title: TRAF3 loss-of-function Reveals the Non-Canonical NF-κB Pathway as a Therapeutic Target in Diffuse Large B-cell Lymphoma

city: Vancouver BC

first: Christian

last: Steidl

state: British Columbia

address: 675, West 10th Ave

department: Department of Lymphoid Cancer Research

institute: BC Cancer

summary: Treatment of diffuse large B-cell lymphoma (DLBCL) remains challenging due to extensive molecular, clinical, and pathological heterogeneity. Here, we report recurrent focal deletions of the chr14q32.31-32 locus, including TRAF3, a negative regulator of NF-κB signaling, in a cohort of uniformly-treated de novo DLBCL (24/324 cases). Integrative analysis uncovered a correlation between TRAF3 copy number loss and TRAF3 reduced expression. CRISPR-mediated TRAF3 loss-of-function (LOF) in DLBCL cell lines enhanced non-canonical NF-κB (NC NF-κB) signaling, rendering cells sensitive to shRNA-induced knockdown of the central NC NF-κB kinase, NIK. NIK pharmacological inhibitors differentially impaired proliferation, and induced apoptosis of TRAF3 LOF cells, further suggesting an acquired onco-addiction to NC NF-κB. Beyond these cell-intrinsic effects, co-culturing of TRAF3 LOF DLBCL cells with primary human CD8+ T-cells revealed an impairment in effector marker induction (Granzyme B, IFNγ) and proliferation in the latter. Accordingly, a reduction in T-cell infiltrates was observed in the microenvironment of TRAF3-low expressing primary DLBCL tumor samples. Neutralization of IL10 produced by TRAF3 LOF cells restored and enhanced GZMB and IFNγ expression in co-cultured CD8+ T-cells. Our findings demonstrate a direct relationship between TRAF3 genetic alterations and NC NF-κB activation, favoring pro-oncogenic cell-intrinsic effects and immune-evasive mechanisms, and highlight NIK as a therapeutic target in defined subset of DLBCL.

overall_design: RNA-seq analysis of 4 cell line systems (3 wildtype (WT) and 3 mutant (MUT)) = 24 samples total

first: Michael

last: Li

first: Lauren

last: Chong


title: Effect of Epstein-Barr Virus DNA on the Transcriptional Profile of BALB/c Mouse Peripheral Blood Mononuclear Cells

status: Public on Apr 09 2024

city: Riad El-Solh

first: Elias

middle: A.

last: Rahal

state: Beirut

department: Experimental Pathology, Immunology and Microbiology

country: Lebanon

institute: American University of Beirut

type: Expression profiling by high throughput sequencing

summary: To examine the effect of DNA from the Epstein-Barr Virus (EBV) on the transcriptional profile of mouse peripheral blood mononuclear cells (PBMCs), BALB/c mouse cells were isolated and cultured in the presence or absence of EBV DNA. RNA was extracted from these cells and then subjected to sequencing. We observed significantly enhanced expression of genes that play roles in proinflammatory processes including ones involved in autoimmune diseases such as rheumatoid arthritis.

overall_design: PBMCs were cultured in the presence or absence of EBV DNA at 37° C in the presence of 5% CO2. Triplicates of the culture conditions were performed. RNA was then extracted from these cells and a TruSeq RNA Sample Prep Kit v2 was used for library preparation. An Illumina NovaSeq 6000 System was then used for sequencing employing the NovaSeq 6000 S4 Reagent Kit. Trimmed reads were mapped to the Mus musculus mm10 reference genome with HISAT2. featureCounts was used to assign sequence reads to genomic features and then Limma-Voom was employed for differential expression (DE) analysis.

first: Marwa

last: Shehab

first: Hadi

last: Hussein

middle: A


title: Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment [CUT & RUN]

status: Public on Apr 10 2024

city: Memphis

first: Daniel

last: Savic

state: TN

address: 262 Danny Thomas pl.

department: Pharmaceutical Sciences

country: USA

institute: St. Jude Children's Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Although acute lymphoblastic leukemia (ALL) is the most prevalent childhood cancer, there is limited understanding of the contribution of inherited genetic variation on inter-individual differences in chemotherapy response, and defining genetic factors impacting therapy failure can help better predict response and identify drug resistance mechanisms. Using inherited noncoding variants associated with chemotherapeutic drug resistance and/or treatment outcome, we mapped these variants to ALL cis-regulatory elements and investigated their gene regulatory potential and genomic connectivity using massively parallel reporter assays and promoter capture Hi-C, respectively. We identified 53 variants with reproducible allele-specific effects on transcription and high-confidence gene targets. Subsequent functional interrogation of the top variant (rs1247117) determined that it disrupted a PU.1 consensus motif and PU.1 binding affinity. Importantly, deletion of the genomic interval containing rs1247117 sensitized ALL cells to vincristine. Together, these data demonstrate that noncoding regulatory variation associated with diverse pharmacological traits harbor significant effects on allele-specific transcriptional activity and impact sensitivity to chemotherapeutic agents in ALL.

overall_design: PU.1 genomic binding in NALM6 cells. N=1 with IgG used for peak calling and E. Coli spike-in for normalization.

first: Kashi

middle: R

last: Bhattarai

first: Robert

middle: J

last: Mobley

first: Kelly

last: Barnett

middle: C

last: Ferguson

first: Jonathan

middle: D

last: Diedrich

first: Brennan

middle: P

last: Bergeron

first: Wenjian

last: Yang

first: Kristine

last: Crews

last: Jabbour

first: Christopher

middle: S

last: Manring

first: Elisabeth

last: Paietta

first: Steven

middle: M

last: Kornblau

first: Wendy

last: Stock

first: Hiroto

last: Inaba

first: Sima

last: Jeha

first: Ching-Hon

last: Pui

first: Cheng

last: Cheng

first: Mary

middle: V

last: Relling

first: William

middle: E

last: Evans

first: Jun


title: Assessing susceptibility for polycyclic aromatic hydrocarbon toxicity in an in vitro 3D respiratory model for asthma

status: Public on Apr 08 2024

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

summary: There is increased emphasis on understanding cumulative risk from the combined effects of chemical and non-chemical stressors as it relates to public health.  Recent animal studies have identified pulmonary inflammation as a possible modifier and risk factor for chemical toxicity in the lung after exposure to inhaled pollutants; however, little is known about specific interactions and potential mechanisms of action.  In this study, primary human bronchial epithelial cells (HBEC) cultured in 3D at the air-liquid interface (ALI) are utilized as a physiologically relevant model to evaluate the effects of inflammation on toxicity of polycyclic aromatic hydrocarbons (PAHs), a class of contaminants generated from incomplete combustion of fossil fuels. Normal HBEC were differentiated in the presence of IL-13 for 14 days to induce a profibrotic phenotype similar to asthma. Fully differentiated normal and asthmatic phenotype HBEC were treated with benzo[a]pyrene (BAP; 1 – 40 ug/mL) or 1% DMSO/PBS vehicle at the ALI for 48 hrs. Cells were evaluated for cytotoxicity, barrier integrity, and transcriptional biomarkers of chemical metabolism and inflammation by quantitative PCR.  Cells with the asthmatic phenotype treated with BAP show some significant (p<0.05) increase in cytotoxicity and significantly (p<0.05) decreased barrier integrity compared to normal cells.  Asthmatic phenotype cells also showed increase sensitivity to BAP metabolism compared to cells with the normal phenotype.  Additionally, RNA sequencing data showed that a large number of genes were uniquely significantly expressed in cells with the induced asthmatic phenotype exposed to BAP.  Future studies will further explore mechanisms of toxicity from global transcriptomics and investigate the role of microRNA in mediating mechanisms of toxicity and inflammation.  These data are the first to evaluate the role of combined environmental factors associated with inflammation from pre-existing disease and PAH exposure on pulmonary toxicity in a physiologically relevant human in vitro model.

overall_design: Fully differentiated bronchial epithelial cells (n=4 replicates) were treated with 40 µg/ml benzo[a]pyrene (BAP) or vehicle control (PBS with 1% DMSO) for 48 hrs.   In addition bronchial epithelial cells differentiated in the presence of 10 ug/mL interluekin-13 were treated with 40 µg/ml benzo[a]pyrene (BAP) or vehicle control (PBS with 1% DMSO) for 48 hrs.  Isolated mRNA were sequenced on BGISEQ-500 platform


title: A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS

city: State College

first: Catherine

last: Douds

state: Pennsylvania

department: BMMB

institute: Penn State University

summary: A key to understanding the roles of RNA in regulating gene expression is knowing their structures in vivo. One way to obtain this information is through probing structures of RNA with chemicals. To probe RNA structure directly in cells, membrane-permeable reagents that modify the Watson-Crick (WC) face of unpaired nucleotides can be used. While dimethyl sulfate (DMS) has led to substantial insight into RNA structure, it has limited nucleotide specificity in vivo, with WC face reactivity only at Adenine (A) and Cytosine (C) at neutral pH. The reagent 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) was recently shown to modify the WC face of Guanine (G) and Uracil (U). While useful at lower concentrations in experiments that measure chemical modifications by reverse transcription stops, at higher concentrations necessary for detection by mutational profiling (MaP), EDC treatment leads to degradation of RNA. Indeed, herein we demonstrate EDC-stimulated degradation of RNA in Gram-negative and Gram-positive bacteria. In an attempt to overcome these limitations, we developed a new carbodiimide reagent, 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide methiodide (ETC), which we show specifically modifies unpaired Gs and Us in vivo without substantial degradation of RNA. We establish ETC as a probe for MaP and optimize the reverse transcription conditions and computational analysis in Escherichia coli. Importantly, we demonstrate the utility of ETC as a probe for improving RNA structure prediction both alone and with DMS.

overall_design: RNA structure probing MaP-seq libraries were constructed for total RNA from in vivo treated E. coli grown in LB at 37°C. To test initial RT conditions, one replicate of both untreated control RNA and 200mM ETC treated RNA libraries were prepared with TGIRT-III at 65°C, TGIRT-III at 70°C, Marathon, SuperScript-II, and HIV-RT, along with 300 mM ETC and 100 mM DMS detected with TGIRT-III at 65°C. Extension temperature was refined with 3 biological replicates of untreated RNA with TGIRT-III at 50°C, ETC treated RNA with TGIRT-III at 50°C, untreated RNA with TGIRT-III at 55°C, ETC treated RNA with TGIRT-III at 55°C, DMS treated RNA with TGIRT-III at 55°C, untreated RNA with TGIRT-III at 60°C, and ETC treated RNA with TGIRT-III at 60°C.

