title: Differential gene expression induced by combined docetaxel and darolutamide in prostate cancer xenografts

city: Rotterdam

first: Stefan

last: Buck

address: Dr Molewaterplein 40

country: Netherlands

institute: Erasmus MC

summary: A total of 64 NMRI nu/nu male mice (Janvier, Le Genest Saint Isle, France) were divided in four equal groups that underwent subcutaneous implantation of tumor fragments of PC346C, PC2400, PC2416 or PC2416-DEC. Tumor volume was measured twice weekly by calipers. At a tumor volume of 300 mm3, mice were randomized 1 to 1 to receive docetaxel once (33 mg/kg bodyweight, i.v.) and darolutamide q.d. (200 mg/kg bodyweight, p.o.) or both vehicles (5% glucose/EtOH/Polysorbate 80 8:1:1 (v/v/v) i.v. and PEG400/propylene glycol/5% glucose 5:3:2 (v/v/v) p.o., respectively) until tumor volume exceeded 1500 mm3 or for maximal 60 days, at which tumors were harvested and frozen. Drug dosages were based on a previously conducted safety experiment. One mouse was excluded from the analysis due to attrition.

overall_design: 63 samples of 4 PDX. Per PDX 7 or 8 treated with docetaxel + darolutamide and 8 ctrls

first: Wesley

last: van de Geer

first: Corrina

last: de Ridder

first: Debra

last: Stuurman

first: Stijn

last: Koolen

first: Harmen

middle: J

last: van de Werken

first: Ronald

last: de Wit

first: Ron

middle: H

last: Mathijssen

first: Elena

middle: S

last: Martens-Uzunova

first: Wytske

last: van Weerden


title: Joint transcriptional disruption of Ret and Ednrb drives cell fate reversal in the Enteric Nervous System in Hirschsprung disease  [scRNA-Seq]

status: Public on Apr 01 2025

city: New York

first: Ryan

middle: D

last: Fine

state: NY

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

country: USA

institute: NYU Langone

type: Expression profiling by high throughput sequencing

summary: Despite extensive genetic heterogeneity, 72% of pathogenic alleles for Hirschsprung disease (HSCR) arise from coding and regulatory variants in genes of the RET and EDNRB gene regulatory network (GRN) in the enteric nervous system (ENS). Reduced signaling of these two receptors below a threshold in enteric neural crest-derived cells (ENCDCs) leads to a molecular tipping point at which otherwise lesser cellular defects result in aganglionosis. To elucidate the mechanisms leading to enteric neuronal loss from these genetic defects, we generated four strains of mice carrying reduced function alleles at Ret or Ednrb or both, along with their wildtype alleles. ENS tissue- and single-cell gene expression profiling of the developing and postnatal gastrointestinal tract in five mouse models, with various combinations of mutant alleles, revealed 3 major insights: (i) Ret and Ednrb deficiency, rather than complete loss, is sufficient to induce HSCR, (ii) Ret and Ednrb demonstrate strong trans interactions, and (iii) disruption of this interaction leads to cellular fate changes to compensate for neuronal loss. This study of targeted mouse models of a multifactorial disorder reveals how increasing dosage of genetic defects within a GRN leads to quantifiably increasing dysregulation from genotype to gene expression to cellular identity to function. Importantly, our studies establish that aganglionosis results only with severely reduced gene expression at both receptor genes and their consequent disruption of normal and compensatory cell fate trajectories.

overall_design: We performed single cell RNA-Seq analysis on 2 WT, 2 Ednrb-s/s, and 2 Ret-CFP/+ Ednrb-s/s intestinal samples at E14.5. This series contains additional technical sequencing replicates for some samples to increase read depth. We also uploaded rds files corresponding to figures in the paper.

first: Rebecca

last: Chubaryov

first: Mingzhao

last: Fu

first: Gabriel

last: Grullon

first: Aravinda

last: Chakravarti


title: Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations.

city: London

first: Luca

last: Biasco

address: 30 Guilford St, Holborn

country: United Kingdom

institute: UCL

summary: Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction.

overall_design: In order to evaluate the extent of phenotypic correction of microglia in the brain, spleen focus forming virus (SFFV) promoter driven lentiviral vectors SFFV.GILT or SFFV.GAAco vector were used to transduce Lin- cells, which were subsequently infused in Busulfex-treated mice.At 32-weeks after infusion, FACS-sorted CD45+CD11b+CXCR3+ microglia cells from the brain of the GILT vs GAAco treated groups (2 mice per group, 2 samples per mouse) were analyzed by single-cell(sc)RNA-seq (10x genomics). We wanted to formally confirm that the cells isolated from the GILT mice carried a transcriptional profile more similar to normal microglia when compared to the GAAco group, as a result of a more efficient genetic correction driven by the GILT-vector. To this aim, we also analyzed by scRNA-seq the microglia isolated from untreated wild type (WT) C57BL/6 mixed background control mice or Pompe mice (2 mice per group).


title: Transcriptome of human dermal endothelial cells treated with control or RAPTOR siRNA

city: Houston

first: Tu N

last: Tran

state: Texas

address: 6670 Bertner Ave,

department: Cardiovascular

institute: Houston Methodist Research Institute

summary: Cultured human dermal endothelial cells were transfected with control or RAPTOR siRNA. RNA was exacted and assessed by RNA-seq.

overall_design: We have two experimental groups: control siRNA and RAPTOR siRNA. We prepared three replicates in each group.

first: Fei

last: Han

first: Weiqing

last: Chen

first: Guangyu

last: Wang

first: Pengchun

last: Yu


title: The intestinal clock controls host’s metabolic response to diet by driving intestinal metabolic functions and the fiber-dependent microbiome

city: Freising

first: Marjolein

last: Heddes

address: Gregor mendel str 2

country: Germany

institute: TUM

summary: Investigating the function of intestinal Bmal1 in regulating the rhythmic jejunal transcriptome

overall_design: We performed gene expression analyses obtained from jejunal tissues at 6 timpeoints over the 24-h day (in constant darkness)

first: Yunhui

last: Niu

first: Kinga

last: Balázs


title: Spatial transcriptome of developmental mouse brain reveals temporal dynamics of gene expressions and heterogeneity of the claustrum

city: Tokyo

first: Yuichiro

last: Hara

address: 2-1-6 Kamikitazawa, Setagaya-ku

department: Research Center for Genome & Medical Sciences

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

summary: We performed a spatial transcriptome analysis of developing mouse brains to identify novel markers for cerebrum substructure and to investigate the spatiotemporal regulation of gene expression during development.

overall_design: Coronal sections of forebrain in two stages of developing ICR mice (E17 and P0) were subject to spatial transcriptome analysis with the 10x Genomics Visium platform. The libraries were sequenced by the Illumina HiSeqX platform with 150-nt paired-end reads.

first: Takuma

last: Kumamoto

first: Naoko

last: Yoshizawa-Sugata

first: Hideya

last: Kawaji

first: Chiaki

last: Ohtaka-Maruyama


title: Evaluating levels of Vaccinia viral mRNA translation

city: Ottawa

first: Adrian

last: Pelin

state: Ontario

address: 501 Smyth Rd.

country: Canada

institute: Ottawa Hospital Research Institute

summary: We have sequenced polysome enriched mRNA to determine levels of viral transcript translation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data enriched for polysomes in Vaccinia infected cells.

first: Taha

last: Azad


title: Dual phosphorylation of DISC1 at Ser58 and Ser713 regulates polarization of cortical neurons via GSK3β

city: Beijing

first: Lin

last: Yuan

address: You'anmenwai,Fengtai District

country: China

institute: Capital Medical University

summary: Disrupted-In-Schizophrenia 1 (DISC1), a susceptibility gene for major psychiatric disorders, encodes a scaffold protein that has complex impacts on neuronal development. However, its role in neuronal polarization remains unclear. Here we show that phosphorylation of DISC1 at Ser58 and Ser713 regulates cortical neuron polarization¬. Expression of phosphor-dead human DISC1 (Ser58Ala, Ser713Ala; hDISC1AA) delays the transition from multipolar to uni/bipolar cells in mouse cortical culture. Mice carrying the hDISC1AA mutant exhibit aberrant orientation of the axon initial segment and reduced thickness of corpus callosum. hDISC1AA knock-in mice exhibit hyperlocomotion activity in an open field, deficits in prepulse inhibition, reduced social interaction, and defective novel object recognition. GSK3β activity is increased in the cortices of the hDISC1AA knock-in mice. Embryonic treatment of the GSK3β inhibitor SB-216763 rescues behavioral deficits in hDISC1AA/+ mice. Our findings support a model in which dual phosphorylation of DISC1 at Ser58 and Ser713 inhibits GSK3β activity and plays a crucial role in neural polarization, potentially contributing to the manifestation of psychiatric disorders related to DISC1 dysfunction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from the PFC of WT and hDISC1AA/+ mice (8-week-old, C57)

first: Jun

last: Ren

first: Yiliang

last: Xu

first: Tian

last: Zhao

first: Qian

last: Chu

first: Jing

last: Tian

first: Haihong

last: Ye


title: Effect of Chaetocin on gene expression in C. elegans

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

summary: To identify transcriptome changes caused by chaetocin

overall_design: Young adult N2 wild type C. elegans were exposed to 25 µM chaetocin or DMSO vehicle control for 5 h in NGM buffer before total RNA isolation.


title: The transcriptional role of TG2-mediated H3Q5ser in CRC [RNA-seq]

city: Shenyang

first: Wanhua

last: Xie

address: Huanghe North Street 146

institute: Shenyang Medical college

summary: We investigated the alteration of H3Q5ser upon RNF40-depleted or TG2-depleted HCT116 cells.

overall_design: mRNA profiles of HCT116 cells following RNF40 or TG2 depeltion. The mRNA-seqencing was performed  in triplicate including the following conditions: siControl, siRNF40, and siTG2

first: Xie

last: Wanhua


title: Spatial and single cell transcriptomics reveals cellular crosstalk changes in ileal Crohn’s disease during inflammation

city: Atlanta

first: Subra

last: Kugathasan

state: GA

address: 1760 Haygood Dr

department: Pediatrics

institute: Emory University

summary: Crohn’s disease is a lifelong disease with no cure that requires a better characterization of the cellular milieu and behavior that drives disease progression if more targeted therapies are to be developed. Our work  with spatial and single cell transcriptomics adds new knowledge and gives spatial context to the cellular behavior and communication occurring within the intestinal mucosa during Crohn’s disease and how it is affected by inflammation.

overall_design: Ileal mucosal biopsies and Ileal surgical tissue from CD patients were used for single cell and spatial Transcriptomic analysis respectively

first: Kolachala

last: Vasantha L

first: Maddipatia

last: Sushma Chowdary

first: Murthy

last: Shanta

first: Dodd

last: Anne

first: Pelia

last: Ranjit Singh

first: Venkateswaran

last: Suresh

first: Anbazhagan

last: Murugadas

first: Jhita

last: Navdeep

first: Joshi

last: Gaurav N

first: Yin

last: Hong

first: Lopez

last: Chrissy A

first: Geem

last: Duke

first: Cutler

last: David J

first: Qiu

last: Peng

first: Matthews

last: Jason D

first: Kugathasan

last: Subra


title: Development of cell therapy against CKD using functionally enhanced hiPSC-derived nephron progenitor cells (hiPSC-NPCs)

city: Kyoto

first: Takeya

last: Otsuki

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Application, Kyoto University.

