title: Macrophages Promote Pre-Metastatic Niche Formation of Breast Cancer through AHR Activity

city: shanghai

first: wang

last: jiaqi

address: 320 Yueyang Road

institute: The Shanghai Institute of Nutrition and Health (SINH) of the Chinese Academy of Sciences (CAS)

summary: Macrophages that acquire an immunosuppressive phenotype are crucial for creating the pre-metastatic niche (PMN), which is essential for facilitating breast cancer metastasis to the distant organ. Our study showed that increased aryl hydrocarbon receptor (AHR) activity in lung macrophages is vital for establishing the immunosuppressive PMN in breast cancer. AHR activation led to higher PD-L1 expression on macrophages through directly binding to the promoter of Pdl1, subsequently, promoting Treg cell differentiation in the PMN. Mice with Ahr conditional deletion in macrophages had reduced lung metastasis of breast cancer. The elevated AHR level in PMN macrophages was induced by GM-CSF released  from breast cancer cells, which activated STAT5 and prevented AHR ubiquitination in macrophages. In breast cancer patients, the expression of AHR and PD-L1 correlated with Treg cell infiltration, and high AHR expression was associated with a poor prognosis. Our findings uncover a previously unknown cellular and molecular mechanism through which macrophages establish the lung PMN in breast cancer.

overall_design: To investigate the role of increased aryl hydrocarbon receptor (AHR) activity in alveolar macrophages in establishing the immunosuppressive pre-metastatic niche (PMN) in breast cancer, we established a 4T1 breast cancer model. We collected alveolar macrophages from mice without 4T1 tumor inoculation and mice inoculated with primary 4T1 tumour for 2 weeks. Then, we performed gene expression profiling analysis using data obtained from RNA seq of alveolar macrophages at two time points.

first: Xu

last: Jiang

first: Jiaqi

last: Wang


title: Gene-environment interaction between Notch1 and oxidative stress disrupts cardiac developmental pathways

status: Public on Oct 18 2024

city: Columbus

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

country: USA

institute: Research Institute at Nationwide Children's Hospital

type: Expression profiling by high throughput sequencing

summary: The majority of congenital heart disease cases lack a definitive cause, suggesting the role of gene-environment interactions (GxE) in disease pathogenesis. Maternal diabetes mellitus (matDM) is among the most prevalent environmental risk factors for CHD and matDM associated oxidative stress is known to disrupt cardiac development. Here, we demonstrate that NOTCH1 haploinsufficient endothelial cells have an altered transcriptomic response to oxidative stress compared to control endothelial cells, with an exacerbated effect on gene regulatory networks crucial for endocardial cushion morphogenesis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NOTCH1WT and NOTCH1+/- iPSC derived endothelial cells in normal culture conditions and with exposure to 50 micromolar hydrogen peroxide for 4 days.

first: Choudhury

last: Talita

first: Greskovich

last: Sarah

first: Rao

last: Anupama

first: Garg

last: Vidu


title: Single-cell RNA-sequencing of angioblasts and endothelial cells from E9.5-E11.5 mouse embryos

city: Oxford

first: Oliver

middle: Andrew

last: Stone

state: Oxfordshire

address: IDRM, Old Road Campus, Roosevelt Drive

department: Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

summary: Background: The formation of the lymphatic system has been a subject of controversy for over a century. Although the accepted view is that lymphatic endothelial cells originate exclusively from veins, there have been reports of non-venous derived lymphatics in multiple tissues. Methods: We performed single-cell RNA sequencing analyses on ~20000 individual cells isolated from Pax3Cre/+;Rosa26tdTomato mouse embryos at E9.5, E10.5 and E11.5, the temporal window in which lymphatic endothelium initially emerges. Results: These analyses revealed the existence of populations of lymphangioblasts which arise from paraxial mesoderm and directly incorporate into the lymph sacs. Our findings support the notion that lymphatic endothelial cells also have non-venous origins and explain the discrepancies between previous studies.

overall_design: Endothelial progenitors and endothelial cells were isolated from Pax3Cre/+;Rosa26tdTomato embryos at ~E9.5, ~E10.5 and ~E11.5, to define transcriptional differences between paraxial mesoderm-derived and and non-paraxial mesoderm-derived endothelium. Single cell gene expression was profiled using the 10x Genomics Chromium Next GEM Single Cell 3' GEM, Library and Gel Bead Kit v3.1.

first: Irina-Elena

last: Lupu

first: David

middle: E

last: Grainger

middle: A


title: RIPseq of proQ-3XFLAG in V. cholerae

city: Jena

first: Rabea

last: Ghandour

address: Winzerlaer Straße 2

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller University

summary: Gene regulation at the post-transcriptional level is prevalent in all domains of life. In bacteria, ProQ-like proteins have emerged as important RNA chaperones facilitating RNA stability and RNA duplex formation. In the major human pathogen V. cholerae, post-transcriptional gene regulation is key for virulence, biofilm formation, and antibiotic resistance, yet the role of ProQ has not been studied. Here, we show that ProQ interacts with hundreds of transcripts in V. cholerae, including the highly abundant FlaX small RNA (sRNA). Global analyses of RNA duplex formation using RIL-Seq (RNA interaction by ligation and sequencing) revealed a vast network of ProQ-assisted interactions and identified a role for FlaX in motility regulation. Specifically, FlaX base-pairs with multiple sites on the flaB flagellin mRNA, preventing 30S ribosome binding and translation initiation. V. cholerae cells lacking flaX display impaired motility gene expression, altered flagella composition, and reduced swimming in liquid environments. Our results provide a global view on ProQ-mediated RNA duplex formation and pinpoint the mechanistic and phenotypic consequences associated with ProQ-associated sRNAs in V. cholerae.

overall_design: To identify proQ-binding RNAs in Vibrio cholerae, we used RNA co-immunoprecipitation followed by RNA-sequencing (RIP-seq). V. cholerae WT and proQ-3XFLAG were cultivated in LB medium to OD600 of 0.2 and 2.0. Three biological replicates for each condition are provided.

first: Kai

last: Papenfort


title: RILseq of proQ-3XFLAG in V. cholerae

overall_design: To investigate the RNA-RNA interactome on ProQ, V. cholerae WT and proQ-3XFLAG were cultivated in LB medium to OD600 of 0.2 and 2.0. Cells were subjected to RNA crosslinking, coimmunoprecipitation and ligation followed by chimeric cDNA synthesis and high-throughput sequencing. Two biological replicates for each condition are provided.

first: Michaela

last: Huber

first: Sahar

last: Melamed

first: Malte

last: Siemers

first: Gisela

last: Storz


title: TCF1 dosage determines cell fate during T cell development

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Loss of function studies have shown that transcription factor T cell factor-1 (TCF1), encoded by the Tcf7 gene, is essential for T cell development in the thymus. We discovered that the Tcf7 expression level is regulated by E  box DNA binding proteins, independent of Notch, and regulates ab and gd T cell development. Systematic  interrogation of the five E-protein binding elements (EPE1-5) in the Tcf7 enhancer region showed lineage-specific  utilization. Specifically, loss-of-function analysis revealed that only EPE3 plays a critical role in supporting ab T cell development, while EPE1, 3 and 5 regulate gd T cell maturation and functional cell fate decision. The  importance of EPE3 in supporting both lineages may stem from its unique capacity to interact with the Tcf7 transcriptional start site. Together these studies demonstrate that the precise dosage of TCF1 expression mediated  by distinct EPEs generates a balanced output of T cells from the thymus.

overall_design: We did H3K27ac HiChIP experiments in bone marrow pro-B cells and DN3 cells.


title: Circulating-miRNAs expression profiles in an endangered Piedmontese sheep breed during the estrus cycle

city: Grugliasco

first: Eugenio

last: Martignani

state: TO

address: Largo Braccini 2

department: Veterinary Science

country: Italy

institute: University of Torino

type: Non-coding RNA profiling by high throughput sequencing

summary: The preservation of locally endangered breeds is essential for ecosystem services that affect both society and the environment. Reproductive fitness becomes a crucial consideration in this regard. MicroRNAs (miRNAs) are small noncoding RNA molecules with a key role in post-transcriptional regulation. They usually act in tissues, where they are produced, but when released in extracellular fluid, they are termed circulating miRNAs (c-miRNAs). C-miRNAs might be potential biomarkers, whose profile changes under different physiological states. The purpose of this work is to establish a connection between distinctive variations in c-miRNAs’ expression and specific estrus cycle phases in Frabosana-Roaschina sheep, an endangered Piedmontese breed. Two trials of twenty ewes with different reproductive efficiency (nulliparous in the first trial, pluriparous in the second trial) were sampled on alternate days, after synchronization, for blood, saliva and feces. Ultrasound scans were performed during the induced estrus cycle. Animals were also video recorded to assess behaviors. Play behaviors and no sexual behaviors were detected in the first trial; sexual behaviors and no play behaviors in the second one. Based on plasma trends of 17β-estradiol and progesterone and ultrasound images, two moments were identified for miRNAs analyses: the beginning of the follicular phase (day 2) and the beginning of luteal phase (day 11). C-miRNAs of 6 representative animals from second trial were sent to be sequenced. Analyses on the sequencing data have highlighted twelve c-miRNAs differentially expressed (DE), comparing day 11 with day 2: five miRNAs resulted upregulated, whereas seven miRNAs are downregulated. An enrichment analysis, based on predicted targets, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases was performed. Many of these genes regulate reproductive pathways with the possible involvement of miRNAs. In the end, qRT-PCR validation of DE miRNAs in all ewes was performed and differences in gene expression between the two sampling points and the two trials emerged, in line with literature. The investigation of these miRNAs’ involvement in the regulation of the estrus could improve reproductive performance and welfare of Frabosana-Roaschina.

overall_design: 20 pluriparous ewes of Frabosana-Roaschina ewes were recruited. Animals were synchronized with a standardised protocol using progesterone sponges. Blood samples were collected every 2 days after sponge removal and 6 representative animals were chosen. Two time points were selected: 2 days and 11 days after removal of progesterone sponges corresponding to the beginning of the follicular phase and the luteal phase respectively. microRNA were extracted from plasma and sequenced.

first: Isabella

last: Manenti

first: Ugo

last: Ala


title: Gene expression profile at single cell level of human control, MPHOSPH8-deficient and MORC2-deficient cerebral organoids at day 27.