first: Paul

last: Babitzke

first: Philip

last: Bevilacqua


title: Transcriptional response of brain cell types to oxygen decline

city: Houston

first: Wei

last: Cao

state: Texas

address: 6431 Fannin St

department: Anesthesiology

institute: UT Health Houston

summary: Brain hypoxia is associated with a wide range of physiological and clinical conditions. Although oxygen is an essential constituent of maintaining brain functions, our understanding of how specific brain cell types globally respond and adapt to decreasing oxygen conditions is incomplete. In this study, we exposed mouse primary neurons, astrocytes, and microglia to normoxia and two hypoxic conditions and obtained genome-wide transcriptional profiles of the treated cells. Analysis of differentially expressed genes under conditions of reduced oxygen revealed a canonical hypoxic response shared among different brain cell types. In addition, we observed a higher sensitivity of neurons to oxygen decline, and dissected cell type-specific biological processes affected by hypoxia. Importantly, this study establishes novel gene modules associated with brain cells responding to oxygen deprivation and reveals a state of profound stress incurred by hypoxia.

overall_design:
To investigate the effect of oxygen decline on mouse brain cells we individually cultured to maturity mouse primary neurons, mouse primary astrocytes and mouse primary microglia and exposed them to different levels of oxygen for 8h. There were 2 sets of experiments per cell type: 5% vs 21% O2 ( 4 samples each-Experiment A) and 1% vs 21% O2 (4 samples each - Experiment B).
We then performed gene expression profiling analysis on the RNA-seq from the 16 samples obtained per cell-type.
Comparative gene expression profiling analysis of RNA-seq data per cell type at 1% vs 5% and 5% vs 21% O2.

first: Srinivas

middle: N

last: Puttapaka

first: Sanming

last: Li

first: Camille

last: Ravel-Godreuil

first: Ethan

last: Roy


title: Comparative 3D genome analysis between neural retina and RPE reveals differential cis-regulatory interactions at retinal disease loci [HiChIP]

city: Sevilla

first: Pedro Manuel

last: Martínez-García

state: Sevilla

address: Ctra. de Utrera, km. 1, 41013 Montequinto, Sevilla

country: Spain

institute: CSIC

summary: Vision depends on the functional interplay between the photoreceptor cells of the neural retina and the supporting cells of the underlying retinal pigment epithelium (RPE). Many genes involved in inherited retinal diseases (IRD) display highly specific spatiotemporal expression within these interconnected retinal components through the local recruitment of cis-regulatory elements (CREs) in 3D nuclear space. To understand the role of differential chromatin architecture in establishing tissue-specific expression patterns at IRD loci in the human neural retina and the RPE, we mapped genome-wide chromatin interactions by applying in situ Hi-C and H3K4me3 HiChIP to human adult post-mortem donor retinas. A comparative 3D genome analysis between neural retina and RPE revealed that almost 60% of known IRD genes were marked by differential cis-regulatory interactions or 3D genome structure. Furthermore, we zoomed in on tissue-specific chromatin interactions at the ABCA4 locus, which is implicated in the most common autosomal recessive IRD. We constructed high-resolution ABCA4 interaction profiles using UMI-4C, which, upon integration with bulk and single-cell epigenomic datasets and in vivo enhancer assays in zebrafish, revealed tissue-specific CREs for ABCA4. In summary, through extensive comparative 3D genome mapping, based on genome-wide (Hi-C), promoter-centric (HiChIP) and locus-specific (UMI-4C) assays of human neural retina and RPE, we have shown that gene regulation at key IRD loci is likely mediated by tissue-specific chromatin interactions. These findings do not only provide insight into tissue-specific regulatory landscapes at retinal disease loci, but also delineate the search space for genomic variation underlying unsolved IRD.

overall_design: HiChIP assays of H3K4me3 in RPE/choroid and neural retina from human adult post-mortem donor samples

first: Eva

last: D’haene

first: Victor

last: López Soriano

first: Pedro

first: Soraya

last: Kalayanamontri

first: Alfredo

last: Dueñas Rey

first: Ana

last: Sousa-Ortega

first: Silvia

last: Naranjo

first: Stijn

last: Van de Sompele

first: Lies

last: Vantomme

first: Sarah

last: Vergult

last: Bastos Neto

first: José

middle: L

last: Gómez-Skarmeta

first: Juan

last: Martínez-Morales

first: Miriam

last: Bauwens

last: Tena

first: Elfride

last: De Baere


title: Comparative 3D genome analysis between neural retina and RPE reveals differential cis-regulatory interactions at retinal disease loci [UMI4C]

overall_design: UMI4C assays in neural retina and RPE/choroid from human adult post-mortem donor samples


title: The long non-coding RNA LINC00941 regulates human epidermal homeostasis through interaction with the MTA2/NuRD complex

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

country: Germany

institute: University of Regensburg

summary: Numerous long non-coding RNAs (lncRNAs) were shown to have functional impact on cellular processes, such as human epidermal homeostasis, but for only a few the mode of action has been elucidated. Here, we report that lncRNA LINC00941 controls keratinocyte differentiation on a global level through association with the MTA2/NuRD complex, one of the major chromatin remodelers in cells. LINC00941 was found to interact with NuRD-associated MTA2, suppressing the expression of the transcription factor EGR3, a regulator of epidermal differentiation. Both, LINC00941 and the MTA2/NuRD complex are enriched in non-differentiated keratinocytes and repress the expression of differentiation genes through epigenetic silencing of EGR3, consequentially repressing premature differentiation of human progenitor cells.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for MTA2 in primary human keratinocytes upon siLINC00941 treatment

last: Morgenstern

first: Markus

last: Kretz


title: Gene expression profile at single neuron level of mouse hippocampal neuron, sampled from ex vivo acute brain slice

status: Public on Apr 06 2024

city: Sendai

first: Haruya

last: Yagishita

state: Miyagi

address: 6-3 Aoba, Aramaki, Aoba-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Tohoku University

summary: Hippocampal neurons exhibit heterogeneous properties, such as physiological and molecular expression patterns. To identify the gene expression patterns related to the physiological properties, we used single-cell RNA sequencing for neurons recorded juxtacellularly in vivo.

overall_design: Hippocampal dorsal CA1 neurons were recorded juxtacellularly and then fluorescently labeled by electrical stimulation in vivo using the ICR mice. The brains were then isolated and sectioned. The somas of the recorded and labeled neurons were manually suctioned with a glass pipette and analyzed using Quartz-seq2.

first: Yasuhiro

last: Go

first: Kazuki

last: Okamoto

first: Nariko

last: Arimura

first: Yuji

last: Ikegaya

first: Takuya

last: Sasaki


title: RNA-seq gene expression profiling of RefSeq genes in nuclear RNA from livers of mice treated with the nuclear receptor CAR (Nr1i3) agonist ligand TCPOBOP for 2 week or for 8 week.

status: Public on Apr 07 2024

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: PolyA-selected RNA was isolated from the nuclear fraction of frozen liver tissue from adult male and female ICR/CD1 mice that were treated with a TCPOBOP delivered using either a Low Corn Oil vehice or a High Corn Oil vehicle regimen. Livers were collected and nuclear RNA purified and analyzed either 2 week or 8 weeks after initiating TCPOBOP treatment. These samples are part of a study designed to elucidate genes and gene-based mechanisms underlying TCPOBOP-disrupted liver metabolic dysfunction, including the pericentral steatosis seen within 2 weeks of the initial TCPOBOP exposure. Major findings of this work included the following: Early (1-day) TCPOBOP transcriptional responses were enriched for CAR-bound primary response genes, and for lipogenesis and xenobiotic metabolism and oxidative stress protection pathways; late (2-wk) TCPOBOP responses included many CAR binding-independent secondary response genes, with enrichment for macrophage activation, immune response and cytokine and reactive oxygen species production. Late upstream regulators specific to TCPOBOP-exposed male liver were linked to pro-inflammatory responses and hepatocellular carcinoma progression. TCPOBOP administered weekly to male mice using a high corn oil vehicle activated carbohydrate-responsive transcription factor (MLXIPL)-regulated target genes, dysregulated mitochondrial respiratory and translation regulatory pathways, and induced more advanced liver pathology. Overall, TCPOBOP exposure recapitulated histological and gene expression changes characteristic of emerging steatotic liver disease, including secondary gene responses in liver non-parenchymal cells indicative of transition to a more advanced disease state.

overall_design: Liver nuclear RNA, polyA-selected, was isolated from frozen liver tissue from 7-8 week old male and female CD-1 mice treated with TCPOBOP or vehicle control for 14 days. Each RNA sample is derived from a single liver, with n=3-4 mice per treatment group.

first: Hong

last: Ma


title: FOXO1 is a master regulator of CAR T memory programming [scRNA_FOXO1_NGFR]

city: Philadelphia

first: Katherine

middle: Paige

last: Mueller

address: 3501 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

summary: Poor CAR T persistence limits CAR T cell therapies for B cell malignancies and solid tumors1,2. The expression of memory-associated genes such as TCF7 (protein name TCF1) is linked to response and long-term persistence in patients3–7, thereby implicating memory programs in therapeutic efficacy. Here, we demonstrate that the pioneer transcription factor, FOXO1, is responsible for promoting memory programs and restraining exhaustion in human CAR T cells. Pharmacologic inhibition or gene editing of endogenous FOXO1 in human CAR T cells diminished the expression of memory-associated genes, promoted an exhaustion-like phenotype, and impaired antitumor activity in vitro and in vivo. FOXO1 overexpression induced a gene expression program consistent with T cell memory and increased chromatin accessibility at FOXO1 binding motifs. FOXO1-overexpressing cells retained function, memory potential, and metabolic fitness during settings of chronic stimulation and exhibited enhanced persistence and antitumor activity in vivo. In contrast, TCF1 overexpression failed to enforce canonical memory programs or enhance CAR T cell potency. Importantly, endogenous FOXO1 activity correlated with CAR T and TIL responses in patients, underscoring its clinical relevance in cancer immunotherapy. Our results demonstrate that memory reprogramming through FOXO1 can enhance the persistence and potency of human CAR T cells and highlights the utility of pioneer factors, which bind condensed chromatin and induce local epigenetic remodeling, for optimizing therapeutic T cell states.

overall_design: Single cell transcriptomic study of HER2.BBz CAR T cells overexpressing empty vector (NGFR) or FOXO1 which were isolated from Her2+ osteosarcoma tumors in NSG mice. 20,000 cells were collected per mouse with 5 total mice per condition. CAR T cells were generated from one human donor.

first: Alice

last: Wang

first: Evan

last: Weber


title: Comparative 3D genome analysis between neural retina and RPE reveals differential cis-regulatory interactions at retinal disease loci

first: Pedro Manuel

last: Martínez-García

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

overall_design: Refer to individual Series


title: Transcriptomic Profiling across Human Serotonin Neuron Differentiation via the FEV Reporter System

city: shanghai

first: yingqi

last: li

address: siping road

country: China

institute: tongji university

summary: This study has successfully established a human FEV reporter system using CRISPR/Cas9 gene-editing technology. We have investigated the precise timing of FEV expression in human SNs. When compared to the previously established TPH2-reporter system, the FEV-reporter system has demonstrated the capacity to yield a greater number of highly-purified SNs, which can be utilized for in-depth exploration of the transcriptomic profiles of SNs during the differentiation process. Moreover, this expanded yield of purified SNs holds promise for facilitating high-throughput drug screening.

