title: Tripotent Lgr5 stem cells in the posterior tongue generate non-taste lingual, taste and salivary gland cells [Bulk RNA-seq]

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

institute: Prinses maxima centrum

summary: The circumvallate papillae (CVP) and foliate papillae (FoP) of the posterior tongue contain taste buds in close proximity to specialized salivary glands, known as von Ebner and minor salivary glands, respectively. The developmental relationship between taste buds and these salivary glands remains largely unexplored. Lineage tracing studies in mice have revealed that Lgr5 marks taste bud stem cells. Here, we report single-cell RNA sequencing of the entire CVP and FoP of mice, yielding transcriptional profiles of cells from tongue surface epithelium, taste buds and the associated salivary glands. We unveiled a developmental trajectory in which taste buds, the associated salivary glands and the non-taste tongue surface epithelium originate from a common Lgr5+ cell. We describe long-term organoid culture conditions for these cells and confirm their tripotency at the clonal level in vitro. CVP and FoP harbor chemosensory units consisting of taste bud and salivary gland cells derived from the same parental Lgr5+ stem cell.

overall_design: Circumvallate papillae (n=20) and foliate papillae (n=40) were send for single-cell RNA seq. Lineage trajectory analysis revealed a potential bi/tripotent Lgr5+ stem cell in the posterior tongue. Subsequent scRNA-seq analysis of clonal cultures derived from a single Lgr5+ stem cell presented its tripotent nature. Next, in-vivo mulitcolour lineage tracing confirmed this phenomenon. Studying the cell fate decisions resulted in a putative role for Foxe1 in the lineage trajectory. Bulk RNA-sequencing of knock-out of Foxe1 in the posterior tongue organoids revealed an ablation of mature saliva markers and a more progenitor-like phenotype.

first: Laurens

last: Verweij

first: Seok-Young

last: Kim

first: Dimitrios

last: Laskaris

first: Lin

last: Lin

first: Femke

last: Ringnalda

first: Chris

last: Winkel

first: Jay

last: Slack

first: Karin

last: Sanders

first: Jacco

last: van Rheenen

first: Marc

last: van de Wetering

first: Hans

last: Clevers


title: Tripotent Lgr5 stem cells in the posterior tongue generate non-taste lingual, taste and salivary gland cells [scRNA-seq]

status: Public on Sep 01 2025

city: Utrecht

country: Netherlands

type: Expression profiling by high throughput sequencing


title: Cardiomyocyte development from human induced pluripotent stem cells (iPSC)

city: Liverpool

first: Richard

last: Barrett-Jolley

address: 6 West Derby Street

country: United Kingdom

institute: University of Liverpool

summary: Induced-pluripotent stem cell-derived cardiomyocyte (IPSC-CM) models can improve understanding of pathophysiology through disease modelling and can be used for cardiotoxicity screening of drugs, ultimately reducing reliance on animal models; however these models have not been extensively functionally characterised, which was the aim of this study. A contracting IPSC-CM model was generated and characterised for atrial and ventricle-specific cardiac gene expression with RNAsequencing.  These data are to be correlated with functional assays.

overall_design: Cryopreserved IPSCs were recovered from liquid nitrogen and thawed into a 6 ml volume of StemFlexTM supplemented with 10 µM rho-associated protein kinase (ROCK) inhibitor (Y-27632 dihydrochloride; Sigma). IPSCs were collected by centrifugation at 100 x g for 90 seconds and the cell pellet gently resuspended in StemFlexTM, before being plated onto vitronectin-coated tissue culture plates.   Spontaneous differentiation of IPSCs was initiated by replacement of StemFlexTM medium with DMEM/F-12 supplemented with 10% (vol/vol) FBS. Medium changes were performed every 3-4 days for up to 15 days. RNA was purified from monolayer cell culture using RNeasy Mini Kit (Qiagen, Manchester, UK) according to the manufacturer’s instructions. Data was the sequenced on a NovaSeq with paired-end protocol.


title: Bioinformatic-experimental screening uncovers multiple targets for increase of MHC-I expression through activating the interferon response in breast cancer

city: Wuhan

first: Zilun

last: RUAN

state: Hubei

address: Donghu Road, No. 115, Wuchang District

department: Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University

country: China

institute: Wuhan University

summary: Expression of major histocompatibility complex I (MHC-I) on tumor cells is extremely important for antitumor immune response for its essential role in activating various immune cells including tumor-specific CD8+ T cells. Cancers of low MHC-I expression are commonly of little immune cell infiltration and exhibit poor prognosis in clinic. In this study, we conducted a bioinformatic-experimental screening to identify potential gene targets to enhance MHC-I expression in breast cancer. Through combination of MHC-I scoring, gene expression correlation analysis, and survival prognostication, we identify 243 genes negatively correlated with MHC-I expression in breast cancer, of which 144 genes were further identified as negative correlation factors for tumor-infiltrated lymphocytes. Finally, we verified partially according to KEGG or gene-dependency analysis in breast cancer MCF7 cells, and figured out multiple genes including PIP5K1A, NCKAP1, CYFIP1, DIS3, TBP and EXOC1 as potent gene targets for increase of MHC-I expression in breast cancer. Mechanistically, knockout each of these genes activates the intrinsic interferon response in breast cancer cells, which not only promoted MHC-I expression but also caused immunogenic death of breast cancer cells. Collectively, we identified multiple gene targets for increase of MHC-I expression in breast cancer.

overall_design:
The HEK-293T cells were purchased from the American Type Culture Collection (ATCC). The MCF7 cells were kindly provided by Dr. Cheguo Cai (Wuhan University). These cell lines were cultured in DMEM (GIBCO) medium supplemented with 10% FBS (Cellmax) and 1% penicillin-streptomycin (HyClone) under an atmosphere of 5% CO2 at 37 °C. All cells were negative for mycoplasma.
CRISPR-Cas9 gRNA plasmids for the indicated 40 candidate genes were constructed by standard molecular biology technique. HEK-293T cells were seeded into plates for 20 hours, and then cells were transfected by standard calcium phosphate precipitation method at a density of 40%–50%.
Gene knockout in MCF7 cells was achieved using a CRISPR-Cas9 system. Briefly, double-stranded oligonucleotides corresponding to the target sequences were cloned into the lenti-CRISPR-V2 vector, and then these lentiviral plasmids were co-transfected with two packaging plasmids into HEK-293T cells. Two days after transfection, the lentiviral supernatants were harvested, ultra-filtrated (0.45 mm filter, Millipore), and then infected MCF-7 cells in the presence of polybrene (8 mg/mL). The infected cells were selected with puromycin (2 mg/ml) for at least 6 days to establish stable cell lines.

first: Xin

last: Li

first: Zi-Lun

last: Ruan

first: Shu-Zhen

last: Yang

first: Qing

first: Jin-Peng

first: Ming-Ming

last: Hu


title: Myeloid TGF-b signaling shapes liver macrophage heterogeneity and metabolic liver disease pathogenesis

city: Ann Arbor

first: Jiandie

state: MI

address: 210 Washtenaw Ave

department: Life Sciences Institute

country: USA

institute: University of Michigan

summary: Cellular heterogeneity of innate immune cells such as macrophages is a hallmark of metabolic dysfunction-associated steatohepatitis (MASH) pathogenesis. The mechanisms shaping liver macrophage heterogeneity and polarization during disease progression remain poorly understood. Here we identified TGF-b signaling as a critical regulator of the bifurcate maturation of TREM2+ and NEGR1+ macrophages in MASH liver. Myeloid-specific inactivation of Tgfbr1 in mice exacerbated diet-induced MASH pathologies, including hepatocyte injury, inflammation, and liver fibrosis. Mechanistically, ablation of TGF-b signaling in myeloid cells resulted in diminished TREM2+ macrophages and a marked expansion of NEGR1+ macrophages in the liver. The latter is characterized by induction of gene signatures associated with inflammasome activation, cytokine signaling, cellular senescence, and immunosuppression. The expansion of NEGR1+ macrophage contributes to effector T cell exhaustion, thereby facilitating the development of MASH-associated hepatocellular carcinoma in Tgfbr1-deficient mice. Together, these studies uncover myeloid TGF-b signaling as a crucial factor within the liver microenvironment that shapes liver macrophage heterogeneity and functional polarization during MASH pathogenesis and the development of MASH-associated liver cancer.

overall_design: Bulk RNA-seq on metabolic-dysfunction associated steatoheptitis (MASH) mouse liver in Control and Tgfbr1 MKO mice ; Single-nucleus RNA-seq on MASH mouse liver in different genotypes

first: Ziyi

last: Meng

first: Xiaoxue

last: Qiu

first: You

last: Lu

middle: D


title: TRiC/CCT Chaperonin Regulates RNA Polymerase II in the Nucleus [RNA-seq]

city: Boston

first: Zlata

last: Gvozdenov

state: MA

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

summary: The molecular chaperonin TRiC/CCT is a large hetero-oligomeric structure that serves an essential role in eukaryotic cells by minimally supporting protein homeostasis including the folding of nascent polypeptides and the assembly/disassembly of protein complexes. TRiC/CCT is typically considered a strict cytosolic machine. Here, we investigated the influence of TRiC/CCT on nuclear features including epigenetic marks, chromatin accessibility, and transcription. Despite being linked to several chromatin modifiers, our work indicates TRiC/CCT does not have a sustained role with these factors. TRiC/CCT did actively contribute to transcription. Inactivation of TRiC/CCT resulted in a significant increase in the production of RNA leading to an accumulation of noncoding transcripts. Our data support a direct role for TRiC/CCT with RNA polymerase II as the chaperonin modulated nascent RNA production both in vivo and in vitro. Overall, our studies reveal a new avenue by which TRiC/CCT contributes to cell homeostasis by regulating the activity of nuclear RNA polymerase II.

overall_design: To assess the influence of the CCT chaperonin on nuclear events, we examined steady-state RNA transcripts in the presence and absence of active CCT. To inactivate CCT, we used the temperature sensitive strain cct1-2. WT and cct1-2 and an established temperature regime of 4 h at 37°C, which prompts cessation of cell growth that is reversible following a return to a permissive temperature (Ursic et al. 1994). In brief, exponentially growing parental and cct1-2 yeast were shifted to 37°C for 4 h. RNA was isolated and subjected to NGS. RNA-Seq analysis was performed: Differential gene expression was done by comparing WT and cct1-2; regions with cryptic transcription events were analyzed.


title: Small nucleolar RNA SNORA67 regulates DLGAP5-activated Wnt pathway to promote colorectal cancer development

city: Shenyang

first: Xiaotong

last: Jiang

address: Nanjing North Street, Heping District

institute: The First Affiliated Hospital of China Medical University

summary: Background Colorectal cancer is a malignancy with high incidence and mortality rates worldwide, posing a serious threat to human life and health.Since tumor progression is usually hidden onset and most CRCs are diagnosed at a late stage, the exploration of new biomarkers can greatly improve the early diagnosis of CRC and is crucial for treatment and prognosis. Small nucleolar RNA (snoRNA), a conserved short non-coding RNA, involves in the regulation of tumorigenesis and progression. Methods Differentially expressed SNORA67 was screened based on colorectal cancer tissue data from GEO and TCGA databases.Clinical significance of SNORA67 was investigated using Cox proportional risk model, work characteristics（ROC） and survival analysis of subjects. The biological function of SNORA67 was studied by CCK8, plate cloning, Transwell, scratch test, flow cytometry and xenotransplantation of nude mouse models.RNA-seq was designed to clarify the pathway and downstream target genes, and the underlying mechanisms were verified by PCR and WB assay analysis. Results We demonstrated that SNORA67 is highly expressed in colorectal cancer, and was a relevant marker for CRC diagnosis and prognosis. Inhibition of SNORA67 in CRC cell line can inhibit proliferation and migration in vitro, promote apoptosis, affect cell cycle and inhibit tumor growth in vivo.Mechanistically, SNORA67 activates the Wnt signaling pathway in J colorectal cancer by regulating DLGAP5.