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

summary: To translate our mouse data and to model the role of MPHOSPH8 and MORC2 in human brain development, we generated human three-dimensional (3D) cerebral organoids lacking MPHOSPH8 and MORC2. These cerebral organoids were compared to control organoids by single cell RNA sequencing (scRNA-seq) to analyze the cell composition and expression of clustered protocadherins.

overall_design: We established two independent clones of MPHOSPH8 as well as MORC2 knockout H9 human ES cell lines by CRISPR-Cas9 engineering and used these clones for cerebral organoid generation. On day 27 single-cell suspensions from two cerebral organoids per condition were prepared and analyzed by scRNA-seq.

first: Astrid

last: Hagelkruys

first: Josef

last: Penninger


title: Transcriptional response of Methanosarcina acetivorans to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED

city: Lincoln

first: Nicole

last: Buan

state: NE

address: 1901 Vine St N200 Beadle N200 Beadle

department: Biochemistry

institute: University of Nebraska-Lincoln

summary: Methane-producing archaea are key organisms in the anaerobic carbon cycle. These organisms, also called methanogens, grow by converting substrate to methane gas in a process called methanogenesis. Previous research showed that reduction of the terminal electron acceptor is the rate-limiting step in methanogenesis by Methanosarcina acetivorans. In order to gain insight into how the cells sense and respond to availability of the terminal electron acceptor, we designed an experiment to deplete cells of the essential terminal oxidase enzyme, HdrED. We found that depletion of HdrED in vivo results in higher abundance of transcripts for methyltransferases (mtaC2, mtaB3, mtaC3), coenzyme B biosynthesis, C1 metabolism, and pyrimidine compounds. In most cases, these changes were distinct from transcript abundance changes observed during the transition from exponential growth to stationary phase cultures. These data implicate MsrC (MA4383) in CoM-S-S-CoB heterodisulfide sensing and indicate cells have a specific mechanism to sense intracellular ratio of CoM-S-S-CoB, coenzyme M and coenzyme B thiols and further suggest transcripts encoding translation and methanogenesis functions are controlled by feed-forward regulation depending on substrate availability.

overall_design:
16 samples were analyzed: +Tet exponential (two technical replicates), +Tet stationary (two technical replicates, -Tet 24h (three biological replicates, -Tet 30h (two biological replicates, -Tet 36h (two biological replicates, -Tet 42h (three biological replicates), -Tet 48h (two biological replicates.
*** Submitter states that only RMA files and the scans of the slides are available for the GEO submission ***

middle: R

first: William

middle: W

last: Metcalf


title: TCF1 dosage determines cell fate during T cell development. [scRNA-Seq]

summary: Loss of function studies have shown that transcription factor T cell factor-1 (TCF1), encoded by the Tcf7 gene, is essential for T cell development in the thymus. We discovered that the Tcf7 expression level is regulated by E box DNA binding proteins, independent of Notch, and regulates ab and gd T cell development. Systematic interrogation of the five E-protein binding elements (EPE1-5) in the Tcf7 enhancer region showed lineage-specific utilization. Specifically, loss-of-function analysis revealed that only EPE3 plays a critical role in supporting ab T cell development, while EPE1, 3 and 5 regulate gd T cell maturation and functional cell fate decision. The importance of EPE3 in supporting both lineages may stem from its unique capacity to interact with the Tcf7 transcriptional start site. Together these studies demonstrate that the precise dosage of TCF1 expression mediated by distinct EPEs generates a balanced output of T cells from the thymus.

overall_design: 10,000 sorted WT-DN and ΔEPE3-DN thymocytes were targeted. Using a Chromium Next GEM Single Cell 3ʹ _GEM, Library & Gel Bead Kit v3.1  and the Chromium Chip G Single Cell Kit, the thymocytes, at 1,000 cells per µl, were loaded onto a chromium single-cell controller to generate single-cell gel beads-in-emulsion according to the manufacturer’s protocol.

first: Anjali

last: Verma

first: Bridget

last: Aylward

first: Fei

last: Ma

first: Cheryl

last: Sherman

first: Laura

last: Chopp

first: Susan

last: Shinton

first: Roshni

last: Roy

first: Shawn

last: Fahl

first: Alejandra

last: Contreras

first: Byron

last: Koenitzer

first: Parirokh

last: Awasthi

first: Krystyna

last: Mazan-Mamczarz

first: Noah

last: Ollikainen

first: Xiang

last: Qiu

first: Remy

last: Bosselut

first: Ranjan

last: Sen

middle: L

last: Wiest

first: Jyoti

last: Misra Sen


title: TCF1 dosage determines cell fate during T cell development. [scATAC-Seq]

first: Supriyo

last: De

overall_design: 100,000 sorted WT-DN and ΔEPE3-DN thymocytes were processed to isolate nuclei. Using the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 and the Chromium Next GEM Chip H Single Cell Kit v1.1, thymocyte nuclei, at 7,000 nuclei per µl, were loaded onto a Chromium controller to generate single-nuclei GEMs after which library construction is performed according to the manufacturer’s protocol.

first: Anjali

last: Verma

last: Aylward

first: David


title: INTS6 controls DNA:RNA hybrids autoregulation at double-strand break through Senataxin

first: Monika

last: Gullerova

address: S Parks Rd

department: Sir William Dunn School of Pathology

summary: The fidelity of transcription is essential for genome stability, especially when DNA damage happens. However, how the transcription cycle is regulated remains unknown. Here, we found that INTS6 is a fundamental player, which recruits PP2A to double-strand breaks (DSBs) and functions together with senataxin (SETX). The in-depth insight of ChromeRNA-seq shows that INTS6 is not only involved in global transcription termination but also the de novo transcription termination. Therefore, INTS6 is a great target for future translational studies.

overall_design: To investigate the importance of INTS6 in regulating transcription at genome-wide level, we emplyed the chromatin associated RNA sequencing to detect the nascent transcripts around DSBs in both mock and INTS6-depleted cells.

first: Qilin

last: Long

first: Kamal

last: Ajit


title: Interferon epsilon as a novel anti-viral agent in the testis

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene expression profile in JAR (HTB-144, ATCC) cells with scrambled control or miR-34a mimic transfection

status: Public on Oct 17 2024

city: Zuoying

first: Sung-Chou

last: Li

state: Kaohsiung

address: No. 386, Dazhong 1st Rd.

department: Department of Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

summary: We examined gene expression variations in JAR cells between scrambled control and miR-34a mimic transfection

overall_design: We had the RNA samples prepared and examined microarray assays.

first: Te-Yao

last: Hsu


title: Interferon epsilon as a novel anti-viral agent in the testis [mouse]

summary: The testis is susceptible to viral infections, which can impair fertility. Spermatogenic cells were thought to lack anti-viral defences, including interferon (IFN) or IFN-stimulated gene (ISG) expression. Challenging this dogma, we discovered that interferon-epsilon (IFNɛ), a type-I IFN first identified in female reproductive epithelia, is constitutively expressed by spermatogenic cells and macrophages in mouse and human testes. Moreover, mice lacking IFNɛ are more susceptible to viral epididymo-orchitis. The mechanisms of IFNɛ-mediated anti-viral protection in the testis were examined in this study.

overall_design: Adult (56d old) wildtype mice (WT) and Ifne-/- mice lacking IFNe received a single intraperitoneal injection of saline (200µl). Mice were culled 7 days later and reproductive organs were collected for analysis.

first: Rukmali

last: Wijayarathna

first: Mark

middle: P

last: Hedger

first: Linden

middle: J


title: RNA-sequencing of primary wild-type (WT) and Pla2g4d-deficient (KO) keratinocytes

city: Graz

first: Johannes

last: Breithofer

state: Styria

address: Heinrichstraße, 31/3

department: Institute for molecular Biosciences

institute: University of Graz

summary: PLA2G4D is a phospholipase and transacylase expressed in epidermal keratinocytes, and its expression is upregulated in inflammatory skin disorders such as psoriasis. Treatment of primary keratinocytes with proinflammarory cytokines IL17A and TNFα markedly increases Pla2g4d-mRNA expression. To investigate the function of PLA2G4D, we conducted bulk RNA sequencing of primary keratinocytes isolated from wild-type and Pla2g4d-deficient mice and studied transcriptional changes under basal and cytokine stimulation. The sequencing data suggests that PLA2G4D modulates fundamental biological processes including cell proliferation, differentiation, and signaling.

overall_design: Primary keratinocytes were isolated from two days old neonatal wild-type (n=5)  and  Pla2g4d-deficient (n=8) C57BL/6NJ mice. Cells from both genotypes were cultured in the abscence and presence of IL17A and TNFα. Total RNA was isolated and bulk RNA sequencing was performed to study transcriptional changes between groups

first: Dominik

last: Bulfon

first: Nermeen

last: Fawzy

first: Martin

last: Tischitz

first: Clara

last: Zitta

first: Lennart

last: Hartig

first: Gernot

middle: F

last: Grabner

first: Anita

last: Pirchheim

first: Hubert

last: Hackl

first: Ulrike

last: Taschler

first: Achim

last: Lass

first: Carmen

last: Tam-Amersdorfer

first: Herbert

last: Strobl

first: Dagmar

last: Kratky

first: Robert

last: Zimmermann


title: Immunomolecular and reactivity landscapes of gut IgA subclasses in homeostasis and inflammatory bowel diseases.

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: The human gut includes plasma cells (PCs) expressing immunoglobulin A1 (IgA1) or IgA2, two structurally distinct IgA subclasses with elusive regulation, function and reactivity. We show here that intestinal IgA1+ and IgA2+ PCs co-emerged early in life, comparably accumulated somatic mutations, and were enriched within short-lived CD19+ and long-lived CD19− PC subsets, respectively. IgA2+ PCs were often clonally related to IgA1+ PCs and a subset of them presumably emerged from IgA1+ precursors. Of note, secretory IgA1 (SIgA1) and SIgA2 dually coated a large fraction of mucus-embedded bacteria, including Akkermansia muciniphila. Disruption of homeostasis by inflammatory bowel disease (IBD) increased newly formed and actively proliferating IgA1+ plasmablasts, depleted long-lived IgA2+ PCs, and increased SIgA1+SIgA2+ gut microbiota. Such increase featured enhanced IgA1 reactivity to pathobionts, including Escherichia coli, combined with depletion of beneficial Akkermansia muciniphila. Thus, gut IgA1 and IgA2 emerge from clonally related PCs and show unique changes of both frequency and reactivity in IBD.

overall_design: scRNA and V(D)J sequencing of alive lamina propria cells from an histological normal human ileal sample.

first: Giuliana

last: Magri

first: Andrea

last: Cerutti

first: Sonia

last: Tejedor-Vaquero

first: Pau

last: Berenguer-Molins


title: Interferon epsilon as a novel anti-viral agent in the testis [human]

first: Jamie

last: Gearing

overall_design: A vial of Sertoli cells isolated from human testis (HSerc) that were cryopreserved at passage one was purchased from ScienCell Research Laboratories, USA (Catalog #4520). The cells were infected with Zika virus (strain PRVABC59) at a multiplicity of infection (MOI) of 5 or 10. Cultures were treated with 100IU recombinant human IFNɛ 12h before infection (prophylactic-IFNɛ) or 1h after infection (therapeutic-IFNɛ), or diluent alone (controls). (IFNɛ was generated in house as described in Stifter et al. 2017; specific activity 3.62 x 104 IU/ml). Cells and media were harvested 24h or 48h post-infection for RNA-seq, qPCR, and plaque assays.

