title: Pseudo-resistant Bacillus cereus uses biofilm-related mechanism to mimic vancomycin resistance during agar diffusion susceptibility testing

city: Graz

first: Paul Jakob

last: Schmid

address: Neue Stiftingtalstraße 6

department: Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine

institute: Medical University of Graz

summary: The glycopeptide vancomycin is a drug of choice for the treatment of severe non-gastrointestinal infections with members of Bacillus cereus sensu lato. Recently, sporadic detection of vancomycin resistant phenotypes emerged, mostly for agar diffusion testing. The food packaging isolate BC70 displayed a pseudo-resistant phenotype for vancomycin in both Etest and disk diffusion. In this work, we used RNA-Seq on the nanopore platform to study differentially expressed genes in BC70 cells, which were able to actively move into the inhibition zone during vancomycin susceptibility testing using Etest and therefore appeared to be resistant. Transcriptomic analysis revealed several key genes of biofilm formation (e.g. calY, tasA, krsEABC) to be upregulated in pseudo-resistant cells suggesting a biofilm-related mechanism of motility. Downregulation of virulence (e.g. hblABCD, nheABC, plcR) and flagellar genes compared to swarming cells also confirmed the non-swarming phenotype of the pseudo-resistant isolate. This type of biofilm-related motility was distinct from swarming motility and joined the list of bacterial strategies interfering with reliable antimicrobial susceptibility testing.

overall_design: We compared the gene expression of pseudo-resistant BC70 with the reference strain ATCC 14579, which did not show resistance during vancomycin susceptibility testing. Furthermore, gene expression of BC70 was compared to swarming BC70 cells as well as BC70 cells on MH agar.

first: Paul

first: Clemens

last: Kittinger


title: FRMD3 deficiency inhibits breast epithelial differentiation by Notch pathway inhibition.

status: Public on Jul 10 2024

city: Beijing

first: Qianchen

last: Li

address: Beijing

country: China

institute: PKU

type: Expression profiling by high throughput sequencing

summary: In order to find the molecular mechanism of FRMD3 in stemness regulation, we knocked down FRMD3 in MCF-7 and T47D luminal A breast cancer cell lines for RNA sequencing.

overall_design: We knocked down FRMD3 in MCF-7 and T47D luminal A breast cancer cell lines for RNA sequencing.

first: Ji

last: Ma

first: Yuqing

last: Gong

first: Xiaoran

last: Sun

first: Hongquan

last: Zhang

first: Jun

last: Zhan


title: CCR1 and CCR2 co-expression on monocytes is nonredundant and delineates a distinct monocyte subpopulation. [RNA-Seq]

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

country: United Kingdom

institute: University of Glasgow

summary: The interactions between chemokines and their receptors, particularly in the context of inflammation, are complex with individual receptors binding multiple ligands and individual ligands interacting with multiple receptors. In addition, there are numerous reports of simultaneous co-expression of multiple inflammatory chemokine receptors on individual inflammatory leukocyte subtypes. Overall, this has previously been interpreted as redundancy and proposed as a protective mechanism to ensure that the inflammatory response is robust. In contrast we have hypothesised that the system is not redundant but exquisitely subtle. Our interests relate to the receptors CCR1, CCR2, CCR3 and CCR5 which, together, regulate non-neutrophilic myeloid cell recruitment to inflammatory sites. Here we demonstrate that, whilst most murine monocytes exclusively express CCR2, there is a small subpopulation, which is expanded during inflammation, which co-expresses CCR1 and CCR2. Combinations of transcript and functional analysis demonstrate that this is not redundant expression and that co-expression of CCR1 and CCR2 marks a phenotypically distinct population of monocytes characterised by expression of genes otherwise typically associated with neutrophils. Single cell RNA sequencing confirms this as a monodisperse population of atypical monocytes. This monocytic population has been previously described as having immunosuppressive activity. Overall, our data confirm combinatorial chemokine receptor expression by a subpopulation of monocytes but demonstrate that this is not redundant expression and marks a discrete monocytic population.

overall_design: Bulk RNA-seq of Monocytes isolated from mouse bone in a resting or inflamed state.

first: Heather

middle: A

last: Mathie

first: Gerry

last: Graham


title: Identification of Chromatin proteins involved in gene repression in lamina-associated domains (RNA-Seq)

city: Milano

first: Stefano

middle: Giustino

last: Manzo

state: MI

address: Via Celoria 26, Dipartimento Bioscienze, Torre A, Piano 4

department: Biosciences

country: Italy

institute: University of Milan

summary: Lamina-associated domains (LADs) are large chromatin regions that are associated with the nuclear lamina and form a repressive environment for transcription. The molecular players that mediate gene repression in LADs are currently unknown. Here we performed a full-genome genetic screen in human cells using LAD-integrated fluorescent reporters to identify such regulators. Surprisingly, the screen identified very few lamina proteins, but revealed roles for dozens of known chromatin regulators. Among these are the negative elongation factor (NELF) complex and interacting factors, suggesting that regulation of RNA polymerase pausing can be a mechanism to repress transcription in LADs. Furthermore, the chromatin remodeler complex BAF and the activation complex Mediator can work both as activators and repressors in LADs, depending on the local context and possibly rewiring of heterochromatin. Our data suggest that fundamental regulatory steps of the transcription process and chromatin remodeling, rather than interaction with NL proteins, have a major role in the regulation of transcription in LADs.

overall_design: RNASEQ experiments were performed on a clonal HAP1 cell line genetically modified to express dCAS9-KRAB domain and transduced with a lentiguide against ADAM22 (pLB187,negative control as not expressed in HAP1) or lentiguides against NELFE or NELFB. RNA was extracted 144 hours following transduction.

last: G Manzo

first: Abdelghani

last: Mazouzi

first: Christ

last: Leemans

first: Tom

last: van Schaik

first: Nadia

last: Neyazi

first: Marjon

middle: S

last: van Ruiten

first: Benjamin

middle: D

last: Rowland

first: Thijn

last: Brummelkamp

first: Bas

last: van Steensel


title: Transcriptional and epigenetic changes from the genesis of the human male germline through to adulthood provide a map of prenatal and postnatal molecular drivers of differentiation and reveal the developmental origin of seminoma.

city: Philadelphia

first: Eoin

middle: Christopher

last: Whelan

state: PA

address: 3800 Spruce St

department: Biomedical Sciences

country: USA

institute: University of Pennsylvania School of Veterinary Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Aberrancies in male germline development can lead to the formation of seminoma, a testicular germ cell tumor. Seminomas are biologically similar to primordial germ cells (PGCs) and many bear an isochromosome 12p [i(12p)] with two additional copies of the short arm of chromosome 12. By mapping of seminoma transcriptomes and open chromatin landscape onto our normal human male germline trajectory, we find that seminoma resembles premigratory/migratory primordial germ cells, but exhibit enhanced germline and pluripotency programs and upregulate genes involved in apoptosis, angiogenesis, and MAPK/ERK pathways. By modeling seminoma using pluripotent stem cell-derived primordial germ cells from Pallister Killian syndrome patients mosaic for i(12p), we identify gene dosage effects that may contribute to transformation. As murine seminoma models do not exist, our analyses provide insights into genetic, cellular and signaling programs driving seminoma transformation and our in vitro platform will permit future evaluation of additional signals required for seminoma tumorigenesis.

overall_design: Human pre- and post-natal testis samples were recovered along with seminoma samples and subjected to single-cell RNA sequencing (10X genomics) and/or single-cell RNA/ATAC ("multiome", 10X Genomics). The goal of this study was to develop the human trajectory of germ cell development and then map the seminoma samples onto it.

first: Keren

last: Cheng

first: Yasunari

last: Seita

middle: C

first: YoungSun

last: Hwang

first: Ryo

last: Yokomizo

first: Antonia

last: Rotolo

first: Katherine

middle: L

last: Nathanson

first: Louisa

last: Pyle

first: Ian

last: Krantz

first: Jill

middle: P

last: Ginsberg

first: Priti

last: Lal

first: Xunda

last: Luo

first: Phillip

middle: M

last: Pierorazio

first: Rebecca

last: Linn

first: Thomas

middle: F

last: Kolon

first: Sandra

last: Ryeom

first: Bangjin

last: Kim

first: Kotaro

last: Sasaki


title: CCN6/WISP3 suppresses metaplastic breast carcinoma by antagonizing a WNT/b-catenin/EZH2 cascade

city: Ann Arbor

first: Bioinformatics

last: Core

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

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

overall_design: Refer to individual Series


title: CCN6/WISP3 suppresses metaplastic breast carcinoma by antagonizing a WNT/b-catenin/EZH2 cascade [RNA-seq]

summary: Metaplastic breast carcinomas (mBrCAs) are a highly aggressive subtype of triple negative breast cancer (TNBC) with histological evidence of epithelial to mesenchymal transition (EMT) and aberrant differentiation, including varied non-glandular features. CCN6/WISP3 tumor suppressor gene inactivation and b-catenin-dependent Wnt pathway activation are often seen in mBrCAs. We have reported MMTV-Cre;Ccn6fl/fl (Ccn6-KO) mice develop spindle mBrCAs with EMT and elevated expression of the Wnt/b-catenin pathway genes HMGA2 and IGF2BP2. The mechanisms by which the secreted CCN6 protein exerts tumor suppressor functions in breast tissues are uncertain. Here, we show recombinant CCN6 protein interacts with Wnt receptor FZD8 and co-receptor LRP6 on mBrCA cells to antagonize Wnt ligand-mediated activation of b-catenin/T-cell-factor (TCF) transcription. We identify the gene for histone methyltransferase EZH2, the catalytic component of polycomb repressive complex 2, as a β-catenin/TCF transcriptional target in Ccn6-KO mBrCA cells. Inhibition of Wnt/β-catenin/TCF function in Ccn6-KO mBrCA cells led to reduced EZH2 levels and decreased histone H3 lysine 27 trimethylation, resulting in deregulation of specific gene targets. Pharmacological inhibition of EZH2 reduced growth and metastasis of Ccn6-KO mBrCA mammary tumors and induced an epithelial phenotype in vivo. In human breast cancer specimens, low CCN6 is significantly associated with activated β-catenin and high EZH2 in spindle mBrCAs compared to other subtypes. Collectively, our findings establish a novel tumor suppressor mechanism for CCN6 as a key negative regulator of a b-catenin/TCF-EZH2 axis and highlight how CCN6 restoration or b-catenin or EZH2 inhibition could have therapeutic relevance for patients with spindle mBrCAs.

overall_design: We identify gene differential expression in breast cancer cells expressing a dominant negative beta-catenin construct (DNTCF4) vs cells without DNTCF4 or cells expressing DNTCF4 plus rescue proteins. A companion experiment (Kleer_kleer_CS3) identified genes differentially associated with H3K27Me3 peaks in DNTCF4 cells vs controls. Those genes will be compared with differentially expressed genes between DNTCF4 and controls identified in this experiment using iPathwayGuide.