overall_design: To investigate the specific mechanisms by which SNORA67 promotes the biological properties of colorectal cancer cells, we performed transcriptome sequencing of control NC and experimental ASO-SNORA67 in the HCT116 cell line.

first: J

last: Xiaotong

first: Y

last: Zhidong

first: K

last: Hui

first: M

last: Lijie

first: C

last: Shitong


title: Distinct hepatocyte adaptations during gestation and lactation

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

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

sample_organism:
Ovis aries
Mus musculus

platform_organism:
Ovis aries
Mus musculus

overall_design: Refer to individual Series


title: TGF-b/Smad3 inhibition synergizes with PPARg agonism to reduce fibrosis and enhance functional beige adipogenesis

city: Bethesda

first: Youngjae

last: Bahn

state: Maryland

address: 10 Center Dr.

institute: NIH

summary: Adipose tissue depots vary markedly in their ability to store and metabolize triglycerides, undergo beige adipogenesis and be susceptibile to metabolic disease. The   molecular mechanisms that underlie such heterogeneity are not entirely clear. Previously, we showed that TGF-b signaling regulates the browning of white adipose tissue via recruitment of dedicated beige progenitors. Here, we find that TGF-b signals dynamically regulate the balance between adipose tissue fibrosis and beige adipogenesis. Elevated basal and high-fat diet inducible activation of TGF-b/Smad3 signaling was observed in the visceral (epididymal) adipose tissue depot. Activation of TGF-b/Smad3 signaling was associated with increased adipose tissue fibrosis. RNA-seq combined with fluorescence-activated cell sorting of stromal vascular fraction of epididymal white adipose tissue depot resulted in identification of TGF-b/Smad3 regulated ITGA5+ fibrogenic progenitors. TGF-b/Smad3 signal inhibition, genetically or pharmacologically, reduced fibrosis and increased functional beige adipogenesis. TGF-b/Smad3 antagonized the beneficial effects of PPARγ  , activation whereas TGF-b receptor 1 inhibition synergized with actions of rosiglitazone, a PPARγ agonist, to dampen fibrosis and promote beige adipogenesis. There was a positive correlation between TGF-b activation and levels of fibrosis marker, ITGA5, in human adipose tissue samples  , with visceral (omental) adipose tissue depot exhibiting higher fibrosis potential than subcutaneous or brown adipose tissue depots. Taken together, out data provide TGF-b/Smad3 signaling operates at the nexus of adipose tissue fibrosis and functional beige adipogenesis.

overall_design:
For CD versus HFD, primary preadipocytes were isolated from eWAT of CD or HFD fed mice. For mock versus TGF-β versus SB, primary preadipocytes from eWAT of wildtype mice were treated by TGF-β with/without SB431542.
For Itga5High versus Itga5 Low, primary preadipocytes were collected by FACS Aria cell sorter by anti-CD49e antibody and induced adipogenic differentiation into adipocytes.

first: YoungJae

first: Sushil

middle: G

last: Rane


title: Effect of knockdown of junctional genes JUP and PLEC on Small Airway Epithelial Cells (SAECs)  in the context of epithelial desquamation in distal bronchioles of Idiopathic Pulmonary fibrosis (IPF) patients

city: New Haven

first: Rolando

last: Garcia-Milian

state: CT

address: 333 Cedar St

department: CWML

institute: Yale University

summary: JUP and PLEC are downregulated in the distal bronchioles of IPF patients. To understand the relevance of this in the epithelial sloughing (desquamation) phenotype observed in distal bronchioles of IPF patients, we knockeddown JUP and PLEC in small airway epithelial cells thats are isolated from distal bronchioles of human airway epithelium (Lonza). Bulk RNA sequencing of JUP vs Scrambled and PLEC vs Scrambled were performed. The transriptomic data suggests that JUP transcriptionally regulates the matrix synthesis and the transcription of other junctional genes in SAECs. However, no significant effect of PLEC knockdown on transcription of matrix genes, a significant reduction in junctional gene transcripts were observed in PLEC knockdown. These findings suggest that JUP and PLEC may play key roles in the regulation of epithelial integrity during homeostasis, and when desrupted can lead to epithelial desquamation.

overall_design: SAECs were cultured in small airway epithelial cell medium (Lonza) and the cells were treated with eaither scrambled RNA or siRNA against JUP or siRNA for PLEC. After 72hrs, total RMA was extracted from SAECs and subjected to bulk RNA sequencing.

first: Rachana

middle: R

last: Chandran

first: Brigitte

middle: N

last: Gomperts


title: The transcriptome of WT and DDX55 knockout CD4 naive T cells that activated for indicated time points

city: 成都

first: ping

last: he

address: 17 Renmin South Road, Wuhou District, Chengdu

institute: sichuan university

summary: WT and DDX55 knockout CD4 naive T cells were stimulated with anti-CD3/CD28 antibodies in vitro for 0, 8, 24 hours, and the transcriptome of these cells were determined by whole-transcriptome sequencing.

overall_design: Purified WT or Ddx55-KO naïve CD4+ T cells were stimulated with plate-bound anti-CD3(5 ug/ml) and anti-CD28(2.5 ug/ml) for 0, 8, and 24 hours followed by total RNA isolation. RNA library preparation and high throughput sequencing were conducted


title: Neuronal CD47 Induces Microglial Phagocytosis Defects and Autism-like Behaviors While Mitigating Aβ-Induced Synaptic Loss

city: Hefei

first: Wenjie

last: Hu

address: No.81, Meishan Road

institute: Anhui Medical University

summary: Neuronal CD47 is a potent "do not eat me" signal that protects synapses from excessive pruning by microglia. We used an adeno-associated viruses gene expression system to induce neuron-specific CD47 overexpression in wild-type and 5xFAD mice,and we used single nucleus RNA sequencing (snRNA-seq) to analyze the diversity of neurons and microglia in the hippocampus.

overall_design: Mice were injected with AAV-mCherry and AAV-CD47 respectively, and the hippocampal tissues of mice were isolated after 2 months and analyzed using SnRNAseq.

first: Mengting

last: Chen

first: Yujie

last: Cheng

first: Wei

last: Shao

first: Shanshan

last: Zhou

first: Panpan

first: Xingqi

last: Wu

first: Yin

first: Kai

last: Wang


title: The chromatin accessibility of WT and DDX55 knockout naive CD4 T cells

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ATAC-seq were used to determine the chromatin accessibility across the genome in WT and DDX55 knockout naive CD4 T cells.

overall_design: ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) were performed on CD4 naive T cells isolated from WT and DDX55 knockout mice.


title: Zebrafish caudal fin amputation models the effects of diabetes on inflammation and regeneration

city: Guiyang

first: Zhao

last: Yanchi

state: Guizhou

address: No. 9 Beijing Road

institute: Guizhou Medical University

summary: Aim: In this study, we aim to establish a diabetic zebrafish model and examine the effects of high glucose on inflammation and tissue regeneration. Materials and Methods:  Tübingen strain zebrafish (wild type, WT), Tg (mpo: EGFP), and Tg (coro1a: EGFP) zebrafish were employed. Caudal fin amputation was performed to study tissue regeneration and inflammation. Results:  Our results showed that high glucose increased the recruitment of neutrophils and macrophages after amputation. Most importantly, limb regeneration was severely impaired after amputation in zebrafish larvae exposed to 222 mM glucose for 14 days. In addition, inflammatory factors IL-1β, IL-6, TNF-α, VCAM-1, and MCP-1, which are closely related to the development of diabetic wound, increased significantly in caudal fin amputation after glucose exposure. The p38 inhibitor SB203580 can reduce the expression of inflammatory factors and promote regeneration in high glucose. It showed that caudal fin amputation after glucose exposure resulted in genes enrichment of several pathways involved in amino acid metabolism, lipid metabolism, and inflammation based on high-throughput transcriptome sequencing. Conclusions:  Overall, this experimental system using zebrafish larvae provides a wide spectrum of genetic and molecular profile recapitulating human diabetes which will be beneficial for basic research of inflammation and regeneration in diabetic background and promote translational research for diabetes therapy.

overall_design: Zebrafish embryos were placed in 30 ml of culture medium in petri plates with 130 mM or 222 nM D-glucose at 6 hours post fertilization (hpf) and control group were maintained in regular culture medium. All embryos were cultured in incubator at 28.5 ℃. The culture medium was replaced at half volume every day.  Caudal fin amputation was performed after glucose exposure for 14 days. Briefly, the larvae were fixed with 3% carboxymethyl cellulose in the culture dish after anesthesia with 0.03% tricaine. The caudal fin was carefully removed at the distal end of the spinal cord of the zebrafish larvae with a 1 mm sapphire blade, without spinal cord injury. After caudal fin amputation, the zebrafish larvae were placed back to original culture condition. Total RNA was extracted using Invitrogen TRizol reagent (California, USA), and generation of the Illumina RNA sequence library and paired end sequencing (300±50 bp) were performed on an Illumina NovaSeq 6000 using aliquots (5 mg) of qualified total RNA. Hisat software was used to compare the sequencing data with the zebrafish referenced genome. To evaluate the expression level of all mRNAs, we first realized sample reads through StringTie, and then calculated the FPKM (fragments per kilobase of transcript per million mapped reads) using stringtie and edgeR software. Finally, the differentially expressed genes (DEGs) were screened by the R software package according to the following criteria: log2 (fold-change) > 1 or <−1 and at p < 0.05. These DEGs were used for further analysis of functions and signaling pathways using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes.

first: Hua

last: Li

first: Yanchi

last: Zhao

first: Dashuang

last: Mo

first: Liping

last: Shu


title: Cross-species cellular mapping and humanization of Fcγ receptors to advance antibody modeling

city: Zwijnaarde

first: Sophie

last: Janssens

address: Technologiepark 71

department: Inflammation Research Center

country: Belgium

institute: VIB/UGhent

summary: Fc receptors mediate the effector functions of therapeutic antibodies. Immunoglobulin G (IgG), the predominant antibody in circulation and clinical use, engages diverse Fc gamma (Fcγ) receptors that are expressed by multiple immune and structural cells. Here, we provide a comprehensive overview of Fcγ receptors and FcRn expression at both the transcriptomic and proteomic level in humans, macaques, and mice. We reveal species-specific differences in both Fcγ receptor diversity and cell-specific expression profile that compromise the translation of mouse and macaque preclinical models for antibody research. To overcome this, we generated a new mouse model in which human FcγRI (hCD64), FcγRIIA (hCD32A), FcγRIIB (hCD32B), FcγRIIIA (hCD16A), FcγRIIIB (hCD16B) is expressed under control of the relevant human promotors, replacing the murine counterparts (FcγRI, FcγRIIB, FcγRIII, and FcγRIV). Furthermore, to improve human antibody pharmacokinetics, murine FcRn was replaced by its human analog. We comprehensively mapped the expression of the knock-in receptors, and found that humanization led to much more faithful cell-specific Fcg receptor expression. We validated the functionality of these knock-in human receptors through in vitro and in vivo antibody-dependent cellular cytotoxicity, anaphylaxis and antigen presentation assays. This cross-species Fcγ receptor atlas and humanized mouse model with refined Fcg  receptor expression and antibody pharmacokinetics will improve the preclinical assessment of antibody-based therapeutics.

