title: Profiling the rat cortical single-cell transcriptome reveals the potential mechanism of specific mode electroacupuncture stimulation opening the blood-brain barrier

first: Congcong

last: Ma

state: Zhejiang

address: No. 548, binwen Road

institute: Zhejiang Chinese Medical University

summary: The existence of the blood-brain barrier (BBB) dramatically limits the drug treatment of central nervous system diseases such as stroke, neurodegenerative diseases, and brain tumors. Due to the complexity of the structure and function of the blood-brain barrier, it has been challenging to develop central nervous system drug delivery strategies and reveal critical biological mechanisms. Our previous studies have confirmed that specific mode electroacupuncture stimulation (EA) can effectively open the BBB in rats. Here, we utilized single-cell RNA sequencing (scRNA-seq) to map the cell population of rat cerebral cortex comprehensively. We identified 23 cell subsets and 8 types of cells in the brain obtained by cell annotation, and explored the potential mechanism of EA to open the blood-brain barrier by bioinformatics analysis of specific cell subsets and cell types, as well as cell communications. In summary, scRNA-seq uncovers the transcriptional changes of the cerebral cortex under EA at the single cell level; our results provide rich insights into the molecular and cellular architecture changes of the brain after EA intervention and provide a new reference for BBB material transport and its drug delivery research in health and disease, providing new potential strategies into the mechanism of BBB opening and provide essential information for designing rational treatment regimens and optimizing drug delivery.

overall_design: Rats were randomly divided into electroacupuncture group and control group ( n = 5 ). Rats in the EA group received electroacupuncture intervention, and rats in the CON group received only the same restraint treatment. The frontal lobe tissues of bilateral cerebral cortex of rats were taken for single cell sequencing.

first: Zhaoxing

last: Jia

first: Lin

last: Gan

first: Xianming

last: Lin


title: Life stage specific poly(A) site selection regulated by Trypanosoma brucei DRBD18

status: Public on Jul 25 2024

city: Buffalo

first: Jonathan

middle: E

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

country: USA

institute: University at Buffalo

type: Expression profiling by high throughput sequencing

summary: In this work, we  examine the function of DRBD18 in T. brucei, here using single cell RNA sequencing (scRNAseq) of uninduced and induced DRBD18 knockdowns. In insect procyclic form, we identified one major and one minor population of cells that dramatically increased upon DRBD18 knockdown. Both of these cell populations were significantly enriched for transcripts that are normally upregulated in the quiescent stumpy bloodstream form and metacyclic (MF) life cycle stages, consistent with a role for DRBD18 in life cycle progression. Furthermore, the 3’ end bias of our sequencing technique allowed us to investigate the effect of DRBD18 on poly(A) site selection, and extension of gene annotations permitted a comprehensive analysis of these changes. We found that 3’UTR shortening upon DRBD18 depletion was prevalent, with over 1500 transcripts exhibiting this this phenotype, and RIPseq analyses showed significant overlap between bound transcripts and those with 3’UTR shortening

overall_design: 10x genomics single cell RNA sequencing (scRNAseq) of uninduced and induced DRBD18 knockdowns

first: Brianna

middle: L

last: Tylec

first: Ashutosh

middle: P

last: Dubey

first: Natalie

middle: A

last: Lamb

first: Donald

last: Yergeau

first: Laurie

middle: K

last: Read


title: MALDI imaging and LC-MS/MS-based fast, high-resolution spatial proteomics demonstrate cellular heterogeneity in situ

status: Public on Jul 24 2024

city: Planegg-Martinsried

first: Axel

last: Imhof

address: Großhadernerstr. 9

country: Germany

institute: BioMedical center

summary: Highly specialized cells are fundamental for proper functioning of complex organs. Variations in cell-type specific gene expression and protein composition have been linked to a variety of diseases. Although single cell technologies have emerged as valuable tools to address this cellular heterogeneity, a majority of these workflows lack sufficient in situ resolution for functional classification of cells and are associated with extremely long analysis time, especially when it comes to in situ proteomics. In addition, lack of understanding of single cell dynamics within their native environment limits our ability to explore the altered physiology in disease development. This limitation is particularly relevant in the mammalian brain, where different cell types perform unique functions and exhibit varying sensitivities to insults. The hippocampus, a brain region crucial for learning and memory, is of particular interest due to its obvious involvement in various neurological disorders. Here, we present a combination of experimental and data integration approaches for investigation of cellular heterogeneity and functional disposition within the mouse brain hippocampus using MALDI Imaging mass spectrometry (MALDI-IMS) and shotgun proteomics (LC-MS/MS) coupled with laser-capture microdissection (LCM) along with spatial transcriptomics. Within the dentate gyrus granule cells we identified two proteomically distinct cellular subpopulations that are characterized by a substantial number of discriminative proteins. These cellular clusters contribute to the overall functionality of the dentate gyrus by regulating redox homeostasis, mitochondrial organization, RNA processing, and microtubule organization. Importantly, most of the identified proteins matched their transcripts, verifying the in situ protein identification and supporting their functional analyses. By combining high-throughput spatial proteomics with transcriptomics, our approach enables reliable near-single-cell scale identification of proteins and profiling of inter-cellular heterogeneity within similar cell-types in tissues. This methodology has the potential to be applied to different biological conditions and tissues, providing a deeper understanding of cellular subpopulations in situ.

overall_design: Wildtype C57BL/6J mouse brains were investigated for regional heterogeneity and correlation of regional transcriptomic and proteomic signatures

first: Shibojyoti

last: Lahiri

first: Raffaele

last: Teperino

first: Archana

last: Tomar

first: Shogo

last: Sato

first: Frederike

last: Schäfer


title: Epigenome editing durability varies widely across cardiovascular disease target genes

city: Philadelphia

first: Yifan

last: Yang

state: PA

address: 3400 Spruce Str

institute: University of Pennsylvania

summary: Background: Hepatic knockdown of the proprotein convertase subtilisin/kexin type 9 (PCSK9) gene or the angiopoietin-like 3 (ANGPTL3) gene has been demonstrated to reduce blood low-density lipoprotein cholesterol (LDL-C) levels, and hepatic knockdown of the angiotensinogen (AGT) gene has been demonstrated to reduce blood pressure. Genome editing can productively target each of these three genes in hepatocytes in the liver, offering the possibility of durable “one-and-done” therapies for hypercholesterolemia and hypertension. However, concerns around making permanent gene sequence changes via DNA strand breaks might hinder acceptance of these therapies. Epigenome editing offers an alternative approach to gene inactivation, via silencing of gene expression by methylation of the promoter region, but the long-term durability of epigenome editing remains to be established. Objectives and Results: We assessed the ability of epigenome editing to durably reduce the expression of the human PCSK9, ANGPTL3, and AGT genes in HuH-7 hepatoma cells. Cells treated with the CRISPRoff epigenome editor and PCSK9 guide RNAs were maintained for up to 124 cell doublings and demonstrated durable knockdown of gene expression and increased CpG dinucleotide methylation in the promoter, exon 1, and intron 1 regions. In contrast, cells treated with CRISPRoff and ANGPTL3 guide RNAs experienced only transient knockdown of gene expression. Cells treated with CRISPRoff and AGT guide RNAs also experienced transient knockdown of gene expression; although initially there was increased CpG methylation throughout the early part of the gene, this methylation was geographically heterogeneous—transient in the promoter, and stable in intron 1.Conclusions: This work demonstrates precise and durable gene regulation via methylation, supporting a new therapeutic approach for protection against cardiovascular disease via knockdown of genes such as PCSK9. However, the durability of knockdown with methylation changes is not generalizable across target genes, likely limiting the therapeutic potential of epigenome editing compared to other modalities.

overall_design: We performed RNA sequencing on HuH-7 cells co-transfected with CRISPRoff mRNA and synthetic PCSK9 P13+P16 gRNAs, compared with control cells, at 27 cell doublings after transfection (n = 3 biological replicates per group).

first: Madelynn

middle: N

last: Whittaker

first: Xiao

last: Wang


title: Defining splicing factor requirements for androgen receptor variant synthesis in advanced prostate cancer

city: Newcastle upon Tyne

first: Luke

last: Gaughan

state: Tyne and Wear

address: Paul O'Gorman Building

department: Translational and Clinical Research Institute

country: United Kingdom

institute: Newcastle University

summary: To understand the function of splcing factor MFAP1 in the transcriptional regulation of anrogen receptor variants, we used the CWR22Rv1 prostate cancer cell line depleted of MFAP1 (siMFAP1) or AR-V7 (siCE3) for 72 hours. We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: To investigate the AR-dependent and -independent global transcriptomic impact of MFAP1-depletion using CWR22Rv1 cells depleted of MFAP1 or AR-V7 using siRNA. We then performed gene expression profiling from the RNA sequencing data in response to MFAP1 or AR-V7 depletion compared to the non-targeting scrambled control.

first: Laura

last: Walker


title: Effect of the gi-2 mutation on Arabidopsis thaliana gene expression

city: Valencia

first: Maria A

last: Nohales

address: Ingeniero Fausto Elio s/n

country: Spain

institute: IBMCP (CSIC/UPV)

summary: This study aimed to characterize the effect of GIGANTEA loss of function on gene expression in Arabidopsis thaliana seedlings genome-wide. To this end, transcriptomic analyses using high-throughput sequencing were carried out in Col-0 wildtype and gi-2 loss-of-function mutants.

overall_design: Three biological replicates (n=40-60 seedlings each) of each wildtype (Col-0) and gi-2 seedlings were grown under short day photocycles for 7 days. Samples were collected at ZT 0 (whole seedlings).

first: Maria


title: Cancer therapy induced effects on mesenchymal stem cells

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

institute: University Hospital Essen

summary: Genotoxic stress-induced senescence of MSCs

overall_design: Cultured MSCs were either treated with radiation or not prior RNAseq analysis

first: Hanna

last: Sentek

first: Annika

last: Braun

first: Diana

last: Klein


title: Engineering spacer specificity of the Cre/loxP system

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

summary: Translational research on the Cre/loxP recombination system focuses on enhancing its specificity by modifying Cre/DNA interactions. Despite extensive efforts, the exact mechanisms governing how Cre distinguishes between substrates remains elusive. Cre recognizes 13 bp inverted repeats, initiating recombination in the 8 bp spacer region. While literature suggests that efficient recombination proceeds between lox sites with non-loxP spacer sequences when both lox sites have matching spacers, experimental validation for this assumption is lacking.  To fill this gap, we investigated target site variations of identical pairs of the loxP 8 bp spacer region, screening 6,000 unique loxP-like sequences. Approximately 84% of these sites exhibited efficient recombination, affirming the flexibility of spacer sequences for catalysis. However, certain spacers negatively impacted recombination, emphasizing sequence dependence. Directed evolution of Cre on inefficiently recombined spacers not only yielded recombinases with enhanced activity but also mutants with reprogrammed selective activity. Mutations altering spacer specificity were identified, and molecular modelling and dynamics simulations elucidated the mechanism behind this specificity switch. These findings highlight the potential to fine-tune site-specific recombinases for spacer sequence specificity, offering a novel concept to enhance the applied properties of designer-recombinases for genome engineering applications.

