title: Transcriptome sequencing of pancreatic cancer cells transfected with SHMT2 knockdown lentivirus (human).

city: Lanzhou

first: Dongao

last: Fan

address: No. 222 South Tianshui Road, Lanzhou 730000, Gansu Province, P.R.China

institute: Lanzhou University

summary: The role of SHMT2 in driving pancreatic cancer progression remains incompletely understood. Our previous findings demonstrated that SHMT2 enhances glycolytic metabolism and promotes proliferative and invasive capacities in pancreatic cancer cells. To delineate the precise molecular mechanism underlying these observations, we performed transcriptomic sequencing.

overall_design: The control group was treated with null virus transfection and the experimental group was treated with SHMT2 knockdown lentivirus.


title: Targeting CDK12 disrupts estrogen-receptor chromatin recruitment and ER-MED1 transcription in advanced ER+ breast cancer

status: Public on Feb 20 2026

city: Dublin

first: Leonie

last: Young

state: Dublin

address: 31A York Street

department: Surgery

country: Ireland

institute: RCSI

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Gene expression panel of oalveolar organoid lung chip microvasculature and alveolar epithelium

city: Chicago

first: Carl

last: Atkinson

state: Illinois

address: 300 e superior st

country: USA

institute: Northwestern University

summary: In the study presented here, a novel model of IRI was used to acquire expression profiles of HAEC and HuLEC-5a via a custom nCounter Expression Panel, leading to the successful characterization of the 3D model.

overall_design: Nanostring human organ transplant nCounter

first: Gill

last: Blake

first: Langerude

last: Logan


title: ARHGEF2 Isoform Switching Couples Intestinal Epithelial Barrier Function with Autophagic Response to Pathogens

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

summary: Maintenance of intestinal epithelial integrity is essential for host defence, yet how epithelial junctional scaffolds connect to antimicrobial autophagy remains unclear. Here we show that distinct isoforms of the guanine nucleotide exchange factor GEF-H1 (mouse Arhgef2-207; human ARHGEF2-219) localize to adherens junctions in polarized intestinal epithelial cells through interaction with the adhesion molecule Nectin-3 and the cytoskeletal scaffold Afadin. Conditional deletion of Arhgef2-207 in the intestinal epithelium induces compensatory expression of the shorter Arhgef2-201, leading to loss of barrier integrity, activation of autophagy, and small-intestinal inflammation.

overall_design: Human organoids before and after 4 hour Listeria infection

first: Shuyuan

last: Chen

first: Alka

last: Diwaker

first: Hans-Christian

last: Reinecker


title: Targeting CDK12 disrupts estrogen-receptor chromatin recruitment and ER-MED1 transcription in advanced ER+ breast cancer [RNA-Seq]

summary: Cyclin-dependent kinase 12 (CDK12) regulates general gene transcription elongation, and plays multiple roles in RNA splicing, DNA damage-response, cell cycle and genomic stability. However, transcriptional partners that guide CDK12-specific gene programs have not been identified. Genomic alterations in CDK12 have been observed in multiple cancers, exhibiting both pro-tumorigenic and tumor-suppressive functions, suggesting a context-dependent mechanism of action. This work describes a novel mechanism for CDK12, suggesting a potential vulnerability in ER+ breast cancer. CDK12 amplifications and gene overexpression were observed in brain metastatic tumors. In ER+ primary patient tumors, high CDK12 protein expression significantly associated with poor overall survival, particularly within the ER+/HER2-negative group. In ER+ endocrine resistant models, CDK12 regulated estrogen signaling pathways, with ER/MED1 identified as the master transcriptional complex directing CDK12-specific pro-tumorigenic gene programs. Pharmacological inhibition of CDK12 significantly reduced viability in endocrine resistant and metastatic cell and organoid models in vitro, and decreased metastatic spread in vivo. These findings provide a basis for further investigation into the role of CDK12 inhibition as a therapeutic approach, particularly in advanced disease settings.

overall_design: RNA-seq profiling of LY2 cells transfected with siRNA targeting CDK12 (siCDK12) and non-targeting control (siCtrl). ChIP-seq of LY2 cells transfected with siCDK12 or siCtrl followed by treatment with β-estradiol.

first: Daniela

last: Ottaviani

first: Mihaela

last: Ola

first: Alessandra

last: Allotta

first: Yasmine

middle: M

last: Chaibi

first: Seán

last: Hickey

first: Petra

last: Jagust

first: Damir

last: Varešlija


title: CUT&Tag profiling of PARIS binding in CamK-PARIS mouse brain

city: Baltimore

first: Ji-Yang

last: Song

state: MD

address: 733 North Broadway St.

institute: Johns Hopkins University School of Medicine

summary: This study used CUT&Tag to profile the genomic binding sites of PARIS in hippocampal tissue from CamK-PARIS transgenic mice. The tissue was fixed, processed for CUT&Tag, and sequenced as paired-end libraries. Signal tracks and SEACR peak calls were generated to characterize PARIS-associated genomic regions and to relate PARIS binding to STAT3 signaling and downstream transcriptional changes in the context of neurodegeneration.

overall_design: CUT&Tag libraries were prepared from hippocampal tissue of CamK-PARIS mice using an anti-FLAG antibody, along with an IgG control. Paired-end sequencing was performed on an Illumina platform. Reads were aligned to the mouse reference genome using Bowtie2, followed by filtering, SEACR peak calling with the IgG control track, and generation of bigWig signal tracks. Processed data include normalized coverage tracks and peak BED files.

first: Jinhee

last: Park

first: Sung-Ung

last: Kang

first: Valina

middle: L

last: Dawson

first: Ted


title: RIP-seq analysis of HUVEC cells overexpressed wild-type or mutanted DDX24

city: Zhuhai

first: Simeng

last: He

address: 52 Meihuadong Road, Xiangzhou

country: China

institute: Sun Yat-sen University

summary: To investigate the impact of DDX24 mutation on the RNA binding activity in HUVEC cells, we conducted RIP-seq analysis.

overall_design: For RIP-seq, RNA interacting with DDX24-WT or DDX24-ΔRBD was isolated following the RIP protocol. The immunoprecipitated RNA was then subjected to mRNA selection using Oligo dT-based Poly(A) mRNA Magnetic Isolation Module (NEB) and prepared for sequencing libraries using Ultra II Directional RNA Library Prep Kit for Illumina (NEB). Libraries were pooled and sequenced on an Illumina Hiseq 3000 PE150 platform.

first: Bin

last: Li


title: IKAROS re-expression modulates transcriptional networks in IKZF1-mutant Ph+ B-ALL [ATAC-seq]

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

summary: With the goal to investigate tumor suppressor mechanisms regulated by IKAROS (IKZF1) in PH chromosome–positive B-cell acute lymphoblastic leukemia (B-ALL) harboring IKZF1 mutations. This dataset includes bulk RNA-seq profiles from human MXP5 and PDX2 cell lines, which were engineered to express doxycycline-inducible wild-type IKAROS (IK1) or an empty vector control. RNA was collected 24 hours post-induction to capture early transcriptional responses to IK1 re-expression. These data are part of a larger multi-omics study integrating RNA-seq, ChIP-seq, CUT&RUN, ATAC-seq, and HiChIP to define IKAROS-regulated transcriptional and chromatin networks in IKZF1-deficient Ph⁺ B-ALL.

overall_design: The experimental design involved the IKZF1-deficient Ph⁺ B-ALL cell lines MXP5 and PDX2, which expresses a doxycycline-inducible wild-type IKAROS (IK1) or an empty control vector. Cells were treated with 1 μg/mL doxycycline for 24 hours to induce IK1 expression. Following induction, cells were used for tagmentation and ATAC-seq analysis. Each condition (IK1-induced and control) was profiled in biological duplicate.

first: Boyd

last: Joseph


title: IKAROS re-expression modulates transcriptional networks in IKZF1-mutant Ph+ B-ALL [RNA-Seq]

overall_design:
The experimental design includes two IKZF1-deficient Ph⁺ B-ALL cell lines (MXP5 and PDX2) expressing either doxycycline-inducible wild-type IKAROS (IK1) or empty control vectors. Cells were treated with 1 μg/mL doxycycline for 24 hours prior to RNA extraction. Each condition was performed in biological duplicate, resulting in eight total RNA-seq libraries. This design supports comparisons between IK1-induced and control samples within and across cell lines to identify IKAROS-regulated transcriptional programs.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************


title: CHD3 and CHD4 coordinate gene expression programs to maintain β-cell function and identity in vivo

city: Indianapolis

first: Jason

last: Spaeth

state: IN

address: 1210 Waterway Blvd

department: Pediatrics

institute: Indiana University

summary: To establish the role of CHD3 and CHD4 on controlling human gene expression programs in the islet, we generated pseudoislets from non-diabetic human donors that were treated with shRNA for CHD3, CHD4 or CHD3+CHD4. mRNA-Seq was performed on isolatd RNA from pseudoislets

overall_design: Human pseudoislets were generated from 12,000 IEQ donor islets using a modified reaggregation protocol. Upon arrival, islets were resuspended and cultured overnight in Standard CMRL 1066 medium (Corning, 15-110-CV) under standard conditions. The following day, floating islets were collected, washed twice with 2mM EDTA in Ca²⁺/Mg²⁺-free PBS, pelleted at 200g and enzymatically dissociated into a single-cell suspension using 0.025% trypsin for 8–9 min with gentle pipetting. The reaction was quenched with an equal volume of VPM, and cells were pelleted, washed once in VPM, and resuspended by gentle flicking to minimize shear stress. For knockdown, dispersed cells were transduced with lentivirus encoding shControl, shCHD3, shCHD4, or shCHD3+shCHD4 at a multiplicity of infection (MOI) of 15 by co-incubation in non–tissue culture-treated 4-well plates (Nunc, 179820) for 3 h at 37°C. Cells were then washed twice with VPM and seeded into ultra-low attachment round-bottom 96-well plates (Nunclon Sphera, PerkinElmer 174925) at 2000 cells per well to allow reaggregation. After 7 days, RNA from pseudoislets were harvested for mRNASequencing

first: Sukrati

last: Kanojia

first: Avinil

last: Das Sharma


title: Targeting CDK12 disrupts estrogen-receptor chromatin recruitment and ER-MED1 transcription in advanced ER+ breast cancer [ChIP-Seq]

first: Leonie

last: Young

first: Daniela

last: Ottaviani

first: Mihaela

last: Ola

first: Alessandra


title: SnRNA seq revealed astrocytic MAGL-KO rescued cognitive impairments in 5xFAD mice

city: San Antonio

first: Chu

last: Chen

state: Texas

address: 7703 Floyd Curl Dr

department: Cellular and Integrative Physiology

institute: UT Health San Antonio

summary: In the brain, 2-Arachidonoylglycerol (2-AG) is the most abundant endogenous cannabinoid. Enhancing 2-AG signaling by inhibiting monoacylglycerol lipase (MAGL) in astrocytes, the primary enzyme that degrades 2-AG in the brain, produces anti-inflammatory and neuroprotective effects in neurodegenerative diseases. However, the effects of astrocytic MAGL inhibition in 5xFAD mice were still unclear. To address this question, behavioral tests were performed and hippocampal nuclei were isolated from WT, TG, TG-aKO, TG-nKO, and TG-tKO mice. Our behavioral and electrophysiological results showed that cognitive and synaptic functions were rescued in TG-aKO mice. Using single-nucleus RNA sequencing analysis, we show here that neuronal MAGL KO mice display distinct gene expression profiles of synaptic DEGs in neurons and glial cells

overall_design: Single nucleus transcriptomics of hippocampus from transgenic mice were analyzed by snRNA-seq.