first: Rukmali

last: Wijayarathna

first: Mark

last: Hedger

first: Linden


title: Girolline is a sequence-context specific modulator of eIF5A activity

city: Wako-shi

first: Tilman

last: Schneider-Poetsch

email: tilman@cal.berkeley.edu, tsp@riken.jp

state: Saitam

address: 2-1 Hirosawa

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

summary: Natural products have a long history of providing potent probes into protein biosynthesis, with numerous molecules serving as valuable therapeutics. The marine natural product girolline has been described as an inhibitor of protein synthesis. Here, we demonstrate that it is not a general translation inhibitor but represents a sequence-specific modulator of translation factor eIF5A. Girolline interferes with ribosome-eIF5A interaction and induces ribosome stalling, primarily on AAA-encoded lysine. Our data furthermore indicate that eIF5A plays a physiological role in ribosome-associated quality control (RQC) and is important in maintaining the efficiency of translational progress. Girolline, therefore, provides a potent tool compound for understanding the interplay between protein production and quality control in a physiological setting and offers a new and selective means of modulating gene expression. numerous molecules serving as valuable therapeutics. The marine natural product girolline has been described as an inhibitor of protein synthesis. Here, we demonstrate that it is not a general translation inhibitor but represents a sequence-specific modulator of translation factor eIF5A. Girolline interferes with ribosome-eIF5A interaction and induces ribosome stalling, primarily on30 AAA-encoded lysine. Our data furthermore indicate that eIF5A plays a physiological role in ribosome-associated quality control (RQC) and is important in maintaining the efficiency of translational progress. Girolline, therefore, provides a potent tool compound for understanding the interplay between protein production and quality control in a physiological setting and offers a new and selective means of modulating gene expression.

overall_design: Ribosome profiling control experiments of human cells treated with low doses of cycloheximide and anisomycin

first: Yongjun

last: Dang

first: Wakana

last: Iwasaki

first: Mayumi

last: Arata

first: Yuichi

last: Shichino

first: Ali

last: Al Mourabit

first: Daniel

last: Romo

first: Jun

middle: O

last: Liu

first: Takuhiro

last: Ito

first: Shintaro

first: Minoru

last: Yoshida


title: TCF1 dosage determines cell fate during T cell development.

first: Supriyo

last: De


title: Gdnf-treated murine intestinal organoids and sorted Ret+ and Ret- single cells

city: Helsinki

first: Toni

last: Lemmetyinen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Adjacent stroma, including subepithelial fibroblasts, are believed to coordinate the differentiation process of epithelial cells, but the mechanisms are not well understood. Glial cell line-derived neurotrophic factor (GDNF) is expressed in the intestinal Pdgfra high subepithelial myofibroblasts (SEMFs), while the GDNF receptor RET is expressed in a subset of enteroendocrine cells (EECs), indicating regulatory crosstalk. In this experiment, single RET+ intestinal cells were sorted the gene expression profile was compared to non-RET cells. This provided knowledge about RET+ cell types. RET+ cells were upregulated with most of the EEC markers, indicating that RET+ cells are expressed in EECs. We also observed the differences in the gene expression profile of stromal-derived GDNF ligand on intestinal organoids. Organoids were derived from intestinal crypts of WT mice C57BL/6J and treated with 500ng/ml of Gdnf and Gfra1. GDNF-treated organoids induced the expression of EEC genes such as Pyy, Tac1, Tph1, and Cck, indicating enhanced differentiation of EC cell and L-I-N cell lineages. This highlights a stroma-epithelium crosstalk pathway regulating the differentiation of intestinal EEC subtypes.

overall_design: 5 samples of 1000 RET+ cells and 5 samples of 1000 RET- cells were sorted for the expreiment from 3 independent mice. Total of 6 control and 6 Gdnf-treated organoids samples from 3 independent expriments treated for 4 days with 500ng/ml of Gdnf and Gfra1.

first: Saara

last: Ollila


title: Methylmalonic acid induces metabolic abnormalities and exhaustion in CD8+ T cells to suppress anti-tumor immunity

city: Tampa

first: Ana

last: Da Silva Gomes

state: Florida

address: 12902 Magnolia Drive

department: Molecular Oncology

institute: H Lee Moffitt Cancer Center

summary: Systemic levels of methylmalonic acid (MMA), a byproduct of propionate metabolism, increase with age and MMA promotes tumor progression via its direct effects in tumor cells. However, the role of MMA in modulating the tumor ecosystem remains to be investigated. The proliferation and function of CD8+ T cells, key anti-tumor immune cells, declines with age and in conditions of vitamin B12 deficiency, which are the two most well-established conditions that lead to increased systemic levels of MMA. Thus, we hypothesized that increased circulatory levels of MMA would lead to a suppression of CD8+ T cell immunity. Treatment of primary CD8+ T cells with MMA induced a dysfunctional phenotype characterized by robust immunosuppressive transcriptional reprogramming and marked increases in the expression of the exhaustion regulator, TOX. Accordingly, MMA treatment upregulated exhaustion markers in CD8+ T cells and decreased their effector functions, which drove the suppression of anti-tumor immunity in vitro and in vivo. Mechanistically, MMA-induced CD8+ T cell exhaustion was associated with a suppression of NADH-regenerating reactions in the TCA cycle and concomitant defects in mitochondrial function. Thus, MMA has immunomodulatory roles, thereby highlighting MMA as an important link between aging, immune dysfunction, and cancer.

overall_design: Global analysis of RNA levels to determine transcriptional reprogramming in mouse CD8+ T cells treated with or without 5 mM methylmalonic acid for 3 days, in triplicate

last: Gomes

first: Joanne

middle: D

last: Tejero

first: Didem

last: Ilter


title: Comparing transcriptomic points of departure to apical effect concentrations for larval fathead minnow exposed to chemicals with four different modes of action

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

institute: United States Environmental Protection Agency

summary: It is postulated that below a transcriptomic-based point of departure, adverse effects are unlikely to occur, thereby providing a chemical concentration to use in screening level hazard assessment.  The present study extends previous work describing a high throughput fathead minnow assay that can provide full transcriptomic data after exposure to a test chemical.  One day post-hatch fathead minnows were exposed to ten concentrations of three representatives of four chemical modes of action: organophosphates, ecdysone receptor agonists, plant photosystem II inhibitors, and estrogen receptor agonists for 24 hours.  Concentration response modeling was performed on whole body gene expression data from each exposure, using measured chemical concentrations when available.  Transcriptomic points of departure in larval fathead minnow were lower than apical effect concentrations across fish species but not always lower than toxic effect concentrations in other aquatic taxa like crustaceans and insects.  The point of departure was highly dependent on measured chemical concentration which were often lower than the nominal concentration.  Differentially expressed genes between chemicals within modes of action were compared and often showed statistically significant overlap.  In addition, reproducibility between identical exposures using a positive control chemical (CuSO4) and variability associated with the transcriptomic point of departure using in-silico sampling were considered.  Results extend a transcriptomic-compatible fathead minnow high throughput assay for possible use in ecological hazard screening.

overall_design:
Fathead minnow larvae (5-6 dpf) were statically exposed to 12 different chemicals (representing 4 different modes of action) for 24 h in 96 well plates.
Total RNA was isolated from each larval homogenate and sequenced using an Illumina NovaSeq 6000.
Processed RNAseq data was analyzed to derive transcriptional points of departure (tPODs) and differentially expressed genes (DEGs) for each sample.

first: Kevin

last: Flynn

first: Michelle

last: Le

first: Monique

last: Hazemi

first: Adam

last: Biales

first: David

middle: C

last: Bencic

first: Brett

last: Blackwell

first: Kendra

last: Bush

first: Robert

last: Flick

first: John

middle: X

last: Hoang

last: Martinson

first: Mackenzie

last: Morshead

first: Kelvin

middle: S

last: Rodriguez

first: Emma

last: Stacy

last: Villeneuve


title: RNA-sequencing reveals novel molecular mechanisms of endometriosis lesion development in a mouse model

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

institute: Australian National University

summary: Our understanding of molecular mechanisms contributing to the pathophysiology of endometriosis, and their upstream regulators, remains limited. Using a C57Bl/6 mouse model of endometriosis in which decidualized endometrial tissue fragments are transferred to subcutaneous sites in recipient mice to mimic endometriosis lesions, we have generated a comprehensive profile of gene expression in decidualized endometrial tissue (n=4), and endometriosis-like lesions at Day 7 (n=4) and Day 14 (n=4) of lesion formation. High throughput mRNA sequencing allowed identification of genes and pathways involved in the initiation and progression of endometriosis-like lesions. We found distinct patterns of gene expression with substantial differences between the lesions and the decidualized endometrium from which they arose, but no differentially expressed genes between the two lesion timepoints. The transcriptional changes at the outset of lesion formation indicated substantial upregulation of immune response-associated canonical pathways. Pathway enrichment analysis indicates multiple potential endogenous upstream regulators, and reveals multiple gene candidates not previously implicated in endometriosis lesion formation suggesting these mediators may have novel roles in disease progression. Collectively, the provided data will be a valuable resource to inform research on the molecular mechanisms contributing to endometriosis development.

overall_design: We performed gene expression profiling using RNA-seq of donor decidualized endometrium (n=4), endometriosis-like lesions at Day 7 (n=4) and Day 14 (n=4) in a C57BL/6 subcutaneous mouse model of endometriosis. There are two additional experimental groups (miR-155 deficient and miR-223 deficient mouse models) also included in this dataset giving a total of 36 samples (4 biological replicates at each timepoint,  12 samples per genotype) These additional samples will reported in a separate manuscript to elucidate the impact of microRNA modulation in endometriosis-like lesion development in mice.

last: Schjenken

first: Kavita

last: Panir

first: Erin

last: Greaves

first: Sarah

last: Robertson

first: Hon

middle: Y

last: Chan

first: Louise

last: Hull


title: Dynamics of the zebrafish tRNAome during the maternal-to-zygotic transition [RNA-Seq]

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry

summary: Time course analysis of tRNA abundance during zebrafish early embryonic development.

overall_design: Wild-type (TLAB strain) zebrafish embryos were grown in standard housing conditions.Unfertilized eggs (0 hours post-fertilization; hpf) were collected or embryos were staged and collected at consecutive developmental time-points, namelyat the 256-cell (2.5 hpf), 1000-cell (3 hpf), sphere (4 hpf), shield (6 hpf) and bud (10 hpf) stages. Eggs and embryos were either flash-frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis, polysome profiling, ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.