overall_design: Comparative gene expression profiling of RNA-seq data from cells differentiated from hESCs to human serotonin neurons at three time points (Day0 (hESCs), Day21, Day 28, Day42)

first: Yingqi

last: Li

first: Jianfeng

last: Lu


title: Transcriptomics analysis highlights potential ways in human pathogenesis in Leishmania braziliensis infected with the viral endosymbiont LRV1

city: Porto Velho

first: kátia

middle: Paula

last: Felipin

state: Rondônia

address: R. da Beira, 7671.

country: Brazil

institute: Fiocruz Rondônia

summary:
Leishmania (Viannia) braziliensis is a parasite prevalent in Brazil and associated with tegumentary leishmaniasis (TL), including cutaneous (CL) and mucosal (ML) forms. The mechanisms of pathogenesis of TL are not fully understood, including some factors related to the host and parasite interaction in response to infection, and especially about Leishmania RNA Virus 1 (LRV1), an endosymbiont virus parasitizing Leishmania species, particularly triggers ML. Molecular approaches are usually applied to compare situations and to understand these interactions. Here, microarray analysis identified 162 differentially expressed genes in LbLRV1+ vs. LbLRV1- infection, with 126 upregulated genes related to IFN signaling, OAS/RNAse L, vitamin D3, and RIG-I type receptors. Additionally, 36 down-regulated genes were observed. Then, two validation assays were performed to confirm these results (RT-qPCR and Cytometric Bead Array). The main results comprise the differential gene expression in cells infected with LbLRV1+ compared to LbLRV1- and control, with overexpression of various genes in LbLRV1+ cells. Cytokine levels showed no significant differences between LbLRV1+ and LbLRV1-. This study highlighted the activation of the OAS/RNase L signaling pathway and the non-genomic actions of vitamin D3 in LbLRV1+ infection compared to LbLRV1- and control. This research contributes to our understanding of the immune response and molecular pathways involved in Leishmania infections, particularly in the presence of LRV1.
We used microarrays to detail the global gene expression program underlying infection of human mnocyte-derived macrophages with LbLRV1-, LbLRV1+ and identified distinct classes of genes upregulated during this process.

overall_design: Comparison of gene expression levels in human macrophages after infection with LbLRV1+ and LbLRV1- in relation to uninfected human macrophages. Samples from three donors were selected to obtain human peripheral blood mononuclear cells (PBMCs). PBMCs from each donor were divided into three sets of cell culture experiments for differentiation into macrophages. The first group consisted of cultures maintained with infection by a LbLRV1+ strain and the second group was maintained with infection by a LbLRV1- strain. As a control for the experiment, a third group of cell cultures was maintained without infection. Gene expression levels were evaluated using microarray analysis.

first: K

last: FELIPIN

first: A

last: OLIVEIRA


title: SUMOylation of zebrafish transcription factor Zbtb21 affects its transcription activitym [ChIP-Seq]

city: Shanghai

first: ZHOU

last: FANG

address: 197, Ruijin Road II

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Phylogenetically conserved lysines 419 and 845 of zebrafish Zbtb21 protein can be conjugated with SUMO molecules. SUMOylation does not affect the subcellular localization and protein stability of Zbtb21, as well as the interaction with Zbtb14 or Zbtb21. Nevertheless, luciferase reporter assays revealed that Zbtb21 is a dual-function transcription factor which exerts activation or repression effect on different promoters, and SUMOylation can modulate the transcriptional activity of Zbtb21 in regulating downstream target genes. Hence, Zbtb21 is identified as a novel substrate of SUMOylation, which would be important for its function.

overall_design: RNA was extracted from cells transfected with wild type Zbtb21 and Zbtb21K419/845R double mutant and analyzed by chromatin immunoprecipitation sequencing.

first: Zhou

last: Fang

first: Yun

last: Deng


title: SUMOylation of zebrafish transcription factor Zbtb21 affects its transcription activitym


title: SUMOylation of zebrafish transcription factor Zbtb21 affects its transcription activity [RNA-Seq]

overall_design: RNA was extracted from three groups of cells transfected with PCS2, wild type Zbtb21 and Zbtb21K419/845R double mutant, and gene expression profiling was performed.


title: Characterization of human pancreatic tissue and organoids reveals subpopulation of intercalated duct cells with progenitor traits

city: Leiden

first: Françoise

last: Carlotti

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

summary: Pancreatic duct organoids have emerged as a valuable tool for investigating pancreas biology and physiology through in vitro modeling. Despite their widespread use, a comprehensive understanding of the cellular heterogeneity of organoids and their underlying tissue remains elusive. Here we performed single-cell transcriptomic profiling of human adult pancreatic exocrine tissue and their derived organoids, revealing a gradient of keratin expression within the ductal network that clustered cells into two distinct low- and high-keratin subpopulations. Keratin-high cells display a higher capacity to form organoids while keratin-low cells express stemness associated markers. Finally, comparative gene expression analysis between ductal tissue and derived organoids revealed a partial recapitulation of the in vivo heterogeneity. These findings further our knowledge on pancreatic duct organoids and pave the way for future investigations into the heterogeneity of the pancreatic ductal syste

overall_design: Pancreatic islet-depleted tissue of 5 donors and 2 organoid lines was sequenced utilizing the SORT-seq platform. Samples of 2 donors were additionally collected using Fluorescence activated cell sorting based on expression of cell surface marker GP2 to study both positive and negative populations.

first: Juri

last: Juksar

first: Eelco

last: de Koning


title: ARID1A suppresses R-loop mediated STING-Type I Interferon pathway activation of anti-tumor immunity (ChIP-Seq)

city: San Diego

first: Diana

last: Hargreaves

state: CA

address: 10010 North Torrey Pines Road

institute: The Salk Institute for Biological Studies

summary: Clinical trials have identified ARID1A mutations as enriched among patients who respond favorably to Immune Checkpoint Blockade (ICB) in several solid tumor types independent of microsatellite instability. We show that ARID1A loss in murine models is sufficient to induce anti-tumor immune phenotypes observed in ARID1A mutant human cancers, including increased CD8+ T cell infiltration and cytolytic activity. ARID1A deficient cancers upregulated an interferon (IFN) gene expression signature, the ARID1A-IFN signature, associated with increased R-loops and cytosolic single stranded DNA (ssDNA). Overexpression of the R-loop resolving enzyme, RNASEH2B, or cytosolic DNase, TREX1, in ARID1A deficient cells prevented cytosolic ssDNA accumulation and ARID1A-IFN gene upregulation. Further, the ARID1A-IFN signature and anti-tumor immunity were driven by STING dependent Type I IFN signaling, which was required for improved responsiveness of ARID1A mutant tumors to ICB treatment. These findings define a molecular mechanism underlying anti-tumor immunity in ARID1A mutant cancers.

overall_design: ChIP-Seq for STAT1, STAT2, and IRF9 was performed in WT and Arid1a -/- MEFs.

first: Matthew

last: Maxwell


title: ARID1A suppresses R-loop mediated STING-Type I Interferon pathway activation of anti-tumor immunity


title: ARID1A suppresses R-loop mediated STING-Type I Interferon pathway activation of anti-tumor immunity (ATAC-Seq)

overall_design: ATAC-seq was performed in sgArid1a or sgScramble B16F10 cells (in vitro).


title: ARID1A suppresses R-loop mediated STING-Type I Interferon pathway activation of anti-tumor immunity (RNA-Seq)

overall_design: RNA-seq of sgScramble and sgArid1a B16F10 tumors (in vivo); RNA-seq of sgScramble + PBS, sgArid1a + PBS, sgScramble + IFNg, and sgArid1a + IFNg treated B16F10 (in vitro); sgScramble, sgArid1a, Cgas dKO, Sting dKO, and sgArid1a + anti-IFNAR B16F10 (in vitro); DMSO treated B16F10, BD98 treated B16F10, BD98 + anti-IFNAR treated B16F10 (in vitro); sgScramble + DMSO, sgArid1a + DMSO, sgArid1a + ruxilitinib (JAK1/2i) B16F10 cells (in vitro); RNA-seq of sgArid1a and sgScramble MC38 cell lines (in vitro); RNA-seq of Arid1a -/- or WT MEF cells (in vitro);  Total-RNA-seq of sgArid1a or sgScramble B16F10 cells (in vitro).


title: Antitumor progenitor exhausted CD8 T cells are sustained with TCR engagement [CUT&Tag]

status: Public on Apr 05 2024

first: Tian

last: Mi

address: 262 Danny Thomas Pl MS351

department: Immunology

summary: Durability of an antitumor immune response is mediated in part by the persistence of progenitor exhausted CD8 T cells (Tpex). Tpex serve as a source for the pool of effector T cells, and in the absence of their cognate antigen, they are able to preserve their quantity through a process of self-renewal. However, it remains unknown how TCR engagement impacts the self-renewal capacity of Tpex in settings of continued antigen exposure. Here, we used a Lewis lung carcinoma model that elicits an optimal or attenuated TCR signal in CD8 T cells to investigate its effect on Tpex persistence during tumor development. Longitudinal phenotyping and single-cell transcriptomics of tumor-specific T cells revealed that formation of the Tpex reservoir in tumor-draining lymph nodes, and its subsequent replenishment of intratumoral Tpex, is dependent on optimal TCR engagement. Notably, adoptive transfer of optimally primed Tpex into a tumor setting with attenuated TCR stimulation significantly accelerates their terminal differentiation, contrasting to the sustained self-renewal occuring with optimal TCR stimulation. This TCR-reinforced Tpex development and self-renewal is coupled to proximal positioning to dendritic cell niches and epigenetic imprinting that involves increased chromatin accessibility at Egr2 and Tcf1 target loci. Collectively, our study highlights the critical role of TCR engagement in sustaining Tpex during tumor progression

overall_design: 2 replicates of Naive CD8 samples, 2 replicates of LN_M9 samples, 2 replicates of TU_M9_Tpex samples

first: Xin

last: Lan

first: Ben

last: Youngblood


title: Antitumor progenitor exhausted CD8 T cells are sustained with TCR engagement [WGBS]

type: Methylation profiling by high throughput sequencing

overall_design: 3 replicates of LN_M9 samples, 3 replicates of LN_C6M9 samples, 1 replicate each of TU_M9, TU_C6M9, TU_M9_TIM3+, TU_M9_TIM3-, TU_C6M9_TIM3+, TU_C6M9_TIM3- samples


title: Antitumor progenitor exhausted CD8 T cells are sustained with TCR engagement [ATACseq]

overall_design: 2 replicates of Naive samples, 4 replicates of LN_M9 samples, 4 replicates of LN_C6M9 samples, 2 replicates of TU_M9_Tex samples, 5 replicates of TU_M9_Tpex samples, 2 replicates of TU_C6M9_Tex samples, 5 replicates of TU_C6M9_Tpex samples, 2 replicates of Naïve CD8 samples


title: Antitumor progenitor exhausted CD8 T cells are sustained with TCR engagement [scRNAseq]

overall_design: 2 replicates of LN_M9 samples, 2 replicates of LN_C6M9 samples


title: Antitumor progenitor exhausted CD8 T cells are sustained with TCR engagement


title: Spatial Transciptomics of human trephine BM samples from AML patients and healthy donors