first: Chen

last: Chu

first: Zhang

last: Jian

first: Hu

last: Mei

first: Zhu

last: Dexiao


title: CHD3 and CHD4 coordinate gene expression programs to maintain β-cell function and identity in vivo [RNA-seq]

summary: To establish the role of CHD3 and CHD4 on controlling gene expression programs in the beta cell, we generated a tamoxifen-inducible, beta-cell-specific knockout mouse models; control (MIP-CreERT; Chd3+/+; Chd4+/+; R26RtdTomato), Chd3Db (MIP-CreERT; Chd3f/f; Chd4+/+; R26RtdTomato) and Chd3/4Db (MIP-CreERT; Chd3f/f; Chd4f/f; R26RtdTomato)

overall_design:
Dispersed islets from tamoxifen treated control, Chd3Db and Chd3/4Db mice were flow-sorted, and RNASeq performed. Chd4Db Samples were uploaded under Series GSE217445.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************


title: Succinate-GPR91 signaling promotes cardiomyocyte metabolic reprogramming and NAD⁺ production to alleviate HFpEF

city: Beijing

first: Yumeng

last: Jia

state: Beijing

address: Youanmen street

institute: Capital Medical University

summary: Disrupted cardiomyocyte energy metabolism underlies HFpEF. We found that cardiac succinate and GPR91 were reduced in HFpEF. In WT mice, succinate supplementation restored metabolism, improved diastolic function, and alleviated hypertrophy and fibrosis, whereas these benefits were abolished in global and cardiomyocyte-specific Gpr91 knockouts. Transcriptomics and mechanistic studies revealed that succinate–GPR91 signaling activated AMPK via Gq, enhanced NAD⁺ production, and promoted glucose–lipid metabolic reprogramming. Thus, the succinate–GPR91 axis is essential for cardiometabolic regulation and represents a promising therapeutic target in HFpEF.

overall_design: RNA-seq was performed on myocardial tissues from Gpr91fl/fl mice and cardiomyocyte-specific Gpr91 knockout mice (Myh6Cre Gpr91fl/fl) under HFpEF conditions, with or without succinate supplementation

first: Jia

last: Yumeng

first: Wang

last: Lei

first: Niu

last: Wenhui

first: Liu

last: Lu

last: Qun

first: Li

last: Dingwei

first: Dai

last: Tangyu


title: Timosaponin AIII enhances CAR-T cell potency and prevents relapse through impairing CAR-Tregs II

city: Hefei

first: Mingqi

last: Hou

institute: USTC

summary: Chimeric antigen receptor (CAR)-T cell therapy has become the standard treatment for refractory and relapsed (r/r) DLBCL in recent years. However, more than half of these patients develop primary or secondary resistance. Given that CAR Tregs are crucial in driving resistant and relapse to CAR-T therapy, but the strategies to overcome are limited. Here, we established a Treg functional high-throughput screening system and identified a natural product, currently in clinical trials, Timosaponin AIII (TAIII), impairs Treg function while activating T cell immune response during CAR-T therapy. Mechanistically, TAIII recruits and blocks the A2AR signaling in CAR-T cells as a novel allosteric inhibitor of A2AR, thereby eliminating CAR-Tregs by suppressing CREB-mediated FoxP3 transcription. Furthermore, TAIII suppresses tumor growth and improves the efficacy of PD-1 immunotherapy by reducing intratumoral Tregs in solid tumor models. Importantly, TAIII increases the Tcm percentage and enhances cytotoxic cytokine secretion of CAR-T cells post-infusion, improving their function. Combining or pretreating CAR-T cells with TAIII enhances their antitumor activity, thereby overcoming late relapses in lymphoma models. These results identify TAIII as a potent adjuvant for CAR-T cell function and manufacturing through eliminating CAR-Tregs proportion, thereby enabling CAR-T therapy to be applied with a broader perspective.

overall_design: CAR -T cells were activated by 1:1 Dynabeads or target cells and treated with 1μM TAIII with or without  5 μM NECA. After 16h treatment, cells were collected for RNA sequencing

first: Jing

last: Yang

first: Wenjun

last: Zhang

first: Guiming

last: Li


title: Interplay between CoREST, p300 and retinoic acid signaling in Acute myeloid leukemia [CUT&Run]

city: Miami

first: Ramin

last: Shiekhattar

state: Florida

address: 1501 NW 10th Avenue

department: Department of Human Genetics

institute: University of Miami - Sylvester Comprehensive Cancer Center

summary: The histone demethylase KDM1A (LSD1), a component of the CoREST corepressor complex, is highly expressed in hematologic malignancies and regulates hematopoietic differentiation. Despite its essential developmental role, LSD1 inhibition has emerged as a promising strategy to enhance retinoic acid (RA)-responsive gene expression in subsets of acute myeloid leukemia (AML). Here, we show that LSD1 physically interacts with RAR/RXR heterodimers at specific genomic loci, restricting chromatin accessibility and transcriptional activation of differentiation programs. Single-agent inhibition of LSD1 or HDACs promotes only partial differentiation. In contrast, Corin, a dual LSD1/CoREST inhibitor, synergizes with all-trans retinoic acid (ATRA) to induce robust myeloid differentiation and apoptosis. Corin treatment increases H3K4me3 and H3K27ac at promoters of ATRA-responsive genes and disrupts CoREST–RAR/RXR complexes, enabling recruitment of the coactivator p300. This epigenetic switch facilitates transcriptional reprogramming essential for terminal differentiation. Our findings identify the functional antagonism between CoREST and p300 as a regulatory axis of RA signaling in AML. Targeting this mechanism with Corin and ATRA re-sensitizes non-APL AML cells to RA-induced differentiation, suggesting a broader therapeutic approach for overcoming resistance in ATRA-refractory leukemias.

overall_design: AML cell lines were treated with ATRA and Corin or DMSO (vehicle control), followed by ChIP-seq, ATAC-seq, RNA-seq, and CUT&RUN to assess transcriptional and epigenomic changes.

first: Mina

last: M. Tayari

first: Helena

last: Gomes Dos Santos

first: Sadat

last: Dokaneheifard

first: Monica

last: Valencia

first: Felipe

last: Beckedorff

first: Arigela

last: Harikumar

first: Justin

last: M. Watts

first: Philip

last: A. Cole


title: IKAROS re-expression modulates transcriptional networks in IKZF1-mutant Ph+ B-ALL

first: Seth

last: Frietze


title: CHD3 and CHD4 coordinate gene expression programs to maintain β-cell function and identity in vivo [ATAC-seq]

first: Jason

last: Spaeth

summary: To establish the role of CHD3 and CHD4 on controlling gene expression programs in the beta cell, we generated a tamoxifen-inducible, beta-cell-specific knockout mouse models; control (MIP-CreERT; Chd3+/+; Chd4+/+; R26RtdTomato) and Chd3/4Db (MIP-CreERT; Chd3f/f; Chd4f/f; R26RtdTomato)

overall_design: Dispersed islets from tamoxifen treated control and Chd3/4Db mice were flow-sorted, and ATAC-Seq performed.

first: Spaeth

last: Jason

first: Kanojia

last: Sukrati

first: Das Sharma

last: Avinil


title: Integrating circulating microRNAs with epidemiological factors enhances breast cancer detection across subtypes: screening phase [miRNA-Seq]

city: Santander

first: Inés

last: Gómez-Acebo

state: CANTABRIA

address: Avda. Cardenal Herrera Oria S/N

country: Spain

institute: Division of Epidemiology and Computational Biology, School of Medicine, University of Cantabria,  IDIVAL, Santander, Spain

type: Non-coding RNA profiling by high throughput sequencing

summary: Exploratory small RNA sequencing analysis of circulating miRNAs in serum samples from 40 women (30 breast cancer cases and 10 controls) recruited within the MCC-Spain study.

overall_design: Serum samples were collected prior to treatment. Total RNA was extracted and small RNA libraries were prepared using QIAseq miRNA Library Kit and sequenced on an Illumina NextSeq 500 platform. Processed miRNA-level count data are provided. This screening phase was used for candidate biomarker selection and excluded from validation analyses. Groups: A (Controls), B (screening), C (free-disease survivorship) and D (without free-disease survivorship).

first: Sara

last: Valero-Domínguez

first: Javier

last: Llorca

first: Jessica

last: Alonso-Molero

first: Thalía

last: Belmonte

first: Gemma

last: Castaño-Vinyals

first: Víctor

last: Moreno

first: Aina

last: Romaguera

first: Pilar

last: Amiano

first: Juan

last: Alguacil

first: Vicente

last: Martín

first: Beatriz

last: Pérez-Gómez

first: Rosana

last: Burgui

first: Ana

last: Molina-Barceló

first: Paz

last: Rodríguez-Cundín

first: Manolis

last: Kongevinas

first: Marina

last: Pollán

first: Trinidad

last: Dierssen-Sotos


title: Interplay between CoREST, p300 and retinoic acid signaling in Acute myeloid leukemia [RNA-seq]

first: Ramin

last: Shiekhattar

first: Mina

last: M. Tayari

first: Helena

last: Gomes Dos Santos

first: Sadat

last: Dokaneheifard

first: Monica

last: Valencia

first: Felipe

last: Beckedorff

first: Arigela

last: Harikumar

first: Justin

last: M. Watts

first: Philip

last: A. Cole


title: Interplay between CoREST, p300 and retinoic acid signaling in Acute myeloid leukemia [ChIP-seq]


title: IKAROS re-expression modulates transcriptional networks in IKZF1-mutant Ph+ B-ALL [HiChIP]

first: Seth

last: Frietze

overall_design: The experimental design involved the IKZF1-deficient Ph⁺ B-ALL cell line MXP5, which expresses a doxycycline-inducible wild-type IKAROS (IK1) or an empty control vector. Cells were treated with 1 μg/mL doxycycline for 24 hours to induce IK1 expression. Following induction, cells were fixed and subjected to H3K27ac HiChIP. Each condition (IK1-induced and control) was profiled in biological duplicate.

