title: The Role of Epithelial IKKβ in the Transition from Normal to Precancerous Tissue in Esophageal Epithelium

city: Chicago

first: Marie-Pier

last: Tetreault

state: IL

address: 300 East Superior Street

department: Medicine/GI&Hep division

institute: Northwestern University

summary: Esophageal cancer is the 6th leading cause of cancer related death with a 5-year survival rate of under 20%. Esophageal squamous cell carcinoma (ESCC) is associated with chronic inflammation and injury. Currently, little is understood about the molecular mechanisms regulating the early stages of esophageal carcinogenesis. The NFB/IKK pathway plays a central role in inflammation and has been implicated in ESCC. However, its functional role in the transition to esophageal precancer is unknown. To investigate this, we utilized ED-L2/Cre mice to knockout IKKβ (IKKβEEC-KO) in the esophagus. These mice and littermate controls were treated with the carcinogen 4-nitroquinoline-1-oxide (4-NQO) or a vehicle for one month. Esophagi were harvested and examined through histological, protein, flow cytometry, and RNA analyses. Histological analysis showed that 4-NQO treatment led to increased inflammation and intraepithelial CD45+ immune cells which was largely attenuated in IKKβEEC-KO mice. Total T cells, Tregs, CD4+, and CD8+ T cells showed a similar trend, while macrophages showed a reverse trend. RNAseq data showed upregulation of inflammatory pathways and downregulation in wound healing related pathways in 4-NQO treated control mice versus knockout. We also saw increased expression of the chemokine CXCL9, a T cell chemoattractant. This increase was blocked in 4-NQO treated IKKβEEC-KO mice or in mice treated with anti-IFN. Additionally, we demonstrated in vitro that IFN upregulates CXCL9 in a NF-ĸB dependent manner in esophageal keratinocytes. So epithelial IKK regulates the immune landscape in the transition to precancer through IFN/CXCL9 signaling and recruitment of T cells to the esophagus.

overall_design: To determine the role of epithelial IKKβ in precancer of the esophagus, we generated mice with IKKβ knocked out in the epithelium of the esophagus using a cre system. Knockout mice were paired with littermate controls and treated with either the carcinogen 4-NQO in their drinking water or a vehicle control for one month. Mice were then sacced and the mucosal tissue of the esophagus was collected. Gene expression profiling was performed on the 4 conditions in a pairwise manner.

first: Hodge

last: Nathan

first: Tsikretsis

last: Lia

first: Tetreault

last: Marie-Pier


title: Augmenting regenerative hematopoietic stem cell self-renewal by intervening in peroxisomal β-oxidation

status: Public on Sep 01 2025

city: NEW YORK

first: Yue

last: Zhang

state: NY

address: 650 W 168th St, New York, NY 10032, black building 1108

country: USA

institute: Columbia University

type: Expression profiling by high throughput sequencing

summary: Robust tissue regeneration relies on extensive stem cell self-renewal. However, the molecular mechanisms promoting stem cell self-renewal during regeneration remain unclear. Here we investigate the role of peroxisomes, a key metabolic organelle, in regulating hematopoietic stem cells (HSCs). We found that disrupting peroxisome biogenesis by deleting Pex5 does not significantly impact HSC number or hematopoiesis at steady state. Strikingly, Pex5-deficient HSCs self-renew extensively and give rise to robust multilineage reconstitution upon multiple rounds of serial transplantation into recipients. Pex5-deficient HSCs are more resistant to stress and have enhanced capacity to regenerate the hematopoietic system following chemo drug treatment or irradiation. Deletion of Pex5 promotes the expansion of HSCs and hematopoietic progenitors with extensive serial ex vivo plating capacity. Pharmacological inhibition of peroxisomal β-oxidation also promotes extensive plating by HSCs and hematopoietic progenitors. We propose that intervening in peroxisomal β-oxidation can be exploited to promote HSC and progenitor function for regenerative medicine.

overall_design: Mx1-cre and Pex5fl mice were obtained from the Jackson Laboratory and maintained on C57BL/6 background. pIpC was injected to young adult mice for five doses every other day to Pex5fl/fl mice and Mx1-cre; Pex5fl/fl mice. Samples were collected at least three weeks after pIpC injection. The mice for sequencing were analyzed at three-month-old. DAPI-lineage-cKit+ cells from bone marrow were double-sorted in a yield-purity order of sorting modes on BD SORP FACSAria. Immediately following FACS isolation, 10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 were used to prepare the library according to the manufacturer’s instructions. Individual libraries were pooled for sequencing on the NovaSeq 6000 Sequencing System (Illumina). Control group samples were collected from Pex5fl/fl mice (LY001, LY003); Mutant group samples were collected from Mx1-cre; Pex5fl/fl mice (LY002, LY004).

first: Emily

last: DiMaulo-Milk

first: Xianwei

last: Chen

first: Longfei

last: Gao

first: Lei

last: Ding


title: Transcriptomic profiling of mouse macrophages treated with recombinant Rv0009, a secretory protein of Mycobacterium tuberculosis

city: Kolkata

first: Joyoti

last: Basu

address: A.P.C. Road

department: Chemistry

country: India

institute: Bose Institute

summary: Peptidyl prolylisomerase (PPIase), a well-conserved protein-folding enzyme, has recently been demonstrated to have a role in virulence of several pathogens. They regulate the cell cycle, chromatin remodelling and transcription factor functions. Mtb has two cyclophilins, PpiA and PpiB coded by ppiA (Rv0009) and ppiB (Rv2582) respectively. PpiA or Rv0009 is secreted during infection and is similar to human cyclophilins. Here, mouse macrophages (RAW264.7) were treated with recombinant Rv0009 or left untreated, followed by RNA isolation and high throughput RNA sequencing.

overall_design: RNA Sequencing in mouse macrophages (RAW264.7) treated with recombinant Rv0009 (4 hour, 8 hour and 24 hour) or left untreated (Biological Triplicate).

first: Manikuntala

last: Kundu

first: Zhumur

last: Ghosh

first: Troyee

last: Das

first: Soumya

last: Mal


title: Gene Expression Data from the Hippocampus of Mice Subjected to Tail Suspension Test

city: Tsukuba

first: Hisako

last: Iwahashi

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

summary:
This study investigates the functional effects of pine needle (PN) extract on depressive-like behavior in a tail suspension test model.
Gene expression profiling was conducted in the hippocampus of control, LPS-induced, and LPS plus PN-treated mice to explore the potential neuroprotective effects of PN.

overall_design: Total RNA was extracted from the hippocampus using an ISOGEN (Nippon Gene Co. Ltd., Tokyo, Japan) following the manufacturer's instructions. Total RNA concentration was determined using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA).Microarray analysis was performed on RNA samples extracted from the hippocampus of mice subjected to the TST, control (water treatment), LPS groups and 50 mg/kg PN administration groups. The Clariom S assay Mouse system (Thermo Fisher Scientific K.K., Tokyo, Japan) was used for triplicate RNA samples from each group. According to the user manual, cDNA for microarray analysis was generated using a GeneChip WT Plus Reagent kit (Thermo Fisher Scientific K.K.). The samples were hybridized using a Clariom S GeneChip Microarray Kit for mouse (Thermo Fisher Scientific K.K.). After washing and staining, images were captured, and raw intensity data were generated using a GeneChip Scanner 3000 (Thermo Fisher Scientific K.K.).Raw image data processing and normalization were performed using Transcriptome Analysis Console (TAC) software version 4.0.2 (Thermo Fisher Scientific, MA, USA) following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. The gene-level analysis was then performed employing the Limma Bioconductor package included with TAC 4.0.2. A one-way ANOVA was applied to identify the differentially expressed genes (DEGs), followed by an empirical Bayes correction to enhance the statistical reliability of the results.A detected above background (DABG) cutoff of 0.05 was set to refine the analysis further to eliminate non-significant signals. Additionally, the positive vs. negative area under the curve (AUC) value was conservatively set at greater than or equal to 0.7 to focus on genes with strong discriminatory potential.The final selection of DEGs was based on stringent filter criteria, requiring a p-value of less than 0.05 (calculated using one-way between-subject ANOVA). −1.2 > linear fold change > 1.2.

first: Farhana

last: Ferdousi

first: Shinji

last: Kondo


title: DRG tissue CSDE1-RIP and bulk RNA sequencing using sciatic nerve injured and uninjured AAV-Control or AAV-shGpr151 injected mice.

city: Daegu

first: Eunsu

last: Jang

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Brain Sciences

country: South Korea

institute: DGIST

summary: To determine the effect of Gpr151 mRNA depletion to rp-mRNA operon including RNA-binding protein CSDE1 after injury, we conducted CSDE1-IP sequencing analysis using the dorsal root ganglions(DRGs) of AAV-control and AAV-shGpr151 injected mice.

overall_design: CSDE1-IP sequencing of the dorsal root ganglion (DRG) tissues using AAV-control and AAV-shGpr151 injected mice. Sciatic nerve injury was conducted for the injured samples.

first: Yewon

last: Jeon

first: Jinyoung

last: Lee

first: Yeonsoo

last: Oh

first: Hoyong

last: Jin

first: Youwon

first: Bohm

first: Ju-Yeon

first: Ju-Hwan

last: Song

first: Jung-Eun

last: Shin

first: Yongcheol

last: Cho


title: Transcriptional changes of adipocyte-deletion of Prmt5 in white adipocytes

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

summary: Adipose tissue (AT) is a crucial regulator of systemic energy homeostasis, and its dysfunction can lead to insulin resistance and other metabolic complications. Protein arginine methyltransferase 5 (PRMT5) catalyzes symmetrical dimethylation of arginine residues to modulate protein stability and function. Here, we explore the function of PRMT5 in AT through RNA sequencing of wildtype and Prmt5 knockout (Prmt5AKO) mice. Our results demonstrate that Prmt5AKO alters the expression of genes related to metabolism and membrane transport. Specifically, Prmt5AKO induces genes enriched in glucose transport and glycolysis pathways, while suppressing genes encoding fatty acid (FA) transporters.

overall_design: RNA-seq profiling of epididymal white adipose tissue (eWAT) from wild-type (WT) and Prmt5 knockout (KO) mice.

first: Xiyue

last: Chen

first: Xiashiyao

last: Zhang

first: Jun

last: Wan


title: RNA-Seq profiles of human prostate cancer PC3 cells with TTC3 knockdown.

city: Saint Petersburg

first: Ranjan

last: Perera

state: FL

address: 600 5th St S

department: Oncology Center

institute: Johns Hopkins All Childrens Hospital

summary: The TTC3 gene is located at 21q22.2, and its protein product functions as an E3 ubiquitin protein ligase, mediating the ubiquitination and subsequent degradation of phosphorylated Akt in the nucleus. TTC3 was reported to play a role in neuronal differentiation inhibition and asymmetric cell division in cancer cells. We found that silencing TTC3 can significantly suppress prostate cancer cell proliferation and growth in vitro and in vivo. To identify targets regulated by TTC3, we performed global gene expression profiling analysis in TTC3-silenced PC3 cells.

overall_design: Expression profiling by high throughput sequencing, using Illumina NextSeq 2000.