overall_design: Characterizing  the activity of Cre and an evolved Cre variant, RecS3. In order to profile the activity, an oligo library of 6000 different target sites are assembled to an E. coli inducible expression vector. The vector carries the recombinase of interest, either Cre (Exp6) or RecS3 (Exp13). Once library plasmids are assembled, they are transformed to E. Coli and expression of the recombinase is induced over night. The subsequent vectors are then purified from the sample. In order to determine how many times each target was either edited (recombined) or not edited (non-recombined) we run a PCR over the target sites then send the amplicon for illumination deep sequencing. Each experiment is done in triplicates at different induction concentrations.

first: Hoersten

last: Jenna

first: Ruiz-Gómez

last: Gloria

first: Paszkowski-Rogacz

last: Maciej

first: Gilioli

last: Giorgio

first: Guillem-Gloria

last: Pedro Manuel

first: Lansing

last: Felix

first: Pisabarro

last: M Teresa

first: Buchholz

last: Frank


title: Heterogeneous liver tissues with biliary branching and vascular elements through organoid bioprinting

city: 北京

first: yixue

last: Luo

state: 北京市

address: Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, China

country: China

institute: 清华大学

summary: Liver is dynamic, heterogeneous, and each cell type acts in concert to regulate its function. In vitro morphogenesis is limited, and self-assembled biliary and blood vessels system are absent from manufactured liver tissues. The combination of bioprinting and organoid technique offers spatial and cellular control over three-dimensional (3D) organ tissue manufacturing, allowing to build liver tissues with self-assembled structure in vitro. We developed a high-throughput PDMS microwell platform (PMP) generating uniform and functional hepatic organoid building blocks (HOBBs) which displayed cellular crosstalk and self-assembled structure. For bioprinting process, we developed three-level temperature control system and new quadratic material, i.e., alginate-gelatin-collagen-laminin (AGCL) biomaterial, realizing reproducible construction of liver tissues with requisite cellular density. Under long-term differentiation, bioprinted liver tissues exhibited enhanced hepatobiliary function, intrahepatic bile duct networks and angiogenic potential. To investigate the regulatory mechanisms of multicellular crosstalk and self-assembled of HOBBS,  biliary branching morphogenesis, biomimetic liver tissue formation, and angiogenesis of HABs, transcriptome analysis  was performed.

overall_design: For 2D culture, HepaRG cells and HUVECs were maintained in growth medium. Hepatic organoid building blocks (HOBBs) were generated by co-culturing HepaRG cells and HUVECs, and cultured in HepaRG growth medium.  HABs were constructed by bioprinting HOBBs and cultured with differentiation media ( HepaRG growth medium supplemented with 0.5% DMSO) for 14 days.  The samples for RNA-seq were collected in TriZol.

first: Shengnan

last: Xue

first: Rui

last: Yao


title: Comparison of transcriptome landscape between adenine-induced and nephrectomy-induced uremic cardiomyopathy

status: Public on Jul 23 2024

city: Guangzhou

first: Jing-Fu

last: Bao

address: 1838 North Guangzhou Ave

institute: Southern Medical University

summary: Adenine and nephrectomy can be used to establish models of uremic cardiomyopathy in rodents. Although these two approaches cause similar phenotypes of heart, adenine may directly act on cardiomyocytes and lead to different molecular changes from nephrectomy-induced uremic cardiomyopathy. Transcriptome analysis on left ventricles showed 789 upregulated and 345 downregulated genes in mice with nephrectomy-induced uremic cardiomyopathy compared to control mice, while 432 upregulated and 155 downregulated genes in mice with adenine diet-induced uremic cardiomyopathy compared to control mice. Functional analysis revealed that these DEGs were involved in pathways related to immune inflammation, metabolic responses, and synaptic transmission. Further analysis demonstrated that nephrectomy-induced uremic cardiomyopathy has enhanced cell cycle process/extracellular matrix remodeling and suppressed fatty acid metabolism, whereas adenine diet-induced uremic cardiomyopathy only exhibits increased inflammatory response/extracellular matrix remodeling. Compared with nephrectomy-induced uremic cardiomyopathy, adenine diet-induced uremic cardiomyopathy showed improved oxidative phosphorylation, aerobic electron transport chain, and tricarboxylic acid cycle, and suppressed cell cycle-related process, indicating that adenine and its derivates may affect the process of chronic kidney induced cardiac changes.

overall_design: To measure transcriptomic changes genome-wide, we performed RNA sequencing using left ventricular apexes of mice with nephrectomy-induced and adenine diet -induced uremic cardiomyopathy


title: Integrated electrophysiological and genomic profiles of single cells reveal spiking tumor cells in human glioma [scRNA-seq]

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Prior studies have described the complex interplay that exists between glioma cells and neurons, however, the electrophysiological properties endogenous to tumor cells remain obscure. To address this, we employed Patch-sequencing on human glioma specimens and found that one third of patched cells in IDH mutant (IDHmut) tumors demonstrate properties of both neurons and glia by firing single, short action potentials. To define these hybrid cells (HCs) and discern if they are tumor in origin, we developed a computational tool, Single Cell Rule Association Mining (SCRAM), to annotate each cell individually. SCRAM revealed that HCs represent tumor and non-tumor cells that have select features of GABAergic neurons and oligodendrocyte precursor cells. These studies are the first to characterize the combined electrophysiological and molecular properties of human glioma cells and describe a new cell type in human glioma with unique electrophysiological and transcriptomic properties that may also exist in the non-tumor brain.

overall_design: Single-cell RNA-sequencing of human glioma

first: Rachel

last: Curry

first: Serin

last: Harmanci Akdes

first: Ganesh

last: Rao

first: Benjamin

last: Deneen


title: Integrated electrophysiological and genomic profiles of single cells reveal spiking tumor cells in human glioma [Patch-Seq]

overall_design: Patch-sequencing of human glioma


title: Analysis of gene expression in the dog macular retina and supporting tissues: comparison with human macular gene expression profiles

city: Madison

first: Freya

last: Mowat

state: WI

address: 1300 University Avenue

department: Ophthalmology and Visual Sciences

institute: University of Wisconsin-Madison

summary: Dogs are commonly used models of human inherited retinal disorders. Because the dog retina contains a macula-like region, dogs are susceptible to maculopathies with many shared genetic etiologies with humans. Human macular gene expression has been characterized and provides insight into the underlying basis of macular disease. We sought to compare macular gene expression profiles in dogs and humans and interrogate macular disease-associated genes for differential expression between macula and periphery. RNA sequencing was performed on 8mm samples of the dog macular region and superior peripheral region, sampling retina and retinal pigmented epithelium/choroid separately. Read sequences were mapped to CanFam3.1 and raw read counts were analyzed to determine significantly differentially expressed genes between macula and periphery within each tissue. A similar analytic pipeline was used with a published dataset of human samples to allow direct dog/human comparisons.  Pathways and processes involved in significantly DEGs were identified using the Database for Annotation, Visualization and Integrated Discovery. Dogs and humans shared the extent and direction of macular retinal differential gene expression, with multiple shared biological pathways implicated in differential expression. There were fewer similarities between dog and human in the supporting tissues of the retina (the RPE, choroid, sclera). Many genes implicated in heritable retinal and macular disorders in both dogs and humans were differentially expressed between macula and periphery. Approximately 2/3 of genes associated with human age-related macular degeneration were differentially expressed in at least one human tissue, whereas approximately half were differentially expressed in at least one dog tissue. This work underpins the dog macular retinal region as analogous to the human macula in terms of differential gene expression. Whilst age-related maculopathy has not been described in dogs, evidence supports the study of aging of the macula and susceptibility to age-associated pathology in dogs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Retina and RPE/choroid for eyes from the macula and periphery from 4 mixed breed dogs and 6 eyes from 3 dogs of RPE/choroid  in the macula with the retina remaining on during sampling (3) or peeled off before sampling (3)

first: Mowat

last: Freya


title: RNA Sequencing of mouse E15.5 Six2-Cre; Irx3/5(loxP/loxP) whole kidneys

city: Toronto

first: Norman

middle: D

last: Rosenblum

address: 686 Bay St

country: Canada

institute: The Hospital for Sick Children

summary: Transcriptional profiling of E15.5 whole kidneys with a conditional deletion of Irx3/5 in the nephron progenitor cell lineage. Irx3/5 were conditionally deleted using Six2-driven Cre-recombinase. Data will provide novel insight into the functional contributions of Irx3/5 towards nephrogenesis.

overall_design: Whole kidney pairs were collected from E15.5 Six2-Cre; Irx3/5(loxP/loxP) and Irx3/5(loxP/+) littermate control embryos. RNA was extracted from the collected kidney samples and processed for RNA-sequencing.

first: Jasmine

last: Bhatti


title: Metabolic enzymes moonlight as selective autophagy receptors to protect plants against viral induced cellular damage

city: Vienna

first: Yasin

last: Dagdas

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

summary: RNA viruses co-opt host intracellular structures to create specialized replication sites and advance infection. The response of the host to this membrane disruption is poorly understood. In this study, we explore Arabidopsis thaliana's reaction to three distinct viruses that commandeer varying cellular compartments. Our findings reveal autophagy is significantly induced within systemically infected tissues, with autophagy disruption rendering plants highly sensitive to infection. Contrary to being an antiviral defense, quantitative analyses of viral RNA and proteomes establish autophagy as a critical component of the host's tolerance mechanism. Further analysis of mitochondrial hijacking by the Turnip Crinkle Virus has shown that despite perturbing mitochondrial integrity, the virus does not trigger a typical mitophagy response. Instead, viral infection activates a distinct selective autophagy mechanism, where oligomeric metabolic enzymes moonlight as selective autophagy receptors and degrade key executors of defense and cell death. Altogether, our study reveals an autophagy-regulated metabolic rheostats that gauges cellular integrity during viral infection.

overall_design: For RNAseq analysis, the same samples as the ones used for TMT proteomics (PRIDE ID #PXD051596) were used to generate 3’TAG seq libraries

first: Marion

last: Clavel


title: Myostatin regulates energy homeostasis through autocrine- and paracrine-mediated microenvironment communications[gastrocnemius]

city: 上海

first: yang

middle: ji

last: ding

address: 淞沪路2005号

institute: fudan university

summary: Myostatin (MSTN) has been discovered as a critical regulator of muscle mass. Recently, there has been an increasing interest in its functions in metabolism. Here, we specific knocked out MSTN in brown adipose tissue (BAT) (MSTNΔUCP1), and found that the MSTNΔUCP1 mice gained more weight than controls on high-fat diet, with progressive hepatosteatosis, and impaired skeletal muscle activity. RNA-seq analysis indicated signatures of mitochondrial dysfunction and inflammation in MSTN-ablation BAT. Further studies demonstrated that KLF4 is required for the metabolic phenotypes and FGF21 contributes to the microenvironment communication between adipocytes and macrophages induced by loss of MSTN in BAT. Moreover, MSTN-SMAD2/3-p38 signaling pathway mediated the expression of KLF4 and FGF21 in adipocytes. Taken together, brown adipocytes-derived MSTN governs metabolic niche in BAT and regulates systemic energy homeostasis.