summary: we identified the differentially expressed genes (DEGs) in hiPSC-NPCs exposed to conditioned media from hiPSC-NPCs transfected with hepatocyte growth factor (HGF-NPCs) by transcriptome analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hiPSC-NPCs cultured in conditioned medium from hiPSC-NPCs and  conditioned medium from HGF-NPCs

first: Yu

last: Hatano

first: Kosuke

last: Toyohara

first: Kenji

last: Osafune


title: Influence of quorum sensing on Klebsiella pneumoniae outer membrane vesicles

city: wenzhou

first: Changrui

last: Qian

state: zhejiang

address: wenzhou medical university

institute: wenzhou medical university

summary:
Purpose: The purpose of this study was to investigate the effect of quorum sensing-related luxS gene on the transcription level of Klebsiella pneumoniae FK6768.
Methods: We constructed the luxS gene knockout strain of FK6768 and its complement strain, and performed transcriptome sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FK6768 strain,  luxS gene knockout strain (FK6768-ΔluxS) and corresponding  complement strain (FK6768-ΔluxS-pluxS).

first: Tieli

last: Zhou


title: The transcriptional role of TG2-mediated H3Q5ser in CRC

first: Wanhua

last: Xie

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Development of cell therapy against CKD using functionally enhanced hiPSC-derived nephron progenitor cells(hiPSC-NPCs)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hiPSC-NPCs cultured in conditioned medium from hiPSC-NPCs,  conditioned medium from HGF-NPCs and conditioned medium from HGF-NPCs with anti-HGF


title: The transcriptional role of TG2-mediated H3Q5ser in CRC [ChIP-seq]

summary: We investigated the alteration of H2Bub1, H3K4me3, and H3Q5ser upon RNF40-depleted or TG2-depleted HCT116 cells.

first: Xie

last: Wanhua


title: Brain changes in responses of mice to intracerebral hemorrhage at the acute stages

city: Changsha

first: En

last: Hu

state: Hunan

address: Kaifu Street, Xiangya Road No.87

department: Xiangya Hospital

institute: Central South university

summary: To investigate the brain changes in responses of mice to intracerebral hemorrhage at the acute stages, we performed gene expression profiling analysis using data obtained from RNA-seq of 6 ICH mice and 6 sham operated controls on day 3.

overall_design: Comparative brain gene expression profiling analysis of RNA-seq data for ICH mice and sham operated controls on day 3

first: Tao

last: Tang

first: Yang

last: Wang

first: Teng

last: Li


title: Mouse heart analysis of Txnip PPXY motif mutated to AAXA

city: NY

first: Yoshinobu

last: Nakayama

address: 160 Convent Ave

institute: City College of New York

summary: Cardiomyocyte specific knock in mouse heart with Txnip PPXY motif mutated to AAXA

overall_design: Wild-type mouse hearts versus Knock-in mouse hearts (n=3 each) The control wild-type hearts are the identical as GSE166252.

first: Jun

last: Yoshioka


title: Dmrt1 regulates mouse expanded potency and facilitates the breaking of embryonic lineage barrier [ChIP-Seq]

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: ChIP-seq for ES, 2iLIF, EPSC; Histone ChIP-seq was performed in E14 cells cultured in ES, 2iLIF and EPSCM

overall_design: Detect the genome region bind by active histone marks

first: Z

last: Zheng

first: Y

middle: Y

first: H

last: Loh


title: Function of LPIN1 in human AML and hematopoiesis

city: Kiel

first: Karin

last: Huber

state: Schleswig-Holstein

address: Arnold-Heller-Straße 3

department: Medical Clinic II

institute: UKSH Kiel

summary: LPIN1 was knocked down in  human acute myeloid leukemia cell line OCI-AML3 and in human CD34+ umbilical cord blood cells after 48 hours of prestimulation using shRNA against human LPIN1 versus shRNA against luciferase (shLuc) as control to determine gene expression changes 48 hours after lentiviral transduction.

overall_design: Transcriptome profiling of shRNA mediated LPIN1 knockdown in AML and healthy hematopoietic cells.

first: Swati

last: Garg

first: Christian

last: Arnold

first: Judith

middle: B

last: Zaugg

first: Caroline

last: Pabst


title: Transcriptomic and metabolomic regulation of temperature-dependent longevity in Drosophila melanogaster

city: Birmingham

first: Alexander

middle: Tate

last: Lasher

state: AL

address: 1300 University Blvd.

department: Biology

institute: University of Alabama at Birmingham

summary: Temperature reduction has been one of the most robust environmental manipulations used to increase lifespan in invertebrates. However, the underlying molecular mechanisms leading to temperature-mediated lifespan extension remains largely unknown. Here, we evaluate how genes and metabolites are altered in response to changes in temperature in the fruit fly, Drosophila melanogaster. Our data show that environmental temperature affects transcriptome much more than the metabolome. Intriguingly, the most affected candidate genes, the Turandot (tot) family genes, have direct effects on longevity in flies.  Specifically, knockdown of tot expression at all temperatures leads to lifespan extension in a sex-specific fashion. Overall, our results imply that individual genes, specifically, the Turandot family of genes that may play a novel role in lifespan regulation in the fruit fly.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for male and female Drosophila melanogaster whole fly body raised at 18, 24, or 28 degrees Celsius.

first: Jessica

middle: M

last: Hoffman

first: Tate

first: Steven

middle: N

last: Austad

first: Liou

last: Sun


title: Effect of pm2.5 maternal exposure on DNA methylation in the offspring myocardium

city: Fuzhou

first: Jingmin

state: Fujian

address: 18 Daoshan Road, Gulou District

department: department of gynecology

institute: Fujian Maternal and Child Health Hospital

summary: The animals were divided into two groups according to exposure of PM2.5 (particulate matter less than 2.5 µm): control group (Non-PM group) or PM exposure group (PM group).PM2.5 at 150 μg/m3were administered by intratracheal instillation during the gestation period of female rats from Day 1 of conception onwards.After the female rat gave birth,the offspring's heart DNA was extracted and anlyzed. DNA promotor methylation profile were determined.The goal was to determine the effects of PM2.5 exposure on the DNA promotor methylation patterns in heart tissue.

overall_design: 3 PM exposure group group/3 control group

first: Xinru

last: Hong


title: Effect of LAIR-1 deficiency on naïve CD8 T cells at baseline

city: Utrecht

first: Akashdip

last: Singh

address: Lundlaan 6

institute: UMC Utrecht

summary: To determine intrinsic differences after genetic ablation of LAIR-1 in naïve CD8 T cells, isolated cells were transcriptionally profiled

overall_design: Naïve CD8 T cells were isolated from wild type and LAIR-1-deficient mice

first: Saskia

last: Vijver

first: Ines

last: Pascoal Ramos

first: Linde

last: Meyaard


title: Dmrt1 regulates mouse expanded potency and facilitates the breaking of embryonic lineage barrier [ATAC-Seq]

first: Yingying

last: Zeng

summary: ATAC-seq for E14 cells cultured in ES, 2iLIF and EPSCM;ATAC-seq was performed on cells E14 cells cultured in ES, 2iLIF and EPSCM

overall_design: Chormatin accssibility were evaluated for E14 cells cultured in ES, 2iLIF and EPSCM

first: Z

first: Y

first: H

last: Li


title: Dmrt1 regulates mouse expanded potency and facilitates the breaking of embryonic lineage barrier [RNA-Seq]

summary: RNA-seq for EPSCM; Bulk RNA-seq were performed on E14 cells cultured in ES, 2iLIF and EPSCM

overall_design: Transcritional profiles of mouse embryonic stem cells stably cultured in different media were shown by RNA-seq

last: Zheng

last: Loh


title: Impact of life under hypoxia on gene expression in mice

city: Vienna

first: Clemens

last: Fürnsinn

address: Währinger Gürtel 18-20

department: Department of Medicine III

country: Austria

institute: Medical University Vienna

summary: Mountain dwellers show a lower prevalence of diabetes, which among countless other factors could be due to lower partial oxygen pressure at high altitude. The present study was to investigate in an experimental setting, if and how reduced oxygen availability affects blood glucose. For hypothesis building, tissue samples were collected from obese mice on high fat diet, which were maintained under normal air (control) or exposed to normobaric hypoxia for three months. Tissue samples were collected and subjected to RNA sequencing and bioinformatics analysis. In a subsequent series of experiments, hypoxia-induced effects on fuel metabolism as well as the mechanism mediating such effects were studied. As compared to controls, hypoxia-treated mice showed reduced blood glucose in association with improved insulin sensitivity, which was the direct consequence of an erythropoietin-mediated increase in the hematocrit.

overall_design: After 3 months on, male obese mice were fed high fat diet (60% of calories as fat). After three months, they were allocated to a hypoxia group (kept in a chamber under 10% oxygen) and a control group (kept at normal air and fed restrictedly so to obtain a mean weight curve as similar as possible to the curve of their hypoxia-exposed counterparts). After another three months, tissue samples were collected approximately 4 h after opening the hypoxia chamber.

first: Thomas

last: Scherer

first: Martin

last: Bilban


title: The miR-15a/16-1 and miR-15b/16-2 clusters regulate early B cell development by limiting IL-7 receptor expression II

city: Innsbruck

first: Sebastian

last: Herzog

address: Innrain 80-82

department: Institute of Developmental Immunology

institute: Medical University of Innsbruck, Biocenter

summary: Pleiotropic functions of miRNAs as transcriptional repressors have been reported for multiple biological processes. One prominent miRNA family is the miR-15 family, which is a well-established tumor-suppressor in B-cell chronic lymphocytic leukemia (CLL). The miR-15 family consists of three bicistronic clusters, miR-15a/16-1, miR-15b/16-2 and miR-497/195, all sharing the same seed sequence suggesting that loss one cluster can be functionally compensated by the remaining miR-15 family members. Thus, a combined deletion may be necessary to reveal its physiological function in vivo. A combined knockout of the most prominent miR-15 clusters, miR-15a/16-1 and miR-15b/16-2 in the hematopoietic system reveals a novel role of the miR-15 family in early B cell development highlighted by an increase of the pro-B cell compartment. Mechanistically, this effect is mediated by enhanced IL-7 receptor expression, which we identified as direct miR-15 target gene. Notably, elevated IL-7 receptor levels were sufficient to trigger increased activation of the STAT5 and PI3K/AKT pathways. Moreover, derepression of directly targeted cell cycle regulators such as Ccne1, Chek1 and Wee1 further facilitates G-to-S transition. Thus, by deregulating a target gene network of cell cycle and signaling mediators, loss of the miR-15 family establishes a pro-proliferative milieu manifesting in an enlarged pro-B cell pool.

overall_design: RNA sequencing data of FACS-sorted pro-B cells of 4 miR-15a/b+/+ Vav-Cre mice (controls) and 4 miR-15a/bfl/fl Vav-Cre mice.