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

summary: We have identified a novel cell subtype within acute myeloid leukemia progression, termed regeneration enrcihed cells (RECs) and aimed to assay its presence and location within the human BM tissue as compared to healthy

overall_design: Identify specific co-localization of hematopoietic cell types within leukemic bone marrow

first: Cameron

last: Hollands

first: Charisa

last: Henly

first: Allison

last: Boyd

first: Mick


title: scRNA seq data from AML PDXs throughout a cytarabine treatment, and directly from AML patients at differnet stages of disease progression

summary: We used scRNA seq on regenerating PDX models and de novo AML patient cells to delineate the heirarchical regeneration of AML following treatment

overall_design: Bone Marrow from AML PDXs were isolated via mechanical dissociation and red blood cell lysis before FACS purification on humanCD45 and CD33 markers prior to scRNA seq protocol. De novo samples were purified by density gradient centrifugation and isolated for live cells via FACS 7AAD exclusion prior to scRNA seq protocol


title: Comparative 3D genome analysis between neural retina and RPE reveals differential cis-regulatory interactions at retinal disease loci [Hi-C]

first: Pedro Manuel

last: Martínez-García

overall_design: in situ Hi-C on RPE/choroid and neural retina from human adult post-mortem donor samples

first: Eva

last: D’haene

first: Victor

last: López Soriano

first: Pedro

first: Soraya

last: Kalayanamontri

first: Alfredo

last: Dueñas Rey

first: Ana

last: Sousa-Ortega

first: Silvia

last: Naranjo

first: Stijn

last: Van de Sompele

first: Lies

last: Vantomme

first: Sarah

last: Vergult

last: Bastos Neto

first: José

last: Gómez-Skarmeta

first: Juan

last: Martínez-Morales

first: Miriam

last: Bauwens

last: Tena

first: Elfride

last: De Baere


title: Exercise-induced beta2 adrenergic receptor activation enhances the anti-leukemic activity of expanded gamma-delta T-Cells via DNAM-1 upregulation and PVR-Nectin-2 recognition

status: Public on Apr 04 2024

city: Tucson

first: Forrest

middle: Lee

last: Baker

state: Arizona

address: 1501 N. Cmapbell Ave CRC Building Room 5340

department: School of Nutritional Sciences and Wellness

institute: The University of Arizona

summary: Exercise mobilizes cytotoxic lymphocytes to blood which may allow superior cell products to be manufactured for cancer therapy. Gamma-delta T-cells have shown promise for treating solid tumors, but there is a need to increase their potency against hematologic malignancies. Here, we show that human gamma-delta T-cells mobilized to blood in response to just 20-minutes of graded exercise have surface phenotypes and transcriptomic profiles associated with cytotoxicity, adhesion, migration and cytokine signaling. Following 14-days ex vivo expansion with zoledronic acid and interleukin (IL)-2, exercise mobilized gamma-delta T-cells had surface phenotypes and transcriptomic profiles associated with enhanced effector functions, and demonstrated superior cytotoxic activity against multiple hematologic tumors in vitro, and in vivo in leukemia bearing xenogeneic mice. Infusing humans with the beta1+beta2-agonist isoproterenol and administering beta1 or beta1+beta2 antagonists prior to exercise revealed these effects to be beta2-adrenergic receptor (AR) dependent. Antibody blocking of DNAM-1 on expanded gamma-delta T-cells, as well as the DNAM-1 ligands PVR and Nectin-2 on leukemic targets, abolished the enhanced anti-leukemic effects of exercise. These findings provide a mechanistic link between exercise, beta2-AR activation, and the manufacture of superior gamma-delta T-cell products for adoptive cell therapy against hematological malignancies. Expanded Vgamma9Vdelta2+ T-cells expanded, from the same participants, after both exercise (n=2) and isoproterenol infusion (n=2) underwent bulk RNA sequencing and gene expression analysis.

first: Kyle

last: Smith

first: Preetesh

last: Mylabathula

first: Tiffany

last: Zuniga

first: Douglass

last: Diak

first: Helena

last: Batatinha

first: Grace

last: Niemiro

first: Michael

last: Seckeler

first: Charles

last: Pedlar

first: Danie

last: O'Connor

first: Jamie

last: Colombo

first: Emmanual

last: Katsanis

first: Richard

last: Simpson


title: Effect of egr3 knockout on gene expression of dissected zebrafish hearts

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild-type siblings.

overall_design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype, we conducted a bulk RNA-seq analysis in dissected zebrafish hearts at 48 hpf.  We dissected 20 hearts for each biological duplicate of egr3 mutant and wild-type sibling samples in cold DMEM with 10% FBS.  Total RNA was isolated using the miRNeasy micro Kit (Qiagen 217084), followed by on-column DNase digestion (DNase-Free DNase Set, Qiagen 79254), and final elution was performed in 12μl of RNase-free water.   Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples.   1. Boezio, G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 (2023). https://doi.org:10.1242/dmm.049571

first: Agatha

last: da Silva

first: Felix

last: Gunawan

first: Giulia

last: Boezio

first: Emilie

last: Faure

first: Alexis

last: Théron

first: Jean-François

last: Avierinos

first: SoEun

last: Lim

first: Shivam

middle: G

last: Jha

first: Radhan

last: Ramadass

last: Guenther

first: Mario

last: Looso

first: Stéphane

last: Zaffran

first: Thomas

last: Juan

first: Didier

middle: Y

last: Stainier


title: Effect of Nr2f6 knockdown in C2C12 myocytes

city: Campinas

first: Dimitrius Santiago

middle: Passos Simoes Froes

last: Guimaraes

state: Sao Paulo

address: Carl von Linneaus

department: BFM

institute: Unicamp

summary:
Investigate the transcriptional landscape changes promoted by Nr2f6 knockdown in C2C12 myocytes.
We performed RNA-seq analysis in control non-target (siScr) and siNr2f6 transfected myocytes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 4 control siScr and 5 siNr2f6 transfected myocytes. Cells were transfected at the time of differentiation media swith and RNA collected by the 3rd day (72h later).

first: Dimitrius

first: Leonardo

middle: R

last: Silveira

first: Juleen

last: Zierath

first: Anna

last: Krook


title: An estrogen receptor α-derived peptide improves glucose homeostasis during obesity

city: College station

first: Shaodong

last: Guo

address: Rm135 Cater-Mattil Hall 2253 TAMU

department: Nutrition

institute: Texas A&M University

summary: Estrogen improves insulin sensitivity and increases energy expenditure, contributing to sexual dimorphism regarding type 2 diabetes mellitus (T2DM) susceptibility. Estrogen receptor α (ERα) plays a crucial role in mediating estrogen action on glucose and energy homeostasis. However, the underlying mechanisms remain incompletely understood. Here, we found a ligand-independent effect of ERα on the regulation of glucose homeostasis and identified an ERα-derived peptide as a potential insulin sensitizer. Deficiency of ERα but not ERβ in the liver impaired glucose homeostasis in male, female, and ovariectomized (OVX) female mice. Mechanistic studies revealed that ERα promoted hepatic insulin sensitivity by suppressing ubiquitination-induced IRS1 degradation. The ERα 1-280 domain mediated the ligand-independent effect of ERα on insulin sensitivity. Furthermore, we designed a peptide based on ERα 1-280 domain and found that ERα-derived peptide interacted with IRS1, increased IRS1 stability through suppressing its ubiquitination, and enhanced insulin sensitivity. Importantly, administration of ERα-derived peptide into obese mice significantly increased insulin sensitivity, attenuated glucose intolerance, and improved serum lipid profiles. These findings pave the way for the therapeutic intervention of T2DM by targeting the ligand-independent effect of ERα and indicate that ERα-derived peptide is a potential insulin sensitizer for the treatment of T2DM.

overall_design: RNA-seq on the livers of db/db male mice treated with control and AF1 peptide

first: Wanbao

last: Yang

first: Wesley

middle: A

last: Brashear


title: Bone Marrow Stromal Cells Induce Chromatin Remodeling in Multiple Myeloma Cells Leading to Transcriptional Changes [Multiome (10X Genomics) - scRNA-Seq & scATAC-Seq]

first: Mehmet

middle: K.

last: Samur

address: 440 Brookline Avenue

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

summary: The natural history of multiple myeloma is characterized by its localization to the bone marrow and its interaction with bone marrow stromal cells. The bone marrow stromal cells provide growth and survival signals, thereby promoting the development of drug resistance. Here, we show that the interaction between bone marrow stromal cells and myeloma cells (using human cell lines) induces chromatin remodeling of cis-regulatory elements and is associated with changes in the expression of genes involved in the cell migration and cytokine signaling. The expression of genes involved in these stromal interactions are observed in extramedullary disease in patients with myeloma and provides the rationale for survival of myeloma cells outside of the bone marrow microenvironment. Expression of these stromal interaction genes is also observed in a subset of patients with newly diagnosed myeloma and are akin to the transcriptional program of extramedullary disease. The presence of such adverse stromal interactions in newly diagnosed myeloma is associated with accelerated disease dissemination, predicts the early development of therapeutic resistance, and is of independent prognostic significance. These stromal cell induced transcriptomic and epigenomic changes both predict long-term outcomes and identify therapeutic targets in the tumor microenvironment for the development of novel therapeutic approaches.

overall_design: Nuclei from MM1S and HS5 cells (co-cultured for 72 hours) were isolated and processed for single-cell Multiome sequencing following 10x Genomics protocols.

first: Moritz

last: Binder

first: Raphael

last: Szalat

first: Srikanth

last: Talluri

first: Mariateresa

last: Fulciniti

first: Hervé

last: Avet-Loiseau

first: Giovanni

last: Parmigiani

middle: K

first: Nikhil

middle: C

last: Munshi


title: ARID1A suppresses R-loop mediated STING-Type I Interferon pathway activation of anti-tumor immunity (scRNA/TCR-seq)

first: Diana

last: Hargreaves

overall_design: Sorted on CD3+ CD8+ T cells and loaded into 10X ChIP K and processed with Chromium Next GEM Single Cell 5’ Reagent Kit v2 and TCR amplification kit.

first: Matthew

last: Maxwell


title: Changes in WT C2C12 Mouse Muscle Myoblast gene expression throughout differentiation.

status: Public on Apr 03 2024

city: Columbus

first: Dominic

last: Kolonay

state: OH

address: 460 W 12th Ave

department: Physiology and Cell Biology

institute: The Ohio State University

summary: Genesis of skeletal muscle relies on the differentiation and fusion of mono-nucleated muscle progenitor cells into the multi-nucleated muscle fiber syncytium. The temporally-controlled cellular and morphogenetic changes underlying this process are initiated by a series of highly coordinated transcription programs. Ultimately, highly specific coordination of these transcription programs is critical for their masterfully timed transitions, which in turn facilitate the intricate generation of skeletal muscle fibers from a naïve pool of progenitor cells. This work aims to categorize changes of gene expression in vitro in C2C12 mouse muscle myoblasts while they begin to form these multinucleated myotubes.