overall_design: The gastrocnemius samples from each group were collected for RNA sequencing. Total RNA was isolated using the Trizol method following the manufacturer's instructions. The quality of the RNA was assessed using the Agilent 2100 Bioanalyzer with the RNA 6000 Nano Kit from Agilent Technologies, Santa Clara, CA, USA. cDNA libraries for each sample were constructed as previously described [35713959]. The libraries were sequenced on the BGIseq500 platform (BGI-Shenzhen, China) using 150 bp paired-end reads with a target of 30 million reads per sample.The raw sequencing data was filtered using trim-galore (v0.6.7) to remove reads containing sequencing adapters and low-quality bases. The resulting clean reads were aligned to the reference genome (mm10) using STAR (v2.5.2b). Gene expression quantification was performed using RSEM (v1.2.28) with commands rsem-calculate-expression --paired-end -p 20 –alignments samples.bam star_index.files. Differential gene expression analysis was conducted to compare MSTNΔUCP1 to MSTNFlox/Flox. DESeq2 (v1.42.0) was used for differential expression analysis, considering genes with an adjusted P value < 0.05 and |FC| > 1.5 as significant. Furthermore, KEGG pathway analysis was conducted using differentially expressed genes in, while gene-set enrichment analysis was performed using the obtained log2FC values to detect pathways enriched with profiling genes.

first: Xingxing

last: Kong


title: Transcriptome analysis of Endothelin-3 or Neurotensin treated MuSCs

city: Bad Nauheim

first: Yundong

last: Peng

state: Hessen

address: Ludwigstrasse, 43

department: I

institute: Max Planck Institute for Heart and Lung Research

summary: GPCRs have emerged as crucial regulators of muscle stem cell (MuSC) quiescence, yet the specific repertoire of GPCRs in quiescent MuSCs and the underlying regulatory network remain largely elusive. By employing pharmacological and inducible-genetic methods, we have identified two niche-derived GPCR ligands, endothelin-3 (ET-3) and neurotensin (NT), which bind to EDNRB and NTSR2 receptors, respectively, reinforcing the maintenance of MuSC quiescence. To comprehensively unravel the molecular mechanisms underlying the inhibitory effects of ET-3 and NT on MuSC activation, we conducted RNA sequencing (RNA-seq) analysis on FACS-purified MuSCs that underwent a 5-day in vitro treatment with ET-3 or NT

overall_design: After 5-day in vitro treatment with ET-3 or NT, mRNA profiles of  the  Ctrl (DMSO)or treated MuSCs were  generated by deep sequencing, in triplicate, using NextSeq500 instrument (Illumina) using v2 chemistry with 1x75bp single end setup.

first: S

last: Guenther

first: Y


title: Molecular organization of autonomic, respiratory, and spinally-projecting neurons in the mouse ventrolateral medulla

city: Charlottesville

first: John

last: Campbell

state: VA

address: 485 MCCORMICK RD, GILMER HALL ROOM 229 PO BOX 400328

department: Biology

institute: University of Virginia

summary: The ventrolateral medulla (VLM) is a crucial region in the brain for visceral and somatic control, serving as a significant source of synaptic input to the spinal cord. Experimental studies have shown that gene expression in individual VLM neurons is predictive of their function. However, the molecular and cellular organization of the VLM has remained uncertain. This study aimed to create a comprehensive dataset of VLM cells using single-cell RNA sequencing in male and female mice. The dataset was enriched with targeted sequencing of spinally-projecting and adrenergic/noradrenergic VLM neurons. Based on differentially expressed genes, the resulting dataset of 114,805 VLM cells identifies 23 subtypes of neurons, excluding those in the inferior olive, and 5 subtypes of astrocytes. Spinally-projecting neurons were found to be abundant in 7 subtypes of neurons, which were validated through in-situ hybridization. These subtypes included adrenergic/noradrenergic neurons, serotonergic neurons, and neurons expressing gene markers associated with pre-motor neurons in the ventromedial medulla. Further analysis of adrenergic/noradrenergic neurons and serotonergic neurons identified 9 and 6 subtypes, respectively, within each class of monoaminergic neurons. Marker genes that identify the neural network responsible for breathing were concentrated in 2 subtypes of neurons, delineated from each other by markers for excitatory and inhibitory neurons. These datasets are available for public download and for analysis with a user friendly interface. Collectively, this study provides a fine-scale molecular identification of cells in the VLM, forming the foundation for a better understanding of the VLM's role in vital functions and motor control.

overall_design: We profiled gene expression in single cell nuclei of the adult male and female mouse ventrolateral medulla using the 10X Chromium Single Cell 3' Gene Expression system, in some cases after sorting cell nuclei labeled by Dbh-Cre activity (A5, C1) or via a retrograde AAV-Cre injected into the spinal cord (SpinalTRAPpos)

first: Dana

middle: C

last: Schwalbe

first: Daniel

middle: S

last: Stornetta

first: Ruei-Jen

last: Abraham-Fan

first: George

middle: M

last: Souza

first: Maira

last: Jalil

first: Maisie

last: Crook

first: Stephen

middle: B

last: Abbott


title: Myostatin regulates energy homeostasis through autocrine- and paracrine-mediated microenvironment communications

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

overall_design: Refer to individual Series


title: scRNAseq of spr-5; met-2 mutant embryos

city: Atlanta

first: David

last: Katz

state: GA

address: 615 Michael St, WBRB Room 435

department: Cell Biology

institute: Emory University

summary: Germline genes are ectopically expressed in the somatic lineages of spr-5; met-2 mutant 100-200 cell embryos

overall_design: N2 wildtype and spr-5; met-2 mutant 100-200 cell embryos were dissociated with chitinase to make single cell cDNA libraries using 10X Genomics Single-Cell Capturing System and analyzed using Cell Ranger and Seurat.

first: Juan

last: Rodriguez

first: Hsaio-Lin

middle: V

last: Wang

first: Emily

middle: J

last: Hill


title: Genome-wide Methylation Patterns in Primary Uveal Melanoma: MethylSig-UM, an Epigenomic Prognostic Signature to Improve Patient Stratification

first: Arupa

last: Ganguly

address: 560 Clinical Research Building 415 Curie Boulevard

type: Methylation profiling by genome tiling array

summary: Despite studies highlighting the prognostic utility of DNA methylation in primary uveal melanoma (pUM), it has not been translated into a clinically-useful tool. We sought to  define a methylation signature to identify newly diagnosed individuals at high risk for developing metastasis. Methylation profiling was performed on 41 pUM with at least three years of follow-up using the Illumina Infinium HumanMethylation450K BeadChip (n=24) and the EPIC BeadChip (n= 17). Findings were validated in the TCGA cohort with known metastatic outcome (n=69). Differentially methylated probes were identified in patients who developed metastasis. Unsupervised consensus clustering revealed three epigenomic subtypes associated with metastasis. To identify a prognostic signature, recursive feature elimination and random forest models were utilized within repeated cross-validation iterations. The 250 most commonly selected probes compose the final signature, named MethylSig-UM. MethylSig-UM can distinguish individuals with pUM at diagnosis who developed future metastasis with an area under the curve of ~81% in the independent validation cohort, and remains significant in Cox proportional hazard models when combined with clinical features and established genomic biomarkers. Altered expression of immune modulating genes were detected in MethylSig-UM positive tumors, providing clues for pUM resistance to immunotherapy. The MethylSig-UM model is available to enable additional validation.


title: RNase R Affects the Level of Fatty Acid Biosynthesis Transcripts Leading to Changes in membrane Fluidity

city: Oeiras

first: Vânia

last: Pobre

address: Av. da República

country: Portugal

institute: Instituto de Tecnologia Química e Biológica

summary: Previous studies on RNase R have highlighted significant effects of this ribonuclease in several processes of Streptococcus pneumoniae biology. In this work we show that elimination of RNase R results in overexpression of most of genes encoding the components of type II fatty acid biosynthesis (FASII) cluster. We demonstrate that RNase R is implicated in the turnover of most of transcripts from this pathway, affecting the outcome of the whole FASII cluster, and ultimately leading to changes in the membrane fatty acid composition. Our results show that the membrane of the deleted strain contains higher proportion of unsaturated and long-chained fatty acids than the membrane of the wild type strain. These alterations render the RNase R mutant more prone to membrane lipid peroxidation and are likely the reason for the increased sensitivity of this strain to detergent lysis and to the action of the bacteriocin nisin. Reprogramming of membrane fluidity is an adaptative cell response crucial for bacterial survival in constantly changing environmental conditions. The data presented here is suggestive of a role for RNase R in the composition of S. pneumoniae membrane , with strong impact on pneumococci adaptation to different stress situations.

overall_design: Global transcriptomic analysis with RNA sequencing to determine the most significant differences between the S. pneumoniae TIGR4 wild type (WT) strain and an isogenic RNase R deletion mutant (Drnr)

first: Alípio

last: André Filipe

first: Bárria

last: Cátia

first: Pobre

last: Vânia

first: Matos

last: Ana Rita

first: Prata

last: Sara Carrera

first: Amblar

last: Mónica

first: Arraiano

last: Cecília Maria

first: Domingues

last: Susana


title: STAT3 inhibition permits epigenetic reprogramming and TLR9/IRF8-driven differentiation of inv(16) acute myeloid leukemia.

