title: Developmental control of rod photoreceptor number via a light-dependent retrograde pathway from intrinsically photosensitive retinal ganglion cells

city: Cincinnati

first: Shane

middle: Peter

last: D'Souza

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital

summary: Photoreception, a form of sensory experience, is essential for normal development of the mammalian visual system. Detecting photons during development is a prerequisite for visual system function - from shaping vision’s first synapse and maturation of retinal vascular networks, to transcriptional establishment and maturation of cell types within the visual cortex.  Consistent with this theme, we find that the lighting environment regulates developmental rod photoreceptor apoptosis via OPN4-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs). Using a combination of genetics, sensory environment manipulations, and computational approaches, we establish a molecular pathway in which light-dependent glutamate release from ipRGCs is detected via a transiently expressed kainate receptor (GRIK3) in rod precursors localized to the inner retina. Communication between ipRGCs and nascent inner retinal rods appears to be mediated by transient hybrid neurites projecting from ipRGCs that sense light before eye-opening. These structures, previously referred to as outer retinal dendrites (ORDs), span the ipRGC-rod precursor distance over the first postnatal week and contain the machinery for sensory detection (melanopsin, OPN4) and anterograde neurotransmitter release (Synaptophysin and VGLUT2). Computational and histological assessment of human mid-gestation development reveal conservation of several hallmarks of an ipRGC-to-rod precursor pathway, including displaced rod precursors, transient GRIK3 expression in the rod lineage, and the presence of ipRGCs with putative neurites projecting deep into the developing human retina. Thus, this analysis defines a retinal retrograde signaling pathway that links the sensory environment to rod precursors via ipRGC photoreceptors, allowing the visual system to adapt to distinct lighting environments prior to eye-opening.

overall_design: Opn4+/- x Opn4+/- harem crosses were used to produce wildtype and knockout littermate pups raised in similar lighting environments (~300 lux). On the day of birth (P0), tail and finger clippings were harvested and mice were genotyped prior to determine appropriate genotypes. At P4, mice were sacrificed between ZT6-7 and retina were dissected in ice-cold oxygenated Ames’ media (95% air, 5% oxygen). Multiple retinas were pooled together from animals of the same genotype (4 retina per sample, 2 animals), and tissue was snap frozen in Trizol (100uL). Post-hoc genotyping was then performed on each sample to confirm genotypes. RNA extraction, library preparation, and sequencing (Illumina HiSeq 2 x 150bp) were all performed at GeneWiz. Samples with >500ng of RNA and a RIN > 8.5 were selected for further processing. The average read depth per sample was 42.7 ± 3.9 million reads. Subsequently, adapters and low-quality reads were trimmed/filtered using Timmomatic v0.39. Reads were pseudoaligned to the mouse reference genome (GRCm38) and counts were quantified using Kallisto v0.46.1. Differential gene expression analysis was performed using Sleuth v0.30.8.

last: Dsouza

first: Richard

last: Lang


title: Effect of ZFP740 knockdown on HepG2 cells

status: Public on Jul 04 2024

city: Guiyang

first: Hao

last: Zhang

address: No.9, Beijing Road City:guiyang

country: China

institute: College of Clinical Medicine

type: Expression profiling by high throughput sequencing

summary: To investigate the effect of ZFP740 gene expression on hepatocellular carcinoma cells, we used the hepatocellular carcinoma cell line HepG2, and then divided into two groups, in which the control group was HepG2, and the intervention group was HepG2 with the knockdown of the ZNF740 gene, and three samples were sent to each group for RNA seq sequencing

overall_design: mRNA profiles of HepG2 cells upon treatment with the knockdown of the ZNF740 gene were generated by deep sequencing,  three samples were sent to for conrtol and ZNF740 knockdown

first: Zhang

last: Hao


title: Differential Anti-Inflammatory Effects of Electrostimulation in a Standardized Setting

city: Rome

first: Christine

last: Nardini

address: Via dei Taurini 9

country: Italy

institute: PICB

summary: To investigate the effects of direct and alternate current on a 3D bioprinted construct containing fibroblasts and keratinocytes in a collagen matrix

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3D bioprinted constructs at time 0, 1, and 48 hours after culture, perfused with TNF-α or in physiological conditions, stimulated with direct current (DC) at 1 or 5V, or alternate current (AC) at 10 or 100 Hz, or without.tab stimuli

first: Biagio

last: Di Pietro

first: Simona

last: Villalta

first: Veronica

last: Ghini

first: Simeone

last: Dal Monego

first: Margherita

last: Degasperi

first: Anna

last: Plaksienko

first: Yuanhua

last: Liu

first: Luigi

last: Manni

first: Tiziana

last: Guarnieri

first: Leonardo

last: Tenori

first: Danilo

last: Licastro

first: Claudia

last: Angelini

first: Lucia

last: Napione

first: Francesca

last: Frascella


title: Identification of epigenetic modifiers essential for growth and survival of AML1/ETO-positive leukemia

city: Freiburg im Breisgau

first: Usama Ur

last: Rehman

address: Breisacher Str. 115

department: ZTZ

country: Germany

institute: Uniklinik Freiburg

summary: Aberrant gene expression patterns in acute myeloid leukemia (AML) with balanced chromosomal translocations are often associated with direct or indirect dysregulation of epigenetic modifiers. Previously, we have shown that the AML1/ETO (RUNX1/MTG8) fusion protein, encoded by the translocation (8;21)(q22;q22), leads to the epigenetic repression of its target genes. We aimed in this work to identify critical epigenetic modifiers, on which AML1/ETO-positive AML cells depend on for proliferation and survival using shRNA library screens and global transcriptomics approaches. Using shRNA library screens, we identified 41 commonly depleted genes in two AML1/ETO-positive cell lines Kasumi-1 and SKNO-1. Among them, several epigenetic regulators as DMAP1, SMYD1, SMYD2, BRD4, SETD8, SETD1A and HDAC8 were depleted. We validated genetically and pharmacologically DNMT1 and ATR using several AML1/ETO-positive and negative cell lines. We also showed in vivo differentiation of myeloblasts after treatment with the DNMT1-inhibitor decitabine in a patient with an AML1/ETO-positive AML. Bioinformatic analysis of global transcriptomics after AML1/ETO induction in 9/14/18-U937 cells identified 973 differentially expressed genes (DEGs) (648 up- and 325 downregulated). Pathway analysis revealed several interferon response pathways and metabolic pathways such as oxidative phosphorylation and hypoxia enriched after AML1/ETO induction. Three genes (PARP2, PRKCD and SMARCA4) were both downregulated after AML1/ETO induction, and also detected in the survival shRNA screens of both cell lines, decreasing survival and proliferation. In conclusion, using unbiased shRNA library screens and global transcriptomics, we have identified several driver epigenetic regulators for proliferation in AML1/ETO-positive AML. Some of these epigenetic regulators, such as DNMT1 and ATR, are susceptible to pharmacological inhibition by small molecules showing promising preclinical and clinical efficacy

overall_design: We compare differential regulated genes after AML1/ETO indution in our generated 9/14/18-U937 cells after Ponasterone A compared to 9/14/18-U937 treated with vehicle (Ethanol), to 9/10/7-U937 LacZ clone treated with Ponasterone A and Ethanol as controls

first: Jesus

last: Duque-Afonso

first: Usama-Ur

first: Michael

last: Lübbert


title: Effect of cell density on HaCaT keratinocyte gene expression

city: Sapporo

first: Yosuke

last: Mai

state: Hokkaido

department: Department of Dermatology

country: Japan

institute: Hokkaido University

summary: Cell density affects keratinocyte behaviors and gene expression. Here, We examines the differential expressed genes regulated by cell density. We performed RNA-seq analysis to compare HaCaT cells cultured under high- or low0density conditions. The Gene Ontology Biological Process terms enriched among differential expressed genes through DESeq2 included cell adhesion and keratinocyte differentiation. Our data provides the understanding of keratinocyte behavior regulated by cell density.

overall_design: HaCaT cells were seeded into 6-cm plastic dishes at the concentration of 2.5 x 105/mL or 7.5 x 105/mL. After the overnight incubation at 37ºC in humidified 5% CO2, RNA was extracted.

first: Wataru

last: Nishie


title: Dor regulates alpha-KG metabolic pathways in mature oligodendrocytes to enhance myelination and reverse age-related remyelination decline

city: Chengdu

first: XueLian

last: He

state: Sichuan

address: Renmin Road

institute: Sichuan University

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Transcriptomic analyses of ChREBPtotal-null mice and ChREBPβ-null mice subcutaneous inguinal white adipose tissue

city: Toulouse Cedex 4

first: Dominique

last: Langin

address: 1 avenue du Professeur Jean Poulhès

country: France

institute: INSERM

summary: The Carbohydrate Responive Element Binding Protein (ChREBP) is a transcription factor sensing glucose. Two isoforms are produced by the same gene, the long isoform ChREBPalpha and the short one ChREBPbeta transcribed from an alternative promoter. ChREBPalpha activates transcription of ChREBPbeta in response to glucose. The latter is thought to mediate most of the ChREBP transcriptional activation of target genes. However, the contribution of ChREBPbeta in metabolic adaptations in vivo is not known. This study aims at dertermining the contribution of the short isoform ChREBPbeta to the changes in gene expression mediated by ChREBP.

overall_design: The study contains 4 groups of mice: total ChREBP knock-out mice, ChREBPbeta knock-out mice, and the respective control wild type littermates of the two transgenic lines.

first: Emeline

last: Recazens

first: Jeremy

last: Dufau

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Transcriptomic analyses of ChREBPtotal-null mice and ChREBPβ-null mice perigonadal white adipose tissue


title: Transcriptomic analyses of ChREBPtotal-null mice and ChREBPβ-null mice


title: RNA-Seq of Planktonic P. aeruginosa in flow

status: Public on Jul 03 2024

city: Princeton

first: Ashwin

last: Ramachandran

state: NJ

address: Department of Molecular Biology, Department of Mechanical and Aerospace Engineering

country: USA

institute: Princeton University

summary: To determine whether flow alters the gene expression of planktonic P. aeruginosa, we designed a long microfluidic channel that enabled us to expose bacteria to flow for significant lengths of time and then be fixed as they exit the channel. The experiments mimic the kinds of shear flows characteristic of a wide variety of confined flow configurations. Using this microfluidic system, we performed bulk RNA-Seq analysis of planktonic bacteria that flowed for 55 min at a shear rate of 20 per second, and compared gene expression of this population with a control population of planktonic bacteria under similar conditions with no flow.

overall_design: We compared gene expression of planktonic bacterial cells that were subject to shear flow versus a control population of cells that were not subject to flow. Three biological replicates were used for each condition.