first: Maria

middle: E

last: Gonzalez

first: Raymond

last: Calvacante

first: Celina

middle: G

last: Kleer

first: Nichoas

middle: J

last: Carruthers


title: CCN6/WISP3 suppresses metaplastic breast carcinoma by antagonizing a WNT/b-catenin/EZH2 cascade [ChIP-seq]

overall_design: This project is to determine by Chip-seq using 3H3K27me3 antibody in 2 CCN6KO Tumor breast cancer cells, parental and transduced with DNTCF4 (a dominant negative Beta catenin construct), how EZH2 can modulate the epigenetics of mice metaplastic breast tumors

first: Nick


title: CCR1 and CCR2 co-expression on monocytes is non-redundant and delineates a distinct monocyte subpopulation. [scRNA-Seq]

first: John

last: Cole

overall_design: CCR1/2+ monocytes (CD45+, CD11b+, Ly6Chi, Ly6G-, SiglecF-, CCR2+, CCR1+) were sorted from the bone marrow of REP mice using BD FACS Aria. Single cell RNA-Seq was performed using 10X Genomics Chromium NextGEM Single Cell 3’ kit (v 3.1) and sequencing on an Illumina NextSeq-2000.  Data analysis was analysed using Seurat, as described in the manuscript.

first: Heather

last: Mathie

first: Gerry

last: Graham


title: CCR1 and CCR2 co-expression on monocytes is nonredundant and delineates a distinct monocyte subpopulation.


title: Polyamine and EIF5A hypusination downstream of c-Myc confers targeted therapy resistance in BRAF mutant melanoma

city: Seoul

first: Tackhoon

state: 서울

address: L3671, KIST, 5 Hwarangro-14-gil, SeongbukGu

country: South Korea

institute: Korea Institute of Science and Tech

summary: BRAF inhibitors are widely employed in the treatment of melanoma with the BRAF V600E mutation. However, the development of resistance greatly compromises their therapeutic efficacy. Here, we elucidate the role of polyamine biosynthesis and its regulatory mechanisms in promoting BRAF inhibitor resistance. Leveraging CRISPR-Cas9 screens, we identify AMD1 (S-adenosylmethionine decarboxylase 1), a critical enzyme for polyamine biosynthesis, as a druggable target whose inhibition reverses vemurafenib resistance. Metabolomic and proteomic analyses reveal that polyamine biosynthesis is upregulated in vemurafenib-resistant cancer, resulting in enhanced EIF5A hypusination, translation of mitochondrial proteins and oxidative phosphorylation. We also identify that sustained c-Myc levels in vemurafenib-resistant cancer are responsible for elevated polyamine biosynthesis. Finally, inhibition of polyamine biosynthesis or c-Myc reversed vemurafenib resistance both in vitro and in vivo in a xenograft model. With the polyamine biosynthesis signature correlated with poor prognosis in BRAF mutant melanoma patients, our findings reveal that the polyamine-hypusination-mitochondrial respiration pathway is an effective therapeutic target that can maximize the therapeutic efficacy of existing BRAF inhibitors.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: The PCR amplicon containing the sgRNA cassette was sequenced with custom primers. The sgRNAs within amplicon was detected with custom codes provided in Github  (https://github.com/tackhoonkim).

first: Byung-Sun

last: Park


title: Transcriptomic profiling of 2 cell lines from Down-Syndrome children with  Acute Lymphoblastic Leukaemia (DS-ALL)

city: Perth

first: Jesse

middle: David

last: Armitage

state: WA

address: 35 Stirling Hwy, Crawley

department: School of Biomedical Sciences

country: Australia

institute: University of Western Australia

summary: Two cell lines derived from 2 Down Syndrome children who developed Acute Lymphoblastic Leukaemia were profiled at the transcriptomic level (bulk RNAseq) and compared against their Patient-Derived Xenograft (PDX) of origin.

overall_design: Libraries were prepared from 500 ng of total RNA isoaled from human DS-PER961 (KRAS G12S mutant)  and DS-PER-962 (CRLF2 + and JAK2 I682F mutant)  cell lines  using the SureSelect Stranded PolyA RNASeq kit. Libraries were sequenced at 40 million paired-end reads  per sample using a NovaSeq 6000 SP 200 cycles reagent kit (Illumina). Raw data was demultiplexed, underwent quality control, aligned and mapped to the trancriptome (GENECODE v34, GRCh38.p13 assembly).

first: Carlos

last: Aya-Bonilla

first: Sébastien

last: Malinge


title: Single-cell analysis reveals alterations in limbal stem cells and niche regulations during cornea wound healing

city: Qingdao,Shandong

first: Di

last: Sun

address: No.5 Yanerdao Road, Shinan District, Qingdao City, Shandong Province

institute: Eye Institute of Shandong First Medical University

summary: The rapid and effective regeneration of corneal epithelial cells depends on limbal stem cells (LSCs). The LSCs of mouse can be subdivided into quiescent LSCs (located on the outer limbus, qLSCs) and active LSCs (located on the inner limbus, aLSCs). Here, we used single-cell RNA sequencing to decipher the transcriptional changes in qLSCs and aLSCs and their niche regulations during the corneal wound healing, and reconstructed the pseudotime trajectory and differentiation of LSCs. Our comparative study identified a transcription factor Creb5, expressed in LSCs, that was significantly upregulated after corneal epithelial injury, and the loss-of-function experiments revealed that silencing Creb5 delayed the corneal epithelial healing. Besides, we predicted a significant increase in the number of ligand-receptor pairs for intercellular communications during corneal epithelial wound healing, especially between immune cells and LSCs, implying the participation of various niche cells in limbal stem cell kinetics during corneal epithelial regeneration. Overall, our research reveals numerous findings on the behavior and functionality of LSCs during corneal wound healing, providing reference for the discovery of mechanisms and potential clinical interventions of ocular surface reconstruction.

overall_design: Single-cell RNA-seq analysis of mouse unwounded and wounded cornea

first: Rong

last: Chen

first: Tian

last: Sang

first: Xiaowen

last: Zhang

first: Qun

last: Wang

first: Lixin

last: Xie

first: Qingjun

last: Zhou

first: Shengqian

last: Dou


title: Abnormal expression profile of plasma exosomal microRNAs in exclusive electronic cigarette adult users

city: Rochester

first: Dongmei

last: Li

state: NY

address: 265 Crittenden Boulevard Cu 420708

department: Clinical and Translational Research

institute: University of Rochester

type: Non-coding RNA profiling by high throughput sequencing

summary: Exposure to electronic cigarette (e-cigarette) aerosol has been linked to a number of health concerns, including DNA damage, elevated oxidative stress, release of inflammatory cytokine, and dysfunctions in epithelial barriers. However, little is known about the effect of exclusive e-cigarette use on expression profiles of exosomal miRNAs, which play critical regulatory roles in many inflammatory responses and disease process including cancer. We aim to compare the exosomal microRNAs expression profile between exclusive e-cigarette users and normal controls without any tobacco product use (non-users). Using blood and urine samples from exclusive e-cigarette users and non-users in the Population Assessment of Tobacco and Health (PATH) Wave 1 study (2013-2014), we examined exosomal microRNAs expression levels through Illumina NextSeq 500/550 sequencing. We identified microRNAs that have significantly higher expression levels in exclusive e-cigarette users than non-users. Gene enrichment analysis of these significant exosomal microRNAs showed their involvement in cancer related pathways, which might indicate a potential elevated risk of cancer among exclusive e-cigarette users.

overall_design: This is a cross-sectional comparison of the impact of exclusive electronic cigarette use on plasma exosomal microRNA expression profiles between exclusive electronic cigarette users and non-users.

first: Zidian

first: Irfan

last: Rahman


title: Competitive Inhibition and Mutualistic Growth in Polymicrobial Infections: Deciphering Staphylococcus aureus – Acinetobacter baumannii Interaction Dynamics

city: Bielefeld

first: Manuel

last: Wittchen

address: Universitaetsstr. 27

department: Center for Biotechnology

country: Germany

institute: Bielefeld University

summary: Staphylococcus aureus (Sa) and Acinetobacter baumannii (Ab) are frequently co-isolated from polymicrobial infections that are severe and recalcitrant to therapy. Here, we apply a combination of wet-lab experiments and in silico modeling to unveil the intricate nature of the Ab/Sa interaction using both, representative laboratory strains and strains co-isolated from clinical samples. This comprehensive methodology allowed uncovering Sa's capability to exert a partial interference on Ab by the expression of phenol-soluble modulins. Additionally, we observed a cross-feeding mechanism, wherein Sa supports Ab's growth by providing acetoin as an alternative carbon source. This study marks the pioneering work to dissect Ab/Sa interaction dynamics wherein competitive and cooperative dynamics can intertwine. Through our findings, we illuminate the ecological mechanisms underpinning their coexistence in the context of polymicrobial infections. Our research not only enriches our understanding but also opens doors to potential therapeutic avenues in managing these challenging infections.

sample_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: Aim of the study is to understand the effect of exposure of Acinetobacter baumannii A118 to  Staphylococcus aureus USA300 and vice versa. Acinetobacter baumannii A118 was cultivated in Cell-Free Conditioned Medium (CFCM) of Staphylococcus aureus USA300, with Acinetobacter baumannii A118 cultivated in TSB medium as control. Furthermore Staphylococcus aureus USA300 was cultivated in CFCM of Acinetobacter baumannii A118, with Staphylococcus aureus USA300 in TSB medium as control. All comparisons were done with Illumina Paired-End RNA-Seq data.

first: Sandra

last: Timme

first: Sindy

last: Wendler

first: Tilman

last: Klassert

first: Joao

last: Saraiva

first: Ulisses

middle: N

last: da Rocha

first: Sareda

last: Schramm

first: Ralf

last: Ehricht

first: Stefan

last: Monecke

first: Birgit

last: Edel

first: Jürgen

last: Rödel

first: Bettina

last: Löffler

first: Soledad

last: Ramirez

first: Hortense

last: Slevogt

first: Marc

middle: T

last: Figge

first: Lorena

last: Tuchscherr


title: Sequence basis of transcription initiation in human genome

city: Dallas

first: Donghong

last: Cai

state: TX

address: Dallas

institute: UTSW

summary: Transcription initiation is an essential process for ensuring proper function of any gene, however, we still lack a unified understanding of sequence patterns and rules that explains most transcription initiation sites in human genome. By explaining transcription initiation at basepair resolution from sequence with a deep learning-inspired explainable modeling approach, here we show that simple rules can explain the vast majority of human promoters. We identified key sequence patterns that contribute to human promoter function, each activating transcription with a distinct position-specific effect curve that likely reflects its mechanism of promoting transcription initiation. Most of these position-specific effects have not been previously characterized, and we verified them using experimental perturbations of transcription factor binding sequences. We revealed the sequence basis of bidirectional transcription at promoters and the links between promoter selectivity and gene expression variation across cell types. Additionally, by analyzing 241 mammalian genomes and mouse transcription initiation site data, we showed that the sequence determinants are conserved across mammalian species. Taken together, we provide a unified model for the sequence basis of transcription initiation at basepair resolution(?) that is broadly applicable across mammalian species, which sheds new light on fundamental questions related to promoter sequence and function.