first: Menglang

last: Yuan

first: Kandarp

last: Joshi

middle: J


title: High-Content Imaging and Transcriptomic Analyses of the Effects of Bisphenol S and Alternative Color Developers on KGN Granulosa Cells

city: Montreal

first: Bernard

last: Robaire

address: 3655 Prom. Sir-William-Osler

country: Canada

institute: McGill University

summary: Concerns about the adverse effects of bisphenol A (BPA), a chemical used for the production of polycarbonate plastics and epoxy resins as well as a color developer in thermal papers, have led to an increase in the use of 4,4-sulfonyldiphenol (bisphenol S; BPS), bis(3-allyl-4-hydroxyphenyl) sulfone (TGSA), 4-hydroxyphenyl 4-isoprooxyphenylsulfone (D-8), and [3-[(4-methylphenyl)sulfonylcarbamoylamino]phenyl] 4-methylbenzenesulfonate (Pergafast-201; PF-201), and 2,4-bis(phenylsulfonyl)phenol (DBSP) as alternative color developers. Data on these chemicals is scarce and little is known about their potential toxicity. We therefore determined the effects of BPS, TGSA, D-8, PF-201, and DBSP on the phenotype, function, and transcriptome of KGN human granulosa cells. Using high-content imaging, we observed that TGSA was the most cytotoxic compound tested, followed by D-8, DBSP, PF-201, and BPS. While the effects of these compounds on lysosomes, mitochondria, and oxidative stress were minimal, TGSA, D-8, and PF-201 drastically increased the number and total area of lipid droplets compared to control. RNA sequencing analyses revealed that TGSA and D-8 exposure differentially regulated 2,414 and 2,563 genes, respectively. PF-201 was the least transcriptionally active chemical, significantly affecting only six genes. Activation of pathways related to the extracellular matrix was the predominant effect of TGSA, while together, TGSA and D-8 commonly inhibited pathways involved in cell cycle regulation, DNA replication, and DNA repair. Such mechanisms may be underlying the cytotoxicity and lipid droplet accumulation observed in KGN cells. These data suggest that alternative color developers such as TGSA, D-8, and PF-201 may not be responsible replacements for BPA and BPS in thermal papers.

overall_design: Total RNA was extracted from KGN human granulosa cells exposed for 48 h to the vehicle control (DMSO) or 30 µM of  TGSA, D-8, or PF-201; n = 5.

first: Lama

last: Iskandarani

first: Stéphane

last: Bayen

first: Barbara

middle: F

last: Hales


title: Erythropoietin Exposure Impairs B Cell Development and Promotes Myeloid-Imprinted Biphenotypic Progenitors

city: Nouzilly

first: Pascal

last: Froment

address: INRAE Nouzilly

department: UMR 7247 INRAE/CNRS/Université de Tours/IFCE

country: France

institute: INRAE

summary: Erythropoietin (EPO) is the major regulator of erythropoiesis, with levels increasing in response to anemia or hypoxia. Recombinant human EPO (rhEPO) is commonly used to treat anemia in patients with chronic kidney disease or cancer. Beyond its role in erythropoiesis, EPO exerts immunomodulatory effects. Emerging evidence suggests that EPO modulates other hematopoietic lineages, such as megakaryocytes while negatively impacting B-cell development. However, its influence on lympho-hematopoiesis remains insufficiently explored. We investigated the effects of EPO on B lymphopoiesis in the context of hyper-EPOemia-induced stress hematopoiesis. Using an EPO supplementation model in C57BL/6 mice, we demonstrate that EPO impairs B lymphopoiesis during Pre-Pro-B to Pro-B transition, by downregulating essential receptor like IL-7 receptor. Conversely, EPO promotes early B-cell development at the common lymphoid progenitor (CLP) and Pre-Pro-B stages. Remarkably, EPO induces the emergence of atypical B-cell precursors with a myeloid imprint, including CSF1R/CD115-expressing CLPs and CD11b and CD16/32-expressing Pre-Pro-B cells. Gene expression profiling revealed that EPO reprograms early B-cell precursors, upregulating a myeloid transcriptional signature while downregulating B-lymphoid identity genes as for instance genes targeted by key transcription factors IRF4, FOXO1, ERG and IRF8. Additionally, EPO exposure impairs hematopoietic stem and progenitor cell proliferation, induces oxidative stress and disrupts iron homeostasis. We additionally observed lymphoid over myeloid progenitor imbalance in the bone marrow and increased extramedullary hematopoiesis in the spleen. In conclusion, hyper-EPOemia reprograms B lymphopoiesis and promotes the emergence of mixed-lineage myeloid-like B cells. Future studies will explore EPO’s effects on lymphoid progenitor fate under hypoxic and infectious conditions.

overall_design: For each cell population, batches of 100 cells (4–5 replicates) were sorted by FACS in 96-well V-bottom plate wells containing 2 mL of lysis buffer (Ultra-pure Water, 10% Triton X-100, RNasinPlus 40Uµ/l; Promega). After evaporation of the lysis buffer at 95ºC for 3 min, first strand cDNA synthesis was performed using the Maxima H Minus Reverse Transcriptase (Thermo Fisher), E3V6NEXT primers (specifiµc primer for each well) and Template Switching Primer: E5V6NEXT. Resulting cDNAs were pooled and purified by the DNA Clean and Concentrator TM-5 kit (Zymo research) and treated with Exonuclease I (New England Biolabs) before amplification using the Advantage 2 PCR kit (Clontech) and the SINGV6 primer (95°C for 1 min, 15 cycles at 95°C for 15 s, 65°C for 30 s, 68°C for 6 min and 72°C for 10 min). PCR products were purified by Agencourt AMPure XP (Beckman Coulter). Libraries were prepared using the Illumina DNA Prep kit (Illumina) according to the manufacturer’s guidelines and sequenced on a NextSeq 2000 (Illumina) at the Genome East Platform of the IGBMC (Strasbourg, France). Image analysis and base calling were performed using RTA 2.7.7 and Bcl-2fastq 2.17.1.14 software and adapter dimer reads were removed using Dimer Remover (https://sourceforge.net/projects/dimerremover/).

first: Andrada

last: Chiron

first: Stéphanie

last: Bessoles

first: Guillaume

last: Sarrabayrouse

first: Kutaiba

last: Alhaj-Hussen

first: Corentin

last: Joulain

first: Thomas

last: Darde

first: Pierre

last: De La Grange

first: Amine

middle: M

last: Abina

first: Bruno

last: Canque

first: Roman

last: Krzysiek

first: Salima

last: Hacein-Bey-Abina


title: TGFβ maintains smooth muscle cell contractile phenotype via PDK4-dpendent regulation of Ac-CoA production [ATAC-Seq_TGF-siPDK4]

city: NEW HAVEN

first: Rongmo

last: Zhang

state: CT

address: 300 George street

institute: Yale

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We find that TGFβ signaling in SMCs induced ACSS2-dependent production of Ac-CoA in a PDK4-dependent manner. TGFb induces SMC contractile phenotype and glycolysis.

overall_design: Human aortic primary smooth muscle cells (HASMCs) were treated with 10 ng/mL of TGFb or 20nM siPDK4 for 7 days with medium changes every other day.

first: Rong-Mo

first: Michael

last: Simons


title: Effect of Pdk4 smooth muscle cell-specific knockout on atherosclerosis analyzed by scRNAseq

summary: Knockout of Pdk4 in smooth muscle cells dramatically decreased inflammation, and increased gene expressions in TGFb signaling and glycolysis in the aorta.

overall_design: Pdk4 was knocked out at age of 4-6 wk, followed high fat diet feeding for 4 months. Fresh whole aorta were digested for scRNAseq.


title: ATAC-seq during the differentiation of BMM cells into osteoclasts

city: Yinchuan

first: Qu

last: XU

state: Ningxia Hui Autonomous Region

address: 804 Shengli South Street, Yinchuan, Ningxia Hui Autonomous Region 750004

country: China

institute: Ningxia Medical University

summary: The transcription factor ETS2 was identified as a hub gene that promotes osteoclast differentiation during the progression of osteoarthritis (OA). Virtual perturbation and in vitro perturbation experiments demonstrated that knockdown of ETS2 can inhibit osteoclast differentiation. Transcriptional regulatory network analysis and combined CUT&Tag with ATAC-seq analysis results indicate that ETS2 promotes osteoclast differentiation by targeting and enhancing the expression of CEBPB.

overall_design: Mouse BMM cells were induced for two days with medium containing 50 ng/ml RANKL and 50 ng/ml M-CSF. ATAC-seq was used to assess the chromatin accessibility of the cells.

last: Xu

first: Penggang

last: Ma

first: Qunhua

last: Jin


title: Chromatin Immunoprecipitation Sequencing of histone modifications (H3K4me3 and H3K27ac) in mouse macrophages (RAW264.7) infected with Mycobacterium tuberculosis

first: Joyoti

last: Basu

summary: Histone modifications plays vital role in the regulation of immune response following Mycobacterium tuberculosis infection. Here, mouse macrophages (RAW264.7) were infected with M. tuberculosis (H37Rv) or left uninfected, followed by Chromatin immunoprecipitation with anti-H3K4me3 or anti-H3K27ac antibody and high throughput sequencing.

overall_design: Chromatin Immunoprecipitation Sequencing of H3K4me3 or H3K27ac modification in M. tuberculosis (H37Rv) infected (6 hrs and 20 hrs) and uninfected mouse macrophages (RAW264.7).

first: Manikuntala

last: Kundu

first: Zhumur

last: Ghosh

first: Manish

last: Kumar

first: Debayan

last: Majumder

first: Byapti


title: Effect of PDK4 or ACSS2 knockdown on HASMC phenotype after 7 days of treatment [RNAseq-siPDK4-siACSS2]

summary: We find that PDK4 knockdown mimics the effect of TGFb in HASMCs, inducing SMC glycolysis and contractile gene expressions. Wherase, ACSS2 knockdown decreases glycolysis and contractile gene expressions.

overall_design: Human aortic primary smooth muscle cells (HASMCs) were treated with 20 nM PDK4 or ACSS2 siRNAs every on day 0 and day 4,  with medium changed every other day.. RNA were collected at day 7.


title: Treatment of prostate cancer with oncolytic virus OH2 [bulkRNA-seq_C4-2]

city: Wuhan

first: Jinzhou

state: Hubei

address: Jiefang Avenue

institute: Tongji Hospital

summary: Prostate cancer is a major challenge due to limited treatment options in advanced stages. Immunotherapy has shown promising prospects in various cancers, but it faces obstacles in prostate cancer due to its immunosuppressive microenvironment and low response rate to current therapies. Oncolytic virus therapy provides a new immunotherapy approach by stimulating anti-tumor immune responses. This study investigated the histological changes of the novel herpes simplex virus type II (HSV-II) oncolytic virus OH2 in prostate cancer tumors.

overall_design: Prostate cancer cell lines (C4-2, 3 vs. 3) were treated with oncolytic virus OH2 intervention

first: Ye

last: An

first: Guichen

last: Ye

first: Zhiyu

last: Xia

first: Shaogang

last: Wang

first: Qidong


title: Effect of TGFb on HASMC phenotype after 7 days of treatment

first: Rongmo

overall_design: Human aortic primary smooth muscle cells (HASMCs) were treated with 10 ng/mL of TGFb for 7 daysm with medium changes every other day.

first: Rong-Mo


title: The transcriptional regulation analysis of ETS2 in mouse BMM cells (Cut&Tag)

first: Qu

overall_design: Mouse BMM cells were induced for two days with medium containing 50 ng/ml RANKL and 50 ng/ml M-CSF. The Cut&Tag experiment was then performed using ETS2 antibodies to explore the transcriptional regulation of ETS2.