overall_design: Total RNA was isolated from n=3 cultured C2C12 myoblasts at D0 and D5 using Tri-Reagent according to the manufacturer’s instructions (Sigma Aldrich). RNA quality was accessed using a 2100 Bioanalyzer System (Agilent), and samples with RNA Integrity Number (RIN) greater than 8.0 were sequenced. Illumina RNA-Seq was performed by the Genomics Services Laboratory (GSL) at Nationwide Children’s Hospital (Columbus, OH). Quality assessment of the RNA-Seq data was performed using NGS-QC-Toolkit (v 2.3.3) with default settings (Patel & Jain 2012). Quality filtered reads were aligned to the mouse reference genome GRCm38 (mm10) using the Tophat2 (v 2.0.0) aligner with default settings (Kim et al. 2013). The R package DESeq2 (v 1.6.3) was used for differential gene expression analysis (Love et al. 2014). Read counts obtained from featureCounts were normalized by taking the median of each gene count across samples and dividing each sample gene count by the relative ratio of library sizes between the calculated median and sample size (Liao et al. 2014). The average normalized expression values of the samples were used to calculate fold change and P values.

first: Kedryn

last: Baskin

first: Keefe

last: McDougal


title: RNA-Seq, WGS, WXS of mouse myeloma tumors derived from Vk*MYC transgenic mice

city: Scottsdale

first: Peter

middle: Leif

last: Bergsagel

address: 13400 E Shea Blvd

institute: Mayo Clinic

summary: Comprehensive genomic analysis (WXS, WGS, RNAseq) identifies shared pathways of progression between human and mouse myeloma.

overall_design: De novo myeloma tumors develop in aged Vk*MYC MYC transgenic mice (summarized by "_O_" in sample name). They may be located in extramedullary locations such as spleen ("_EM_"), or intramedullary in the bone marrow ("_BM_"). They can be passaged in recipient mice ("_R_"). Rarely we are able to establish cell lines that can grow in vitro ("_V_"). Tumors from the mice undergo CD138-selection and are analyzed by RNA-Seq, WGS and WXS

first: Leif

first: Marta

last: Chesi


title: Single-cell RNA-seq data of human PBMC from Myasthenia Gravis patients

city: FUJISAWA

first: Yuumi

last: Okuzono

state: KANAGAWA

address: 26-Muraoka-higashi 2-chome

institute: Takeda Pharmaceutical Company Limited

summary: Myasthenia Gravis (MG) is a chronic autoimmune disorder characterized by severe muscle weakness. However, the seronegative MG patient subgroup, which accounts for about 15% of MG patients, remains challenging diagnosis, and the immunopathology is understudied. Therefore, we performed single-cell RNA-sequencing analysis by peripheral blood and plasma proteome analysis for the seronegative MG patients. Numerical abnormalities were observed in multiple immune cells including B-cells compared to healthy controls (HC) and correlated with disease activities. Additionally, plasma protein of CD22 that was reported to be expressed in the lineage of B-cell maturation, such as mature B-cells and memory B-cells was decreased compared to HC, and had correlation with disease severity, B-cells frequency, and the RNA expression level. These results suggest that the seronegative MG patients have immune disorders centered on B-cells. This is the first large-scale and innovative study to elucidate the immunopathology of the seronegative MG patients.

overall_design: Examination of gene expression profile of human PBMC from Myasthenia Gravis patients.

first: Shigeaki

last: Suzuki

first: Tatsuo

last: Ito

first: Ai

last: Maejima


title: Improvement of immune dysregulation and health-related quality of life in individuals with long COVID at 24-months following SARS-CoV-2 infection

city: Kensington

first: Sara

last: Ballouz

state: NSW

address: High St

country: Australia

institute: UNSW

summary: This study investigated the humoral and cellular immune responses in individuals with long COVID (LC) compared to age and gender matched recovered COVID-19 controls (MC) over 24-months. LC participants showed elevated spike and nucleocapsid IgG levels, higher neutralizing capacity, and increased spike- and nucleocapsid-specific CD4+ T cells, PD-1, and TIM-3 expression on CD4+ and CD8+ T cells at 3- and 8-months, but these differences did not persist at 24-months. Some LC participants had detectable IFN-γ and IFN-β, that was attributed to reinfection and antigen re-exposure. Single-cell RNA sequencing at 24-month timepoint revealed similar immune cell proportions and reconstitution of naïve T and B cell subsets in LC. No significant differences in exhaustion scores or antigen-specific T cell clones were observed. These findings suggest resolution of immune activation in LC and return to comparable immune responses between LC and MC over time. Improvement in self-reported health-related quality of life at 24-months was also evident in the majority of LC (62%). PTX3, CRP levels and platelet count were associated with improvements in health-related quality of life.

overall_design: ADAPT is an ongoing prospective, observational cohort study of patients seen at St Vincent’s Hospital Sydney (Australia) who tested PCR positive for SARS-CoV-2 infection. Each patient is followed for a period of 24-months from the time of diagnosis, with up-to 8 pre-specified timepoint collections. This analysis studied 10 individuals with long-COVID and 10 age and sex matched controls, all of which had an acute COVID19 infection in March 2020. PBMCs collected at 4, 8 and 24 month timepoints were sequenced with 10x and assessed for transcriptional differences.

first: Chansavath

last: Phetsouphanh

first: Brendan

last: Jacka

first: Katherine

middle: J

last: Jackson

first: Daniel

middle: B

last: Wilson

first: Bikash

last: Manandhar

first: Vera

last: Klemm

first: Hyon-Xhi

last: Tan

first: Adam

last: Wheatley

first: Anupriya

last: Aggarwal

first: Anouschka

last: Akerman

first: Vanessa

last: Milogiannakis

first: Mitchell

last: Starr

first: Phillip

last: Cunningham

first: Stuart

last: Turville

first: Stephen

last: Kent

first: Anthony

last: Byrne

first: Bruce

last: Brew

first: David

last: Darley

first: Gregory

last: Dore

middle: D

last: Kelleher

first: Gail

middle: V

last: Matthews


title: The TP53-activated E3 ligase RNF144B is a tumour suppressor that prevents genomic instability

status: Public on Apr 02 2024

city: Barcelona

first: Gerard

last: Romero

state: Catalonia

address: Doctor Aiguader, 88

department: Dpt of Medicine and Life Sciences, Universitat Pompeu Fabra (MELIS/UPF)

institute: Universitat Pompeu Fabra

summary: Background: TP53, the most frequently mutated gene in human cancers, orchestrates a complex transcriptional program crucial for cancer prevention. While certain TP53-dependent genes have been extensively studied, others, like the recently identified RNF144B, remained poorly understood. This E3 ubiquitin ligase has shown potent tumor suppressor activity in murine Eμ Myc-driven lymphoma, emphasizing its significance in the TP53 network. However, little is known about its targets and its role in cancer development, requiring further exploration. In this work, we investigate RNF144B's impact on tumor suppression beyond the hematopoietic compartment in human cancers.  Methods: Employing TP53 wild-type cells, we generated models lacking RNF144B in both non-transformed and cancerous cells of human and mouse origin. By using proteomics, transcriptomics, and functional analysis, we assessed RNF144B's impact in cellular proliferation and transformation. Through In vitro and in vivo experiments, we explored proliferation, transformation potential, DNA repair, cell cycle control, mitotic progression, and treatment resistance. Findings were contrasted with clinical datasets and bioinformatics analysis. Results: Our research underscores RNF144B's pivotal role as a tumor suppressor, particularly in lung adenocarcinoma. In both human and mouse oncogene-expressing cells, RNF144B deficiency heightened cellular proliferation and transformation. Proteomic and transcriptomic analysis revealed RNF144B's novel function in mediating protein degradation associated with cell cycle progression, DNA damage response and genomic stability. RNF144B deficiency induced chromosomal instability, mitotic defects, and correlated with elevated aneuploidy and worse prognosis in human tumors. Furthermore, RNF144B-deficient lung adenocarcinoma cells exhibited resistance to cell cycle inhibitors that induce chromosomal instability.  Conclusions: PRJNA1092607Supported by clinical data, our study suggests that RNF144B plays a pivotal role in maintaining genomic stability during tumor suppression.

overall_design:
MEFs were infected with the corresponding shRNAs in three independent biological replicas and sorted for GFP by flow cytometry using a BD Influx cell sorter (BD Biosciences).
cells were trypsinized and the pellet was snap frozen. RNA from 1 million cells was extracted using the Purelink RNA kit (10307963, Invitrogen) and submitted for analysis
Libraries were prepared using the TruSeq stranded mRNA Library Prep (20020594, Illumina) according to the manufacturer's protocol.
We were interested in the expression differences between RNF144B KD MEFs and those with shCTRL (shRENILLA)

first: Etna

last: Abad

first: Jérémy

last: Sandoz

first: Ivan

last: Zadra

first: Júlia

last: Urgel-Solas

first: Pablo

last: Borredat

first: Savvas

last: Kourtis

first: Laura

last: Ortet

first: Carlos

middle: M

last: Martínez

first: Donate

last: Weghorn

first: Sara

last: Sdelci

first: Ana

last: Janic


title: RNA Sequencing Analysis of Wild Type and Non-phosphorylatable CARM1 mutation knock-in HEL cells

city: Miami

first: Hidehiro

last: Itonaga

state: FL

address: 1501 NW 10th Ave

department: Department of Biochemistry and Molecular Biology

institute: Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami

summary: CARM1 is essential for the development and maintenance of myeloid neoplasms. We found that non-phosphorylatable CARM1 mutation impairs cell cycle progression, induces apoptosis, and downregulates stemness in JAK2-mutant cell lines, suggesting that CARM1 phosphorylation is required for maximal proliferation of myeloid neoplasms.

overall_design: Gene expression profile of wild-type or non-phosphorylatable CARM1 mutation (Y149F or Y334F single, or Y149F/Y334F double mutation) knock-in HEL cells.All cell lines sequencing experiments were repeated in triplicate. Differential expression of each non-phosphorylatable CARM1 mutation expressing cell line was performed independently comparing to wild-type.

first: Stephen

last: Nimer


title: Knockdown of METTL14 inhibits the development of neuroblastoma

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: We investigated the mechanism by which the m6A methyltransferase METTL14 functions in neuroblastoma. To explore the downstream target genes of METTL14, we performed RNA-seq analysis and found that the expression profile of the gene was significantly altered in METTL14 knockdown SK-N-BE(2) cells. We found that overexpression of METTL14 in neuroblastoma patients was a detrimental factor.

overall_design: mRNA profiles of SK-N-BE(2) cells transfected with scramble shRNA (sh-NC) or sh-METTL14 were generated by RNA sequencing, in duplicate, using Novaseq 6000.

first: Jianwei

last: Wang

first: Jian

last: Pan


title: A comprehensive analysis of pneumcoccal two-component system regulatory networks

city: Odense M

first: Jens

middle: Sivkær

last: Pettersen

state: Danmark

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

summary: This study investigates the regulons of 11 pneumococcal response regulators (RRs) by RNA-sequencing of RR-overexpression mutants.