first: Howard

last: Stone

first: Zemer

last: Gitai


title: Rexinoids Induce Differential Gene Expression in Human Glioblastoma Cells

city: Glendale

first: Pamela

middle: A

last: Marshall

state: AZ

address: 4701 W Thunderbird Rd

institute: Arizona State University

summary: Rexinoids are compounds that bind to the rexinoid X receptor (RXR) to modulate gene expression and have been proposed as a new class of therapeutics to treat Alzheimer's disease.  Different rexinoids will initiate downstream effects that can be quite marked even though such compounds can be structurally similar and have comparable RXR binding affinities.  RXR can both homo- and heterodimerize and these protein-protein interactions and subsequent transactivating potential leads to differential gene expression, depending on the RXR dimeric partner, additional cofactors recruited, and downstream transcription factors that are up- or down-regulated.  Expression analysis was performed in the U87 human glioblastoma cell line treated with a panel of rexinoids, and our analysis demonstrated that rexinoids with similar RXR EC50 values can have pronounced differences in differential gene expression.   Negative control was ethanol, positive control was Bexarotene, and rexinoid compounds were A34, A41, A80, and A98, concentration of 1 X 10-7 M for 24 h treatment (rexinoids synthesized at Arizona State University).

overall_design: U87 cells were treated with ethanol or 1 X 10-7 rexinoid for 24 hours, RNA was extracted, and subjected to RNA-seq.  Samples were analyzed in triplicate. Ethanol and Bexarotene were controls.

first: Jennifer

middle: F

last: Hackney

first: Peter

middle: W

last: Jurutka

first: Carl

middle: E

last: Wagner


title: Integrative phenotyping approaches to unmask the Phyb-PIF4 pathway in Arabidopsis thaliana reproductive organs at high ambient temperatures

city: Brno

first: Helene

middle: S.

last: Robert

address: Kamenice 5

country: Czech Republic

institute: CEITEC Masaryk University

summary:
The increasing ambient temperature significantly impacts plant growth, development, and reproduction. Uncovering the temperature-regulating mechanisms in plants is of high importance, not only for boosting our plant biology knowledge but also for assisting plant breeders in improving plant resilience to these stress conditions. Numerous studies on the molecular mechanisms by which plants regulate temperature responses revealed that plants employ distinct transcription factors to regulate thermomorphogenesis specific to each tissue type. A significant discovery in this field was the identification of PHYTOCHROME-INTERACTING FACTORs (PIFs) as key regulators of thermomorphogenesis during vegetative growth. PIF4, a regulator of auxin-mediated signaling pathways, is crucial in controlling high-temperature responses.
In this study, we screened the temperature responses of the wild type and several PhyB-PIF4 pathway Arabidopsis mutant lines in combined and integrative phenotyping platforms for root in soil, shoot, inflorescence, and seed. We demonstrated that high ambient temperature differentially impacts vegetative and reproductive organs through this pathway. Suppression of the PhyB-PIF4 components mimics the response to a high ambient temperature in wild-type plants. We also identified correlative responses to high ambient temperature between shoot and root tissues. This integrative and automated phenotyping was complemented by monitoring the changes in transcript levels in reproductive organs. Transcriptomic profiling of the pistils from plants grown under high ambient temperature identified key elements that may provide clues to the molecular mechanisms behind temperature-induced reduced fertilization rate, such as a downregulation of auxin metabolism, upregulation of genes involved auxin signalling, miRNA156 and miRN160 pathways, pollen tube attractants.

overall_design: The aim of the study was to identify DEGs in pistils from plants grown at high ambient temperature and the involvement of the PhyB PIF4 signaling pathway. Plants were grown in a Fytoscope growth chamber (FS WI, Plant Systems Instruments (PSI), Czech Republic) under growth conditions with a longday regime (16 h light and 8 h dark), LED illumination with an intensity of 150 umol.m-2.s-1, and 35% 45% humidity. For normal conditions (nAT), the temperature was set at 21oC during the day and 18oC at night. For high ambient temperature conditions (hAT), the temperature wat set at 28oC during the day and 24oC at night. Plants were grown at nAT until flowering is induced and moved to hAT. Gynoecium samples from flowers at stages 11 and 12 (before anthesis) were collected from wild type, phyb and 35S::PIF4 plants grown at nAT and hAT. Total RNA was extracted from 100 mg of ovules using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's protocol. RNA isolates were treated with rDNAse Macherey Nagel) to remove traces of contaminant DNA and purified using a RNeasy MinElute Cleanup Kit (Qiagen). RNA quality was assessed using a NanoDrop2000 spectrophotometer and agarose gel electrophoresis. Samples, four biological replicates each, were sent to the Novogene Genomic Sequencing Labs (Cambridge Sequencing Center) for sequencing. All samples passed Novogene quality control threshold for library preparation and RNA-seq. mRNAseq libraries were constructed by Novogene, starting with 100 ng of high-quality RNA per sample. mRNA purification was performed using oligo(dT) attached magnetic beads, followed by fragmentation and first-strand cDNA synthesis. Second strand cDNA synthesis, end repair, adapter ligation, and size selection were performed. PCR enrichment yielded in the final cDNA library. Sequencing was conducted on the Illumina NovaSeq platform, generating 150bp 150bp paired-end read.

first: Shekufeh

last: Ebrahimi Naghani

middle: S


title: Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the transcript life cycle

city: Cambridge

first: Robert

last: Ietswaart

state: MA

address: 700 Main Street

institute: Cellforma, Inc

summary: Series of regulatory mechanisms control eukaryotic mRNAs, from their production on chromatin to their eventual degradation. Dissecting these pathways requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and the cytoplasm. All rates displayed substantial variability genome-wide, and transcripts from genes with related functions flowed across subcellular compartments with similar kinetics. For some genes, most transcripts were rapidly degraded within the nucleus, while the remaining molecules were exported and persisted with stable lifespans. With compartment-specific measurements of poly(A) tail lengths, we found that relationships between tail length and stability differ across the cell. The targets of RNA binding proteins experience distinct RNA flow kinetics, and we found that two, DDX3X and PABPC4, act by controlling the nuclear export of their targets. Finally, we developed a machine learning model to propose additional molecular features that underlie the diverse life cycle of mammalian mRNAs.

overall_design: RNA-seq on nuclear wash and subcellular fractions

first: Brendan

middle: M

last: Smalec

first: Chantal

middle: K

last: Guegler

first: Autum

middle: R

last: Baxter-Koenigs

first: L

last: Churchman


title: Analysis of different mouse P14 CD8+T cell subset gene signatures in presence and absence of Tim-3+ Treg during LCMV CL13 infection

city: Pittsburgh

first: Lawrence

middle: P.

last: Kane

state: PA

address: 5051 Centre Ave.

department: Immunology

institute: University of Pittsburgh

summary: Treg-specific Tim-3 deletion alters the transcriptional profile of specific major WT P14 Tex subsets early during chronic infection.

overall_design: Splenic live CD45.1 congenically marked P14 cells were stained, as described above, and FACS-sorted from a female CD45.1/CD45.2 P14 mouse. Sorted P14 cells were then transferred into tamoxifen-pretreated congenically-distinct WT and Tim-3 Treg KO mice (1,500 P14/mouse, i.v.). One day after transfer, mice were infected with LCMV Cl-13 and analyzed at indicated timepoints.

first: Hector

last: Nieves-Rosado

first: Hridesh

last: Banerjee

first: Angela

last: Gocher-Demske

middle: P


title: Dysregulation of cholesterol homeostasis is an early signal of beta cell proteotoxicity characteristic of type 2 diabetes.

city: Los Angeles

first: Montgomery

last: Blencowe

address: 610 Charles E Young Drive East

institute: UCLA

summary: Type 2 diabetes (T2D) is a common metabolic disease due to insufficient insulin secretion by pancreatic beta cells in the context of insulin resistance. Islet molecular pathology reveals a role for protein misfolding in beta cell dysfunction and loss with islet amyloid derived from islet amyloid polypeptide (IAPP), a protein co-expressed and co-secreted with insulin. The most toxic form of misfolded IAPP is intracellular membrane disruptive toxic oligomers present in beta cells in T2D and in beta cells of mice transgenic for human IAPP (hIAPP). Prior work revealed a high degree of overlap of transcriptional changes in islets from T2D and pre-diabetic 9-10-week-old mice transgenic for hIAPP with most changes being pro-survival adaptations and therefore of limited therapeutic guidance. Here we investigated islets from hIAPP transgenic mice at an earlier age (6 weeks) to screen for potential mediators of hIAPP toxicity that precede predominance of pro-survival signaling. We identified early suppression of cholesterol synthesis and trafficking along with aberrant intra-beta cell cholesterol and lipid deposits, and impaired cholesterol trafficking to cell membranes. These findings align with comparable lipid deposits present in beta cells in T2D and increased vulnerability to develop T2D in individuals taking medications that suppress cholesterol synthesis.

overall_design:
RNA-seq of bulk pancreatic islets from 6 week old hIAPP, rIAPP, and WT mice (18 samples; n = 6 per group)
Treatment descriptions:
hIAPP: Transgenic expression of human IAPP under insulin II promoter
rIAPP: Transgenic expression of rodent IAPP under insulin II promoter

first: Tatyana

last: Gurlo

first: Ruoshui

last: Liu

first: Zhongying

last: Wang

first: Jonathan

last: Hoang

first: Sergey

last: Ryazantsev

first: Marie

last: Daval

first: Alexandra

last: Butler

first: Xia

last: Yang

middle: C


title: Transcriptomic analyses of ChREBPtotal-null mice and ChREBPβ-null mice brown adipose tissue

first: Dominique

last: Langin

first: Emeline

last: Recazens

first: Jeremy

last: Dufau

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Pharmacological impacts of Mucopolysacccharide Polyphosphates in skin involves inhibition of Amphiregulin-mediated signals in keratinocytes

city: shimogyo-ku

first: Ryo

last: Hirase

address: chudoji, awatacho

institute: Maruho

summary: The epidermis, the most superficial layer of human skin, serves a critical barrier function, protecting the body from external pathogens and allergens. Dysregulation in the epidermal differentiation process contributes to barrier dysfunction and is implicated in the pathology of various dermatological diseases, including atopic dermatitis (AD). Mucopolysaccharide polysulfate (MPS) is used as a moisturizing agent for xerosis in AD patients. However, its mechanism of action on keratinocytes, the main constituent of the epidermis, remains unclear. In this study, we investigated the impact of MPS on keratinocytes by subjecting adult human epidermal keratinocyte (HEKa) cells and three-dimensional cultured keratinocytes to MPS treatment, followed by transcriptome analysis. The analysis revealed that MPS treatment enhances keratinocyte differentiation and suppresses proliferation. We focused on amphiregulin (AREG), a membrane protein that belongs to the epidermal growth factor (EGF) family and possesses a heparin-binding domain, as a significant target of the MPS among the genes altered by MPS. It is revealed that MPS exerts an inhibitory effect directly on AREG, rather than on the EGF receptor or other members of the EGF family. Furthermore, it is suggested that AREG leads to a reduction in epidermal barrier function, whereas MPS contributes to barrier enhancement through AREG inhibition. Collectively, these findings suggest that MPS modulates barrier function through the inhibition of AREG, offering insights into potential therapeutic strategies for skin barrier restoration.