overall_design: We carried out single-cell RNA sequencing (BD Rhapsody platform; sequenced using NovaSeq6000) on magnetically cell enriched (MagniSort) and fluoresence-activated cell sorted (FACS; BD Symphony S6) splenocytes of C57BL/6J female mice

first: Karel

last: Van Damme

first: Victor

last: Bosteels

first: Clint

last: De Nolf

first: Bart

last: Lambrecht


first: ping

last: he

summary: Genome-wide distribution of H3K9me3, RNA polymerase II, Rloop, DDX55 and HA-tagged DDX55 in WT and DDX55 knockout CD4 naive T cells were determined by cleavage under targets and tagmentation (CUT&Tag) assays followed by deep sequencing (CUT&Tag-seq) with corresponding antibodies.

overall_design: Cleavage under targets and tagmentation (CUT&Tag) assays were performed using antibodies of H3K9me3, RNA polymerase II, Rloop, DDX55 and HA-tag, respectively on naive T cell isolated from WT and DDX55 knockout mice. The tagmentation products were purified and sequenced on NovaSeq 6000 sequencer (Illumina) with the PE150 model.


title: Nuclear compression-mediated DNA damage drives ATR-dependent Lamin expression and mouse ESC differentiation

city: Mumbai

first: Shamik

last: Sen

state: Maharashtra

address: Powai

department: Biosciences and Bioengineering

country: India

institute: IIT Bombay

summary: Embryonic stem cells (ESCs) which are susceptible to DNA damage depend on a robust and highly efficient DNA damage response (DDR) mechanism for their survival. However, the implications of physical force-mediated DNA damage on ESC fate remains unclear. Here we assessed the importance of DNA damage in ESC differentiation by culturing mouse ESCs (mESCs) on substrates of varying stiffness, which has been shown to induce stem cell differentiation. We show that stiffness-dependent mESC spreading induces DNA damage through nuclear compression that leads to loss of pluripotency, expression of Lamin A/C and germline markers. DNA damage and induction of Lamin A/C are observed in the presence of differentiating agents, as well as during mESC differentiation on cell derived matrices, identifying DNA damage as an early event in differentiation. Differentiation was also associated with reduction of DNA damage and activation of the DDR factor – ATR. While ATR is typically known to play roles in DDR pathway, its role during stiffness-mediated nuclear compression and mESC differentiation is unknown. Nuclear enrichment of activated ATR on stiff substrates and reduction of Lamin A/C expression due to ATR inhibition suggests that mESC differentiation is driven by nuclear compression-mediated DNA damage and involves ATR-dependent modulation of Lamin A/C.

overall_design: To probe the effect of stiffness mediated mechanoadaptation on Tg2A mouse embryonic stem cells (mESCs), we cultured mESCs on gels of varying stiffnesses (0.6 kpa, 4 kPa and 33 kpa) coated with fibronectin. RNA isolation of whole cell lysates was done at different timepoints (3hrs, 6 hrs, 24 hsr and 72 hrs) and compared with a pluripotent control which was cultured on gelatin coated dish in presence of LIF. A DNA damage positive control was used by treating the cells with etoposide (ETO) on 0.6 kPa for 24 hrs. Samples were pooled from 3 independent experiments and run as 2 replicates.

first: Tanusri

last: Roy

first: Sayak

last: Dhar

first: Niharika

last: Tiwary

first: Priya

last: Singh

first: Divya

middle: T

last: Sowpati

first: P

middle: C

last: Shekar

first: Sushil

last: Kumar


title: Electroacupuncture at PC6 Acupoint Adjusts Genome-Wide Gene Expressions and Alters Carfilzomib-Induced Cardiotoxicity in Mice

city: Nanjing

first: Yuxuan

last: Chen

state: Jiangsu

address: 138 Xianlin Rd

institute: Nanjing University of Chinese Medicine

summary: Carfilzomib (CFZ) is a proteasome inhibitor commonly used in the treatment of multiple myeloma, but its clinical application is limited due to its cardiotoxicity. The Neiguan acupoint (PC6) stimulation has been reported to effectively improve cardiac function, but its regulatory mechanism remains unclear. The aim of this study was to investigate the effect and underlying mechanism of electroacupuncture (EA) against CFZ-induced cardiotoxicity in C57BL/6 mice. According to our results, EA treatment significantly reversed CFZ-induced ejection fraction and fractional shortening reduction, which showed great potential effect for heart protection. By using RNA-sequencing, we compared the transcriptome profile of heart samples from DMSO control, CFZ injection, and EA treatment mice, and nearly 40,000,000 valid sequence reads aligned with 20,000 genes from six libraries were obtained. A total of 770 differentially expressed genes (DEGs) were identified in the CFZ (vs. Control) group, including 65 up-regulated and 705 down-regulated genes. Meanwhile, 329 DEGs were obtained in the EA (vs. CFZ) group, including 251 up-regulated and 78 down-regulated genes. Our results shed new insights into the regulatory mechanism of EA at PC6 against CFZ-induced cardiotoxicity, which could further provide theoretical basis for clinical EA therapy.

overall_design: The transcriptome profiles of heart samples from DMSO control, CFZ injection, and EA treatment mice were generated in duplicate, using Illumina NovaSeq 6000.

first: Shengfeng

last: Lu

first: Wei

last: Wu

first: Yi

last: Qian

first: Yizhou


title: High-plex spatial transcriptomic profiling of mismatch repair-deficient endometrial cancer [GeoMx]

city: Chengdu

first: Xue

last: Xiao

state: Sichuan

address: 32# W. Sec 2, 1st Ring Rd

department: Department of Pathology

institute: Sichuan provincial people's hospital

summary: Tumors bearing mismatch repair deficiency (MMRd) are characterized by a high load of neoantigens and are believed to trigger immunogenic reactions upon immune checkpoint blockade treatment. However, multiple cancers with MMRd exhibit variable responses to immune checkpoint inhibitors (ICIs). In endometrial cancer (EC), a distinct tumor microenvironment (TME) exists that may correspond to treatment-related efficacies. Since pre-existing CD8+T cells in the TME are critical for effective treatment of ICI, and lack of T cell infiltration can make MMRd tumor insensitive to ICI therapy, we characterized MMRd ECs with different level of CD8+T cells infiltration. Our analysis identified a gene signature in the MMRd tumor-enriched regions stratifying tumors into “hot”, “intermediate” and “cold” groups according to their distinct immune profiles, a finding highly consistent with the corresponding CD8+ T-cell infiltration status.

overall_design:
We applied digital spatial profiling, a high-plex spatial transcriptomic approach covering over 1,800 genes, to obtain a highly resolved TME landscape in 45 MMRd-EC patients.
Please note that none of the patients (in the records) were treated with ICI.  Since pre-existing CD8+T cells in the TME are critical for effective treatment of ICI, MMRd ECs with different level of CD8+T cells infiltration were analyzed. The CD8+T cells infiltration status is provided in each sample records.


title: Mitochondrial serine metabolism fuels epigenetic remodelling in osteoclast differentiation and is the main target of methotrexate

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

summary: Osteoclasts are specialized myeloid cells with crucial roles in skeletal homeostasis and disease. Differentiation of precursor cells to osteoclasts requires extensive metabolic and epigenetic rewiring, but pathways governing these processes are poorly characterized. Here, we found that transdifferentiation into osteoclasts crucially depends on the generation of one carbon units from serine catabolized by SHMT2. Serine mediatedde novopurine synthesis fuels increased mitochondrial ATP production and ultimately SAM generation necessary for epigenetic repression of macrophage lineage genes. Intriguingly, methotrexate restrains osteoclast precursors from engaging in serine mediated one carbon metabolism, unravelling a hitherto unknown therapeutic mechanism of action. Supplementation of purine precursor metabolites which restore mitochondrial ATP generation fully rescues osteoclastogenesis of SHMT2 knockout or methotrexate inhibited cells. Together, we show an essential role of serine catabolism for metabolic epigenetic coupling in osteoclast differentiation and provide a framework how methotrexate prevents osteoclast-mediated joint destruction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bone marrow derived cells treated with MCSF+RANKL with or without certain amino acids or inhibitors

first: Markus

last: Kieler

first: Stephan

last: Blüml


title: TENT-5 regulates the expression of male-specific genes in Caenorhabditis elegans

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

summary: Polyadenylation is an important post-transcriptional process that governs mRNA stability and expression. Advancements in direct RNA sequencing in recent years have clarified many aspects of this intricate regulation, revealing the influence of various factors. Here, we used Nanopore Direct RNA Sequencing to investigate the association between genome-wide mRNA poly(A) tail profiles and sexual dimorphism in Caenorhabditis elegans. Our results demonstrate sex-dependent differences in both gene expression and poly(A) tail metabolism. Notably, we discovered that cytoplasmic poly(A) polymerase TENT-5 regulates multiple male-specific transcripts, predominantly encoding putative seminal fluid components with predicted extracellular localization. TENT-5 expression in male-specific tissues, such as seminal vesicle and vas deference, corroborates its functional significance. Intriguingly, despite extensive TENT-5-mediated polyadenylation of male-specific transcripts, males devoid of TENT-5 show no abnormalities in mating behavior, sperm morphology, or fertility. Our findings suggest that TENT-5 plays a role in regulating sex-related processes in males, although the physiological consequences remain to be fully elucidated.

overall_design: We implemented Nanopore Direct RNA Sequencing to investigate sex-related differences in gene expression and poly(A) tail metabolism in C. elegans. We performed analysis of wild type (N2) hermaphrodites and males at the young adult stage. Additionally, we compared wild type (N2) males and tent-5(tm3504) males and showed that male-specific genes in C. elegans are regulated by TENT-5.

first: Zuzanna

last: Mackiewicz

first: Vladyslava

last: Liudkovska


title: Comparing the salivar microbiota composition between healthy subjects and HIV patients

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: Those FASTQ are used in a paper where are primarily compared the variations in the oral microbiota composition between HIV patients and healthy controls (HC). In addition, it is performed a longitudinal evaluation of the oral-gut microbiota-immunity axis from HIV-infected patients before starting ART (T0) and after reaching virological suppression (T24 weeks).

overall_design: Total DNA was extracted from the saliva of the subjects, amplified to collect amplicons of variable V3–V4 regions (primers 341F and 805R) of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

first: Amedeo

last: Amedei

first: Edda

last: Russo

first: Leandro

last: Di Gloria

first: Giulia

last: Nannini


title: Activation of Cannabinoid CB2 Receptor in Spinal Microglia alleviates chronic itch

city: Shenzhen

first: Zilong

last: Wang

address: XueyuanDadao

institute: Southern University of Science and Technology

summary: To explore the effects of Cannabinoid CB2R on microglia function in DNFB-induced atopic and contact dermatitis (ACD) mice model, we performed single-cell RNA sequencing (scRNA-seq) analysis of spinal cord samples from three groups, including the naïve control group, ACD model treated with i.t. vehicle (DNFB + Vehicle) group and ACD model treated with i.t. 10 μg AM1241 (DNFB + AM1241) group

overall_design: Spinal dorsal horn (SDH) samples from naïve group,DNFB + Vehicle group, and DNFB + AM1241 group mice. 3 male mice for each group were used to perform the scRNA-Seq (1 sample containing 3 male mice's SDH).