title: Single cell transcriptional profiling of monocytes from asthma patients show a predisposition for an inflammatory response

city: Atlanta

first: Edwin

last: Horwitz

state: Georgia

address: 1570 Haygood Drive NE

institute: Emory University

summary: Background: Asthma is the most common chronic lung disorder among children and young adults worldwide.  Standard of care therapies are only partially effective and have side effects. Despite highly effective new biologic therapies, ~10% of patients continue to be poorly controlled. Methods. We isolated monocytes from peripheral blood obtained from an asthma patient who received an infusion of interferon γ-activated mesenchymal stromal cells (γMSCs), before and at 15 and 35 days after the infusion. We similarly isolated blood monocytes from otherwise healthy subjects with asthma and healthy controls for comparison. We interrogated the monocyte samples with single cell RNA sequencing followed by data analysis using the Seurat pipeline. Findings: A single infusion of γMSCs induced a profound change in circulating monocyte gene expression, including reduction of HLA Class I expression and reduction of gene expression associated with type 1 and type 3 interferon signaling. Further examination of CD14+ and CD16+ monocytes from asthma patients revealed higher expression of proinflammatory genes compared to healthy controls, most notably increased expression of interferon response pathway genes. Within the asthma patients, several viral and interferon response pathways were significantly enriched in severe versus mild asthma. Interpretation: Circulating monocytes from asthma patients may be intrinsically programmed with a dysregulated interferon response. Monocyte directed therapy may be beneficial, especially for patients who are poorly controlled on currently available therapy. Finally, our data suggest that additional studies of γMSC therapy for patients with poorly controlled asthma is warranted.

overall_design: scRNAseq of PBMC isolated from patients with asthma and healthy controls. Preliminary data include patient receiving gMSC infusion with scRNAseq conducted pre-infusion, 15 days and 35 days post-infusion.

first: Kyndal

last: Goss

first: Melanie

middle: L

last: Grant

first: Lokesh

last: Guglani

first: Hannah

last: Miller

first: Cherish

last: Caldwell

first: Anne

last: Fitzpatrick


title: Effect of Pdk4 smooth muscle cell-specific knockout on atherosclerosis

last: Zhang

overall_design: Pdk4 was knocked out at age of 4-6 wk, followed high fat diet feeding for 4 months. Fresh ascending aorta sections were dissected and embedded for spatial sequencing using curio.

first: Michael

last: Simons


title: Dysregulation of Vitamin D and Its Signaling in Hashimoto's Thyroiditis in Korean Population

city: Goyang

first: Dong-Woo

last: Lim

address: Dongguk-ro 32

institute: Dongguk university

summary: Hahimoto’s thyroiditis (HT) is the most common thyroid disease leads to hypothyroid in developed countries. Recent studies highlighted the Vitamin D as the potential risk factor or the therapeutic agents for the HT due to its role in modulating immune responses, while the concrete evidence has not been presented. Patients eligible for the surgery of papillary thyroid cancer (PTC) with or without HT were recruited for the study. We analyzed serum thyroid biomarkers including serum vitamin D, anti-TG, anti-TPO for HT patients. Using the RNA-seq the gene expression profile of thyroid tissue, potential correlation between HT and vitamin D or its signaling was investigated.  HT cohort showed common clinical characteristics known for the HT in serum biomarkers and enrichment analysis of BP terms and KEGG pathways. Serum vitamin D level was significantly lower in HT patients. However, vitamin D receptor (VDR) expression and genes involved in vitamin D-associated BP terms were significantly upregulated in HT. Real-time PCR and Immunofluorescence staining confirmed enhanced VDR expression throughout the thyroid tissue of HT cohort.   This study demonstrated dysregulated vitamin D signaling in thyroid tissue of HT cohort. Further study need to be performed to elucidate etiology, susceptibility, and development of HT in relation with vitamin D signaling.

overall_design: RNA-seq profiling of isolated thyroid tissue from papillary thyroid cancer (PTC) patients eligible for surgery with or without HT etiology.

first: Seok-Mo

last: Kim


title: MSCs can alleviate ferroptosis and improve DKD through the Smad2/3/METTL3/S1PR1 axis.

city: Kunming

first: Yihua

last: Bai

state: 云南省

address: No. 374, Dianmian Road, WuhuaDistrict

institute: The Second Affiliated Hospital of Kunming Medical University

type: Methylation profiling by high throughput sequencing

summary: Diabetic kidney disease (DKD) is a significant cause of end-stage renal disease (ESRD), markedly increasing the risk of cardiovascular disease and all-cause mortality. Although mesenchymal stem cells (MSCs) have demonstrated potential in mitigating DKD through various pathways, their specific mechanisms remain unclear. In this study, we observed increased Smad2 phosphorylation and ferroptosis in DKD models, which were alleviated by MSC intervention. Dot blot analysis and the EpiQuik M6A RNA Methylation Quantification Kit revealed elevated m6A modification levels in DKD. Bioinformatics analysis, receiver operating characteristic (ROC) curves, and Western blot (WB) assays indicated a correlation between METTL3 expression and changes in m6A modification in DKD. Knockdown of METTL3 and Smad2 reduced m6A modification and ferroptosis levels. Furthermore, knockdown of METTL3 reversed the increase in m6A modification caused by Smad2 overexpression. Notably, transcriptome and m6A-seq analysis identified S1pr1 as a target gene. Using the GEPIA database, we found a close association between S1pr1 expression and both Smad2 and METTL3 in kidney tissues. The SRAMP tool predicted nine m6A modification sites on S1pr1 mRNA, eight with over 95% credibility and one at position 688 with over 90% credibility. Knockdown of S1pr1 reversed the protective effect of METTL3 knockdown against ferroptosis in DKD, increasing Fe2+, ROS, and ACSL4 levels while decreasing GPX4 and SLC7A11 expression. Finally, MSC intervention and shRNA-mediated METTL3 knockdown increased the reduced S1pr1 levels in DKD kidney tissue. Our findings suggest that upon nuclear translocation, Smad2 promotes S1pr1 gene m6A modification by binding to METTL3, thereby affecting S1pr1 expression and positively regulating cellular ferroptosis in DKD models. MSC intervention can reduce this process, further elucidating the mechanism by which MSCs regulate podocyte ferroptosis in DKD.

overall_design: This study employed m6A-seq technology to identify relevant m6A methylated differential genes through a comprehensive series of data processing and screening steps. Specifically, cellular samples from three groups—the MPC5 group (MPC5 cells cultured in regular medium), the MPC5sh_METTL3 group (MPC5 cells transfected with sh-METTL3 virus), and the MPC5sh_METTL3_G group (MPC5 cells transfected with sh-METTL3 virus and subsequently treated with 25 µmol/L glucose for 72 hours in the culture medium)—were subjected to Total RNA extraction and quality control. Following this, sequence analysis libraries were constructed and evaluated, and the samples were sequenced and screened. The sequencing data were then aligned to the reference sequence for comparative analysis. Peak calling and differential peak (diff Peak) analysis were conducted to identify changes in m6A methylation sites between the groups. Additionally, transcriptome sequencing analysis was performed, and an integrated analysis of the transcriptome and m6A-seq data was carried out to identify genes with differential m6A methylation that may be associated with alterations in gene expression.


title: The SIK2/SIK3 inhibitor GLPG3970 increases bone formation and trabecular bone mass in hypogonadal female mice and rats

city: Dallas

first: Jialiang

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Currently, there are no orally available bone anabolic therapies to treat osteoporosis. Intermittent parathyroid hormone injections stimulate bone formation through a signaling pathway that inhibits the actions of salt inducible kinase (SIK) isoforms 2 and 3. Therefore, direct small molecule SIK2/SIK3 inhibitors represent a promising treatment strategy to mimic PTH actions. Here we tested GLPG3970, a potent and selective SIK2/SIK3 inhibitor developed for clinical use in inflammatory diseases, in rodent models of post-menopausal osteoporosis. In bone cells, GLPG3970 reduces phosphorylation levels of SIK substrates and regulates gene expression patterns, as assessed by RNA-sequencing, in a PTH-like manner. GLPG3970 was administered to female mice and rats rendered hypogonadal via surgical oophorectomy (OVX) via twice daily oral gavage. In parallel, separate groups of rodents were treated with once daily subcutaneous PTH injections. Skeletal endpoints, serum bone turnover markers, micro-CT, histomorphometry, and mechanical testing, were assessed after study termination. In both OVX-operated mice and rats, GLPG3970 treatment increased markers of bone formation and cancellous bone mass, and increased rat vertebral body bone strength. These results provide strong justification for further development of orally available SIK2/SIK3 inhibitors to treat post-menopausal osteoporosis.

overall_design: Ocy454 cells were treated with vehicle or GLPG3970 for 4 hours. RNA samples were collected and purified for bulk RNA-seq.

middle: S

first: Marc

middle: N

last: Wein


title: Ferroptotic neutrophils eradicate chemotherapy-induced immunity in breast cancer (Neutrophils)

city: Guangzhou

first: Penghan

last: Huang

address: 107 Yan Jinag West Road

institute: Sun Yat-Sen University

summary: Inducing ferroptosis in tumor cells serves as a promising strategy for treating malignancies that are refractory to traditional treatment modalities. However, the consequences of ferroptosis in immune cells in the tumor microenvironment (TME) are not completely understood. In this study, we found that neutrophils in chemoresistant breast cancer exhibited notable vulnerability to ferroptosis. In chemoresistant neutrophils, the cellular phospholipid profile was reprogrammed owing to a deficiency in membrane-bound O-acyltransferase domain-containing 1 (MBOAT1), shifting the preference of the phospholipid fatty acid pattern from monounsaturated fatty acids (MUFAs) to polyunsaturated fatty acids (PUFAs), thereby increasing susceptibility to ferroptosis. Ferroptotic neutrophils significantly suppress the proliferation and cytotoxicity of antitumor CD8 T cells via PGE2, IDO, and oxidized lipids. Furthermore, we found that neutrophil ferroptosis was closely associated with a distinctive subset of IL-1+ CXCL3+ CD4 (Fer-CD4) T lymphocytes that were enriched in chemoresistant tumors. Fer-CD4 T cells regulated neutrophil ferroptosis through MBOAT1 modulation via IL-1/IL-1R1/NF-B signaling. Moreover, we revealed that there is crosstalk between neutrophils and Fer-CD4 T cells, during which Fer-CD4 T cells replenish the neutrophil pool of the TME via CXCL3, IL-8, and S100A9. The ferroptotic neutrophils in turn promote Fer-CD4 T cell differentiation, resulting in extensive neutrophil ferroptosis. In spontaneously tumorigenic mice, targeting IL-1+ CD4 T cells or IL-1R1+ neutrophils disrupted this crosstalk, suppressed neutrophil ferroptosis, enhanced antitumor immunity, and overcame chemoresistance. Our findings revealed the immune-reshaping capacity of neutrophil ferroptosis and its reciprocal feedback regulation with Fer-CD4 T cells, identifying promising targets for restoring anticancer immunosurveillance and reversing chemoresistance

overall_design: Isolation and transcriptome sequencing of sensitive and resistant patient neutrophil

first: Wenfeng

last: Zeng

first: Ruihua

first: Liyan

last: Lao


title: Tau hyperphosphorylation in Locus Coeruleus mediates early-onset sleep disruption in mouse model of AD amyloidosis by causing neuronal hyperexcitability

city: Shanghai

first: Ziyue

last: Zhou

address: 100 Haike Road, Zhangjiang Hi-Tech Park, Pudong

institute: The Interdisciplinary Research Center on Biology and Chemistry

summary: Sleep disturbances are common in patients with neurodegeneration, including Alzheimer's disease (AD), which can occur at early stages of AD and are proposed as potent risk factors for disease onset and progression. The underlying causes of this early-onset sleep disturbances remain unclear. Here we found that 5xFAD transgenic mice display significantly reduced sleep and prolonged wakefulness as early as 2 months of age. This early-onset sleep disruption correlates with increased tonic neuronal activity in the Locus Coeruleus (LC), which is mediated by heightened neuronal excitability due to impaired Kv4 and Kv7 channel conductance. Notably, we discovered that these young transgenic mice develop brain region-specific tau hyperphosphorylation (p-tau) in the LC. To investigate the pathological role of LC p-tau, we induce p-tau by inoculating synthetic human tau fibril into the LC of wild-type mice. This fibril inoculation replicated the reduction in Kv conductance and increased LC neuronal excitability in a tau-dependent manner. Modulating Kv4 and Kv7 channels restored normal excitability in both fibril-inoculated wild-type mice and young 5xFAD mice. Furthermore, fibril inoculation was sufficient to induce 5xFAD-like sleep disruptions in wild-type mice. Finally, pharmacological reduction of p-tau, both ex vivo and in vivo, effectively restored normal electrophysiological properties of LC neurons and normalized sleep/wake patterns in fibril-inoculated wild-type mice and young 5xFAD mice. Therefore, our findings identify a neural mechanism underlying early-onset sleep disturbances in a mouse model of AD amyloidosis and highlight the pathological consequences of LC tau hyperphosphorylation.