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 E Durate Rd

department: Shared Resources Department

institute: City of Hope National Medical Center

type: Methylation profiling by high throughput sequencing


title: Effect of IL-33 in human microglia cell line (HMC3)

city: Detroit

first: Nikhlesh

last: Singh

state: MI

address: 6135  Woodward Avenue

institute: Wayne State University School of Medicine

summary: To investigate the expression prolfile of genes regulated by IL-33 in HMC3.

overall_design: HMC3 cells were treated with IL-33 for 24 hours and gene expression profiling was performed using 3 prime RNA sequencing.

first: Shivantika

last: Bisen


title: Effect of recombinant IL-33s, particularly IL-3395-270, IL-3399-270,IL-33109-270, and IL-33112-270 in HRMVECs

summary: To investigate the expression prolfile of genes regulated by IL-3395-270, IL-3399-270, IL-33109-270, and IL-33112-270  in HRMVECs.

overall_design: Human Retinal microvascular endothelial cells (HRMVECs) were exposed to IL-3395-270, IL-3399-270, IL-33109-270, and IL-33112-270 for 24 hours. The RNA was isolatedand then gene expression profiling was performed using 3 prime RNA sequencing.


title: Effect of ADAM10 depletion in human retinal microvascular endothelial cells (HRMVECs)

summary: To investigate the expression prolfile of genes regulated by ADAM10 in HRMVECs.

overall_design: HRMVECs were transfected with control and ADAM10 siRNA and after 48 hours gene expression profiling was performed using 3 prime RNA sequencing.


title: Targeting oncogene-dependent TIM-3 induces T cell reprogramming thereby enhancing graft-versus-leukemia immunity - scRNAseq

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: We use a mouse model for AML treatment in mice, based on injection of WEHI-3B AML cells followed by allogeneic transplantation of bone marrow and T cells. Allogeneic donor T cells will elicit anti-leukemic GVL effect. We want to decipher the importance of TIM-3 expression on T cells, therefore we used donor BM and donor T cells that contains a deletion for TIM-3 in CD8+ T cells (Havcr2fl/fl;E8icre/+).  We performed single cell RNA sequencing and compared T cells isolated from Havcr2fl/fl;E8icre/+ or Havcr2fl/fl (control).

overall_design: A total of two mice for each group were analyzed. Two Mice received WEHI-3B AML cells and additional allogeneic BM and T cells from Havcr2fl/fl (control). Two Mice received WEHI-3B AML cells and additional allogeneic BM and T cells from Havcr2fl/fl;E8icre/+. T cells were isolated on day 23 after BMT and cells were stained with H2K-b (donor haplotype) antibody (Biolegend, reference 116603) labelled with an oligotag (TotalSeq™-B0952, Biolegend, reference 405287), allowing scRNA-seq analysis of selected engrafted donor T cells.

first: Melanie

last: Boerries

first: Nana

last: Talvard-Balland

first: Lukas

last: Braun

first: Robert

last: Zeiser


title: Endomucin marks quiescent long-term multi-lineage repopulating hematopoietic stem cells and is essential for their transendothelial migration

city: Copenhagen

first: Kim

last: Theilgaard-Mönch

address: Ole maaløes vej 5

department: BRIC & The Finsen Laboratory

country: Denmark

institute: University of Copenhagen & Rigshospitalet/National University hospital

summary: Endomucin (EMCN) currently represents the only hematopoietic stem cell (HSC) marker expressed by both murine and human HSCs. Here, we report that EMCN+ long-term repopulating HSCs (LT-HSCs; CD150+CD48−LSK) have a higher long-term multi-lineage repopulating capacity compared to EMCN− LT-HSCs. Cell cycle analyses and transcriptional profiling demonstrated that EMCN+ LT-HSCs were more quiescent compared to EMCN− LT-HSCs. Emcn−/− and Emcn+/+ mice displayed comparable steady-state hematopoiesis, as well as frequencies, transcriptional programs, and long-term multi-lineage repopulating capacity of their LT-HSCs. Complementary functional analyses further revealed increased cell cycle entry upon treatment with 5-fluorouracil and reduced granulocyte colony-stimulating factor (GCSF) mobilization of Emcn−/− LT-HSCs, demonstrating that EMCN expression by LT-HSCs associates with quiescence in response to hematopoietic stress and is indispensable for effective LT-HSC mobilization. Transplantation of wild-type bone marrow cells into Emcn−/− or Emcn+/+ recipients demonstrated that EMCN is essential for endothelial cell-dependent maintenance/self-renewal of the LT-HSC pool and sustained blood cell production post-transplant.


title: Phenotype and function of ex vivo expanded liver progenitor-like cells through biliary epithelial cells reversion

city: Shanghai

first: hexin

last: Yan

address: Pujian Road

institute: Shanghai Reji Hospital

summary: The current study combined genetic lineage tracing with in vitro small-molecule-based reprogramming to define liver progenitor cells (LPCs) derived from hepatic parenchymal and non-parenchymal cells (NPCs). tdTom+ hepatocytes were isolated from ROSA26tdTomato mice following AAV8-Tbg-Cre-mediated recombination, ALB/GFP-EpCAM- NPCs were isolated from AlbCreERT/R26GFP mice and EpCAM+ biliary epithelial cells (BECs) from wild-type intrahepatic bile ducts. A cocktail of small molecules was used to convert the isolated cells into LPCs.

overall_design:
Global expression analysis of RNA sequencing data of expression levels of liver progenitor-like cells derived from hepatocytes and non-parenchymal cells.
Global expression analysis of RNA sequencing data of expression levels of Epcam+ progenitor-like cells derived from intrahepatic bile ducts.

first: Wei

last: Huang

first: He

middle: X


title: A single RRM domain-containing protein SARP1 is required for the separation zone establishment in Arabidopsis

city: Daegu

first: Ju

last: Yun

address: 333, Techno jungang-daero

department: New Biology

country: South Korea

institute: DGIST

summary: Abscission is a developmental process that sheds organs in response to developmental and environmental cues. Abscission involves cell separation between two neighboring cell types in the abscission zone (AZ), residuum cells (RECs) and secession cells (SECs). However, the regulatory mechanisms for spatial determination governing cell separation are poorly understood. BREVIPEDICELLUS (BP) is one of the key transcription factors regulating the AZ cell size and number. To identify molecular components of abscission, we performed a genetic screen using a weak complementation line of bp-3 carrying activation T-DNA tagging. We identified an ebp1 (enhancer of bp1) mutant displaying delayed floral organ abscission. The ebp1 mutants show concaved surface in SECs and abnormally stacked cells on the top of RECs, in contrast to the precisely separated surface in WT. Molecular and histological analyses revealed that the transcriptional programming during cell differentiation in the AZ is compromised in the ebp1 mutant, where SECs of the ebp1 mutant appear to acquire REC-like activities, including cuticle formation and superoxide production. Here we present that SEPARATION AFFECTING RNA-BINDING PROTEIN1 (SARP1) is up-regulated in ebp1 and plays a role in the establishment of the cell separation layer during floral organ abscission in Arabidopsis.

overall_design: RECs (Residuum cells, abscission zone cells of the receptacle) and SECs (Secession cells, abscission zone cells of separated floral organs) of ebp1 mutants were isolated using fluorescence-activated cell sorting of cells from transgenic plants harboring proQRT2::nlsGFP–GUS construct, and their transcriptomes were analyzed by RNA-sequencing.

first: Inhye

last: Lee

first: JaeHo

first: Sunghwan

last: Kim

first: SuHyun

last: Jung

first: Jiyoun

first: Soonki

last: Park

first: Moon-Soo

last: Soh

first: Yuree

first: June

last: Kwak


title: Itaconate mediates a metabolic crosstalk between osteoclasts and osteoblasts

first: Andrea

last: Komljenovic

address: Schwarzspanierstrasse 17

institute: Medical University of Vienna

summary: Bone remodeling is a highly dynamic process dependent on the precise coordination of osteoblasts and hematopoietic-cell derived osteoclasts. Emerging evidence indicates that cellular differentiation is associated with a metabolic rewiring in conjunction with the acquisition of specific effector functions. Changes in core metabolic pathways during osteoclastogenesis, however, are largely unexplored and it is unknown whether and how these processes are involved in bone homeostasis. We show that during differentiation preosteoclasts rearrange their tricarboxylic acid (TCA) cycle, a process crucially depending on both glucose and glutamine. This rearrangement is characterized by induction of immunoresponsive gene 1 (Irg1) and production of itaconate, which accumulates intra- and extracellularly. While the IRG1-itaconate axis is dispensable for osteoclast generationin vitroandin vivo, we demonstrate that itaconate stimulates osteoblasts by accelerating osteogenic differentiation, reducing proliferation and shifting ATP production from mitochondrial respiration to glycolysis. Additionally, supplementation of itaconate increases bone formation by boosting osteoblast activity in mice. Conversely,Irg1deficient mice exhibit decreased bone mass and have reduced osteoproliferative lesions in experimental arthritis. In summary, we identify itaconate, generated as a result of the metabolic rewiring during osteoclast differentiation, as a previously unrecognized regulator of the crosstalk between osteoclasts and osteoblasts

overall_design: human osteoblast progenitor cells cultivated with three different media (normal growth medium, osteogenic differentiation media, osteogenic differentiation media+5mM itaconic acid )

first: Markus

last: Kieler

first: Stephan

last: Blüml


title: Identification of RNF213 as a potential suppressor of local invasion in intrahepatic cholangiocarcinoma

city: Bangkok

first: Khajeelak

last: Chiablaem

state: State...

address: 270 Rama VI Road, Toong Phayathai, Ratchathewi

country: Thailand

institute: Faculty of Medicine Ramathibodi Hospital, Mahidol University

summary: Intrahepatic cholangiocarcinoma (ICC) is a lethal cancer arising from intrahepatic bile ducts in the liver. In the intraductal growth (IDG) type, also referred to as intraductal papillary neoplasm of the bile duct (IPNB), a rare subtype of ICC, cancer cells originating within the bile duct usually invade and infiltrate the nearby liver tissues, resulting in local invasion. IPNB can serve as a good disease model to study the mechanism of local invasion, which is the earliest step of metastasis. Here, we aimed to identify the genes associated with local invasion by comparing the somatic mutations of the matched IPNB tissues with and without local invasion from a set of 11 patients using the Ion AmpliSeq Comprehensive Cancer Panel. Somatic mutation profiling analysis identified RNF213 as a potential candidate gene associated with local invasion in ICC patients. We established stable RNF213-knockdown and shControl cholangiocarcinoma (CCA) cell lines (HuCCT1, YSCCC, and KKU-100). Next, the expression profiling of the RNF213-knockdown and shContol CCA cell lines was analyzed by RNA sequencing.

overall_design: We established stable RNF213-knockdown and shControlI CCA cell lines using 3rd generation lentivirus systems in HuCCT1, YSCCC, and KKU-100. RNA-Sequencing experiments were performed with three biological replicates.

first: Natini

last: Jinawath


title: AOS10-FMT could rescure the adverse effects induced by STZ on the kidney

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We report the side-effects of STZ on the liver, and found that the AOS10-FMT could rescure the side-effect of STZ in many factors,such as lipid metabolism and oxidative stress

overall_design: Exploration of the FMT effects on the damaged kidney induced by STZ

first: Yanan

last: Hao


title: The DNA-repair protein APE1 contributes with hnRNPA2B1 to motif-enriched miRNA secretion