first: Katharina

last: Hutter

last: Rülicke

first: Lill

last: Andersen

first: Tamas

middle: G

last: Szabo

first: Andreas

last: Villunger


title: Joint transcriptional disruption of Ret and Ednrb drives cell fate reversal in the Enteric Nervous System in Hirschsprung disease  [bulkRNA-seq]

city: New York

first: Ryan

last: Fine

address: 435 E 30th Street

institute: NYU Langone

summary: Despite extensive genetic heterogeneity, 72% of pathogenic alleles for Hirschsprung disease (HSCR) arise from coding and regulatory variants in genes of the RET and EDNRB gene regulatory network (GRN) in the enteric nervous system (ENS). Reduced signaling of these two receptors below a threshold in enteric neural crest-derived cells (ENCDCs) leads to a molecular tipping point at which otherwise lesser cellular defects result in aganglionosis. To elucidate the mechanisms leading to enteric neuronal loss from these genetic defects, we generated four strains of mice carrying reduced function alleles at Ret or Ednrb or both, along with their wildtype alleles. ENS tissue- and single-cell gene expression profiling of the developing and postnatal gastrointestinal tract in five mouse models, with various combinations of mutant alleles, revealed 3 major insights: (i) Ret and Ednrb deficiency, rather than complete loss, is sufficient to induce HSCR, (ii) Ret and Ednrb demonstrate strong trans interactions, and (iii) disruption of this interaction leads to cellular fate changes to compensate for neuronal loss. This study of targeted mouse models of a multifactorial disorder reveals how increasing dosage of genetic defects within a GRN leads to quantifiably increasing dysregulation from genotype to gene expression to cellular identity to function. Importantly, our studies establish that aganglionosis results only with severely reduced gene expression at both receptor genes and their consequent disruption of normal and compensatory cell fate trajectories.

overall_design: We performed bulk-RNA-seq gene expression analysis of mouse intestine at E14.5 and P0 timepoints and both sexes. All assays were performed in biological triplicate.

first: Rebecca

last: Chubaryov

first: Mingzhou

last: Fu

first: Gabriel

last: Grullon

first: Aravinda

last: Chakravarti


title: mRNA profiling on CART19 produced from normal donors treated with vecabrutinib

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

department: Hematology Research

institute: Mayo Clinic

summary: RNA sequencing was performed on three biological replicates of 1) CART19 + vehicle, 2) CART19 + 1 uM vecabrutinib, 3) CART19 + 10 uM vecabrutinib.

overall_design: T cells from normal donors were transduced with a replication-incompetent lentiviral vector expressing a second-generation chimeric antigen receptor (CAR) consisting of an anti-CD19 single chain variable fragment (FMC63) fused to 4-1BB and CD3ζ intracellular domains as previously described.  CART19 were activated for 72 hours in the presence of vehicle, 1 uM vecabrutinib, or 10 uM vecabrutinib prior to isolating RNA.

first: Claudia

last: Manriquez Roman

first: Mohamad

last: Adada

first: Michelle

last: Cox


title: Transcriptome responses of benthic microbial communities after chronic and/or acute exposure to diuron

city: Villeurbanne

first: Philippe

last: Veber

address: 16 rue Raphael Dubois

country: France

institute: CNRS

summary: This experiment aimed to understand stress responses of microbial communities differing in chronic exposure to the photosynthesis inhibitor diuron, combining untargeted metatranscriptomics (RNA-seq) and dose-response design. First, river microbial communities were incubated for 5-weeks in microcosms 1/ under constant exposure to 4µg/L of diuron (stressed community) or 2/ without contamination (non-stressed community). Then, both communities were exposed for 1 hour to a gradient of diuron concentrations to investigate differences in stress responses after chronic exposure. This experimental design enabled the determination of contig response trends as well as sensitivity thresholds.

overall_design: Aquatic microbial communities were sampled in a nearby river and then, shared in two groups. One group grown for 5 weeks under 4µg/L of diuron (stressed-community, chronic expoure) while the second group was not exposed to diuron (non-stressed community). Then, the two groups were exposed for one hour to a gradient of 9 diuron concentration (dose-response design) in duplicate such as: 0, 10-4, 10-3, 10-2, 10-1, 1, 10, 50, 100 µg/L).

first: Floriane

last: Larras

first: Stefan

last: Lips

last: Schreiber

first: Elise

last: Billoir

first: Marie-Laure

last: Delignette-Muller

first: Mechthild

last: Schmitt-Jansen


title: Liver tissue RNA-seq of costunolide (COS) on APAP induced liver injury

city: Wenzhou

first: meihong

last: wang

state: Zhejiang

address: Central North Road

institute: Wenzhou Medical University

summary: To elucidate the potential mechanism of COS inhibiting hepatocyte death, RNA-seq technology was employed to compare the gene expression profiles of liver tissues from CON group mice, APAP group mice, and 20 mg/kg COS treatment mice.

overall_design: The effect of COS on APAP induced liver injury

first: Zhongxiang

last: Xiao

first: Yali

last: Zhang

first: Meihong

last: Wang


title: Genome-wide analysis of long noncoding RNA expression profile in gastric cancer peritoneal metastasis

city: Wuhan

first: Sihao

last: Huang

address: Donghu Road 169

institute: Gastric cancer peritoneal metastasis Tissue

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

summary: Gastric cancer (GC) remains one of the most prevalent tumor worldwide, and ranks third in cancer-related deaths globally. Long non-coding RNAs (lncRNAs) have been reported to play significant role in the progression and metastasis in gastric cancer (GC), however, the molecular mechanism are largely elusive. We aim to identify up-regulated lncRNA in gastric cancer peritoneal metastasis and study their function in promoting tumor progression and metastasis.

overall_design: Microarray expression profiling of mRNAs and lncRNAs were conducted using RNA extracted from three peritoneal metastasis samples and  gastric cancer samples.

first: Jialin

last: Song

first: Yan

last: Fang

first: Lei

last: Han

first: Zaihuan

last: Lin

first: Rongzhang

last: Dou

first: Panyi

last: Zhong

first: Chaogang

last: Yang

first: Zhenxian

last: Xiang

first: Jinseng

last: Zhen

first: Xinyao

first: Shuyi

first: Bin

last: Xiong


title: Heterogeneity of neutrophils in tissues

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

summary: To identify transcriptional diversity of neutrophils in steady state we performed single cell sequencing analysis on 13033 individual neutrophils across 6 different body compartments (bone marrow, blood, spleen, lung, liver and intestine). Dimensional reduction analysis identified unprecedented heterogeneity of the mature neutrophil compartment in healthy mice. Maturation state and tissue origin were both highly associated with neutrophil diversity. Moreover, we found that transcriptional profiles of discrete neutrophil clusters were enriched in genes associated with specific functions or disease states, These results identified preexisting heterogeneity in neutrophils under steady state and suggest that a wide array of ready-to-use functional programs regulate neutrophil function both in health and disease.

overall_design: For single cell analysis of neutrophils, 8 weeks old and 20 months old C57BL6 mice were sacrificed, the lung, liver, spleen and intestine were dissected and dissociated into a single-cell suspension by enzyme digestion. Blood and bone marrow were colected either from the heart of from the femur. Cell strainer-filtered single-cell solution were sorted in BD Aria Cell Sorter as DAPI-CD11b+Ly6G+ cells and loaded into a BD Rhapsody cartridge. For the generation of single-cell whole-transcriptomes we used a BD Rhapsody system according to manufacture instructions. The experiment was perfromed twice and samples were multiplexed and loaded in two different BD cartridges for single cell library generation,

first: Iván

last: Ballesteros

first: Andrea

last: Rubio-Ponce


title: Immune profiling and label-free detection of 2D MXenes at the single-cell and tissue level

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

summary: There is a critical unmet need to image 2D materials within single cells and tissues. Here we propose a versatile label-free single-cell detection strategy based on mass cytometry. We use single-cell mass cytometry by time-of-flight (CyTOF), imaging mass cytometry, and multiplexed ion beam imaging by time-of-flight (MIBI-TOF) with three representative MXenes.  Nb4C3, Mo2Ti2C3, and Ta4C3 were selected to ensure mass-detection within the range and to avoid overlap with currently available tags. We demonstrated their biocompatibility, detection, and quantification in 16 primary human immune cell subpopulations also showing the impact of MXene lateral size on the detection signal and cell binding. We report the biological and  immune functional compatibility of MXenes. In vivo biodistribution experiments in mice using a mixture of MXenes revealed their presence in liver, blood, spleen, and lungs. Lastly, we applied MIBI-TOF to capture the presence of MXenes in different organs. The label-free detection of 2D materials by mass cytometry at the single cell level, on multiple subpopulations and in multiple organs in vivo opens exciting new opportunities in biomedicine.

overall_design: PBMCs were harvested from ethylenediamine tetraacetic acid (EDTA)-venous blood from informed healthy donors (25–50 years old) using a Ficoll-Paque (GE Healthcare, CA, USA) standard separation protocol. Then the PMBCs were treated with medium control, LPS, ConA, Ta4C3, Mo2Ti2C3, Nb4C3 in triplicated conditions for 24 h. The RNA were extracted and sequenced using Illumina Hiseq4000.

first: Laura

last: Fusco

first: Arianna

last: Gazzi

first: Christopher

middle: E

last: Shuck

first: Marco

last: Orecchioni

first: Dafne

last: Alberti

first: Sènan

last: D'Almeida

first: Eiman

last: Ahmed

first: Ofer

last: Elhanani

first: Martina

last: Rauner

first: Barbara

last: Zavan

first: Jean-Charles

last: Grivel

first: Bengt

last: Fadeel

first: Leeat

last: Keren

first: Giulia

last: Pasqual

first: Davide

last: Bedognetti

first: Klaus

last: Ley

first: Yury

last: Gogotsi

first: Lucia

last: Delogu


title: Diagnostic value and predictors of severity in circulating exosomal lncRNAs of white matter hyperintensities

city: Qingdao

first: Xiang

last: Xu

address: 127 Siliunan Road

institute: The Affiliated Qingdao Central Hospital of Qingdao University

type: Non-coding RNA profiling by high throughput sequencing

summary: Exosomal long noncoding RNAs (lncRNAs) play an important role in the diagnosis and treatment of diseases. High-throughput sequencing was performed to determine the differential expression (DE) profiles of lncRNAs and mRNAs in plasma exosomes from patients with white matter hyperintensities (WMH) and healthy controls. Next, functional enrichment analysis and network interaction prediction were performed for DE RNAs, which were verified in a validation cohort (100 WMH and 100 healthy controls) using qRT–PCR. The diagnostic potential of candidate RNAs was evaluated by receiver operating characteristic (ROC) curves. The WMH group was then divided into subgroups according to the Fazekas scale and white matter lesion site, and the correlation of DE exo-lncRNAs in the subgroup was evaluated. We selected 6 DE RNAs (exo-lnc_011776, exo-lnc_011797, exo-lnc_004326, exo-lnc_013222, exo-WNK1 and exo-RPL18), and qRT–PCR confirmed that the expression trends of the differentially expressed genes (DEGs) was consistent with the RNA sequencing results. ROC curve analysis revealed that exo-lnc_011776, exo-lnc_011797, exo-lnc_004326, exo-WNK1 and exo-RPL18 exhibited diagnostic efficacy for WMH. Furthermore, exo-lnc_011797 was positively correlated with the severity of WMH and was significantly elevated in paraventricular matter hyperintensities patients. Our study found that five exosomal RNAs that have potential diagnostic value for WMH. Moreover, exo-lnc_011797 may be a predictor of the severity and location of WMH.