overall_design: Mice were anesthetized with isoflurane vapor and rapidly sacrificed. Brain slices containing LC region were collected by a vibratome (1200S, Leica) in ice-cold dissection buffer. LC regions were micro-dissected on ice with sterile disposable biopsy punch (#33-31, Integra Lifesciences) then quickly frozen with liquid nitrogen and stored at −80°C until used. TRIzol® Reagent (Invitrogen Life Technologies) was used to retrieve total RNA. RNA concentration and quality were determined by NanoDrop spectrophotometer (Thermo Scientific). Only high-quality RNA samples (OD260 / 280 = 1.8 ~ 2.2, OD260 / 230 ≥ 1.9, RIN ≥ 9.0) were used for the library and bulk RNA sequencing (Shanghai Personal Biotechnology Cp. Ltd.).


title: RNASeq analysis of eosinophils with IL33 or (and) SID26681509

city: Hangzhou

first: Yinling

last: Han

address: Jiefang Road

institute: Key Laboratory of Respiratory Disease of Zhejiang Province

summary: Eosinophils are the predominant immune cells implicated in asthma pathogenesis, highlighting the necessity for strategies to mitigate their effects. Previous studies have indicated a potential relationship between lysosomes and eosinophils, while the precise role of lysosomes in eosinophil activation during asthma remains insufficiently understood. Here, we used RNA-seq to analyze transcriptomic expression difference between IL33 or (and) SID26681509-stimulated eosinophils to find out what genes involved in the regulation of inflammation.

overall_design: To analyze transcriptomic expression difference between IL33 or (and) SID26681509-stimulated eosinophils to find out what genes involved in the regulation of inflammation.


title: Multi-omics of resting and anti-CD3/CD28-stimuated Jurkat cells

first: Mulin Jun

last: Li

state: Guangdong

address: No. 9 Jinsui Road, Guangzhou

institute: Guangzhou Women and Children's Medical Center

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

overall_design: Refer to individual Series


title: Non-destructive transcriptomics via vesicular export (NTVE)

city: Munich

first: Gil

middle: Gregor

last: Westmeyer

address: Arcisstrasse 21

country: Germany

institute: Technical University Munich

summary: Transcriptomics is a valuable technique for multiplexed monitoring of cellular states. Using an engineered RNA adapter, NTVE exports cellular transcripts from inducible human and murine reporter cell lines with high concordance to conventional lysate-derived RNA-seq. NTVE allows monitoring of transcriptome changes in response to genetic and chemical perturbations (Interferon gamma; ASCL1 transactivation) in the same cells over time using standard sequencing workflows.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Samples originate either from cell lysates or were prepped from the supernatant by using a viral RNA preparation kit (see method section https://doi.org/10.1101/2024.11.11.622832)

first: Niklas

last: Armbrust

first: Martin

last: Grosshauser

first: Jeffery

last: Truong


title: INO80/SWR Remodelers Regulate Pol II Transcription through BRD2 and Chromatin Landscape (TT-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 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.

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

first: Meitong

last: Liu

first: Qiqin

last: Xu


title: The X-linked chromatin modifier SMC1A is deregulated in lupus female monocytes and promotes autoimmunity [RNA-Seq]

city: Heraklion

first: George

last: Bertsias

address: Andrea Kalokerinou 13

department: Medical School

country: Greece

institute: University of Crete

summary: Biological sex underlines the onset of autoimmunity yet the underlying molecular mechanisms remain ill-defined. Female susceptibility is prominent in systemic lupus erythematosus (SLE), an autoimmune disease of substantial burden. Herein we demonstrate that SMC1A, a subunit of the cohesin complex that escapes X-chromosome inactivation, exhibits female-biased expression in monocytes from SLE patients and those cultured under lupus-inducing stimulus. By altering SMC1A dosage, the expression of immune-related genes, particularly those responsive to lupus environment, was affected. Active enhancers of immune and inflammatory pathways showed widespread SMC1A redistribution in lupus-like monocytes, as revealed by integrated analysis of SMC1A binding, chromatin activity and accessibility. Our data support SMC1A as a sex-biased chromatin modifier that enhances inflammatory responses in lupus.

overall_design:
RNA-seq data from peripheral blood of 15 individuals in each of four groups -healthy male, healthy female and SLE male, SLE female- was analyzed to identify sexually differential gene expression in SLE patients compared to healthy controls. Some of these samples were previously published, with 20 of the total samples being analyzed for the first time in this study.
To investigate the role of SMC1A in gene transcription regulation in human monocytes during lupus-like inflammation, we silenced SMC1A in CD14+ monocytes isolated from blood of three healthy donors. The cells were treated  with IFNa and TNF for 18h and LPS for 3h and  RNA-seq was perfromed on cells from the following conditions: si_control unstimulated, si_control IFNa TNF LPS stimulated, si_smc1a unstimulated, si_smc1a IFNa TNF LPS stimulated.
Focusing on the whole blood-derived monocytes, we analyzed the transciptomic differences between monocytes from healthy donors and SLE patients by conducting RNA-seq on CD14+ monocytes isolated form the blood of 5 healthy donors and 6 SLE patients.
To delineate the sexually differential expressed genes in SLE monocytes, blood CD14+ monocytes were isolated from 10 male and 8 female patients with SLE, cultured with 10 ng/ml MCSF for 18 h and QuantSeq 3' mRNA sequencing was performed

first: Despoina

last: Kosmara

first: Sofia

last: Papanikolaou

first: Chrysoula

last: Stathopoulou

first: Giannis

last: Vatsellas

first: Aggelos

last: Banos

first: Prodromos

last: Sidiropoulos

first: Matthieu

middle: D

last: Lavigne

first: Dimitrios

last: Boumpas

first: Charalampos

last: Spilianakis

first: Dimitris

last: Konstantopoulos

first: Christoforos

last: Nikolaou


title: The X-linked chromatin modifier SMC1A is deregulated in lupus female monocytes and promotes autoimmunity [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for the cohesin complex member protein SMC1A and the histone modification H3K27ac in blood CD14+ monocytes unstimulated and stimulated with IFNa TNF (18h) and LPS  (1h)


title: CRISPR library screening analysis on DMSO and Erlotinib 10µM treated samples

city: Melbourne

first: Goknur

last: Giner

state: VIC

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Triple-negative breast cancers (TNBCs) are the most aggressive subtype of breast cancer that have poor prognosis and very few treatment options. Although approximately 40-70% of TNBC patients have EGFR overexpression, anti-EGFR therapies exerted little to no clinical benefit. This could be due to (i) the presence of an inherent resistance mechanism, (ii) the presence of EGFR protein in its inactive form, or (iii) lack of EGFR on the surface of plasma membrane. Several studies have shown that EGFR is present in the intracellular compartments, instead of the plasma membrane surface, in TNBC patients. Previous studies have demonstrated that intracellular EGFR renders TNBC tumors resistant to anti-EGFR therapies. Here, we used genome wide CRISPR library screening to identify the markers of resistance to EGFR inhibitors. Our CRISPR screening identified a redox protein, thioredoxin reductase 3 (TXNRD3), to be depleted in erlotinib-treated MDA-MB-231 cells suggesting that loss of TXNRD3 may sensitize TNBC cells to EGFR inhibitors. siRNA-induced knockdown and pharmacological inhibition of TXNRD3 using an FDA-approved drug auranofin significantly sensitized EGFR-high TNBC cells to EGFR inhibitors. Mechanistically, TXNRD3 knockdown or inhibition increased oxidative stress resulting in increased EGFR phosphorylation at Y1068 (active EGFR protein). Moreover, auranofin also increased surface accumulation of EGFR and sensitized SUM159PT cells to cetuximab-induced ADCC. Auranofin and erlotinib combination therapy exerted a significant anti-cancer activity in vivo in MDA-MB-231 cell line-derived xenograft and in murine syngeneic 4T1.2 TNBC model. Collectively, these data suggests that TXNRD3 inhibition using auranofin activates EGFR and increases its surface localization, which then sensitizes TNBC cells to anti-EGFR therapies. Hence, auranofin combined with anti-EGFR therapies may be a viable approach for the treatment of TNBC patients.

overall_design: To to identify the markers of resistance to EGFR inhibitors, we performed CRISPR library screening analysis and compared DMSO samples with the samples treated with Erlotinib  10µM. Sequencing experiments were run for three replicates on 4 lanes for each sample in vivo in MDA-MB-231 cell line-derived xenograft and in murine syngeneic 4T1.2 TNBC model cell lines.

first: Giner

last: Goknur


title: Analysis of the low salt transcriptome of Haloferax volcanii

city: Frankfurt am Main

first: Andreas

last: Borst

address: Max-von-Laue-Str. 9

institute: Goethe-Universität Frankfurt

summary: Archaea are well known for inhabiting areas of our planet that are usually hostile for any form of life, hence they are often termed as “extremophiles”. Although also found in common soil or the digestive tract of vertebrates, some species thrive on acidic or alkaline grounds, in submarine black smokers with temperatures surpassing 100°C or live in aquatic areas with a very high salinity.Haloferax volcanii is a halophilic and mesophilic archaeon that was first discovered in the 1930s and isolated from the hypersaline environment of the Dead Sea. Its optimal growth conditions are at 42 °C in around 2 M NaCl and complex nutrient medium, however it can also grow in different synthetic media and at a wide range of temperatures and NaCl concentrations. While NaCl concentrations up to 0.7 M inhibit growth in synthetic glucose media, a concentration of 0.9 M is sufficient to sustain growth at a reduced rate.Here we show for the first time a transcriptome-wide analysis of differential gene expression of cells grown under low salt condition. We cultivated cells at an optimal NaCl concentration of 2.1 M in glucose media and compared the expression profile of these to cells grown in 0.9 M NaCl after 26 and 68 h.