overall_design: We developed a new assay, which we named CRISPR-Cap, to determine the effects of CRISPR-mediated editing of endogenous motif sequences in vivo


title: Liver X receptor controls a bifurcated transcriptional program where lipogenesis genes overshoot upon refeeding while cholesterol biosynthesis genes return to pre-fasting levels [lxr_rna]

city: Rehovot

first: Ido

last: Goldstein

address: POB 12

department: Institute of Biochemistry, Food Science and Nutrition

country: Israel

institute: The Hebrew University of Jerusalem

summary: Transitions from a fed to a fasted state are common in mammals. The liver orchestrates adaptive responses to feeding/fasting by transcriptionally regulating metabolic pathways of energy usage and storage. Transcriptional and enhancer dynamics following cessation of fasting (refeeding) were never explored.  We aimed to inspect the transcriptional and chromatin events occurring upon refeeding, their kinetic behavior and their molecular drivers. We found that the refeeding response is temporally-organized with an early response focused on ramping up protein translation while later stages of refeeding drive a bifurcated lipid synthesis program. While both lipid synthesis pathways were inhibited during fasting, cholesterol biosynthesis genes returned to their basal levels upon refeeding while lipogenesis genes significantly overshoot above pre-fasting levels. Lipogenic gene overshoot is dictated by Liver X Receptor alpha (LXRα) which directly binds and activates lipogenic enhancers. These findings unravel the mechanism behind the long-known phenomenon of refeeding fat overshoot.

overall_design: RNA-seq floxed refed 24h and LXR dko refed 24h

first: Noga

last: Korenfeld


title: Liver X receptor controls a bifurcated transcriptional program where lipogenesis genes overshoot upon refeeding while cholesterol biosynthesis genes return to pre-fasting levels [lxr_atac]

overall_design: ATAC-Seq of floxed mice fasted for 24h followed by refeeding of 24h and LXR dko mice fasted for 24h followed by refeeding of 24h


title: Liver X receptor controls a bifurcated transcriptional program where lipogenesis genes overshoot upon refeeding while cholesterol biosynthesis genes return to pre-fasting levels [kinetics_rna]

overall_design: Males, 8 weeks-old mice (C57BL/6J) were randomly assigned to either group (6 mice per group). The experiment started after 1 week of acclimation. The Adlib group had ad libitum access to food (Teklad TD2018) and water throughout the experiment. For the rest of the groups, food was removed at the beginning of the inactive phase (shortly after lights on, zeitgeber time 1). For the Refed groups, food was put back in the cage 24 h later while the fasted group was anesthetized and euthanized. The Refed groups were euthanized 3 h, 10 h and 24 h after food reintroduction. At each group endpoint, mice were anesthetized and euthanized (ketamine:xylazine 30:6 mg/ml) and the liver was excised.


title: scRNA-seq analysis of biopsy tissue from Interstitial Lung Disease patients who took EGCG

city: San Francisco

first: Max

last: Cohen

state: CA

address: 513 Parnassus Ave, Box 0111

department: Medicine

institute: UCSF

summary: Trihydroxyphenolic compounds, such as Epigallocatechin Gallate (EGCG), cause fibroblast-specific TGFb1 receptor kinase and lysyl oxidase like 2 (LOXL2) inhibition, reducing fibroblast activation and collagen cross-linking in fibrotic mice lungs and in cultured human precision cut lung slices (PCLS) derived from Interstitial Lung Disease (ILD) / Idiopathic Pulmonary Fibrosis (IPF) patients. When taken for two weeks, EGCG reduced protein markers of pro-fibrotic signaling in spare tissue from diagnostic surgical biopsies from ILD patients. Here, we report the result of single-cell RNA sequencing on lung tissue from ILD patients who took EGCG (600mg by mouth daily) for two weeks prior to diagnostic surgical biopsy and donated spare tissue and from control/untreated biopsy samples, including comparison to normal donor and end-stage ILD explant lung tissues.

overall_design: scRNA-seq was performed on spare biopsy tissue from four fibrotic lung disease patients who took EGCG (600mg by mouth daily) prior to diagnostic surgical lung biopsy, four fibrotic lung disease control biopsies, tissue from one normal/healthy donor lung, and one end-stage IPF explant lung. Following tissue digestion with dispase and collagenase, flow cytometry  was performed for live epithelial (EPCAM+/CD45-/CD31-) and mesenchymal (EPCAM-/CD45-/CD31-) cells, which were combined 1:1 for scRNA-seq.

first: Harold

last: Chapman

first: Claude

last: Le Saux

first: Ying

last: Wei

first: Alexis

last: Brumwell


title: Effect of VDR knockdown on the gene expression of K562 cells after 48h

city: Jinan City

first: Yan

last: Xu

address: No. 44 Wenhua West Road

institute: Shandong University

summary: To investigate the effect of VDR in the regulation of K562 cells. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for K562 cells from shNC and shVDR after 48h.

first: Baobing

last: Zhao


title: Distinct modes of heat shock transcription factor interactions with mitotic chromosomes

city: Vancouver

first: Sheila

last: Teves

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

country: Canada

institute: Life Science Institute

summary: TBP is required for efficient reactivation of Pol I following mitosis but is generally not required

overall_design: Cleavage Under Target and Tagmentation (CUT&Tag) for Pol I

first: James

middle: Z

last: Kwan

first: Thomas

last: Nguyen


title: Liver X receptor controls a bifurcated transcriptional program where lipogenesis genes overshoot upon refeeding while cholesterol biosynthesis genes return to pre-fasting levels [lxr_chip]

overall_design: ChIP-Seq floxed mice fasted for 24h followed by refeeding of 24h and LXR dko mice fasted for 24h followed by refeeding of 24h


title: Molecular differences between tumor endothelial cells from low- and high-grade gliomas

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

overall_design: Refer to individual Series


title: Low- and high-grade glioma-associated vascular cells differentially regulate tumor growth [project3]

summary: Glioma vascular cells (GVC) from high-grade IV gliomas (HG) are molecularly and functionally distinct from normal brain EC, and secrete higher levels of pro-tumorigenic factors that promote glioma growth and progression. However, it remains unclear whether GVC  from Low- Grade II/II gliomas (LG) also express pro-tumorigenic factors, and to what extent they functionally contribute to glioma growth. Here, we profile the transcriptomes of GVC from IDH-mutant (mIDH) LG and IDH-wildtype (wIDH) HG and show that they exhibit significant molecular and functional heterogeneity. LG-GVC show enrichment of extracellular matrix and cell cycle-related gene sets and sensitivity to anti-angiogenic drugs, whereas HG-GVC display an increase in immune response-related gene sets and anti-angiogenic resistance. Strikingly, conditioned media from LG-GVC inhibits the growth of wIDH glioblastoma cells, whereas HG-GVC promotes growth. In vivo co-transplantation of LG-GVC with tumor cells reduces growth, whereas HG-GVC enhances tumor growth in orthotopic xenografts. We identify ASPORIN (ASPN), a small leucine-rich repeat proteoglycan, enriched in LG-GVC as a growth suppressor of wIDH glioblastoma cells in vitro and in vivo. Together, these findings indicate that GVC from LG and HG gliomas are heterogeneous and differentially regulate tumor growth.

overall_design: To determine the molecular identity of GVC isolated from primary GBM tumors by CD31-MACS sorting. CD31-positive GVC and CD31-negativeGBM tumor cell fractions were isolated and cultured for RNA extraction. Differential gene expression analysis was performed to characterize the enrichment of endothelial markers in GVC fractions. We also performed transcriptmic profiling of GVC cultured at different passages, early (EP, P2) and late passage (LP, P7) to determine if they maintain their identity in culture over long-term

first: Harley

middle: I

last: Kornblum

first: Sree

last: Muthukrishnan


title: Liver X receptor controls a bifurcated transcriptional program where lipogenesis genes overshoot upon refeeding while cholesterol biosynthesis genes return to pre-fasting levels


title: Low- and high-grade glioma-associated vascular cells differentially regulate tumor growth [project2]


title: Faecalibaterium prausnitzii strain EXL01 boosts efficacy of Immune Checkpoint Inhibitors

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

country: France

institute: Parean Biotechnologies

summary: Gut microbiota impacts responses to immune checkpoint inhibitors (ICI). High level of Faecalibacterium prausnitzii has been associated with a positive response to ICI in multiple cancer types. Here, we show in two independent cohorts of patients with non-small cell lung cancer and advanced melanoma that high level of F. prausnitzii at baseline is positively associated with a better clinical response to ICI. In a mouse preclinical model, we show that the F. prausnitzii strain EXL01, already in clinical development for Inflammatory Bowel Disease, restores the anti-tumor response to ICI in the context of antibiotic-induced microbiota perturbation at clinical and tumor transcriptomics level. In vitro, EXL01 strain enhances T cell activation in the presence of ICI. Interestingly, oral administration of EXL01 strain is not associated with a change in fecal microbiota diversity or composition suggesting a direct effect on immune cells in the small intestine.

overall_design: To investigate the effects of EXL01 strain at the tumor level, we conducted RNA sequencing analysis on the tumors biopsies collected 13 days post tumor inoculation

first: Marius

last: Bredon

first: Camille

last: Danne

first: Hang

last: Pham

first: Pauline

last: Ruffié

first: Alban

last: Bessede

first: Nathalie

last: Rolhion

first: Laura

last: Creusot

first: Loic

last: Brot

first: Iria

last: Alonso

first: Philippe

last: Langella

first: Lisa

last: Derosa

middle: B

last: Cortot

first: Bertrand

last: Routy

first: Laurence

last: Zitvogel

first: Nicola

last: Segata

first: Harry

last: Sokol


title: Low- and high-grade glioma-associated vascular cells differentially regulate tumor growth [project1]

first: Riki

last: Kawaguchi

first: Harley

last: Kornblum

first: Sree

middle: D

last: Muthukrishnan


title: Genome-wide chromatin binding of ARNTL2 in nasopharyngeal carcinoma  cell line HONE1 [CHIP-seq]

city: Guangzhou

first: Yanping

last: Mao

state: Guangdong

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

summary: Abnormal expression of circadian genes is known to be engage in tumor initiation and progression through disrupting rhythms of cellular processes. Here, we determined a significant role of the core circadian transcription factor ARNTL2 in nasopharyngeal carcinoma metastasis. To further investigate the downstream targets of ARNTL2 in nasopharyngeal carcinoma, chromatin immunoprecipitation (ChIP) sequencing was performed in ARNTL2-overexpression HONE1 cell.

overall_design: Chromatin immunoprecipitation (ChIP) sequencing was performed in human nasopharyngeal carcinoma cell line HONE1 with ARNTL2 overexpression  to explore the genome-wide chromatin binding of ARNTL2

first: Wenqing

last: Zou

last: Liu


title: mRNA expression profiling of  nasopharyngeal carcinoma cell line HONE1 upon ARNTL2 knockdown [RNA-seq]

summary: Abnormal expression of circadian genes is known to be engage in tumor initiation and progression through disrupting rhythms of cellular processes. Here, we determined a significant role of the core circadian gene ARNTL2 in nasopharyngeal carcinoma metastasis. To further investigate the underlying mechanism of ARNTL2 in nasopharyngeal carcinoma, High-throughput RNA sequencing was performed in ARNTL2-knockdown HONE1 cell.