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

type: Non-coding RNA profiling by high throughput sequencing

summary: The base excision repair (BER) Apurinic/apyrimidinic endonuclease 1 (APE1) enzyme is endowed with several non-repair activities, such as the cell response to genotoxic stress, the regulation of gene expression and miRNAs processing. We recently demonstrated that APE1 can be actively secreted by mammalian cells through exosomes. The role of APE1 in exosomes is still unknown, especially regarding the molecular mechanism involving small non-coding RNAs vesicular secretion. miRNAs loading into exosomes is a regulated and selective process, since not all the expressed miRNAs are indistinctly conveyed into exosomes. Through a dedicated transcriptomic analysis on cellular and vesicular small RNAs, we identified secreted miRNAs characterized by enriched sequence motifs and possible binding sites for APE1. In 50 out of 53 DE-miRNA precursors, we surprisingly found EXO motifs and proved that APE1 cooperates with hnRNPA2B1 for the EV-sorting of a subsets of miRNAs, including miR-1246, through a direct binding to GGAG stretch. We provide evidence of a new post-transcriptional role for this ubiquitous DNA-repair enzyme towards miRNAs secretion mechanisms, that could be exploited to interfere with tumor microenvironment.

overall_design: In the study presented here, the miRNome profiling was analyzed in A549 cells following the transient APE1 silencing to identify DEmiRNAs candidates. The experiment was performed in triplicates.

first: Giovanna

last: Mangiapane

first: Michela

last: Notarangelo

first: Emiliano

last: Dalla

first: Giulia

last: Antoniali

first: Monica

last: Degrassi

first: Fabrizio

last: Fabbiano

last: Canarutto

first: Vito

last: D'Agostino

first: Gianluca

last: Tell


title: Signalling pathways drive heterogeneity of ground state pluripotency

city: London

first: Kirsten

middle: R

last: McEwen

address: Du Cane Road

department: MRC Clinical Sciences Centre

institute: Imperial College London

summary: Pluripotent stem cells (PSCs) can self-renew indefinitely while maintaining the ability to generate all cell types of the body. This plasticity is proposed to require heterogeneity in gene expression, driving a metastable state which may allow flexible cell fate choices. Contradicting this, naive PSC grown in fully defined ‘2i’ environmental conditions, containing small molecule inhibitors of MEK and GSK3, show homogenous pluripotency and lineage marker expression. Here we report that 2i induces greater genome-wide heterogeneity than traditional serum-containing growth conditions at the population level across both male and female PSCs. Heterogeneity is dynamic and reversible over time, consistent with a dynamic metastable equilibrium of the pluripotent state. We further show that 2i conditions increase heterogeneity specifically in the calcium signalling pathway at both the population and single-cell level. This is driven by loss of robustness regulators in the form of negative feedback to the upstream EGF receptor. Our findings show that metastability occurs in both 2i and serum PSCs which has implications for our understanding of the nature of the pluripotent state and the role of signalling pathways in the control of transcriptional heterogeneity. Furthermore, our results have critical implications for the current use of kinase inhibitors in the clinic, with induced heterogeneity potentially inducing cancer metastasis and drug resistance.

overall_design: Pluripotent stem cell lines including embryonic stem cells and embryonic germ cells were grown in either serum (FCS) or 2i conditons. Transcriptomes of 22 samples (9 in serum and 13 in 2i) were profiled in batch 1, including 10 female and 12 male cell lines. Transcriptomes of 18 samples (9 in serum and 9 in 2i) were profiled in batch 2 across passages 11, 14 and 17 for three cell lines for each growth condition. All cell lines were derived from Oct4ΔPE-GFP transgenic male mice crossed with with 129SvEv female mice.

first: Sarah

last: Linnett

first: Harry

middle: G

last: Leitch

first: Prashant

last: Srivastava

first: Lara

last: Al-Zou’abi

first: Maxime

last: Rotival

first: Alex

last: Sardini

first: Thalia

last: Chan

last: Filippi

first: Michael

last: Stumpf

first: Enrico

last: Petretto

first: Petra

last: Hajkova


title: Negative selection allows human primary fibroblasts to tolerate high somatic mutation loads induced by N-ethyl-N-nitrosourea

status: Public on Jul 22 2024

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1300 Morris Park Ave

department: Genetics & Biochemistry

institute: Albert Einstein College of Medicine

summary: Single-cell sequencing has shown that thousands of mutations accumulate with age in most human tissues. While there is ample evidence that some mutations can clonally amplify and lead to disease, the total burden of mutations a cell tolerates without functional decline remains unknown. Here we addressed this question by exposing human primary fibroblasts to multiple, low doses of N-ethyl-N-nitrosourea (ENU) and analyzed somatic mutation burden using single-cell whole genome sequencing. The results indicate that individual cells can sustain ~60,000 single-nucleotide variants (SNVs) with only a slight adverse effect on growth rate.  We provide evidence that such high levels of mutations are only tolerated through negative selection against variants in gene coding regions, and in sequences associated with genetic pathways for maintaining basic cellular function and growth. Since most tissues in adults are non-dividing, these results suggest that somatic mutations in the absence of negative selection may have functionally adverse effects.

overall_design: To determine the impact of increased somatic mutation burden on primary human cells in vitro, we repeatedly treated human fetal lung fibroblasts (IMR-90) a total of 9 times with a sublethal dose of 50 µg/mL of N-ethyl-N-nitrosourea (ENU), followed by a recovery period. We then performed RNA-Sequencing of cells collected at the begining of the experiment (1st cycle) or end of the experiment (9th cycle) from the control or ENU-treated groups. Samples collected from 3 independent replicates.

first: Johanna

last: Heid

first: Shixiang

last: Sun

first: Moonsook

last: Lee

first: Alexander

last: Maslov

first: Xiao

last: Dong

first: Simone

last: Sidoli

first: Jan

last: Vijg


title: Small RNA sequencing Analysis of lung Reveals Novel tRNA-derived Small RNAs with Biomarker Potential for Pulmonary Arterial Hypertension

city: Changsha

first: Yusi

last: Chen

state: Hunan

address: 139 Renmin Road

institute: The Second Xiangya Hospital of Central South University

summary: Transfer RNA-derived small RNAs (tsRNAs) are important regulators of a variety of biological functions, however, it is yet unclear how tsRNAs work to cause pulmonary arterial hypertension (PAH). The goal of the current study was to gain a better understanding of how tsRNAs contribute to PAH pathogenesis.

overall_design: A rat model of PAH induced by monocrotaline (MCT) was established, and right ventricular tissues were obtained. Small RNA sequencing was used to get the tsRNA expression profiles of the PAH group and the control group. Quantitative reverse transcription-PCR (real-time PCR) was used to confirm the results. Subsequently, the target genes of the 10 selected tsRNAs and their biological functions were then predicted using bioinformatics techniques.

first: Yi

last: Tang

first: Tengteng

last: Zhu

first: Jiang

last: Li


title: Gene expression profile at single cell level of non-parenchymal cells from Fibrosis and Tumor (FAT) Metabolic Dysfunction-Associated Steatohepatitis (MASH) model vs healthy liver at 12- and 24-week timepoints.

city: New York

first: Chittampalli

middle: Narayanan

last: Yashaswini

address: 1425 Madison Avenue, 11-76

department: Liver

institute: Icahn School of Medicine at Mount Sinai

summary: MASH is a subtype of metabolic dysfunction-associated steatotic liver disease, characterized by inflammation and fibrosis. Non-parenchymal cells in this dataset include mostly immune cells, as well as some other cell types like endothelial cells, cholangiocytes, stellate cells, etc.

overall_design: Single cell suspensions from MASH vs healthy murine livers were made using enzymatic digestion with Dnase I and Collagenase IV, as well as mechanical digestion, followed by filtering. Non-parenchymal cells were enriched by using percoll gradients (70% and 25%). Most hepatocytes are removed with this protocol, and red blood cells are lysed. Samples were submitted for scRNAseq, and were analyzed for uPAR expression in this study.

first: Scott

last: Friedman


title: Myostatin regulates energy homeostasis through autocrine- and paracrine-mediated microenvironment communications[BAT]

city: 上海

first: yang

last: ding

address: 淞沪路2005号

institute: fudan university

summary: Myostatin (MSTN) has been discovered as a critical regulator of muscle mass. Recently, there has been an increasing interest in its functions in metabolism. Here, we specific knocked out MSTN in brown adipose tissue (BAT) (MSTNΔUCP1), and found that the MSTNΔUCP1 mice gained more weight than controls on high-fat diet, with progressive hepatosteatosis, and impaired skeletal muscle activity. RNA-seq analysis indicated signatures of mitochondrial dysfunction and inflammation in MSTN-ablation BAT. Further studies demonstrated that KLF4 is required for the metabolic phenotypes and FGF21 contributes to the microenvironment communication between adipocytes and macrophages induced by loss of MSTN in BAT. Moreover, MSTN-SMAD2/3-p38 signaling pathway mediated the expression of KLF4 and FGF21 in adipocytes. Taken together, brown adipocytes-derived MSTN governs metabolic niche in BAT and regulates systemic energy homeostasis.

overall_design: The brown adipose tissue (BAT) tissue samples from each group were collected for RNA sequencing. Total RNA was isolated using the Trizol method following the manufacturer's instructions. The quality of the RNA was assessed using the Agilent 2100 Bioanalyzer with the RNA 6000 Nano Kit from Agilent Technologies, Santa Clara, CA, USA. cDNA libraries for each sample were constructed as previously described [35713959]. The libraries were sequenced on the BGIseq500 platform (BGI-Shenzhen, China) using 150 bp paired-end reads with a target of 30 million reads per sample.The raw sequencing data was filtered using trim-galore (v0.6.7) to remove reads containing sequencing adapters and low-quality bases. The resulting clean reads were aligned to the reference genome (mm10) using STAR (v2.5.2b). Gene expression quantification was performed using RSEM (v1.2.28) with commands rsem-calculate-expression --paired-end -p 20 –alignments samples.bam star_index.files. Differential gene expression analysis was conducted to compare MSTNΔUCP1 to MSTNFlox/Flox. DESeq2 (v1.42.0) was used for differential expression analysis, considering genes with an adjusted P value < 0.05 and |FC| > 1.5 as significant. Furthermore, KEGG pathway analysis was conducted using differentially expressed genes in, while gene-set enrichment analysis was performed using the obtained log2FC values to detect pathways enriched with profiling genes.

first: Xingxing

last: Kong


title: The developmentally timed decay of an essential microRNA family is seed-sequence dependent

city: Bethesda

first: Katherine

last: McJunkin

state: MD

address: 50 South Drive, Building 50 Room 3148

institute: National Institutes of Health

summary: MicroRNA (miRNA) abundance is tightly controlled by regulation of biogenesis and decay. Here, we show that the mir-35 miRNA family undergoes selective decay at the transition from embryonic to larval development in C. elegans. The seed sequence of the miRNA is necessary and largely sufficient for this regulation. Sequences outside the seed (3' end) regulate mir-35 abundance in the embryo but are not necessary for sharp decay at the transition to larval development. Enzymatic modifications of the miRNA 3' end are neither prevalent nor correlated with changes in decay, suggesting that miRNA 3' end display is not a core feature of this mechanism and further supporting a seed-driven decay model. Our findings demonstrate that seed-sequence-specific decay can selectively and coherently regulate all redundant members of a miRNA seed family, a class of mechanism that has great biological and therapeutic potential for dynamic regulation of a miRNA family's target repertoire.