first: Boyd

last: Joseph


title: Transcriptome sequencing of adipose tissue isolated from facial infiltrating lipomatosis or control

city: Shanghai

first: Hongrui

last: Chen

address: 639 Zhizaoju Road, Shanghai 200011, P.R.China.

department: Plastic and reconstruction surgery

institute: Shanghai ninth people's hospital

summary: Facial infiltrating lipomatosis is a congenital malformation characterized primarily by the excessive proliferation of adipose tissue. However, the pathogenesis of it remains unclear. To compare the gene expression differences between the adipose tissue of facial infiltrating lipomatosis and normal facial subcutaneous adipose tissue, we collected a total of 14 adipose tissue samples for high-throughput RNA sequencing, aiming to identify potential pathogenic genes.

overall_design: Group 1: FIL adipose tissue. Group 2: Normal adipose tissue

first: Chen

last: Hua

first: Xiaoxi

last: Lin


title: EOLA1, a novel mitochondria-localized protein critical for heart functions via regulating mitochondrial translation

city: Shenzhen

first: Hao

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology (SUSTech)

summary: Mitochondria has its own mRNA translation system, which is mediated by mitochondria-specific protein synthesis machinery – ‘mitoribosomes’. Dysregulation of mitochondrial translation disrupts the metabolic homeostasis and has been implicated in pathologies including metabolic syndromes, neurological disorders and cardiac diseases. Here, we identify that EOLA1 (Endothelium and lymphocyte associated ASCH domain 1) as a novel mitochondrial protein and exclusively localizes to mitochondria matrix. We further show that knockout of EOLA1 dramatically affects mitochondrial translation and subsequently the oxidative phosphorylation in mammalian cells. Mechanistically, EOLA1 interacts with mt-rRNA (mitochondrial ribosomal RNA) and EFTU, which maintains the translation elongation of mitochondrial mRNAs. Importantly, we generated a Eola1 knocked-out mice model and found that heart functions are obviously abnormal upon depletion of EOLA1 homolog in mouse, implying that EOLA1 are important for proper functions of heart via regulating mitochondrial translation. Taken together, our work demonstrates that EOLA1 is a novel regulator for mt-RNA and mitochondrial translation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To systematically identify novel molecules involved in the regulation of mitochondrial function, an unbiased positive screening was performed in a cancer cell model using a CRISPRi/Cas9 library. Secondly, considering that EOLA1’s ASCH domain likely binds with RNA2, we decided to identify the RNAs targeted by EOLA1 via UV-RIP-seq. We found that EOLA1 protein abundantly interacts with 12S mt-rRNA, which is the RNA component of mitochondrial mt-SSUs.

first: Xiaoyan

last: Shi


title: Extracellular vesicles and their RNA cargo facilitate bidirectional cross-kingdom communication between human and bacterial cells [smallRNA-Seq]

city: Saarbrücken

first: Shusruto

last: Rishik

state: Saarland

address: Informatik Campus E2.1

department: Zentrum für Bioinformatics

country: Germany

institute: Universität des Saarlandes

summary: Extracellular vesicles (EVs), released by both eukaryotic and prokaryotic cells, have emerged as key mediators of cell-to-cell communication. Recent advances highlight their crucial role in cross-kingdom communication, bridging the microbial world with human biology. Here, we investigated the molecular mechanisms underlying EV-mediated bidirectional communication within the gastrointestinal ecosystem. Using a model that includes human colon cells and both Gram-positive and Gram-negative gut bacteria, we reveal an intricate exchange of information between these kingdoms. Our analysis uncovered highly specific responses of host cells to bacterial EVs (BEVs) and BEV-RNA cargo, including uptake rates by human cells, impact on human cell viability, and alterations in their transcriptomic landscape. In parallel, we discovered that host-derived EVs and miR-192-5p are internalized by gut bacteria, leading to changes in their growth pattern. These findings highlight the precision with which EVs and their RNA cargo mediate interkingdom communication. Our results underscore the importance of tailored, context-specific analyses for understanding the scope of EV-mediated interactions in complex biological systems.

overall_design: Sequencing of smallRNAs isolated from EVs purified from Caco-2 cell culture supernatant (conditioned medium) and fresh cell culture medium (unconditioned medium). EVs were isolated via ultracentrifugation and purified using size-exclusion chromatography. RNA was isolated from EVs and used for smallRNA-seq.

first: Laura

last: Gröger

first: Nicole

last: Ludwig

first: Amila

last: Beganovic

first: Marcus

last: Koch

first: Stefanie

last: Rheinheimer

first: Martin

last: Hart

first: Petra

last: König

first: Tabea

last: Trampert

first: Pascal

last: Paul

first: Annette

last: Boese

first: Claus-Michael

last: Lehr

first: Sören L.

last: Becker

first: Gregor

last: Fuhrmann

first: Andreas

last: Keller

first: Eckart

last: Meese


title: Extracellular vesicles and their RNA cargo facilitate bidirectional cross-kingdom communication between human and bacterial cells [RNA-Seq]

overall_design: RNA-seq profiling of Caco-2 cells after incubation with BEVs from Lacticaseibacillus casei, Enterococcus faecalis, and Proteus mirabilis, or transfection with RNA isolated from the respective BEVs for 10 h, 24 h or 48 h. Controls used included PBS, AllStars Negative Control siRNA (ANC), and LPS from Proteus mirabilis. RNA was isolated from cells and used for RNA-seq.


title: The transcriptome of Dermacentor andersoni salivary glands at single cell resolution

city: Hamilton

first: Lucas

last: Tirloni

state: MT

address: 903 S 4th Street

department: LB

institute: NIAID

summary: Applications of transcriptomics have significantly advanced the identification of numerous tick salivary molecules involved in feeding and the transmission of tick-borne pathogens. In this study, we analyze the salivary gland transcriptome of Dermacentor andertsoni, the vector of Rickettsia rickettsii in the U.S., at single cell resolution.

overall_design: Dermacentor andersoni adult ticks were collected in May 2023 from vegetation near Lake Como, Montana, USA. Ticks were sampled using the flagging method, where a white flannel cloth was swept over low-lying vegetation and bushes. After collection, ticks were transported to the laboratory and maintained in an environmental incubator at 21°C and 85% relative humidity, with a 12h/12h light/dark cycle. Ticks were removed from incubator and salivary glands were dissected. Salivary glands (SGs) were isolated and stored in fresh, ice-cold, nuclease-free HBSS buffer (Invitrogen, Carlsbad, CA, USA). To prepare a single-cell suspension, the salivary glands were dissociated following a mechanical and enzymatic protocol. The resulting cell suspension was filtered through a 40 µm Flowmi cell strainer and centrifuged at 600 rcf for five minutes to pellet the cells. The pellet was then resuspended in an appropriate volume of HBSS media to achieve the target cell concentration. Cell counting and viability were assessed using trypan blue staining and a Neubauer chamber for visualization. The single cell suspensions were loaded (7,000 cells) onto a Chromium Controller for GEM (Gel Bead-In-EMulsion) generation and barcoding using the Chromium Single Cell 3’ Reagent Kits according to the manufacturer's protocol (10x Genomics). After cDNA synthesis, amplification, and library construction, the library was sequenced by the Illumina NovaSeq 6000 System. The raw sequencing data were demultiplexed and processed using the Cell Ranger Software Suite (10x Genomics). Raw sequencing data were aligned to the D. andersoni (GCF_023375885.1) reference genome and quantified using Cell Ranger tool (v7.0.1). Low-quality cells (4,405 cells) were excluded using a threshold of three median absolute deviations (MAD) from the median of the overall cell population for both unique molecular identifier (UMI) or feature counts and mitochondrial content. Putative doublets were identified and removed using scDblFinder R package (v 1.18.0), yielding 14,400 high-quality cells for downstream analyses. Cell clustering was performed following routine steps provided in the Seurat (v4.3) pipeline. Counts were natural log (log1p)-transformed, followed by scaling and dimensionality reduction (1:10), with visualization using PCA and UMAP. Cells were clustered using the shared nearest-neighbor approach based on the Louvain algorithm (resolution = 0.15), and the results were projected onto UMAP. Differential gene expression analysis (min.pct = 0.25, logfc.threshold = 0.25, q < 0.05) across cell clusters were conducted using the Wilcoxon rank-sum test via the ‘FindMarkers’ and ‘FindAllMarkers’ functions, respectively.


title: Persistence of alveolar fibroblast-derived ADAMTS4+ cells during delayed resolution of pulmonary fibrosis

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary: Idiopathic pulmonary fibrosis is a severe interstitial lung disease with limited therapeutic options. This study traced fibroblast growth factor 10 (Fgf10+) alveolar fibroblasts (AFs) in aged mice subjected to bleomycin injury, analyzing histology and single-cell transcriptomics at peak fibrosis and during resolution phases. Ex vivo models and human lung tissue data were also examined. Results showed Fgf10+ AFs transitioning from lipofibroblasts (LIF) to myofibroblasts (MyoFBs) during fibrogenesis, and reversing during resolution. An ADAM metallopeptidase with thrombospondin type 1 motif 4 (Adamts4+) AF population was linked to delayed resolution. ADAMTS4 emerged as a key target in fibrotic lung diseases, highlighting its therapeutic potential.

overall_design: Aged female Fgf10Cre-ERT2/+; tdTomatoflox mice received tamoxifen injections three successive injections two weeks prior to intratracheal instillation of saline or bleomycin. Lungs were collected on days 14, 30 and 60 post bleomycin injury for further analysis.

first: Ali

last: Khadim

first: Mahsa

last: Zabihi

first: Elie

last: El Agha


title: RNA-seq of Ixodes scapularis salivary glands [bulkRNA-dissociated-SG]

summary: Applications of transcriptomics have significantly advanced the identification of numerous tick salivary molecules involved in feeding and the transmission of tick-borne pathogens. In this study, we analyze the salivary gland transcriptome of Ixodes scapularis, the main vector of Borrelia burgdorferi in the U.S. We use next-generation sequencing to provide a more detailed view.