overall_design: High-throughput RNA sequencing analysis was performed in human nasopharyngeal carcinoma cell line HONE1 transiently transfected with siARNTL2 or  control siRNA.


title: Targeting TNF/IL-17/MAPK Pathway in hE2A-PBX1 Leukemia: effects of OUL35, KJ-Pyr-9, and CID44216842

first: Wei

state: Guangdong Province

address: 382 Waihuan E Rd, Panyu District

department: School of Medicine

institute: South China University of Technology

summary: t(1;19)(q23;p13) is one of the most common translocation genes in childhood acute lymphoblastic leukemia (ALL) and is also present in acute myeloid leukemia (AML) and mixed-phenotype acute leukemia (MPAL). This translocation results in the formation of the oncogenic E2A-PBX1 fusion protein, which contains a trans-activating domain from E2A and a DNA-binding homologous domain from PBX1. Despite its clear oncogenic potential, the pathogenesis of E2A-PBX1 fusion protein is not fully understood (especially in leukemias other than ALL), and effective targeted clinical therapies have not been developed. To address this, we established a stable and heritable zebrafish line expressing human E2A-PBX1 (hE2A-PBX1) for high-throughput drug screening. Blood phenotype analysis showed that hE2A-PBX1 expression induced myeloid hyperplasia by increasing myeloid differentiation propensity of hematopoietic stem cells (HSPCs) and myeloid proliferation in larvae, and progressed to AML in adults. Mechanistic studies revealed that hE2A-PBX1 activated the TNF/IL-17/MAPK signaling pathway in blood cells and induced myeloid hyperplasia by up-regulating the expression of the runx1. Interestingly, through high-throughput drug screening, three small molecules targeting the TNF/IL-17/MAPK signaling pathway were identified, including OUL35, KJ-Pyr-9, and CID44216842, which not only alleviated the hE2A-PBX1-induced myeloid hyperplasia in zebrafish but also inhibited the growth and oncogenicity of human pre-B ALL cells with E2A-PBX1. Overall, this study provides a novel hE2A-PBX1 transgenic zebrafish leukemia model and identifies potential targeted therapeutic drugs, which may offer new insights into the treatment of E2A-PBX1 leukemia and improve the quality of life of leukemia patients.

overall_design: Kidney marrow of the wild type, Tg(hsp70:E2A-PBX1-EGFP) zebrafish after 3-month heat shock were isolated separately. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.

first: Haiping

last: Luo

last: Zhang


title: Cholestasis-induced neutrophil phenotypic transformation contributes to the immune escape of colorectal liver metastasis

city: Guangzhou, China

first: Wangjun

last: Liao

address: Guangzhou Dadao North Road No.1838, Baiyun District

institute: Nanfang Hospital

summary: Cholestasis, a serious complication of liver metastasis (LM), contributes to dismal prognosis in patients with colorectal cancer and LM. However, the mechanism underlying the effect of cholestasis on the development of LM or pre-metastatic microenvironment in the liver remains elusive. In this study, we discovered that cholestasis accelerated the progression of LM and is associated with increased neutrophil infiltration, T-cell exclusion, and exhaustion. Besides, Tβ-MCA and GCA promoted the expression of Arg1 and iNOS in neutrophils via the p38/MAPK signaling pathway. The significant suppression of the activation and cytotoxic effects of CD8+ T cells during co-culture with BA-pretreated neutrophils indicated that BAs directly induce the polarization of immunosuppressive neutrophils. Importantly, targeting BA anabolism with Obeticholic acid effectively suppressed the LM of colorectal cancer in a cholestasis mouse model. Our findings suggest that cholestasis, associated with the failure to achieve drainage of primary BAs, accelerates the progression of LM by remodeling the tumor immune microenvironment. Moreover, targeting BA anabolism with OCA may represent a therapeutic strategy for cholestasis-associated LM of colorectal cancer.

overall_design:
To investigate the influence of primary bile acids on the phenotypic transformation of neutrophils, we treated mouse neutrophils with GA, TCA, and TβMCA, respectively for 24 h.
We then performed RNA-seq on the neutrophils under 4 different treatments, including control.

first: Li

last: Sun

first: Nanyan

last: Yang


title: Transcriptome analysis of mesenchymal glioma-propagating cells treated with p38MAPK inhibitor (SB202190)

city: Singapore

first: Hong Sheng

last: Cheng

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine,

country: Singapore

institute: Nanyang Technological University

summary: To examine the underlying mechanism and treatment effect of p38MAPK inhibition in patient-derived glioma-propagating cells of the mesenchymal subtype.

overall_design: Mesenchymal glioma-propagating cells were cultured as neurosphere suspensions in serum-free growth medium supplemented with growth factors. 1*10^6 cells were seeded in a 10 cm dish overnight. The cells were treated the next day with either DMSO or 100 nM SB202190 daily for 72 h.

first: Hong

middle: S

first: Nguan

last: Tan


title: Whole transcriptome analysis of prostatic urethra of rats after thulium laser prostatectomy [miRNA]

city: GuiYang

first: XiaoHu

last: Tang

address: No. 83 Zhongshan East Road

institute: Guizhou Provincial People's Hospital

summary: To investigate the repair mechanism of urethral wound after prostatectomy, we used microarray RNA sequences and bioinformatics methods to analyze the entire transcriptome of post-urethral resection trauma tissue in the rat prostate.

overall_design: Two-group experiment (miRNA_Sham = only abdominal median incision was performed (control) vs miRNA_TULP = simulating transurethral laser prostatectomy. Four biological replicas of each group in rat prostatic urethra.

first: Guangheng

first: Xiaohu

first: Zhiyan

first: Hao

first: Heng


title: Whole transcriptome analysis of prostatic urethra of rats after thulium laser prostatectomy

type:
Non-coding RNA profiling by array
Expression profiling by array

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


title: Whole transcriptome analysis of prostatic urethra of rats after thulium laser prostatectomy [mRNA, lncRNA, circRNA]

type:
Expression profiling by array
Non-coding RNA profiling by array

overall_design: Two-group experiment (Sham = only abdominal median incision was performed (control) vs TULP = simulating transurethral laser prostatectomy. Four biological replicas of each group in rat prostatic urethra.


title: Transcriptomic analysis revealed genes involved in response to drought stress in Zizyphus jujuba var. Spinosa

city: Shenyang

first: Shengjun

last: Dong

address: No.120 Dongling Road, Shenhe District, Shenyang, Liaoning Province, P.R.China.

institute: Shenyang Agricultural University

summary: Through transcriptome sequencing analysis, drought-resistant genes were excavated to lay a foundation for the cultivation of excellent lineage of Zizyphus jujuba var. Spinosa.There were a total of 10136 differential expressed genes were obtained by transcriptome sequencing of the two families No.1 and No.5, among which 5254 genes were up-regulated and 4882 genes were down-regulated.Several gene families related to drought resistance were found, including ERF, bZIP, MYB, WRKY, NAC, ZFP, F-box, HSP, and bHLH.There are 926 entries commented to the Go function.There are 122 metabolic pathways annotated for KEGG function.The results of PCR fluorescence quantitative verification of 19 drought-related genes were consistent with the results of transcriptome sequencing, among which 15 genes were up-regulated in  No. 1 family.

overall_design: Transcriptome sequencing was performed on two Zizyphus jujuba var. Spinosa  families No. 1 (treatment group) and No. 5 (control group) under drought stress for 15 days.There were 3 biological replicates in each family

first: Quangang

first: Jianhua

last: Chen

first: Jie

last: Lu


title: Intermittent fasting alleviates photoreceptor degeneration and retina inflammation in oxidative stress-induced model of Age-Related Macular Degeneration

status: Public on Jul 09 2024

city: xu zhou

first: Jingzhen

last: Li

address: huang shan road

department: Life science

institute: xuzhou medical university

summary: Age-related macular degeneration (AMD), a prevalent neurodegenerative disorder, remains the leading cause of vision loss among the elderly population. Despite the urgent need, effective treatments or preventive strategies for AMD are not available. Recent studies have highlighted the potential neuroprotective benefits of intermittent fasting (IF) in several models of aging and age-associated disorders. However, its efficacy in AMD has not been established. Our current research reveals that IF alleviated neurodegeneration  by reducing RPE and photoreceptor cell damage  in an oxidative stress-induced mouse model of AMD. The assessment of visual capabilities in mice through optomotor response (OMR) tests indicates that IF markedly preserved visual function in NaIO3-treated mice. To understand the mechanism by which IF exerts its protective effects, we performed transcriptome analyses and found that IF can counteract numerous transcriptional alterations induced by NaIO3, predominantly affecting genes involved in photoreceptor structure, inflammatory pathways and reactive oxygen species (ROS) process. Further, we demonstrated through multiple experiments that IF could effectively reduce ROS levels and restraining the hyperactivation of microglia and Müller cells within the RPE and retina. Moreover, we explored the initiation of IF at a later stage in an individual's lifespan and found that benefits were also obtained in the AMD model. Collectively, this study indicates IF exerts neuroprotective effects by reducing ROS production and inflammation in the retina, and is expected to become a new strategy for retinal degenerative diseases caused by oxidative damage, incluiding AMD.

overall_design: We examined the transcriptional profiles of IF-treated degenerative retina to explore the underlying mechanism. RNA was isolated from the RPE/choroid/sclera complex, which was either subjected to PBS or NaIO3 induction, with and without IF intervention, and subjected to RNA-seq analysis

first: Meng

first: Beibei

last: Wang


title: Transcriptome Changes and Metabolic Outcomes After Bariatric Surgery in Adults With Obesity and Type 2 Diabetes

city: Riyadh

first: Abderrezak

last: Bouchama

address: Ahmad Ibn Hanbal Street, Ar Rimayah

department: Experimental Medicine

country: Saudi Arabia

institute: KAIMRC

summary: We aimed to characterize bariatric surgery-induced transcriptome changes associated with diabetes remission and the predictive role of the baseline transcriptome.

overall_design: We performed a whole-genome microarray in peripheral mononuclear cells at baseline (before surgery) and 2 and 12 months after bariatric surgery in a prospective cohort of 26 adults with obesity and type 2 diabetes. We applied machine learning to the baseline transcriptome to identify genes that predict metabolic outcomes.

first: Mamoon

last: Rashid

first: Ali

last: Al Qarni

first: Saeed

last: Al Mahri

first: Sameer

last: Mohammad

first: Altaf

last: Khan

first: Mashan

last: Abdullah

first: Cynthia

last: Lehe

first: Reem

last: Al Amoudi

first: Omar

last: Aldibasi


title: Single-cell sequencing of CD45-positive and CD45 negative cells from the lungs of WT, Trex1 KO, Trex1;Ifngr1 DKO, and cGas-KI/+;Vav-icre mice

city: Hefei

first: Jinghe

last: Zhang

state: Anhui

address: Huangshan Road 443

institute: University of Science and Technology of China

summary: Trex1 KO is one of the animal models with activated cGAS. Here, we will compare the lung tissue of mice with hematopoietic overexpression of cGAS to see if it exhibits a phenotype similar to that of Trex1 KO.