overall_design: exosomal lncRNAs profiles of white matter hyperintensities(WMH) patients and controls

first: Xudong

last: Pan

first: Aijun

last: Ma

first: Xiaoyan

last: Zhu


title: Gene expression profiling of whole blood in patients with severe leptospirosis

city: Bangkok

first: Umaporn

last: Limothai

state: Thailand

address: 1873 Rama IV Rd, Pathum Wan, Pathum Wan District, Faculty of Medicine, Chulalongkorn University

country: Thailand

institute: Chulalongkorn University, Faculty of Medicine

summary: Background: Leptospirosis is a global zoonotic infectious disease with various clinical manifestations ranging from mild self-limiting illness to life-threatening infection with multi-organ damage. This study was aimed at investigating transcription profiles from whole blood samples of patients with leptospirosis and identifying genes as novel biomarkers for predicting severe leptospirosis.  Methods: In a discovery cohort, 12 serum samples of patients with severe and non-severe leptospirosis at initial clinical presentation were selected for gene expression profiling using the NanoString nCounter PanCancer IO 360 gene expression panel. In a validated cohort of 99 samples, top candidate genes were selected and further tested by qRT-PCR in whole blood samples of 30 and 69 individuals with severe and non-severe leptospirosis, respectively.  Results: The discovery set identified 20 differentially expressed genes (DEGs) among the two groups. The top three down-regulated candidate genes including programmed cell death 1 (PDCD1), interleukin 4 (IL4), and nitric oxide synthase 2 (NOS2) were selected and further validated. In the validated cohort, PDCD1 levels were significantly lower in the severe group compared with the non-severe group(Stats?). Based on the ROC analysis, PDCD1 levels could discriminate between the severe and non-severe groups. Additionally , PDCD1 levels displayed good predictive power of subsequent pulmonary hemorrhage with an AUROC of 0.86 (95% CI;0.76-0.96, p = 0.007). PDCD1 also emerged as an independent prognostic factor of severe leptospirosis in the multivariate regression analysis..  Conclusion: Our data indicated that whole blood gene expression profiles were significantly different between the severe and non-severe leptospirosis groups. PDCD1 expression levels at presentation could potentially serve as a biomarker for predicting severe leptospirosis.

overall_design: A total of 12 serum samples (8 and 4 samples from the severe and non-severe groups, respectively) were randomly selected from the stored samples to investigate the gene expression profile using the nCounter PanCancer IO 360 panel (NanoString Technologies, Seattle, WA). The samples were tested according to the manufacturer’s protocol.

first: Janejira

last: Dinhuzen

first: Sasipha

last: Tachaboon

first: Patcharakorn

last: Kiatamornrak

first: Watchadaporn

last: Chaisuriyong

first: Bangon

last: Laosatiankit

first: Suppalak

last: Brameld

first: Nuttha

last: Lumlertgul

first: Sadudee

last: Peerapornratana

first: Nattachai

last: Srisawat


title: RNA sequencing analysis of prostate cancer cells with ectopic expression of circ0003553

first: Gang

last: Luo

state: Hubei

address: 26 Shengli Street

institute: Huazhong University of Science and Technology

summary: Transcriptome analysis was performed to determine the effect of overexpression of circ0003553 in prostate cancer cells

overall_design: Prostate cancer cells PC3 and DU145 transfected with expression vector containing circ0003553 were used for RNA-seq analysis.


title: Whole transcriptome analysis of human CD4 T cell subsets

city: Cambridge

first: William

last: Foster

state: County (optional)

address: Babraham Research Campus

institute: Babraham Institute

summary:
Whole transcriptome analysis of in vitro TFH versus naïve CD4 T cells, tonsillar TFH (CXCR5hiPD1hiCD25-TNFR2-) and TFR (CXCR5hiPD1+CD25hiTNFR2+)
We used microarray analysis to compare naïve CD4 T cells to in vitro differentiated TFH, which we then compared to ex vivo Tonsillar TFH and TFR.

overall_design: This dataset contains 4 groups of samples, as detailed in the summary, with 6-8 samples per group.

first: James

middle: A

last: Harker


title: mRNA profiling on TNFR2 knockout CART19 compared to wildtype CART19 produced from normal donors

first: Saad

last: Kenderian

summary: RNA sequencing was performed on three biological replicates of untransduced (UTD) T cells, CART19 (TNFR2 wildtype) and TNFR2 knockout CART19 produced from normal donors.

overall_design: T cells from normal donors were transduced with a replication-incompetent lentiviral vector expressing a second-generation chimeric antigen receptor (CAR) consisting of an anti-CD19 single chain variable fragment (FMC63) fused to 4-1BB and CD3ζ intracellular domains as previously described.  TNFR2 knockout CART19 were also transduced with TNFR2 CRISPR Guide RNA in a pLentiCRISPR v2 backbone as previously described.  RNA was isolated on Day 8 of production.

first: Claudia

last: Manriquez Roman

first: Michelle

last: Cox


title: Characterization of a new class of RNA products from the Pax-5 oncogene: circular RNAs

city: Moncton

first: Eric

middle: P

last: Allain

state: New Brunswick

address: 330 University ave

department: Medical Genetics

institute: Vitalité Health Network

summary: Circular RNAs (circRNAs) represent a relatively new class of RNA products, which are gaining interest due to their involvement in many biological processes and cancer disease. Due to their innate ability to bind and modulate co-interacting proteins and microRNAs (miRs), circRNAs represent an additional layer of complex intracellular signaling and regulatory networks supporting cell biology and cancer phenotypes. In this study, we identify and characterize various circRNA products, which derive from the Pax-5 oncogene (circPax-5) in B lymphocytes. We establish the expression profiles of multiple circPax-5 variants in a collection of previously reported Pax-5 expressing tissues in addition to cell models and clinical samples from B cell cancer lesions. For example, we observe that circPax-5 products are overexpressed (up to 13-fold) in chronic lymphocytic leukemia (CLL) where the majority of these circRNAs consists of a specific circPax-5 isoform containing the sequence of exons 2 to 5 (circPax-5_2-5) of the Pax-5 locus. Given the established role of Pax-5 gene products in cancer biology, we also we set out to assess the impact of circPax-5 in cancer processes using conditional expression of circPax-5_2-5 in B cell lines. Interestingly, we found that circPax-5_2-5 was associated with cancer cell growth rates, which were dependent on B cell differentiation and cancer subtypes. We also characterized mechanistic features of circPax-5 in B cell lines based on common molecular features of circRNAs (ex: miR sequestering and sponging). CircPax-5 complexes from B cells were thus isolated by circRNA precipitations and submitted to deep sequencing analysis to identify co-interacting miRs. In addition to miR sponging profiles, circPax-5 were also studied for potential translation of novel peptides through putative internal ribosome entry sites (IRES). Using a dual IRES-dependent reporter gene assay, we found that circPax-5_2-5 harbors IRES motifs capable of encoding uncharacterized proteins. Altogether, our study introduces a new category of Pax-5 gene products which provide an extension of Pax-5-dependant signaling and function in B lymphocytes. This is particularly important in cancer cells given our observations of elevated circPax-5 levels in specific B cell cancer lesions. Furthermore, the elucidation of new players from the Pax-5 oncogene could provide the mapping of unknown cancer pathways, which could be targeted for therapeutic and/or diagnostic strategies in B cell cancer lesions.

overall_design: DNA probes targeting circular PAX5 RNA or non-specific probes (control) were pre-incubated with cell lysates from Raji and Reh cells prior to pulldown with streptavidin-conjugated magnetic beads. miRNAs interacting with PAX5 circular RNA were then subjected to small-RNA sequencing.

first: Gilles

last: Robichaud

first: Nicholas

last: Finn

first: Nicolas

last: LeBlanc

first: Laura-Kim

last: Landry

first: Vanessa

last: Veilleux

first: Brandon

last: Hannay

first: Danick

last: Martin

first: Shruti

last: Srivastava

first: Gabriel

last: Wajnberg


title: The global fusarium graminearum gene expressional responses to different nitrogen source and the gene expression changes between histone methylation defective mutants and wild type strain

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

institute: Shanghai Inst. Plant Phys. & Eco.

summary:
Purpose: To assess global changes of  fusarium graminearum gene expressional responses to different nitrogen source and gene expression changes after removal different histone methylation hallmarks.
Methods: For RNA seq of fusarium, three biological replicates of hyphae  after 48/72 hours cultured were sequenced.
Results: For each sample, 5.83-8.31G RNA-seq clean reads were obtained mapped to the Fusarium graminearum genome sequence.

overall_design: Three biological replicates of  wild type and knock out mutants  after 48/72 hours cultured in different medium were sequenced using Illumina Hiseq-PE150 Sequencing System.

first: Wan-Qiu

last: Wang

first: Dong

last: Zhang

first: Yu-Feng

first: Wei-Hua


title: The global wheat gene expressional responses to fusaoctaxin B

summary:
Purpose: To assess global changes of wheat coleoptiles gene expression in response to fusaoctaxin B which is a linear, C-terminally-reduced and D-amino acid residue-rich octapeptide, as the product of the two non-ribosomal peptide synthetases encoded by Fusarium graminearum fg3_54 cluster.
Methods: For RNA seq of wheat coleoptiles, three biological replicates of  after 3 hours fusaoctaxin B-treated coleoptiles, after 3 hours control (0.5% Tween-20) treated coleoptiles, after 24 hours fusaoctaxin B-treated coleoptiles and after 24 hours control (0.5% Tween-20) treated coleoptiles were sequenced.
Results: For each sample, 33-95 M RNA-seq clean reads were obtained mapped to the Triticum aestivum Chinesespring genome sequence.
Conclusions: Fusaoctaxin B represents an unprecedented virulence factor.

overall_design: Three biological replicates of  after 3 hours fusaoctaxin B-treated coleoptiles, after 3 hours control (0.5% Tween-20) treated coleoptiles, after 24 hours fusaoctaxin B-treated coleoptiles and after 24 hours control (0.5% Tween-20) treated coleoptiles were sequenced using Illumina NovaSeq 6000 Sequencing System.


title: Evidence of DNA methylation in Aspergillus oryzae [RNA-seq]

city: Koto-ku

first: Yutaka

last: Saito

state: Tokyo

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary: DNA methylation is an important epigenetic modification widespread in eukaryotes and bacteria. However, genomic methylation levels show a dramatic diversity throughout the evolution of life, varying even between closely-related species and strains. In Aspergillus, a genus of filamentous fungi, the existence of DNA methylation has been controversial with previous studies reporting different conclusions using different species and detection methods. Here, we report DNA methylation analysis of Aspergillus oryzae, an important species in the Japanese fermentation industry, and a close relative of the pathogen Aspergillus flavus whose DNA methylation has been denied by the recent previous study using bisulfite sequencing. In this study, we conduct bisulfite-seq and RNA-seq of A. oryzae using three biological replicates from each of liquid and solid culture conditions. The statistical analysis of these data reveals thousands of highly-confident methylated cytosines (mCs), while the re-analysis of data from A. flavus detects few mCs being consistent with the previous study. Based on the comparative genome analysis of A. oryzae and A. flavus, we find that a substantial fraction of mCs are observed in syntenic segments including the aflatoxin biosynthesis gene cluster. Together, our results are the first evidence of DNA methylation in A. oryzae, providing a new example of the evolutionary diversity of DNA methylation as well as a new insight into its industrial applications.