first: Madalena

middle: M

last: Reimão-Pinto

first: Andrew

last: Behrens

first: Sergio

last: Forcelloni

first: Klemens

last: Fröhlich

first: Selay

last: Kaya


title: Stem Cell Activity-Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration [ChIP-seq/hMeDIP]

city: Houston

first: Yejing

last: Ge

state: Texas

department: Cancer Biology

institute: The University of Texas, MD Anderson Cancer Center

summary: Mammalian retrotransposons constitute 40% of the genome. During tissue regeneration, adult stem cells coordinately repress retrotransposons and activate lineage genes, but how this coordination is controlled is poorly understood. Here, we observed that dynamic expression of histone methyltransferase SETDB1 (a retrotransposon repressor) closely mirrors stem cell activities in the murine skin. SETDB1 ablation leads to reactivation of endogenous retroviruses (ERVs, a type of retrotransposon) and assembly of viral-like particles, resulting in hair loss and stem cell exhaustion that is reversible by antiviral drugs. Mechanistically, at least two molecularly and spatially distinct pathways are responsible: antiviral defense mediated by hair follicle stem cells and progenitors, and antiviral independent response due to replication stress in transient amplifying cells. ERV reactivation is promoted by DNA demethylase TET-mediated hydroxymethylation and recapitulated by ablating cell fate transcription factors. Together, we demonstrated ERV silencing is coupled with stem cell activity and essential for adult hair regeneration.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Setdb1 in MIK cells and P30 mouse hair follicle cells; for H3K9me3 in P30 mouse hair follicle cells or in P0 mouse skin epithelium. Hydroxymethylated DNA Immunoprecipitation (hMeDIP) in P30 mouse hair follicle cells or in P0 mouse skin epithelium.

first: Ying

last: Lyu


title: Stem Cell Activity-Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration

type: Methylation profiling by high throughput sequencing


title: Stem Cell Activity-Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration [RNA-seq]

overall_design:
Gene expression profiling analysis of RNA-seq data for C57BL/6J mouse skin epithelium between different groups (control and knockout groups, control and drug treatment groups).
Comparative gene expression profiling analysis of RNA-seq data for hair follicle stem cells (HF-SCs) from C57BL/6J mice second telogen skin between Setdb1 heterozygous (Het) and conditional knock-out (cKO) groups.


title: In vivo RNA sequencing reveals a crucial role of Fus3-Kss1 MAPKpathway in Candida glabrata pathogenicity

status: Public on Oct 16 2024

city: Wuhan

first: Hao

last: Cui

address: Wuhan University, 299 Bayi Road, Wuchang District, Wuhan, Hubei, P.R. China

country: China

institute: Wuhan University

summary: Candida glabrata is an important and increasingly common pathogen of humans, particularly in immunocompromised hosts. Despite this, little is known about how this fungus causes disease. Here, we applied RNA sequencing and an in vivo invasive infection model to identify the attributes that allow this organism to infect hosts. Fungal transcriptomes show a dramatic increase in the expression of Fus3 and Kss1, two mitogen-activated protein kinases (MAPKs), during invasive infection. We further demonstrate that they are both highly induced under a combination of serum and high CO2 condition. Deletion of both FUS3 and KSS1, but neither gene alone, results in a reduced fungal burden in organs, as well as in gastrointestinal tract in the DSS (Dextran Sulfate Sodium)-induced colitis model. Similarly, the defect in persistence in macrophages and attenuated adhesion to epithelial cells are observed when FUS3 and KSS1 are both disrupted. The fus3 kss1 double mutant also displays defects in the induction of virulence attributes such as genes required for iron acquisition and adhesion, and in the anti-fungal drug tolerance. The putative downstream transcription factors Ste12(1), Ste12(2), Tec1 and Tec2 are found to be involved in the regulation of these virulence attributes. Collectively, our study indicates that an evolutionary conserved MAPK pathway which regulates mating and filamentous growth in Saccharomyces cerevisiae, is critical for C. glabrata pathogenicity.

overall_design: To uncover the signaling pathway contributing to the virulence of C. glabrata, the gene expression profiles of this fungal pathogen at 24 h and 48 h post invasive infection from RNA-seq experiment. The RNA-seq analysis was applied on the kidney, which is frequently the most heavily infected organ with hematogenously disseminated candidiasis.

first: Xinreng

last: Mo

first: Xiangtai

last: Yu

first: Kang

last: Xiong

first: Shan

last: Yang

first: Chang

last: Su

first: Yang

last: Lu


title: Stem Cell Activity-Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration [ATAC-seq]

overall_design:
The assay for transposase-accessible chromatin with sequencing (ATAC-Seq) for skin anagen hair follicle cells from P30 Setdb1 heterozygous (Het) and P30 conditional knock-out (cKO) mice.
The assay for transposase-accessible chromatin with sequencing (ATAC-Seq) for hair follicle stem cells from second telogen skin of Setdb1 heterozygous (Het) and conditional knock-out (cKO) mice.


title: Dynamic behavior and lineage plasticity of the pulmonary venous endothelium

city: Philadelphia

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

summary: Repair of the pulmonary vascular bed and the origin of new vasculature remains underexplored despite the critical necessity to meet oxygen demands after injury. Given their critical role in angiogenesis in other settings, we investigated the role of venous endothelial cells in endothelial regeneration after adult lung injury. Using single cell transcriptomics, we identified the norepinephrine transporter Slc6a2 as a marker of pulmonary venous endothelial cells and targeted that locus to generate a venous-specific, inducible Cre mouse line. Contributions of the venous endothelial cells to angiogenesis were examined during postnatal development, adult viral injury, and adult hyperoxia injury. Remarkably, we observed that venous endothelial cells proliferate into the adjacent capillary bed upon influenza injury and hyperoxia injury, but not during normal postnatal development. Imaging analysis demonstrated that venous endothelial cells exhibit the ability to proliferate and differentiate into general capillary and CAR4 expressing aerocyte capillary endothelial cells after infection, thus contributing to repair of the capillary plexus vital for gas exchange. Single cell transcriptomic analysis of Slc6a2 lineage traced cells confirmed these observations, with progeny exhibiting significant loss of venous identity and gain of capillary marker expression upon injury resolution. Our studies thus establish that venous endothelial cells exhibit demonstrable progenitor capacity upon respiratory viral injury and sterile injury, contributing to repair of the alveolar capillary bed responsible for pulmonary function.

overall_design: 10X 3’-biased gene expression (v3.1) scRNA-seq libraries prepared from primary mouse lung tissue post-influenza infection, with fluorescent labelling of venous endothelial cells using Slc6a2-CreERT2 x R26-CAG-LSL-tdTomato-WPRE transgenic mice.

first: Joanna

last: Wong

first: David

middle: B

last: Frank

last: Vaughan


title: Metabolic reprogramming tips vaccinia virus infection outcomes by stabilizing interferon-g induced IRF1

city: Dallas

first: Dustin

last: Hancks

address: 5323 Harry Hines Blvd MC 9093

institute: UT Southwestern Medical Center

summary: Interferon (IFN) induced activities are critical, early determinants of immune responses and infection outcomes. A key facet of IFN responses is the upregulation of hundreds of mRNAs termed interferon-stimulated genes (ISGs) that activate intrinsic and cell-mediated defenses. While primary interferon signaling is well-delineated, other layers of regulation are less explored but implied by aberrant ISG expression signatures in many diseases in the absence of infection. Consistently, our examination of tonic ISG levels across uninfected human tissues and individuals revealed three ISG subclasses. As tissue identity and many comorbidities with increased virus susceptibility are characterized by differences in metabolism, we characterized ISG responses in cells grown in media known to favor either aerobic glycolysis (glucose) or oxidative phosphorylation (galactose supplementation). While these conditions over time had a varying impact on the expression of ISG RNAs, the differences were typically greater between treatments than between glucose/galactose. Interestingly, extended interferon-priming led to divergent expression of two ISG proteins: upregulation of IRF1 in IFN-γ/glucose and increased IFITM3 in galactose by IFN-α and IFN-γ. In agreement with a hardwired response, glucose/galactose regulation of interferon-γ induced IRF1 is conserved in unrelated mouse and cat cell types. In galactose conditions, proteasome inhibition restored interferon-γ induced IRF1 levels to that of glucose/interferon-γ. Glucose/interferon-γ decreased replication of the model poxvirus vaccinia at low MOI and high MOIs. Vaccinia replication was restored by IRF1 KO. In contrast, but consistent with differential regulation of IRF1 protein by glucose/galactose, WT and IRF1 KO cells in galactose media supported similar levels of vaccinia replication regardless of IFN-γ priming. Also associated with glucose/galactose is a seemingly second block at a very late stage in viral replication which results in reductions in herpes- and poxvirus titers but not viral protein expression. Collectively, these data illustrate a novel layer of regulation for the key ISG protein, IRF1, mediated by glucose/galactose and imply unappreciated subprograms embedded in the interferon response. In principle, such cellular circuitry could rapidly adapt immune responses by sensing changing metabolite levels consumed during viral replication and cell proliferation.

overall_design: To gain insights into how secondary cues may alter deployed ISG responses, we infected cells, which were primed with different IFNs in combination with metabolites established to modulate mitochondrial activities, with biomedically relevant viruses

first: Tyron

last: Chang

first: Sruthi

last: Chappidi

first: Mahsa

last: Sorouri


title: Stem Cell Activity-Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration [WGBS]

last: Ge

overall_design: Whole-genome bisulfite sequencing (WGBS) for skin anagen hair follicle cells from P30 control and Setdb1 conditional knock-out mice, and Enzymatic Methyl-seq for mouse skin epithelium from P0 control and Dnmt1 conditional knock-out mice.


title: Effect of Myh9 knockdown and PEG950 treatment on in vitro differentiated hepatocyte gene expression

city: Dresden

first: Marino

last: Zerial

address: Pfotenhauerstr. 108

institute: MPI-CBG

summary: Myh9 knockdown reduces the strength of the apical actomyosin cortex from hepatocytes, which causes isotropic growth of the bile canaliculus (BC) and ultimately results in the formation of hepatocyte cysts with a large central apical lumen. Treatment of hepatocytes with the osmotically active bioinert polymer PEG950 causes and increase in intraluminal pressure, which causes expansion of the bile canaliculus (BC) and ultimately results in the formation of hepatocyte cysts with a large central apical lumen. In these cysts, hepatocytes have common apico-basal polarity, such as observed for simple epithelia like cholangiocytes. To investigate whether this change in apical lumen morphology and polarization is associated with alterations in gene expression we compared hepatocytes with and without Myh9 knockdown and with and without PEG950 treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for in vitro differentiated hepatocytes with or without Myh9 knockdown and with or without PEG950 treatment (10 mM). RNA-seq data was obtained for day 5 after plating of the hepatoblasts.

first: Maarten

last: Bebelman

first: Lenka

last: Belicova

first: Andre

last: Gohr


title: Stem Cell Activity-Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration [scRNA-seq]

first: Yejing

overall_design:
We used single cell RNA sequencing (scRNA-seq) to analyze cell population difference in C57BL/6J mouse skin between Setdb1 heterozygous (Het) and conditional knock-out (cKO) groups during the anagen stage.
We used single cell RNA sequencing (scRNA-seq) to analyze skin epithelium cell population difference between the vehicle control and ATR inhibitor (Ceralasertib, AZD6738) treatment groups on Setdb1 conditional knock-out (cKO) mice.