overall_design:
To invastigate the mechanism of MPS on keratinocyte, primary keratinocytes (HEKa) and 3D-cultured keratinocyte were treated by MPS. We then perform RNA-seq at 24hrs after treatment
To invastigate AREG inhibitory effect of MPS on keratinocyte, primary keratinocytes (HEKa) were treated by MPS, AREG, AREG antibody. We then perform RNA-seq at 24hrs after treatment


title: Transcriptomic analyses of ChREBPtotal-null mice and ChREBPβ-null mice liver


title: Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle [RNAseq]

city: San Francisco

first: Albert

last: Xu

state: CA

address: 513 Parnassus Ave, HSW 640

department: Cell and Tissue Biology

institute: University of California, San Francisco

summary: Dissecting the myriad regulatory mechanisms controlling eukaryotic transcripts from production to degradation requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and cytoplasm. These rates varied substantially, yet transcripts from genes with related functions or targeted by the same transcription factors and RNA binding proteins flowed across subcellular compartments with similar kinetics. Verifying these associations uncovered roles for DDX3X and PABPC4 in nuclear export. For hundreds of genes, most transcripts were degraded within the nucleus, while the remaining molecules were exported and persisted with stable lifespans. Transcripts residing on chromatin for longer had extended poly(A) tails, whereas the reverse was observed for cytoplasmic mRNAs. Finally, a machine learning model identified additional molecular features that underlie the diverse life cycles of mammalian mRNAs.

overall_design: Cellular fractionation and RNAseq in human K562 cell lines. 2 replicates for each fraction. Either DDX3 or target genes from GI map were knocked down with CRISPRi. In the DDX3 mutant experiments, DDX3 WT or Mutants were overexpressed with lentiviral transgene and endogenous DDX3 was knocked down.

first: Brendan

last: Smalec

first: Robert

last: Ietswaart

first: Karine

last: Choquet

first: Erik

last: McShane

first: Ziad

last: Jowhar

first: Emma

last: West

first: L

last: Churchman

first: Stephen

middle: N

last: Floor


title: Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.

overall_design: Ribosome profiling in human K562 cell lines with CRISPRi knockdown of DDX3X or a sgGal4 control. 2 replicates for each time point and 3 time points. Day 0, Day 3 post knock-down, and Day 14 post knock-down.

first: Xu

last: Albert

first: Smalec

last: Brendan M.

first: Ietswaart

last: Robert

first: Choquet

last: Karine

first: McShane

last: Erik

first: Jowhar

last: Ziad

first: West

last: Emma R.

first: Churchman

last: L Stirling

first: Floor

last: Stephen N.


title: Epigenetic profiling of primary human peripheral blood NK cell populations

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus Medical Center

summary: Human peripheral blood NK cell popiulations were seperated on the basis of CD56 expression with flowcytometry. Sorted CD56-bright (CD56Br) and CD56-dim (CD56Dim) NK cells were subjected to H3K4Me2 ChIPmentation to obtain epigenome profiles for downstream analyses.

overall_design: 2 biological replicate ChIP-Seq experiments.

first: Laura

last: Surace

first: James

last: di Santo


title: Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle

first: Albert

last: Xu

overall_design: Genome-wide CRISPR-interference screens in human K562 cell lines (in background of sgDDX3X or sgGal4 control lines). 2 replicates each for Initial and Final time points were taken for each cell line.

first: Brendan

last: Smalec

first: Robert

last: Letswaart

first: Karine

last: Choquet

first: Erik

last: McShane


title: Context-dependent roles for autophagy in myeloid cells in tumor progression [Atg5_Pymt]

status: Public on Jul 02 2024

first: Seungmin

middle: "Sam"

last: Hwang

address: 415 Main st.

institute: Broad Institute of MIT and Harvard

summary: Autophagy is known to suppress tumor initiation by removing genotoxic stresses in normal cells. Conversely, autophagy is also known to support tumor progression by alleviating metabolic stresses in neoplastic cells. Centered on this pro-tumor role of autophagy, there have been many clinical trials to treat cancers through systemic blocking of autophagy. Such systemic inhibition affects both tumor cells and non-tumor cells, and the consequence of blocked autophagy in non-tumor cells in the context of tumor microenvironment is relatively understudied. Here, we examined the effect of autophagy-deficient myeloid cells on the progression of autophagy-competent tumors. We found that blocking autophagy only in myeloid cells modulated tumor progression markedly but such effects were context dependent. In a tumor implantation model, the growth of implanted tumor cells was substantially reduced in mice with autophagy-deficient myeloid cells; T cells infiltrated deeper into the tumors and were responsible for the reduced growth of the implanted tumor cells. In an oncogene-driven tumor induction model, however, tumors grew faster and metastasized more in mice with autophagy-deficient myeloid cells. These data demonstrate that the autophagy status of myeloid cells plays a critical role in tumor progression, promoting or suppressing tumor growth depending on the context of tumor-myeloid cell interactions. This study indicates that systemic use of autophagy inhibitors in cancer therapy may have differential effects on rates of tumor progression in patients due to effects on myeloid cells and that this warrants more targeted use of selective autophagy inhibitors in a cancer therapy in a clinical setting.

overall_design: Gene expression from Atg5 WT Tumor associated macrophages (TAMs) and Atg5 KO TAMs were analyzed by RNA-seq. PyMT tumor tissues were harvested from Atg5 WT (MMTV-PyMT + Atg5flox/flox) and Atg5 KO (MMTV-PyMT + Atg5flox/flox+LysMcre) female mice in FVB/NJ background at 65 days of age. TAMs, CD11b+ F4/80+ Ly6G- Ly6C-, were isolated by FACS from the tumor tissues.

first: Jayoung

last: Choi


title: Context-dependent roles for autophagy in myeloid cells in tumor progression [Atg5_MC38]

overall_design: Gene expression from Atg5 WT Tumor associated macrophages (TAMs) and Atg5 KO TAMs were analyzed by RNA-seq. 1x1e5 MC38 cells were implanted subcutaneously into the right flank of female mouse at 6~8 week of age. Tumor tissues were harvested at 21 days post implantation from Atg5 WT (Atg5flox/flox) and Atg5 KO (Atg5flox/flox+LysMcre) female mice in C57BL/6J background. TAMs, CD11b+ F4/80+ Ly6G- Ly6C-, were isolated by FACS from the tumor tissues.


title: Mutations in linker-2 of KLF1 impair expression of membrane transporters and cytoskeletal proteins causing hemolysis

city: Brisbane

first: Stephen

last: Huang

state: Queensland

address: 37 Kent Street Woolloongabba

department: Mater Research institute

country: Australia

institute: University of Queensland

summary: The SP/KLF family of transcription factors harbour three C-terminal C2H2 zinc fingers interspersed by two linkers which confers DNA-binding to a 9-10bp motif. Mutations in KLF1, the founding member of the family, are common. Missense mutations in linker two result in a mild phenotypes. However, when co-inherited with loss-of-function mutations, they result in severe non-spherocytic hemolytic anemia. We generated a mouse model of this disease by crossing Klf1+/- mice with Klf1H350R/+ mice that harbour a missense mutation in linker-2. Klf1H350R/- mice exhibit severe hemolysis without thalassemia. RNA-seq demonstrated loss of expression of genes encoding transmembrane and cytoskeletal proteins, but not globins. ChIP-seq showed no change in DNA-binding specificity, but a global reduction in affinity, which was confirmed using recombinant proteins and in vitro binding assays. This study provides new insights into how linker mutations in zinc finger transcription factors result in different phenotypes to those caused by loss-of-function mutations.

overall_design:
RNAseq and ChIPseq in 14.5DPC fetal livers
---------------------------------
The comparisons in cuffdiff corresponds as follows:
Q1 KLF1 D45/- mRNAseq
Q2 KLF1 -/- mRNAseq
Q3 KLF1 +/- mRNAseq

first: Kevin

last: Gillinder

first: Andrew

last: Perkins

first: Graham

middle: G

last: Magor


title: CRISPR screen for regulators of cadherin based cell to cell adhesion

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Pooled Crispr based genome wide screen to find potential (transcriptional) regulators and pathways underlying the regulation of cadherin based cell to cell adhesion.

overall_design: A spontaneously immortalized human keratinocyte line (HaCaT) expressing Cas9 was transduced with lentivirus containing the Brunello library encoding for 76441 sgRNAs inclusive 1000 non-targeting controls at a coverage of approximately 400 cells/sgRNA. The transduced cells were selected and expanded maintaining a library coverage of approximately 600 cells/sgRNA. 50-60x10^6 cells were stained Desmoglein 3 (Dsg3), and the 10 % cells with the lowest and the 10 % cells with the highest expression of Dsg3, respectively, were isolated by FACS. 50-60 x10^6 cells served as a control before FACS. Two technical replicates were done (repl 1 and 2).

first: Chiara

last: Stuedle

first: Florian

last: Geier

first: Volker

last: Spindler

first: Henriette

last: Franz

first: Maitreyi

last: Rathod

first: Aude

last: Zimmermann

first: Vivien

last: Beyersdorfer

first: Karen

middle: L

last: Fischer


title: ADBP-1 regulates ADR-2 nuclear localization to control editing substrate selection

city: Haifa

first: Ayelet

last: Lamm

address: Technion st

department: Biology

country: Israel

institute: Technion

summary: We generated RNA-seq libraries from three biological replicas of adbp-1 mutant worms at the embryo and L4 developmental stages. We wanted to identify editing sites globally in adbp-1 mutant worms and understand the preferable ADR-2 5’ and 3’ nearest neighbors of editing sites in wild-type worms in contrast to adbp-1 mutant worms. In addition, we wanted to test if the cytoplasmic localization of ADR-2 causes the downregulation of 3’UTR edited genes and lncRNAs, and test the effect of lacking ADBP-1 on global gene expression.

overall_design: A-to-I RNA editing detection of known and de-novo editing sites and  gene expression analysis in adbp-1 mutant worms.