first: Kangtai

last: Xu


title: Understanding the mechanisms of resistance to BRAF inhibitors in colorectal cancer

city: Lexington

first: Yekaterina

last: Zaytseva

state: KY

address: 760 Press ave

department: Toxicology and Cancer Biology

institute: University of Kentucky

summary: Mutations in proto-oncogene BRAF occur in about 10-15% of CRC patients and BRAFV600E is the most common. Most patients with BRAFV600E metastatic CRC show reduced survival compared to patients with wild-type BRAF. For patients who undergo BRAF-targeted therapy, resistance develops 4-6 months after treatment initiation and results in more aggressive disease. We established  PT130 cells resistant to PLX8394, a novel BRAF inhibotor, and tested them in vitro and in vivo.

overall_design: To invesigate the differences in PT130 Parental and PT130 PLX 8394 Resistant cells both in vitro and in vivo

first: Mariah

last: Geisen

first: Daheng

last: He

first: Chi


title: Injured sensory neurons-derived Galectin-3 contributes to neuropathic pain via programming microglia in the spinal dorsal horn

summary: Gal3 plays an important role in chronic pain through the activation of microglia. We used single nucleus RNA sequencing (snRNA-Seq) to uncover the mechanisms of Gal3-activated microglia in pain regulation.

overall_design: Spinal dorsal horn (SDH) from 6-days vehicle or Gal3-treated mice, 3 male mice for each group were used to perform the snRNA-Seq (2 groups: vehicle control (1 sample containing with 3 male mice's SDH) and Gal3-treatment (1 sample containing 3 male mice's SDH)).

first: Leyan

last: Shan

first: Luyao

last: Ji


title: Iron supplementation in zebrafish models of mucopolysaccharidoses type III

city: Adelaide

first: Karissa

last: Barthelson

state: South Australia

address: North Terrace Campus

country: Australia

institute: The University of Adelaide

summary: Sanfilippo Syndrome Type B, characterized by a deficiency in N-acetylglucosaminidase (NAGLU) enzyme, represents a debilitating genetic disorder which causes childhood dementia. In this study, we employed zebrafish models carrying the naglu A603fs mutation to investigate the potential of intraperitoneal (i.p.) injection of ferric citrate to rescue whole brain transcriptomes relative to an i.p. injection of saline vehicle control. Zebrafish, aged 6 months, were either homozygous (MPS IIIB) and heterozygous (unaffected control) genotypes, and each group was subjected to either ferric citrate or saline injection. A total of 10 fish per genotype and treatment were examined via RNA-seq. Although initial findings identified sex-specific differences in inflammation pathways and regeneration which may be rescued in female samples (but not in males), the sample size of fish per genotype, sex, and treatment limited the ability to draw definitive conclusions.

overall_design: Whole-brain profiles from heterozygous (naglu A603fs/+, unaffected control) and homozygous mutant siblings (naglu A603fs/A603fs, MPS IIIB) zebrafish 7 days after an i.p. injection of ferric citrate (10 micrograms) or 0.85% saline control. Brains were taken from zebrafish aged at 6 months.

first: Michael

last: Lardelli


title: Activation of a nongenetic AHR-ELMSAN1 axis optimizes BET-targeting therapy and suppresses leukemia stem cells in preclinical models [RNA-Seq2]

city: Birmingham

first: xinyue

last: zhou

state: Alabama

address: WTI 510G 1824 6th Ave S

department: hematology and oncology

institute: university of alabama at birmingham

summary: Developing strategies to enhance the response to bromodomain and extraterminal domain (BET) inhibitors and effectively eradicate cancer stem cells would represent a major cancer treatment advance against leukemia. Through a functional CRISPR screen, we identified the aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor, as a critical regulator of MYC expression and BET inhibitor sensitivity in human acute myeloid leukemia (AML). Constitutive or pharmacological activation of AHR repressed MYC and synergized with BET inhibitors to inhibit MYC transcription and suppress leukemia growth across diverse AML models. Mechanistically, AHR directly up-regulated a noncanonical target, ELMSAN1, a component of the MiDAC histone deacetylase complex, which promotes histone deacetylation at MYC regulatory elements. ELMSAN1 depletion led to up-regulation of MYC and impaired AHR signaling–induced BET inhibitor sensitization. In vivo, AHR agonists enhanced BET inhibitor efficacy in patient-derived xenografts and murine leukemia models, enabling the use of lower BET inhibitor doses while preserving therapeutic benefit and reducing toxicity. This combination suppressed leukemia stem cell (LSC) gene signatures and reduced LSC frequency, with minimal impact on normal hematopoietic stem and progenitor cells in both human cord blood xenografts and immunocompetent mouse models. Together, these findings uncover a MYC-repressive, nongenetic AHR-ELMSAN1 axis that enhances BET-targeting therapies and selectively impairs LSCs, providing a compelling rationale for clinical translation in AML and potentially other MYC-driven cancers.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DMSO, FICZ, JQ1, or combinational treated AML cells.

first: Xinyue

last: Zhou

first: Steven

last: Moreira

first: Kristin

last: Hope

first: Rui

last: Lu


title: Activation of a nongenetic AHR-ELMSAN1 axis optimizes BET-targeting therapy and suppresses leukemia stem cells in preclinical models [RNA-Seq]


title: Shifts in the epigenomic landscapes of co-existing DNA phosphorothioates and methylation in Pseudomonas

city: Shanghai

first: Lili

last: Liu

address: 301 Yanchang Middle Road

institute: Shanghai Tenth People's Hospital, Tongji University School of Medicine

summary: PT modification is widely distributed in the bacterial genome, in which a sulfur atom replaces a non-bridging oxygen atom in DNA backbone. Its function is related to restriction modification, oxidative stress, and regulation of gene expression. By heterologously expressing the GpsATC modification system and the Gm6ATC modification system in E. coli HST04 strain, previous studies found that the PT modification and another restriction modification, the methylation modification, can share the same motif. However, bacteria in which both modifications naturally coexist in the same motif do not exist in nature. We found a bacterial strain S1 that naturally contains the GpsATC modification and used this strain to construct multiple modification systems to study the interactions between the multiple modifications. Our results showed that when the dam gene (G6mATC) is introduced, the two modifications can coexist in the same motif (Gps6mATC) and produce the new modification types (GpsATC); when another PT modification system (GPS GCC) is introduced, the two types of PT modification motifs (GpsGCC, GpsATC) coexist, with GpsGCC dominating. It also led to the emergence of the novel modification type CpsTGG/CpsCAG. All three models of multisystem coexistence resulted in shifts in modification sites and differences in gene expression. This study sheds light on the understanding of modification interactions and epigenetic networks.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Pseudomonas qingdaonensis strain S-1 and mutants

first: Qinghua

last: Zhang

first: Zheng

last: Jiao

first: Peiyu

first: Yanran

last: Hu

first: Yong

last: Lai

first: Bo

last: Cao


title: Activation of a nongenetic AHR-ELMSAN1 axis optimizes BET-targeting therapy and suppresses leukemia stem cells in preclinical models [CUT&RUN]

overall_design: CUT&RUN-sequencing for AHR in DMSO or FICZ treated U937 AML cells and FICZ treated K562 AHR-overexpressing cells.


title: Intracellular Fusobacterium nucleatum infection increases METTL3-mediated m6A methylation to promote the metastasis of esophageal squamous cell carcinoma

city: Guangzhou

first: Songhe

last: Guo

address: 132 Waihuan Road East, Guangzhou, China.

institute: Sun Yat-sen University

type: Methylation profiling by high throughput sequencing

summary: In order to examine the alterations of m6A modifications in particular genes during Fn infection, we conducted differential transcriptome sequencing and differential m6A-sequencing with the aim of analyzing the alterations in expression and map the m6A modification in Fn-infected Eca109 cell and control Eca109 cell.

overall_design: m6A-RIP-seq of mRNA in in Fn-infected Eca109 cell and control Eca109 cell


title: Type I interferons dominate cutaneous lichen planus inflammatory landscape driving the interface dermatitis reaction.

city: Paris

first: Chloé

last: Grolleau

address: 1 avenue Claude Vellefaux

department: Hopital saint Louis

country: France

institute: INSERM U1342, eq 16

summary: Cutaneous lichen planus (LP) is a chronic inflammatory skin disease histologically characterized by an interface dermatitis with lymphocyte infiltration and keratinocyte cell-death. Previous studies suggest that LP inflammation is dominated by a type I immune response involving IFN-g but its pathogenesis remains not fully elucidated yet. To investigate the inflammatory mechanisms underlying LP, we performed single-cell RNA sequencing on LP compared with healthy control skins. We demonstrate that lesional skin from patient with LP is imprinted by a type I interferon (IFN-I)-rich environment, involving all the main skin cell components. While all immune cells are imbued with this interferon signature, we highlight unique subsets of inflammatory keratinocytes and fibroblasts highly influenced by IFN-I near the epidermis-dermis junction. We also show a unique CD8+CXCL13+ T cell population exhibiting cytotoxic and epidermis-homing markers together with an enrichment in inflammatory CD16+ myeloid cells in LP skin. Herein, we illustrate that IFN-I education on all major skin cell types and particularly in keratinocytes drives the interface dermatitis reaction, thus orchestrating the cross-talk between immune and stromal cells in LP skin. Last, we suggest the effectiveness of targeting the common IFN-I receptor, IFNAR1, to switch off the activation of inflammatory pathways in an ex-vivo model of LP skin and in on patient with lupus lichen skin lesions. Together, our data provide a comprehensive characterization of LP immunopathogenesis and demonstrate the strong involvement of IFN-I in its inflammatory landscape, providing arguments for the therapeutic use of drugs targeting IFN-I pathway in patients with LP.

overall_design: A skin biopsy from one patient with active lichen planus was cut in half and cultured with either anti-IFNAR1 antibody (anifrolumab, 10 mm/ml AstraZeneca) or control isotype (IgG1 kappa, abcam) in RPMI enriched medium (10% FCS with 60UI/ml of IL2) for 72 hours. 3 healthy control skins from plastic surgery waste were cultured in the same condition without antibody. After 72h culture RNA was extracted for microarray analysis.

first: Hélène

last: Le Buanec

first: Jean-David

last: Bouaziz


title: INO80 / SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape (RNA-Seq)

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

summary: INO80 / SWR remodelers, including INO80, P400 / TIP60, and SR CAP, ha v e been vie w ed to regulate H2A.Z dynamics, but how they control specific gene expression remains unclear. Here, we reveal distinct phenotypes arising from short- and long-term perturbations f ollo wing the depletion of INO80 / SWR remodelers. We identified the direct target genes of INO80, P400, and SRCAP remodelers. Mechanistically, we found that INO80 / SWR remodelers interact and facilitate the chromatin occupancy of the H2A.Zac reader protein BRD2, thereby elucidating the regulation of Pol II transcription b y INO80 / SWR remodelers. A dditionally, while the degradation of P400 or SRCAP led to a reduction in H2A.Zac, INO80 depletion did not affect H2A.Zac occupancy but decreased the occupancy of P400 and SRCAP. Collectively, our findings suggest that INO80 / SWR remodelers primarily regulate the chromatin landscape and influences BRD2 chromatin binding, thereby shedding light on their mechanisms in Pol II transcription regulation during de v elopment and disease.

overall_design: We performed ChIP-Seq, Cut&Tag, ATAC-Seq, ChAR-Seq and RNA-Seq to investigate the functions of INO80/SWR remodelers.