first: Ying

last: Lyu


title: The Influence of Melanoma Extracellular Vesicles on Benign Melanocytes: A Role for PRAME in Modulation of the Tumor Microenvironment

city: Oklahoma City

first: Jeffrey

middle: Don

last: McBride

state: OK

address: 1000 NE 13th St

department: Dermatology

institute: University of Oklahoma

summary: This study investigates the role of PRAME (Preferentially Expressed Antigen in Melanoma), a cancer-testis antigen, in melanoma progression, particularly its function in melanoma-derived extracellular vesicles (EVs) and its impact on benign primary melanocytes.

overall_design: To investigate the effects of extracellular vesicles from melanoma cells on neighboring benign cells, we treated primary melanocytes with melanoma-derived EVs from A375 cells. We then extracted total RNA and performed RNA sequencing.

first: Xiaochen

last: Liu

first: Ralf

last: Janknecht

first: Sepideh

last: Asadbeigi

first: Lisa

last: Perry

first: Adul-Rafeh

last: Naqash

first: Wei-Qun

last: Ding


title: The mouse endothelial cell lines

city: Kumamoto

first: Saori

last: Morino-Koga

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: The bEnd.3 and UV♀2 cells were mouse endothelial cell lines. The bEnd.3 cells were derived from the endothelial cells of the mouse brain and the UV♀2 cells were established from an angioendothelioma-like tumor that developed on the skin of mice. We performed bulk RNA-seq analysis of these two cell lines to investigate the difference between these cells.

overall_design: RNA-seq analysis of two mouse endothelial cell lines, bEnd.3 and UV♀2. In detail, these cells were plated on a 10-cm dish. After confluency, cells were washed three times and cultured in serum-free conditions for 3 days.

first: Minetaro

last: Ogawa


title: The para-aortic splanchnopleure (P-Sp) of mouse embryos

summary: The hematopoietic stem cells (HSCs) arise from hemogenic endothelial cells (HECs) in the para-aortic splanchnopleure (P-Sp)/aorta-gonad-mesonephros (AGM) region of mouse embryos. HECs differentiate into HSC precursors and blood progenitors and form intra-aortic hematopoietic clusters (IAHCs) in the aorta. To identify HECs in distinction from endothelial cells, we performed single-cell RNA-seq analysis of cells isolated from the dorsal aorta and its surrounding tissues at E9.5. We found the population of HECs in the arterial endothelial cell cluster. Therefore, our data might elucidate the mechanism of HEC development.

overall_design: Single-cell RNA-seq analysis of para-aortic splanchnopleura (P-Sp) from the mouse embryos at E9.5

first: Tomomasa

last: Yokomizo

first: Toshio

last: Suda


title: Excessive adventitial stress drives inflammation-mediated fibrosis in hypertensive aortic remodelling in mice

city: Maastricht

first: Bart

last: Spronck

address: Universiteitssingel 40

department: Dept. of Biomedical Engineering

country: Netherlands

institute: Maastricht University

summary: Hypertension induces significant aortic remodelling, often adaptive but sometimes not. To identify immuno-mechanical mechanisms responsible for differential remodelling, we studied thoracic aortas from 129S6/SvEvTac and C57BL/6 J mice before and after continuous 14-day angiotensin II infusion, which elevated blood pressure similarly in both strains. Histological and biomechanical assessments of excised vessels were similar at baseline, suggesting a common homeostatic set-point for mean wall stress. Histology further revealed near mechano-adaptive remodelling of the hypertensive 129S6/SvEvTac aortas, but a grossly maladaptive remodelling of C57BL/6 J aortas. Bulk RNA sequencing suggested that increased smooth muscle contractile processes promoted mechano-adaptation of 129S6/SvEvTac aortas while immune processes prevented adaptation of C57BL/6 J aortas. Functional studies confirmed an increased vasoconstrictive capacity of the former while immunohistochemistry demonstrated marked increases in inflammatory cells in the latter. We then used multiple computational biomechanical models to test the hypothesis that excessive adventitial wall stress correlates with inflammatory cell infiltration. These models consistently predicted that increased vasoconstriction against an increased pressure coupled with modest deposition of new matrix thickens the wall appropriately, restoring wall stress towards homeostatic consistent with adaptive remodelling. By contrast, insufficient vasoconstriction permits high wall stresses and exuberant inflammation-driven matrix deposition, especially in the adventitia, reflecting compromised homeostasis and gross maladaptation.

overall_design: 2x2 design of genotype (C57BL/6J vs. 129S6/SvEvTac) and treatment (control vs. AngII-induced hypertension)

first: Marcos

last: Latorre

first: Mo

last: Wang

first: Sameet

last: Mehta

first: Alexander

last: Caulk

first: Pengwei

last: Ren

first: Abhay

last: Ramachandra

first: Sae-Il

last: Murtada

first: Alexia

last: Rojas

first: Chang-Shun

last: He

first: Bo

last: Jiang

first: Matthew

last: Bersi

first: George

last: Tellides

first: Jay

last: Humphrey


title: Leukocyte kinetics and bacterial clearance during S. pneumoniae pneumonia and contributions of ICAM-1

city: Chapel Hill

first: Claire

last: Doerschuk

state: NC

address: 125 Mason Farm Rd.

institute: University of North Carolina

summary: Streptococcus pneumoniae is a leading cause of community-acquired pneumonia. Intercellular adhesion molecule-1 (ICAM-1) is an adhesion molecule that is highly expressed on the pulmonary capillary endothelium, alveolar epithelium and other cell types within the lung. ICAM-1 is known to play important roles in leukocyte adhesion, migration, and motility. To determine the contributions of ICAM-1 to bacterial clearance and leukocyte kinetics during pneumonia, mice were inoculated with S. pneumoniae and evaluated 1, 4 and 7 days later. Our results show that Icam1-/- mice have a greater number of viable bacteria within the lung at each time point. The impaired clearance observed in Icam1-/- mice was not due to an impediment in leukocyte recruitment. In fact, Icam1-/- mice had a greater number of neutrophils and recruited inflammatory macrophages in the lung tissue and the alveoli/airways on day 7. In contrast, fewer alveolar macrophages were present in the BAL of Icam1-/- mice. The loss of body weight and the concentrations of inflammatory mediators in the BAL were also significantly greater in Icam1-/- mice. Mechanistic studies to understand the defect in clearance show that neutrophils and macrophage subpopulations had no defect in phagocytosis or acidification of phagosomes. RNA sequencing reveals many differences in gene expression, but does not suggest° a defect in phagocytosis. Thus, ICAM-1 is necessary for the clearance of S. pneumoniae and for the resolution of pneumonia, but is not required for the recruitment of neutrophils or inflammatory macrophages into the pneumonic lung parenchyma or the alveoli/airways during S. pneumoniae-induced pneumonia.

overall_design: Gene expression profiling analysis was performed on 1) naïve primary alveolar macrophages isolated from ICAM-1 null or wild type mice or 2) primary alveolar macrophages isolated from ICAM-1 null or wild type mice following exposure to Staphylococcus aureus pHrodo-labeled bioparticles for 1 hour.

middle: K

last: McPeek

first: John

last: Gomez

first: Jessica

last: Martin

first: Marie

middle: A

last: Iannone

first: Hong

last: Dang


title: tRNA hypomodification facilitates 5-fluorocytosine resistance via cross-pathway control system activation in Aspergillus fumigatus.

city: Jena

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

institute: Leibniz Institute for Natural Product Research and Infection Biology

summary: Increasing antifungal drug resistance is a major concern associated with human fungal pathogens like Aspergillus fumigatus. Genetic mutation and epimutation mechanisms clearly drive resistance, yet the epitranscriptome remains relatively untested. Here, deletion of the A. fumigatus tRNA-modifying isopentenyl transferase ortholog, Mod5, led to altered stress response and unexpected resistance against the antifungal drug 5-fluorocytosine (5-FC). After confirming the canonical isopentenylation activity of Mod5 by LC-MS/MS and Nano-tRNAseq, we performed simultaneous profiling of transcriptomes and proteomes to reveal a comparable overall response to 5-FC stress; however, a premature activation of cross-pathway control (CPC) genes in the knockout was further increased after antifungal treatment. We identified several orthologues of the A. nidulans Major Facilitator Superfamily (MFS) transporter nmeA as specific CPC-client genes in A. fumigatus. Overexpression of Mod5-target tRNATyrGΨA in the ∆mod5 strain rescued select phenotypes but failed to reverse 5-FC resistance, whereas deletion of nmeA largely, but incompletely, reverted the resistance phenotype, implying additional relevant exporters. In conclusion, 5-FC resistance in the absence of Mod5 and i6A likely originates from multifaceted transcriptional and translational changes that skew the fungus towards premature CPC-dependent activation of antifungal toxic-intermediate exporter nmeA, offering a potential mechanism reliant on RNA modification to facilitate transient antifungal resistance.

overall_design: Nano-tRNAseq analysis performed by Immagina Biotechnology on purfied total tRNA from A. fumigatus wild type and 𝚫mod5 knockout strains.

middle: G

last: Bruch

first: Valentina

last: Lazarova


title: Quantification of global DNA methylation using EPIC array

city: Clayton

first: Laura

last: Perlaza-Jimenez

state: Victoria

address: 15 Innovation Walk

institute: Monash University

type: Methylation profiling by genome tiling array

summary: The level of dNA methylation in BRE80-BRE80-T5 and T47D cells expressing active and inctive DNMT3A was quantified using EPIC array across more than 850,000 CpGs

overall_design: Bisulphite converted DNAs from the 24 samples were hybridised to theInfinium Human Methylation EPIC BeadChip v2.0


title: Loss of CD4 T cell responses to prior vaccines associate with inflammation and altered transcriptional signatures in HIV infection

city: Erlangen

first: Krystelle

last: Nganou-Makamdop

address: Schlossgarten 4

department: Virology institute

institute: Universitätsklinikum Erlangen

summary: The preference of HIV to infect activated CD4 T cells has been proposed to contribute to a numerical reduction of antigen-specific T cells and the loss of T cell-mediated immunity. To date, our understanding of how HIV impact on vaccine-induced cellular immunity is limited. Moreover, the influence of chronic inflammation, that persist in treated HIV infection, is still unclear. Here, we investigated inflammation, immune activation and antigen-specific T cell responses in HIV-uninfected and cART-treated HIV people with prior measles virus and tetanus toxoid immunity. Our findings highlight lower antigen-induced T cell activation and lower cytokine production of antigen-specific CD4 T cells in the HIV group. These lower recall CD4 T cell responses associated with high plasma levels of multiple cytokines and with T cell hyperactivation. Transcriptome analysis of sorted antigen-specific CD4 T cells revealed that upon antigen reencounter, HIV people on cART had a reduced expression of gene sets previously reported to associate with vaccine-induced protective immunity against various pathogens. We further identified a consistent impairment of the IFN and IFN signaling pathways as a mechanism for the functional loss of antigen-specific CD4 T cell responses in cART-treated people with HIV. Together, our findings suggest that vaccine-induced cellular immunity may benefit from strategies to counteract inflammation in HIV infection.pecific

overall_design: T cell subsets sorted after stimulation with MV, TT or a no stim control underwent RNA extraction, followed by NEB next library prep and illuminy sequencing

last: Nganou Makamdop


title: Co-option of transcriptional hub expanded triangular functional interactions among nutrients during plant terrestrialzation

city: Singapore

first: Yating

last: Dong

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: Plant nitrate, phosphate, and sucrose responses create a complex molecular network fine-tuned for growth and survival. This triangular interplay, crucial for the adaptability of terrestrial plants, allows the availability of one nutrient to influence plant responses to others. However, the origins and functional repurposing of this complex network for plant terrestrialization remain scarcely understood. By delving into the time-series transcriptome responses to nitrate, phosphate, and sucrose in the bryophyte Marchantia polymorpha and its streptophycean algal relatives Klebsormidium nitens, we observed convergent yet largely species-specific regulatory circuits in nutrient response. A key gene regulatory network (GRN) module centered on MpCSD, MpERF20, and MpHD9 was found to govern the hierarchical responses and crosstalk among the three nutrients in M. polymorpha. In K. nitens, these transcription factors were involved in nutrient responses but were co-opted during phytoterrestrialization to serve additional functions. Further network perturbation experiments validated the extensive evolution of transcriptional targets of these regulatory circuits, with cytokinin responsive genes being recruited exclusively into macronutritional GRNs in M. polymorpha thus optimizing nutrient response. Our findings illuminate the evolutionary strategies employed to redeploy the triad of nutrient interactions during the adaptation of ancestral green plants to terrestrial habitats.