overall_design: D39 wild type (WT), and RR-overexpression mutants (CEP:rr) was inoculated in triplicates in C+Y media and grown at 37°C to an OD 0.4 before RNA extraction.

middle: S

first: Flemming

last: Nielsen

first: Mikkel

last: Jørgensen


title: Biological Control of Root-Knot Nematode Meloidogyne incognita Infection of Tomato (Solanum lycopersicum L.) by the Oomycete Biocontrol Agent Pythium oligandrum

status: Public on Apr 01 2024

city: Nanjing

first: Paul

last: Daly

address: 50 Zhongling St

institute: Jiangsu Academy of Agricultural Sciences

summary: The biocontrol agent Pythium oligandrum, which is a member of phylum Oomycota, can control diseases caused by a taxonomically wide range of plant pathogens, including fungi, bacteria, and oomycetes. However, whether P. oligandrum could control diseases caused by plant root-knot nematodes (RKNs) was unknown. We investigated a recently isolated P. oligandrum strain GAQ1, and the P. oligandrum CBS530.74 strain, for the control of RKN Meloidogyne incognita infection of tomato (Solanum lycopersicum L.). Initially, P. oligandrum culture filtrates were found to be lethal to M. incognita second-stage juveniles (J2s) with up to 84% mortality at 24 h after treatment compared to 14% in the control group. Consistent with the lethality to M. incognita J2s, tomato roots treated with P. oligandrum culture filtrates reduced the attraction of nematodes, and the number of nematodes penetrating the roots was reduced by up to 78%. In a greenhouse pot trial, P. oligandrum GAQ1 inoculation of tomato plants significantly reduced the gall number by 58% in plants infected with M. incognita. Notably, P. oligandrum GAQ1 mycelial treatment significantly increased tomato plant height (by 36%), weight (by 27%), and root weight (by 48%). Transcriptome analysis of tomato seedling roots inoculated with the P. oligandrum GAQ1 strain identified ~2,500 differentially expressed genes. The enriched GO terms and annotations in the up-regulated genes suggested modulation of plant hormone-signaling and defense-related pathways in response to P. oligandrum. In conclusion, our results support that P. oligandrum GAQ1 can serve as a potential biocontrol agent for M. incognita control in tomato. Multiple mechanisms appear to contribute to the biocontrol effect involving direct inhibition of M. incognita, potential priming of tomato plant defenses, and plant growth promotion.

overall_design: Triplicate sets of pooled tomato seedling roots grown in Petri dishes with or without Pythium oligandrum GAQ1.

first: Yuwei

last: Xue

first: Weishan

last: Li

first: Mengnan

first: Ningchen

last: Ru

first: Siqiao

last: Chen

first: Min

last: Jiu

first: Hui

last: Feng

first: Lihui

last: Wei

first: Dongmei

last: Zhou


title: Individual transcription factors modulate both the micromovement of chromatin and its long-range structure [RNA-Seq]

city: Lausanne

first: David

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

country: Switzerland

institute: École polytechnique fédérale de Lausanne

summary: The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear how nucleus-wide chromatin organization responds dynamically to the activity of specific TFs. Here we examined how two TFs with opposite effects on local chromatin accessibility modulate chromatin dynamics nucleus-wide. We combine High-resolution Diffusion mapping (Hi-D) and Dense Flow reConstruction and Correlation (DFCC) in living cells to obtain an imaging-based, nanometer-scale analysis of local diffusion processes and long-range coordinated movements of both chromatin and TFs. We show that the expression of either an individual transcriptional activator (CDX2) or repressor (SIX6) with large numbers of binding sites increases chromatin mobility nucleus-wide, yet they induce opposite coherent chromatin motions at the micron scale. Hi-C analysis of higher-order chromatin structures shows that induction of the pioneer factor CDX2 leads both to changes in local chromatin interactions and the distribution of A and B compartments, thus relating the micromovement of chromatin with changes in compartmental structures. Given that inhibition of transcription initiation and elongation by RNA Pol II has a partial impact on the global chromatin dynamics induced by CDX2, we suggest that CDX2 overexpression alters chromatin structure dynamics both dependently and independently of transcription. Our biophysical analysis shows that sequence-specific TFs can influence chromatin structure on multiple architectural levels, arguing that local chromatin changes brought by TFs alter long-range chromatin mobility and its organization.

overall_design: Nuclear RNA-Seq in 3T3 with a doxycycline-inducible expression of CDX2, treated or not with doxycycline

first: Haitham

last: Shaban

first: Elias

middle: T

last: Friman

first: Cedric

last: Deluz

first: Armelle

middle: I

last: Tollenaere

first: Natalya

last: Katanayeva


title: Single cell methylation, RNA, and ATAC sequencing of amygdala brain tissue from inbred mouse strains

city: Los Angeles

first: Patrick

address: 635 Charles E Young Dr S

department: Psychiatry

institute: UCLA

summary: Knowing the genes involved in quantitative traits provides a critical entry point to understanding the biological bases of behavior, but there are very few examples where the pathway from genetic locus to behavioral change is known. Here we address a key step towards that goal by deploying a test that directly queries whether a gene mediates the effect of a quantitative trait locus (QTL). To explore the role of specific genes in fear behavior, we mapped three fear-related traits, tested fourteen genes at six QTLs, and identified six genes. Four genes, Lsamp, Ptprd, Nptx2 and Sh3gl, have known roles in synapse function; the fifth gene, Psip1, is a transcriptional co-activator not previously implicated in behavior; the sixth is a long non-coding RNA 4933413L06Rik with no known function. Single nucleus transcriptomic and epigenetic analyses implicated excitatory neurons as likely mediating the genetic effects. Surprisingly, variation in transcriptome and epigenetic modalities between inbred strains occurred preferentially in excitatory neurons, suggesting that genetic variation is more permissible in excitatory than inhibitory neuronal circuits. Our results open a bottleneck in using genetic mapping of QTLs to find novel biology underlying behavior and prompt a reconsideration of expected relationships between genetic and functional variation.

overall_design: Adult male animals (Jackson Laboratories) were euthanized at 10-16 weeks old in an isoflurane chamber and decapitated. The brain was removed and the amygdala was microdissected, snap frozen in dry ice, and stored at -80oC until processing. Tissue from ~2 animals were combined into a single tube and considered a replicate, with 2 replicates per strain for snmC-seq2, snRNA-seq, and snATAC-seq experiments. snmC-seq2 on microdissected tissue as previously described (Luo et al 2018). We selected for a 75-25 enrichment of neuronal vs non-neuronal nuclei during FACS sorting using NeuN-488/DAPI counterstains. For snRNA-seq, single nuclei suspension and library generation were completed at the Cedars Sinai Applied Genomics, Computation and Translational Core and followed the 10X protocol for the Chromium Next GEM Automated Single Cell 3’ Library and Gel Bead Kit v3.1 (cat# PN-100014) as described except for the following modifications: Suspensions from cell nuclei were generated using the recommended method from the 10X scMultiome protocol (CG000375 Rev C) to lyse cells and obtain nuclei. Following single nuclei suspension generation, nuclei were counterstained for 7-AAD and NeuN-405 antibody (Novus Biologicals, 1:200) and sorted on a MACSQuant Tyto prior to GEM generation. We selected for a 75-25 split of NeuN+/7-AAD+ nuclei for neurons and NeuN-/7-AAD+ for non-neuronal nuclei respectively. We captured ~10,000 nuclei per genotype per region per replicate on a single 10X GEM chip. All downstream library preparation was done according to the 10X protocol (CG000286) and sequenced on a Novaseq 6000 with a target of ~40-50k reads per nucleus. For snATAC-seq, single nuclei suspension and library generation were completed at the Cedars Sinai AGCT core and followed the 10X protocol for Next GEM scATAC-Seq v1.1 (PN-1000175) as described except for the following modifications: Nuclei suspensions were generated using the recommended method from the 10X scMultiome protocol (CG000375 Rev C) to lyse cells and obtain nuclei Following single nuclei suspension generation, nuclei were counterstained for 7-AAD and sorted on a MACSQuant Tyto prior to GEM generation. NeuN was not used for neuronal enrichment due to dye incompatibility between our NeuN antibody and a nuclear counterstain. After the sort, we carried out permeabilization of nuclei as per the protocol. We aimed to capture 10,000 nuclei per well x 8 wells, for a total of 80,000 nuclei over 8 total samples (~10,000 nuclei per genotype per region per replicate). All downstream library preparation was done according to the 10X protocol (CG000209) and sequenced on a Novaseq 6000 with a target of >35k reads per nucleus.

first: Jonathan

last: Flint

first: Chongyuan

last: Luo


title: Individual transcription factors modulate both the micromovement of chromatin and its long-range structure [ChIP-Seq]

overall_design: Chromatin immunoprecipitation on CTCF in 3T3 with a doxycycline-inducible expression of CDX2, treated or not with doxycycline


title: NKX2-2 based nuclei sorting on human archival pancreas enables the enrichment of islet endocrine populations for single nucleus RNA sequencing

city: Tallahassee

first: Yue

middle: Julia

last: Wang

address: 1115 West Call Street

department: Biomedical Sciences

institute: Florida State University

summary: Current approaches to profile the single-cell transcriptomics of human pancreatic endocrine cells almost exclusively rely on freshly isolated islets. However, human islets are limited in availability. Furthermore, the extensive processing steps during islet isolation and subsequent single cell dissociation might alter gene expressions. In this work, we cross-compared five nuclei isolation protocols and selected the citric acid method as the best strategy to isolate nuclei with high RNA integrity and low cytoplasmic contamination from human pancreata. We innovated fluorescence-activated nuclei sorting (FANS) based on the positive signal of NKX2-2 antibody to enrich for nuclei of the endocrine population from the entire nuclei pool of the pancreas. Our sample preparation procedure generated high-quality single-nucleus gene-expression libraries while preserving the endocrine population diversity. We observed comparable endocrine cellular composition and cell type signature gene expression between our snRNA-seq libraries and conventional scRNA-seq libraries generated with live cells from freshly isolated human islets. Our work fills a technological gap and helps to unleash archival pancreatic tissue for molecular profiling targeting the endocrine population. We expect that our protocol can be used to enrich nuclei for transcriptomics study from various populations in the pancreas and in different organs/tissues.

overall_design: Nuclei were isolated using citric acid method from archival frozen human pancreata. Islet endocrine population was enriched by FANS based on the positive signal of NKX2-2 labelling. Resulting nuclei were processed using 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v 3.1.