first: Hui

last: Wang

first: Qiqin

last: Xu


title: Injury Induced Paracrine Effects on the Podocyte’s Transcriptome

city: Cleveland

first: Oliver

last: Wessely

state: OH

address: 9500 Euclid Avenue/NC10

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundation

summary: Although injury in glomerular disease might only damage a subset of podocytes in any given glomerulus, the response of the healthy neighboring podocytes to the injured podocytes oftentimes determines the course of the disease. To investigate this relationship, we designed a dual chamber open microfluidic co-culture device to specifically examine paracrine signaling to healthy podocytes from podocytes targeted injured by either Adriamycin, Puromycin Aminonucleoside or a cytopathic anti-podocyte antibody. Global transcriptomic analysis measured by RNA-sequencing revealed shared and unique pathways between the three forms of targeted injury, with temporal differences in the transcriptomic responses to each form of injury. Paracrine-induced injury to neighboring podocytes was similar to the targeted primary injured podocytes and was specific for each podocyte injury model. Ligand-receptor analysis of ligands secreted by the insult targeted podocytes and receptors expressed by the responsive, paracrine injured counterparts identified 23 candidate mediator pairs. These findings critically define a new concept for future studies to understand the pathways involved in secondary cellular injury fields in animal models and ultimately human studies.

overall_design: Primary, human podocytes were seeded into a two-chamber microfluidic device. The podocytes in the outer chamber were injured using either (i) a cytopathic anti-podocyte antibody (IgG), (ii) puromycin aminonucleoside (PAN), or (iii) Adriamycin/doxorubicin (ADR). The podocytes in the inner chamber remained naïve (uninjured). After 24-hours post-injury, the two chambers were connected by flooding with shared media. Autocrine and paracrine effects of the injury models were assessed with mRNA sequencing at 24- and 96-hours post-injury.

first: Yuting

last: Zeng

first: R

middle: A

last: Schweickart

first: Jeffrey

middle: W

last: Pippin

first: Stuart

last: Shankland


title: Type I interferons dominate cutaneous lichen planus inflammatory landscape driving the interface dermatitis reaction [lupus_lichen]

overall_design: We collected paraffined-embebded skin biopsies of lupus-lichen keratoderma before and after anifrolumab infusions and 3 healthy control skin samples for RNA extraction and hybridization on Affymetrix microarrays.


title: INO80 / SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape

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

overall_design: Refer to individual Series


title: Mitochondrial N-formylmethionine instructs tissue-inflammatory CD4+ T cells by redirecting endolysosomal pathways

city: Rochester

first: Yanyan

last: Zheng

state: Minnesota

address: 839 16th ST SW, Apt421

institute: Mayo Clinic

summary: Rheumatoid arthritis (RA) is a T-cell dependent autoimmune disease that causes tissue damaging joint inflammation. Mechanisms through which T cells from RA patients mediate tissue injury are poorly understood, but one of their distinguishing features is their poor mitochondrial performance. We performed RNAseq analysis of stimulated CD4+ T cells from 8 RA (ATPlow) and 8 RA (ATPint) patients. CD4+ T cells from RA (ATPlow) (n=4 each) were stimulated and treated with vehicle or the mPTP inhibitor CsA (5uM).CD4+ T cells from RA (ATPint) (n=4 each) were stimulated and treated with vehicle or the fMet (5 ng/ml) for 24 hrs

overall_design: We performed RNAseq analysis of stimulated CD4+ T cells from four RA (ATPlow) and four RA (ATPint) patients. CD4+ T cells from RA (ATPlow) (n=4 each) were stimulated and treated with vehicle or the mPTP inhibitor CsA (5uM).CD4+ T cells from RA (ATPint) (n=4 each) were stimulated and treated with vehicle or the fMet (5 ng/ml) for 24 hrs

first: Cornelia

middle: M

last: Weyand


title: INO80 / SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape (ATAC-Seq)


title: INO80/SWR Remodelers Regulate Pol II Transcription through BRD2 and Chromatin Landscape (ChIP-Seq)

summary: INO80/SWR remodelers, including INO80, P400/TIP60, and SRCAP, have been viewed to regulate H2A.Z dynamics, but how they control specific gene expression remains unclear. Here, we reveal distinct phenotypes arising from short- and long-term perturbations following the depletion of INO80/SWR remodelers. We identified the direct target genes of INO80, P400, and SRCAP remodelers. Mechanistically, we found that INO80/SWR remodelers interact and facilitate the chromatin occupancy of the H2A.Zac reader protein BRD2, which is crucial for Pol II initiation through TFIID. Additionally, while the degradation of P400 or SRCAP led to a reduction in H2A.Zac, INO80 depletion did not affect H2A.Zac occupancy but decreased the occupancy of P400 and SRCAP. Collectively, our findings suggest that INO80/SWR remodelers primarily regulate the chromatin landscape and influences BRD2 chromatin binding, thereby shedding light on their mechanisms in Pol II transcription regulation during development and disease.

first: Meitong

last: Liu


title: INO80 / SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape (ChAR-Seq)


title: Transcriptomic profiling of PSEN2 mutation

city: Palo Alto

first: Yu

state: CA

address: 1215 Welch Road

department: CVI

institute: Stanford University

summary: Here we compared the transcriptomic profiles of cardiomyocytes derived from human induced pluripotent stem cells with or with presenilin 2 mutation (S130L).

overall_design: Four isogenic pairs were compared. Each pair came from the same donor. The only difference is on the PSEN2 mutation.

first: Chi

middle: K

last: Lam

first: Lei

last: Tian

first: Joseph

last: Wu


title: Circadian Reprogramming by High-Fat Diet Signifies Temporal Coordination of Metabolic Cycles in the Kidney

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

summary: The circadian gene expression in peripheral tissue displays rhythmicity which is reprogrammed by feeding rhythms and dietary composition in mammals. In this study, circadian transcriptome was performed to investigate how high fat diet influences circadian gene regulation in the mouse kidney.

overall_design: 6-week-old, male C57BL/6 mice were subjected to ad libitum normal chow diet or to high-fat diet under 12hr light/ 12hr dark schedule. Kidney was harvested every 4 hours over the circadian cycle at ZT0, 4, 8, 12, 16, 20 (n=3 per time point per group). Total RNA was extracted from kidney, and used for RNA-seq.

first: Kenichiro

last: Kinouchi

first: Ekaterina

last: Deyneka

first: José

last: Monroy Kuhn

first: Carolina

last: Greco

first: Kristin

last: Eckel-Mahan

first: Kenneth

last: Dyar

first: Dominik

last: Lutter

first: Pierre

last: Baldi

first: Hiroshi

last: Itoh

first: Paolo

last: Sassone-Corsi


title: Transcriptomic profile of  WT and Mthfd2 KO alloreactive CD4+ T cells [RNA-seq]

city: Wuhan

first: Chen

last: zhang

address: Jiefang road 1037

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: To investigate the effect of  Mthfd2 KO in alloreactive CD4+ T cells. We performed in vitro mixed lymphocyte to induce alloreactive T cells. CD4+ T cells were respectively purified from the spleens of 8-week-old TEaWT and TEaMthfd2 KO mice by magnetic-activated cell sorting (MACS) positive selection. APCs were sorted from the spleens of 8-week-old F1 (BALB/c x C57BL/6) mice. CD4+ T cells were cocultured with APCs three days and then performed RNA-sequencing.

overall_design: CD4+ T cells were respectively purified from the spleens of 8-week-old TEaWT or TEaMthfd2 KO mice by magnetic-activated cell sorting (MACS) positive selection. APCs were sorted from the spleens of 8-week-old F1 (BALB/c x C57BL/6) mice and stained with mitomycin for 30 min at 37 °C with 5% CO2. Then, CD4+ T cells were then cocultured with APCs  for 3 days at 37 °C and 5% CO2 in RPMI 1640 medium supplemented with 10 mM HEPES, 50 mM 2-mercaptoethanol, 100 U/mL penicillin/streptomycin, and 2 mM glutamine.

first: Yuan

last: Li

first: Zhang

first: Jiahong

last: Xia

first: Jie


title: Neuroendocrine control of planarian regeneration

first: yue

last: chen

state: Shanghai

address: 320 Yue-Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology


title: neuroendocrine control of planarian regeneration (Spatial transcriptome)

summary: Effective tissue regeneration requires cells to perceive the surrounding context and make internal state adaptations that enable context-dependent fate changes in time and space, but the mechanisms underlying this complex process remain unclear. Here, transcriptom sequencing was used for study neuroendocrine control of planarian regneration

overall_design:
Examine gene expression profiles of regenerated asexual planarian fragments after amputation at different time points, wild type intact asexual planarian and 3dpa tail after RNAi.
Stereo-seq data for six time points (0h, 12h, 1.5d, 3d, 5d, 10d) and the 10X Visium data for five time points (0h, 12h, 1.5d, 3d, 5d).

Please note that the 'regeneration (mixed sample)' raw data are non-demultiplexed files generated from all samples (5 time-point; 0h, 12h, 1.5d, 2.5d, 5d) and the details of splited 5 time-point samples are included in '10X_Visium_filtered_feature_bc_matrix_and_image.zip'.

Schmidtea mediterranea include both asexual and sexual types. Our experiments used asexual Schmidtea mediterranea (strain CIW4) animals, and sequencing data were matched using transcriptome (GSE72389_smed_20140614.fa.gz).

first: Yue

first: Yuxiaofei

last: Wang

first: An

last: Zeng


title: neuroendocrine control of planarian regeneration (single-cell transcriptome)

summary: Effective tissue regeneration requires cells to perceive the surrounding context and make internal state adaptations that enable context-dependent fate changes in time and space, but the mechanisms underlying this complex process remain unclear. Here, transcriptom sequencing was used for study neuroendocrine control of planarian regeneration.

overall_design:
Examine gene expression profiles of regenerated asexual planarian fragments after amputation at six time points (0h, 12h, 1.5d, 3d, 5d 10d).
Schmidtea mediterranea include both asexual and sexual types. Our experiments used asexual Schmidtea mediterranea (strain CIW4) animals, and sequencing data were matched using transcriptome (GSE72389_smed_20140614.fa.gz).

last: Chen


title: Genome-wide maps of H3K4me3 mofification in wild type and Mthfd2 KO alloreactive T cells [ChIP-seq]

summary: This study aims to characterize the H3K4me3 modification in wild type and Mthfd2 KO activated T cells, and find the potential mechanism of the Mthfd2 KO in alloreactive T cells.

overall_design: CD4+ T cells cocultured with APCs for 3 days to induce  alloreactive T cells in vitro. CD4+ T cells were purified from the spleens of TEaWT and TEaMthfd2 KO mice by magnetic-activated cell sorting (MACS) positive selection. APCs were sorted from the spleens of F1 (BALB/c x C57BL/6) mice and stained with mitomycin for 30 min at 37 °C with 5% CO2.