sample_organism:
Marchantia polymorpha
Klebsormidium nitens

overall_design: To study the macronutritional GRN co-option during terrestrialization, parrallel transcriptome study was performed in K. nitens and M. polymorpha, in which five time points including cotrol, nitrate/phosphate/sucrose stravation for five days, and then nutrient resupply for 6h, 24h, and 72h. Three important transcription factors MpCSD, MpERF20, and MpHD9 were identified in this analysis. Furthermore, RNAseq experiments were performed in the three different knock-out mutants by exposure to nitrate/phosphate/sucrose stravation for 5 days.

first: Daisuke

last: Uraono


title: Transcription Factor (TF)EB mediates a mTORC1OFF-induced ECM degradation program of breast cancer cells

city: Paris

first: Philippe

last: Chavrier

address: 12 rue Lhomond

country: France

institute: Institut curie

summary: We show that mTORC1 repression in breast cancer cells potentiates an invadopodia-based metastatic program

overall_design: mTORC1 is central to nutrient sensing and controls endolysosomal biogenesis and exocytosis. To identify genes dysregulated upon mTORC1 repression, we silenced the mTORC1 tethering factor, RagC, in the human MDA-MB-231 breast  cancer cell line. Two independent siRNAs againt RagC were used. We then performed RNA-sequencing to have a comparative analysis of gene expression.

first: David

last: Remy


title: Spatial transcriptomics analysis of adult hippocampal neurogenesis in the human brain

city: Montreal

first: Naguib

last: Mechawar

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

summary: Adult hippocampal neurogenesis (AHN) has been extensively characterized in rodent models, but its existence in humans remains controversial. We sought to assess the phenomenon in post-mortem human hippocampal samples by combining spatial transcriptomics and fluorescent in situ hybridization. We detected very few cells expressing neural stem cell- and proliferation-specific genes in the human dentate gyrus (DG) from childhood to middle age, suggesting very low levels of hippocampal neurogenesis throughout life. However, we observed at all ages a significant number of DG cells expressing the immature neuronal marker DCX. The majority of DCX+ cells displayed an inhibitory phenotype, while the remainder were non-committed or excitatory in nature. Overall, our study investigates for the first time the extent of AHN in the human brain with spatial transcriptomic tools and reveals important insight into the distribution and phenotype of cells expressing neurogenesis markers in the adult human hippocampus.

overall_design: Four fresh-frozen dentate gyrus samples from neurologically healthy male control subjects (21, 26, 42 and 43 years old) were used for spatial transcriptomics and analyzed.

first: Sophie

last: Simard

first: Reza

last: Rahimian

first: Maria

last: Davoli

first: Stéphanie

last: Théberge

first: Natalie

last: Matosin

first: Gustavo

last: Turecki

first: Corina

last: Nagy


title: Amniotic fluid stem cell extracellular vesicle therapy improves lung growth and branching morphogenesis in fetal hypoplastic lungs secondary to oligohydramnios

city: Toronto

first: Fabian

last: Doktor

address: 555 University Avenue

institute: The Hospital for Sick Children

summary: Oligohydramnios is known to cause fetal pulmonary hypoplasia. Amniotic fluid stem cell extracellular vesicles (AFSC-EVs) have shown beneficial effects on hypoplastic lungs secondary to congenital diaphragmatic hernia. Herein, we investigated, whether AFSC-EVs also foster antenatal lung development in hypoplastic lungs secondary to oligohydramnion. We therefore induced surgically oligohydramnion in rat dams and harvested their fetuses. Controls underwent surgery without amniotic fluid drainage. The hypoplastic lungs were assigned to ex vivo to either medium alone or medium + AFSC-EV as a lung explant. Those samples were harvested 24h later and subjected to RNA extraction for subsequent RNA-seq.

overall_design: We subjected three fetal control lungs, three fetal hypoplastic lungs and three fetal hypoplastic lungs treated with AFSC-EVs to RNA-seq experiments

first: Lina

last: Antounians

first: Augusto

last: Zani


title: Interplay between nutrient stress and lysosomal signaling imprints immune memory in tissues [microarray4]

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: Uncovered organelle signaling and metabolic processes shaping CD8+ tissue-resident memory (TRM) development

overall_design: We used microarrays to compare the global transcription profiles of OT-1 cells activated in control or arginine-deficient culture medium with or without stimulation of 5 ng/ml TGF-b for 2.5 days

first: Hao

last: Shi

first: Jana

middle: L

last: Raynor


title: Interplay between nutrient stress and lysosomal signaling imprints immune memory in tissues [microarray3]

overall_design: OT-1 cells from WT-Cas9-KI-Flcnfl/fl or Cd4Cre-Cas9-KI-Flcnfl/fl mice were transduced with sgNTC, sgTfeb, or sgTfe3 in various combinations as indicated and transferred into WT mice, followed by LM-OVA infection. At day 7.5 p.i., siIEL OT-1 cells were sort purified for microarray analysis


title: Interplay between nutrient stress and lysosomal signaling imprints immune memory in tissues [microarray1]

overall_design: sgNTC (Ametrine+) and sgFlcn (GFP+)-transduced OT-1 cells were sort-purified from spleen and siIEL of the same LM-OVA-infected mice at day 7.5 p.i. for microarray analysis


title: Effect of Rab35 knockdown on in vitro differentiated hepatocyte gene expression (time-course)

first: Scientific Computing

last: Facility

address: Pfotenhauerstrasse 108

summary: Rab35 knockdown results in a loss of apical bulkheads from hepatocytes, which causes isotropic growth of the bile canaliculus (BC) and ultimately results in the formation of hepatocyte cysts. In these cysts, hepatocytes have  common apico-basal polarity, such as observed for simple epithelia like cholangiocytes. To investigate whether this change in polarization is associated with alterations in gene expression we compared hepatocytes with and without Rab35 knockdown in a previous RNA-sequencing experiment and found changes in gene expression after 5 days of culture. In this experiment, we want to investigate when Rab35 knockdown starts to affect gene expression. For this, we performed a time-course RNA-sequencing experiment in hepatocytes with and without Rab35 knockdown.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for in vitro differentiated hepatocytes with or without Rab35 knockdown. RNA-seq data was obtained every day between day 1 and day 5 after plating of the hepatoblasts.

first: Maarten

last: Bebelman

first: Lenka

last: Belicova

first: Andre

last: Gohr

first: Marino

last: Zerial


title: Centralized control of dynamic gene regulatory circuits governs human T cell rest and activation [Perturb-CITE-seq]

status: Public on Oct 15 2024

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 1650 Owens St

institute: UCSF Gladstone Institutes

summary: The ability of individual cells to maintain a distinct identity and respond to transient environmental signals requires tightly controlled regulation of gene networks. However, how discrete sets of gene regulators coordinate circuits that respond to extracellular cues remains poorly defined. The need for context-dependent regulation is prominent in human CD4+ T cells, where distinct cell lineages must respond to diverse signals to orchestrate effective adaptive immune responses and maintain homeostasis. Here, we performed CRISPR screens in multiple primary human CD4+ T cell contexts to identify regulators that control expression of IL2RA, which is a canonical marker of T cell activation in pro-inflammatory effector T cells (Teffs) and constitutively expressed in anti-inflammatory regulatory T cells (Tregs) where it is required for fitness. Strikingly, the majority of identified regulators are required in discrete cell type and stimulation timepoints, and a subset even had opposite functional effects in different conditions. Using single-cell transcriptomics after pooled perturbation of context-specific screen hits, we characterized specific factors as regulators of overall rest or activation and constructed state-specific regulatory networks. Upstream of these networks, MED12 – a component of the Mediator complex – serves as a dynamic orchestrator of regulators across conditions, governing both cell type- and stimulation-specific gene expression. MED12 interacts with the histone modifying complex COMPASS, affecting chromatin state and expression of genes encoding key context- and lineage-specific regulators; including rest maintenance factor KLF2 and activation promoting genes. We demonstrated that CRISPR ablation of MED12 blunted this cell state transition and protected T cells from activation-induced cell death. Overall, this work leverages CRISPR screens performed across primary cell conditions to identify context-specific regulators and dynamic gene circuits required to establish resting and activated T cell states.

overall_design: Perturb-CITE-seq performed with 2 donors including resting and stimulated CD4+ Tregs and Teffs

first: Maya

last: Arce

first: Jennifer

last: Umhoefer

first: Nadia

last: Arang

first: Sivakanthan

last: Kasinathan

first: Jacob

middle: W

last: Freimer

first: Zachary

last: Steinhart

first: Haolin

last: Shen

first: Minh T.N

last: Pham

first: Mineto

last: Ota

first: Anika

last: Wadhera

first: Dmytro

last: Dorovskyi

first: Yuan

last: Zhou

first: Dajani

last: Rama

first: Yan Yi

last: Chen

first: Qi

last: Liu

first: Brian

middle: R

last: Shy

first: Ansuman

middle: T

last: Satpathy

first: Julia

last: Carnevale

first: Nevan

middle: J

last: Krogan

first: Jonathan

last: Pritchard


title: Multiscale Drug Screening for Cardiac Fibrosis Identifies MD2 as a Therapeutic Target

city: Palo Alto

first: Yu

address: 1215 Welch Road

department: CVI

institute: Stanford University

summary: The ATAC-seq aims to examine the antifibrotic effects of artesunate on the epigenetic level in human primary fibroblasts

overall_design: Three human primary fibroblast lines were treated with vehicle control, TGFβ，TGFβ+ART

first: Hao

last: Zhang

first: Joseph

middle: C

last: Wu


title: Multiscale drug screening for cardiac fibrosis identifies MD2 as a therapeutic target

summary: The RNA-seq aims to examine the antifibrotic of artesunate in human primary fibroblasts

overall_design: We used 6 primary fibroblasts lines treated with vehicle ctrl, TGFβ，TGFβ+artesunate


title: Dynamics of the zebrafish tRNAome during the maternal-to-zygotic transition [Ribo-Seq]