overall_design: The Ixodes scapularis ticks used in this study were obtained from the tick-rearing facility at Oklahoma State University (Stillwater, OK, USA). Prior to infestation, unfed ticks were maintained at 21°C and 85% relative humidity. One day before feeding, female ticks were paired with males to allow mating. Adult ticks were placed on the outer ear of four naïve female New Zealand rabbits, restricted by orthopedic stockinets that were glued in place. A total of 20 female and 20 male ticks (40 ticks per ear, 80 ticks per rabbit) were allowed to attach. To classify ticks by blood-feeding index, partially fed ticks were collected from the host based on engorgement size, sorted by weight, and divided into biological triplicates: an unfed group (UF) (15 females per replicate, weighing 1.6 mg in average), group G2 (5 females per replicate, weighing 7.2 mg in average), and group G5 (4 females per replicate, weighting 41.5 mg in average). After removal from the host, ticks were rinsed sequentially with 1% bleach, nuclease-free water, 70% ethanol, and a final rinse with nuclease-free water. Ticks were dissected within two hours of removal. Salivary glands (SGs) were isolated and stored in fresh, ice-cold, nuclease-free HBSS buffer (Invitrogen, Carlsbad, CA, USA). To prepare a single-cell suspension, the salivary glands were dissociated following a mechanical and enzymatic protocol. The resulting cell suspension was filtered through a 40 µm Flowmi cell strainer and centrifuged at 600 rcf for five minutes to pellet the cells. The pellet was then resuspended in an appropriate volume of HBSS media to achieve the target cell concentration. Cell counting and viability were assessed using trypan blue staining and a Neubauer chamber for visualization. Total RNA was isolated using the Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific) according to the manufacturer's instructions. RNA integrity and quantity were assessed using a 4200 TapeStation system (Agilent Technologies). Illumina libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit with polyA selection, and sequencing was performed on an Illumina NovaSeq 6000 DNA sequencer. Raw sequencing data were trimmed and aligned to the Ixodes scapularis reference genome (ASM1692078v2). We used the RNA-seek workflow  https://github.com/skchronicles/RNA-seek), which performs multiple steps including quality assessment with FastQC, FQScreen, Kraken, and BBTools; adaptor removal and quality trimming with Cutadapt; read alignments using STAR in 2-pass mode; and read quantification with RSEM.


title: Transcriptomic alterations induced by low-intensity ultrasound (LIUS) in OSCC.

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

summary: Ultrasound therapy has emerged as a promising, non-invasive modality for cancer treatment, although its underlying mechanisms remain incompletely understood. Immunoblotting analysis revealed that low-intensity ultrasound (LIUS) alters global levels of histone modifications, including monoubiquitinated H2B (H2Bub1), H3K4me3, and H3K27me3, in oral squamous cell carcinoma (OSCC) OC3 cells. Given the pivotal role of histone marks in transcriptional regulation, we further investigated the effect of LIUS on transcriptional control in OC3 cells.

overall_design: Total RNA was harvested from OC3 cells 48 hours after LIUS (T1) treatment, with untreated OC3 cells serving as the control

first: Chia-Huei

first: Pin-Feng

last: Hung

first: Gin-Shin

last: Chen

first: Bikash

middle: C

last: Mallick


title: Influence of TAK1 signaling on the cardiac fibroblasts transcriptome

city: Louisville

first: Richa

last: Singhal

state: KY

address: 580 S Preston Street, Baxter II Building, Office 321B

department: Medicine

institute: University of Louisville

summary: Organ health and function depend on communication between cell types to coordinate tissue growth and repair. Recent studies have indicated that fibroblasts are critical to this process; however, their role in regulating inflammatory responses to injury have remained ambiguous.  Here, we demonstrate that transforming growth factor β-activated kinase 1 (TAK1) is a gatekeeper of the inflammatory cardiac fibroblast phenotype. We find that TAK1 propagates IL-1β and TNF-α signaling in cardiac fibroblasts and coordinates the synthesis and secretion of chemokines  as well as inflammatory and pro-resolving lipid mediators. Deletion of TAK1 specifically in fibroblasts improves cardiac structural and functional remodeling after MI in male mice, which is associated with decreased immune cell recruitment and lower levels of resident macrophages . Nevertheless, we found the effects of TAK1 deletion to be sexually dimorphic in nature, providing support to the idea that the protected phenotype of the female sex may be based in disparate immune and inflammatory responses. Moreover, TAK1 signaling controlled the acquisition of novel markers of the inflammatory fibroblast phenotype, having a biological basis in redox stress, chemokine  and lipid mediator biosynthesis, metalloproteinase activity, and damage-associated molecular pattern recognition. Using genes associated with these processes as guides, we find that cardiac inflammatory fibroblasts arise xxx after MI in both mouse models and humans . Collectively, these results further resolve the nature and function of inflammatory cardiac fibroblasts  in cardiac responses to injury and identify TAK1 signaling in fibroblasts as a potential target for therapy.

overall_design: Isolated cardiac fibroblasts from TAK1fl/fl mice were transduced with LacZ or iCre prior to stimulation with bFGF, TNFa, IL-1b, or TGFb for 24 hours.

first: Bradford

middle: G

last: Hill

first: Daniel

last: Nguyen

middle: A


title: RNA-seq of Ixodes scapularis salivary glands [bulkRNA-intact-SG]

overall_design: Ixodes scapularis ticks were purchased from the tick-rearing facility at Oklahoma State University (Stillwater, OK, USA). Unfed ticks were maintained at 21°C and 85% relative humidity before infestation on rabbits. One day prior to feeding, female ticks were paired with males to mate. Adult ticks were restricted to feed on the outer part of the ear of four naïve female New Zealand rabbits, using orthopedic stockinets glued in place. A total of 20 adult females and 20 males (40 ticks per ear, 80 ticks per animal) were placed into the tick containment apparatus and allowed to attach. To group ticks by blood-feeding index, partially fed ticks were collected from the host during feeding, selected by engorgement size, sorted by weight, and divided into biological triplicates: unfed group (UF) (20 females per replicate, weight 1.6 ± 0.2 mg), group G1 (5 females per replicate, weight 2.8 ± 0.6 mg), group G2 (5 females per replicate, weight 7.3 ± 0.8 mg), group G3 (3 females per replicate, weight 15.9 ± 1.7 mg), group G4 (3 females per replicate, weight 24.6 ± 2.9 mg), group G5 (3 females, weight 44.5 ± 5.8 mg), and group G6 (2 females, weight 105.6 ± 15.9 mg). After removal from the host, ticks were rinsed sequentially with 1% bleach, nuclease-free water, and 70% ethanol, followed by a final rinse with nuclease-free water. Ticks were dissected within two hours after removal from the host. Tick salivary glands (SGs) were dissected in fresh, ice-cold, nuclease-free phosphate-buffered saline (PBS), pH 7.4 (Invitrogen, Carlsbad, CA, USA). After dissection, the salivary glands were gently washed in fresh, ice-cold, nuclease-free PBS, pH 7.4, and then immediately stored in RNAlater (Invitrogen, Carlsbad, CA, USA) prior to RNA extraction. After removal from RNAlater, SGs were gently washed in nuclease-free PBS, pH 7.4. Total RNA was isolated using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to the manufacturer's instructions. RNA integrity and quantity were assessed using a 4200 TapeStation system (Agilent Technologies). Illumina libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit with polyA selection, and sequencing was performed on an Illumina NovaSeq 6000 DNA sequencer. Raw sequencing data were trimmed and aligned to the Ixodes scapularis reference genome (ASM1692078v2). We used the RNA-seek workflow (https://github.com/skchronicles/RNA-seek), which performs multiple steps including quality assessment with FastQC, FQScreen, Kraken, and BBTools; adaptor removal and quality trimming with Cutadapt; read alignments using STAR in 2-pass mode; and read quantification with RSEM.


title: Multiomic single nuclei profiling of a mouse model of Alzheimer’s disease reveals that ACSS2 confers neuronal resilience to tauopathy

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

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

overall_design: Refer to individual Series


title: Spatial transcriptomics for CD36/FABP5/PPARδ signaling axis defines spontaneously proliferating cardiomyocytes in neonatal stages

city: Houston

first: Tamer

last: Mohamed

address: 6770 Bertner Avenue

institute: Baylor College of Medicine

summary: Spontaneously cycling cardiomyocytes (CMs) represent a rare and unique population in the neonatal heart with the potential to drive cardiac regeneration in adulthood. While previous studies have observed their existence, the mechanisms regulating their cell cycle activity remain poorly understood. Here, we aim to identify the signaling axis that defines the spontaneously proliferating CMs in the neonatal stage.

overall_design: Using single-cell RNA sequencing of neonatal mice CMs at postnatal day 1 (NMCMs-P1) we identified CD36 as a marker of the spontaneously proliferating CMs and those who respond to the cell cycle induction. Both Cd36 global and CMs-specific knockout mice (CD36KO, CD36CKO) exhibited smaller hearts, fewer CMs, impaired CM proliferation, and limited regenerative capacity at P1 following apical resection. Bulk-RNAseq in CD36KO and CD36CKO showed downregulation of cell cycle genes, as well as Fabp5, Pparδ, and Rxrs. Spatial transcriptomics for P1 wild-type (WT) mice hearts identified and localized a subpopulation of CMs with high cell cycle activity and co-expression of Cd36, Fabp5, and Pparδ. To define the upstream modulator of this signaling pathway, we conducted spatial metabolomics which revealed a decrease in CD36KO and CD36CKO cardiac intracellular contents of retinyl ester which was further confirmed with quantitative internalization assays. At Nano molar concentrations, retinoic acid (RA) enhanced the cell cycle activity of WT-P1 NMCMs but not the CD36KO. Knockdown of Fabp5 abolished the RA effect on CM proliferation, while its overexpression enhanced the effect of RA. Crossbreeding CD36KO mice with Pparδ-cardiac specific overexpressing mice rescued the proliferative phenotype, restoring CM proliferation and regenerative capacity after apical resection in P1 to the WT levels. Furthermore, Pparδ overexpression in neonatal mice resulted in enhanced CM proliferation and improved regenerative capacity following apical resection.