last: Wu


title: Single-cell dissection of ex vivo human heart tissue reveals pro-inflammatory microvascular changes in the right atrium in ischemic heart disease and heart failure

city: Kuopio

first: Minna

last: Kaikkonen-Määttä

country: Finland

institute: A. I. Virtanen Institute

summary: Timecourse analysis of the impact of inflammatory stimulus on human aortic endothelial cells using RNA-seq

overall_design:
RNA-seq analysis of HAEC under IL1b stimulus for 2 hours, 8 hours, 14 hours and 32 hours.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: P

last: Moreau

first: M

middle: U


title: Pharmacological Inhibition of EZH2 Suppresses Tumor Growth and Pulmonary Metastasis in Melanoma Cells in vitro and in vivo

city: Cheng Du

first: Yongxia

last: Zhu

state: Si Chuan

address: Ren Min Road Numer 17

institute: Sichuan Cancer Hospital

summary:
To explore the anticancer mechanism of ZLD1039, RNA-seq was performed to identify global changes in gene expression in tumors treated with ZLD1039 (100 mg/kg) compared with that in vehicle-treated controls in the A375 xenograft model.
The incidence and mortality rate of malignant melanoma are increasing worldwide. Metastasis limits the efficacy of current melanoma therapies and leads to poor prognosis for patients. EZH2 is an epigenetic regulator that promotes the proliferation, metastasis, and drug resistance of tumor cells by regulating transcriptional activity. EZH2 inhibitors could be effective in melanoma therapies. Herein, we aimed to investigate whether the pharmacological inhibition of EZH2 by ZLD1039, a potent and selective S-adenosyl-l-methionine-EZH2 inhibitor, suppresses tumor growth and pulmonary metastasis in melanoma cells. Results showed that ZLD1039 selectively reduced H3K27 methylation in melanoma cells by inhibiting EZH2 methyltransferase activity. Additionally, ZLD1039 exerted excellent antiproliferative effects on melanoma cells in 2D and 3D culture systems. Administration of ZLD1039 (100 mg/kg) by oral gavage caused antitumor effects in the A375 subcutaneous xenograft mouse model. RNA sequencing and GSEA analysis revealed that the ZLD1039-treated tumors exhibited changes in the gene sets enriched for “Cell Cycle” and “Oxidative Phosphorylation”, whereas the “ECM receptor interaction” gene set had a negative enrichment score. Mechanistically, ZLD1039 induced G0/G1 phase arrest by upregulating p16 and p27 and inhibiting the functions of the cyclin D1/CDK6 and cyclin E/CDK2 complex. Moreover, ZLD1039 induced apoptosis in melanoma cells via the mitochondrial reactive oxygen species apoptotic pathway, consistent with the changes in transcriptional signatures. ZLD1039 also exhibited excellent antimetastatic effects on melanoma cells in vitro and in vivo. Our data highlight that ZLD1039 may be effective against melanoma growth and pulmonary metastasis and thus could serve as a therapeutic agent for melanoma.

overall_design: ZLD1039 (100 mg/kg) or vehicle (n = 3)

first: Luoting

last: Yu


title: Cold-induced expression of a truncated Adenylyl Cyclase 3 acts as rheostat to brown fat function [iBAT_WT_AT_HFD_cold]

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Promoting brown adipose tissue (BAT) activity has been recognized as innovative therapeutic approach to improve obesity and metabolic disease. Whilst the molecular circuitry underlying thermogenic activation of BAT is well understood, the processes underlying rheostatic regulation of BAT to maintain homeostasis and avoid excessive energy dissipation remain ill-defined.  Increasing cyclic AMP (cAMP) biosynthesis is key for BAT activation. Here, we demonstrate that ADCY3, an adenylyl cyclase whose expression is induced during cold exposure and regulates cAMP homeostasis in thermogenic fat, is dispensable for BAT function in lean mice, but becomes critical during obesity. Furthermore, by combining RNA-seq with epigenomic H3K4me3 profiling, we detected a novel, cold-inducible promoter that generates a 5’ truncated Adcy3-at mRNA isoform, Adcy3-at. Mice lacking only Adcy3-at, but not full-length Adcy3, displayed increased energy expenditure already under lean conditions and were protected against obesity and ensuing metabolic imbalances. Subcellularly, translated ADCY3-AT proteins are retained in the endoplasmic reticulum (ER), did not translocate to the cell membrane, and lacked enzymatic activity. By interacting with ADCY3, ADCY3-AT retained ADCY3 in the ER and, thereby, reduced the plasma membrane pool of ADCYs available for G-protein mediated cAMP synthesis. Thereby, ADCY3-AT acts as a signaling rheostat in BAT, limiting adverse consequences of uncurbed cAMP activity after long-term BAT activation. Adcy3-at induction was driven by a cold-induced, truncated isoform of the transcriptional cofactor PPARGC1A (PPARG Coactivator 1 Alpha, PPARGC1A-AT). Expression of Ppargc1a-at and Adcy3-at are evolutionary conserved, indicating that transcriptional rewiring by commissioning of alternative promoters is key for thermogenic fat function.

overall_design: Inguinal brown adipose tissue (iBAT) Total RNA profiles of 20-week old C57BL/6N wild-type or Adcy3-AT KO (ADCY3∆AT) mice on HFD diet (D12492), cold exposed were generated by deep sequencing on NovaSeq6000.

first: Sajjad

last: Khani

first: Hande

last: Topel

first: Ajeetha

last: Josephrajan

first: Bjørk

last: Larsen

first: Ana

last: Albuquerque de Almeida Tavanez

first: Michael

middle: J

last: Gaudry

first: Philipp

last: Leyendecker

first: Natasa

last: Stanic

first: Isabella

last: Gaziano

first: Nils

last: Rouven Hansmeier

first: Elena

last: Schmidt

first: Paul

last: Klemm

first: Lara-Marie

last: Vagliano

first: Christoph

last: Engelhard

first: Søren

last: Nielsen

first: Naja

last: Zenius Jespersen

first: Rizwan

last: Rehimi

first: Sabrina

last: Gohlke

first: Peter

last: Frommolt

first: Thorsten

last: Gnad

first: Alvaro

last: Rada-Iglesias

first: Marta

last: Pradas-Juni

first: Tim

last: Schulz

first: Thomas

last: Wunderlich

first: Alexander

last: Pfeifer

first: Martin

last: Jastroch

first: Dagmar

last: Wachten

first: Jan-Wilhelm


title: Cold-induced expression of a truncated Adenylyl Cyclase 3 acts as rheostat to brown fat function [iBAT_WT_AT]

first: Jan

last: Kornfeld

overall_design: Inguinal brown adipose tissue (iBAT) polyA RNA profiles of 20-week old C57BL/6N wild-type or Adcy3-AT KO (ADCY3∆AT) mice on chow diet were generated by deep sequencing on NovaSeq6000  in triplicates.

first: Sajjad

last: Khani

first: Hande

last: Topel

first: Ajeetha

last: Josephrajan

first: Bjørk

last: Larsen

first: Ana

last: Albuquerque de Almeida Tavanez

first: Michael

last: Gaudry

first: Philipp

last: Leyendecker

first: Natasa

last: Stanic

first: Isabella

last: Gaziano

first: Nils

last: Rouven Hansmeier

first: Elena

last: Schmidt

first: Paul


title: Cold-induced expression of a truncated Adenylyl Cyclase 3 acts as rheostat to brown fat function [iBAT_WT_AdKO_cold]

overall_design: Inguinal brown adipose tissue (iBAT) polyA RNA profiles of 20-week old C57BL/6N wild-type (Adcy3-fl/fl) or Adipocyte specific Adcy3 KO (Adipoq-Cre-Adcy3-fl/fl) mice on chow diet were generated by deep sequencing on NovaSeq6000 in quadruplicates.

last: Klemm

first: Lara-Marie

last: Vagliano

first: Christoph

last: Engelhard

first: Søren

last: Nielsen

first: Naja

last: Zenius Jespersen

first: Rizwan

last: Rehimi

first: Sabrina

last: Gohlke

first: Peter

last: Frommolt

first: Thorsten

last: Gnad

first: Alvaro

last: Rada-Iglesias

first: Marta

last: Pradas-Juni

first: Tim

last: Schulz

first: Thomas

first: Alexander


title: Cold-induced expression of a truncated Adenylyl Cyclase 3 acts as rheostat to brown fat function

first: Jan

last: Kornfeld


title: Transcriptomes of Wild Type tomato and sllbd40 fruit on different fruit stages

first: Jialong

last: Zhang

address: Malianwa Street

institute: China Agricultural University

summary: In order to find the gene which were regulated by SlMYC2, the fruits of WT and SlMYC2-KO line were collected at 25 DDA to do the RNA-Seq. Total RNA was extracted from above tomato fruits by TRIzol reagent and three biological replicates were taken. The clean data were aligned to the tomato reference genome release SL3.0. According to the RNA-Seq data, many development-related genes were down-regulated in SlMYC2-KO fruit. We find the potential SlMYC2-regulated genes.

overall_design: Fruit mRNA profiles of 25 DAA fruits of wild type (Ailsa Craig) and  slmyc2 mutant

first: Lun

last: Liu

first: Yang-Dong

last: Guo


title: Cold-induced expression of a truncated Adenylyl Cyclase 3 acts as rheostat to brown fat function [iBAT_WT_AdKO]

overall_design: Inguinal brown adipose tissue (iBAT) polyA RNA profiles of 20-week old C57BL/6N wild-type (Adcy3-fl/fl) or Adipoq-Cre-Adcy3-fl/fl (Adipocyte specific Adcy3 conditional KO) mice on chow diet were generated by deep sequencing on NovaSeq6000 in quadruplicates.

first: Sajjad

last: Khani

first: Hande

last: Topel

first: Ajeetha

last: Josephrajan

first: Bjørk

last: Larsen

first: Ana

last: Albuquerque de Almeida Tavanez

first: Michael

last: Gaudry

first: Philipp

last: Leyendecker

first: Natasa

last: Stanic

first: Isabella

last: Gaziano

first: Nils

last: Rouven Hansmeier

first: Elena

last: Schmidt

first: Paul

first: Lara-Marie

last: Wunderlich

last: Pfeifer

first: Martin

last: Jastroch

first: Dagmar

last: Wachten

first: Jan-Wilhelm


title: Cohesin is essential for the timely activation of condensin and anaphase segregation

city: London

first: Jonay

last: Garcia-Luis

state: London

address: Du Cane Road

department: London Institute of Medical Sciences

institute: UKRI

summary: Yeast chromosome organization is dominated by the SMC complexes cohesin and condensin. Yeast cohesin has a dual function on metaphase chromosomes, holding sister chromatids together and organising individual chromatids into loops. After metaphase, most of the cohesin is cleaved and the condensin complex takes over the main role of organizing chromosomes. Condensin organized chromosomes into larger loops, producing chromosome condensation. How chromosome organization transits from a cohesin centric environment to a condensin centric environment is not well understood. Here we show that there is a crosstalk between cohesin and condensin through the Cdc5 kinase. Cohesin bound Cdc5 is released upon cohesin s Scc1 cleavage. Released Cdc5, in turn, hyperphosphorylates multiple condensin subunits, leading to a fine-tuned condensin activation. Failure in condensin fine-tuning activation leads to condensin impairment and chromosome missegregation.

overall_design: Hi-C


title: Gardenia Jasminoides induce paraptosis

city: Shenzhen

first: Yan

last: Zhao

address: No. 1088,Xueyuandadao

department: BIology

institute: Southern University of Science and Technology

summary: We treated breast cancer MCF7 cell line with different Gardenia Jasminoides and found that they can induce paraptosis of cMCF7 cells.

overall_design:
3' mRNA-seq was taken for MCF-7 cells under treated by different Gardenia Jasminoide drugs
The file metadata_with_compound_structures.xlsx includes the images of the compound structures.

first: Wencheng

last: Wei

first: Yuhui

last: Hu


title: Hypoxia differentially accelerates cognitive impairment related features in cerebral cortex revealed by single cell sequencing in APP/PS1 mice

first: Junchao

last: Xie

address: Middle 301 Yanchang Road

department: Neurology

institute: Shanghai Tenth People's Hospital

summary: Here we aimed at exploring the effect of hypoxia on cognitive impairment progression in a single cell resolution through single cell RNA sequencing (ScRNA seq). We exposed the APP/SP1 transgenic AD model mice to hypoxia condition and explored the cell heterogeneity and interactions in cerebral cortex with single cell RNA sequencing (10X genomics). We further analyze the differently expressed genes and signaling pathways related with cognitive impairment by different cell types and subclusters.