overall_design: Using cell sorting technology, CD45-positive and CD45 negative cells were isolated from the lung tissues of WT, Trex1 KO, Trex1;Ifngr1 DKO, and cGas-KI/+;Vav-icre mice.

first: Ruibo

last: Zhao

first: Daxing

last: Gao


title: Andrographis paniculata standardized extract attenuates transcriptome, proteome, and metabolome changes caused by SARS-CoV-2 infection in golden hamster kidney

city: Bangkok

first: Arnatchai

last: Maiuthed

state: Bangkok

address: 447 Thanon Si Ayutthaya, Thung Phaya Thai, Ratchathewi

department: Pharmacology

country: Thailand

institute: Faculty of Pharmacy, Mahidol University

summary: SARS-CoV-2 was the cause of the COVID-19 global pandemic that resulted in millions of deaths worldwide. SARS-CoV-2 infection is often accompanied by renal manifestations such as acute kidney injury and kidney fibrosis, however there is a lack of effective treatment options that also address renal involvement. In this study, golden hamsters were inoculated with Delta variant SARS- CoV-2, and given either vehicle or Andrographis paniculata (AP) standardized extract as treatment. Hamster kidney tissues were then subjected to transcriptomics, proteomics, and metabolomics analysis. Results showed that AP potentially ameliorates kidney fibrosis mediated by ECHS1-induced mTOR activation and LHX1-HDAC8 promotion. This was supported by observations of lipid metabolism alterations that may have been a result of mTOR activation in metabolomics study. Transcriptomics analysis revealed less enrichment of viral infection pathways in AP-treated groups. Overall, AP appears to attenuate SARS-CoV-2 infection and development of kidney fibrosis.

overall_design: The animal study was conducted within an AAALAC International-accredited facility and abided to ARRIVE guidelines. Briefly, 8-week old male golden hamsters were split into 5 groups, which were: 1. SARS-CoV-2- infected, orally received vehicle treatment (2 mL/kg/day dimethyl sulfoxide), and sacrificed 1 day post inoculation (Delta control day 1), 2. Delta control day 3, 3. SARS-CoV-2-infected, orally administered 1000 mg/kg/day Andrographis paniculata (AP) 95% ethanol standardized extract, and sacrificed 1 day post inoculation (Delta AP day 1), 4. Delta AP day 3, and 5. Delta AP day 7. Kidney tissue was collected during necropsy.

last: Yang

first: Nichawadee

last: Sandech

first: Sucheewin

last: Krobthong

first: Chanat

last: Aonbangkhen

first: Yodying

last: Yingchutrakul

first: Supasek

last: Kongsomros

first: Phisit

last: Khemawoot


title: Downstream-of-gene (DoG) transcripts contribute to an imbalance in the cancer cell transcriptome

city: Chicago

first: Mannan

last: Bhola

state: IL

address: 303 E Superior St

department: BMG

institute: Northwestern university

summary: In this study, we reveal insights into the biogenesis of downstream-of-gene (DoG)-containing RNAs in human cancers.

overall_design: Examination of RNAPII and TOP1, catalytically engaged TOP1-sequencing, and nascent RNA sequencing in paired COADs and non-neoplastic colon tissue, SW480, HCT116, and FHC cells. RNAPII binding and nascent RNA sequencing upon TOP1 depletion in SW480 colon cancer cells.

first: Shannon

last: Lauberth

first: Yaping

last: Lu

first: David

last: Katz

first: Guang-Yu

first: Nefertiti

last: Muhammad

first: Jessica

last: Xu

first: Pedro

last: Avila-Lopez

first: Brian

last: Maunze

first: Kouki

last: Abe


title: The Clinical and Molecular Rersponse of Pyoderma Gangrenosum to Interleukin 23 Blockade: results from a proof-of-concept open-label clinical trial

city: Liverpool

first: John

last: Frew

address: Elizabeth St

department: Dermatology

institute: Liverpool Hospital

summary: Open Label Clinical Trial

overall_design: Tissue Gene Expression Response to Interleukin 23 Blockade of skin biopsies of Pyoderma Gangrenosum at Baseline and Week 12.

first: J

middle: W


title: Expression Profiling of Heart (NH, TAC and TAC-R)

city: Saitama

first: Manabu

last: Shiraishi

address: Omiya

country: Japan

institute: Jichi Medical University

summary:
Transcriptome analysis of  RNA samples from whole heart
Transverse aortic constriction (TAC) is a well-established method for studying the pathomechanisms of heart failure in animal models of cardiac hypertrophy. A number of studies have shown that the treatment of heart failure in this animal model of cardiac hypertrophy suggests that hypertrophy and fibrosis may be reversible. However, since TAC-release protocols that improve hemodynamics by releasing physical stenosis remain undefined, the histological characteristics and molecular biological regulatory mechanisms of the reversibility of cardiac hypertrophy and fibrosis are unknown. Therefore, this study aimed to establish a TAC release model and investigate the reversibility and plasticity mechanisms of myocardial hypertrophy, fibrosis, and angiogenesis. Four weeks post-TAC surgery, TAC release was conducted by cutting the aortic stenosis sutures. The TAC group exhibited severe myocardial hypertrophy, fibrosis, and increased angiogenesis, along with diastolic dysfunction. Conversely, the TAC-release group showed reduced hypertrophy and fibrosis, and improved diastolic function. Gene expression analysis highlighted Regulator of Calcineurin 1 as a key player in cardiac function and histological changes post-TAC release. Rcan1 knockdown exacerbated myocardial hypertrophy and fibrosis in the TAC-release group. This study sheds light on the functional, structural, and histological changes in the heart induced by TAC release and elucidates some of its regulatory mechanisms.

overall_design: We analyzed whole heart  using the Affymetrix GeneChip Arrays platform with ClariomTM S Assyay, Rat platform. Array data was processed by Affymetrix  Array Computational Tool. Normal heart: Normal heart as control. TAC: TAC-subjected heart. TAC-R:  Heart released from TAC.


title: ZMAT2 condensates regulate the alternative splicing of TRIM28 to promote the proliferation of hepatocellular carcinoma cells

city: Changsha

first: Jiong

last: Li

address: No.138, Tongzipo Road

department: Department of Radiology

institute: The Third Xiangya Hospital, Central South University

summary: Dysregulation of splicing factor expression plays a crucial role in the progression of hepatocellular carcinoma (HCC). Our research found that the expression level of splicing factor ZMAT2 is increased in HCC, promoting the proliferation of hepatocellular carcinoma cells. RNA-seq data indicated that ZMAT2 regulated exon skipping of mRNA, while RIP-seq data further revealed the binding motifs of ZMAT2. A comprehensive analysis of RNA-seq and RIP-seq data indicateed that ZMAT2 plays a crucial role in the maturation process of TRIM28 mRNA. Deletion of ZMAT2 led to the deletion of 25 bases in exon 11 of TRIM28, ultimately resulting in nonsense-mediated decay (NMD). Previous studies have demonstrated a close association between TRIM28 and the proliferation of hepatocellular carcinoma. Our experiments have revealed that TRIM28 serves as a critical factor for ZMAT2 in facilitating the proliferative process of hepatocellular carcinoma. Studies have demonstrated a close correlation between the mRNA splicing process and the occurrence of phase separation. Our research discovered that ZMAT2 is capable of undergoing phase separation, resulting in the formation of liquid droplet condensates within hepatocellular carcinoma cells. Additionally, it was found that ZMAT2 is able to form protein-nucleic acid condensates with TRIM28 mRNA. In summary, we hypothesize that ZMAT2 and TRIM28 mRNA form protein-nucleic acid condensates, thereby regulating the splicing of TRIM28 mRNA. The augmented expression of ZMAT2 in hepatocellular carcinoma cells results in the upregulation of TRIM28 expression, ultimately driving the proliferation of hepatocellular carcinoma cells.

overall_design: To investigate whether ZMAT2 influences the progression of HCC via its mRNA splicing function


title: Ribosomal S6 kinase 1 regulates 'inflammaging' via the senescence secretome III.

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: Inhibition of the nutrient-responsive mTOR (mammalian target of rapamycin) signalling pathway including the key downstream S6 kinase 1 (S6K1) extends lifespan and improves healthspan in mice.  However, the underlying mechanisms contributing to the profound age-related benefits observed with loss of S6K1 signalling are unclear. Cellular senescence is a stable growth arrest accompanied by an inflammatory phenotype (termed the senescence-associated secretory phenotype, or SASP). Whileboth cellular senescence and SASP-mediated chronic inflammation contribute to age-related pathology the specific role of S6K1 signalling in these process have not been determined . Here, focussing on mouse liver a key target tissue for the beneficial health effects of loss of S6K1 signalling, we show that S6K1 deletion does not reduce senescence but ameliorates inflammation and immune cell infiltration in aged livers. Using human and mouse models of senescence, we demonstrated that reduced inflammation is a liver intrinsic effect associated with S6K deletion. Furthermore, gene expression analysis suggested that downregulated cGAS/STING and IRF3 activation might mediate the impaired SASP observed upon S6K deletion. Using a hepatic oncogene induced senescence model, we showed in vivo that S6K1 deletion results in reduced IRF3 activation, impaired production of cytokines such as IL1 and reduced immune infiltration. Overall, deletion of S6K reduces inflammation in the liver suggesting that suppression of the inflammatory SASP by S6K could contribute to explain the beneficial effects of inhibiting these pathways on healthspan and lifespan.

overall_design: Transcriptomics data from whole liver homogenates from S6K1 WT and KO mice derived from young (90 days)  and old (600 days) mice. Transcriptomics data from mouse embryonic fibroblasts undergoing replicative senescence or RAS-induced senescence derived from S6K1 WT/KO mice or S6K1/S6K2 WT/DKO mice.

first: D

last: Withers

last: Gil

first: M

last: Heikenwalder


title: Neutrophils facilitate the epicardial regenerative response after zebrafish heart injury

city: Atlanta

first: Elizabeth

middle: A

last: Peterson

state: GA

address: 1760 Haygood Dr NE

institute: Emory University

summary: Despite extensive studies on endogenous heart regeneration within the past 20 years, the players involved in initiating early regeneration events are far from clear. Here, we assessed the function of neutrophils, the first-responder cells to tissue damage, during heart regeneration. We detected rapid neutrophil mobilization to the injury site after ventricular amputation, peaking at 1-day post-amputation (dpa) and resolving by 3 dpa. Further analyses indicated neutrophil mobilization coincides with peak epicardial cell proliferation and recruited neutrophils associated with activated, expanding epicardial cells at 1 dpa. Neutrophil depletion inhibited myocardial regeneration and significantly reduced epicardial cell expansion, proliferation, and activation. To explore the molecular mechanism of neutrophils on the epicardial regenerative response, we performed scRNA-seq analysis of 1 dpa neutrophils and identified enrichment of the FGF and ERK signaling pathways. Pharmacological inhibition of FGF signaling indicated its’ requirement for epicardial cell expansion, while neutrophil depletion blocked ERK signaling activation in epicardial cells. Altogether, our studies revealed that neutrophils quickly induce epicardial cells, which later accumulate at the injury site and contribute to heart regeneration.

overall_design: Neutrophils from the zebrafish heart were isolated by fluorescence-activated cell sorting (FACS) according to the presence or absence of eGFP signal and analyzed using scRNAseq.