first: Abou Bakr

last: Salama


title: Confirmation of CDK8/19 inhibitor selectivity and activity in colorectal cancer [in vitro]

city: Sutton

first: Konstantinos

last: Mitsopoulos

state: London

address: 15 Cotswold Road

department: Cancer Therapeutics Unit

country: United Kingdom

institute: The Institute of Cancer Research

summary: We verified the selectivity of two chemical series of inhibitors of the Mediator kinases using a combination of high-quality chemical probes and genetic knockouts.  Knockout of CDK8 and/or CDK19 resulted in a range of overlapping and differential effects on gene expression or colony formation implying both shared and unique functions.  Analysis of molecular responses following knockout or inhibitor treatment revealed that many of the changes measured were attributable to CDK8 inhibition.  Knockout of both kinases resulted in enrichment of oncogene-associated gene expression consistent with a role gene expression associated with oncogene-dependence.  Knockout of both kinases abrogated in vitro anti-tumour activity resulting from inhibitor treatment, while loss of CDK8 alone was sufficient to block inhibitor effects on colony growth in vitro.  Overall, we demonstrated that our potent chemical probes are highly selective for the Mediator kinases in cancer cells and that many of the tumour-related responses to inhibitor treatment resulted from CDK8 inhibition.

overall_design: Using orthogonal approaches that combined chemical and genetic tools (CDK8 and CDK19 single and double knockouts), we validated the selectivity of small-molecule inhibitor CCT251545 (350nM, 6hours) versus DMSO in the colorectal cell line SW620 in vitro.

first: Costas

first: Robert

last: Te-Poele

first: Paul

last: Clarke


title: Study on the potential impact of sustained high temperatures during non-breeding season on largemouth bass

city: haikou

first: yue

last: chen

address: No. 58 Renmin Avenue, Meilan District

institute: Hainan University

summary: With the growing scale of largemouth bass breeding, the demand for seedlings is increasing. As global temperatures rise, it is crucial to study the effects of high temperature their regulatory mechanisms in largemouth bass. In this study, we simulated a high water temperature (28 ℃) in the non-breeding season in aquaculture ponds for 28 days to examine the growth, reproduction, metabolism, apoptosis, and methylation markers in largemouth bass; transcriptome analysis was also performed. The results showed no significant difference in body weight between male and female largemouth bass. However, the high-temperature exposed females had reduced growth hormone (GH) and estradiol (E2) levels and elevated cortisol levels. They also showed upregulated expression of AR, cyp19a, igf, fshβ, and lhβ in ovarian tissue. Transcriptomic comparisons between temperature treatments revealed 963 differentially expressed genes in females and 700 in males. Both the ECM receptor interaction and PPAR signaling pathways were significantly enriched. High-temperature enhanced the lipid metabolism process through the PPAR signaling pathway. High temperatures increased oxidative stress in females, which corresponded with increases in SOD, CAT, and GSH-Px, likely to counteract the excess reactive oxygen species. Moreover, endoplasmic reticulum stress was activated, indicated by increases in IRE1 and ATF6, leading to the upregulation of apoptosis-related genes and ovarian cell apoptosis. At high temperature, 5-MC%, demethylase, and methyltransferase were not different in females, while 5-MC% and methyltransferase were higher and demethylase was lower in males. In summary, sustained high temperature affected ovarian development by altering the expression of hormone and gonad related genes and inducing endoplasmic reticulum stress leading to ovarian cell apoptosis. However, low demethylase activity and high genome-wide methylation in the testis suggested that high temperatures may affect testis development via methylation, potentially impacting offspring production.

overall_design: A total of 216 fish were randomly divided into the 12 tanks, with 18 fish per tank, separate males and females. This experiment sets up 2 groups (three tanks/group), the temperature in the control group is maintained at 20°C, while in the high-temperature group, the temperature is increased to 28°C within 2 hours. Samples are taken at the beginning of the experiment as the IC group. After 28 days, the control group sample is taken as NC group, and the high-temperature group sample is taken as HT group

first: Yue


title: Kitl/kit signaling pathway regulate meiosis in mouse female gonad

city: TianJin

first: Liu

last: Chang

address: Weijin Road

institute: Nankai University

summary: The initiation of meiotic division, proper homologous chromosome pairing, and recombination are essential for maintaining genome stability in gametes. Numerous genes are involved in regulating these key processes during meiosis. However, the role of gonad somatic cells in regulating the initiation and progression of germ cell meiosis remains poorly understood. In this study, we identify the Kitl/Kit signaling pathway as a critical regulator of meiotic in female gonads. Disruption of Kitl/Kit signaling, both in vivo and in vitro, impairs the initiation of meiosis and leads to abnormalities in meiotic progression. We also observed that the mTOR/S6 signaling pathway is inhibited when Kitl/Kit signaling is blocked. Notably, adding a mTOR activator to in vitro cultures of Kitl conditional knockout gonads partially rescued germ cell numbers and improved meiotic initiation efficiency. Our findings highlight the essential role of the Kitl-Kit-mTOR-S6 signaling axis in meiotic initiation and progression. This study reveals a novel function of Kitl/Kit signaling in regulating embryonic meiosis and provides a new framework for future research on how somatic cells influence germ cell meiosis.

overall_design: Single cell sequencing of f/+ cre and f/f cre female gonads in E14.5 was performed to explore the transcriptome changes

first: Chang

last: Liu


title: Transcriptome analysis of the course of ischemic stroke from acute to chronic phase in mice [2]

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka university

summary: We conducted an examination of alterations in gene expression in the ischemic brain of mice at 3 and 14 days after cerebral infarction, in comparison to the control and sham operation groups at  single nucleus-transcriptomic levels. By cell type annotation, we obtained neurons (glutamatergic and GABAergic), fibroblast-like cells, astrocytes, oligodendrocyte progenitor cells (OPCs), oligodendrocytes, microglia, endothelial cells, and pericytes. We observed survival signals in neurons in addition to extensive inflammatory changes and neuronal death signals. A massive change was observed on day3, showing the loss of glutamatergic neuron and the increase of endothelial cells. This tendency was slightly recovered towards day14. Our findings revealed elevated expression of autophagy and cAMP signaling in surviving neurons within the penumbra region.

overall_design: Mouse cerebral infarcts were produced in a model of distal middle cerebral artery occlusion (dMCAO). The mice were divided into four groups: 3 days post-stroke, 14 days post-stroke, the control group, and the sham surgery group. Each brains brain tissue is mechanically dissociated, and cell membranes are lysed using enzymatic treatment and detergents to isolate and purify the nuclei. After confirming the quality of the nuclei, a library is prepared, and single nucleus RNA sequencing is performed.

first: Takeshi

last: Ikegami

first: Tsutomu

last: Sasaki


title: Confirmation of CDK8/19 inhibitor selectivity and activity in colorectal cancer [in vivo]

summary: We verified the selectivity of two chemical series of inhibitors of the Mediator kinases using a combination of high-quality chemical probes and genetic knockouts.  Knockout of CDK8 and/or CDK19 resulted in a range of overlapping and differential effects on gene expression or colony formation implying both shared and unique functions.  Analysis of molecular responses following knockout or inhibitor treatment revealed that many of the changes measured were attributable to CDK8 inhibition.  Knockout of both kinases resulted in enrichment of oncogene-associated gene expression consistent with a role gene expression associated with oncogene-dependence.  Knockout of both kinases abrogated in vivo anti-tumour activity resulting from inhibitor treatment, while loss of CDK8 alone was sufficient to block inhibitor effects on colony growth in vitro.  Overall, we demonstrated that our potent chemical probes are highly selective for the Mediator kinases in cancer cells and that many of the tumour-related responses to inhibitor treatment resulted from CDK8 inhibition.

overall_design: Using orthogonal approaches that combined chemical and genetic tools (CDK8 and CDK19 single and double knockouts), we validated the selectivity of small-molecule inhibitor CCT251921 (42 mg/kg p.o. q.d, 3days) versus vehicle control (0.5% Methocel, 0.25% Tween 20 in sterile phosphate buffered saline) in the colorectal cell line SW620 in vivo.


title: Ribo-seq analysis of HUVECs upon DDX24 knockdown

city: Zhuhai

first: Simeng

last: He

address: 52 Meihuadong Road, Xiangzhou

institute: Sun Yat-sen University

summary: To investigate the impact of DDX24 silencing on the translation landscape in HUVEC cells, we conducted Ribo-seq analysis.

overall_design: To investigate changes in translation in response to DDX24 knockdown, we performed ribosome profiling (Ribo-seq) and matched RNA-seq in HUVEC cells subjected to DDX24 knockdown for 48 h using siRNAs. Both Ribo-seq and the matched RNA-seq experiments performed in 3 replicates.

first: Bin

last: Li


title: Transcriptome analysis of the course of ischemic stroke from acute to chronic phase in mice

summary: We examined comprehensive gene expression in the mouse brain under physiological conditions at  single cell-transcriptomic levels. In addition, Sytox-negative cells were sorted and analyzed for gene expression. We performed single cell RNA-seq for mouse brain and found that the neurons could no recovered for further analyses. We successfully obtained oligodendrocyte progenitor cells (OPCs), oligodendrocytes, microglia, endothelial cells, and pericytes, but were unable to obtain neurons.  Additionally, we were only able to obtain astrocytes to a limited extent.We were able to examine comprehensive gene expression in the physiological brain.

overall_design: B6.129S4-Pdgfratm11(EGFP)Sor/J mouse brain were dissociated enzymatically, and then the cell suspensions were isolated by cell sorting (FACS) according to absence of Sytox signal. The sorted cells were analyzed using single cell RNA sequencing.


title: Transcriptome of embryonic hearts with cardiomyocyte-specific deficiency of Pcbp1

city: Los Angeles

first: Yao Wei

last: Lu

state: CA

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

summary: We generated cardiomyocyte-specific Pcbp1 knockout mice, and observed ventricular non-compaction defects and abnormal cardiac morphogenesis at E12.5 and E16.5. Majority of homozygous mutant mice died shortly after birth. We sought to identify the transcriptome changes at E16.5 by Pcbp1-deficiency in cardiomyocytes.

overall_design: We cross Pcbp1-Flox mice with Ctnt-Cre to generate cardiomyocyte-specific deletion of Pcbp1. On embryonic day (E) 16.5, cardiac ventricles from mutant mice and littermate controls were dissected, snap frozen and processed for RNA isolation. Genotype of individual embryos were confirmed by PCR from DNA isolated from yolk-sacs or tail tips. E16.5 heart RNA were processed for rRNA-depleted library construction and RNA-sequencing.