overall_design: differential gene expression profiles of the halophilic archaeon Haloferax volcanii should be analysed as response to low salt conditions in glucose medium (2.1 M vs 0.9 M NaCl) after a short (26 h) and prolonged (68 h) period of time. RNA-Seq was done in duplicates of 3 Samples (2.1 NaCl M after 26h; 0.9 M NaCl after 26h and 0.9 M NaCl after 68 h). Key player genes involved in low salt stress response (26h at 0.9 M NaCl) and low salt adaption (68h at 0.9 M NaCl) shluld be identified.


title: Non-cell-autonomous control of gastruloid development by the lncRNA T-UCstem1 through DKK1-dependent modulation of WNT signalling

city: Basel

first: Edoardo

last: Sozzi

address: Klingelbergstrasse 48

country: Switzerland

institute: ETH Zurich

summary: The role and the mechanisms of long non-coding RNA (lncRNAs) in early mammalian embryogenesis remain unclear; this is mostly due to the complexity of the regulatory mechanism of lncRNAs and the limited availability of early embryo samples. The emergence of stem cell-based models of early mammalian embryogenesis offers new opportunities to address these challenging questions. Here we use mouse gastruloids to investigate the role of an ultraconserved lncRNA, T-UCstem1, in the formation of the mammalian body plan. Combining morphological and immunofluorescence analysis with bulk and single cells transcriptomics, we provide unprecedented evidence that T-UCstem1 is a key regulator of gastruloid development and is required for the extension of the anteroposterior axis. Specifically, knock down of T-UCstem1 results in aberrant gastruloid development, which is characterized by altered spatiotemporal expression of the differentiation markers and persistence of pluripotency genes. Single-cell analysis reveals higher cellular heterogeneity in T-UCstem1 KD gastruloids. Notably, the presence of cell populations characterized by the co-expression of pluripotency and differentiation markers points to a key role of T-UCstem1 in establishment and maintenance of proper cellular identity. Mechanistically, we show that T-UCstem1 acts non-cell autonomously through Dickkopf-related protein 1 (DKK-1)-dependent modulation of WNT pathway. Our findings highlight a previously unexplored role for ultraconserved lncRNAs in gastruloid development and open the way for using gastruloids to dissect the functions of lncRNAs in early mammalian development.

overall_design: Bulk RNA seq of mouse gastruloids derived from KD for an ultraconserved lncRNA, T-UCstem1, vs Ctrl. 3 biological replicates per group, 1 time point (5days).

first: Alessandro

last: Fiorenzano

first: Arianna

last: Coppola

first: Annalisa

last: Fico


title: Synergistic antibacterial mechanism of benzyl isothiocyanate and resveratrol against Staphylococcus aureus revealed by transcriptomic analysis

city: Dalian

first: Jianan

last: Liu

state: Liaoning

address: NO.1 Light-Industry Garden, Ganjingzi Borough

institute: Dalian Polytechnic University

summary: The transcriptomics results showed that the BITC_RES groups had 245 and 1150 more differential genes than the BITC group and RES group, respectively. Among them, the serine protease (splD) in the BITC_RES group was down-regulated about 259.8-fold, which was 259.8-fold and 86.6-fold higher than that in the BITC group and RES group.

overall_design: The library construction process was carried out in several ways. Total RNA sample identification, mRNA enrichment, duplex cDNA synthesis, end repair, A-addition and splicing, fragment selection and PCR amplification, library construction and Illumina sequencing..Raw sequence data was obtained by throughput sequencing, and low qualified reads were removed to obtain clean reads for final use. The filtered sequences were analyzed for genomic localization using Bowtie2 software. Differentially expressed genes (DEGs) between the control group and each treatment group were screened by DESeq2 software, statistical modeling was performed for the calculation of probability of hypothesis testing (p-value), and finally multiple hypothesis testing was performed for correction to obtain FDR values. The DEGs obtained after screening were imported into the Gene Ontology (GO) comprehensive database and the Kyoto Encyclopedia of Genes and Genomes (KEGG) comprehensive database to find the corresponding functional annotations and metabolic pathways for enrichment analysis.

first: Jinle

last: Ma

first: Junya

last: Zhu

first: Yingrui

last: Wang

first: Hongshun

last: Hao

first: Jingran

last: Bi

first: Hongman

last: Hou

first: Gongliang

last: Zhang


first: Mulin Jun

last: Li

summary: To investigate the internal regulatory mechanisms governing the CD28 gene region during T cell activation and to screen for truly active dynamic chromatin regulatory elements responsive to stimulation, we employed the CRISPRa gene editing technology to design specific sgRNAs targeting this region and conducted a tilling CRISPRa screen sequencing on the CD28 gene region.

overall_design: We performed tilling CRISPRa screening of CD28 gene region in Jurkat cells. Anti-CD28 and anti-CD3 antibodies were utilized to activate T cells as previously described (Simeonov et al. Nature, 2017). Briefly, the culture plate was coated with 10 µg/ml of anti-CD28 (TONBO Biosciences, 40-0289) for 12 hours at 4°C prior to cell inoculation. Jurkat or CD4+ T cells were then seeded with 10 µg/ml of anti-CD3 (40-0038). The cells were harvested 24 hours later for subsequent experimental analysis.

first: Zhao

first: Wei

last: Dong


title: RNA-Seq shows the effect of EGFR-TKIs Dacomitinib on HaCaT cells

city: 杭州市

first: zhou

middle: wan

last: ying

state: 浙江省

address: Banshan street

institute: 浙江省肿瘤医院

summary: Dacomitinib treated HaCaT for 48 hours, Dacomitinib significantly increased Retinol metabolism pathway in HaCaT

overall_design: When the HaCaT cell confluence reached 70%, the cells were treated with Dacomitinib for 48 h, and the experimental group was treated with 0.1%DMSO. The differences in cell pathways between the two groups were detected by RNA-Seq technology.

first: Luo

last: Fang

first: Jiaqi

first: Wanying

last: Zhou


title: ChIP-seq of resting and anti-CD3/CD28-stimuated Jurkat cells

summary: To finely dissect the dynamic changes in the epigenome and chromatin state during T cell activation, we utilized the Jurkat cell line as a model and performed ChIP-seq on both resting and anti-CD3/CD28-stimulated Jurkat cells, targeting various histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K27me3), RNA PolII, and CTCF.

overall_design:
We performed ChIP-seq on both resting and anti-CD3/CD28-stimulated Jurkat cells for distinct histone modifications and TFs. Anti-CD28 and anti-CD3 antibodies were utilized to activate T cells as previously described (Simeonov et al. Nature, 2017). Briefly, the culture plate was coated with 10 µg/ml of anti-CD28 (TONBO Biosciences, 40-0289) for 12 hours at 4°C prior to cell inoculation. Jurkat or CD4+ T cells were then seeded with 10 µg/ml of anti-CD3 (40-0038). The cells were harvested 24 hours later for subsequent experimental analysis.

**Please note that the records have been updated as below on Sep 22, 2025:
[1] both raw and processed data for GSM8522707-GSM8522720 have been replaced
[2] additional sample records have been included


title: Multi-level transcriptional regulation of embryonic sex determination and dosage compensation by the X-signal element sex-1

city: Ann Arbor

first: Gyorgyi

last: Csankovszki

state: MI

address: 1105 N University Ave

department: MCDB

institute: University of Michigan

summary: The C. elegans nuclear hormone receptor sex-1 is known to be an embryonic X-signal element that represses xol-1, the sex-switch gene that is the master regulator of sex determination and dosage compensation. Several prior studies on sex-1 function have suggested that sex-1 may have additional downstream roles beyond the regulation of xol-1 expression. In this study we characterize some of these additional roles of sex-1 in regulating the dual processes of sex determination and dosage compensation during embryogenesis. Our study reveals that sex-1 acts on many of the downstream targets of xol-1 in a xol-1-independent manner. Further analysis of these shared but independently regulated downstream targets uncovered that sex-1 mediates the expression of hermaphrodite- and male-biased genes during embryogenesis. We validated sex-1 binding on one of these downstream targets, the male-developmental gene her-1. Our data suggests a model where sex-1 exhibits multi-level direct transcriptional regulation on several targets downstream of xol-1 to reinforce the appropriate expression of sex-biased transcripts in XX embryos. Furthermore, we found that xol-1 sex-1 double mutants show defects in dosage compensation. Our study provides evidence that this is caused by the misregulation of dpy-21, one of the components of the dosage compensation complex, and the subsequent misregulation of H4K20me1 enrichment on the X chromosomes.

overall_design: RNA-seq profiles of early embryo, L1 and L3 larval stage C. elegans samples. The following genotypes are included: N2 Bristol strain (wild type), WM458 xol-1 (ne4472) X, and EKM198 xol-1 (ne4472) sex-1 (gk829) X. Genotype and developmental stage for each sample are listed separately.

first: Eshna

last: Jash

first: Zoey

last: Tan

first: Audry

middle: I

last: Rakozy

first: Anati Alyaa

last: Azhar

first: Hector

last: Mendoza

first: Györgyi


title: 4C-seq of resting and anti-CD3/CD28-stimuated Jurkat cells

summary: To investigate the interacting loci within the region containing rs5837875, we employed the circularized chromosome conformation capture (4C) assay to elucidate the spatial interactions and regulatory networks associated with rs5837875, utilizing this specific region as the bait in Jurkat cells.

overall_design: We performed 4C-seq on both resting and anti-CD3/CD28-stimulated Jurkat cells. Anti-CD28 and anti-CD3 antibodies were utilized to activate T cells as previously described (Simeonov et al. Nature, 2017). Briefly, the culture plate was coated with 10 µg/ml of anti-CD28 (TONBO Biosciences, 40-0289) for 12 hours at 4°C prior to cell inoculation. Jurkat or CD4+ T cells were then seeded with 10 µg/ml of anti-CD3 (40-0038). The cells were harvested 24 hours later for subsequent experimental analysis.


title: Therapeutic reduction of RAD23A extends lifespan and mitigates pathology in TDP-43 mice

city: London

first: Ravindra

middle: Singh

last: Prajapati

state: UK

address: 2nd floor, Maurice Wohl Clinical Neuroscience Inst, 5 Cutcombe Road

department: BCN, Maurice Wohl Clinical Neuroscience Ins

country: United Kingdom

institute: King's College London

summary: Protein misfolding and aggregation are cardinal features of neurodegenerative disease (NDD) and they contribute to pathophysiology by both loss-of-function (LOF) and gain-of-function (GOF) mechanisms.  This is well exemplified by TDP-43 which aggregates and mislocalizes in several NDDs.  The depletion of nuclear TDP-43 leads to reduction in its normal function in RNA metabolism and the cytoplasmic accumulation of TDP-43 leads to aberrant protein homeostasis.  A modifier screen found that loss of rad23 suppressed TDP-43 pathology in invertebrate and tissue culture models.  Here we show in a mouse model of TDP-43 pathology that genetic or antisense oligonucleotide (ASO)-mediated reduction in the RAD23A confers benefits on survival and behavior, histological hallmarks of disease and reduction of mislocalized and aggregated TDP-43.  This results in improved function of the ubiquitin-proteasome system (UPS) and correction of transcriptomic alterations evoked by pathologic TDP-43.  RAD23A-dependent remodeling of the insoluble proteome appears to be the key event driving pathology in this model.  As TDP-43 pathology is prevalent in both familial and sporadic NDD, targeting RAD23A may have therapeutic potential.