middle: T

first: Berta

last: Eliad


title: BHLHE40 regulates myeloid cell polarization through IL-10-dependent and independent mechanisms

city: St. Louis

first: Christina

last: Stallings

state: MO

address: 425 South Euclid ave

institute: Washington University in Saint Louis

summary: Better understanding of the host responses to Mycobacterium tuberculosis (Mtb) infections is required to prevent tuberculosis and develop new therapeutic interventions. The host transcription factor BHLHE40 is essential for controlling Mtb infection, in part by repressing Il10 expression, where excess IL-10 contributes to the early susceptibility of Bhlhe40-/- mice to Mtb infection. Deletion of Bhlhe40 in lung macrophages and dendritic cells is sufficient to increase the susceptibility of mice to Mtb infection, but how BHLHE40 impacts macrophage and dendritic cell responses to Mtb is unknown. Here we report that BHLHE40 is required in myeloid cells exposed to GM-CSF, an abundant cytokine in the lung, to promote the expression of genes associated with a pro-inflammatory state and better control of Mtb infection. Loss of Bhlhe40 expression in murine bone marrow derived myeloid cells cultured in the presence of GM-CSF results in lower levels of pro-inflammatory associated signaling molecules IL-1b, IL-6, IL-12, TNFα, iNOS, IL-2, KC, and RANTES, as well as higher levels of the anti-inflammatory associated molecules MCP-1 and IL-10 following exposure to heat-killed Mtb. Deletion of Il10 in Bhlhe40-/- myeloid cells restored some, but not all, pro-inflammatory signals, demonstrating that BHLHE40 promotes pro-inflammatory responses via both IL-10-dependent and independent mechanisms. In addition, we show that macrophages and neutrophils within the lungs of Mtb-infected Bhlhe40-/- mice exhibit defects in iNOS production compared to infected WT mice, supporting that BHLHE40 promotes pro-inflammatory responses in innate immune cells, which may contribute to the essential role for BHLHE40 during Mtb infection in vivo.

overall_design: To investigate the role of BHLHE40 in inflammatory responses in GM-CSF-cultured cells and determine what effects were dependent on excess IL-10 in the absence of BHLHE40, we generated GM-CSF cultures from WT,  Bhlhe40-/-, and Bhlhe40-/-Il10-/- GM-CSF mice and collected samples in the following conditions: naïve, mock-treated, and heat-killed Mycobacterium tuberculosis (HKTB)-treated.

first: Skyler

last: Hendrix

first: Yassin

last: Mreyoud

first: Michael

last: McNehlan


title: Sequential redox vulnerabilities with therapeutic potential during the acquisition of drug resistance in BRAFV600E lung adenocarcinoma

city: Bordeaux

first: ELodie

last: Darbo

address: 229 cours de l'Argonne

department: INSERM

institute: University of Bordeaux

summary: The current targeted therapy for lung cancer patients harbouring BRAFV600E alterations consists of a dual blockade of RAF and MEK kinases often combining dabrafenib with trametinib (D/T). This regimen results in extended survival when compared to single agent treatments but, as with other targeted therapies, disease progression is unavoidable. There is limited information of how BRAFV600E-driven lung adenocarcinomas adapt to this targeted treatment and persist before clinical relapse is detected. At this point, a significant fraction of these resistant tumours display mutations in other members of the RAS-ERK pathway and counteract the inhibitors effect by reactivating oncogenic signalling. We demonstrate here that oxidative stress together with the concomitant induction of antioxidant responses is a prominent and early feature boosted by D/T treatment. However, the nature of the oxidative damage and the choice of redox detoxification systems elicited by cancer cells display substantial differences during the process leading to the onset of drug resistance. While persister cells suffer from lipid peroxidation and strongly rely on GPX4 to prevent ferroptosis-driven cell death, D/T resistant tumours harbouring NRAS secondary mutations enhance cystine transport to boost antioxidant responses. Accordingly, timely inhibition of these detox programs by GPX4 or HDAC inhibitors decrease resistant cell viability and extend therapeutic efficacy.

overall_design: HCC364-DTP and DTEP were generated by treating HCC364 cells with 250 nM dabrafenib and 5 nM trametinib for 3 and 40 weeks, respectively. Total RNA were extracted and submitted to Illumina RNA sequencing (30M single reads 50 bases).

first: Marie-Julie

last: Nokin

first: Elodie

first: David

last: Santamaría

last: Ambrogio


title: single nucleus RNA-seq for mice septal area

city: Shenzhen

first: Gaowei

last: Chen

address: 1056 Xueyuan avenue

institute: ShenZhen Institute of Advanced technology Chinese Academy of sciences

summary: To characteirze the cell types in the septal area of mice using single nuclues RNA-seq

overall_design: Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.


title: Targeting fatty acid metabolism to abrogate differentiation block in pre-leukemia induced by AML1-ETO [2]

city: Tianjin

first: Yu

last: Liu

state: -- None selected --

address: 288 Nanjing Road

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: To gain the underlying insight into the functional impact of AML1-ETO expressed in hematopoietic stem cells and progenitors (HSPCs), we employed single-cell transcriptome sequencing to elucidate the characteristics of  purified Lin-c-kit+ cells (HSPCs) from the bone marrow (BM) of both AML1-ETO expressed (AML1/ETO) and Wild-Type (control) C57 mice.

overall_design: The conditional inducible knock-in C57BL/6 murine model was established with an inducible Cre recombinase (Mx1-Cre) and heterozygous conditional knock-in of Runx1-Run1t1 in hematopoietic system. Mice with the Runx1-Runx1t1 genotype carry the mCherry sequence downstream of the Runx1-Runx1t1 sequence. Upon Poly[I:C] induction, the Runx1-Runx1t1 protein with mCherry fluorescence will be expressed (mCherry+) , while cells which have not responsed by Poly[I:C] will not express Runx1-Runx1t1 protein and fluoresce without mCherry (non_mCherry). Single-cell RNA-seq was performed on purified Lin-c-kit+ cells from the bone marrow (BM) of both AML1-ETO expressed (AML1/ETO) and Wild-Type (control) C57 mice.The BM cells were sorted using AriaIII as follows: DAPI-Lin-c-kit+ cells from the control mouse, DAPI-mCherry-Lin-c-kit+ cells from the AML1/ETO mouse (non-mCherry group) and DAPI-mCherry+Lin-c-kit+  cells from the AML1/ETO mouse (mCherry+ group). And the cells of non-mCherry group and mCherry+ group were derived from the same AML1/ETO mouse.

first: JianXiang

last: Wang

first: Shaowei

last: Qiu

first: Xiaoyu


title: CyCoNP lncRNA establishes cis and trans RNA-RNA interactions to supervise neuron physiology

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

institute: Sapienza University of Rome

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

overall_design: Refer to individual Series


title: Immune landscape of oncohistone-mutant gliomas reveals diverse myeloid populations and tumor-promoting behavior

city: Montréal

first: Claudia

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

summary: Histone H3-mutant gliomas are deadly brain tumors characterized by a dysregulated epigenome and stalled differentiation. In contrast to the extensive datasets available on tumor cells, limited information exists on their tumor microenvironment (TME), including the immune infiltrate. Here, we characterize the TME of H3.3K27M and G34R/V-mutant gliomas, and multiple H3.3K27M mouse models, using transcriptomic and proteomic, including spatial single-cell approaches. Resolution of immune lineages indicates uniform high-infiltration of H3-mutant gliomas with diverse myeloid populations, high-level expression of immune checkpoints, and scarce lymphoid cells, findings uniformly reproduced in all H3.3K27M models tested. We show these myeloid populations communicate with H3-mutant cells mediating immunosuppression and sustaining tumor formation and maintenance. Dual inhibition of myeloid cells and immune checkpoints showed significant therapeutic benefit in pre-clinical syngeneic models. Our findings provide valuable characterization of the TME of oncohistone-mutant gliomas, and insights into means to modulate the myeloid infiltrate for the benefit of patients.

overall_design: 4 mouse tumor models of K27M pHGG generated by in-utero electroporation of mutations, sequenced for single-cell. These mutations include H3.3K27M, ATRX LOF, P53 LOF and PDGFRA WT overexpression (annotated as KAPP). 2 replicates of de-novo KAPP and 2 replicates of KAPP engrafted tumor; generated by engrafting the de-novo tumor in a new mouse.

first: Augusto

last: Andrade

first: Danai

last: Topouza

last: McNicholas

first: Antonella

last: De Cola

first: Damien

last: Faury

first: Steven

last: Hebert

first: Nada

last: Jabado

first: Manav

last: Pathania


title: Spatial Transcriptomics reveals that cells that experience intratumoral hypoxia retain hypoxia-associated transcriptional programs after invading into oxygenated tumor regions.

city: Baltimore

first: Ines

last: Godet

state: MD

address: 1650 Orleans Street, CRB1, room 128

department: Oncology

institute: Johns Hopkins University

summary: To understand the role of hypoxia in metastatic progression, we sought to spatially map gene expression in hypoxic cells compared with cells that migrated to oxygenated tumor regions. We adapted the Visium spatial transcriptomics protocol to perform concurrent transcriptional profiling and fluorescent imaging of our hypoxia fate-mapping system.

overall_design: Hypoxia fate-mapping MDA-MB-231 tumors (Godet et. al, 2019) were harvested 18 days post-implantation and immediately frozen in clear OCT. 10 μm tumor slices were placed within the fiducial frame of the Visium slide. The tissue was pre-fixed in cold methanol and imaged at 10X magnification using a Cytation5 in the RFP and GFP channels to acquire native fluorescence. The slide was immediately transferred to cold methanol with DAPI. DAPI staining was imaged at 10X using Cytation5.

first: Daniele

last: Gilkes


title: Skeletal Muscle-On-A-Chip in Microgravity for Sarcopenia Modeling and Advanced Drug Screening

city: PALO ALTO

first: Soochi

last: Kim

state: California

address: Bldg 101 Rm 141, Miranda

institute: Stanford University

summary: Microgravity has been shown to lead to both muscle atrophy and impaired muscle regeneration. The purpose was to study the efficacy of microgravity to model impaired muscle regeneration in an engineered muscle platform and then to demonstrate the feasibility of performing drug screening in this model. Engineered human muscle was launched to the International Space Station National Laboratories, where the effect of microgravity exposure for 7 days was examined by transcriptomics.

overall_design: Gene expression profiling analysis of skeletal muscle-on-a-chip in microgravity and in gravity at day 7 with or without drug treatment (IGF-1 and SW033291), and human muscle tissue obtained from healthy and with sarcopenia.

first: Mahdis

last: Shayan

first: Bugra

last: Ayan

first: Thomas

middle: A

last: Rando

first: Ngan

last: Huang


title: Missense mutations in linker-2 of KLF1 impair expression of membrane transporters and cytoskeletal proteins to cause hemolysis

city: Melbourne

first: Graham

middle: William

last: Magor

state: Victoria

address: 99 Commercial Rd

institute: ACBD

overall_design:
Compound heterozygous mice for KLF1 mutations develop hemolytic anemia accompanied with splenomegaly and expanded erythroid progenitors in the spleen (CD71+/TER119+ erythroblasts).
We performed RNAseq on CD71+/TER119+ erythroblasts sorted from spleens of the 5 indicated genotypes. We performed differential gene expression analysis from 3 or more biological replicates across the 5 genotypes.

first: Stephen

first: Kevin

last: Gillinder

first: Andrew

last: Perkins


title: Iron capture through CD71 dictates perinatal and tumoral Treg expansion modulating iron homeostasis and gut microbiota colonization