first: Jisheng

last: Sun

first: Jinhu

last: Wang


title: Ribosomal S6 kinase 1 regulates 'inflammaging' via the senescence secretome II.


title: Ribosomal S6 kinase 1 regulates 'inflammaging' via the senescence secretome I.


title: Engrailed transcription factors direct embryonic medial excitatory cerebellar nuclei neuron identity and survival

city: New York

first: Alexandra

middle: L.

last: Joyner

state: New York

address: 430 E 67th St

department: Developmental Biology Program

institute: Sloan Kettering Institute

summary: In the cerebellum, the excitatory neurons of the three cerebellar nuclei (eCN) form the primary output for the circuit. The medial eCN (eCNm) were recently divided into molecularly defined subdomains in the adult, however how they are established during development is not known. We define molecular subdomains of the eCNm using scRNA-seq and spatial expression analysis during embryogenesis. Our analysis shows that the eCNm are transcriptionally divergent from the rest of the eCN by E14.5. We previously showed that conditional loss of the homeobox genesEn1andEn2leads to death of a subset of embryonic eCNm. We demonstrate that loss ofEn1/2in embryonic eCNm results in cell death of a specific posterior eCNm molecular subdomain and loss of TBR2 expression in an anterior subdomain, as well as reduced synaptic gene expression. We further reveal a similar function for EN1/2 in mediating TBR2 expression, neuron differentiation and survival in the two other cerebellar excitatory neuron types. Thus, our work defines embryonic eCNm molecular diversity and reveals conserved roles for EN1/2 in the cerebellar excitatory neuron lineage.

overall_design: Atoh1-lineage neurons of the cerebellum labeled by tdTomato in control or Engrailed 1/2 knockout E14.5 embryos were isolated by FACS, and scRNA-seq using the 10X Genomics' Chromium Next GEM Single Cell 3' Reagent Kits (v3.1). Samples were then sequenced on a NovaSeq 6000.

first: Anjana

last: Krishnamurthy

first: Andrew

last: Lee

first: N

last: Bayin

first: Daniel

last: Stephen

first: Olivia

last: Nasef

first: Zhimin

last: Lao

middle: L


title: Astrocyte morphology driven improvements to OCD phenotypes

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

institute: University of California, Los Angeles

summary: We investigated the consequences of striatal astrocyte Gi-GPCR activation in the SAPAP3 KO mouse model of OCD

overall_design: 16 whole striatum tissue samples for whole tissue bulk transcriptomics. 4 mice per experimental group, 4 experimental groups: wild-type + tdT, wild-type + hM4Di, KO + tdTomato, KO + hM4Di all treated with DCZ, the agonist of hM4Di.

first: Baljit

last: Khakh

first: Joselyn

last: Soto

first: Chiranjivi

last: Neupane

first: Muskan

last: Kaur

first: Vijaya

last: Pandey

first: James

last: Wohlschlegel


title: Next-generation sequencing facilitates quantitative analysis of wild and acute renal failure mice

city: hainan

first: Yaochen

last: Cao

address: Xueyuan Road

institute: Hainan Medical University

summary: The goals of this study are to compare NGS-derived renal transcriptome profiling (RNA-seq) to microarray and to evaluate protocols for optimal high-throughput data analysis.

overall_design: Methods: Renal mRNA profiles of 21-day-old Wild and Acute renal failure mice were generated by deep sequencing, in triplicate. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.

first: Cao

last: Yaochen


title: Gene expression changes in response to microparticle treatment in mouse macrophages

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

summary: To investigate the potential molecular mechanisms of the microparticles' ability to rescue TLR4-deficient mice under Gram-negative infection, we performed RNA-seq experiments in J774A.1 mouse macrophage cell lines, under MP, LPS, and LPS+MP treatments. As expected, ~2000 genes were induced in response to LPS, and the degree of upregulation is significantly higher than down-regulation. In the presence of MP, LPS still upregulated ~1800 genes, similar to LPS treatment alone, but there were significantly more downregulated genes, indicating that MP has profound effects under LPS challenge, primarily through down-regulation of gene expression. A total of 1267 DEGs were found in the MP-treatment group, including 631 upregulated genes and 636 downregulated genes. The average fold change is much smaller than LPS and LPS+MP groups. Functional category analyses of these MP-upregulated genes revealed significant enrichment of immune-related GO terms, including response to stress, toxic substances, and homeostatic process. The results suggest that the MP upregulated the expression of ~600 genes, fine-tuning the immune profile.

overall_design: J774A.1 mouse macrophages were mock-treated (control), or treated by microparticles (MP), lipopolysaccharide (LPS), and both compounds (LPS+MP). As the major component of the outer membrane of Gram-negative bacteria, LPS triggers Toll-like receptor 4 and the innate immune response. We conducted RNA-seq with three biological replicates in each group, and identified significantly differentially expressed genes (DEGs, FDR<0.05, fold-change>2).

first: Bernhard

last: Kaltenboeck


title: Expression data from in vitro HIV-1-infected macrophages responding to two SalmonellaTyphimurium bacteria

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

summary: We used microarrays to detail the global programme of gene expression in human macrophages infected in vitro with HIV-1 or not and then subjected to contact with Salmonella Typhimurium ST313 or ST19 strains; we identified distinct classes of differentially regulated genes during this process

overall_design: Primary human macrophages from 3 different donors were infected with HIV-1ADA WT or mock-infected for 8 days. They were incubated or not (basal) with Salmonella Typhimurium (4/74 strain) or Salmonella Typhimurium (D23580 strain) during 2 h at 37°C, then lysed and RNA of each sample was analyzed with microarrays

first: Chantal

last: Deschamps

first: Audrey

last: Dumas

first: Gabrielle

last: Lê-Bury

first: Florence

last: Niedergang


title: Homeostatic SOCE prevents complex cell stress responses

city: Würzburg

first: Robert

last: Blum

address: Josef-Schneider-Str. 11

department: Department of Neurology

institute: University Hospital Würzburg

summary: We report the application of bulk RNA-seq for detection of changes in the mRNA-transcriptome of cultured primary, cortical astrocytes when homeostatic calcium fluxes are modulated. We investigated three conditions: (1) control (2) glial cells treated with thapsigargin, a blocker of the SERCA. This causes the depletion of ER calcium and induces store-operated calcium entry (SOCE). (3) Calcium-free extracellular solution. This causes an acute interruption of homeostatic calcium influx and thereby also causes ER calcium depletion. The aim was to detect immediate changes in the cellular transcriptome. Therefore, we treated the cells for just 60 min with the different conditions. The data show that about 8% (calcium-free condition) or 16% (SERCA blockade) of the whole mRNA transcriptome is changed within one hour, when homeostatic calcium fluxes are affected. Regulated are biological processes associated with cell health, differentiation, metabolism, ER stress responses, gene expression, and many more processes.

overall_design: Profiling of calcium signaling components that are changed in cultured cortical astrocytes of the mouse based on 4 biological replicates under three different conditions: control, SERCA blockade, Calcium-free solution. Cells were treated for 60 min before total RNA was prepared. We have sequenced four biological replicates.

first: Thorsten

last: Bischler


title: Gut lymphatics functionally adapt to the region they drain and are altered by helminths [BEC_LEC_NI-Sv_RNAseq]

status: Public on Jul 08 2024

first: Daria

last: Esterhazy

address: 924 E 57th Street

department: Pathology

institute: University of Chicago

summary: Tissue lymphatics are crucial for fluid homeostasis and immunosurveillance. We asked whether the lymphatics are adapted to the organ in which they reside, such as along the gut. Duodenal lymphatic capillaries (lacteals) displayed the mot discontinuous tight junction composition versus lacteals at other sites, resulting in a dependence on duodenal lacteals for rapid dietary lipid uptake. Duodenal helminths abrogated these features. RNAseq of LECs and the mucosa along the intestine revealed that LEC transcriptomes matched the functional profile of the local mucosa. Helminth infection reverses key duodenal signatures like lipid metabolism and immune activation, instead triggering lymphangiogenic and mucosal antimicrobial responses. We identified a putative VEGFR2/3 signaling gradient that may explain differences in tight junction along the small intestine at homeostasis. Inflammation-induced lymphangiogenesis and decreased fat exposure likely underlie duodenal lymphatic impermeability upon helminth infection, while microbial depletion acted additively on lymphatic restructuring. Our study provides molecular insights into lymphatic function along the intestine and stages lymphatic permeability as subject to dynamic regulation by environmental queues.

overall_design: We sought to interogate two questions: 1. Is the blood and lymphatic along the intestine transcriptionally distint between segments. 2. How does infection with the helminth S. venezeluensis impact the blood and lymphatic vasculature transcriptionally?

first: Jorden

last: Lane

first: Elida

last: Nieves-Ortiz

first: Aliia

last: Fatkhullina

first: Ornella

last: Ndatabaye

first: Terrance

last: Dermody


title: ARL4C remarkably promotes the tumorigenesis of Uveal Melanoma and may represent a potential therapeutic target

city: Shanghai

first: Man

last: Xiao

address: No.24, Lane 1400, Beijing West Road

department: Department of Clinical Laboratory

institute: Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Uveal melanoma is the most common primary intraocular neoplasm, arising from melanocytes of the choroid plexus, ciliary body, and iris of the eye. The mechanism of tumorigenesis in uveal melanoma still remains unclear, resulting in poor outcomes of systemic therapies available for the treatment of uveal melanoma. Currently, ADP-ribosylation factor-like 4C (ARL4C), an ARF-Like small GTP-binding protein, has been confirmed to be closely involved in the occurrence of various tumors, including colorectal, lung, liver, gastric and ovarian cancers as well as glioblastoma. Here, we found that ARL4C was strongly expressed in uveal melanoma cells and widely distributed in the cytosol and nucleus. The proliferation and metastasis capabilities of OCM-1 and 92-1 uveal melanoma cells were significantly decreased after ARL4C knockdown both in vitro and in vivo. Furthermore, over-expression of ARL4C in ARL4C-depleted cells can significantly rescue the abilities of proliferation and metastasis in above both cells. In addition, direct injection of ARL4C small interfering RNA (siRNA) into OCM-1 cell-derived tumors inhibited tumor growth in immunodeficient mice. Therefore, ARL4C tightly participates in tumorigenesis and might represent a novel therapeutic target to uveal melanoma. We believe that small molecule drugs targeting ARL4C could be explored and further applied to clinical therapy of uveal melanoma in years or decades to come.

overall_design: Wild type and ARL4C knockdown OCM-1 cells using lentivirus expressing shRNA were collected to investigate the function and molecular mechanism of ARL4C in the tumorigenesis of Uveal Melanoma.

first: Shaoping

last: Ji

first: Maosen

last: Dou


title: microRNA expression data of ascencding central auditory pathway from noise-induced hearing loss rat model

city: Seoul

first: Sohyeon

last: Park

state: Seoul

address: 71, Daehak-ro

department: Interdisciplinary Program in Neuroscience

institute: Seoul National University College of Natural Sciences

summary:
115 dB SPL of  noise exposure for 2 hours causes high threshold shift at day 1 and recovers rapidly at day 3.
Microarray was performed to identify up or down-regulated genes during rapid recovery of hearing.