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry

summary: Time course analysis of tRNA abundance during zebrafish early embryonic development.

overall_design: Wild-type (TLAB strain) zebrafish embryos were grown in standard housing conditions.Unfertilized eggs (0 hours post-fertilization; hpf) were collected or embryos were staged and collected at consecutive developmental time-points, namelyat the 256-cell (2.5 hpf), 1000-cell (3 hpf), sphere (4 hpf), shield (6 hpf) and bud (10 hpf) stages. Eggs and embryos were either flash-frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis, polysome profiling, ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.

first: Madalena

last: Reimão-Pinto

first: Andrew

last: Behrens

first: Sergio

last: Forcelloni

first: Klemens

last: Fröhlich

first: Selay

last: Kaya

middle: D


title: Centralized control of dynamic gene regulatory circuits governs human T cell rest and activation [Bulk_RNA]

first: Alexander

last: Marson

overall_design: Bulk RNAseq performed on resting and stimulated CD4+ Tregs and Teffs following arrayed CRISPR KO of Mediator complex subunits.

first: Maya

last: Arce

first: Jennifer

last: Umhoefer

first: Nadia

last: Arang

first: Sivakanthan

last: Kasinathan

first: Jacob

last: Freimer

first: Zachary

last: Steinhart

first: Haolin

last: Shen

first: Minh

last: Pham

first: Mineto

last: Ota

first: Anika

last: Wadhera

first: Dmytro

last: Dorovskyi

first: Yuan

last: Zhou

first: Dajani

first: Yan


first: Yu

last: Liu

summary: In this project, we used single nucleus RNA-sequenicng to delineate the effects of artesunate on multiple types of cells in the heart.

overall_design: For each group, the n = 3 of ventricular heart tissues were pooled together. The group setting is Sham, TAC, TAC + ART.

first: Hao

last: Zhang

first: Joseph

last: Wu


title: Centralized control of dynamic gene regulatory circuits governs human T cell rest and activation [CRISPR_Screens]

first: Alexander

overall_design: Pooled CRISPR KO screens for IL2RA. Screens were performed using a library targeting trans regulators and immune genes in CD4+ T cell subsets.

first: Maya

last: Rama

last: Chen

first: Qi

first: Brian

last: Shy

first: Ansuman

last: Satpathy

first: Julia

last: Carnevale

first: Nevan

last: Krogan

first: Jonathan

last: Pritchard


title: Centralized control of dynamic gene regulatory circuits governs human T cell rest and activation [ChIPseq_MED12_RNAPol_CXXC1]

last: Marson

overall_design: ChIPseq experiment comparing changes in Teff after MED12 KO compared to AAVS1 KO control samples. Each assay was performed for resting and stimulated Teffs from two human donors.

last: Arce

first: Jennifer

last: Umhoefer

first: Nadia

last: Arang

first: Sivakanthan

last: Kasinathan

first: Jacob

last: Freimer

first: Zachary

last: Steinhart

first: Haolin

first: Minh

first: Mineto


title: Centralized control of dynamic gene regulatory circuits governs human T cell rest and activation [MED12_KO_CUTnRUN_H3K4]

overall_design: CUT&RUN experiment comparing changes in Teff after MED12 KO compared to AAVS1 KO control samples or kinase inhibitor treatment (SEL120-24A) compared to H2O control treatment. Each assay was performed for resting and stimulated Teffs from three human donors.

last: Shen

last: Pham

last: Ota

first: Anika

last: Wadhera

first: Dmytro

last: Dorovskyi

first: Yuan

last: Zhou

first: Dajani

first: Yan

last: Liu


title: Adipose tissue biology and effect of weight loss in women with lipedema

city: Saint Louis

first: Silvia

last: Gonzalez-Nieves

state: Missouri

department: Pharmacology & Physiology

institute: Saint Louis University

summary: Lipedema is a lipodystrophic disease characterized by marked increases in lower-body subcutaneous adipose tissue, anecdotally reported to: i) increase inflammation and fibrosis and impair microvascular and lymphatic circulation in the affected adipose tissue, ii) reduce risk of developing obesity-related cardiometabolic abnormalities; and iii) be resistant to diet-induced weight loss. To further our understanding of lipedema, we examined body composition, metabolic health and adipose tissue bology in women with obesity and lipedema (Obese-LIP) at baseline and following ~9% diet-induced weight loss. At baseline, people with Obese-LIP had ~23% greater leg fat mass, ~11% lower android-to-gynoid ratio and ~54% greater insulin sensitivity compared to women matched on age, body mass index and whole-body fat mass. In the Obese-LIP group, total and proinflammatory macrophage content and expression of inflammation and fibrosis-related genes were greater while lymph/angiogenesis-related genes were lower in subcutaneous femoral compared to abdominal adipose tissue. Diet-induced weight loss improved insulin sensitivity and decreased total fat mass due to similar reductions in abdominal and leg fat masses, with minimal effect on markers of adipose tissue inflammation/fibrosis and lymph/angiogenesis. Our study provides important insights into the pathophysiology of lipedema and suggests diet-induced weight loss should be the cornerstone therapy in people with Obese-LIP.

overall_design: Subcutaneous abdominal and femoral adipose tissue  (SAAT and SFAT)  samples were isolated by biopsy of obese-lipedema patients before and after mild weight-loss (9%).

first: Vincenza

last: Cifarelli

first: Gordon

middle: I

last: Smith

first: Jun

last: Yoshino

first: Hector

middle: H

last: Palacios

first: Anja

last: Fuchs

first: Thomas

middle: F

last: Wright

first: Samuel

last: Klein


title: MicroRNAs in plasma-derived extracellular vesicles as non-invasive biomarkers for eosinophilic esophagitis

first: Elena

last: Grueso-Navarro

state: Ciudad Real

address: Vereda de Socuéllamos s/n

department: Gastroenterology

institute: Hospital General de Tomelloso

summary: Background: The lack of non-invasive biomarkers imposes the dependence on endoscopy with biopsies for the diagnosis and monitoring of eosinophilic esophagitis (EoE), a prevalent chronic inflammation of the esophagus mediated by a type 2 immune response. We aimed to identify potential non-invasive biomarkers using microRNAs (miRNAs) in plasma-derived extracellular vesicles (pEVs).   Methods: This is a prospective single-center observational study including a discovery cohort of EoE patients (n=26) with active disease (EoE.Basal) and after anti-inflammatory treatment (EoE.Post.tx), and control subjects (n=16). Small-RNA-seq of RNA-pEVs was performed to identify differentially regulated small-RNAs (sRNAs) in EoE.Basal vs. controls and EoE.Basal vs. EoE.Post.tx comparisons. Candidate miRNAs were validated in an independent cohort (EoE patients, n=33; controls, n=14), and the diagnostic potential of miRNAs-pairs was assessed.   Results: the pEVs-sRNA cargo differed among controls, EoE.Basal and EoE.Post.tx conditions. Compared with controls, Ser_Comb_22, Leu_Comb_5, miR-10b-5p and miR-125a-5 were upregulated in EoE.Basal, and miR-224-5p, miR-221-3p, let-7d-5p and miR-191-5p were downregulated. Combination of miR-221-3p and miR-10b-5p showed the best diagnostic performance in discovery (AUC=0.87) and validation (AUC=0.70) cohorts. Comparing EoE.Basal and EoE.Post.tx paired samples, miR-374a-5p and miR-30a-3p were upregulated in EoE.Basal, while miR-15a-5p and let-7d-5p were downregulated. Here, combination of mi-30a-3p and miR-15a-5p showed AUC values of 0.90 and 0.71 in discovery and validation cohorts respectively. MiR-30a-3p remained highly upregulated in EoE.Basal when compared to EoE.Post.tx in the validation cohort (p=0.001).   Conclusions: The sRNA cargo of pEVs is related to the inflammatory activity in EoE. This study pioneers the use of pEVs as a non-invasive biomarker for EoE.

overall_design: To investigate the potential of  extracellular vesicle (EVs) dervied small-RNA as non-invasive biomarker for EoE we obtained plasma samples from control subjects, and paired samples from patients with EoE with active inflammation (EoE.Basal) and after succesful anti-inflammatory treatment (EoE.Post.tx). Total RNA from plasma EVs of participants was subjected to small-RNAseq to identify differentially regulated smallRNAs, and performed two comparisons: 1) unpaired analysis for comparing controls with EoE.Basal samples to identify potential diagnostic biomarkers, and 2) paired analysis for EoE.Basal and EoE.Post.tx. Identified small-RNAs, to identify potential monitoring biomarkers. Data from sRNA-seq was analyzed to identfy microRNA and transference fragment RNAs (tRFs). Finally, Finally,  was used to best combinations of two miRNAs were selected to discriminate between the groups compared.

first: Leticia

last: Rodríguez-Alcolado

first: Laura

last: Arias-González

first: Ana

middle: M

last: Aransay

first: Juan

last: Lozano

first: Julia

last: Sidorova

first: Rocío

last: Juárez-Tosina

first: Jesús

last: González-Cervera

first: Alfredo

last: Lucendo

first: Emilio

last: Laserna-Mendieta


title: Autoimmune inflammation causes hematopoietic stem cells to generate a trained immunity program inherited by BMDMs [RNAseq_secondary_data]

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: Trained immunity occurs when inflammatory stimulation reprograms myeloid cells to have increased effector functions upon secondary stimulation.  Interestingly, the secondary stimulation can occur well beyond the lifetime of an individual myeloid cell, thus memory of immune training must reside in the hematopoietic system. After showing that long-term hematopoietic stem cells (HSCLT) from mice treated with pristane for eight weeks generate trained macrophages, we sought to uncover mechanisms underlying the heritable trained immunity program in myeloid cells. To do this we transplanted HSCLT from pristane mice into congenic recipients, and after 18 weeks of engraftment we generated bone marrow derived macrophages (BMDMs) in vitro. We then analyzed the chromatin landscape and transcriptome using low input chromatin accessibility and transcriptomics sequencing (LiCAT-seq) which allows for the co-generation of RNA-seq and ATAC-seq libraries from the same cellular pool. With this approach we found a unique epigenetic phenotype of reduced chromatin accessibility at metabolic genes in BMDMs from pristane HSCLT, which resulted in reduced transcription of metabolic genes, leading to reduced metabolism in BMDMs.

overall_design: Mice were treated ± pristane for eight weeks, then HSCLT were sorted out and transplanted into lethally irradiated congenic recipients. After 18 weeks of engraftment BMDMs were generated for LiCAT-seq analysis.