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary:
Beside suppressing immune responses, regulatory T cells (Tregs) maintain tissue homeostasis and control systemic metabolism. Whether iron, a fundamental element for all living cells, is required for Treg expansion, is completely unknown. Here, we showed that the transferrin receptor CD71 was upregulated on activated proliferating Tregs infiltrating human liver cancer. Mice with a Treg-restricted CD71 deficiency spontaneously developed a scurfy-like disease, caused by a severe impairment in perinatal Treg expansion.
CD71-null Tregs display decreased proliferation and mitochondrial functions, and a tissue-Treg signature loss. In the perinatal life, CD71 deficiency in Tregs triggered a hepatic response to iron overload, characterized by increased hepcidin transcription and iron accumulation in macrophages. A lower bacterial diversity, and a reduction of beneficial species, were detected in the faecal microbiota of CD71 conditional knock-out neonates. Our findings indicate that the CD71-mediated iron absorption is required for Treg perinatal expansion and controls the systemic iron homeostasis, which in turn shapes the bacterial gut colonization.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sorted CD4+ YFP+ Tregs from splenocytes of Foxp3Cre/+ Tfrcfl/fl and Foxp3Cre/+ Tfrc+/+ female mice

first: Ilenia

last: Pacella

first: Silvia

last: Piconese


title: Investigating the transcriptional regulation of intratumoral hypoxia in CTCs

summary: Using a hypoxia-fate mapping system that causes a fluorescent switch from DsRed to GFP expression,  we isolated CTCs from the blood of 2 NSG mice 40 days post orthotopic tumor implantation. The CTCs were sorted into DsRed+ or GFP+ populations by fluorescence-activated cell sorting (FACS).

overall_design: Mice were inoculated with hypoxia fate-mapping MDA-MB-231 cells (described in Godet et. al, Nat Comm, 2019) orthotopically to generate breast tumors. After 40 days, whole blood was collected, lysed to eliminate red blood cells and washed. Samples were immediately sorted into DsRed+ or GFP+ populations and submitted to RNA extraction.


title: Hfq mediates transcriptome-wide RNA structurome reprogramming under virulence-inducing conditions in a phytopathogen

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Although RNA structures play important roles in regulating gene expression, the mechanism and function of mRNA folding in plant bacterial pathogens remain elusive. Therefore, we perform dimethyl sulfate sequencing (DMS-seq) on the Pseudomonas syringae under nutrition-rich and deficient conditions, revealing that the mRNA structure changes substantially in the minimal medium (MM) that tunes global translation efficiency (TE), thereby inducing virulence. This process is led by the increased expression of hfq, which is directly activated by transcription regulators RpoS and CysB. The co-occurrence of Hfq and RpoS in diverse bacteria and the deep conservation of Hfq Y25 is critical for RNA-mediated regulation and implicates the wider biological importance of mRNA structure and feedback loops in the control of global gene expression.

sample_organism: Pseudomonas savastanoi pv. phaseolicola 1448A

first: Canfeng

last: HUA

first: Jiadai

first: Yue

last: Sun

first: Tingting

last: Wang

last: Deng


title: MTGR1 is required to maintain small intestinal stem cell populations - scRNA sequencing

status: Public on Jul 01 2024

city: Nashville

first: Christopher

last: Williams

state: Tennessee

address: 2215-B Garland Ave, 1075 MRB4

institute: Vanderbilt University Medical Center

summary: Loss of MTGR1 broadly skews intestinal cell lineages. Here, we used sc-RNA sequencing to analyze MTGR1-dependent changes in intestinal cell and stem cell populations.

overall_design: Cells from WT and Mtgr1 null duodenums were collected and encapsulated for analysis by scRNA-sequencing.

first: Sarah

last: Short

first: Ken

last: Lau

first: Alan

last: Simmons


title: MTGR1 is required to maintain small intestinal stem cell populations - RNA-sequencing

summary: Undifferentiated intestinal stem cells (ISCs), particularly those marked by Lgr5, are crucial for maintaining homeostasis and resolving injury. Lgr5+ cells in the crypt base constantly divide, pushing daughter cells upward along the crypt axis where they differentiate into specialized cell types. Coordinated execution of complex transcriptional programs are necessary to allow for the maintenance of undifferentiated stem cells while permitting differentiation of the wide array of intestinal cells necessary for homeostasis. Previously, members of the myeloid translocation gene (MTG) family have been identified as transcriptional co-repressors that regulate stem cell maintenance and differentiation programs in multiple organ systems, including the intestine. One MTG family member, myeloid translocation gene related 1 (MTGR1), has been recognized as a crucial regulator of secretory cell differentiation and response to injury. However, whether MTGR1 contributes to the function of ISCs has not yet been examined. Here, using Mtgr1-/- mice, we have assessed the effects of MTGR1 loss specifically in ISC biology. Interestingly, loss of MTGR1 increased the total number of cells expressing Lgr5, the canonical marker of cycling ISCs, suggesting higher overall stem cell numbers. However, expanded transcriptomic and functional analyses revealed deficiencies in MTGR1 null ISCs, including deregulated ISC-associated transcriptional programs. Ex vivo, intestinal organoids established from Mtgr1 null were found nearly completely unable to survive and expand, likely due to aberrant differentiation and loss of stem and proliferative cells. Together, these results indicate that MTGR1’s role in intestinal differentiation is likely to be stem cell intrinsic and identify a novel role MTGR1 in maintaining ISC function.

overall_design: Small intestine crypts were isolated from 3 WT and 3 Mtgr1-/- mice. Following crypt isolation, a portion of the samples were collected and homogenized in TRIzol reagent while the remaining crypts were plated for enteroid culture. After 24 hours, half of the plated enteroids were collected for RNA extraction, while the remaining enteroids were cultured for an additional 48 hours and harvested at 72 hours post-plating. Gene expression changes between WT and Mtgr1 null samples was assessed by bulk RNA-sequencing.


title: Gain-of-function Variants in SMAD4 compromise Respiratory Epithelial cells

city: Boston

first: Hongmei

last: Mou

address: 55 Fruit Street, Jackson 1402

department: The Mucosal Immunology & Biology Research Center

institute: Massachusetts General Hospital

summary: To investigate how SMAD4 mutations associated with Myhre syndrome impact SMAD4 protein levels, activation and physiological functions in patient derived nasal epithelial cells. We derived primary nasal basal stem cells from inferior turbinate brushings of healthy subjects and Myhre syndrome patients (SMAD4-Ile500Val, Arg496Cys, Ile500Thr).  After ALI differentiation, RNA was collected from healthy nasal basal epithelial cells and Myhre syndrome-epithelial cells to perform mRNA Deep sequencing. We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Total RNA was extracted from nasal basal epithelial cells (passage P1). Comparative gene expression profiling analysis was done of RNA-seq data for nasal basal epithelial cells and Myhre syndrome-epithelial cells.

first: Mark

last: Lindsay

first: Eleanor

last: Scimone

first: Joseph

last: Lawton

first: Rashmi

last: Richa

first: Lael

last: Yonker

first: YP

last: Di

first: Kenny

last: Ouyang

first: Xiulei

last: Mo

first: Angela

last: Lin


title: Early-life infection depletes preleukemic cells in a mouse model of hyperdiploid B-cell acute lymphoblastic leukemia

city: Vancouver

first: Ali

last: Farrokhi

state: BC

address: BC Childrens Hospital Research Institute, 950 west 28th Ave- Ro0m 3062

institute: University of British Columbia

summary: Epidemiological studies report opposing influences of infection on childhood B cell acute lymphoblastic leukemia (B-ALL). Although infections in the first year of life appear to exert the largest impact on leukemia risk, the effect of early pathogen exposure on the fetal preleukemia cells (PLC) that lead to B-ALL has yet to be reported. Using cytomegalovirus as a model early-life infection, we show that virus exposure within one week of birth induces profound depletion of transplanted B-ALL cells in two mouse models and of in situ-generated PLC in Eu-ret mice. The age_x0002_dependent depletion of PLC results from an elevated STAT4-mediated cytokine response in neonates, with high levels of IL-12p40-driven IFN-g production inducing PLC death. Similar PLC depletion can be achieved in adult mice by impairing viral clearance. These findings provide mechanistic support for an inhibitory effect of early-life infection on B-ALL progression and could inform development of therapeutic or preventative approaches.

overall_design:
To investigate the specific cellular changes in PLC affected by an anti-MCMV immune response and the effector molecules driving them, we infected 6 day-old Eμ-ret pups with 3x10^3 plaque-forming unit (PFU) of K181-luc MCMV via intraperitoneal (i.p.) injection.
We then performed RNA-seq on PLC flow-sorted from the spleens of 6 MCMV-infected and 4 PBS-infected mice 6 days after infection. RNA was isolated from 2x10^5 cells per mouse.

first: Tanmaya

last: Atre

first: Samuel

last: Salitra

first: Maryam

last: Alteha

first: Ana

last: Citlali Márquez

first: Matthew

last: Gynn

first: Mario

last: Fidanza

first: Sumin

last: Jo

first: Nina

last: Rolf

first: Karen

first: Jesus

last: Duque-Afonso

first: Michael

last: Cleary

first: Alix

last: Seif

first: Tobias

last: Kollmann

first: Soren

last: Gantt

first: Gregor

last: Reid


title: Activation of S1P2 is protective against cisplatin-induced peripheral neuropathy

city: Singapore

first: wan Shing Brenda

last: Lam

address: MD3 #04-01 16 Medical Drive

department: Pharmacology

country: Singapore

institute: National University of Singapore Yong Loo Lin School of Medicine

summary: To elucidate the molecular mechanisms underlying the neuroprotective role of S1P2, we conduct RNASeq on dorsal root ganglions (DRGs) collected from a cisplatin-induced peripheral neuropathy (CIPN) rat model.

overall_design: 4 biological replicates with three treatment groups

first: Brenda

middle: W

first: Ping

last: Xiang

first: Ling

middle: J

last: Soon

first: Amelia

middle: Y

last: Yam

first: Claudine

last: Lim

first: Long

last: Nguyen

first: Deron

last: Herr

first: Minh

last: Lea


title: Transcriptomic Analysis of the Spatiotemporal Axis of Oogenesis and Fertilization in C. elegans

city: Charlotte

first: Yangqi

last: Su

state: NC

address: 9201 University City Blvd

department: Bioinformatics

institute: UNC Charlotte

summary: The oocyte germline of the C. elegans hermaphrodite presents a unique model to study the formation of oocytes. However, the size of the model animal and difficulties in retrieval of specific stages of the germline have obviated closer systematic studies of this process throughout the years. Here, we present a transcriptomic level analysis into the oogenesis of C. elegans hermaphrodites. We dissected a hermaphrodite gonad into seven sections corresponding to the mitotic distal region, the pachytene, the diplotene, the early diakinesis region and the 3 most proximal oocytes, and deeply sequenced the transcriptome of each of them along with that of the fertilized egg using a single-cell RNA-seq protocol. We identified specific gene expression events as well as gene splicing events in finer detail along the oocyte germline and provided novel insights into underlying mechanisms of the oogenesis process. These results expand our knowledge of the transcriptomic space of the C. elegans germline and lay a foundation on which future studies of the germline can be based upon.