overall_design: Cochlear Nucleus, Superior Olivary Complex, Inferior Colliculus, Auditory Cortex, Peripheral Blood were extracted at day1 and day3 after noise exposure. Total RNA was extracted to conduct microarray analysis.

first: Kwangsoo

last: Kim

first: Sunah

last: Yang

first: Moo-kyun


title: Transcriptomic analysis of neural-induced SHED cells with/without HCMV infection

city: Shenyang

first: Jingui

last: Deng

state: Liaoning

address: No.36 Sanhao Street, Heping District

department: Virus Laboratory

institute: the Affiliated Shengjing Hospital, China Medical University

summary: To study the molecular mechanism of neural differentiation disorder caused by HCMV infection.

overall_design: RNA sequencing were performed to determine the  transcriptomes of neural-induced stem cells from human exfoliated deciduous teeth (SHED) with/without human cytomegalovirus (HCMV) infection.

first: Jianming

last: Li

first: Mingyi

last: Xu

first: Yujing

last: Huang

first: Qiang

last: Ruan


title: Human papillomavirus-associated head and neck squamous cell carcinoma cells lose viability during triggered myocyte lineage differentiation

city: Bielefeld

first: Ingo

last: Todt

address: Morgenbreede 1

department: Ear, nose and throat medicine

institute: University of Bielefeld

summary: Head and neck squamous cell carcinoma (HNSCC) is a highly malignant disease, and death rates have remained at approximately 50% for decades. New tumor-targeting strategies are desperately needed, and a previous report indicated the triggered differentiation of HPV-negative HNSCC cells to confer therapeutic benefits. Using patient-derived tumor cells, we created a similar HNSCC differentiation model of HPV+ tumor cells from two patients. We observed a loss of malignant characteristics in differentiating cell culture conditions, including irregularly enlarged cell morphology, cell cycle arrest with downregulation of Ki67, and reduced cell viability. RNA-seq showed myocyte-like differentiation with upregulation of markers of myofibril assembly. Immunofluorescence staining of differentiated and undifferentiated primary HPV + HNSCC cells confirmed an upregulation of these markers and the formation of parallel actin fibers reminiscent of myoblast-lineage cells. Moreover, immunofluorescence of HPV+ tumor tissue revealed areas of cells co-expressing the identified markers of myofibril assembly, HPV surrogate marker p16, and stress-associated basal keratinocyte marker KRT17, indicating that the observed myocyte-like in vitro differentiation occurs in human tissue. We are the first to report that carcinoma cells can undergo a triggered myocyte-like differentiation, and our study suggests that the targeted differentiation of HPV+ HNSCCs might be therapeutically valuable.

overall_design: Primary head and neck squamous cell carcinoma cell cultures were established in a serum-free medium to investigate the differentiation potential of HNSCC. The cells were differentiated with a serum medium and cultured for 8 days until full differentiation was achieved. Both cultures under the control condition (PNEU) and the differentiation condition (CFM) have been analyzed using RNA-seq.

first: Sarah

last: Gendreizig

first: Felix

last: Oppel


title: Gut lymphatics functionally adapt to the region they drain and are altered by helminths [NI-Sv_5-8_dpi_Mucosa_RNAseq]

first: Daria

last: Esterhazy

overall_design: We sought to investigate two questions: 1. How is the small intestine mucosa transcriptionally distinct at each segment? 2. How does the transcriptional state of the small intestine mucosa change when S. venezeluensis reaches the duodenum (5 dpi) and upon height of S. venezeluensis infection in the duodenum (8 dpi).

first: Jorden

last: Lane

first: Elida

last: Nieves-Ortiz

first: Aliia

last: Fatkhullina

first: Ornella


title: Identification of the role of PTP1B in acute kidney injury and its regulation via siRNA delivery with milk-derived extracellular vesicles

first: Hochung

last: Jang

address: 5 Hwarang-ro 14-gil

institute: Korea Institute of Science and Technology (KIST)

summary: Acute kidney injury (AKI) is a critical condition marked by a sudden decline in kidney function,  often triggered by ischemia-reperfusion (IR) injury. Its pathophysiology involves inflammation, oxidative stress, and endoplasmic reticulum (ER) stress. Recently, protein tyrosine phosphatase 1B (PTP1B) has been highlighted as a therapeutic target for ischemic disease due to its potential implication in activating ER stress. In this study, we observed significant overexpression of PTP1B in human kidney tissues during AKI. Additionally, in mouse models of AKI, we confirmed that this overexpression is associated with the upregulation of ER stress and inflammatory pathways mediated by Src. To explore the effect of PTP1B inhibition in AKI, we employed PTP1B-targeting siRNA (PTPi) delivered via extracellular vesicles derived from commercial milk (mEVs). PTPi@mEVs effectively reduced PTP1B expression in proximal tubular cells, decreasing ER stress and Src kinase activation. In an IR-AKI mouse, PTPi@mEVs alleviated renal dysfunction, reduced cell death, and restored gene expression related to inflammation, ROS, and ER stress. Histological analysis confirmed that PTP1B knockdown mitigated tight junction disruption in renal tissue. These findings underscore the therapeutic potential of targeting PTP1B to mitigate AKI symptoms, highlighting the efficacy of mEVs-mediated PTPi delivery in reducing acute inflammatory responses and renal dysfunction.

overall_design: To verify the role of PTP1B in AKI, we formulated PTP1B siRNA-loaded milk-derived extracellular vesicles and administered them to AKI mouse model.


title: Biochemical characterization, biosynthesis mechanism, and functional evaluation of selenium-enriched Aspergillus oryzae A02

city: Tianjin

first: Jinyang

address: No. 32, Xiqi Road, Tianjin Airport Economic Park

institute: Chinese Academy of Sciences

summary: Selenium-enriched A. oryzae A02 was observed to primarily upregulate peroxisome activity while downregulating estrogen 2-hydroxylase activity in mice hepatocytes, suggesting its potential in fortifying antioxidant physiological functions and upholding metabolic balance.

overall_design: To assess the regulatory impact of selenium-enriched A. oryzae A02 on mice metabolism and scrutinize its potential regulatory mechanisms, we administered selenium-enriched A. oryzae A02 to mice for 8 weeks and scrutinized its effects on growth performance and liver physiological metabolism.

first: Le

last: Gao

first: Xin

last: Wu


title: A DGCR8/FLII-dominated on-off switch for immediate-early genes governs embryo implantation in mouse and human [eCLIP]

city: Beijing

first: Xuehui

last: Lv

address: No.5 Yiheyuan Road, Haidian district, Beijing, 100871, China

institute: Peking University

summary: As an essential checkpoint for successful pregnancy, mammalian embryo implantation initiates fetal-maternal communication. However, the underlying transcriptional regulation governing such a fast transition is still unknown. Here, we identify a DGCR8/FLII-dominated on-off switch for immediate-early genes (IEGs) governing pluripotency transition and morphogenesis of epiblasts upon embryo implantation. In mouse naïve embryonic stem cells (mESCs), we find the Microprocessor component DGCR8, but not DROSHA, can recognize mRNA stem-loop structures and further interact with and occupy transcriptional activator FLII to directly suppress transcription of non-miRNA target genes. Interestingly, when mESCs exit from naïve pluripotency, ERK signaling is quickly activated to induce FLII phosphorylation and disrupt DGCR8/FLII interaction. Phosphorylated FLII then binds to AP1, a typical IEG, to mediate the transcriptional activation of cell migration-related genes to establish poised pluripotency. Re-occupation of FLII by DGCR8 drives poised ESCs into formative pluripotency. Disruption of the DGCR8/FLII-mediated transcriptional activation inhibits the naïve-poised-formative ESC transition and the corresponding embryonic morphogenesis during implanting period, which is conserved in mouse and human.

overall_design: To investigate the role of DGCR8 in transcriptional repression, the global RNA-binding sites of DGCR8 were identified by sCLIP which were used to capture RBP binding sites and distinguish nascent RNAs from RBP-binding signals. Meanwhile, the global RNA-binding sites of FLII were also captured by eCLIP.

last: Lyu


title: in vitro construction of an embryonic caudal organizer

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

summary: Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods:  Single cell transcriptomes of bmp4 explants were harvested at 6 hpf, 8 hpf,10 hpf, 12 hpf, 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 (10x Genomics, Cat# PN-1000121) according to the manufacturer’s protocol for 10000 cell recovery. Results: paraxial mesoderm, lateral plate mesoderm, and their derivatives were detected in bmp4 explants, and NMP, somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well-organized caudal-like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: bmp4 injected zebrafish explants or BMP4 induced human embryoids  were harvested  for scRNA-seq.

last: Cheng

first: Yan-Yi

last: Xing

first: Ying


title: Unveiling the Role of KSHV-Infected Human Mesenchymal Stem Cells in Kaposi's Sarcoma Initiation

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: Kaposi's sarcoma (KS) may derive from Kaposi's Sarcoma Herpesvirus (KSHV)-infected human Mesenchymal Stem Cells (hMSCs) that migrate to sites characterized by inflammation and angiogenesis, promoting the initiation of KS. By analyzing the RNA sequences of KSHV-infected primary hMSCs, we have identified specific cell subpopulations, mechanisms, and conditions involved in the initial stages of KSHV-induced transformation and reprogramming of hMSCs into KS progenitor cells. Under pro-angiogenic environmental conditions, KSHV can reprogram hMSCs to exhibit gene expression profiles more similar to KS tumors, activating cell cycle progression, cytokine signaling pathways, and endothelial differentiation indicating the involvement of KSHV infection in inducing the Mesenchymal-to-Endothelial (MEndT) transition of hMSCs. This finding underscores the significance of this condition in facilitating KSHV-induced proliferation and reprogramming of hMSCs towards MEndT and closer to KS gene expression profiles, providing further evidence of these cell subpopulations as precursors of KS cells that thrive in a pro-angiogenic environment.

overall_design: To evaluate the impact of different growth conditions in KSHV infection of bone marrow-derived human Mesenchymal Stem Cells (hMSC), we infected these cells with KSHV in different environments. We performed KSHV (KSHVr.219) infection of hMSC in MEM alpha medium, basal MSC growth conditions (MSC-KSHV MEM), or KS-like pro-angiogenic conditions (MSC-KSHV KS). After 72 hours of infection (short-term infection) or after one month of infection and selection for KSHV-infected cells (long-term infection), we extracted RNA to perform a whole RNA-sequencing analysis. As controls for both time points, we included mock-infected hMSCs growing under basal MSC growth conditions (MSC MEM) and mock-infected hMSCs growing in KS-like pro-angiogenic conditions (MSC KS) to study the effects of the pro-angiogenic environment.