overall_design: RNA-seq was conducted for Aspergillus oryzae RIB40 in liquid (CD-Glc) and solid (WB) culture conditions with three biological replicates.

first: Koichi

last: Tamano

first: Yoshiyuki

last: Nishimiya

first: Toshitaka

last: Kumagai

first: Momoe

last: Suyama

first: Wataru

last: Kitagawa

first: Yoshiaki

last: Yasutake

first: Naoyuki

last: Tajima

first: Toutai

last: Mituyama

first: Tomohiro

last: Tamura

first: Tomoshi

last: Kameda


title: Analysis of transcripts expressed during log and stationary phases in Xenorhabdus szentirmaii

status: Public on Mar 31 2025

city: Milwaukee

first: Madhusudan

last: Dey

state: WI

address: 3209 N Maryland Ave

department: Biological Sciences

institute: UW-Milwaukee

summary: To understand the molecular details of the biosynthesis, secretion, and/or mode of action of antimicrobials, we performed a comparative analysis of transcripts expressed during log and stationary phases of growth of in Xenorhabdus szentirmaii to identify the deferentially expressed genes. Total RNA was isolated from X. szentirmaii grown at log and stationary phases (Fig 3A, four biological replicates referred here Dey1, Dey2, Dey3 and Dey4 for the log phase and Dey5, Dey6, Dey7 and Dey8 for the stationary phase, Supplemental Table 1). The equal amount of total RNA was subjected to RNA sequencing analysis.

overall_design: RNA seq profiling of  log and stationary phases of growth of in Xenorhabdus szentirmaii

first: Dey

last: Ritisha

first: Valle

last: Domonique Olivia

first: Chakraborty

last: Abhijit

first: Mayer

last: Kimberly A

first: Uppala

last: Jagadeesh

last: Anish

first: Mirza

last: Shama

first: Forst

last: Steven

first: Skwor

last: Troy

last: Madhusudan


title: DNA methylation profiling of germ cells from mice exposed to chronic social defeat stress

city: Fujisawa

first: Shu

last: Aizawa

state: Kanagawa

address: 1866 Kameino

department: Department of Zoological Science

institute: Nihon University College of Bioresource Sciences

type: Methylation profiling by high throughput sequencing

summary: Mice exposed to chronic social defeat stress (CSDS), an animal model of depression, exhibit dysfunction of the male reproductive system. However, the mechanism by which exposure to CSDS contributes to male reproductive abnormalities remains poorly understood. We investigated the effects of CSDS on DNA methylation profiles of male germ cells using the reduced representation of bisulfite sequencing (RRBS).

overall_design: Methylation profiling of germ cells from control and CSDS-exposed mice by reduced representation of bisulfite sequencing

first: Hikari

last: Ohno


title: ATF4 drives regulatory T cell functional specification in homeostasis and obesity [ChIP-seq]

city: La Jolla

first: Chunyu

last: Jin

address: 9500 Gilman Dr. MC0648

institute: University of California, San Diego

summary: Regulatory T cells (Tregs) have diverse functional specification in homeostasis and disease. However, how liver Tregs function and are transcriptionally regulated in obesity is not well understood. Here, we identified that effector Tregs expressing activating transcription factor 4 (ATF4) were enriched in the livers of obese mice. ATF4 was critical for driving an effector Treg transcriptional program, and ATF4-expressing Tregs promoted the development of obesity-induced liver fibrosis by enhancing transforming growth factor–β activation via integrin αvβ8. Treg-specific deletion of Atf4 resulted in reduced liver Tregs and attenuation of obesity-induced liver abnormalities. Furthermore, ATF4 was required to promote the differentiation of nonlymphoid tissue Treg precursors under steady state. These findings demonstrate that ATF4 is important for regulating Treg functional specification in homeostasis and obesity.

overall_design: To elucidate how ATF4 regulates Treg effector function, we performed ATF4 ChIP-seq on CD4+CD25+ Treg cells isolated from spleen and LNs.


title: In Vitro Fertilization induces reproductive changes in male mouse offspring and has multigenerational effects [RNA-seq II]

city: Philadelphia

first: Eric

middle: Alejandro

last: Rhon Calderon

state: Pennsylvania

address: 3400 Civic Center Blvd, Bldg 421, Floor 9-175

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: In vitro fertilization (IVF) is a non-coital method of conception used to treat infertility. Although safe, IVF has been associated with adverse outcomes in the fetus, placenta, and adult life, but studies focusing on the male reproductive system are limited. Here, we used a mouse model to assess the morphological and molecular effects of IVF on male offspring. We evaluated three developmental stages: 18.5-day fetuses and 12- and 39-week adults. Regardless of age, we observed changes in the testicular-to-body weight ratio, serum testosterone levels, testicular morphology, transcriptome, and DNA methylation. Also, sperm showed changes in morphology and DNA methylation. To assess multigenerational phenotypes, we mated IVF and naturally conceived males with wild-type females. Offspring from IVF males exhibited a decreased fetal weight-to-placental weight ratio regardless of sex. At 12-weeks-of-age, offspring showed higher body weights, differences in glucose, triglycerides, insulin, total cholesterol, HDL and LDL/VLDL levels. Both sexes showed changes in gene expression in liver, testes and ovaries, and decreased global DNA methylation. Collectively, our findings demonstrate that male IVF offspring exhibit abnormal testicular and sperm morphology and molecular alterations and transmit defects multigenerationally. These experiments contribute to our understanding of the long-term impacts of IVF on adult offspring health.

overall_design: Gene expression analysis using Total RNA extracted from F2 E18.5 placentas (Males (n=12, Natural=6 and IVF=6), and females (n=10, Natural=4 and IVF=6) NextSeq1000.

last: Rhon-Calderon

first: Cassidy

last: Hemphill

first: Alexandra

last: Savage

first: Laren

last: Narapareddy

first: Richard

last: Schultz

first: Marisa

last: Bartolomei


title: Loss of NOL10 leads to impaired disease progression of NUP98::DDX10 leukemia

city: Toyoake

first: Yutaka

last: Shima

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake-cho

institute: Fujita Health University

summary: NUP98 rearrangements associated with acute myeloid leukemia and myelodysplastic syndromes generate NUP98-fusion proteins. One such fusion protein, NUP98::DDX10, contains the putative RNA helicase DDX10. The molecular mechanism by which NUP98::DDX10 induces leukemia is not well understood. Here, we show that 24 amino acids within the DDX10 moiety of NUP98::DDX10 are crucial for cell immortalization and leukemogenesis. NOL10, nucleolar protein 10, interacts with the 24 amino acids, and NOL10 is a critical dependency of NUP98::DDX10 leukemia development. Studies in a mouse model of NUP98::DDX10 leukemia showed that loss of Nol10 impaired disease progression and improved survival. We also identified a novel function of NOL10 in that it acts cooperatively with NUP98::DDX10 to regulate serine biosynthesis pathways and stabilize ATF4 mRNA. Collectively, these findings suggest that NOL10 is a critical regulator of NUP98::DDX10 leukemia, and that targeting NOL10 (or the serine synthesis pathway regulated by NOL10) may be an effective therapeutic approach.

overall_design: We established murine NUP98::DDX10 leukemia model. To investigate the role of Nol10 in the leukemia cells expressing NUP98::DDX10, The leukemia cells purified from the bone marrow of the leukemia model were trasduced with shRNA against Nol10 to knockdown the expression of Nol10

first: Issay

last: Kitabayashi

first: Kazutsune

last: Yamagata


title: In Vitro Fertilization induces reproductive changes in male mouse offspring and has multigenerational effects [array]

overall_design: Bisulfite converted DNA from 12 mice 12 weeks sperm and 12 mice 39 weeks sperm from 2 different groups (12 weeks: Natural N=6, IVF N=6. 39 weeks:Natural N=6, IVF N=6) were hybridized to the Illumina Mouse Methylation285 12v1-0 BeadChip Array


title: lncRNA-seq profiling for primary mouse cortical neurons

city: Stanford

first: Mengting

last: Han

state: CA

address: 290 Jane Stanford Way  ChEM-H/Neuroscience Building W117

department: Bioengineering

institute: Stanford University

summary: To understand the factors influencing gRNA performance for CRISPR-TO system, we performed lncRNA-seq profiling through Novogene Corporation Inc for total RNA extracted from 6 DIV primary mouse cortical neurons dissected from 3 litters of P0 pups of C57BL/6J mice.

overall_design: We performed lncRNA-seq profiling through Novogene Corporation Inc for total RNA extracted from 6 DIV primary mouse cortical neurons dissected from 3 litters of P0 pups of C57BL/6J mice.

first: Jon

last: Bezney

first: Lei

last: Qi


title: In Vitro Fertilization induces reproductive changes in male mouse offspring and has multigenerational effects

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

overall_design: Refer to individual Series


title: Evidence of DNA methylation in Aspergillus oryzae

last: Saito


title: In Vitro Fertilization induces reproductive changes in male mouse offspring and has multigenerational effects [RNA-Seq]

overall_design: Gene expression analysis using Total RNA extracted from F1: E18.5 testis (n=10, Natural=4 and IVF=6), 12 weeks testis (n=10, Natural=5 and IVF=5) and 39 weeks testis (n=10, Natural=4 and IVF=6). F2: 12 weeks testis (n=12, Natural=5 and IVF=7), 12 weeks male livers (n=10, Natural=5 and IVF=5), 12 weeks ovaries (n=9, Natural=4 and IVF=5), 12 weeks female livers (n=10, Natural=4 and IVF=4), using either Illumina NovaSeq6000 or NextSeq1000.


title: Evidence of DNA methylation in Aspergillus oryzae [bisulfite-seq]

overall_design: Bisulfite-seq was conducted for Aspergillus oryzae RIB40 in liquid (CD-Glc) and solid (WB) culture conditions with three biological replicates.

first: Koichi

last: Tamano

first: Yoshiyuki

last: Nishimiya

first: Toshitaka

last: Kumagai

first: Momoe

last: Suyama

first: Wataru

last: Kitagawa

first: Yoshiaki

last: Yasutake

first: Naoyuki

last: Tajima

first: Toutai

last: Mituyama

first: Tomohiro

last: Tamura

first: Tomoshi

last: Kameda


title: Transcriptomic changes associated with SIRT1-based therapy in a model of retinal neurodegeneration

first: Brahim

last: Chaqour

state: PA

address: 422 Curie Blvd

department: Ophthalmology

summary: The aim of this study was to examine retinal transcriptomic changes associated with optic neuritis and identify those that are reversed upon targeted expression of SIRT1 in RGCs. Conceptually, identification of transcriptional differences between SIRT1-treated and non-treated retinas will help identify genes correlating with resilience and resistance to neurodegeneration and/or the molecular pathways affected by SIRT1 overexpression. To achieve this, we used a mouse model of experimental autoimmune encephalomyelitis (EAE)-induced optic neuritis, a commonly used model of multiple sclerosis, in which myelin oligodendrocyte-specific immune responses are induced by injecting myelin oligodendrocyte glycoprotein peptide (MOG35-55) . EAE mice develop an autoimmune demyelinating reaction characteristic of multiple sclerosis and optic neuritis which include optic nerve inflammation, axon demyelination, and loss of RGCs and visual acuity.Using this disease model and bulk RNA sequencing, we identified genes whose expression is affected by constitutive ubiquitous SIRT1 expression in SIRT1 knock-in mice, and in wild-type mice upon either targeted adeno-associated virus (AAV)-mediated SIRT1 expression in RGCs or oral gavage with resverotrol (RSV), a SIRT1 activator.