overall_design: we combined microdissection with scRNA-seq technique, and profiled the transcriptomes in the proliferative zone, pachytene zone, diplotene zone, early diakinesis zone (before -3 oocyte stage), later diakinesis zone (-3, -2, -1 oocytes), and the zygote. We identified not only many genes that were known to play roles in oogenesis and fertilization, but also many novel candidate genes that may be significant in each of the stages.

first: Jonathan

last: Shea

first: Darla

last: DeStephanis

first: Zhengchang


title: RORC RNA Switch Mechanisms

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF


title: Transcriptomic analysis to identify genes associated with hypothalamus vulnerability in aging mice with cognitive decline

city: Beijing

first: Cuige

last: Shi

address: No.12, Dahuisi Road, Haidian District

institute: National Research Institute for Family Planning

summary: Normal aging process is accompanied by cognitive decline. Studies have shown that the hypothalamus plays an important role in regulating aging and cognition. However, the exact molecular mechanism remains unclear. Therefore, the present study aimed to identify predictors of aging cognitive decline in the hypothalamus. The behavioral experiment was used to identify learning and memory differences between young and old mice. Transcriptome sequencing was performed on the hypothalamus of young and old mice to identify potential genes.Our data provide the  related genes ,which may be potential predictors of cognitive function in the elderly population, which will establish an important foundation for us to further explore the molecular mechanism.

overall_design: To identify predictors of aging cognitive decline in the hypothalamus, five young mice (12 weeks old) and five aging mice (22 months old) were used to establish animal models.After the behavioral experiment,  three of each group were randomly selected for transcriptome sequencing.


title: Transcriptional profiling of NK cells from tuberculosis patients

city: beijing

first: lu

last: z

state: - 选择 -

address: beijing

institute: institution of microbology

summary: NK cells were purified from peripheral blood of healthy controls (n = 5), individuals with latent tuberculosis infection (n = 5), and active tuberculosis patients (n = 5). Total RNA was isolated from purified NK cells using RNA Isolation Kit (Dongsheng, R1061) according to the manufacturer's instructions. RNA Sequencing was conducted using the Illumina HiSeq X Ten platform (Novogene Bioinformatics Technology Co., Ltd.) with paired-end 150-bp reads.

overall_design: Patients with ATB were diagnosed by significant symptoms of TB with a positive result of T-SPOT.TB test (a commercially available IGRA method) , and were further confirmed by Mtb culture of respiratory specimens. LTBI individuals were healthcare workers with positive T-SPOT.TB results but without any clinical TB symptoms.  The individuals without known history of exposure to Mtb were included as healthy control (HC) subjects based on negative results of both T-SPOT.TB and PPD skin reactivity tests. ATB patients and LTBI individuals were recruited from Beijing Chest Hospital, a TB specialized hospital in China. All Hhealthy control individuals were recruited form Institute of Microbiology, Chinese Academy of Sciences. All participants aged ≥16 years, and had no significant other medical history such as human immunodeficiency virus (HIV) infection, cancers and diabetes.

first: Cui

middle: H

last: Liu


title: Characterization of Residual MicroRNAs in AAV Vector Batches Produced in HEK293 Mammalian Cells and Sf9 Insect Cells

status: Public on Jun 30 2024

city: Nantes

first: Jean-Baptiste

last: Dupont

address: 22 boulevard Benoni Goullin

institute: Nantes Université

summary: With more than 130 clinical trials and eight approved gene therapy products, AAVs stand as one of the most popular vehicles to deliver therapeutic DNA in vivo. One critical quality attribute analyzed in AAV batches is the presence of residual DNA, as it could pose genotoxic risks or induce immune responses. Surprisingly, the presence of small cell‑derived RNAs, such as micro‑RNAs, has not been previously investigated. In this study, we examined the presence of miRNAs in purified AAV batches produced in mammalian or in insect cells. Our findings revealed that miRNAs were present in all batches, regardless of the production cell line or capsid serotype (2 and 8). Quantitative assays indicated that miRNAs were co‑purified with the rAAV particles in a proportion correlated with their abundance in the production cells. The level of residual miRNAs was reduced via an immunoaffinity chromatography purification process including a tangential flow filtration step or by RNase treatment, suggesting that most miRNA contaminants are likely non encapsidated into AAV particles. In summary, we demonstrate, for the first time, that miRNAs are co-purified with AAV particles. Further investigations are required to determine whether these miRNAs could interfere with the safety or efficacy of AAV-mediated gene therapy.

sample_organism: unclassified Adeno-associated dependoparvovirus A

overall_design: This dataset includes results of a Taqman Low Density Array experiment performed on three samples: HEK293 cells and two replicate AAV-derived samples, The objective is to compare the miRNA profile of the AAV samples to the one of the producer HEK293 cell line.

first: Magalie

last: Penaud-Budloo

first: Emilie

last: Lecomte

first: Quentin

first: Simon

last: Pacouret

first: Frederic

last: Broucque

first: Aurélien

last: Guy-Duché

first: Laurence

last: Jeanson-Leh

first: Cécile

last: Robin

first: Véronique

last: Blouin

first: Eduard

last: Ayuso

first: Oumeya

last: Adjali


title: Cell type and expression independent spatial enhancer-promoter proximity

city: bethesda

first: Efsun

last: Arda

state: Maryland

address: 41 medlars drive

institute: National Institutes of Health

summary: We explored the relationship between enhancer-promoter pairs,  spatial proximity and cell specific gene expression

overall_design: We performed HiChIP using the H3K27ac antibody in two cell lines, EndoC-bH1 and PANC-1. We followed the HiChIP protocol described in Mumbach et al (PMID: 27643841)

first: Li

last: Wang

first: Konnie

last: Guo

first: Songjoon

last: Baek

first: H

middle: E


title: Clariom D gene array of Bone Marrow derived macrophages

city: Lund

first: Mattias

last: Belting

state: Skåne

address: Barngatan

department: Clinical Sciences Lund

country: Sweden

institute: Lund University

summary: Glioblastoma multiforme (GBM) presents a formidable clinical challenge due to its complex microenvironment. Here, we introduce lipid droplet (LD)-loaded macrophages, or tumor-associated foam cells (TAFs), as a previously unidentified immune cell population in GBM. Through extensive analyses of patient tumors, together with in vitro and in vivo investigations, we reveal that TAFs exhibit distinct pro-tumorigenic characteristics related to hypoxia, mesenchymal transition, angiogenesis, and impaired phagocytosis. Moreover, TAF presence correlates with worse patient outcome. Our mechanistic investigations demonstrate that TAF formation is facilitated by lipid cargo from extracellular vesicles released by GBM cells. Importantly, we demonstrate that targeting key enzymes involved in LD formation, such as DGAT1 or ACSL, effectively disrupts TAF functionality. This study establishes TAFs as a prominent immune cell entity in GBM and provides valuable insights into their interplay within the microenvironment. Disruptin

overall_design: 12 samples from patient-derived peripheral blood monocytes, in triplicates, out of which: 3 are hypoxic in vitro differentiated macrophages, 3 are hypoxic in vitro differentiated macrophages treated with DGAT1 inhibitor for 24 hours, 3 are hypoxic in vitro differentiated macrophages treated with GBM-derived EVS, 3 are hypoxic in vitro differentiated macrophages treated with GBM-derived EVs and DGAT1 inhibitor for 24 hours.

first: Valeria

last: Governa

first: Kelin

last: de Oliveira

first: Svenja

last: Offer

first: Myriam

last: Magaña

first: Anna

middle: B

last: Rudenstam

first: Jiaxin

last: Li

first: Sarah

last: Beyer

first: Maria

last: Johansson

first: Ann-Sofie

last: Månsson

first: Charlotte

last: Edvardsson

first: Faris

last: Durmo

first: Axel

last: Boukredine

first: Emelie

last: Gezelius

first: Julien

last: Menard

first: Raquel

last: Garza

first: Johan

last: Jakobsson

first: Therese

last: de Neergaard

first: Pia

last: Sundgren

first: Pontus

last: Nordenfelt

last: Darabi

first: Karin

last: Forsberg-Nilsson

first: Hugo

last: Talbot

last: Bengzon


title: Leukemic initiation in Jam-C-deficient HSPC reveals AP-1/TNF- gene expression signature as a biomarker for AML

city: Marseille

first: Michel

last: Aurrand-Lions

address: 27 Bd Leï Roure

institute: Cancer Research Center of Marseille (CRCM)

summary: The leukemic stem cell score 17 (LSC-17) based on stemness gene expression signature is recognized as indicator of poor disease outcome in acute myeloid leukemia (AML). However, our understanding of the relationships between LSC and pre-leukemic cells is still incomplete. In particular, it is not known whether “niche-anchoring” of pre-leukemic cell affects disease evolution. To address this issue, we conditionally inactivated the adhesion molecule Jam-C expressed by haematopoietic stem cells (HSC) and LSC in an inducible iMLL-AF9-driven AML mouse model. Deletion of Jam-C in HSC before activation of the leukemia-initiating iMLL-AF9 fusion resulted in a shift from long term (LT-HSC) to short term-HSC (ST-HSC) expansion, suggesting that transcriptional programs of leukemic HSC were altered. RNA sequencing performed on leukemic HSC and GMP isolated from diseased mice revealed that genes upregulated in Jam-C-deficient animals belonged to Activation Protein-1 (AP-1) and TNF-/NFB signalling pathways. Using three publicly available datasets of AML gene expression, we further showed that human orthologs of dysregulated genes belonged to a gene regulon distinct from the LSC-17 signature. A prognosis 14-genes score from the AP-1/TNF-/NFB gene expression signature was established and called ATIC for “AP-1/TNF- initiating cell”.  ATIC was independent of the LSC-17 score and improved the stratification of AML patients obtained with the LSC-17 score suggesting that the ATIC score reflected the presence of ST-HSC-initiating AML cells at diagnosis. Collectively we provide a novel tool for understanding AML disease heterogeneity through the identification of specific transcriptional programs for leukemic stem and progenitor cells.

overall_design: BM cells were recovered from femur and tibia, red blood cells were lysed using 1X RBC lysing buffer (eBioscience) and stained with a cocktail containing Live/dead marker, Sca-1, CD150, CD16/32, CD34, CD117, CD135, CD48, and a biotinylated lineage cocktail containing: CD4, CD8, CD3, CD19, CD11c, DX5, Ter119, CD11b, B220 and Gr1.

middle: M

last: Grenier


title: Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation

first: Melissa

middle: McCalley

last: Inge

state: Massachusetts

address: 24 Cummington Mall

institute: Boston University

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

overall_design: Refer to individual Series


title: Effect of Gram Negative Anaerobic Bacteria on Normal Human Skin Keratinocytes (HEKa cells)