title: Immunometabolic adaptation in monocytes underpins functional changes during pregnancy [metabolism]

city: Swansea

first: April

last: Rees

address: Room 203 ILS1, Singleton Park

country: United Kingdom

institute: Swansea University

summary: Metabolic heterogeneity is a determinant of immune cell function. The normal physiological metabolic reprogramming of pregnancy that ensures the fuel requirements of mother and baby are met might also underpin changes in innate and adaptive immunity that occur with pregnancy and manifest as altered responses to pathogens and changes to autoimmune disease symptoms.     Here, we use peripheral blood monocytes, susceptible to microenvironmentally determined reprogramming of metabolism, to determine if pregnancy at term provokes an altered metabolic profile that underpins functional change.    Focusing on late gestation where any effect will be most profound, we reveal that monocytes lose M2-like and gain M1-like properties accompanied by reductions in mitochondrial mass, maximal respiration and cardiolipin content in pregnancy; glycolysis is unperturbed. We establish that muramyl dipeptide (MDP)-stimulated cytokine production relies on oxidative metabolism then show that reduced monocyte oxidative metabolism with pregnancy compromises the production of TNF and IL-6 in response to MDP but not LPS.     Overall, mitochondrially centred metabolic capabilities of late gestation monocytes are downregulated revealing natural plasticity in monocyte phenotype and function that could reveal targets for improving pregnancy outcomes but also yield new therapeutic approaches to diverse metabolic and/or immune-mediated diseases beyond pregnancy.

overall_design: Monocytes isolated from human peripheral blood of non-pregnant females (aged 18-40) and pregnant females at term (37+ weeks)

first: Benjamin

last: Jenkins

first: Roberto

last: Angelini

first: Luke

last: Davies

first: James

middle: G

last: Cronin

first: Nicholas

last: Jones

first: Catherine

last: Thornton


title: Isolation of mature adipocytes from in vitro differentiated human adipose stem cells

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: Obesity and associated metabolic outcomes define the metabolic syndrome. Interestingly, an under-appreciated fact is that body fat distribution, rather than total body fat amount, is a key determinant of metabolic disease. Indeed, in contrast to upper-body obesity, lower-body fat accumulation inversely correlates with metabolic risks. Understanding processes regulating upper- vs. lower-body fat expansion is paramount to predict (and prevent) these risks. We combine functional, proteomics, transcriptomics and epigenomics analyses to identify chromatin-associated mechanisms of adipose depot-specific fat expansion. Here, we analyze by RNA-seq the transcriptome of adipocytes differentiated in vitro from human gluteal (lower-body) and abdominal subcutaneous (upper-body) depots-derived adipose stem cells. We aim to identify adipose depot-specific and temporal differences in the up- or down-regulation of gene expression, and relate these differences to changes in chromatin states.

overall_design: Analysis of the transcriptome by RNA-seq in adipose tissue-derived stem cells (ASCs) induced to differentiate in vitro into the adipocyte lineage. ASCs were collected at the proliferating stage, day 0 (confluent, cell cycle-arrested stage, time of differentiation induction), and on days 1, 3, 9 and 15 of differentiation. ASCs were isolated from two donors (1 from gluteofemoral subcutaneous adipose tisse, 1 from abdominal subcutaneous adipose tissue), cultured and subjected to three independent differentiation experiments for each donor. Cells were collected at indicated time points and processed for RNA-seq analysis.  Code for data processing and analysis are available at https://github.com/sarahhp/nucleolus_paper.

first: Evdokiia

last: Potolitsyna

first: Sarah

last: Hazell Pickering

first: Nolwenn

last: Briand


title: Single cell gene expression profile of tumor-associated fibroblasts from macrophage-depleted PDAC liver metastasis

city: Liverpool

first: Michael

last: Schmid

state: Merseyside

address: Ashton Street

department: Molecular and Clinical Cancer Medicine

institute: University of Liverpool

summary: We used single cell RNA sequencing to investigate how macrophages regulate tumor-associated fibroblast heterogeneity in PDAC liver metastasis

overall_design:
Experimental liver metastasis in Pdgfrb-GFP reporter mouse model for 14 days. Macrophages were depleted with CSF1R neutralizing antibody, or IgG control, from Day 7 to 14. GFP+ metastasis-associated fibroblasts and GFP+ cells from naive liver were enriched by fluorescence activated cell sorting (FACS) and analyzed by single cell RNA sequencing
Contributor:  Centre for Genomics Research, Liverpool

first: Meirion

last: Raymant

first: Yuliana

last: Astuti

first: Daniel

last: Green


title: Early amyloid-induced changes in microglia gene expression in APP/PS1 mice [scRNA-seq]

city: Groningen

first: Takuya

last: Oshima

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences of Cells & Systems

institute: University Medical Center Groningen

summary: Alzheimer’s disease (AD) is a progressive neurodegenerative disease and the most common cause of dementia, characterized by deposition of extracellular amyloid-beta (Aβ) aggregates and intraneuronal hyperphosphorylated Tau. Many AD risk genes, identified in genome-wide association studies (GWAS), are expressed in microglia, the innate immune cells of the central nervous system. Specific subtypes of microglia emerged in relation to AD pathology, such as disease-associated microglia (DAMs), which increased in number with age in amyloid mouse models and in human AD cases. However, the initial transcriptional changes in these microglia in response to amyloid are still unknown. Here, to determine early changes in microglia gene expression, hippocampal microglia from APPswe/PS1dE9 (APP/PS1) mice and wildtype littermates were isolated and analyzed by RNA sequencing (RNA-seq). By bulk RNA-seq, transcriptomic changes were detected in hippocampal microglia from 6-months-old APP/PS1 mice. By performing single cell RNA-seq of CD11c-positive and negative microglia from 6-months-old APP/PS1 mice and analysis of the transcriptional trajectory from homeostatic to CD11c-positive microglia, we identified a set of genes that potentally reflect the initial response of microglia to Aβ.

overall_design: Smart-seq2 single cell RNA sequencing analysis of FACS-isolated CD11c-positive and negative microglia from cortex and hippocampus of 6-month-old APPswe/PSEN1dE9 (APP/PS1, transgenic) and controls. N =  4 per condition.

first: Mandy

last: Kater

first: Christiaan

last: F Huffels

first: Evelyn

last: Wesseling

first: Jinte

last: Middeldorp

first: Elly

last: Hol

first: Mark

middle: H

last: Verheijen

first: August

last: Smit

first: Erik

middle: W

last: Boddeke

first: Bart

last: Eggen


title: Early amyloid-induced changes in microglia gene expression in APP/PS1 mice [bulk RNA-seq]

overall_design: Bulk RNA sequencing analysis of FACS-isolated microglia from hippocampus of APPswe/PSEN1dE9 (APP/PS1, transgenic) and controls at different ages ( 4-, 6-, 9-month-old). N = 3 or 4 per condition.

middle: F

last: Huffels


title: Transcriptome data of monocytes from adolescents with obesity and age / sex matched controls

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

institute: Murdoch Children's Research Institute

summary: Trained immunity is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to certain microbial components, diets, or metabolites, altering their responses to future exposures. Trained immunity is observed in hypercholesterolemia, dislipidemia, and in response to high fat diet. In this study monocytes from obese adolescents and controls were exposed to microbial stimulation in vitro or media alone, and transcriptional profiles were generated.

overall_design: Blood was collected using venapuncture and PBMCs were isolated and viably frozen. Upon analysis, PBMCs were thawn, viable monocytes isolated with negative isolation and monocytes were stimulated for 4 hours with medium alone or purified LPS (TLR4 ligand). RNA from purified monocytes was isolated and the RNA-seq data was analysed. Comparisons for differentially expressed genes were made using either the unstimulated sample  as reference (for stimulated vs unstimulated) or controls (for adolescents with obesity vs controls)

first: Siroon

last: Bekkering

first: Christoph

last: Saner

first: Toby

last: Mansell

first: Danielle

last: Longmore

first: Zoe

last: McCallum

first: Anne-Louise

last: Ponsonby

first: Markus

last: Juonala

first: Mihai

last: Netea

first: Matthew

middle: A

last: Sabin

first: Richard

last: Saffery

first: Niels

middle: P

last: Riksen

first: David

last: Burgner


title: Wnt/β-catenin signaling regulates amino acid metabolism through the suppression of CEBPA and FOXA1 in liver cancer cells [ChIP-seq]

status: Public on Mar 31 2024

city: Tokyo

first: Kiyoshi

last: Yamaguchi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Clinical Genome Research

institute: The University of Tokyo

summary: In this study, we showed that activated Wnt/β-catenin signaling suppressed HAL and ARG1, genes associated with cellular metabolism, via CEBPA and FOXA1 transcription factors. In contrast, inhibition of the Wnt signaling pathway increased HAL and ARG1, resulting in decreased intracellular levels of histidine and arginine in liver cancer cells. These data gain an insight into a new role of the Wnt signaling pathway in amino acid metabolism in liver cancer.

overall_design: Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) for CEBPA or FOXA1 in HuH-7 cells.

first: Saya

last: Nakagawa

first: Yoichi

last: Furukawa


title: Hepatocytes differentiate into intestinal epithelial cells through a hybrid epithelial/mesenchymal cell state in culture II

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

summary: We found that hepatocytes isolated from adult mouse livers can dedifferentiate into progenitor-like cells and exhibit a hybrid epithelial/mesenchymal phenotype in monolayer culture. dediHeps can re-differentiate into mature hepatocytes by forming aggregates and fetal intestinal progenitor cells (FIPCs) by forming organoids in three-dimensional culture. We conducted RNA-seq analyses to investigate the characteristincs of hepatocytes, dediHeps, dediHep aggregates, dediHep derived spherical organoids, dediHep derived budding organoids, FIPC derived spherical organoids, intestinal stem cell (ISC) derived budding organoids, and CLiP cells (Katsuda, 2016).

overall_design: We performed RNA-seq analyses for hepatocytes, dediHeps, dediHep aggregates, dediHep-derived spherical organoids, dediHep-derived budding organoids, FIPC-derived spherical organoids, ISC-derived budding organoids, and CLiPs.

first: Shizuka

last: Miura

first: Kenichi

last: Horisawa

first: Yasuyuki

last: Ohkawa


title: Wnt/β-catenin signaling regulates amino acid metabolism through the suppression of CEBPA and FOXA1 in liver cancer cells

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

overall_design: Refer to individual Series


title: Single-cell RNA sequencing of CD45 positive cells in spleen, bone marrow, colon and periphral blood from WT and Wnt5 DKO mice under DSS treatment

city: New Haven

first: Yi

last: Luan

state: CT

address: 10 Amistad, Room 324

institute: Yale University

summary: We use single-cell RNA sequencing to analyze cell composition and DEGs of CD45+ cells from spleen, BM, blood, and colon of WT and Wnt5 DKO mice under DSS treatment

overall_design: CD45 positive cells were isolated by flow cytometry from various tissues of WT and Wnt5 DKO mice under DSS treatment and analyzed by scRNA-seq


title: Wnt/β-catenin signaling regulates amino acid metabolism through the suppression of CEBPA and FOXA1 in liver cancer cells [Array]

overall_design: Microarray expression analysis using HepG2 hepatoblastoma cells transfected with β-catenin, TCF7, TCF7L1, TCF7L2, and/or LEF1 siRNAs


title: Tyrosine phosphorylation of CARM1 promotes its enzymatic activity and alters its target specificity

first: Jun

last: Sun

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

summary: CARM1 Y149F, Y334F or Y149F/Y334F mutants have decreased activtiy to dimethylate RUNX1.

overall_design: CARM1 Y149F, Y334F or Y149F/Y334F mutations were introduced into HEL cells. ChIP-seq analyses for RUNX1 and RUNX1 R319me2a were performed in wild type and CAMR1 mutant HEL cells.

first: Hidehiro

last: Itonaga

first: Stephen

last: Nimer


title: Effects of CDK8/19 Mediator Kinase inhibition on gene expression in castration-resistant prostate cancer cell line 22Rv1 and its derivatives grown in vitro.

