Ruijin Er Road

institute: Ruijin Hospital

summary: Erosive Esophagitis (EE) is one of the common forms of gastroesophageal reflux disease (GERD). We performed transcriptomic analysis (RNA sequencing) of esophageal biopsies from patients with EE and healthy controls to increase understanding of complex cellular and molecular pathways in EE.

overall_design: Patients with persistent symptoms suggestive of GERD (acid regurgitation and/or heart burn) and no previously antisecretory or prokinetic therapy were advised to undergo 24 h pH monitor and endoscopy in sequence. EE was defined as abnormal 24 h pH parameters and LA grade C or D, according to the LA classification. Healthy voluntary controls were those with absence of GERD symptoms and normal endoscopic appearance. In each subject, specimen was taken at 5 cm above the squamo-columnar junction, from macroscopically intact mucosa, prior to any antisecretory and/or prokinetic therapy. In total, mucosal biopsies from patients with EE (n=8)  and healthy controls (n=8) underwent RNA sequencing.

first: Teng

first: Di

last: Ge

first: Duowu

last: Zou


title: PD-L1 regulation of colonic inflammation and colorectal cancerdevelopment

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

summary: PD-L1 acts as an immune checkpoint that inhibits T cell activation and suppresses colonic inflammation. We aimed at determine the cellular and molecular mechanisms underlying PD-L1 function in colon epithelium and colon cancer. scRNA-seq was perform to determine the gene expression profiles in epithelial cells and immune cells in the single-cell level. Tumors were induced in WT and PD-L1 KO mice. Analysis of WT and PD-L1 KO tumors revealed that loss of PD-L1 alters T cells, myeloid cells, B cells, and tumor-associated fibroblast subpopulations. Our finding determines that PD-L1 regulates multiple cellular populations to regulates host immune response and tumor development.

overall_design: Tumor tissues were dissected from mice and digested with collagenase to make single cells. The single cells were collected using a 10xGenomics system for cDNA libraray preparation and high throughout DNA sequencing.

first: Dakota

last: Poschel

first: John

last: Klement

first: Alyssa

last: Merting

first: Kebin

last: Liu


title: Topoisomerase I (TOP1) is a functional mitotic interactor of the bookmarking factor HNF1B [ChIPseq_786O]

first: Marco

last: PONTOGLIO

overall_design: HNF1B-ChIPseq was performed in asynchronous and mitotic 786-O cells fixed with NAQC (non-aqueous crosslinking) or AQC (aqueous crosslinking) methods. Free cycling mIMCD3 cells were admixed either to asynchronous or mitotic 786-O cells just before the crosslinking step as a calibrating internal control.

first: Alessia

last: Bagattin

first: Salvina

last: Tammaccaro

first: Magali

last: Chiral

first: Munevver

last: Makinistoglu

first: Jonathan

last: Lerner

first: Serge

last: Garbay

first: Nicolas

last: Kuperwasser

last: Pontoglio