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: Objectives: To define the inflammatory signature of healthy keratinocytes induced by gram-negative anaerobe bacteria commonly found in HS and investigate pathways of activation.  Methods: Type strains of P. nigrescens, P. melanogenica, P. intermedia, P. asaccharolytica, F. nucleatum, as well as S. aureus and the normal skin commensal S. epidermidis were heat-killed and co-incubated with normal human keratinocytes.  RNA was analyzed using RNAseq and RT-qPCR.  TLR4 and JAK inhibitors were used to investigate mRNA and protein inhibition of inflammatory cytokines. Results: All GNAs tested induced significantly higher levels of CXCL8 than S. epidermidis or negative control.  P. nigrescens, P. melanogenica, and F. nucleatum were the most stimulatory and produced CXCL8 levels much higher than S. aureus.  RNASeq revealed a broad inflammatory profile most strongly induced by F. nucleatum.  All three bacteria strongly activated the IL-17 pathway and correlated with HS skin transcriptomes.  Both TLR4 and JAK inhibition significantly reduced keratinocyte inflammation.  Results: All GNAs tested induced significantly higher levels of CXCL8 than S. epidermidis or negative control.  P. nigrescens, P. melanogenica, and F. nucleatum were the most stimulatory and produced CXCL8 levels much higher than S. aureus.  RNASeq revealed a broad inflammatory profile most strongly induced by F. nucleatum.  All three bacteria strongly activated the IL-17 pathway and correlated with HS skin transcriptomes.

overall_design: To compare gene signatures induced by anaerobes we stimulated keratinocytes for 3 hours with 2*10^9 bacteria and then harvested RNA and subjected the samples to RNASeq

first: Samuel

last: Williams


title: Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation (microarray)

summary: Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced H3K27ac. Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data supports clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.

overall_design: Recruitment of transcription cofactors to 346 canonical TF binding sites and all possible single nucleotide variants was profiled. Three cofactors (BRD4, P300, and TBL1XR1) were profiled in three cell types (Jurkat, HEK293, and SUDHL4), and seven histone lyisne acetyltransferases (CBP, GCN5, MOF, MOZ, P300, PCAF, and TIP60) were profiled in both resting and 45 min TCR-stimulated Jurkat cells. All experiments were performed in duplicate or in triplicate.

first: Rebekah

last: Miller

first: Heather

last: Hook

first: David

last: Bray

first: Jessica

last: Keenan

first: Rose

last: Zhao

first: Thomas

middle: D

last: Gilmore

first: Trevor

last: Siggers


title: Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation (ChIP-Seq)

summary: Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced H3K27ac. Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data supports clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.

overall_design: Chromatin Immunopreciptation DNA-sequencing (ChIP-seq) of H3K27ac in resting Jurkat T cells and Jurkat T cells stimulated for 45 minutes using soluable CD2/CD3/CD28


title: Randomized phase II trial of preoperative fulvestrant with or without enzalutamide for ER+/Her2- primary breast cancer

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: Most ER+ breast cancers (BC) express androgen receptors (AR).  This randomized phase II trial of 4 months of neoadjuvant fulvestrant (Fulv) alone or with enzalutamide (Combo) was performed to determine if the addition of AR blockade to Fulv would increase the percentage of patients with limited residual tumor at time of surgery, as measured by modified preoperative endocrine predictive index (PEPI) score. Eligible patients were women with ER+/HER2- primary BC cT2 or greater.  Stratification factors were clinical node and T-stage.  Fresh tumor biopsies were required at study entry, after 4 weeks on therapy (W5), and at surgery (week 17).

overall_design: 86 total samples had gene expression analyzed using tempo-seq across the Fulv or Combo arms at prior to (B) or post treatment (W)

first: Jennifer

middle: K

last: Richer

first: Anthony

last: Elias


title: Blood transcriptional response to treatment-resistant depression during electroconvulsive therapy

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

institute: Tel Aviv University

summary:
This study aimed to elucidate the transcriptional differences in peripheral blood mononuclear cells (PBMC) between individuals with treatment-resistant depression (TRD) and a control group without a psychiatric illness; and between patients with TRD, treated with either standard antidepressant drugs alone, or in combination with electroconvulsive therapy (ECT) or ketamine. Additionally, PBMC transcriptomics were compared between treatment responders, following completion of their treatment protocols.
PBMC transcriptomics were compared between treatment responders, following completion of their treatment protocols.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PBMC under 3 different treatments (Serotonin, electroconvulsive therapy, ketamine)

first: Noam

last: Shomron

last: Gurwitz


title: The role of Rack1 in microglia in AD

first: Zengqiang

last: yuan

address: No. 27 Taiping Road, Haidian District

institute: Beijing Institute of Basic Medical Sciences

summary: We found that Rack1 increased in microglia in AD mouse model. Conditional knockout of Rack1 in microglia reduced Aβ aggregation, alleviated neuroinflammation, and rescued cognitive impairments in AD mouse model. Mechanism investigation revealed that knockout of Rack1 in microglia decreased microglial numbers but increased astrocytic numbers and phagocytic activities via IGF1-IGF1R signaling.

overall_design: To study the role of Rack1 in microglia in AD, we used conditional knockout of Rack1 in microglia in AD mouse model,and studied it effects on Aβ aggregation, neuroinflammation, and cognitive impairments. Moreover, we performed microglial and astrocytic transcriptome profile and coculture system to study the mechanism.

first: Jingdan

last: Zhang

first: Jinbo

last: Cheng

last: Yuan


title: Expression data from spermatogonia enriched from 12 dpc mouse testes

city: Kyoto

first: mito

last: shinohara

state: Kyoto

address: Sakyo-ku, Yoshida Konoe

department: Medicine

institute: Kyoto University

summary:
Spermatogonial stem cells (SSCs) cotinues to produce sperm throughout life by self-renewal division. Although it is possible to expand SSCs from most of the mouse strains in vitro for a long-term period by supplementing GDNF and FGF2, SSCs from a 129 background do not proliferate under the same culture conditions.  Since it suggested that they have distinct self-renewal requirements, gene expressions of spermatogonia enriched from testes of DBA/2, C57BL/6, and 129 strains were compared.
In this dataset, we include the expression data obtained from spermatogonia enriched from 12dpc testes of DBA/2, C57BL/6, and 129.  Enrichment was performed by magnetic activated-cell sorting using anti-Ecadherin (CDH1) antibody (ECCD2). These data are used to obtain 359 genes that are differentially expressed among DBA/2, C57BL/6, and 129.

overall_design: 3 Total samples were analyzed. We generated the following comparisons using GeneSpring: 129<B6; 129>B6; 129<DBA/2; 129>DBA/2. Genes with an FDR≤20% and a fold-change ≥2 were selected.

first: Mito

last: Kanatsu-Shinohara

first: Takashi

last: Shinohara


title: Persistent dysfunction of Th17 cells in people with HIV on ART and in elite controllers

city: Montréal

first: Jean-Philippe

last: Goulet

address: C.P. 6128, succursale Centre-ville

institute: Université de Montréal

summary: Th17 cells are rapidly depleted during HIV infection and their frequencies and functions are not fully restored by antiretroviral therapy (ART). In addition, Th17 cells contribute to viral persistence during ART. However, molecular mechanisms underlying these observations remain understudied. MemCCR6+ cells from STs vs. HDs showed alterations in the NOTCH and TGF-β1/smad2-3 pathways, indicative of impairments in their differentiation and stability. Consistently, the RORγt/C2 repressor NR1D1 was upregulated, while Semaphorin 4D, a RORγt/C2 inducer, was decreased in MemCCR6+ cells from STs vs. HDs. Frequencies of Th17 and Th1/Th17 cells within total MemCCR6+ cells were lower in STs and ECs compared to HD individuals, and expressed higher levels of activation and senescence/exhaustion markers. As a result, MemCCR6+ cells from STs produced less IL-17A/F, IL-22, and IFN-γ in vitro compared to HDs. Downregulation of HIV restriction factors (SERINC3, KLF3, and RNF125) and HIV inhibitors (tetraspanins), along with increased expression of MRE11 in MemCCR6+ cells from ST individuals supported higher susceptibility/permissiveness to HIV infection. MemCCR6+ cells from STs and ECs had lower TFAP4 expression and increased expression of EED and TP53BP1 vs. HDs, which is associated to HIV persistence. Markers of DNA damage/modification were elevated in STs and ECs compared to HDs, including NASP, RPA2, H2AX, PARP, and DNA methylases DNMT1/DNMT3A. Similar to the ST group, MemCCR6+ cells in ECs showed decreased expression of Semaphorin 4D and Notch1, along with higher expression of NR1D1 compared to HD donors. Despite successful ART, the transcriptional signature of MemCCR6+ cells revealed impaired differentiation, stability, functions, DNA damage/modifications, and higher susceptibility to HIV infection and viral persistence.

overall_design: FACS-sorted cells (Th17 and Treg populations) from 14 individuals : 5 HDs, 6 STs, and 3 ECs

first: Alexis

last: Yero

first: Tao

last: Shi

first: Cecilia

last: Costiniuk

first: Jean-Pierre

last: Routy

first: Cecile

last: Tremblay

first: Ralph-Sydney

last: Bouassa

first: Yulia

last: Alexandrova

first: Amélie

last: Pagliuzza

first: Nicolas

last: Chomont

first: Petronela

last: Ancuta

first: Mohammad-Ali

last: Jenabian


title: Omics analyses of stromal cells from ACM patients reveal alterations in chromatin organization and mitochondrial homeostasis [Bisulfite-Seq]

city: Milan

first: Mattia

last: Chiesa

address: Via Parea 4

department: Bioinformatics and Artificial Intelligence facility

institute: Centro Cardiologico Monzino IRCCS

type: Methylation profiling by high throughput sequencing

summary: Arrhythmogenic cardiomyopathy (ACM) is a genetic disorder, characterized by ventricular ar-rhythmias, contractile dysfunctions and fibro-adipose replacement of the myocardium. Cardiac mesenchymal stromal cells (CMSC) participate to disease pathogenesis by differentiating towards adipocytes and myofibroblasts. Some altered pathways in ACM are known, but many are yet to be discovered. In order to define changes in the gene expression profiles between ACM- and HC-CMSC, we performed a high throughput Bisulfite-seq on 6 ACM and 6 HC samples. Out of 12466 expressed peaks, 30 resulted differentially expressed. Through enrichment and gene network analyses, we identified differentially regulated pathways, some of which never associated with ACM, including mitochondrial functioning and chromatin organization. Functional validations confirmed that ACM-CMSC exhibited a higher amount of active mitochondria and ROS production, a lower proliferation rate and a more pronounced epicardial-to-mesenchymal transition, compared to controls. In conclusion, ACM-CMSC -omics revealed some additional altered molecular pathways, relevant in the disease pathogenesis, which may constitute novel targets for specific therapies.