overall_design: To test the role of miRISC-mediated slicing in invertebrates, we used CRISPR/Cas9-mediated genome editing to mutate the DEDH catalytic tetrad to AEDH in the major C. elegans microRNA Argonautes, ALG-1 and ALG-2 (alg-1(AEDH); alg-2(AEDH)). To determine the impact of mutating Argonautes’ catalytic residues on C. elegans microRNAs, we profiled small RNAs from embryos, L4 stage larvae and young adults. We also profiled small RNAs from embryos that were single mutants, with catalytic residues mutated in either ALG-1 or ALG-2. To test whether Target-directed microRNA degradation contributed to downregulation of select miRNAs in alg-1(AEDH); alg-2(AEDH), we added mutations to this background that theoretically inactivate all TDMD (ebax-1(null)) or TDMD of a mir-243 alone (Y47(mir-243bs_del)) and sequenced small RNAs in young adults.

first: Bridget

middle: F

last: Donnelly

first: Bing

last: Yang

first: Acadia

last: Grimme

first: Karl-Frederic

last: Vieux

first: Chen-Yu

last: Liu

first: Lecong

last: Zhou


title: Apigenin inhibits tumor angiogenesis by suppressing microvesicle biogenesis

city: hefei

first: Wanying

last: Zhang

address: JinZhai Road 96, Hefei, Anhui, China

institute: University of Science and Technology of China

summary: Apigenin regulates multiple pathways related to microvesicle biogenesis without affecting the expression of small Rho GTPase activator  guanine nucleotide exchange factors (GEFs). However, apigenin can primarily targets ARHGEF1 protein, a GEF of the small GTPases, thereby inhibiting the activity of small G proteins such as Cdc42, which is essential in regulating the signaling for the release of microvesicles from tumor cells. Targeting ARHGEF1, apigenin effectively prevents tumor cells from releasing microvesicles. This, in turn, inhibits tumor angiogenesis related to VEGF90K transport on microvesicles, ultimately impeding tumor progression.

overall_design: To investigate the effect of apigenin on transcriptional regualtion, we performed gene expression profiling analysis using data obtained from RNA-seq of HCC-LM3 cells treated with or without apigenin.

first: Qiyu

last: Feng

first: Hongyang

last: Wang


title: STAT3 inhibition permits epigenetic reprogramming and TLR9/IRF8-driven differentiation of inv(16) acute myeloid leukemia [scRNA-seq]

first: Haiqing

address: 1500 E Durate Rd

institute: City of Hope National Medical Center

summary: Cultured acute myeloid leukemia (AML) blasts can differentiate into antigen-presenting cells but achieving leukemic cell immunogenicity proved challenging in clinical setting. Despite expressing multiple immunostimulatory receptors, such as Toll-like Receptor 9 (TLR9), AML cells resist immunostimulation. We previously demonstrated that eliminating Signal Transducer and Activator of Transcription 1 and 3 (STAT1/3) signaling in AML cells using decoy DNA strategy (CpG-STAT3dODN) synergized with TLR9 stimulation and resulted in T cell-mediated leukemia regression. Here, we interrogated the molecular underpinnings of CpG-STAT3dODN-driven differentiation and immunogenicity of mouse Cbfb/MYH11/Mpl AML. The transcriptional profiling of AML cells isolated from mice after inducible Stat3 silencing plus TLR9 stimulation or CpG-STAT3dODN treatment, revealed comparable upregulation of genes related to myeloid cell differentiation (Irf8, Cebpa) and immune stimulation (Gadd45a, Ciita, Il12a, Ifng) but decreased expression of leukemia-promoting Runx1 and Run1t1. The conditional Irf8 silencing in AML cells almost completely abrogated TLR9-driven leukemia cell differentiation. The AML cell reprogramming by CpG-STAT3dODN was likely regulated epigenetically as revealed by reduced global promoter hypomethylation of crucial myeloid cell differentiation and immune activation genes. These changes were associated with reduced expression of known STAT3 targets, DNMT1 and DNMT3a/b. Finally, we provide initial evidence of anti-leukemic effects of CpG-STAT3 inhibitor against human AML model in humanized mice. Our studies suggest that, beyond oncogenic functions, STAT3 in AML cells may be a primary checkpoint in control of immune-stimulatory and differentiation driving effects. These findings support further development of CpG-STAT3 inhibitors as a new bi-functional agents for AML immunotherapy.

overall_design: GFP+c-Kit+ double-positive CMM cells were sorted out of spleens harvested from mice treated short-term (three times every other day) using CpG-STAT3dODN or control PBS and  analyzed using scRNAseq.

first: Dongfang

first: Karol

last: Jacek

first: Marcin

last: Kortylewski


title: Transcription inhibition in Aedes Albopictus C6/36 cells

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: To determine codon optimality in Aedes Albopictus C6/36 cells, we blocked transcription using three independent transcription inhibitors (5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB), Flavopiridol and Triptolide) and measured the RNA level at 6 hours post treatment using RNA-seq.

overall_design: RNA-seq was performed at 6 hours after mock treated (DMSO) or blocking transcription with Flavopiridol, Triptolide or DRB.

first: Luciana

last: Castellano


title: Uncoupled H3K9me3 nucleation and reinforcement during early zebrafish embryogenesis

city: Athens

first: Mary

last: Goll

address: 130 East Green Street

department: Genetics

institute: University of

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The structural organization of eukaryotic genomes is contingent upon fractionation of DNA into transcriptionally active euchromatin and repressive heterochromatin. However, we still have a limited understanding of how these distinct states are first established during animal embryogenesis. Histone lysine 9 trimethylation (H3K9me3) is critical to heterochromatin formation and bulk establishment of this mark is thought to help drive large-scale remodeling of the initially naive chromatin state during animal embryogenesis. However, a detailed understanding of this process is lacking. Here, we leverage CUT&RUN to define the emerging H3K9me3 landscape of the zebrafish embryo with high sensitivity and temporal resolution. We find that despite the prevalence of DNA transposons in the zebrafish genome, LTR transposons are preferentially targeted for H3K9me3 deposition in the embryo, with different families showing distinct establishment kinetics. High signal-to-noise ratios afforded by CUT&RUN revealed emerging sites of low-amplitude H3K9me3 nucleation prior embryonic genome activation (EGA), with early nucleation primarily at a subset of transposon sequences, loci enriched for maternal piRNAs, and pericentromeres. Unexpectedly, the number of nucleated H3K9me3 sites increases linearly across blastula development while quantitative comparison revealed a >10-fold genome-wide increase in H3K9me3 signal at established sites over just 30 minutes precisely at the onset of major EGA. Later stage analysis revealed continued maturation of the H3K9me3 landscape beyond the initial wave of bulk establishment. Our findings uncover distinct mechanisms of pre- and post-EGA H3K9me3 targeting and reveal decoupling of H3K9me3 establishment from reinforcement during de novo heterochromatin formation.

overall_design: CUT&RUN for H3K9me3 across developmental timecourse in zebrafish embryogenesis as well as confirmation H3K9me3 CUT&RUN experiments in manually-dechorionated cell-number-normalized samples using multiple H3K9me3 antibodies

middle: L

last: Duval

first: Ashley

last: Artis


title: Cell state and transcription factor modulation during extended CD8+ T-cell expansion ex vivo

city: Oxford

first: Simon

last: Davis

address: MRC Weatherall Institute of Molecular Medicine

department: Radcliffe Department of Medicine

institute: University of Oxford

summary: Adoptive cell therapy is fast becoming a cornerstone of modern tumour immunotherapy. It relies on the relatively long-term (>2 week) ex vivo expansion of T cells either in the form of tumour-infiltrating cells, or bulk cells modified with the expression of heterologous signaling proteins, e.g., chimeric antigen receptors. However, relatively little is known about the developmental trajectories of T cells under these conditions at the systems level, and whether entire genetic pathways could be manipulated for clinical advantage. Using bulk RNA-seq analysis of T cells expanded and rested over a 17-day period, we provide a resource of how gene expression changes as cells transition through distinct cellular states over the course of activation and ex-vivo expansion. We also performed experiments to investigate the role of FOSL1 in T-cell function.

overall_design: We used naive CD8+ T cells as a starting population to reduce heterogeneity for bulk RNA-seq measurements, and because their use as a starting population (vs. unfractionated subsets of T cells) exhibits superior capacity to expand, persist and eliminate tumors. Naive cells were stimulated with anti-CD3/CD28 beads for seven days with RNA extracted at defined time-points (i.e., 30 mins, 3 hours, 12 hours, 24 hours, 48 hours, 72 hours, 7 days). Beads were then removed and RNA extracted at either 2, 7, or 10 days. For each time-point we extracted total RNA and performed bulk RNA-seq in three replicates. For the FOSL1 experiments, we generated FOSL1 overexpression and FOSL1 KO lines in immortalized human Jurkat T cells and compared them with the parental Jurkat cell lines using bulk RNA-seq. We also transduced three donor CD8+ T-cells with lentivirus encoding FOSL1 and performed bulk RNA-seq to assess the transcriptional changes in the cells overexpessing FOSL1 compared to the parental donors.

first: Yuan

last: Lui

first: Sumana

last: Sharma

first: Ana

last: Mafalda Santos

first: Edward

last: Jenkins


title: STAT3 inhibition permits epigenetic reprogramming and TLR9/IRF8-driven differentiation of inv(16) acute myeloid leukemia [RRBS]

city: Duarte

last: Li

overall_design: We assessed whether levels of DNMTs present in CMM cells will change specifically in sorted CpG-STAT3dODN-induced CD11b+ CMM cell subset compared to the bulk CD11b-CMM cells or to the untreated CMM cells in control mice.