first: Julian

last: Naipauer

first: Ezequiel

last: Lacunza

first: Martín


title: Chromatin regulates alternative polyadenylation via the RNA polymerase II elongation rate

city: Boston

first: Zarmik

last: Moqtaderi

state: MA

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

summary: The Pol II elongation rate influences poly(A) site selection, with slow and fast Pol II derivatives causing upstream and downstream shifts, respectively, in poly(A) site utilization.  In yeast, depletion of either of the histone chaperones FACT or Spt6 causes an upstream shift of poly(A) site use that strongly resembles the poly(A) profiles of slow Pol II mutant strains. Like slow Pol II mutant strains, Spt6- and FACT-depleted cells exhibit processivity defects, indicating that both Spt6 and FACT stimulate the Pol II elongation rate.  Poly(A) profiles of some genes show atypical downstream shifts; this subset of genes overlaps well for FACT- or Spt6- depleted strains, but it is different from the atypical genes in Pol II speed mutant strains.  In contrast, depletion of histone H3 or H4 causes a downstream shift of poly(A) sites for most genes, indicating that nucleosomes inhibit the Pol II elongation rate in vivo.  Thus, chromatin-based control of the Pol II elongation rate is a potential mechanism, distinct from direct effects on the cleavage/polyadenylation machinery, to regulate alternative polyadenylation in response to genetic or environmental changes.

overall_design: 3' READS to obtain mRNA 3'-isoform-specific sequence data for determining cleavage/polyadenylation site preferences transcriptome-wide in mutant and shutoff yeast strains.

first: Joseph

middle: V

last: Geisberg

first: Kevin

last: Struhl


title: A DGCR8/FLII-dominated on-off switch for immediate-early genes governs embryo implantation in mouse and human [smallRNA-seq]

overall_design: To investigate the role of DGCR8 overexpression in miRNA biogenesis, we overexpressed DGCR8 protein during EB differentiation. Next, the samples in EB-Day0/1/2/4 were used to perform miRNA expression profiling analysis from small RNA-seq.


title: A DGCR8/FLII-dominated on-off switch for immediate-early genes governs embryo implantation in mouse and human [RNA-seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Re-analysis of GSM1679300 (ie, Dicer-/- mESC, Rep3).


title: A DGCR8/FLII-dominated on-off switch for immediate-early genes governs embryo implantation in mouse and human [Cut&Tag]

overall_design: To investigate the role of FLII/AP1/DGCR8 in FLII/JUN-mediated gene activation, we performed cut&tag assay of JUN/RNAPII/H3K27ac in different cells including FLII knockout or FLII/JUN overexpression cells during naïve-poised transition and DF-dKO naïve mESC with coexpression of FLII phosphorylation mutants and DGCR8.


title: ATACseq of TNBC cell lines treated with EZH2i (tazemetostat) and/or AKTi (ipatasertib)

first: Simon

last: Knott

address: 8687 Melrose Ave.

institute: Cedars Sinai

summary: Triple negative breast cancer (TNBC) is the most aggressive breast cancer subtype and has the highest rate of recurrence1. The predominant standard of care for advanced TNBC is systemic chemotherapy with or without immunotherapy, however responses are typically short-lived1,2. Thus, there is an urgent need to develop more effective treatments. PI3K pathway components represent plausible therapeutic targets, as approximately 70% of TNBCs have PIK3CA/AKT1/PTEN alterations3–6. However, unlike hormone receptor-positive tumors, it is still unclear if or how PI3K pathway inhibitors will be effective in triple-negative disease7. Here we identify a promising AKT inhibitor-based therapeutic combination for TNBC. Specifically, we show that AKT inhibitors potently synergize with agents that suppress the histone methyltransferase, EZH2, and promote robust tumor regression in multiple TNBC models in vivo. AKT and EZH2 inhibitors exert these effects by first cooperatively driving basal-like TNBC cells into a more differentiated, luminal-like state, which cannot be effectively induced by either agent alone. Once differentiated, these agents kill TNBCs by hijacking signals that normally drive mammary gland involution. Finally, using machine learning approach, we developed a classifier that can be used for patient selection. Together these findings identify a promising therapeutic strategy for this highly aggressive tumor type and illustrate how deregulated epigenetic enzymes can insulate tumors from oncogenic vulnerabilities. These studies also reveal how developmental tissue-specific cell death pathways may be co-opted for therapeutic benefit.

overall_design: TNBC cell lines were treated EZH2i (5 uM tazemetostat), AKTi (5 uM ipatasertib) or EZH2i+AKTi.  On day -5, MDA-MB-468 cells were seeded at 40% confluency and treated with 5uM tazemetostat or DMSO. On day -3, cells were passaged again at 40% confluency and maintained in DMSO or tazemetostat. On day -1, cells were seeded into 6cm plates at 250,000 cells per plate and maintained in DMSO or tazemetostat. On day 0, cells were treated in media containing 2% FBS with AKTi (ipatasertib) and/or EZH2i (tazemetostat). Cells were collected at 24 hours, cells were isolated and then prepared for ATACseq.


title: Age, Sex and Alzheimer’s disease: a longitudinal study of 3xTg-AD mice reveals sex-specific disease trajectories and inflammatory responses mirrored in postmortem brains from Alzheimer’s patients

city: Lebanon

first: Arti

last: Gaur

state: NH

address: 1 Medical Center Dr

department: Neurology

institute: Dartmouth-Hitchcock Medical Center

summary: Aging and sex are major risk factors for developing late-onset Alzheimer’s disease. Compared to men, women are not only nearly twice as likely to develop Alzheimer’s, but they also experience worse neuropathological burden and cognitive decline despite living longer with the disease. It remains unclear how and when sex differences in biological aging emerge and contribute to Alzheimer’s disease pathogenesis. We hypothesized that these differences lead to distinct molecular Alzheimer’s disease signatures in males and females, which could be harnessed for therapeutic and biomarker development. We aged male and female, 3xTg-AD and B6129 control mice across their respective lifespans while longitudinally collecting brain samples. We conducted RNA sequencing analysis on bulk brain tissue and examined differentially expressed genes between 3xTg-AD and B6129 samples and across ages in each sex. 3xTg-AD males experienced an accelerated upregulation of immune-related gene expression in the brain relative to females, especially in genes involved in complement system activation, suggesting distinct inflammatory disease trajectories between the sexes. Our data demonstrate that chronic inflammation and complement activation are associated with increased mortality, revealing that age-related changes in immune response act as a primary driver of sex differences in Alzheimer’s disease trajectories.

overall_design: To examine molecular changes throughout disease progression, we collected brain tissue from male and female, 3xTg-AD and B6129 control mice, between the ages of 6- and 24-months-old.

first: Alicia

last: Barber


title: Regulation mechanism  of POX08340 and POX01907 in  Penicillium oxalicum HP7-1 at the transcriptional level

city: Nanning

first: shen

last: xin

address: Daxue Road

institute: College of Life Science and Technology, Guangxi University

summary: In order to studing molecular mechanism of  Raw Starch Digesting Glucoamylase production in Penicillium oxalicum ,we deleted POX01907 and POX08340  and analyzed the co-expression network of POX08340 and POX01907 at transcriptional level.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of  at 24h after tansfer to the enzyme production medium with raw starch (the only carbon source).

last: Shen

first: Xue

last: Liang

first: Shuai

last: Zhao


title: Interferon subverts an AHR-JUN axis to promote CXCL13+ T cells in lupus [JUN IFN]

city: Chicago

first: Calvin

last: Law

address: 303 E Superior St Lurie 5-220

institute: Northwestern University

summary: SLE is prototypical autoimmune disease driven by pathologic T cell-B cell interactions. Expansion of B cell-helper T cells including T follicular helper (Tfh) and T peripheral helper (Tph) cells is a prominent feature of systemic lupus erythematosus (SLE). Human Tfh and Tph cells characteristically produce high levels of the B cell chemoattractant CXCL13 yet regulation of T cell CXCL13 production and the relationship between CXCL13+ T cells and other T cell states remains unclear. Here, we identify an imbalance in CD4 T cell phenotypes in SLE patients, with expansion of PD-1+/ICOS+ CXCL13+ T cells and reduction of CD96hi IL-22+ T cells. Using CRISPR screens, we identify the aryl hydrocarbon receptor (AHR) as a potent negative regulator of CXCL13 production by human CD4 T cells. Transcriptomic, epigenetic, and functional studies demonstrate that AHR coordinates with AP-1 family member JUN to prevent CXCL13+ Tph/Tfh cell differentiation and promote an IL-22+ phenotype. Type I interferon (IFN), a pathogenic driver of SLE, opposes AHR and JUN to promote T cell production of CXCL13. These results place CXCL13+ Tph/Tfh cells on a polarization axis opposite from Th22 cells and reveal AHR, JUN, and IFN as key regulators of these divergent T cell states.

overall_design: Primary human CD4+ memory T cells were stimulated with CD3/CD28 dynabeads with  either PBS or IFN-alpha (1000U/mL) for 72 hours.

first: Jaehyuk

last: Choi

first: Deepak

last: Rao


first: Di

last: Tian

address: DaXue east road

institute: College of Life Science and Technology,GuangXi university

first: Yuanni

last: Ning


title: Increased RNA and protein degradation is required for counteracting transcriptional burden and proteotoxic stress in human aneuploid cells

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

institute: Istituto Italiano di Tecnologia

summary: Aneuploidy, an abnormal chromosome composition, results in a stoichiometric imbalance of protein complexes, which jeopardizes the fitness of aneuploid cells. Aneuploid cells thus need to compensate for the imbalanced DNA levels by regulating their RNA and protein levels, a phenomenon known as dosage compensation. However, the molecular mechanisms involved in dosage compensation in human cells – and whether they can be targeted to selectively kill aneuploid cancer cells – remain unknown. Here, we addressed this question via molecular dissection of multiple diploid vs. aneuploid cell models. Using genomic and functional profiling of a novel isogenic system of RPE1-hTERT cells with various degrees of aneuploidy, we found that aneuploid cells cope with both transcriptional burden and proteotoxic stress. At the mRNA level, aneuploid cells increased RNA synthesis, but concomitantly elevated several RNA degradation pathways, in particular the nonsense-mediated decay (NMD) and the microRNA-mediated mRNA silencing pathways. Consequently, aneuploid cells were more sensitive to the genetic or chemical perturbation of several key components of these RNA degradation pathways. At the protein level, aneuploid cells experienced proteotoxic stress, resulting in reduced translation and increased protein degradation, rendering them more sensitive to proteasome inhibition. These findings were recapitulated across hundreds of human cancer cell lines and primary tumors, confirming that both non-transformed and transformed cells alter their RNA and protein metabolism in order to adapt to the aneuploid state. Our results reveal that aneuploid cells are dependent on the over- or under-activation of several nodes along the gene expression process, identifying these pathways as clinically-actionable vulnerabilities of aneuploid cells.

overall_design: miRNA profiling of aneuploid cells compared to diploid counterpart

first: Marica

last: Rosaria Ippolito

first: Johanna

last: Zerbib

first: Yonatan

last: Eliezer

first: Eli

last: Reuveni

first: Sonia

last: Viganò

first: Giuseppina

last: De Feudis

first: Anouk

last: Savir Kadmon

first: Ilaria

last: Vigorito

first: Sara

last: Martin

first: Kathrin

last: Laue

first: Yael

last: Cohen-Sharir

first: Carmela

last: Rubolino

first: Simone

last: Scorzoni

first: Francisca

last: Vazquez

first: Stefano

last: Santaguida

first: Uri

last: Ben-David

first: Ottavio

last: Croci