overall_design: APP/PS1 mice was subjected to a hypoxia condition of 8% O2 for 5 hours. The cerebral cortex was then harvested and subjected to scRNA seq with 10X Genomics platform. Two samples of hypoxic or normoxic cortical tissue, respectively, were included in the analysis.

first: Yunxiao

last: Dou

first: Yichen

first: Yongzhe

last: Gu

first: Kangshuai

last: Du

first: Fang

last: Wang

first: Shuai

last: Yang

first: Yanxin


title: Gene expression profile level of mRNA of brain organoid at day56 of ctrl and WS

city: hangzhou

first: zhao

last: xingsen

address: kaixuan road 268

institute: zhejiang university

summary: Brain organoid is consist of many different cells,w e used single cell RNA sequencing (scRNA-seq) to analyze the diversity of each neural cluster

overall_design: we performed bulk RNA sequencing (RNA-seq) with both CTRL and WS forebrain organoids to reveals the altered gene expression relating to neuronal development

first: Xingsen

last: zhao

first: Xue

middle: k

last: li


title: Gene expression profile of brain organoid at day56 of ctrl and WS

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

overall_design: Refer to individual Series


title: Short hairpin RNAs artifactually impair cell growth and suppress clustered microRNA expression

city: Boston

first: Edroaldo

last: Lummertz da Rocha

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

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

platform_organism:
Homo sapiens
synthetic construct


title: Short hairpin RNAs artifactually impair cell growth and suppress clustered microRNA expression [miRNA expression]

summary: Gene disruption is a central tenet of cancer research, where novel drug targets are often identified and validated through cell-growth based knockdown studies or screens. Short hairpin RNA (shRNA) mediated mRNA knockdown is widely used in both academic and pharmaceutical cancer research settings. However, off-target effects of shRNAs as well as interference with endogenous small RNA processing have both been reported. We show here that both gene-specific and control shRNA expression impair in vitro cell growth and preferentially decrease clustered microRNA levels, significantly reducing oncogenic microRNA cluster expression. In addition, exogenous shRNAs induce a depressed cell-cycle-gene expression signature that is shRNA-sequence independent and present across several studies. The collective impact of these observations is important to cancer research, given the widespread historical use of shRNAs in the field and the common goal of interrogating genes that regulate proliferation. We therefore recommend that for future shRNA use, care be taken to titrate lentiviral dose, use hairpin-expressing controls, perform gene-of-interest rescue experiments and/or validate shRNA-derived results by small interfering RNA (siRNA) knockdown or CRISPR/Cas9-mediated genetic knockout.

overall_design: Study the sequence dependent and independent growth effects of shRNAs

first: John

last: Powers


title: Gene expression profile at single cell level of brain organoid at day56 of ctrl and WS [scRNA-seq]

summary: Brain organoid is consist of many different cells, we used single cell RNA sequencing (scRNA-seq) to analyze the diversity of each neural cluster.

overall_design: We used three sets of human D56 forebrain organoids derived from three sets of CTRL and WS iPSCs to get changes of WS


title: TNFR1 signaling  in sympathetic nerves  dampens the inflammatory response  in the bone marrow

status: Public on Aug 31 2025

city: Dresden

first: Tatyana

last: Grinenko

address: Fetscherstraße 74

country: Germany

institute: IKL , Carl Gustav Carus Universitätsklinikum, TU Dresden

summary: Hematological malignancies and cytotoxic therapy induce sympathetic neuropathy in the bone marrow (BM), leading to niche remodeling, disease progression, and impaired hematopoiesis regeneration after myeloablative therapy. Vincristine induces pro-inflammatory cytokine production in the BM, including tumor necrosis factor a (TNF-a), impairs hematopoietic stem cell function, and harms sympathetic neurons. Deleting TNF receptor R1 (TNFR1) in sympathetic nerves exacerbated hematopoietic stem cell exhaustion. Mechanistically, loss of sympathetic nerve-specific TNFR1 signaling prevented the increase of norepinephrine levels in the BM after vincristine treatment, leading to delayed inflammation resolution due to elevated IL-6 production by BM endothelial cells. Therefore, TNFR1 signaling in sympathetic nerves plays a role in the resolution of the inflammatory state after vincristine treatment. Therapeutic strategies meant to reduce inflammation should be considered to prevent long-term hematopoietic damage in cancer patients.

overall_design: 3000 hematopoietic stem cells (Lin- Kit+ Sca-1+ CD48- Cd150+) from TH:cre-TNFR1f/f and TH:cre+TNFR1f/f mice were sorted for bulkRNAseq 48h after 6 weeks vincristine treatment. 1500 mesenchymal stromal cells (CD45- Ter119- Sca1+ CD31-) and 1500 endothelial cells (CD45- Ter119- Sca1+ CD31+) from TH:cre-TNFR1f/f and TH:cre+TNFR1f/f mice were sorted for bulkRNAseq 72h after vicristine injection.

first: Iryna

last: Kovtun

first: Anupam

last: Sinha


title: Leptosphaeria maculans gene expression at the beginning of primary oilseed rape leaf infection

city: Thiverval-Grignon

first: Isabelle

last: Fudal

address: avenue Lucien Bretignieres

institute: INRA

summary: The transcriptome of Leptosphaeria maculans was analysed in mycelium and during oilseed rape leaf infection. The array probes were designed from gene models from the L. maculans whole genome annotation. One aim of this study was to verify the expression of the automatically annotated gene models in various conditions. Another goal was to monitor gene expression profiles during oilseed rape leaf infection and to highlight tissue-specific transcripts, e.g. in plant up-regulated transcripts for further analyses.

sample_organism:
Brassica napus
Plenodomus lingam

overall_design: We performed 3 hybridizatiosn (NimbleGen) with samples derived from oilseed rape infected leaves. Samples from infected oilseed rape leaves were harvested 3 days post infection. Three replicates each. All samples were labeled with Cy3.

first: Juliette

last: Linglin


title: PPAR agonist, DTMB reduces chronic neuroinflammation in 5xFAD mice model.

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

summary: Abnormal production of amyloid-beta (Aβ) plaque and chronic neuroinflammation are commonly observed in the brain of patients with Alzheimer’s disease, and both of which induce neuronal cell death, loss of memory, and cognitive dysfunction. However, many of the drugs targeting the production of Aβ peptides have been unsuccessful in treating Alzheimer’s disease. In this study, we identified synthetic novel peroxisome proliferator activating receptor (PPAR) agonist, DTMB, which can ameliorate the chronic inflammation and Aβ pathological progression of Alzheimer’s disease. We discovered that DTMB attenuated the proinflammatory cytokine production of microglia by reducing the protein level of NF-κB. DTMB also improved the learning and memory defects and reduced the amount of Aβ plaque in the brain of 5xFAD mice. This reduction in Aβ pathology was attributed to the changes in gliosis and chronic inflammation level. Additionally, bulk RNA sequencing showed that genes related to inflammation and cognitive function were changed in the hippocampus and cortex of DTMB treated mice. Our findings demonstrate that DTMB has the potential to be a novel therapeutic agent for Alzheimer’s disease.

overall_design: Total 4 experimental groups: Wild type (WT) Vehicle, Wild type - DTMB, Tg (5xFAD) Vehicle, and Tg-DTMB. Hippocampus and cortex tissues of 3 mice in each group were used to gene expression analysis.

first: Kyong-Tai

last: Kim

first: Eun-Ji

last: Oh

first: Kyung-Won

last: Jo

first: Byunghee

last: Kang


title: Deciphering the role of tumor cell-intrinsic Sema4D in TNBC mouse tumor using single-cell RNA sequencing

city: Hefei

first: Jinguo

last: Zhang

state: Anhui Province

address: No. 17 Lujiang Road Luyang District Hefei Anhui Province

institute: University of Science and Technology of China

summary: Sema4D (Semaphorin 4D, also known as CD100) is a member of the class IV semaphorin family and is predominantly expressed on the surface of lymphocytes, monocytes, macrophages, and endothelial cells. The current understanding of Sema4D function is focused on its receptor-mediated signaling activities with limited data on its intrinsic mechanisms. However, the immunological roles and functional mechanism of tumor cell-intrinsic Sema4D regulating immune escape remain largely unknown. This study employs single-cell RNA sequencing (scRNA-seq) to investigate cellular and regulatory role of Sema4d in TNBC mouse tumors.

overall_design: Comparative gene expression profiling analysis of single cell sequencing data for the NC and Sema4d-knockdown tumor tissues, using the shRNA to knock down Sema4d.

first: Yueyin

last: Pan


title: Invasive properties of patient-derived glioblastoma cells after reversible electroporation in vitro

city: Ljubljana

first: Anja

last: Blažič

address: Tržaška cesta 25

country: Slovenia

institute: University of Ljubljana, Faculty of electrical engineering

summary:
Background. Electroporation-based therapies are being explored in glioblastoma (GB) treatment, as means of enhancing drug delivery or achieving nonthermal ablation. Yet, little is known about how sublethal exposure affects the invasive behaviour of GB tumour cells.

Materials and methods. Five patient-derived GB cell lines were initially screened for intrinsic invasive potential, and two most invasive (NIB140 CORE and NIB216 CORE) were selected for further experiments with electroporation treatment. Cells in suspension were exposed to bursts of high-frequency biphasic electric pulses resulting in electric field strength of 1 kV/cm, which corresponded to conditions of reversible electroporation. Changes in cell invasion and gene regulation were assessed 24 hours after electro-poration using transwell assay and RNA transcriptome analysis, respectively.

Results. Reversible electroporation at 1.0 kV/cm enhanced invasion in a cell line-dependent manner. NIB140 CORE showed a consistent and pronounced increase, with a median of 3.74-fold (274 %) higher number of invading cells compared to sham control. In contrast, NIB216 CORE exhibited only a modest increase in invasion (1.30-fold; 30 %). Transcriptomic profiling identified modulation of genes linked to extracellular matrix or-ganization and ion channel activity in NIB140 CORE, and cytoskeletal remodelling in NIB216 CORE, indicating the activation of invasion-related pathways.