overall_design: Four weeks after MOG immunization, RSV-gavagged and  SIRT1 KI and AAV-SIRT1-injected WT mice and their respective controls were sacrificed, and retinas were rapidly isolated and snap frozen in liquid nitrogen. Total RNA was extracted from homogenized mixtures of retinas using RNeasy purification kit according to the manufacturer’s instructions (Qiagen). Sample RNA concentrations and purity were measured using the Thermo Scientific NanoDrop 8000 UV-Vis Spectrophotometer. RNA sequencing was performed with three biological replicates per group of mice by Genewiz/Azenta (New Jersey, USA) where the cDNA libraries were prepared and sequenced using Illumina Hiseq, 2 × 150 bp paired-end chemistry

first: Kenneth

last: Shindler

first: Ahmara

last: Ross

first: Kimberly

last: Dine


title: FLI1 and GATA1 govern TLN1 transcription: new insights into FLI1-related platelet disorders

city: Marseille

first: Julien

last: Maurizio

address: Bd Jean Moulin

summary: Germline variations in FLI1, essential for megakaryopoiesis, are linked to bleeding disorders, platelet aggregation defects and mild thrombocytopenia. However, the mechanisms behind these abnormalities remain unclear. This study aims to elucidate the impact of FLI1 variants on human megakaryocytes and platelets.

overall_design: We assessed the impact of one FLI1 variant (Arg337Gln) on megakaryopoiesis using single-cell RNA sequencing, and defects were confirmed in platelet samples obtained from the five patients belonging to four different families carrying the Arg337Gln, Lys345Asp Arg340Cys and Lys345Asp and cell lines.

first: E

last: Gabinaud

first: M

last: Poggi


title: Extracellular Vesicle exposure induced DNA methylation changes in normal Hematopoietic Stem Progenitor Cells: the first proof of concept in Acute Myeloid Leukemia model

city: Rionero in Vulture

first: Ilaria

last: Laurenzana

address: via Padre Pio, 1

country: Italy

institute: IRCCS CROB, Centro di Riferimento Oncologico della Basilicata

type: Methylation profiling by genome tiling array

summary: To analyze the impact of AML derived-extracellular vesicles (EVs) on hematopoietic progenitor stem cell methylation (HPSCs), we used DNA isolated from primary CD34+ cells, purified from umbilical cordon blood, treated with EVs derived from AML cell line KG1.

overall_design: Bisulphite converted DNA from the 6 samples were hybridised to the Illumina Infinium 850k Human Methylation

first: G

last: Calice

first: I

first: D

last: Lamorte


title: Nicotinic Acetylcholine Receptors Regulate Growth Hormone in Pituitary Somatotrophs of Tigers

city: Haerbin

first: Lulu

last: Liu

address: No. 26, Hexing Road, Xiangfang District, Haerbin City, Heilongjiang Province, China

institute: Northeast Forestry University

summary: We used single nucleus RNA sequencing (snRNA-seq) to analyze the diversity of Siberian tiger pituitary gland.

overall_design: Siberian tiger pituitary snRNA-seq data were analysed to explore species-specific differential genes that differ from those of other mammals.

first: Shilong

last: Yang

first: Guangshun

last: Jiang

first: Shiyu

last: Chen


title: Evaluation of the effects of FGF8, Endothelin-1, and BMP4 (FEDB) on induced pluripotent stem cell (iPSC)-derived neural crest cells (NCCs) induced in two-dimensional (2D) conditions

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

institute: Kyoto University

summary: To evaluate the effects of FEDB on NCCs induced in 2D conditions, we sampled 2D cultured cells and cell aggregates during FEDB treatment and compared gene expression patterns.

overall_design: RNA sequencing profiles of 1231A3 iPSC-derived NCC aggregates, NCC aggregates treated with FEDB, CD271high+ NCCs sorted from 2D induction protocols (2D NCC CD271high), and 2D NCC CD271high treated with FEDB in 2D culture (2D 271H+FEDB).

first: S

last: Motoike


title: Induction of osteogenic lineage cells from human induced pluripotent stem cell (iPSC)-derived neural crest cell (NCC) aggregates through mandibular prominence ectomesenchyme (mdEM)

summary: To clarify the changes in cell properties during the differentiation process from iPSC-derived NCC aggregates into osteogenic cells through mdEM, we sampled cell aggregates during the  differentiation and compared gene expression patterns.

overall_design: RNA sequencing profiles of 1231A3 iPSC-derived NCC aggregates (day 5), mdEM (day 9), and day 38 clusters.


title: Recapitulation of regional patterning using human induced pluripotent stem cell (iPSC)-derived mandibular prominence ectomesenchyme (mdEM)

summary: To ascertain the induction of developmentally accurate mdEM, we sampled cell aggregates during regional patterning induction and compared gene expression patterns.

overall_design: RNA sequencing profiles of 1231A3 iPSC-derived neural crest cell (NCC) aggregates (day 5), mdEM (day 9), distal cap (day 13), proximal-oral domain (day 13), and dental mesenchyme (day 17).


title: Medium RNAseq from patient DM1 cell line

city: Paris

first: Florent

last: Hubé

address: 9 quai saint Bernard

department: LBD

institute: Sorbonne Université, CNRS, Paris, France

summary: Recently, the repertoire of human small nucleolar noncoding RNAs (snoRNAs) and their potential functions has expanded with the discovery of new snoRNAs and messenger RNA (mRNA) targets, for which snoRNA-guided modifications may influence their stability, translatability, and splicing. We previously identified snoRNAs that are abundant in healthy human muscle progenitor cells. In this study, we demonstrated that SNORA40 and SNORA70 loss-of-function impairs myogenic differentiation. Interestingly, gain-of-function can rescue impaired differentiation muscle progenitor cells in myotonic dystrophy type 1 (DM1). We identified cyclin D3 (CCND3) mRNA, which is partially located in the nucleolus, as a target for SNORA40 and SNORA70, which are required for its pseudouridylated status. Expression of the CCND3 protein is required for muscle progenitors to exit the cell-cycle when they are induced to differentiate. We revealed that this switch requires SNORA40/70. Finally, we observed that DM1 cells show reduced levels of SNORA40/70 and undetectable CCND3 protein. However, restoring normal levels of SNORA40/70 partially restored CCND3 protein expression, coinciding with improved cell fusion capacity in DM1 muscle progenitors. Collectively, these data suggest that this effect may stem from SNORA40/70-dependent pseudouridylation of CCND3 mRNA, emphasizing snoRNAs as key players in normal and pathological muscle differentiation.

overall_design:
Total RNA were purified then RNA >50 nt (gel purification) and <200 nt (columns) were fractionnated and sequenced
MB1 and MB2 data are from GSE178649 series.

first: Claire

last: Francastel


title: Genome-wide mRNA profile of human gastric normal and gastric cancer tissues

city: Madurai

first: Jaishree

last: Pandian

state: Tamil Nadu

address: School of Biological Sciences, Madurai Kamaraj University.

department: Unit of Excellence in Cancer Genetics, Department of Genetics, School of Biological Sciences, MKU, Department of Surgery and Surgical Gastroenterology and Histopathology Division, Department of Laboratory Services, MMHRC.

country: India

institute: Madurai Kamaraj University & Meenakshi Mission Hospital & Research Centre, Madurai.

summary: Gastric cancer is the fourth common cancer and second leading cause of cancer related mortality. The survival probability of gastric cancer patients is often less due to the diagnosis at late stage and also due to the heterogenous nature of tumors. Molecular and transcriptome-wide understanding of the dysregulations in gastric tumors from different populations is highly required to delineate the heterogeneity. To delineate the key oncogenic dysregulations in terms of the transcripts, transcription programs and signaling pathways, we performed genome-wide mRNA profiling of human gastric normal and gastric cancer tissues using Affymetrix Human Transcriptome 2.0 arrays.

overall_design: Gastric cancer and adjacent gatric normal tissues were freshly collected in RNAlater solution and stored at -80°C. Total RNA was isolated from gastric normal and tumor tissues. 50 gastric tumor and 15 adjacent gastric normal tissues, with the RIN value (≥5) were profiled using GeneChip® Human Transcriptome Array 2.0 (HTA-2_0). The differentially expressed genes (DEG's) were analyzed using Transcriptome Analysis Console V4.0. Gene-set enrichment analysis and Gene Ontology analysis of DEG's were used to identify the enrichment of biological pathways and processes involved in gastric carcinogenesis.

first: Madhusudhanan

last: Gnanasekaran

first: Vikash

last: Vittal

first: Ponmathi

last: Panneerpandian

first: Karthikeyan

last: Selvarasu

first: Satyajit

last: Patwardhan

first: N

last: Mohan

first: P

middle: L

last: Alagammai

first: Ramesh

last: Ardhanari

first: Kumaresan

last: Ganesan


title: Dissecting tissue-specific transcriptional response to 20E in Drosophila by E23 expression

city: Moscow

first: Nadezhda

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

summary: Transcriptional activation by 20-hydroxyecdysone (20E) in Drosophila provides an excellent model for studying tissue-specific response to steroids. An increase in 20E titer controls degradation of larval and proliferation of adult tissues during metamorphosis. To study 20E-dependent transcription, we used the natural system for controlling the 20E titer – E23 membrane transporter, which exports 20E from the cell. We artificially expressed the E23 in tissues to suppress the first wave of 20E-inducible transcription at metamorphosis.  Expression of E23 revealed a plethora of 20H dependent genes in salivary glands, but mildly affected the transcription in brain/eye-antennal discs. We described the mechanisms controlling the transcriptional activation by 20E in Drosophila salivary glands. 20E depletion caused a decreased binding of Pol II and TFIID subunit, TBP, to target promoters, demonstrating 20E role in the stimulation of transcription initiation. At the target loci 20E depletion resulted in a malfunctioning of sites co-bound with EcR and CBP/Nejire and enriched with H3K27Ac histone mark inherent to active enhancers. At these sites, 20E titer was found to control chromatin accessibility and acetylation. We presume that the activity of these ‘active’ ecdysone-sensitive elements – (ESEs) is responsible for an active status of 20E targets in the salivary glands of wandering larvae.

overall_design: RNA-Seq and ChIP-Seq analysis were performed on tissues (salivary glands and brains/eye-antennal discs) of wandering larvae (4-6h before puparium formation). All experiments were done using hsp-e23 larvae, treated with the double heat shock (with 1-hour rest) 20-22 h before puparium formation, and in control conditions, without heat shocks

first: Aleksandra

last: Evdokimova


title: ATF4 drives regulatory T cell functional specification in homeostasis and obesity [RNA-seq]

first: Chunyu

last: Jin

overall_design: To elucidate how ATF4 regulates Treg activation and function, we performed bulk RNA-seq on spleen YFP+ Treg cells isolated from control mice and Atf4fl/flFoxp3YFPcre/wt mice.


title: ATF4 drives regulatory T cell functional specification in homeostasis and obesity [ATAC-seq]

overall_design: To study the transcriptional regulation of Treg functional specification in the obese liver, we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) on sorted hepatic Treg cells from lean and obese mice.