overall_design: In order to gain insight into the mechanisms underlying RAD23A actions in a TDP-43-based mouse model of ALS/FTD (TDP-43Tg/+), we utilized antisense oligos to knock down Rad23a in the mouse motor cortex. Scrambled antisense oligos were used as a control. Both wild-type (WT) and TDP-43Tg/+ mice's motor cortex were treated with scrambled and rad23a knockdown ASOs. We used ten biological replicates for each condition. To identify genes associated with the disease, we compared WT scrambled with TDP-43Tg/+ scrambled, and to identify genes associated with the treatment, we compared TDP-43Tg/+ scrambled with TDP-43Tg/+ rad23a knockdown ASO-treated mice.

first: Xueshui

last: Guo

first: Jiyeon

last: Chun

first: Insuk

last: Byun

first: Kamil

middle: K

last: Gebis

first: Yi-Zhi

first: Karen

last: Ling

first: Casey

last: Dalton

first: Jeff

last: Blair

first: Anahid

last: Hamidianjahromi

first: Jeffrey

last: Savas

first: Min

last: Lee

first: Jemeen

last: Sreedharan

first: Robert

last: Kalb


title: Oncostatin-M: A Novel Leukocyte-Derived Factor Facilitating the Ovulatory Process in the Human Ovary

city: Lexington

first: Yohan

last: Choi

state: KY

address: 800 Rose St

department: OB/GYN

institute: University of Kentucky

summary: Leukocytes, known as key effectors for ovulation, were found to specifically express oncostatin-M (OSM), while its receptors (OSMR and IL6ST) were abundant in granulosa cells, as shown in single-cell transcriptomics of follicular aspirates. OSM levels in the follicular fluid ranged 20.99 to 429.81 pg/ml. Increases in OSM-positive cells and OSMR and IL6ST expression were detected in ovulatory follicles post-hCG administration. Treating recombinant human OSM protein (rhOSM) to hCG-primed human granulosa/lutein cells activated signaling mediators, e.g., STATs. This treatment enabled hGLC cultures to mimic the in vivo ovulatory steroidogenesis dynamic, characterized by increased progesterone and reduced estradiol, unlike hCG alone. Additionally, rhOSM modulated gene expression associated with various ovulatory changes. This evidence suggests that leukocyte-derived OSM is a groundbreaking factor in human ovulation.

overall_design: Cultured human granulosa-lutein cells treated with hCG and hCG+rhOSM were used to perform RNA-seq analysis.

first: Mats

last: Brännström

first: James

middle: W

last: Akin

first: Ashley

last: Teates

first: Lane

last: Christenson

first: Thomas

middle: E

last: Curry

first: Misung

last: Jo


title: Toxoplasma gondii dictates placental trophoblast lineage specification through induction of decidual signaling cues [single nuclei multiome]

city: Pittsburgh

first: Leah

last: Cabo

state: PA

address: 4249 Fifth Avenue

institute: University of pittsburgh

summary: Pregnancy is a critical point of vulnerability to infection and other insults that could compromise proper fetal development. The placenta acts as a protective and nutrient-permeable barrier to most infectious agents, but a few are capable of bypassing its defenses. Remarkably little is known about how exposure to these select pathogens might impact ongoing placental development. Here we demonstrate thatToxoplasma gondii entirely misdirects the developmental program of trophoblast stem cells. Infection of progenitor cytotrophoblasts prevents fusion and differentiation to infection-resistant syncytiotrophoblast. Rather, T. gondii elicits a unique transcriptional identity that polarizes cytotrophoblasts to the infection-permissive extravillous trophoblast fate. Strong evidence of developmental disruption is found in multiple orthogonal models, including trophoblast stem cells, trophoblast organoids, and chorionic villi. Manipulation of cell fate by the parasite is most dramatic in trophoblast organoids, where we see robust outgrowth of HLA-G(+) extravillous trophoblasts. Collectively, these data show thatToxoplasmaantagonizes differentiation of an infection-resistant cell type by inducing formation of an infection-permissive cell type, therefore potentiating its own transmission to the fetus.

overall_design: To investigate the impact of Toxoplasma gondii infection on trophoblast development, we infected or mock-infected cytotrophoblasts (CTB) and compared them to intermediately and terminally differentiated extravillous trophoblast (EVT)

first: Cabo

last: Leah

first: Boyle

last: Jon


title: ATAC-seq of resting and anti-CD3/CD28-stimuated Jurkat cells

first: Mulin Jun

last: Li

summary: The majority of genetic risk variants associated with autoimmune diseases are located in chromatin regions that are accessible during T cell stimulation. To systematically investigate the dynamic changes in chromatin accessibility during T cell activation, we utilized the Jurkat cell line as a model and performed ATAC-seq on both resting and anti-CD3/CD28-stimulated Jurkat cells.

overall_design: We performed ATAC-seq on both resting and anti-CD3/CD28-stimulated Jurkat cells.Anti-CD28 and anti-CD3 antibodies were utilized to activate T cells as previously described (Simeonov et al. Nature, 2017). Briefly, the culture plate was coated with 10 µg/ml of anti-CD28 (TONBO Biosciences, 40-0289) for 12 hours at 4°C prior to cell inoculation. Jurkat or CD4+ T cells were then seeded with 10 µg/ml of anti-CD3 (40-0038). The cells were harvested 24 hours later for subsequent experimental analysis. The ATAC-seq library was prepared with the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) and the TruePrep Index Kit V2 for Illumina (Vazyme, TD202), following the kit’s instructions.

first: Zhao

last: Wang

first: Wei

last: Dong


title: CD28 region-capture HiC of resting and anti-CD3/CD28-stimuated Jurkat cells

summary: To meticulously explore how local chromatin architecture influences T cell activation, we conducted high-resolution regional capture Hi-C by designing tiling capture probes that span the CD28, CTLA4, and ICOS genes along with their distal regulatory sequences (chr2:204300000-205000000, GRCh37) in both resting and stimulated Jurkat cells.

overall_design: We performed CD28 region-capture HiC on both resting and anti-CD3/CD28-stimulated Jurkat cells. Anti-CD28 and anti-CD3 antibodies were utilized to activate T cells as previously described (Simeonov et al. Nature, 2017). Briefly, the culture plate was coated with 10 µg/ml of anti-CD28 (TONBO Biosciences, 40-0289) for 12 hours at 4°C prior to cell inoculation. Jurkat or CD4+ T cells were then seeded with 10 µg/ml of anti-CD3 (40-0038). The cells were harvested 24 hours later for subsequent experimental analysis.


title: RNA-seq of resting and anti-CD3/CD28-stimuated Jurkat cells

summary: To investigate the dynamics of gene expression during T cell activation and identify essential genes responsive to stimulation, we conducted RNA sequencing on both resting and stimulated Jurkat cells.

overall_design: We performed RNA-seq on both resting and anti-CD3/CD28-stimulated Jurkat cells, with each sample including two replicates. Anti-CD28 and anti-CD3 antibodies were utilized to activate T cells as previously described (Simeonov et al. Nature, 2017). Briefly, the culture plate was coated with 10 µg/ml of anti-CD28 (TONBO Biosciences, 40-0289) for 12 hours at 4°C prior to cell inoculation. Jurkat or CD4+ T cells were then seeded with 10 µg/ml of anti-CD3 (40-0038). The cells were harvested 24 hours later for subsequent experimental analysis. The freshly extracted total RNAs with high qualities were sent to the Novogene (Beijing, China) for constructing libraries and sequencing.


title: NOTCH-driven oscillations control cell fate decisions during intestinal homeostasis

city: Utrecht

first: Amir

last: Giladi

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Intestinal homeostasis requires tight regulation of stem cell maintenance and commitment to absorptive and secretory cells, two key intestinal lineages1,2. While major signalling pathways critical for this control have been identified3, how they achieve such a tight balance in cell type composition remains unclear. Here, we uncover dynamic expression of Hes1, a direct NOTCH target3, in intestinal stem and progenitor cells, and investigate its role in vivo and in vitro. A knock-in reporter4 reveals distinct, cell-specific period lengths in Hes1 oscillations that form a gradient along the crypt-villus axis. Whereas secretory precursors oscillate at low periods, absorptive precursors oscillate at higher periods before transitioning to a differentiated state. To test the function of different oscillation periods, we innovated a microfluidic system that modulates Hes1 oscillations in organoids. We find that varying the oscillation period modulates secretory cell differentiation: While 90-min oscillations promote Paneth cells, 130-min oscillations increase formation of other secretory subtypes. Moreover, low-period oscillations support stemness and a proliferative state. Our study provides the first clear evidence that information for tissue homeostasis in the intestine is encoded in the temporal dynamics of signalling components.

overall_design: To identify potential subtle changes in cell type composition upon modulation of Notch-driven oscillations, we performed bulk RNA sequencing (bulk RNAseq) after entraining oscillations to 3 different periods (90-, 130- and 170-min) for 3 different durations (24-, 48- and 72-hours).

first: Sonja

last: Weterings

first: Hiromune

last: Eto

first: Jan

last: de Leede

first: Mirjam

last: Hoekstra

first: Wouter

last: Beijk

first: Esther

last: Liefting

first: Karen

middle: B

last: van den Anker

first: Jacco

last: van Rheenen

first: Alexander

last: van Oudenaarden

first: Katharina

last: Sonnen


title: Oxytocin Receptor Enhances Adipocyte Browning and Energy Metabolism in Mice

city: Shenyang,China

first: Dan

address: No. 146, Huanghe North Street, Yuhong District, Shenyang City, Liaoning Province，China

institute: Shenyang Medical College

summary: Obesity is characterized by abnormal adipose development and disruptive energy metabolism, and with many factors involved. Oxytocin receptor (OXTR) affects social behaviors, mammary gland development and cancers. In this study, transgenic overexpression of OXTR under β-actin promoter (++Oxtr) exhibited a lean phenotype with reduced fat accumulation and without significant change in food consumption. OXTR overexpression enhanced energy expenditure, adaptive thermogenesis and glucose tolerance. Morphologically, OXTR overexpression displayed a browning phenotype in adipose tissue accompanied by higher cell counts and smaller adipocytes. Gene expression analysis revealed elevated levels of Brown Adipose Tissue (BAT) markers, fatty acid transport proteins and glucose transporters in adipose tissues. High OXTR ameliorated high-fat-diet induced obesity with improvement of metabolic parameters. Furthermore, OXTR overexpression led to an activation of PPAR signaling, increased energy consumption, reduced fat accumulation and weight loss. We have identified OXTR to be a critical regulator of energy metabolism and thermogenesis. That OXTR enhances adaptive thermogenesis and energy metabolism may present a novel therapeutic target for metabolic disorders.

overall_design: To explore the molecular mechanism of OXTR regulating adipose development and energy metabolism, RNAseq was used to analyze differentially expressed genes (DEGs) of ++Oxtr against WT gWAT of mice. 365 DEGs were identified, 286 up and 79 down.