first: Taylor

middle: S

last: Mills

first: Etienne

last: Danis

first: Eric

last: Pietras


title: Autoimmune inflammation causes hematopoietic stem cells to generate a trained immunity program inherited by BMDMs [RNAseq_primary_data]

summary: Trained immunity occurs when inflammatory stimulation reprograms myeloid cells to have increased effector functions upon secondary stimulation. We found that autoimmune inflammation indiced trained immunity in bone marrow derived macrophages (BMDMs) in mice treated with pristane for eight weeks. We then analyzed the chromatin landscape and transcriptome using low input chromatin accessibility and transcriptomics sequencing (LiCAT-seq) which allows for the co-generation of RNA-seq and ATAC-seq libraries from the same cellular pool. With this approach we found that BMDMs had increased chromatin accessibility at metabolic genes and inflammatory related genes in BMDMs from pristane treated mice, which resulted in increased transcription of metabolic and inflammatory genes, leading to enhanced metabolism and inflammatory functions in BMDMs.

overall_design: Mice were treated ± pristane for eight weeks, then BMDMs were generated for LiCAT-seq analysis.


title: Autoimmune inflammation causes hematopoietic stem cells to generate a trained immunity program inherited by BMDMs [ATACseq_primary_data]


title: Autologous transplantation of P63+ lung progenitor cells in patients with bronchiectasis: a randomized, single-blind, controlled trial

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

summary: Non-cystic fibrosis bronchiectasis is a severe respiratory disease characterized by progressive loss of lung function, resulting in high morbidity and even early mortality. Current treatments cannot repair progressive lung damage, which encouraged the exploration of stem and progenitor cell-based regenerative therapies. In current study, we found that the P63+ progenitor cells normally located in airway basal layer could appear in the alveolar spaces of bronchiectasis patients. We successfully cloned and expanded the progenitor cells from the airway brushing tissues of patients. Then we conducted a randomized, single-blind, controlled, phase 1/2 trial to evaluate the safety and efficacy of autologous P63+ progenitor cells transplantation in bronchiectasis patients.

overall_design: Via bronchoscopy, a small amount of 3-5th level bronchi tissue sample were collected from patients. The obtained tissue was washed and enzymatically digested to form a single-cell suspension, which was then cultured under regenerative cell cloning system. In total, we conducted whole-genome RNA sequencing to analyze the transcriptome of P63+ progenitors from 7 patients with non-cystic fibrosis bronchiectasis for comparative analysis.

first: Weipan

last: Zhang


title: miRNA expression in extracellular vesicles  from mouse adipose tissues

city: Nanjing

first: Xiaohong

last: Jiang

address: 163 Xianlin Rd.

institute: Nanjing University

summary: We used microarrays to analyze  the global programme of miRNA expression in extracellular vesicles  from different types of tissue of 8-week male C57BL/6 mice.

overall_design: Here we tested miRNA expression in in extracellular vesicles of epididymal white adipose tissue, inguinal white adipose tissue andbrown adipose tissue of C57BL/6 mice under room temperature

first: Ruixue

last: Shi


title: Metabolic regulation of the glioblastoma stem cell epitranscriptome by malate dehydrogenase 2 (MDH2)

city: Pittsburgh

first: Jeremy

last: Rich

address: 5115 Centre Ave

department: Hillman Cancer Center

institute: University of Pittsburgh Medical Center

summary: Glioblastoma (GBM) ranks among the most lethal of human cancers with current therapies offering only palliation. GBM displays striking intratumoral heterogeneity with diversity of cell state, metabolism, and molecular regulation. Here, we demonstrate that stem-like tumor cells, designated GBM stem cells (GSCs), display higher activity of the malate aspartate shuttle (MAS) through increased expression of malate dehydrogenase 2 (MDH2). Genetic and pharmacologic targeting of MDH2 reduced GSC proliferation, self-renewal, and in vivo tumor growth. MDH2 targeting induced accumulation of alpha-ketoglutarate (αKG), a critical enzymatic co-factor. Mechanistically, MDH2 regulated post-transcriptional regulation of mRNA, specifically N6-Methyladenosine (m6A) with platelet-derived growth factor receptor- (PDGFR) as a regulated transcript. Leveraging these observations, targeting MDH2 and PDGFR displayed combinatorial efficacy against GSCs. Collectively, these results suggest that stem-like tumor cells reprogram their metabolism to induce changes in their epitranscriptomes that reveal possible therapeutic paradigms.

overall_design:
RNA-seq:
TRIzol reagent (Sigma Aldrich) was used to isolate total cellular RNA from cell pellets according to the manufacturer's instructions. RNA was purified from 387 GSCs, transduced either with a nontargeting or two independent, non-overlapping shRNAs targeting MDH2 and were subjected to RNA-seq. The experiment was performed in biological duplicates.

MeRIP-seq:
GSCs were tranduced either with a nontargeting or two independent, non-overlapping shRNAs targeting MDH2 and were subjected to m6A-seq. The experiment was performed in biological duplicates.

first: Deguan

last: Lv

first: Deobrat

last: Dixit

first: Andrea

last: Cruz

first: Akanksha

last: Chilukuri

first: Sameer

last: Agnihotri

middle: N


title: Extracellular Vesicle miR-1 Delivery from Skeletal Muscle to Adipose Tissue Modifies Lipolytic Pathways in Response to Resistance Exercise in Humans

city: Lexington

first: Benjamin

last: Burke

state: KY

address: 741 S. Limestone

institute: University of Kentucky

summary: Extracellular vesicles (EVs) have emerged as important mediators of inter-tissue signaling and exercise adaptations. In this human study (n=32), muscle-specific microRNA-1 (miR-1) was delivered to adipose tissue via EVs following an acute bout of resistance exercise. Using a multi-model machine learning automation tool, we discovered muscle primary miR-1 transcript and CD63+ EV count in circulation as top explanatory features for changes in adipose miR-1 levels in response to resistance exercise. RNA-sequencing (RNA-seq) and in-silico prediction of miR-1 target genes identified CAV2 and TRIM6 as miR-1 target genes upregulated in adipose tissue of participants with high increases in miR-1 levels following resistance exercise. Overexpression of miR-1 in differentiated human adipocyte-derived stem cells downregulated these miR-1 targets and enhanced catecholamine-induced lipolysis. These data identify a novel mechanism by which skeletal muscle communicates to adipose tissue and modulates lipolysis via delivery of miR-1-containing EVs.

overall_design: We performed RNA-sequencing of human adipose tissue following a single bout of resistance exercise.

first: B

first: Y

last: Wen


title: Interplay between nutrient stress and lysosomal signaling imprints immune memory in tissues [microarray2]

first: Hongbo

last: Chi

overall_design: sgNTC (GFP+) and sgLamtor4, sgRraga, or sgRragc (all Ametrine+)-transduced OT-1 cells were sort purified from the siIEL of the same LM-OVA-infected mice (with their respective sgNTC controls) at day 7.5 p.i for microarray analysis

first: Hao

first: Jana

last: Raynor


title: Centralized control of dynamic gene regulatory circuits governs human T cell rest and activation [H3K27ac_CUTnRUN]

first: Alexander

last: Marson

summary: The ability of individual cells to maintain a distinct identity and respond to transient environmental signals requires tightly controlled regulation of gene networks. However, how discrete sets of nuclear regulators coordinate dynamic circuits that respond to extracellular cues remains poorly defined. This is prominent in CD4+ T cells, where cells must respond to diverse immunogenic signals to orchestrate effective adaptive immune responses and maintain immune homeostasis. Here, we performed CRISPR screens in multiple primary human CD4+ T cell contexts to identify nuclear regulators that control expression of IL2RA, a canonical marker of T cell activation that is differentially regulated between pro-inflammatory effector T cells and anti-inflammatory regulatory T cells. Strikingly, we discovered that the majority of identified regulators function within discrete cell type and stimulation timepoints, and a subset even had opposite effects across conditions. Using single-cell transcriptomics and surface proteomics after pooled perturbation of context specific screen hits, we characterized many factors as regulators of overall rest or activation and constructed state-specific regulatory networks. KLF2, MYB, and SOCS3 were distinguished as interconnected repressors of activation in resting T cells while GATA3 and MYC are required for proper stimulation response. Upstream of these circuits, MED12 – a component of the Mediator complex – serves as a dynamic orchestrator of trans regulators across conditions, governing both cell type and stimulation specific gene expression. Chromatin analysis revealed how MED12 coordinates key regulators as T cells transition to and from rest and activation. We demonstrated that CRISPR ablation of MED12 blunted this transition and protected T cells from activation-induced cell death.

overall_design: H3K27ac CUT&RUN for CRISPR KO primary human CD4+ Teffs and CD4+ Tregs. Samples include both resting and stimulated Teffs and Tregs.  AAVS1 KOs samples serve as wild-type controls for the dataset.

first: Maya

last: Arce

first: Jennifer

last: Umhoefer

first: Jacob

last: Freimer

first: Zachary

last: Steinhart

first: Mineto

last: Ota

first: Anika

last: Wadhera

first: Dmytro

last: Dorovskyi

first: Yan

middle: Y

last: Chen

first: Qi

last: Liu

first: Brian

last: Shy

first: Julia

last: Carnevale

first: Jonathan

middle: K

last: Pritchard


title: The transcriptome of hand2 loss- and gain-of-function embryonic cardiomyocytes

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: To gain mechanistic insight into how Hand2 regulates cardiac fusion, we performed transcriptomic analyses of  hand2 loss- and gain-of-function 20 hpf cardiomyocytes.

overall_design: 1. hand2 loss-of-function: hand2 mutant CMs vs WT sibling CMs, each group has 3 replicates. 2. hand2 gain-of-function: hand2 OE CMs vs WT sibling CMs, each group has 3 replicates.

first: Yanli

last: Xu

first: Didier

last: Stainier


title: Autoimmune inflammation causes hematopoietic stem cells to generate a trained immunity program inherited by BMDMs [ATACseq_secondary_data]

first: Andrew

last: Goodspeed

first: Taylor

last: Mills

first: Etienne

last: Danis

first: Eric

last: Pietras


title: Dynamics of the zebrafish tRNAome during the maternal-to-zygotic transition

first: Danny

last: Nedialkova

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

overall_design: Refer to individual Series


title: Dynamics of the zebrafish tRNAome during the maternal-to-zygotic transition [tRNA-Seq]

overall_design: Wild-type (TLAB strain) zebrafish embryos were grown in standard housing conditions.Unfertilized eggs (0 hours post-fertilization; hpf) were collected or embryos were staged and collected at consecutive developmental time-points, namelyat the 256-cell (2.5 hpf), 1000-cell (3 hpf), sphere (4 hpf), shield (6 hpf) and bud (10 hpf) stages. Eggs and embryos were either flash-frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis, polysome profiling, ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.

first: Madalena

last: Reimão-Pinto

last: Behrens

first: Sergio

last: Forcelloni

first: Klemens

last: Fröhlich

first: Selay

last: Kaya