title: SINE-MIR enhancer rewiring by Esrrb architecturally reprogram the pluripotency spectrum [ATAC-Seq]

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

institute: Institute of Molecular and Cell Biology

summary: ATAC-seq were performed during EPSC differentiation to 3dESC

middle: O

last: Cipta

first: Y

first: H

last: Li

last: Loh


title: Comparative microarray of wild-type and Parp3-/- C2C12 cells

city: Illkirch

first: Françoise

last: DANTZER

address: 300 boulevard S. Brant

institute: CNRS

summary: Wild-type and two different Parp3-/- clones of C2C12 cells were induced to differentiate for 72h. Microarray was performed to compare the transcriptomic profile of the two Parp3-deficient clones versus the wild-type control at T72h post-differentiation.

overall_design: The wild-type C2C12 and the two Parp3-/- C2C12 cell lines were induced to differentiate for 72h. Total RNA was extracted at T72h post-differentiation and processed for microarray. Three biological replicates (= 3 differentiations) were performed.

last: Dantzer


title: SINE-MIR enhancer rewiring by Esrrb architecturally reprogram the pluripotency spectrum [HiChIP]

summary: Esrrb HiChIP were performed on E14 cells cultured in different media conditions or shRNA knockdown

overall_design: Esrrb HiChIP experiments on E14 mESCs

first: Yi

last: Yao


title: SINE-MIR enhancer rewiring by Esrrb architecturally reprogram the pluripotency spectrum [Hi-C]

summary: Hi-C were performed on E14 cells cultured in different media conditions

overall_design: Hi-C experiments on E14 mESCs


title: SINE-MIR enhancer rewiring by Esrrb architecturally reprogram the pluripotency spectrum [ChIP-Seq]

summary: ChIP-seq was performed in wildtype or treated (using shRNA or CRISPRi) E14 cells

overall_design: Detect the genome region bound by Esrrb, Cas9 or Yy1


title: The role of splicing factor PTBP1 in mechanotransduction

status: Public on Mar 30 2025

city: Sheffield

first: Pei Li

last: Tseng

state: Sheffield

address: Western Bank

institute: University of Sheffield

summary: Mechanical cues play a vital role in numerous biological processes, including embryonic development, aging, cellular homeostasis, and disease progression. Cells sense and convert these mechanical signals into biochemical responses that regulate cell behaviours like proliferation and migration through a process known as mechanotransduction. In this study, we present a comprehensive, large-scale approach to identify proteins with a mechanosensitive nuclear localisation and therefore a potential role in mechanotransduction. Our screening method is based on inducing acute changes in cellular traction forces, combined with in situ biotinylation of nuclear proteins, followed by mass spectrometry analysis. This screen approach identified among other proteins the splicing factor PTBP1 as a protein with mechanosensitive nuclear localisation, and we show that its nuclear abundance can be regulated by mechanical cues such as cell density, cell size, and extracellular matrix (ECM) stiffness. Moreover, we demonstrate that PTBP1 is essential for ECM stiffness-driven mesenchymal stem cell differentiation into osteoblasts, as well as for epithelial cell spreading and stiffness-induced proliferation. Furthermore, we show that PTBP1 mediates mechanosensitive alternative splicing of the endocytic adapter protein Numb, and that this splicing event affects the membrane trafficking of the mechanosensor integrin beta1 and is critical for matrix stiffness-induced stem cell differentiation and epithelial cell proliferation and cell spreading. Our findings support the emerging concept that alternative splicing plays a crucial role in mechanotransduction, offering new mechanistic insights into how matrix stiffness influences cellular mechanoresponses.

overall_design:
In order to discover potential mechanoregulators, we developed an unbiased screen to identify proteins which translocate between the nucleus and cytoplasm acoording to the changes of mechanical property controlled by a Tetracycline-inducible promoter, and we identified splicing factor PTBP1 as a mechanoregulator.
We conducted PTBP1 KD experiments in MCF10A and performed RNA-seq analysis to identify the alternative splicing of Numb exon 9 can be regulated by PTBP1 and ECM stiffness.
We performed cell proliferation, cell spreading, and Integrin b1 recycling experiments to clarify the role of PTBP1 in the control of cellular responses through regulation of alternative splicing of Numb exon 9.

first: Pei-Li

first: Weiwei

last: Sun

first: Ahmed

last: Salem

first: Mubarak

last: Alaklobie

first: Sarah

last: Macfarlane

first: Annica

last: Gad

first: Mark

last: Collins

first: Kai

last: Erdmann


title: Efficient DNA- and virus-free engineering of cellular transcriptomic states using dCas9 ribonucleoprotein (dRNP)-complexes

status: Public on Mar 29 2025

city: Planegg

first: Anna

last: Danese

address: Grosshaderner strasse 9

institute: Ludwig Maximilians University

summary:
For genome editing, the use of CRISPR ribonucleoprotein (RNP) complexes is well established and often the superior choice over plasmid-based or viral strategies. RNPs containing dCas9 fusion proteins, which enable the targeted manipulation of transcriptomes and epigenomes remain significantly less accessible. Here, we describe the production, delivery and optimization of second generation CRISPRa RNPs (dRNPs). We characterize the transcriptional and cellular consequences of dRNP treatments in a variety of human target cells and show that the uptake is very efficient. The targeted activation of genes demonstrates remarkable potency, even for genes that are strongly silenced, such as developmental master transcription factors. In contrast to DNA based CRISPRa strategies, gene activation is immediate and characterized by a sharp temporal precision. We also show, that dRNPs allow very high target multiplexing, enabling undiminished gene activation of multiple genes simultaneously. Applying these insights, we find that intensive target multiplexing at single promoters synergistically elevates gene transcription. Finally, we demonstrate in human stem and differentiated cells that the preferable features of dRNPs allow to instruct and convert cell fates efficiently without the need for DNA delivery or viral vectors.

Please cite:
Tobias Schmidt, Maximilian Wiesbeck, Luisa Egert, Thi-Tram Truong, Anna Danese, Lukas Voshagen, Simon Imhof, Matilde Iraci Borgia, Deeksha, Andrea M Neuner, Anna Köferle, Arie Geerlof, André Santos Dias Mourão, Stefan H Stricker, Efficient DNA- and virus-free engineering of cellular transcriptomic states using dCas9 ribonucleoprotein (dRNP) complexes, Nucleic Acids Research, Volume 53, Issue 6, 11 April 2025, gkaf235, https://doi.org/10.1093/nar/gkaf235

overall_design: RNAseq of WT HAF cells (NHDF-Ad, Lonza) after transfection of CRISPR dCas9 -VPRRNPs (dRNPs) targeting gene activation of EPCAM (EPCAM condition) vs. empty dCas9-VPR protein (Control condition)

first: Stefan

last: Stricker

first: Tobias

last: Schmidt


title: Dmrt1 regulates mouse expanded potency and facilitates the breaking of embryonic lineage barrier

first: Yingying

last: Zeng

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

overall_design: Refer to individual Series


title: Comparison of CRISPR-Cas9 genome-edited JEG-3 TAZ/WWTR1 knockout and wild type choriocarcinoma cells

status: Public on Mar 28 2025

city: Vienna

first: Martin

last: Knöfler

address: Währinger Gürtel 18-20, 5Q,

department: Department of Obstetrics and Gynaecology, Reproductive Biology Unit

institute: Medical University of Vienna

summary: The transcriptional co-activator TAZ/WWTR1 plays a central role in the Hippo signaling pathway and acts as crucial mediator in maintaining organ size and tissue homeostasis. Changes in its activity can lead to diseases, including cancer, due to uncontrolled cell growth or aberrant cellular behavior. The aim of this study was to identify gene signatures that are specifically regulated by TAZ in human trophoblast cells. This was achieved by comparing JEG-3 wild-type and TAZ knockout choriocarcinoma cells, generated with CRISPR-Cas9 technology.

overall_design: The JEG-3 TAZ wild-type and knockout cell lines were generated using CRISPR-Cas9 genome-editing, resulting in two wild-type and two TAZ knockout lines. Next-Generation Sequencing was employed to analyze the gene expression differences across 8 samples, comprising the two wild-type cell lines and the two knockout cell lines, each measured in duplicates.

first: Gudrun

last: Meinhardt

first: Péter

last: Király

first: András

last: Szilágyi


title: Single-cell transcriptomic analysis Treg cells in peripheral lymph nodes

city: zhangzhou

first: xiaoyu

last: meng

address: Institute of Immunology Zhejiang University School of Medicine Medical Research Building A812 388 Yuhang Tang Road, Hangzhou

institute: mxy

summary: Treg cell-specific ablation of Cxxc1 leads to the development of a lethal inflammatory disease characterized by spontaneous T-cell activation.Cxxc1-deficient Treg cells showed reduced immunosuppressive capacity without affecting Treg cell numbers.To investigate the role of Cxxc1 as a transcriptional regulator of Treg subsets, we performed single-cell RNA-seq (scRNA-seq) paired with T cell receptor sequencing (TCR-seq) .

overall_design: CD4+YFP+ Treg cells from WT and Foxp3Cre Cxxc1fl/fl mice were isolated for scRNA-seq.

first: Xiaoyu

last: Meng

first: Yezhang

last: Zhu

first: Kuai

last: Liu

first: Lie

last: Wang


title: Endometrial assembloid model reveals endometrial adenogenesis regulation by estradiol-driven WNT7B expression [scRNA-seq]

city: Hong Kong

first: Yimeng

last: Li

address: 21 Sassoon Road, Pokfulam Hong Kong

institute: The university of Hong Kong

summary: To establish an in vitro endometrial co-culture model, endometrial organoid was co-cultured with endometrial stromal cells in a 3D hydrogel matrix. During this co-culture process, tubular gland development was identified from endometrial organoids, which showed the molecular, morphological and functional properties of human endometrial glands. To further characterize the genetic drive for this phenomenon, we conducted single-cell RNA sequencing analysis at day 1 and day 9 after co-culture.

overall_design: Three-dimensional co-culture models were collected separately at day 1 and day 9 after co-culture, digested into single cells and send for single-cell RNA sequencing analysis to identify the regulatory genes.

first: Xintong

first: Jianlin

first: Cheuk

last: Lee

first: Philip

middle: C

last: Chiu


title: FAO-fueled OXPHOS and NRF2-mediated stress resilience in MICs drive lymph node metastasis

first: Xin

middle: Yuan

last: Guan

state: -- Country other than USA or Canada --

address: Room L10-56, 10/F, Laboratory Block, 21 Sassoon Road, Hong Kong

department: Department of Clinical Oncology

institute: The University of Hong Kong

summary: The lymph nodes (LN) are the most frequent metastatic sites of esophageal squamous cell carcinoma (ESCC), but the associated mechanisms are poorly understood. Tumor cells lodge and survive at the metastatic site during the early adaptation step, which is the bottleneck for successful metastasis. However, the phenotypic and molecular characteristics of tumor cells that contribute to this key process remain elusive. Here, we established a robust human xenograft spontaneous LN metastasis model to capture individual cancer cells and used single-cell RNA sequencing to profile transcriptomic changes in cancer cells during different steps of metastasis.