Conclusions. These findings highlight a potential risk of pro-invasive responses in GB cells. In tumour ablation with irreversible electroporation, this concern relates to cells in the pe-ripheral zone that may experience only sublethal electric fields, while in electrochemo-therapy, a similar risk may arise if permeabilized cells are not effectively eliminated due to insufficient local drug delivery. Nevertheless, the two tested cell lines responded differ-ently, underscoring patient-specific heterogeneity and the need for validation in more physiologically relevant models.

overall_design: RNA-seq profiling of non-treated (no exposure) and with electroporation-treated (exposure to 200 V) patient-derived glioblastoma cells (NIB140 CORE and NIB216 CORE) using H-FIRE pulses 24 hours upon the treatment

first: Bernarda

last: Majc

first: Metka

last: Novak

first: Barbara

last: Breznik

first: Lea

last: Rems


title: Short hairpin RNAs artifactually impair cell growth and suppress clustered microRNA expression [gene expression]

first: Edroaldo

last: Lummertz da Rocha

state: MA

first: John

last: Powers


title: Blocking PD-1 engagement rapidly upregulates innate antiviral and immune functions that associate with HIV reservoir decay [scRNA-seq]

city: PHOENIX

first: Aarthi

last: Talla

state: ARIZONA

address: 2448 W ROWEL RD

institute: IMMUNASYST

summary: The HIV reservoir, a small pool of PD-1+CD4+ T cells that carry integrated HIV genomes, remains a formidable obstacle to HIV cure. The clinical use of PD-1 inhibitors has shown promising results in curbing the HIV reservoir in people with HIV (PWH) and cancer, but the underlying mechanisms are unknown. Here, we demonstrate that anti-PD-1 therapy leads to a decay in the frequency of cells harboring HIV DNA at the end of a two-year follow-up in 9 of 14 PWH receiving pembrolizumab within the CITN-12 clinical trial (NCT02595866). This reduction correlates with an innate immune response, characterized by increased monocyte frequencies and enhanced myeloid cell-specific transcription of interferon-stimulated genes (ISGs), chemokines, antiviral restriction factors, and TLR signaling. These changes emerge as early as 24 hours post-treatment and persist until the end of therapy. Within 24 hours of treatment, we also observe an increase in proliferating effector HIV-specific CD8+ T cells, increased expression of effector T cell genes, and a decline in plasma TGF-β levels. We validate the generalizability of these ISG expression modules across >1,000 publicly available scRNA-seq samples, revealing a consistent association between high ISG expression in peripheral blood mononuclear cells (PBMCs) and lower expression of WNT pathway and Treg gene sets - pathways known to regulate immune quiescence and persistence of the HIV reservoir - in PBMCs from uninfected controls, as well as in samples from individuals with cancer or infections. Furthermore, we demonstrate that ISGs triggered by TLR ligands protect CD4+ T cells from HIV infection in vitro. These findings support a mechanism by which ISGs restrict the HIV reservoir in vivo and define a set of immune signaling pathways that can be used to identify PWH in whom the HIV reservoir may decay upon anti-PD-1 therapy.

overall_design: Single cell RNA sequencing was performed on Peripheral blood mononuclear cells (PBMCs) on a subset of participants that had bulk RNA sequencing data, at the following timepoints: C01D01 (pre-treatment), C01D02 (hours after the first treatment cycle ), and one week after the first cycle (C01D08).

first: Joao

middle: L

last: Azevedo

first: Muhammad

middle: B

last: Latif

first: Ana

last: Enriquez

first: Gabriela

middle: P

last: Sanchez

first: Ashish

last: Sharma

first: Rafick-Pierre

last: Sekaly


title: Regulation by LTTRs LrhA, YafC, YdcI, and YhaJ in Escherichia coli K12

city: Cologne

first: Karin

last: Schnetz

address: Zuelpicher Str. 47a

department: Institute for Genetics

institute: University of Cologne

summary: LrhA, YafC, YdcI, and YhaJ are LysR-type transcription regulator in Escherichia coli K12. In this study the transcriptomes of E. coli K12 strain U4 (MG1655 derivative, rph+ flhDC(IS1) dgcJ∷IS1 crl::IS1 ilvG+ ΔlacZ; Yilmaz et al. 2020, J. Bacteriol 203 e00427-20, https://doi.org/10.1128/JB.00427-20) and isogenic ΔlrhA, ΔyafC, ΔydcI, and ΔyhaJ mutants  grown in Tryptone medium to OD600 0.8 were determined. The data revealed few loci that may be specifically affected in one deletion mutant only, while most differentially expressed loci were up or down regulated in several of the mutants.

overall_design: RNA-sequencing analyses were performed of five different E. coli K12 strains in three biological replicates each. The strains included E. coli K12 MG1655 derivative U4 (Yilmaz et al. 2020, J. Bacteriol 203 e00427-20, https://doi.org/10.1128/JB.00427-20) as reference strain and isogenic ΔlrhA, ΔyafC, ΔydcI, and ΔyhaJ deletion mutants.

first: Ria Basu

last: Roy


title: easyPairedTag: A Comprehensive Pipeline for Paired-Tag Data Quality Control and Analysis

city: Shanghai

first: Yifei

last: Zang

address: 2005 Songhu Road

institute: Fudan University

summary: Paired-Tag is an ultra-high throughput single-cell method for simultaneous profiling of gene expression and histone modifications, enabling identification of cell-type-specific cis-regulatory elements and correlation of their chromatin states with the expression levels of putative target genes. However, the lack of an automated end-to-end pipeline has limited its application. Here, we present easyPairedTag, a Snakemake pipeline for Paired-Tag data processing and quality control. Key features include flexible configuration for diverse experimental setups, automated sub-library merging and sample demultiplexing, and comprehensive quality control metrics. When applied to published mouse brain datasets, easyPairedTag improves overlapping gene quantification via strand-specific analysis for precise cell clustering. In mouse hypothalamus datasets,  easyPairedTag is compatible with the processing of paired-end sequencing data to detect histone modification peaks with higher sensitivity and specificity, facilitating the discovery of putitive cell-type-specific cis-regulatory elements.

overall_design: Joint profiling of RNA and histone modifcations in single-cells

first: Ziyin

last: Chen

first: Jiehui

last: He

first: Yuanming

last: Zheng

first: Kaiwen

last: Shao

first: Miao

last: Yu


title: Blocking PD-1 engagement rapidly upregulates innate antiviral and immune functions that associate with HIV reservoir decay [bulkRNA-seq]

overall_design: Bulk RNA sequencing was performed on whole blood collected in PAXgene tubes from participants at the following timepoints: C01D01 (pre-treatment), C01D02 (hours after the first treatment cycle ), and EOT (end of therapy).


title: A new class B synthetic multivulva gene, ccar-1 works through the Ras pathway to regulate vulva development

city: Baltimore

first: Nikita

middle: Sudhir

last: Jhaveri

address: 3400 N Charles Street

department: Biology

institute: Johns Hopkins University

summary: Conserved Ras and Notch cell-signaling pathways promote Caenorhabditis elegans vulval cell fates. Ras pathway activity promotes the 1º vulval fate and inhibits the 2º vulval fate, and Notch pathway activity promotes the 2º vulval fate and inhibits the 1º vulval fate. Vulval cell fates are inhibited by the parallel-acting synthetic multivulva (synMuv) genes, which are grouped into either class A or B genes.  We identified a new synMuv class B gene ccar-1, that works redundantly with class A genes to regulate vulva development. ccar-1 is activated by the Notch pathway to inhibit the Ras pathway in presumptive 2º vulval cells to ensure low levels of Ras pathway activity and proper 2º vulval fate specification. Our findings indicate that ccar-1 might inhibit the Ras pathway by repressing the transcription of the Ras pathway ligand lin-3 EGF. By analogy, we suggest that CCAR-1 might act as a tumor suppressor by inhibiting the expression of growth factor signals. Our study also highlights the identification of a first gain-of-function mutation that suppresses the synMuv phenotype.

overall_design: RNA-seq profiling of C. elegans wild strain N2, mutant Cel-ccar-1(gk433), and mutant Cel-ccar-1(n2070) at mixed stage.

first: Erik

last: Andersen

middle: S

first: Scott

last: Clark

first: Melanie

last: Worley

first: Howard

last: Horvitz


title: Transcriptomics characterizes the expression profile of rat liver tissue on the third day after partial hepatectomy

city: Kunming

first: Liyan

last: Li

state: Yunnan

address: No. 1168, Chunrong West Road

department: Institute of Neuroscience

institute: Kunming Medical University

summary: Background: Liver regeneration (LR) after partial hepatectomy (PHx) involves complex molec-ular mechanisms, but the key regulatory networks remain incompletely understood. This study aims to characterize the multi-stage dynamics of LR after PHx and its core drivers. Methods: A PHx rat model was established for systematic assessment of histologic changes and serum biomarkers during regeneration. Transcriptomic analysis of liver tissues on the third day after PHx was performed to identify differentially expressed genes (DEGs). Moreover, the functions of key hub genes (Dcn and Hif1a) were verified by in vitro experiments, including the use of over-expression/knockdown plasmids, H2O2-induced hepatocyte injury model, and HIF1A inhibitor (LW6). Results: PHx triggered time-dependent inflammation, hepatocyte proliferation, and liver tissue remodeling. After the PHx procedure, the early phase was dominated by inflammation-driven and cellular proliferation, with a shift to liver tissue remodeling and functional recovery in the mid- to late phase. Transcriptomics identified 8,392 DEGs that were enriched in proliferation, autophagy, oxidative stress, apoptosis, inflammation, and metabolic reprogramming. Interaction analyses highlighted a critical sub-network consisting of 44 genes that regulate angiogenesis, LR, autophagy, and growth factor activity, including Dcn and Hif1a. In in vitro experiments, Dcn overexpression alleviated H2O2-induced BRL cell damage, including cell activity, cycle, autophagy, and oxidative stress. Dcn knockdown exhibited the opposite regulatory pattern. Mechanistically, Dcn upregulated HIF1A, and LW6-mediated HIF1A inhibition reversed the protective effect of Dcn on H2O2-induced hepatocyte injury. Conclusion: Dcn modulates hepatocyte proliferation, apoptosis, autophagy and oxidative stress through upregulating HIF1A, thereby alleviating hepatocyte injury. These findings reveal that the Dcn/HIF1A axis is a key therapeutic target for LR after PHx.

overall_design: Liver tissues from the Sham and PHx-3 groups were analyzed by transcriptomics to identify potential molecular mechanisms of LR.

first: Hailei

last: Wang

first: Kuangpin

last: Liu

first: Wei

last: Ma

first: Ke

first: Kuan

first: Yuqing

last: Zhang

first: Yundong

first: Hongqiang

last: Gao


title: The Parkinson's Disease Variant rs356182 Regulates Neuronal Differentiation Independently from Alpha-Synuclein

city: Grand Rapids

first: Jordan

last: Prahl

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

summary: One of the most significant risk variants for Parkinson's disease (PD), rs356182, is located at the PD-associated locus near the alpha-synuclein (α-syn) encoding gene, SNCA. SNCA-proximal variants, including rs356182, are thought to function in PD risk through enhancers via allele-specific regulatory effects on SNCA expression. However, this interpretation discounts the complex activity of genetic enhancers and possible nonconical functions of α-syn. Here we investigated a novel risk mechanism for rs356182. We use CRISPR-Cas9 in LUHMES cells, a model for dopaminergic midbrain neurons, to generate precise hemizygous lesions at rs356182. The PD-protective (A/-), PD-risk (G/-), and wildtype (A/G) clones were neuronally differentiated and then compared transcriptionally and morphologically. Among the affected genes was SNCA, whose expression was promoted by the PD-protective allele (A) and repressed in its absence. In addition to SNCA, hundreds of genes were differentially expressed and associated with neurogenesis and axonogenesis- an effect not typically ascribed to α-syn. We also found that the transcription factor FOXO3 specifically binds to the rs356182 A-allele in differentiated LUHMES cells. Finally, we compared the results from the rs356182-edited cells to our previously published knockouts of SNCA and found only minimal overlap between the sets of significant differentially expressed genes. Together, the data implicate a risk mechanism for rs356182 in which the risk-allele (G) is associated with abnormal neuron development, independent of SNCA expression. We speculate that these pathological effects manifest as a diminished population of dopaminergic neurons during development leading to the predisposition for PD later in life.

overall_design: To determine the role of rs356182 in dopaminergic neurons, we generated three biological replicate hemizygous clones for the Parkinson's disease protective allele (A/-) and PD risk allele (G/-), as well as 3 sorted and cloned WT controls using the LUHMES cell line. The clones were expanded and differentiated to day 6 before being submitted for RNA-sequencing.

first: Steven

middle: E

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