first: Da-Zhi

last: Wang


title: Dual Targeting of STING and PI3Kγ Eliminates Regulatory B Cells to Overcome STING Resistance for Pancreatic Cancer Immunotherapy [RNA-seq]

city: Ann Arbor

first: Chengyi

state: Michigan

address: B520, 1600 Huron Pkwy

institute: University of Michigan

summary: The immune suppression in tumors and lymph nodes of pancreatic ductal adenocarcinoma (PDAC), regulated by suppressive myeloid cells and regulatory B (Breg) cells, hinders the effectiveness of immunotherapy. Although STING agonists activate myeloid cells to overcome immune suppression, it expands Breg cells, conferring STING resistance in PDAC. We discovered that blocking PI3Kγ during STING activation abolished IRF3 phosphorylation to eliminate Breg cells, while PI3Kγ inhibition sustained STING-induced IRF3 phosphorylation to preserve STING function in myeloid cells. Therefore, we developed a dual functional compound SH-273 and its albumin nanoformulation Nano-273, which stimulates STING to activate myeloid cells and inhibits PI3Kγ to eliminates Breg cells overcoming STING resistance. Nano-273 achieved systemic antitumor immunity through intravenous administration, which decreases Breg cells and remodels microenvironment in tumors and lymph nodes. Nano-273, combined with anti-PD-1, extended median survival to 200 days in transgenic KPC PDAC mice (KrasG12D-P53R172H-Cre), offering potential for PDAC treatment.

overall_design: B and Bone marrow dendritic cells from KPC mice are harvest and incubate with (MSA2 or MSA2 plus IPI-549) or without treatments. RNA sequencing are conducted to check their differential gene expressions.

first: Duxin

last: Sun


title: A bifunctional, moonlighting RNA coordinates pathways to regulate human embryonic development [snRNA-seq]

city: Redwood City

first: Jin

last: Chen

address: 2800 Bridge Parkway

institute: Altos Labs

summary: Early embryogenesis and cellular differentiation require complex choreography between nuclear and cytoplasmic pathways. Through integrative analysis and a short open reading frame functional screen, sORF-seq, we identified lncPRESS1, a bifunctional long-non-coding RNA that also encodes a microprotein. In the nucleus, lncPRESS1 binds BRG1 to regulate chromatin remodeling and modulate the expression of pluripotency and differentiation genes. In the cytoplasm, lncPRESS1 is translated into a microprotein that binds to IFT57, regulating ciliogenesis and SHH signaling pathways to control lineage commitment. Together, these results reveal a novel mechanism where the dual functions of lncPRESS1 simultaneously coordinate chromatin remodeling and signaling pathways. This coordination co-regulates the initial developmental decisions specifying neuroectoderm and mesoderm fates during human embryonic development, underscoring the underappreciated complexity of multifunctional RNAs.

overall_design: The lncPRESS1 WT, KO, and ΔATG hESCs with matrigel (medium:matrigel=1:1) were injected into the flank of NSG™ immunodeficient mice for teratoma development. The teratoma were flash frozen and sent for scRNA-seq analysis.

first: Kaiyuan

last: Zhu

first: Wan-Chen

first: Jamin

first: Benjamin

last: Yang

first: Elmer

last: Guzman

first: Morgane

first: Rene

last: Sit

first: Rose

last: Yan

first: Shi-An

first: Udit

last: Parekh

first: Mia

last: Pulos-Homes

first: Yeyun

last: Ouyang

first: Ana

last: Granat

first: Maya

last: Yamazaki

first: Carla

last: Mulas

first: Renato

last: Minopoli

first: Stefka

last: Tyanova

first: Daniel

last: Itzhak

first: Diego

last: Acosta-Alvear


title: Aberrant alternative splicing of AARS2 in congenital cardiomyopathy is regulated by PCBP1

first: Yao Wei

last: Lu


title: Transcriptome of adult hearts with cardiomyocyte-specific deficiency of Aars2

summary: We generated cardiomyocyte-specific Aars2 knockout mice using Myh6-Cre, and observed progressive cardiac function decline starting at postnatal day (P) 28, with severe chamber dilation, and  phenotypes reminance of mitochondrial cardiomyopathy. All homozygous mutant mice died before reaching P70. We sought to identify the transcriptome changes by Aars2-deficiency at P14 and P21 in adult, prior to the onset of the cardiomyopathy.

overall_design: We cross Aars2-Flox mice with Myh6-Cre to generate cardiomyocyte-specific deletion of Aars2. At P14 or P21, heart apex from mutant mice, heterozygous and cre-negative controls were dissected, snap frozen and processed for RNA isolation. Genotype of individual embryos were confirmed by PCR from DNA isolated from tail tips. RNA were processed for rRNA-depleted library construction and RNA-sequencing.

first: Da-Zhi

last: Wang


title: A bifunctional, moonlighting RNA coordinates pathways to regulate human embryonic development [scRNA-seq]

first: Jin

last: Chen

overall_design: The lncPRESS1 WT, KO, and ΔATG hESCs were pretreated with 3.25 uM of CHIR99021 for 24 hours and then 0.5 uM of CHIR99021 for 72 hours to develop 3D gastruloids. These gastruloids were dissociated into single cells using ACCUTASE and then sent for scRNA-seq analysis.

first: Kaiyuan

last: Zhu

first: Wan-Chen

last: Li

first: Jamin

last: Liu

first: Benjamin

first: Elmer


title: Dual Targeting of STING and PI3Kγ Eliminates Regulatory B Cells to Overcome STING Resistance for Pancreatic Cancer Immunotherapy [scRNA-seq]

first: Chengyi

overall_design: Tumor tissues were harvest from KPC tumor bearing mice with (MSA2 or IPI-549 or SH-273 or Nano-273) or without treatments for single cell suspension for single cell RNA sequencing

first: Duxin

last: Sun


title: Transcriptome of embryonic hearts with cardiomyocyte-specific deficiency of Aars2

summary: We generated cardiomyocyte-specific Aars2 knockout mice, and observed ventricular non-compaction defects and abnormal cardiac morphogenesis at E16.5. All homozygous mutant mice died before birth. We sought to identify the transcriptome changes at E16.5 by Aars2-deficiency in cardiomyocytes.

overall_design: We cross Aars2-Flox mice with Ctnt-Cre to generate cardiomyocyte-specific deletion of Aars2. On embryonic day (E) 16.5, cardiac ventricles from mutant mice and littermate controls were dissected, snap frozen and processed for RNA isolation. Genotype of individual embryos were confirmed by PCR from DNA isolated from yolk-sacs or tail tips. E16.5 heart RNA were processed for rRNA-depleted library construction and RNA-sequencing.


title: A bifunctional, moonlighting RNA coordinates pathways to regulate human embryonic development [ATAC-seq]

overall_design: The hESCs, including the WT, KO, and ΔATG, were differentiated into the two germ layers (neuroectoderm: treated with SMADi; mesoderm: treated with BMP4). Daily samples were collected for 5 days for ATAC-seq.

last: Yang

last: Guzman

first: Morgane

first: Rene

last: Sit

first: Rose

last: Yan

first: Shi-An

first: Udit

last: Parekh

first: Mia

first: Yeyun

first: Ana


title: RNA-seq in HUVECs upon DDX24 knockdown

first: Simeng

last: He

summary: DEAD-box (DDX) RNA helicases play crucial roles in gene regulation by interacting with RNAs and influencing RNA fate and function. Previously, we have associated DDX24 with vascular development, but its precise role in RNA metabolism remains unclear. In this study, we demonstrate that DDX24 modulated endothelial cell functions by binding to and regulating mRNAs crucial for vascular morphogenesis and angiogenesis. These results establish a link between DDX24-dependent regulation of mRNA stability and endothelial cell function, providing novel therapeutic targets for angiogenesis.

overall_design: To investigate the role of DDX24 in vascular endothelial cells, RNA-seq of HUVEC with DDX24 knockdown by siRNA was performed. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different processed cells.Comparative gene expression profiling analysis of RNA-seq data for HUVECs(siNC) and its derivative (siDDX24).

first: Bin


title: Single cell Transcriptomes Reveals Aberrant Airway cell-cell interations in Pulmonary Fibrosis

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

institute: Francis Crick Institute

summary: We used single-cell RNA-seq to compare epithelial and immune cell populations in non-manipulated brushings of the proximal airway mucosa in patients newly-diagnosed with IPF (n=9) as compared to healthy controls (n=7). 60,313 cells were profiled including 22,487 cells from healthy controls and 37,826 cells from patients with IPF.

overall_design: Exploratory single-cell RNA-seq analysis of proximal airway mucosa cell populations from patients with idiopathic pulmonary fibrosis (IPF) and health controls.

first: Richard

middle: J

last: Hewitt

first: Anne

last: O'Garra

first: Clare

last: Lloyd


title: Enhanced cross-linked immunoprecipitation follow by sequencing (eCLIP-seq) of PCBP1 in embryonic mouse heart

first: Yao Wei

last: Lu

summary: PCBP1 is an RNA-binding protein abundantly expressed in the embryonic heart. We sought to determine the RNA interaction of Pcbp1 in embryonic heart.

overall_design: Embryonic day (E) 16.5 C57BL/6N hearts ventricles were snap-frozen follow by cryogrinded, UV crosslinking, and sonication. 20 x E16.5 hearts were pool per biological replicate (40 hearts total, n=2). Immunoprecipiation was performed by a pre-validated PCBP1 antibody (Abcam cat #ab168377). 2% of the sample was taken as the paired input sample. IP and input samples were cut from the membrane at the relative band size of 40kDa to 75kDA above that band size. RNA adapter ligation, reverse transcription, DNA adapater ligation and PCR amplification were performed.

first: Da-Zhi


title: Nanostring analysis of the effect of administration of IL-4 on murine Ly6Chi blood monocytes

city: Edinburgh

first: Stephen

last: Jenkins

address: 47, Little France Crescent

department: Centre For Inflammation Research

institute: University of Edinburgh

summary:
C57BL/6JCrl mice were injected intraperitoneally with CCl4, which causes liver injury, or olive oil vehicle control.
24hrs later the CCl4-treated group were then given an intravenous injection of IL-4complex or PBS control and then 24hrs later the Ly6Chi blood monocytes were sorted for Nanostring analysis.

overall_design: Nanostring transcriptomic data are presented from FACS-sorted Single Live CD45+ CD11b+ CSF1R+ SiglecF-, CD19-, CD3-, Ly6G- Ly6Chi, Treml4- blood monocytes

first: Ruairi

middle: W

last: Lynch


title: RNA half-life seq in HUVECs upon DDX24 knockdown

summary: DEAD-box (DDX) RNA helicases play crucial roles in gene regulation by interacting with RNAs and influencing RNA fate and function. Previously, we have associated DDX24 with vascular development, but its precise role in RNA metabolism remains unclear. In this study, we demonstrate that DDX24 facilitates the decay of the target mRNAs, in a CCR4-NOT deadenylase complex dependent manner. These results establish a link between DDX24-dependent regulation of mRNA stability and endothelial cell function, providing novel therapeutic targets for angiogenesis.