overall_design: DNA was extracted 6 ACM and 6 control CMSC, and methylome analyses were performed by bisulfite conversion of DNA combined with next generation sequencing (NGS).

first: Melania

last: Lippi

first: Elena

last: Sommariva

first: Angela

middle: S

last: Maione

first: Lara

last: Iengo

first: Gianluca

last: Perrucci

first: Tommaso

last: Sattin

first: Chiara

last: Cencioni

first: Matteo

last: Savoia

first: Andreas

last: Zeiher

first: Fabrizio

last: Tundo

first: Claudio

last: Tondo

first: Giulio

last: Pompilio


title: Omics analyses of stromal cells from ACM patients reveal alterations in chromatin organization and mitochondrial homeostasis


title: COMPASS core subunits MpSet1 and MpSwd3 regulate Monascus pigments synthesis in Monascus purpureus

city: Shanghai

first: Zhongling

last: Wu

address: Building 2, No. 1518 Jiangchang West Road, Jing'an District, Shanghai

institute: Bright Dairy & Food Co., Ltd.

summary: In eukaryotes, methylation of histone H3 at lysine 4 (H3K4me) catalyzed by the complex of proteins associated with Set1 (COMPASS) is crucial for the transcriptional regulation of genes and the development of organisms. In Monascus, the functions of COMPASS in establishing H3K4me remain unclear. This study first identified the conserved COMPASS core subunits MpSet1 and MpSwd3 in Monascus purpureus and confirmed their roles in establishing H3K4me2/3. Loss of MpSet1 and MpSwd3 resulted in slower growth and development and inhibited the formation of cleistothecia, ascospores, and conidia. The loss of these core subunits also decreased the production of extracellular and intracellular Monascus pigments (MPs) by 94.2%, 93.5%, 82.7%, and 82.5%, respectively. In addition, RNA high-throughput sequencing and quantitative real-time polymerase chain reaction (qRT-PCR) showed that the loss of MpSet1 and MpSwd3 altered the expression of 2646 and 2659 genes, respectively, and repressed the transcription of MPs synthesis-related genes. In addition, the ΔMpset1 and ΔMpswd3 strains demonstrated increased sensitivity to cell wall stress with the downregulation of chitin synthase-coding genes. These results indicated that the COMPASS core subunits MpSet1 and MpSwd3 help establish H3K4me2/3 for growth and development, spore formation, and pigment synthesis in Monascus. These core subunits also assist in maintaining cell wall integrity.

overall_design: To investigate the functions of COMPASS core subunits MpSet1 and MpSwd3 in the regulation of Monascus pigments, we established the MpSet1 and MpSwd3 deletion mutants. We then performed gene expression profiling analysis using data from RNS-seq of WT, SET1 and Swd3 mutant strains. Comparative gene expression profiling of RNA-seq data for WT and its knock out mutans (Set1 and Swd3).

first: Hongyan

last: Gao

first: Zhenmin

last: Liu


title: Omics analyses of stromal cells from ACM patients reveal alterations in chromatin organization and mitochondrial homeostasis [RNA-Seq]

summary: Arrhythmogenic cardiomyopathy (ACM) is a genetic disorder, characterized by ventricular ar-rhythmias, contractile dysfunctions and fibro-adipose replacement of the myocardium. Cardiac mesenchymal stromal cells (CMSC) participate to disease pathogenesis by differentiating towards adipocytes and myofibroblasts. Some altered pathways in ACM are known, but many are yet to be discovered. In order to define changes in the gene expression profiles between ACM- and HC-CMSC, we performed a high throughput RNA-seq on 6 ACM and 6 HC samples. Out of 15031 expressed genes, 529 resulted differentially expressed. Through enrichment and gene network analyses, we identified differentially regulated pathways, some of which never associated with ACM, including mitochondrial functioning and chromatin organization. Functional validations confirmed that ACM-CMSC exhibited a higher amount of active mitochondria and ROS production, a lower proliferation rate and a more pronounced epicardial-to-mesenchymal transition, compared to controls. In conclusion, ACM-CMSC -omics revealed some additional altered molecular pathways, relevant in the disease pathogenesis, which may constitute novel targets for specific therapies.

overall_design: Cells were obtained through the digestion of endomyocardial biopsies and they were characterized. The culture medium for CMSC maintenance was Iscove’s Modified Dulbecco’s Medium (Thermo Fisher Scientific), supplemented with 20% Fetal Bovine Serum (EuroClone), 10 ng/mL basic fibroblast growth factor (Peprotech), 10,000 U/mL Penicillin (EuroClone), 10,000 µg/mL Streptomycin (EuroClone), and 0.02 M L-Glutamine (EuroClone). All the assays were per-formed on CMSC cultured in these conditions. For sequencing via Illumina HiSeq (50-100 Million reads/sample), we extracted total RNA of CMSC from the 6 ACM and 6 control subjects, using the total RNA purification kit (Norgen Biotek Corp.) and following the recommended protocol. High-quality libraries were prepared using the PrepXTM RNA-Seq Library Kit for Illumina platforms. Sequential aligning of raw reads was performed against the GRCh38 Human Genome reference (version 99) with ‘STAR’, and ‘Bowtie 2’ to locally align any reads not mapped by STAR. Gene expression quantification and annotation was computed by “featureCounts”. Then, when less than 10 reads aligned in at least 40% of the gene, that gene was deemed as not expressed. The expressed genes were further normalized (variance stabilizing normalization) by the ‘DaMiRseq R package.


title: Circulating tumor extracellular vesicles to monitor metastatic prostate cancer genomic and transcriptomic evolution

city: Barcelona

last: Nonell

address: C/ NATZARET, 115-117

department: VHIOinformatics

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

summary: Extracellular vesicles (EVs) secreted by tumors are abundant in plasma, but their potential for multi-omic profiling remains widely unexplored.   Here, we pursued next-generation sequencing of circulating EV-DNA and EV-RNA in metastatic prostate cancer (mPC), using a range of in-vitro and in-vivo models, validating our findings in 35 mPC patients with longitudinal samples collected during androgen receptor signaling inhibitor (ARSI) therapy.     EV-DNA copy-number (CN) profiles matched same-patient biopsies and ctDNA (p<0.001) and EV-DNA tumor fraction (TF) associated with shorter time to progression.  We developed a novel approach for studying mRNA in circulating EVs (RExCuE), showing high correlation between EV-RNA and tumor biopsies (r>0.7, p<0.001). EV-RNAseq signatures at 4 weeks of therapy associated with clinical responses. Last, we derived a specific signature of ARSI response in EV-RNA in vivo that predicted response to therapy.    In conclusion, EV profiling enables the study of mPC evolution at transcriptomics level in liquid biopsies.

overall_design: Gene expression profiling analysis of RNA-seq data for C4-2 cells and matching EVs treated with Vehicle (VH) or Enzalutamide (EZ)

first: Joaquin

last: Mateo

first: Irene

last: Casanova-Salas


title: Pre-clinical spheroid models identify BMX as a therapeutic target for metastatic MYCN non-amplified neuroblastoma (ChIP-Seq)

city: Illkirch

first: Anais

middle: Flore

last: Bardet

address: 1 rue Laurent Fries

institute: IGBMC

summary: The development of targeted therapies has provided new hope for an increasing number of cancer patients affected by previously incurable diseases. The clinical success of this approach, however, is limited by numerous challenges, including a better control of cell plasticity, particularly in refractory and metastatic patients. Here we addressed this question in Neuroblastoma (NB), an aggressive pediatric malignancy, which remains a clinical challenge for high-risk patients. NB originates from neural crest-derived progenitors through defective differentiation programs combined with oncogenic activity due to genetic and epigenetic alterations. In order to identify critical genes responsible for tumor aggressiveness we performed combined chromatin and transcriptome analyses on matched primary xenografts, spheroids and differentiated adherent cultures, which we derived from metastatic non-MYCN amplified (nMNA) NB patients. Our approach identified the kinase BMX among the most differentially regulated genes between patient-derived xenografts and spheroids versus adherent models. We further found that BMX expression is associated with high tumor stage and poor patient survival in multiple NB transcriptomic datasets and critical to maintain the self-renewal and tumorigenic potential of NB spheroids. Moreover, we uncovered a positive correlation between BMX expression and the mesenchymal tumor cell phenotype, which was previously associated with increased chemo-resistance. Finally, we show that BMX inhibitors can readily reverse this cellular state, increase the sensitivity of NB spheroids toward standard of care chemotherapy, and reduce tumor growth in preclinical NB models. Altogether, our study identifies BMX as a novel promising therapeutic target for high-risk patients with relapsed or refractory nMNA NB tumors.

overall_design:
H3K4me3 ChIP-seq of matched neuroblastoma xenografts, spheroids and cells in adherent culture conditions
-------------------------------------------------
Raw patient data is deposited on zenodo https://doi.org/10.5281/zenodo.7431535 due to privacy restrictions

first: Santhoshkumar

last: Sundaramoorthy

first: Daniele

last: Colombo

first: Annick

last: Mühlethaler-Mottet

first: Anaïs

middle: F

first: Nicolò

last: Riggi


title: Cell size regulates human endoderm specification through actomyosin-dependent AMOT-YAP signaling

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

institute: WuHan university

summary: Size, as a key physical property of the cell, has enormous impacts on cellular physiology and function. However, whether and how cell size influences stem cell specification is largely unknown. Here, we have analyzed the dynamic changes in cell size during definitive endoderm (DE) differentiation from human pluripotent stem cells. Interestingly, the cell size becomes smaller and with higher stiffness as the differentiation progresses. More importantly, accelerating the cell size diminution with hypertonic pressure significantly improves DE differentiation. Through functional intervention of mechanosensitive elements, we have identified actomyosin activity as a key mediator of DE differentiation and cell size diminution. Mechanistically, the diminution of cell size leads to AMOT nuclear translocation in an actomyosin-dependent manner, which represses YAP activity and thereby permits and facilitates DE differentiation. Together, our study has established a novel connection between cell size diminution and DE differentiation mediated by myosin-dependent AMOT nuclear translocation and suggests application of osmotic pressure an effective facilitator for human endoderm lineage differentiation.

overall_design: human ESC lines, H9, were cultured in mTeSR1 medium (STEMCELL Technologies, #AB217641) on Matrigel-coated plates. The endoderm differentiation protocol of human ESCs was based on the previous reports. IMDM (Gibco, #C12440500BT) and F12 (Gibco, #C11765500BT) mixed at the ratio of 1:1 (IMDM/F12), was used as basal medium, supplemented with 0.2% BSA (YEASEN, #36106ES76), 1% B27 (without Vitamin A, Shanghai BasalMedia Technologies, S441J7), 1% penicillin-streptomycin and Activin A (100 ng/ml, PeproTech, #120-14P) was added for 4 days for endoderm differentiation. When indicated, 10μM Blebbistatin and 2% sucrose was added for 4 days for endoderm differentiation.

first: Lai

last: Jiang

first: Chenchao

last: Yan

first: Wei