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary: RNA-Seq analysis was carried out to investigate the effects of selective CDK8/19 inhibitor SNX631 on gene expression in different 22RV1 derivatives grown in cell culture, under androgen-supplemented and androgen-deprived conditions. The 22Rv1 derivatives were generated as following: Parental 22Rv1 (Rv1-WT) were transduced with a lentivirus expressing luciferase, yielding the derivative Rv1-Luc. 22Rv1 cells with a double knockout of CDK8 and CDK19 (Rv1-dKO) were made via CRISPR/Cas9.  Rv1-dKO cells were further transduced with lentiviruses to generate Rv1-dKO re-expression derivatives that express wild-type CDK8 or CDK19 (Rv1-dKO-CDK8 or Rv1-dKO-CDK19) and kinase-inactive D173A mutants (Rv1-dKO-CDK8M or Rv1-dKO-CDK19M).

overall_design: The effects of CDK8/19 inhibition on gene expression in 22Rv1 derivatives were evaluated as follows: (1) For effects under androgen-supplemented conditions, cells were seeded in FBS media, incubated overnight, and then treated with 0.1% DMSO (vehicle control) or 500 nM SNX631 in FBS media for 3 days. (2) For effects under androgen-deprived conditions, cells were first sub-cultured in CSS media for one passage (3-4 days) and then seeded in CSS media, incubated overnight, and then treated with 0.1% DMSO (vehicle control) or 500 nM SNX631 in CSS media for 3 days.  Each treatment condition was done in biological triplicate.

first: Jing

last: Li

first: Hao

last: Ji

first: Igor

last: Roninson

first: Mengqian

last: Chen


title: Wnt/β-catenin signaling regulates amino acid metabolism through the suppression of CEBPA and FOXA1 in liver cancer cells [RNA-seq]

overall_design: Transcriptome analysis of HuH-7 cells transfected with control, CEBPA, or FOXA1 siRNAs.


title: Effects of CDK8/19 Mediator Kinase inhibition by Senexin B and SNX631 on androgen-regulated gene expression in LNCaP cells

summary: RNA-Seq analysis was carried out to investigate the effects of selective CDK8/19 inhibitor Senexin B and SNX631 on gene expression in LNCaP prostate cancer cells treated with or without androgen.

overall_design: Androgen-deprived LNCaP cells were treated with vehicle control (0.1% DMSO), CDK8/19 inhibitors (1 μM Senexin B or 500 nM SNX631), synthetic androgen R1881 (0.1 or 1 nM),  or a combination of CDK8/19 inhibitior and R1881 for 24 or 72 hours. Each treatment condition was done in biological triplicate or quadruplicate.


title: Early amyloid-induced changes in microglia gene expression in APP/PS1 mice

first: Takuya

last: Oshima


title: Immunometabolic adaptation in monocytes underpins functional changes during pregnancy. [MYELOID]

first: April

last: Rees

first: Benjamin

middle: J

last: Jenkins

first: Roberto

last: Angelini

first: Luke

middle: C

last: Davies

first: James

last: Cronin

first: Nicholas

last: Jones

first: Catherine

last: Thornton


title: Individual transcription factors modulate both the micromovement of chromatin and its long-range structure [Hi-C]

first: David

last: Suter

overall_design: Hi-C in 3T3 with a doxycycline-inducible expression of CDX2, treated or not with doxycycline

first: Haitham

last: Shaban

first: Elias

last: Friman

first: Cedric

last: Deluz

first: Armelle

last: Tollenaere

first: Natalya

last: Katanayeva


title: Circulating miRNA analysis in Pulmonary Arterial Hypertension patients, overexpression of miR-3168 downregulates BMPR2 and impairs angiogenesis in vitro

city: Stanford

first: Mauro

last: Lago Docampo

state: California

address: 269 Campus Dr.

department: Pediatrics

institute: Stanford University

type: Non-coding RNA profiling by high throughput sequencing

summary: Pulmonary Arterial Hypertension (PAH) is a rare disease where the thickening of the precapillary pulmonary arteries ends up inducing right heart failure. Nowadays, getting an early diagnosis is complicated and usually delayed until performing right-heart catheterization. In this work, we performed small RNA sequencing in the plasma of idiopathic PAH patients and controls. We were able to find 29 differentially expressed microRNAs and validate 7 of them in a nationwide cohort (let-7a-5p, let-7b-5p, let-7c-5p, let-7f-5p, miR-9-5p, miR-31-5p, miR-3168). We then used classification models to analyze their potential as PAH predictors. In the first half of our cohort, we obtained a model with an AUC of 0.888. Although, this value lowered to 0.738 after using this model in the whole cohort of patients. Also, we validated the effect of miR-3168, a novel upregulated miRNA in PAH patients that targets the BMPR2 and impairs angiogenesis as measured in tube formation assay. In conclusion, we found novel downregulated and upregulated microRNAs in idiopathic PAH patients. We developed a 3-microRNA signature for diagnosis and validated in vitro that miR-3168 targets BMPR2 and impairs angiogenesis.

overall_design: Differential expression analysis between Pulmonary Arterial Hypertension patients and healthy donors matched by age

last: Lago-Docampo

first: Ainhoa

last: Iglesias-López

first: Carlos

last: Vilariño

first: Adolfo

last: Baloira

first: Isabel

last: Blanco

first: Joan

last: Barberá

first: Diana

last: Valverde


title: Single-cell RNA sequencing of MMTV-neu mammary cancer cell line

status: Public on Mar 29 2024

city: Nashville

first: Justin

last: Balko

state: TN

address: 658 Preston Research Building

institute: Vanderbilt University Medical Center

summary: MMTV-neu cells consist of epithelial-like and mesenchymal-like cell populations with distinct genetic signatures.

overall_design: MMTV-neu parental cancer cells were collected and subjected to single-cell RNA sequencing to identify gene expression.

first: Elizabeth

last: Wescott


title: Individual transcription factors modulate both the micromovement of chromatin and its long-range structure


title: RNA-Seq analysis of adventitious rooting zone of Arabis alpina main stem during extended cold exposure.

city: Köln

first: Maria

last: Albani

address: Carl-von-Linné-Weg 10

department: Botanical institute

institute: University of Cologne

summary:
Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximise fitness and ensure reproductive success. We used the arctic alpine perennial Arabis alpina to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4 °C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4 °C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developingin specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in A. alpina stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of DR5 auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone
responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism.
Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.

overall_design: 27 samples, 3 biological replicates per condition

first: Priyanka

last: Mishra


title: Chromatin Landscape Instructs Precise Transcription Factor Regulome during Embryonic Lineage Specification [CUT&RUN]

city: Shanghai

first: Liping

last: Wang

address: 1239 Siping Road

institute: Tongji University

summary: Embryos, originating from fertilized eggs,  undergo continuous cell division and differentiation, accompanied by dramatic changes in transcription, translation, and metabolism. Epigenetic information and transcription factors (TFs) play indispensable roles in regulating these processes. Recently, the trophoblast regulator TFAP2C was identified as crucial in initiating early cell fate decisions. However, Tfap2c transcripts persist in both the inner cell mass (ICM) and trophectoderm (TE) of blastocysts, prompting inquiry into its function in post-lineage establishment. In this study, we delineate the dynamics of TFAP2C during the mouse peri-implantation stage and elucidate its collaboration with the key lineage regulators CDX2 and NANOG. Importantly, we propose that de novo formation of H3K9me3 in the extraembryonic ectoderm during implantation antagonizes TFAP2C binding to crucial developmental genes, thereby maintaining its lineage identity. Together, this research highlights the plasticity of the epigenetic environment in designating the genomic binding of highly adaptable lineage-specific TFs and regulating embryonic cell fates.

overall_design: we utilized an ultra-low-input CUT&RUN (uliCUT&RUN) strategy to delineate the dynamics binding of CDX2/NONOG/SOX2 at certain key developmental stages: morula, inner cell mass and trophectoderm in embryonic day (E3.5) blastocyst, as well as the epiblast (Epi) and extraembryonic ectoderm (ExE) in E6.5 post-implantation embryos.

first: Shanru

last: Yi

first: Guang

last: Yang

first: Rui

last: Gao


title: TFE3-SLC36A1 axis promotes resistance to glucose starvation in kidney cancer cells [ChIP-Seq]

city: Wuhan

first: suli

last: LV

address: Wuhan, Hubei, China

institute: Huazhong University of Science and Technology

summary: "Starving cancer to death" is pursued for cancer therapy. An intriguing regime is to inhibit glucose transporter GLUT1 in cancer cells. But past attempts are challenged by that cancer cells can somehow tolerate starvation. In addition, during cancer progression, cancer cells may suffer from insufficient nutrient supply, for example due to insufficient angiogenesis. So uncovering mechanism of starvation resistance shall not only shed insight into cancer progression but also benefit cancer therapy. TFE3 is known as a transcription factor capable of activating autophagic genes. Physiological TFE3 activity is regulated by phosphorylation-triggered translocation, which is sensitive to nutrient status. We recently reported TFE3 constitutively localizes to cell nucleus in kidney cancer, promoting cell proliferation even under replete condition. But whether and how TFE3 affects kidney cancer cell sensitivity to starvation is unclear. In this study, we find TFE3 promotes kidney cancer cell resistance to glucose starvation. We show starvation triggers TFE3 protein stabilization through increasing its O-GlcNAcylation. Furthermore, through unbiased functional genomic study, we identify genes sensitive to TFE3 protein level, including SLC36A1, a lysosomal amino acid transporter. We find SLC36A1 is overexpressed in kidney cancer, promotes mTOR activity and kidney cancer cell proliferation. Importantly, SLC36A1 level is directly upregulated by TFE3 upon starvation, which enhances cellular resistance to starvation. Suppressing TFE3 or SLC36A1 significantly increased cellular sensitivity to GLUT1 inhibitor in kidney cancers. Collectively, we uncover a TFE3-SLC36A1 axis that responds to starvation and enhances starvation tolerance in kidney cancer.

overall_design: To examine the effect on transcriptome by TFE3, we performed ChIP-Seq and RNA-Seq to identify TFE3 directly-regulated genes. For ChIP-Seq, we stably expressed HA-TFE3 in Caki-1 kidney cancer cells. HA antibody was used for Chromatin IP. ChIP DNA was analyzed with Next generation sequencing. For RNA-Seq, Caki-1 cells were transduced with lentiviruses expressing TFE3-shRNA or control sequences. Total RNA was extracted for RNA-Seq.

first: Suli

last: Lv

first: Lidong

last: Sun

first: Tanjing

last: Song


title: TFE3-SLC36A1 axis promotes resistance to glucose starvation in kidney cancer cells [RNA-Seq]