title: Chronic alcohol drinking compromises lung immunity by altering immunometabolism in both human and mouse lungs

city: Gothenburg

first: Muhammad

last: Arif

state: Västra Götaland

address: Blå Straket 5/WLAB

department: Department of Molecular and Clinical Medicine

country: Sweden

institute: University of Gothenburg

summary: Heavy alcohol drinking dysregulates lung immunity and host defense, which makes individuals with AUD more susceptible to develop inflammatory condition in lungs with poor prognosis. Current study, we focused on exploring the effects of chronic alcohol consumption on lungs using NIAAA alcohol feeding model in mice with 10 days of a Lieber-DeCarli liquid diet containing 5% ethanol followed by a single ethanol binge (5 g/kg) and population based human lung transcriptome data from Genotype-Tissue Expression (GTEx) project consist of 328 alcohol drinkers and 110 non-drinkers. Flow cytometry and transcriptomics analysis in mice lungs revealed that alcohol consumption dysregulates cellularity of immune cell levels and lung immunity. Transcriptomics analysis both in lungs and liver at 9-, 24- hours and 14 days post ethanol binge in mice uncovered that the lungs were more sensitive to alcohol effect to down-regulate pathways of immune system regulations than liver. Comparative data analysis of lung transcriptomes between mice and human subjects not only confirmed similar dysregulation on lung immunity but also provided evidence that immunometabolic changes are the central driver of alterations in lung transcriptome with down regulating immune pathways and upregulating metabolic pathways. Since the NIAAA model recapitulates multiple changes in the lung transcriptome that had been observed in human subjects with chronic alcohol drinking, this makes the mouse model suitable for experimental studies exploring role of alcohol drinking in lung health. Chronic alcohol drinking reduced mTOR signaling and cellularity of immune cells, which can be further attenuated by selective inhibition of mTOR. BCAA-mTOR signaling axis can be an upstream regulator of alcohol induced dysregulation in lung immunity

overall_design: We conducted transcriptomics analysis in lungs and liver from the same mice in different time points following single binge at 9- and 24-hours. Additionally, to investigate the long-term effect of such model, we decided to check the transcriptomics status 14 days after the single binge while mice were continued chronic alcohol drinking.

first: Lenny

last: Pommerolle

first: Madeline

last: Beehee

first: Corynn

last: Appolonia

first: Abhishek

last: Basu

first: Kaelin

last: Wolf

first: Charles

last: Zawatsky

first: Olivia

last: Rivellini

first: Joshua

middle: K

last: Park

first: Resat

last: Cinar


title: STAT3 inhibition permits epigenetic reprogramming and TLR9/IRF8-driven differentiation of inv(16) acute myeloid leukemia [RNASEQ_AML_DECSCR]

first: Haiqing

overall_design: To unravel the molecular mechanism underlying leukemic cell differentiation in response to combined STAT3-inhibition/TLR9-stimulation, we compared global gene expression in sorted GFP+/c-Kit+CMM cells derived from spleens of mice treated three times every other dayin vivousing CpG-STAT3dODN, CpG-scrODN or PBS.

first: Dongfang

last: Wang

first: Karol

last: Jacek

first: Marcin

last: Kortylewski


title: Neutralization of truncated procalcitonin by antibody treatment protects vascular barrier integrity during systemic inflammation

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

summary: Differentially expressed genes were identified in lung endothelial cells of CLP-treated mice compared to sham-treated controls and after treatment with an antibody against truncated murine procalcitonin.

overall_design: Sepsis was induced in mice by CLP (Cecal Ligation Puncture). Some mice were treated with an antibody against murine truncated procalcitonin. Endothelial cells from the lungs of CLP-treated, CLP plus antibody treatment, sham-treated and untreated mice were isolated and subjected to RNAseq analysis.

first: Nana-Maria

last: Wagner

first: Laura

last: Brabenec

first: Katharina

middle: E

last: Hellenthal


title: Endomucin marks quiescent long-term multi-lineage repopulating hematopoietic stem cells and is essential for their transendothelial migration [RNA-seq: EMCN_KO]

city: Copenhagen

first: Kim

last: Theilgaard-Mönch

address: Ole maaløes vej 5

institute: University of Copenhagen & Rigshospitalet/National University hospital

summary: Endomucin (EMCN) currently represents the only hematopoietic stem cell (HSC) marker expressed by both murine and human HSCs. Here, we report that EMCN+ long-term repopulating HSCs (LT-HSCs; CD150+CD48−LSK) have a higher long-term multi-lineage repopulating capacity compared to EMCN− LT-HSCs. Cell cycle analyses and transcriptional profiling demonstrated that EMCN+ LT-HSCs were more quiescent compared to EMCN− LT-HSCs. Emcn−/− and Emcn+/+ mice displayed comparable steady-state hematopoiesis, as well as frequencies, transcriptional programs, and long-term multi-lineage repopulating capacity of their LT-HSCs. Complementary functional analyses further revealed increased cell cycle entry upon treatment with 5-fluorouracil and reduced granulocyte colony-stimulating factor (GCSF) mobilization of Emcn−/− LT-HSCs, demonstrating that EMCN expression by LT-HSCs associates with quiescence in response to hematopoietic stress and is indispensable for effective LT-HSC mobilization. Transplantation of wild-type bone marrow cells into Emcn−/− or Emcn+/+ recipients demonstrated that EMCN is essential for endothelial cell-dependent maintenance/self-renewal of the LT-HSC pool and sustained blood cell production post-transplant.

overall_design: LT-HSCs were purified from Emcn-/- mice and Emcn+/+ littermate controls for RNA sequencing (3000-5000 cells per replicate, 3-4 biological replicates (mice) per group.

first: Sophia

last: Engelhard

first: Montserrat

last: Estruch Alrich

first: Shuyu

last: Qin

first: Christoph

middle: A

first: Francisco

last: Rodriguez-Gonzalez

first: Martine

last: Drilsvik

first: Javier

last: Martin-Gonzalez

first: Jeng-Wei

last: Lu

first: David

last: Bryder

first: Claus

last: Nerlov

first: Joachim

last: Weischenfeldt

first: Kristian

last: Reckzeh


title: Targeting the Epigenome Reduces Keloid Fibroblast Cell Proliferation, Migration and Invasion

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Keloids are pathological fibroproliferative scars resulting from abnormal collagen deposition within and beyond the margins of the initial cutaneous insult. Keloids negatively impact quality of life cosmetically and functionally and have unsatisfactory treatment modalities with adverse side effects and high reoccurrence rates. Recent studies indicate that epigenetic dysregulation is involved in the development and progression of keloids, suggesting that this could be a viable therapeutic target. The purpose of this study was to evaluate epigenetic targeting drugs, HDACi, LSD1i, Corin, and A-485, as potential therapies for keloids using in-vitro model systems with patient-derived keloid fibroblasts. Results demonstrated that both dual-acting CoREST inhibitor, corin, and HDAC inhibitor, MS-275, reduced fibroblast proliferation more than the LSD1 inhibitor. Corin was the most effective inhibitor of keloid fibroblast migration and invasion across keloid cell lines and primary cells. RNA-seq analysis showed that corin treatment upregulated a significant number of genes with an enrichment in neural differentiation and cell adhesion gene sets. Specifically, corin increased the expression of claudins, which may cause increased cell adhesion and contribute to corin-induced reductions in migration and invasion. Corin downregulated gene sets involved in cell cycle progression, confirmed by reductions in Cyclin A1 and Cyclin B2 at the protein level compared to DMSO. These results highlight the significant role for epigenetic regulation in pathogenic keloid fibroblasts properties and indicate that the epigenetic inhibitor corin may be useful in the prevention and/or treatment of keloids.

overall_design: Gene expression profiling analysis of RNA-seq data for patient keloid cells 1, 2, 3 & 4 (PK1, PK2, PK3, PK4) and patient normal fibroblasts 4 (PNF4) and how epigenetic drug (Corin) affects these cells compared to DMSO.

first: Nedaa

last: Almier

first: Marianne

last: Collard

first: Rhoda

last: Alani


title: Endomucin marks quiescent long-term multi-lineage repopulating hematopoietic stem cells and is essential for their transendothelial migration [RNA-seq: wildtype_EMCN]

first: Kim

overall_design: RNA was isolated from 3000-5000 FACS sorted EMCN+CD150+CD48-LSK (EMCN+ LT-HSCs) and EMCN-CD150+CD48-LSK (EMCN- LT-HSCs) for RNA sequencing. Granulocyte-Monocyte progenitors (GMPs) were additionally sorted as well characterised population to serve as more differentiated population for comparison. BM cells were isolated from C57Bl6 mice purchased at Taconic (Denmark). 4 biological replicates for each population, one EMCN-LT-HSC replicate was removed from analysis due to poor quality of the sequenced library.


title: Comparative single-cell transcriptional and proteomic atlas of clinical-grade injectable mesenchymal source tissues

city: La Jolla

first: Samuel

middle: Richard

last: Ward

address: 9500 Gilman Drive (0863)

department: Orthopaedic Surgery, Radiology, and Bioengineering

institute: University of California San Diego

summary: Bone marrow aspirate concentrate (BMAC) and adipose-derived stromal vascular fraction (ADSVF) are the most marketed stem cell therapies to treat a variety of conditions in the general population and elite athletes. Both tissues have been used interchangeably clinically even though their detailed composition, heterogeneity, and mechanisms of action have neither been rigorously inventoried nor compared. This lack of information has prevented investigations into ideal dosages and has facilitated anecdata and misinformation. Here, we analyzed single-cell transcriptomes, proteomes, and flow cytometry profiles from paired clinical-grade BMAC and ADSVF. This comparative transcriptional atlas challenges the prevalent notion that there is one therapeutic cell type present in both tissues. We also provide data of surface markers that may enable isolation and investigation of cell (sub)populations. Furthermore, the proteome atlas highlights intertissue and interpatient heterogeneity of injected proteins with potentially regenerative or immunomodulatory capacities.

overall_design: Bone marrow aspirate concentrate (BMAC) and the adipose-derived stromal vascular fraction (ADSVF) from the same donors were run on the 10x Chromium Controller at the day of tissue collection.

first: Severin

last: Ruoss

first: Chanond

last: Nasamran

first: Scott

middle: T

last: Ball

first: Jeffrey

last: Chen

first: Kenneth

middle: N

last: Halter

first: Kelly

last: Bruno

first: Thomas

last: Whisenant

first: Jesal

last: Parekh

first: Mary

last: Esparza

first: Shanelle

last: Dorn

first: Shannon

last: Bremner

first: Kathleen

last: Fisch

first: Adam

last: Engler


title: Structural Basis for Cytoplasmic Factors Required for Integrator and CPSF Function

city: Rochester

first: Eric

middle: John

last: Wagner

address: 575 Elmwood Avenue

department: Biochemistry and Biophysics

institute: University of Rochester Medical Center

summary: The object of this study (or experiment) was to determine the impact of BRAT1 depletion on the transcriptome during differentiation into neuroprogenitor cells. Two control and two BRAT1 knockout H7-human ESC lines were differentiated for 14 days, total RNA isolated and polyA enriched Click-seq libraries generated. Broad transcriptional misregulation was observed between differentiated knockout and control lines. Specifically, the precocious upregulation of several neurogenesis-driving transcription factors indicates the mistiming of differentiation.

overall_design: Samples are human H7 embryonic stem cells (ESCs) that have been ventrally differentiated for 14 days. There are two groups, Day 0 (undifferentiated ESCs) and Day 14 (neural progenitors), with 2 control lines and 2 BRAT1 knockout lines at each. There are three biological replicates of each sample at each condition. MJPro1-3 are three biological replicates of Control Line 1 at Day 14, and MJPro4-6 are Control line 2. MJPro7-9 are three biological replicates of BRAT1 knockout Line 1 at Day 14, and MJPro10-12 are BRAT1 knockout 2 at Day 14. MJPro25-27 are biological replicates of Control line 1 at Day 0, and MJPro28-30 are Control line 2 at Day 0.  Finally, MJPro31-33 are biological replicates of BRAT1 knockout line 1 at Day 0, and MJPro34-36 are BRAT1 knockout line 2 at Day 0.