first: XinYue

last: Bao

first: ShuiLian


title: Gene expression clusters change and molecular correlation via STING pathway between orbital MALT lymphoma and orbital IgG4-related eye diseases

city: Ube

first: Keishiro

last: Isayama

state: 山口県

institute: Yamaguchi　University

summary: Purpose: MALT lymphoma orbital region and IgG4-related eye disease (IGG4ROD) account for the majority of mass lesions in the orbital region. They may show similar shadows on radiological images, and many cases are difficult to differentiate clinically. We investigated what kind of gene expression cluster(RNA-seq) and molecular differences are responsible for two diseases. Methods: Total RNA was extracted from fresh tissues in 20 cases which were histopathologically diagnosed from 20XX to 20XX, and a sequence library was created. Next-generation sequencing analysis (RNA-seq, NovaSeq6000) was performed to compare gene expression between the two groups, and principal component analysis and cluster hierarchy analysis were performed. Results: In principal component analysis, orbital MALT lymphoma and IgG4ROD were clustered in component 2in PCA analysis. Clear cluster differences were observed, except for one case that appeared to be IgG4-producing MALT lymphoma. In addition, cluster analysis showed that one case that appeared to be IgG4-producing MALT lymphoma was located just between the IGG4ROD and MALT lymphoma clusters. Furthermore, in a comparison of up regulator analysis between IgG4ROD and MALT lymphoma, 582 genes were identified as candidates(p<0.01). Pathway analysis of MALT lymphoma suggested that the Sting pathway be activated. Sting pathway-down-stream analysis were significant eight  gene expression changes)P<0.05). In addition, STING immunohistochmical analysis were detected different formed staining pattern using quantitative evaluation in IgG4ROD and MALT(P<0.01). Conclusion: MALT lymphoma orbital and IgG4-related eye disease (IGG4ROD) can be divided into two clusters of gene expression. The Sting pathway may be a important pathway specific to orbital MALT lymphoma compared with orbital IgG4ROD.

overall_design: Total RNA was extracted from fresh tissues of orbital MALT lymphomas and IgG4-ROD.

first: Mizuki

last: Tagami

first: Mizuho

last: Nishio

first: Atsuko

last: Yoshikawa

first: Norihiko

last: Misawa

first: Atsushi

last: Sakai

first: Yusuke

last: Haruna

first: Mami

last: Tomita

first: Yoichi

last: Mizukami

last: Azumi

first: Shigeru

last: Honda


title: Single-cell transcriptomics of Smad4fl/fl and Smad4fl/fl;Rosa26-creERT2 (Smad4iko) mice.

city: Guangzhou

first: lei

last: zeng

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: SUN YAT-SEN UNIVERSITY

summary: We report a comprehensive cell atlas of the lungs from Smad4fl/fl and Smad4fl/fl;Rosa26-creERT2 (Smad4iko) mice.

overall_design: The mouse lung tissue blocks were dissected from Smad4fl/fl and Smad4fl/fl;Rosa26-creERT2 (Smad4iko) mice and dissociated to yield single cell suspension. A total of 3 Smad4fl/fl and 4 Smad4iko mouse samples were used for single cell RNA sequencing.


title: Transcriptome regulation in the brain of a transgenic Alzheimer mouse model treated by lactate

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

summary: To investigate the potential effect of lactate in Alzheimer disease (AD) therapy, we established  a transgenic Alzheimer disease mouse model, and  analyse the transcriptome regulation induced by lactate compared to vehicle treatment in AD mice. In parallel, the lactate induced transcriptome regulaltion also were analyzed in wild type mice compared to vehicle treatment.

overall_design: Comparative gene expression profiling in mice brain RNA-seq data between wild type (WT)  and AD mice in condition of lacate (Lac) or vehicle (V) treatment. Each condition in each phenotype mice included 3 male (M) and 3 femlae (F).  Thus, the samples consists of total 8 groups with triplicates in each group, e.g. group "AD_Lac_F, rep 1" represents the AD mice by lactate treatment  in female, replicate 1.

first: Imen

last: Belhaj

first: Ingrid

last: Åmellem

first: Can

middle: H

last: Tartanoglu

first: Hanne

last: Weidemann

first: Evan

last: Vallenari

first: Farrukh

middle: A

last: Chaudhry

first: Jon

last: Storm-Mathisen

first: Magnar

last: Bjørås

first: Linda

last: Bergersen


title: Arsenic-sensing domain regulates trafficking and function of the arsenite transporterACR3 in the liverwortMarchantia polymorpha

city: Cambridge

first: Ignacy

last: Bonter

address: Downing site

institute: University of cambridge

summary: Study focused on N-terminal domain of MpACR3

overall_design: Six RNA-seq samples, three of which are As(III) treated plants, three are plants grown on clean Half gamborg medium


title: STAT3S727 Phosphorylation in VTA Dopaminergic Neurons Competed by  O-GlcNAcylation Regulates Acute Stress-Induced Anxiety and Reward Inhibition [ATAC-Seq]

city: Shanghai

first: Shao

middle: Ming

last: Shuo

address: 138 Yixueyuan Road

institute: Fudan university

summary: Acute stress can inhibit the activity of dopaminergic neurons in the ventral tegmental area (VTA), leading to increased anxiety and reduced sensitivity to natural rewards. However, the molecular mechanisms underlying this effect remain unclear. Our study shows that acute restraint stress increases the phosphorylation of the transcription factor STAT3 at Ser727 and Tyr705 in VTA dopaminergic neurons, enhancing its transcriptional activity. This modulation contributes to the inhibition of dopaminergic neuron activity, heightened anxiety, and reduced reward sensitivity. Furthermore, acute stress also promotes O-GlcNAcylation in VTA neurons, which competes with STAT3 Ser727 but not Tyr705 phosphorylation and modulates its transcriptional activity, leading to alterations in GABA receptor expression.  This reveals a complex molecular feedback mechanism where O-GlcNAcylation regulates STAT3 activity to maintain brain homeostasis during acute stress responses.

overall_design: To investigate the differential chromatin accessibility changes in VTA dopaminergic neurons induced by Ogt knockdown.Ogt flox+/Y and Ogt flox-/Y mice were injected with AAV-TH-Cre and AAV-DIO-H2B-EGFP in the VTA, and EGFP+ nuclear fractions were sorted for ATAC-seq.

first: Mingshuo

last: Shao

first: Yi

last: Wu

first: Haiyang

last: Wang

first: Chenchun

last: Zhang

first: Yan

last: Jiang

first: Ying

last: Zhu


title: Self-tolerance maintained by self-reactive CD8+ T cells

city: hangzhou

first: wang

last: pengfei

address: yuhangtang road 866

institute: zhejiang university

summary: CD8+ T cells play a critical role in immune tolerance maintainnance after immune activation. It is known to function through targeting activated CD4+ T cells, in both Qa-1- and MHC-Ia-restricted9 manner. However, the exact nature of this targeting process, i.e., the specific peptides and the corresponding reactive CD8 TCRs, remains unknown. In this study, we identified the self-peptides on activated CD4+ T cells that could mediate the CD8+ T cells immunosuppressive activity. By cloning the corresponding CD8 TCRs and the generation of TCR transgenic mice , we were able to validate the immunosuppressive function of CD8+ T cells carrying the self-reactive TCRs both in vitro and in vivo. The therapeutic potential of peptide vaccination and CD8+ T cell transfer were confirmed in a mouse EAE model. This study suggest that self-tolerance can be maintained by self-reactive CD8+ T cells recognizing self-antigenic peptides through specific TCRs, thus redefine the nature of CD8+ regulatory T cells as self-reactive CD8+ T cells.

overall_design: To investigate the gene expression changes in CD4+ T cells before and after activation, we stimulated C57/B6 mouse splenocytes with 1 μg/ml ConA for 48 hours, then sorted the CD4+ T cells from both the stimulated and unstimulated groups.Then we performed gene expression profiling analysis using data obtained from RNA-seq of stimulated and unstimulated CD4+ T cells.

first: Yadan

last: Bai

first: Pengfei

first: Fan

last: Zhao

first: Linrong

last: Lu


title: Identification of hepatocyte-primed biliary epithelial cells in the homeostatic liver by in vivo lentiviral gene transfer to mice and non-human primates [scRNA-Seq]

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

summary: Liver regeneration is supported by hepatocytes and, in certain conditions, biliary epithelial cells (BEC). BEC are facultative liver stem cells, able to form organoids in culture and engraft in damaged livers. However, BEC heterogeneity in the homeostatic liver remains to be fully elucidated. Here, we exploited in vivo systemic lentiviral vector (LV) administration to achieve efficient and life-long gene transfer to BEC in mice. We found that LV-marked BEC retain organoid-formation potential and predominantly respond to liver damage, however, are less clonogenic and display more hepatocyte-primed transcriptome compared to untransduced BEC. We thus identify a BEC subset committed to hepatocyte lineage in the absence of liver damage, characterized by a transcriptional network orchestrated by hepatocyte nuclear factor 4a. We also report in vivo targeting of such BEC in non-human primates. This work highlights intrinsic BEC heterogeneity and that in vivo LV gene transfer to the liver may persist following BEC-mediated repair of hepatic damage.

overall_design: Single-cell experiment of two samples of biliary epithelial cells (BEC) from non-human primates (NHP) livers enriched in cholangiocytes.

first: Michela

last: Milani

first: Francesco

last: Starinieri

first: Alessio

last: Cantore


title: STAT3S727 Phosphorylation in VTA Dopaminergic Neurons Competed by  O-GlcNAcylation Regulates Acute Stress-Induced Anxiety and Reward Inhibition [RNA-Seq stress]

overall_design: To explore the changes in signaling pathways in VTA dopaminergic neurons induced by acute restraint.VTA brain tissue was collected from male C57BL/6 mice with or without 30 min of acute restraint stress. Ribosome-associated mRNA from dopaminergic neurons expressing NBL10-HA was enriched and subjected to RNA sequencing.


title: Single-nucleus RNA sequencing combined with fluorescence in situ hybridization reveals Stat3 as a therapeutic target for ventilator-induced diaphragm dysfunction

city: Wuhan

first: Bing

last: Yang

address: No.1 Shizishan Street, Hongshan District

department: College of Vetirinary Medicine

institute: Huazhong Agricultural University

summary: snRNA-seq revealed that MV induced significant changes in the cellular composition and transcriptional profiles of diaphragm tissue. Specifically, fibroblasts and type IIb myofibers showed increased proportions, while type IIx myofibers and other cell types, such as fibro/adipogenic progenitors (FAPs), showed a decrease in their representation. Transcriptionally, MV led to the upregulation of key muscle atrophy-related genes such as Atrogin-1 and Murf-1, as well as fibrosis-related genes including collagen and fibronectin. Stat3 emerged as a central player, with its expression significantly elevated in both myofibers and fibroblasts. Further analysis of gene regulatory networks demonstrated that Stat3 activation was associated with disrupted muscle metabolism, increased fibroblast activity, and enhanced fibrotic signaling pathways. FISH confirmed the spatial localization of these transcriptional changes, corroborating the snRNA-seq findings. The increased activity of Stat3, particularly in promoting fibrosis and muscle degradation, suggests that it is a key regulator in the pathogenesis of VIDD.

overall_design: To induce anesthesia in mice, a 1% solution of pentobarbital (Sigma-Aldrich, St. Louis, MO) was administered via intraperitoneal injection. After shaving and disinfecting the neck area, a tracheostomy was performed, and the mouse’s trachea was connected to a small animal ventilator (VentElite, Harvard Apparatus, USA) for controlled mechanical ventilation. The ventilator settings during MV were as follows: a tidal volume of 10 mL/kg, a respiratory rate (RR) of 150 breaths per minute, and a positive end-expiratory pressure (PEEP) of 2 cm H2O1. Throughout the entire process of MV, mouse body temperature was maintained at approximately 37°C using a mouse-specific temperature maintenance device. Continuous anesthesia was provided to the mice. The control group of mice did not undergo MV.