overall_design: To establish an LN metastasis mouse model, 1-3×10^6 tumor cells tagged with GFP in 20 µl PBS were injected into the right hind foot pad of nude mice. Metastases were evaluated frequently through in vivo imaging. Mice were harvested between 2 weeks and 2 months post-injection. Primary tumors at the injection site and right-side popliteal lymph nodes (draining LNs) were excised for subsequent examination. The absence or presence of LN metastases was confirmed by FACS or examination of 100-µm LN sections for the presence of a GFP signal in the LNs. The single tumor cells were rinsed with DPBS on ice before loading into the Gel Bead & Multiplex Kit and Chip Kit (10× Genomics, Pleasanton, CA, USA) for the construction of a chromium single-cell 3′-library according to the manufacturer’s instructions. Libraries were sequenced on an HiSeq X Ten system and mapped to the human reference genome (build GRCh38) using CellRanger-4.0.0 (10× Genomics).

first: Shanshan

first: Baifeng

last: Zhang

first: Xinyuan


title: Impact of TAZ (WWTR1) depletion on gene expression during primary first-trimester extravillous trophoblast differentiation

first: Martin

summary: Human placental cytotrophoblasts undergo differentiation into extravillous trophoblasts (EVTs) that anchor the placenta to the uterine wall and establish blood flow to the developing fetus. The transcriptional co-activator TAZ (WWTR1) is one of the main effectors of the Hippo signaling pathway, which regulates organ size by controlling important cellular processes such as cell proliferation, apoptosis, stem cell self-renewal and differentiation. Additionally, TAZ is involved in mechano-sensing and cell contact inhibition. In order to gain deeper insights into the function of TAZ in the EVT differentiation process, siRNA (small interfering RNA) treatment was employed to reduce TAZ levels in cytotrophoblasts, which were collected from placentae between 8th and 10th weeks of pregnancy, and underwent EVT differentiation in vitro. The objective of the study was to elucidate the influence of TAZ on the differentiation and function of EVTs by comparing the gene expression profiles of TAZ gene-silenced cells to those with normal TAZ levels.

overall_design: Cytotrophoblasts were isolated from first trimester placental tissue (8th-10th weeks of gestation). Differentiated, HLA-G-positive extravillous trophoblasts were removed by HLA-G PE magnetic bead sorting (MACS Miltenyi Biotec). The remaining HLA-G- negative trophoblasts were plated onto fibronectin-coated cell culture dishes and transfected with non-targeting (ntc) or TAZ siRNAs one hour after seeding. RNA was isolated from the differentiated TAZ siRNA- and ntc-treated cells after 72 hours of cultivation, at the time when the majority of cells developed into EVTs. Subsequently, gene expression analysis was conducted using Next Generation Sequencing, encompassing six samples, three replicates each, derived from three independent cell preparations.

first: Gudrun

first: Peter

last: Kiraly

first: Andras

last: Szilagyi


title: SINE-MIR enhancer rewiring by Esrrb architecturally reprogram the pluripotency spectrum

first: Yingying

last: Zeng


title: Whole-transcriptome analysis of bovine leukemia virus-infected cows with contrasting proviral load levels.

city: Hurlingham

first: Hugo

last: Carignano

address: DR. NICOLAS REPETTO Y DE LOS RESEROS S/N

country: Argentina

institute: Instituto de Virología e Innovaciones Tecnológicas (INTA-CONICET)

summary: Bovine leukaemia virus (BLV) is a retrovirus that infects cattle, causing Bovine Enzootic Leukosis, a chronic disease characterized by the proliferation of infected B cells. BLV proviral load (PVL) is a key determinant of disease progression and transmission risk. Cattle can exhibit distinct phenotypes of low PVL (LPVL) or high PVL (HPVL), which remain stable throughout their lifetime. Differential expression analysis performed in edgeR identified 1,908 differentially expressed genes (DEGs) between HPVL and LPVL animals, including 774 downregulated (DReg) and 1134 upregulated (UReg) genes.

overall_design: We performed a whole-transcriptome analysis of peripheral blood mononuclear cells (PBMCs) obtained from BLV-infected Argentinian Holstein cows. The study compared two contrasting phenotypes: samples from three animals with a high proviral load (HPVL) were analyzed against those from four animals with a low proviral load (LPVL).

first: Marcos

middle: I

last: Petersen

first: Karina

last: Trono


title: Chromatin dynamics at cis-regulatory elements dictate cell fate identities in early embryos [CUTTAG]

city: Milan

first: Yinxiu

last: Zhan

address: via Adamello, 16

institute: European Institute of Oncology (IEO)

summary: The establishment of germ layers during early development is crucial for body formation. The Drosophila zygote serves as a model for investigating these transitions in relation to the chromatin landscape. However, the cellular heterogeneity of the blastoderm embryo poses a challenge for gaining mechanistic insights. Using 10× Multiome, we simultaneously analyzed the in vivo epigenomic and transcriptomic states of wild-type, E(z)-, and CBP-depleted embryos during zygotic genome activation at single-cell resolution. We found that pre-zygotic H3K27me3 safeguards tissue-specific gene expression by modulating cis-regulatory elements. Furthermore, we demonstrate that CBP is essential for cell fate specification functioning as a transcriptional activator by stabilizing transcriptional factors binding at key developmental genes. Surprisingly, while CBP depletion leads to transcriptional arrest, chromatin accessibility continues to progress independently through the retention of stalled RNA Polymerase II. Our study reveals fundamental principles of chromatin-mediated gene regulation essential for establishing and maintaining cellular identities during early embryogenesis.

overall_design: Two biological replicates were performed for each CUT&Tag.

first: Francesco

last: Cardamone

first: Annamaria

last: Piva


title: Chromatin dynamics at cis-regulatory elements dictate cell fate identities in early embryos [bulk RNA-seq]

overall_design: Three biological replicates were performed for each sample.


title: The ZBTB24-CDCA7-HELLS axis suppresses the totipotent 2C-like cell reprogramming by maintaining Dux methylation and repression

city: Kunming

first: meiqi

last: Lin

address: Kunming, Yunnan province

institute: LPBR

summary: Two-cell-like cells (2CLCs), a rare population (~0.5%) in murine embryonic stem cell (mESC) cultures, are in a transient totipotent-like state resembling that of 2C-stage embryos, and their discovery and characterization have greatly facilitated the study of early developmental events, such as zygotic genome activation. However, the molecular determinants governing 2C-like reprogramming remains to be elucidated. Here, we show that ZBTB24, CDCA7 and HELLS, components of a molecular pathway that is involved in the pathogenesis of immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome, function as negative regulators of 2C-like reprogramming by maintaining DNA methylation of the Dux cluster, a master inducer of the 2C-like state. Disruption of the ZBTB24-CDCA7-HELLS axis results in Dux hypomethylation and derepression, leading to dramatic upregulation of 2C-specific genes, which can be reversed by site-specific re-methylation in the Dux promoter. We also provide evidence that CDCA7 is enriched at the Dux cluster and recruits the CDCA7-HELLS chromatin remodeling complex to constitutive heterochromatin. Our study uncovers a key role for the ZBTB24-CDCA7-HELLS axis in safeguarding the mESC state by suppressing the 2C-like reprogramming.

overall_design: To investigate the inhibitory effects of ICF-related genes on 2C-like reprogramming, we generated stable cell lines with Dnmt3b-, Zbtb24-, Cdca7- and Hells-knockouts by CRISPR-Cas9 technology. RNA-seq was conducted on WT, Dnmt3b-KO, Zbtb24-KO, Cdca7-KO and Hells-KO cells to assess the transcriptional profile. To explore whether the facilitation of 2C-like reprogramming in the deficiency of ZBTB24-CDCA7-HELLS axis is Dux dependent, we employed CRISPR-Cas9 technology to knockout Dux cluster in Zbtb24-KO, Cdca7-KO and Hells-KO cells individually to generate Zbtb24/Dux double knockout (DKO), Cdca7/Dux-DKO and Hells/Dux-DKO cell lines. We performed gene expression profiling analysis using data obtained from RNA-seq of WT cells, single-KO and double-knockout cells. Additionally, we treated WT mESCs with DMSO control or 2 μM DNMT1 protein degrader GSK-3484862 for three days for inducing global DNA demethylation.

first: Dan

last: Guo

first: Zeling

last: Du

first: Youqi

first: Meiqi

first: Jiameng

last: Dan


title: Shared requirement for MYC upstream super-enhancer region in tissue regeneration and cancer

city: Stockholm

first: Inderpreet

last: Sur

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Cancer has been characterized as a wound that does not heal. Malignant cells are morphologically distinct from normal proliferating cells but have extensive similarities to tissues undergoing wound healing and/or regeneration. The mechanistic basis of this similarity has, however, remained enigmatic. Here we show that the genomic region upstream of Myc, which is required for intestinal tumorigenesis, is also required for intestinal regeneration after radiation damage. The region is also critical for growth of adult intestinal cells in 3-D organoid culture, indicating that culture conditions that recapitulate most aspects of normal tissue architecture still reprogram normal cells to proliferate using a mechanism similar to that employed by cancer cells. Our results uncover a genetic link between tissue regeneration and tumorigenesis, and establish that normal tissue renewal and regeneration of tissues after severe damage are mechanistically distinct.

overall_design: Crypt enriched fractions of adult mouse intestine or organoids from fetal intestine of wild-type and mice with deletion of the MYC regulatory region were analysed with scRNA-seq. Adult mice with or  without 12 Gy irradiation were used. Intestines were collected 2 days after irradiation (2dpi) for scRNA-seq. For fetal organoid 3Dcultures, epithelium was harvested from E16.5 intestine and cultured in matrigel. Single cell suspensions were prepared on day 11 of culture. Wild-type cultures predominantly contained budding organoids with mature crypt like structures  and few small dense sheroids. These were separately picked and analysed. These did not show major differences and were considered as WT1 and WT2 respectively. The 3D cultures from the mutant mice only contained large spherical structures.


title: Nanobody engineered and photosensitiser loaded bacterial outer membrane vesicles potentiate anti-tumor immunity and immunotherapy

city: CHICAGO

first: Peng

middle: of

last: Xia

state: ILLINOIS

address: 929 E 57TH ST

department: chemistry

institute: University of chicago

summary: Bacterial outer membrane vesicles (OMVs) are promising as antitumor agents, but their clinical application is limited by toxicity concerns and unclear mechanisms. We engineered OMVs with CDH17 tumor-targeting nanobodies, enhancing tumor selectivity and efficacy while reducing adverse effects. These engineered OMVs function as natural stimulator of interferon genes (STING) agonists, activating the cyclic GMP-AMP synthase (cGAS)-STING pathway in cancer cells and tumor-associated macrophages (TAMs). Loading engineered OMVs with photoimmunotherapy photosensitizers further enhanced tumor inhibition and STING activation in TAMs. Combining nanobody-engineered OMV-mediated photoimmunotherapy with CD47 blockade effectively suppressed primary and metastatic tumors, establishing sustained antitumor immune memory. This study demonstrates the potential of nanobody-engineered OMVs as STING agonists and provides insights into novel OMV-based immunotherapeutic strategies harnessing the innate immune system against cancer. Our findings open new avenues for OMV applications in tumor immunotherapy, offering a promising approach to overcome current limitations in cancer treatment.

overall_design: To investigate the function of engineered bacterial outer membrane vesicles (OMVs) in tumor cells, we established a Colon26 cell mouse subcutaneous tumor model. By comparing the differentially expressed genes between the control group and the OMV group, we explored the mechanism by which OMVs play a role in tumors.