overall_design: To investigate the role of DDX24 in mRNA stability, RNA half-life-seq of HUVEC with DDX24 knockdown by siRNA was performed. We performed gene expression profiling analysis using data obtained from RNA-seq of 2 different processed cells at 3 time points. Comparative gene expression profiling analysis of RNA-seq data for HUVECs(siNC) and its derivative (siDDX24).


title: Quiescence and self-renewal of muscle stem cells require a type 2 deiodinase-mediated cell-autonomous surge in intracellular thyroid hormone signaling.

city: Napoli

first: Maria

middle: Angela

last: Da Stefano

address: Via S. Pansini, 5

country: Italy

institute: University of Naples "Federico II"

summary: Stem cells are critical for the regeneration and homeostasis of adult tissues. Thyroid hormone (TH), whose intracellular concentration is increased by type 2 deiodinase (D2), is involved in many cell functions but its role in quiescence is unknown. Here we show that D2 marks the quiescent stem cells in muscle and skin, and that its activity is required to maintain quiescence. Genetic D2-depletion in quiescent muscle stem cells triggers their spontaneous transition from G0 to a GAlert –like state. D2-depletion increases the proliferative potential of stem cells upon muscle injury, but impairs their self-renewal capacity, leading to depletion of the stem cell pool over time and regenerative failure. Mechanistically, TH sustains Notch signalling by directly promoting the expression of Notch receptors and their canonical target genes. In the acute setting, transient pharmacological inhibition of D2 accelerates muscle regeneration and skin wound healing by promoting stem cell expansion. In conclusion, D2-dependent sustained intracellular TH concentration is critical for maintaining stem cell quiescence and in regulating self-renewal.

overall_design: To investigate the mechanisms by which D2 controls quiescence we performed RNA-seq analysis of freshly isolated quiescent muscle stem cells from 3 cD2KO mice versus 3 controls booth in resting conditions. Muscle stem cells were isolated from hindlimb muscles of 3-4 month old Pax7nGFP/+;Pax7+/+;Dio2Fl/Fl (control) and Pax7nGFP/+;Pax7-CreERT2/+;Dio2Fl/Fl (cD2KO) mice.

last: De Stefano

first: Raffaele

last: Ambrosio

first: Cristina

last: Luongo

first: Tommaso

last: Porcelli

first: Domenico

last: Salvatore


title: IL-4 treatment induces apoptosis of blood monocytes and proliferation of reparative macrophages to resolve liver injury.

summary: IL-4 can have significant therapeutic benefit in many injury settings, but its mechanism of action is unclear. Here, we show that, in a model ofCCl4-mediatedacuteliver injury, exogenous IL-4 caused adramatic shift from recruited Ly6Chimonocytes to an abundance of monocyte-derived macrophages. This shift in macrophage dynamics was associated with accelerated clearance of necrotic tissue and enhanced hepatocyte regeneration that required IL-4 receptor-signalling to leukocytes. IL-4 did not alter monocyte recruitment or differentiation but instead stimulated monocyte apoptosis and acted on previously-recruited macrophages to drive proliferation and pro-repair characteristics, including expression of key genes involved in dismantling necrotic tissue. Further scRNA-seq analysis of the impact of IL-4 on all hepatic myeloid lineages revealed injury and cell-type specific responses. Together, our data reveal a novel pathway by which IL-4 alters the composition and functional specification of injury-associated myeloid cells and resolves injury in the liver.

overall_design: To examine the effect of IL-4 treatment on the composition and activation state of hepatic myloid cells and whether this differs in healthy or  injured liver, we performed scRNAseq on CD45+CD19-CD3-CD31-NK1.1- liver leukocytes from naive mice 48hrs after injection of IL-4c or PBS, or from mice given CCl4-mediated liver injury followed by IL-4c or PBS 24 hrs later, and cells harvested after a further 48 hours.

first: R

first: S

last: J Jenkins

first: L

last: Martens


title: A bifunctional, moonlighting RNA coordinates pathways to regulate human embryonic development [RNA-seq]

first: Jin

last: Chen

overall_design: The hESCs, including the WT, KO, and ΔATG, were differentiated into the three germ layers (neuroectoderm: treated with SMADi; mesoderm: treated with BMP4; definitive endoderm: treated with STEMdiff™ Definitive Endoderm Kit). Daily samples were collected for 5 days for bulk RNA-seq. The gain-of-function variants of lncPRESS1 hESCs were collected at early, intermediate, and late stages for RNA-seq.

first: Kaiyuan

last: Zhu

first: Wan-Chen

last: Li

first: Jamin

last: Liu

first: Benjamin

last: Yang

first: Elmer

last: Guzman

first: Morgane

first: Rene

last: Sit

first: Rose

last: Yan

first: Shi-An

first: Udit

last: Parekh

first: Mia

last: Pulos-Homes

first: Yeyun

last: Ouyang

first: Ana

last: Granat

first: Maya

last: Yamazaki

first: Carla

last: Mulas

first: Renato

last: Minopoli

first: Stefka

last: Tyanova

first: Daniel

last: Itzhak

first: Diego

last: Acosta-Alvear


title: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for Zmiz1 in Neuro-2a (N2a) cells

city: new orleans

first: Rajan

last: K C

state: LA

address: 6602 Freret St

department: Cell and Molecular Biology

institute: Tulane University

summary:
Purpose: Zinc Finger MIZ-Type Containing 1 (Zmiz1) is a member of the PIAS family of protein and function as a transcriptional coactivator of Notch, Androgen Receptor (AR), p53, Estrogen Receptor (ER), and Smad3/4 . Here, we use Neuro-2a cell line to perform ChIP sequencing on Zmiz1 bound, direct or indirect to profile Zmiz1 associated genomic regulation.
Methods: Neuro-2a (N2a) (ATCC, CCL-131) were cultured in DMEM-high glucose (Cytiva, SH30022) supplemented with 5 % FBS (Cytiva, SH3008803) and 50 U/ml Penicillin-Streptomycin (Thermo Fisher Scientific, 15070063) at 37 °C and 5% CO2. Zmiz1-HA was overexpressed in N2a cells and subsequently, ChIP DNA samples were obtained by using ChIP-IT Express Enzymatic Kit (Active Motif, 53009) and processed according to manufacturer specifications. Anti-HA-Tag Antibody (Cell Signaling, 3724S) was used for immunoprecipitation. Pull down DNA quantity was measured using Qubit DNA HS kit (Thermo Fisher Scientific, Q32851). The sequencing library was prepared using TruSeq ChIP Library Preparation Kit (Illumina, IP-202–1012). Ten nanograms of starting material were used for library preparation. Library quality and quantity were assessed using Agilent DNA 1000 chip (Agilent 5067-1504) and Qubit DNA HS kit respectively. Libraries were sequenced using the NextSeq1000/2000 P2 Reagents (200 Cycles) v3 (Illumina, 20046812) on a Nextseq1000/2000 system. Sequencing analysis was done using the ChIPSeq App from BaseSpace Labs (Illumina), which uses MACS2 for region enrichment and HOMER for motif analysis.
Results: ChIP-seq peaks analysis identified thousands of peaks which are mostly located in intergenic regions followed by introns.
Conclusions: We identify Zmiz1 bound DNA (direclty or indireclty) in Neuro-2a cells thus providing genomic regulation in neurodevelopmental events.

overall_design: Zmiz1-HA plasmid was transfected in Neuro-2a cell followed by chromatin immunoprecipitation (ChIP enzymatic kit from Active Motif), library prepraration, and sequencing.

first: K

last: Rajan

first: Stryder

last: Meadows

first: Maria

last: Galazo


title: Transcriptomes of premetastatic tumor-draining lymph nodes with or without denervation of TDLN-innervating nociceptive nerves

city: Shanghai

first: Yu

last: Zhang

address: No.150  Rd. Fenglin

institute: Zhongshan Hospital, Fudan University

summary: We compared the mice tumor-draining lymph nodes(TDLNs) with or without orthotopic tongue xenografts, and with or without  denervation of TDLN-innervating nociceptive nerves

overall_design: T represents mice with B16F10 tongue innoculation; NT represents mice without B16F10 tongue innoculation; NDE represents mice with inhibition of TDLN-innervating nociceptive nerves, and NC represents mice without inhibition of TDLN-innervating nociceptive nerves.Rep 1,2,3 represents biological independent repetitions.

first: Yibo

last: Guo

first: Tong

last: Ji


title: irCLIP-seq of DDX24 in HUVECs

first: Simeng

last: He

summary: DEAD-box (DDX) RNA helicases play crucial roles in gene regulation by interacting with RNAs and influencing RNA fate and function. Previously, we have associated DDX24 with vascular development, but its precise role in RNA metabolism remains unclear. In this study, we demonstrate that DDX24 modulated endothelial cell functions by binding to and regulating mRNAs crucial for vascular morphogenesis and angiogenesis. We further identify DDX24-bound mRNAs in endothelial cells using crosslinking immunoprecipitation (CLIP) sequencing. Mechanistically, DDX24 facilitates the decay of the target mRNAs, such as CLEC14A and ERG, by recruiting the deadenylase complex CCR4-NOT. These results establish a link between DDX24-dependent regulation of mRNA stability and endothelial cell function, providing novel therapeutic targets for angiogenesis.

overall_design: To investigate the role of DDX24 in vascular endothelial cells, CLIP-seq of HUVEC with DDX24-FLAG transfected followed by FLAG pull-down. We then identify DDX24-binding targets using data obtained from CLIP-seq of HUVECs.