title: FOXJ1 regulates microtubule dynamics in nonciliated cells and is a mediator of taxane resistance

city: Boston

first: Steven

middle: P

last: Balk

state: MA

address: 3 Blackfan Circle

department: Hematology/Oncology

institute: Harvard Medical School

summary: Docetaxel is the first-line chemotherapy for metastatic castration-resistant prostate cancer (PC) and taxanes are broadly used in other cancers, but mechanisms of resistance remain to be established. In our study, we generated docetaxel-resistant PC xenografts and found increased expression of genes that drive development of multiciliated cells. These genes included FOXJ1, its upstream activator GMNC, and multiple FOXJ1-regulated genes that are associated with microtubules (MTs). Notably, FOXJ1 gene amplification was more frequent in taxane-exposed PC patients, and its overexpression conferred resistance to docetaxel both in vitro and in vivo. This resistance was associated with a decrease in docetaxel-mediated MT bundling, indicating that FOXJ1-regulated genes act at the level of tubulin to mitigate abnormal MT aggregation. Additionally, overexpression of an MT-associated FOXJ1-regulated gene (TPPP3) had similar effects. Conversely, FOXJ1 knockdown impaired basal MT function, enhanced taxane binding to MTs, and increased docetaxel sensitivity. Finally, analysis of data from the CHAARTED clinical trial showed that higher expression of FOXJ1 was predictive of decreased survival in PC patients treated with docetaxel. Together these findings highlight FOXJ1’s role in regulating MT dynamics in non-ciliated cells and that its increased expression mediates taxane resistance.

overall_design: Mice with LuCaP35CR or LuCaP70CR xenograft tumors were treated with either vehicle or docetaxel (DTX) at 30 mg/kg by i.p. injection every 21 days starting at day 0 as indicated. Docetaxel and vehicle treated xenografts were harvested when they reached ~1500 mm3. The treated tumors were harvested 2 weeks after their final dose of docetaxel. Mice bearing LNCaP FOXJ1_OE and LNCaP EV xenografts were treated with docetaxel (DTX, 30 mg/kg, i.p., 6 mice per each group). The first dose was administered when tumors reached ~250 mm3 (Day 9), and a second dose was given on Day 30. Mice for both groups were  sacrificed 5 days after the second dose, and the tumors were harvested for RNA sequencing.

first: Fang

last: Xie

first: Larysa

last: Poluben

first: Olga

last: Voznesensky


title: STAT3S727 Phosphorylation in VTA Dopaminergic Neurons Competed by  O-GlcNAcylation Regulates Acute Stress-Induced Anxiety and Reward Inhibition [RNA-Seq Ogt]

first: Shao

last: Shuo

overall_design: To explore the differential gene signaling pathway changes in VTA dopaminergic neurons caused by Ogt knockdown.Ogt flox+/Y and Ogt flox-/Y mice were injected with AAV-TH-Cre and AAV-Flex-NBL10 in the VTA, and ribosome-associated mRNA expressing NBL10-HA was enriched and subjected to RNA sequencing.

first: Mingshuo

last: Shao

first: Yi

last: Wu

first: Haiyang

last: Wang

first: Chenchun


title: RNA-seq data of ginsenoside Rg3-treated BGC823 gastric cancer cells

city: changchun

first: 富强

last: 李

state: 吉林省

address: 前进

institute: 吉林大学

summary: This study aims to explore the potential mechanism of Ginsenoside Rg3 against gastric cancer,we first found that the anti-GC cell proliferation by Rg3 in part is via inhibiting the formation of E2F-DP heterodimers, and suppressing the p53-p21-cyclin/CDKs-RB signaling pathway. These find-ings highlight the potential of Rg3 as a natural product with low toxicity and anti-tumor activity in cancer treatment.

overall_design: Total RNA from DMSO or Rg3 treated (48 hours) BGC823 GC cells (3 repeats) was extracted using the RNAiso Plus (9109, Takara, Tokyo, Japan) and sent to Biomarker Technologies Co., Ltd. (Beijing, China) for RNA-Seq analysis.

first: Fuqiang

last: Li

first: Chengyu

last: Cai

first: Yong

first: Jingji

last: Jin


title: Single cell RNA-sequencing of male and female dorsal root ganglia (DRG) following Bortezomib (BTZ) or vehicle (VEH) administration.

city: St. Louis

first: Valeria

last: Cavalli

state: MO

address: 1 Bookings Dr.

institute: Washington University in St. Louis

summary: Peripheral neuropathies are the most common neurodegenerative diseases affecting more than 20 million people in the USA alone. Chemotherapy, including treatment with the highly effective drug bortezomib (BTZ), is a frequent cause of peripheral neuropathy. We demonstrated recently that while some chemotherapeutics exert direct toxic effects on axons, BTZ leads to axon degeneration via signals from neuronal somata, which reside in the dorsal root ganglia (DRG). However, what these signals are and how they arise is unknown. To address this question, we treated mice intravenously with BTZ twice weekly for 8 weeks and determined the impact on DRG gene expression via single cell RNA-sequencing.

overall_design: In these experiments we used wild-type mice (Balb/cJ mice own colony, average age 13 weeks) to test the effects of bortezomib treatment on peripheral neuropathy. Vehicle (5% 100% EtOH, 5% Tween-80, 90% Sterile Saline) or bortezomib (2 mg/ml in 100% ethanol) (Millipore Sigma) dissolved in 5% Tween-80, 90% Sterile Saline (0.1 mg/ml) was administered intravenously by tail vein injection twice weekly at a dose of 0.8 mg/kg for 8 weeks. Following administration, DRG tissues were isolated and analyzed using scRNAseq.

first: Michael

last: Thomsen

first: Stefanie

last: Geisler

first: Oshri

last: Avraham


title: Spatially profiling the molecular effects of repetitive transcranial magnetic stimulation in aged rodent brains.

city: Perth

first: Alexander

last: Tang

state: Western Australia

address: 35 Stirling Highway, University of Western Australia

department: School of Biomedical Science

institute: University of Western Australia

summary: Repetitive transcranial magnetic stimulation (rTMS) is a widely adopted non-invasive tool used to study the brain and as an alternative treatment for neurological disorders. However, the molecular mechanisms affected in the brain regions at and beyond the stimulation site, and how this varies with different rTMS protocols in an aged brain remains unclear. Here we use a combination of bulk RNA-sequencing and spatial transcriptomics to map the molecular changes across a mouse brain in response to two commonly used rTMS protocols: intermittent (iTBS) and continuous theta burst stimulation (cTBS).

overall_design: Wild-type aged (57-72 weeks old), male C57BL/6J mice were treated with a single session of intermittent theta-burst (iTBS), continuous theta-burst (cTBS), or sham stimulation, with four mice used for each stimulation group. Animals were euthanised three hours post-stimulation and the brains were removed and dissected along the midline. Coronal sections from the right brain hemisphere, taken approximately 0.26 - 0.74 mm anterior from bregma, were analysed using spatial transcriptomics.

first: Rebecca

middle: C

last: Ong


title: Identification of prognostic biomarkers for endometrioid endometrial carcinoma based on the miRNA and mRNA co‐expression network regulated by estradiol [RNA]

city: Beijing

first: Li

state: -- None selected --

address: Department of Obstetrics and Gynecology

institute: peking union medical college hospital

summary: Endometrioid endometrial carcinoma (EEC), an estradiol-related disease, remains a serious health threat to women because of its high incidence and trend of rejuvenation. Accumulating evidence has highlighted that microRNAs (miRNAs) and messenger RNAs (mRNAs) play important roles in various biological processes involved in the pathogenesis of EEC. This study aimed to identify the potential prognostic biomarkers associated with EEC regulated by estradiol.

overall_design: To investigate the pathway through which estrogen participates in the the pathogenesis of EEC, microRNA sequencing were performed on EEC samples treated with or without estradiol (250 nM). We then performed gene expression profiling analysis of RNA-seq obtained from above two groups.

first: Qiu

last: Xie


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

first: Zlata

last: Gvozdenov

address: 240 Longwood Ave

department: BCMP

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 chromatin 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. Cell nuclei were isolated and subjected to DNase-Seq. WT and cct1-2 chromatin states were analyzed to detect chromatin changes upon CCT inactivation.


title: TRiC/CCT Chaperonin Regulates RNA Polymerase II in the Nucleus [4tU-Seq]

overall_design: To assess the influence of the CCT chaperonin on nuclear events, we examined active RNA transcripttion in the presence and absence of functional 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. The cells were then spiked with 4tU (or DMSO for control) for 5 min. 4tU-containing RNA was isolated, RNA libraries were constructed and subjected to NGS. Active transcription analysis was performed by comparing steady-state (RNA-Seq) and 4tU-Seq samples in WT and cct1-2; regions with elevated or reduced active transcription were identified. The unitless constant of RNA half-life was estimated from the number of transcripts (RNA-Seq) divided by the production of new mRNA (4tU-Seq).


title: Spatially profiling the molecular effects of repetitive transcranial magnetic stimulation in aged rodent brains. [bulkRNA]

overall_design: Whole transcriptome sequencing data generated from RNA extracted from the sensorimotor cortex of wildtype aged (57-72 weeks old) C57BL/6J mice that received a one-off stimulation session of either intermittent theta-burst (iTBS), continuous theta-burst (cTBS) or sham stimulation. A total of five animals were included in each treatment group. Animals were euthanised three hours post-stimulation, after which the brain was removed and the sensorimotor cortex was dissected and extracted for RNA.


title: Topology regulates cell differentiation in situ

first: Jiayi

last: Mao

address: Zhi Zao Ju road

institute: shanghai ninth people's hospital

summary: To study the topology regulation of cell differentiation in situ, mesh-like flap spacers with different diameters and spacing were prepared by near-field electrostatic printing. Firstly, the structural characteristics and biocompatibility of the materials were studied. The effect of the flap shim prepared by in vivo near-field electrostatic printing technology on skin tissue was analyzed by mRNA-seq, and the related genes and proteins were detected by flow cytometry, qPCR, and Western blotting to clarify the mechanism of the topological structure on the flap. Finally, it was explored in animals.

overall_design: 1. Mesh-like flap gaskets with different diameters and spacings were prepared by near-field electrostatic printing; 2. The spacer was placed under the flap, and the skin tissue was collected after 7 days of treatment. 3, transcriptome sequencing was performed to investigate the topology regulating cell differentiation in situ.

first: Tao

last: Zan

first: Wenguo

last: Cui


title: Mature optic nerve regeneration requires ligand-independent expression of the LIF receptor

city: Changsha

first: Qian

last: Jiang

state: 湖南省

address: 湖南省长沙市芙蓉区解放中路有色院小区研究生宿舍

institute: 中南大学湘雅二医院

summary: To investigate the molecular consequences of LIFR expression, RGCs were FACS-isolated from vglut2-tdTomato mice two weeks following intraocular AAV2-LIFR, AAV2-Ctrl or AAV2-shLIFR, AAV2-shScramble and then analyzed by bulk RNA-seq. AAV2-LIFR and AAV2-shLIFR had a pronounced transcriptional effect on adult RGCs compared to the control group.

overall_design: To compare transcriptional changes in adult RGCs isolated from mice two weeks following intravitreal injection of AAV2-LIFR, AAV2-Ctrl, AAV2-shLIFR or AAV2-shScramble (AAV2-LIFR vs. AAV2-Ctrl; AAV2-shLIFR vs. AAV2-shScramble, n=3 replicates each group).

first: Lili

first: Bing