first: Madeline

last: Jensen

first: Christoph

last: Pröschel


title: Increased ROS levels in mitochondrial outer membrane protein Mul1-deficient oocytes result in abnormal preimplantation embryogenesis

city: Fukuoka

first: Takumi

last: Koshiba

address: 8-19-1 Nanakuma, Jonan-ku

country: Japan

institute: Fukuoka University

summary: Loss of Mul1 in oocytes evoke high ROS concentration and results in abnormal embryogenesis before implantation.

overall_design: In order to compare the expression profiles between wildtype oocyte and mul1-deficient oocyte, we used 213 of wild type unfertalized oocytes and 123 of Knockout unfertalized oocytes.

first: Ann

last: Nakai

first: Toshio

last: Watanabe


title: Identification of constitutively-expressed immune effectors in the house fly (Musca domestica) and the transcription factors that regulate them

city: Houston

first: Richard

last: Meisel

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: In this study we fed groups of female house flies one of two Gram-negative bacteria (Pseudomonas aeruginosa and Escherichia coli) or control broth and used RNA-seq to determine differential gene expression at 4 hours post-feeding. Flies that ingested P. aeruginosa induced expression of genes encoding digestive proteins in the gut but did not induce AMPs. Flies in all treatment groups constitutively expressed some paralogs of lysozyme and AMP genes at the transcript level.

overall_design: RNA-seq performed on flies infected with either Pseudomonas aeruginosa, Escherichia coli, or control medai 4 hours after infection

first: Danial

last: Asgari

first: Christopher

last: Saski

middle: P

first: Dana

last: Nayduch


title: RNA-Seq based transcriptome analysis of colorectal cancer cells in response to lactate treatment

city: Guangzhou

first: Hua-shan

last: Liu

state: Guangdong

address: 26 Yuancun Erheng Road

department: Department of Colorectal Surgery

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

summary: Recently, the presence of lactate in colorectal cancer (CRC) has been rediscovered as crucial signalling molecule which plays key roles in the regulation of the metabolic pathways, the immune response, and cell-to-cell communication within the tumour microenvironment. We here report the RNA-Seq based transcriptome analysis of DLD1 and SW480 cells in response to lactate treatment. By a number of statistical tests, a series of genes were statistically significant, indicating a gene set profoundly responded to lactate in CRC. To unveil the molecular mechanism associated with the effects of lactate on CRC development and progress, these genes were annotated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment analyses. Our data demonstrate that targeting lactate metabolism and transport represents a promising approach for CRC therapeutics.

overall_design: Examination of transcriptome in 2 CRC cell lines. For each cell line, 6 samples are analyzed RNA sequencing (3 biological replicates for control samples and 3 biological replicates for lactate treated samples).

first: Liang

last: Kang


title: Global transcriptional profiling of wild type and LATS1/2 KO CAL27 cells in response to indisulam

status: Public on Jul 21 2024

city: Hiroshima

first: Toshinori

last: Ando

address: 1-2-3 Kasumi, Minami-ku

institute: Hiroshima University Hospital

summary: mRNA sequencing of WT and LATS1/2 KO CAL27 cells were treated with indisulam 1 μM for 24hr to profile and characterize dysregulated pathways and alternative splicing in response to indisulam

overall_design: WT and LATS1/2 CAL27 cells treated with 24h indisulam or DMSO control in a 3 vs 3 sample design


title: Single-cell RNA sequencing reveals a role of Phf2 in promoting the exit of postnatal neural stem cell from shallow quiescence.

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

summary: Dentate gyrus single cell mRNA profiles of 30-day-old wild-type (WT) and Phf2 conditional knockout (Phf2−/−) mice were generated by single cell sequencing. We performed data filtering: i) for the genes expressed in at least 30 cells and cells with detected expression of at least 200 genes and no more than 8000 genes; ii) cells with the percentage of expressed mitochondrial genes no more than 10%. Potential cell doublets were filtered out using scrublet (https://pypi.org/project/scrublet/). Single cell clustering was done using scanpy package (https://scanpy.readthedocs.io/en/stable/).

overall_design: Single cell mRNA profiles of 30-day old Nestin-Cre Tg wild type (Phf2+/+) control mice and conditional KO (Nestin-Cre Tg, Phf2flox/flox) mutant mice.

first: Jeehyun

last: Yoon

first: Jia

last: Feng

first: Ker Zhing

last: Lok

first: Niranjan

last: Shirgaonkar

first: Derrick Sek Tong

last: Ong


title: The regulation of transcriptome in HCC cells by SRSF10 [Huh7_shSRSF10_RNAseq]

city: shanghai

first: JL

last: CAI

address: shanghai

institute: fudan university

summary: We investigated the impact of SRSF10 knockdown on transcriptome in HCC cells through RNA-seq assays

overall_design: we analyzed gene expression profiles using RNA-seq assays in Huh7 cells with downregulated SRSF10

first: J

last: Cai

first: L

last: Song

first: Z

last: Dai


title: The Role of LINGO1 in Epithelial Wound Repair

city: Philadelphia

first: De'Broski

last: Herbert

state: PA

address: 3900 Spruce Street

department: Pathobiology

institute: University of Pennsylvania

summary: Leucine-rich repeat and IgG-like domain containing NOGO-receptor interacting protein 1 (LINGO1) has an inhibitory role in neuronal growth and regeneration following injury; yet LINGO1 involvement in the injury response of other tissues has not been thoroughly explored.  Previous studies have demonstrated that the reparative cytokines of the Trefoil factor family interact with members of the LINGO receptor family in maintenance of gastrointestinal barrier integrity, suggesting a role for LINGO receptors in epithelial repair processes. In this study, we investigated whether LINGO1 had a role in alveolar epithelial repair. A mouse alveolar epithelial cell line, MLE-12, was utilized in an in vitro scratch assay as a model of epithelial injury and repair.  CRISPR/Cas9-mediated deletion of Lingo1 resulted in significantly reduced wound closure at both 24 and 48 h post-scratch in comparison to parental (WT) cells. We preformed RNA sequencing of 24h post-scratch cells or un-scratched cells, and revealed a set of 147 differentially expressed genes between WT and Lingo1KO cells following scratch.

overall_design: 4 samples total, 4 conditions, 1 sample per condition.

first: Ray

last: Saunders

first: Annabel

last: Ferguson


title: STAT3 inhibition permits epigenetic reprogramming and TLR9/IRF8-driven differentiation of inv(16) acute myeloid leukemia [RNASEQ_AML_CPGDOX]

first: Haiqing

last: Li

department: Shared Resources Department

institute: City of Hope National Medical Center

summary: Cultured acute myeloid leukemia (AML) blasts can differentiate into antigen-presenting cells but achieving leukemic cell immunogenicity proved challenging in clinical setting. Despite expressing multiple immunostimulatory receptors, such as Toll-like Receptor 9 (TLR9), AML cells resist immunostimulation. We previously demonstrated that eliminating Signal Transducer and Activator of Transcription 1 and 3 (STAT1/3) signaling in AML cells using decoy DNA strategy (CpG-STAT3dODN) synergized with TLR9 stimulation and resulted in T cell-mediated leukemia regression. Here, we interrogated the molecular underpinnings of CpG-STAT3dODN-driven differentiation and immunogenicity of mouse Cbfb/MYH11/Mpl AML. The transcriptional profiling of AML cells isolated from mice after inducible Stat3 silencing plus TLR9 stimulation or CpG-STAT3dODN treatment, revealed comparable upregulation of genes related to myeloid cell differentiation (Irf8, Cebpa) and immune stimulation (Gadd45a, Ciita, Il12a, Ifng) but decreased expression of leukemia-promoting Runx1 and Run1t1. The conditional Irf8 silencing in AML cells almost completely abrogated TLR9-driven leukemia cell differentiation. The AML cell reprogramming by CpG-STAT3dODN was likely regulated epigenetically as revealed by reduced global promoter hypomethylation of crucial myeloid cell differentiation and immune activation genes. These changes were associated with reduced expression of known STAT3 targets, DNMT1 and DNMT3a/b. Finally, we provide initial evidence of anti-leukemic effects of CpG-STAT3 inhibitor against human AML model in humanized mice. Our studies suggest that, beyond oncogenic functions, STAT3 in AML cells may be a primary checkpoint in control of immune-stimulatory and differentiation driving effects. These findings support further development of CpG-STAT3 inhibitors as a new bi-functional agents for AML immunotherapy.

overall_design: Mice engrafted with CMM-tetON-shStat3cells (AML cells >1% in blood) were treated IV three times every other dayusing PBS, CpG oligonucleotide, doxycycline (Dox) or a combination of CpG plus doxycycline (CpG+Dox).

first: Dongfang

last: Wang

first: Karol

last: Jacek

first: Marcin

last: Kortylewski


title: Rejuvenation of aged oocyte through exposure to young follicular microenvironment

first: Rong

address: 5A Engineering Drive 1

department: Mechanobiology Institute (MBI)

institute: National University of Singapore

summary: Reproductive aging is a major cause of fertility decline, attributed to decreased oocyte quantity and competence. Follicular somatic cells play crucial roles in the growth and development of the oocyte by providing nutrients and regulatory factors. Here we investigated how oocyte quality is affected by its somatic cell environment by creating chimeric follicles, whereby an oocyte from one follicle was transplanted into and cultured within another follicle whose native oocyte was removed. Somatic cells within the chimeric follicle re-establish connections with the oocyte and support oocyte growth and maturation in a three-dimensional (3D) culture system. We show that young oocytes transplanted into aged follicles exhibited reduced meiotic maturation and developmental potential, whereas the young follicular environment significantly improved the rates of maturation, blastocyst formation and live birth of aged oocytes. Aged oocytes cultured within young follicles exhibited enhanced interaction with somatic cells, more youth-like transcriptome, remodelled metabolome, improved mitochondrial function, and enhanced fidelity of meiotic chromosome segregation. These findings provide the basis for a future follicular somatic cell-based therapy to treat age-associated female infertility.

overall_design:
To investigate how oocyte quality is affected by its somatic cell environment by creating chimeric follicles, whereby an oocyte from one follicle was transplanted into and cultured within another follicle whose native oocyte was removed.
We then perform RNA-sequencing analysis on individual oocytes isolated from reconstituted chimeric follicles (RCFs), which include young oocytes with young somatic cells (RCF-YY), aged oocytes with aged somatic cells (RCF-AA), and aged oocytes with young somatic cells (RCF-AY). Additionally, we perform RNA-sequencing analysis on oocytes from young mice, with and without in vitro culture, serving as controls.

first: HaiYang

first: Yaelim

last: Lee

first: Jin

last: Zhu