first: Bin

last: Li


title: Biosacetalin 1,1-Diethoxyethane enhances aerobic respiration via activation of AMP-activated protein kinase

status: Public on Feb 19 2026

city: Jeollanam-do

first: Seung-Rock

last: Lee

address: Seoyang-ro, Hwasun-eup, Hwasun-gun

department: Biochemistry

country: South Korea

institute: Chonnam National University Medical school

summary: The enzyme 5ʹ-adenosine monophosphate (AMP)-activated protein kinase (AMPK) is a key regulator of cellular energy metabolism, playing a protective role in cardiovascular remodeling and diseases. Here, 1,1-Diethoxyethane (1,1-DEE), a compound traditionally known as a flavoring agent in wine and distilled spirits, was identified as an AMPK activator. By analyzing AC16 cardiomyocytes with the Seahorse Mito Stress Test, we found that 1,1-DEE induced a transient inhibition of both mitochondrial respiration and glycolysis, resulting in reduced ATP production. This metabolic disturbance triggered AMPK activation in a time- and concentration-dependent manner, leading to adaptive increases in the phosphorylation of acetyl-CoA carboxylase and 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2, which promotes fatty acid oxidation and glycolysis. AMPK activation also enhanced mitochondrial biogenesis by upregulating peroxisome proliferator-activated receptor gamma coactivator 1-alpha and mitochondrial transcription factor A. These alterations led to a sustained increase in both mitochondrial respiration and glycolysis. Overall, our findings unravel the important physiological role of 1,1-DEE in energy homeostasis through AMPK activation and aerobic respiration. This mechanism may hold therapeutic potential for the prevention and treatment of metabolic and cardiovascular diseases.

overall_design: RNA-seq of profiling of heart tissues of C57BL/6J mice (normal diet (ND) group and 1,1-DEE-treated group) after 8 weeks of treatment.

first: Thang

last: Nguyen Huu


title: RNA sequencing of E15.5 isolated progenitors cells from wildtype and Zmiz1-KO cortex

summary:
Purpose: Zinc Finger MIZ-Type Containing 1 (Zmiz1) is a member of the PIAS family of protein and function as a transcriptional coactivator of Notch, Androgen Receptor (AR), p53, Estrogen Receptor (ER), and Smad3/4 . Despite Zmiz1 mutations association with neurodevelopmental disorders such as ASD, ADHD, and intellectual disability, its role in physiological and pathological neurodevelopment  is significantly unknown. Here, we use murine model to knockout Zmiz1 using Emx1Cre and performed basal progenitors isolation at E15.5 and RNA sequencing to profile transcriptional changes upon Zmiz1 deletion.
Timed pregnancy was carried out. Mice was euthanized using CO2 and embryos brain were extracted at E15.5. Cortex was dissected and dissociated into single cell suspension using Neural Tissue Dissociation Kit (P) (Miltenyi Biotec, 130-092-628) following manufacture instruction. Intermediate progenitors were magnetically selected and isolated using Anti-Prominin-1 MicroBeads, mouse (Miltenyi Biotec, 130-092-333). Total RNA was extracted from wildtype and Zmiz1-KO samples. RNA concentration and RNA integrity number were determined. RNA library was prepared, quantified, and verified using TruSeq RNA Library Prep Kit v2, Qubit dsDNA High Sensitivity Assay kit and Bioanalyzer DNA1000 assay kit respectively. Verified samples were sequenced using the NextSeq1000/2000 P2 Reagents (200 Cycles) v3 on a Nextseq1000/2000. RNA-seq data analysis was performed using illumina BaseSpace Sequence Hub. Briefly, sequenced reads were aligned to mouse (mm10) reference genome with RNA-Seq alignment tool (STAR aligner) and differentially expressed genes (DEG) were determined using the RNA-Seq Differential Expression tool (version 1.0.1).
Results: We found 261 differentially expressed genes of which 67 genes were upregulated while 194 genes were downregulated. Downregulated genes were enriched in biological processes such as central nervous system differentiation, axon development, neuron migration, progenitors proliferation, etc.
Conclusions: We assessed cortical intermediate progenitors transcriptional profile potentially regulated by Zmiz1.

overall_design: E15.5 isolated WT and Zmiz1-KO progenitors RNA sequencing


title: Endothelial GARP Governs Longevity of Lung-resident CD8 T cell memory

city: Kunming

first: Xiaolong

state: Yunnan

address: 935 Jiaoling road

institute: Peking Union Medical College

summary: Tissue-resident memory CD8 T (Trm) cells provide frontline defense against respiratory viral infections, yet their persistence in the lung is remarkably short-lived compared to other barrier sites. The stromal cues that maintain these cells remain poorly defined. Here, we identify lung endothelial cells as a critical niche that sustains antiviral CD8 Trm cells through the activation of TGF-β. We found that the transmembrane protein GARP, highly expressed on lung endothelial cells, is essential for activating latent TGF-β and promoting the expression of the tissue-retention molecules CD103 and CD69 on CD8 Trm cells. Endothelial-specific deletion of GARP impaired CD8 Trm maintenance and compromised heterologous immunity against influenza, whereas its overexpression enhanced CD8 Trm populations. Mechanistically, we discovered that influenza-induced TNF triggers persistent, epigenetic repression of the GARP gene in endothelial cells, leading to a loss of TGF-β signaling and CD8 Trm cell waning. Consequently, neutralization of TNF restored GARP expression and boosted Trm retention. These findings provide a mechanistic basis for the transient nature of lung Trm cells and suggest that modulating the TNF-GARP-TGF-β axis could be a strategy to achieve durable respiratory immunity.

overall_design: scRNA-seq profiling of the lung cells from a 6 weeks old naïve C57BL/6J mouse.


title: DNA methylation patterns reveal cellular mechanisms underlying neurologic risk in inflammation-sensitized hypoxic ischemic encephalopathy

city: Wilmington

first: Elizabeth

last: Wright-Jin

state: Delaware

address: 200 Powder Mill Road

department: Neurology

institute: Nemours Children's Health

summary: Neonatal hypoxic ischemic encephalopathy (HIE) is a common birth complication that can cause death or lifelong disability due to cerebral palsy, epilepsy, and autism. Maternal infection or inflammation is a leading risk factor for diagnosis of HIE and cerebral palsy. However, the reasons for this increase in neurological risk to the offspring remain unknown. Inflammation or infection are known to cause epigenetic changes and may contribute to the increased risk of neurodevelopmental disability in exposed offspring. We hypothesized that differential methylation occurs in brain monocytes in a mouse model of inflammation-sensitized hypoxic ischemic encephalopathy. We compared DNA methylation in brain monocytes isolated from control, maternal immune activation (MIA), and inflammation sensitized HIE at postnatal day 7 (P7). Maternal inflammation induced significant methylation differences relative to control samples. MIA samples showed FDR-significant enrichment at loci involving craniofacial development and transcription factors important for regulating neurodevelopment and immune function. MIA and HIE samples were not significantly different. These results suggest that maternal inflammation or infection may increase the risk of HIE or neurological sequelae via gene methylation resulting in altered neurodevelopment.

overall_design: Illumina Infinium Mouse Methylation BeadChip of monocyte cells from 4 samples each of P7-aged  C57bl/6 mice brains treatment groups of Maternal Immune Activation, Hypoxic Ischemic Encephalopathy, and Controls. Bisulfite Conversion by QIAGEN, EPItect Bisulfite Kit. Bead Arrary name and version: Infinium MouseMethylation-12 v1.0.

first: Andrew

middle: T

last: Ebenezer

first: Jonathan

last: Hicks

first: Brooke

last: Hollander

first: Alexander

last: Hone

first: Mona

last: Batish

first: Robert

last: Akins

first: Adam

last: Marsh


title: RNA sequencing of P1 and P14 enriched neurons from wildtype and Zmiz1-KO cortex

first: Rajan

last: K C

summary:
Purpose: Zinc Finger MIZ-Type Containing 1 (Zmiz1) is a member of the PIAS family of protein and function as a transcriptional coactivator of Notch, Androgen Receptor (AR), p53, Estrogen Receptor (ER), and Smad3/4 . Despite Zmiz1 mutations association with neurodevelopmental disorders such as ASD, ADHD, and intellectual disability, its role in physiological and pathological neurodevelopment  is significantly unknown. Here, we use murine model to knockout Zmiz1 using Emx1Cre and performed neuron enrichment on P1 and P14 cortex followed by RNA sequencing to profile transcriptional changes upon Zmiz1 deletion.
Mice was euthanized using ice (P1) or CO2 (P14) and brain were extracted at P1 or P14. Cortex was dissected and dissociated into single cell suspension using Neural Tissue Dissociation Kit (P) (Miltenyi Biotec, 130-092-628 (P1) or 130-107-677 (P14)) following manufacture instruction. Neurons were magnetically isolated/enriched by negative selection through depletion of non-neuronal cell types using  cocktail of antibodies for non-neuronal cell types (Miltenyi Biotec, 130-115-390). Total RNA was extracted from wildtype and Zmiz1-KO samples. RNA concentration and RNA integrity number were determined. RNA library was prepared, quantified, and verified using TruSeq RNA Library Prep Kit v2, Qubit dsDNA High Sensitivity Assay kit and Bioanalyzer DNA1000 assay kit respectively. Verified samples were sequenced using the NextSeq1000/2000 P2 Reagents (200 Cycles) v3 on a Nextseq1000/2000. RNA-seq data analysis was performed using illumina BaseSpace Sequence Hub. Briefly, sequenced reads were aligned to mouse (mm10) reference genome with RNA-Seq alignment tool (STAR aligner) and differentially expressed genes (DEG) were determined using the RNA-Seq Differential Expression tool (version 1.0.1).
Results: For P1 enriched neurons, we found 291 differentially expressed genes of which 124 genes were upregulated while 167 genes were downregulated. Downregulated genes were enriched in biological processes such as neuron development, central nervous system differentiation, and axon development. For P14 enriched neurons,  we found 2,116 differentially expressed genes of which 749 genes were upregulated while 1,367 genes were downregulated. Downregulated genes were enriched in biological processes such as synaptic signalling and organization and neuron development and differentitation.
Conclusions: We assessed P1 and P14 cortical neurons transcriptional landscape following Zmiz1 deletion in the cortex.

overall_design: P1 and P14 enriched neurons from WT and Zmiz1-KO cortex RNA sequencing

first: K

last: Rajan

first: Stryder

last: Meadows

first: Maria


title: Characterization of sensitivity and resistance mechanisms to DHX9 inhibitor in endometrial and ovarian cancer cell lines

city: Bethesda

first: Tzu-Ting

last: Huang

state: MD

address: 10 Center Dr., Bldg 10, Rm 6B05

institute: National Cancer Institute

summary: To investigate the DHX9i response across endometrial and ovarian cancer cell lines with diverse backgrounds, total RNA was isolated from three biological replicates of cells treated with or without ATX968 (a DHX9 inhibitor). The RNA samples were then subjected to paired-end RNA sequencing on the NovaSeq X Plus (Illumina) platform.

overall_design: Total RNA was isolated from three replicate cultures of endometrial and ovarian cancer cells treated with or without ATX968 (DHX9 inhibitor) and then subjected to paired-end RNA sequencing on the NovaSeq X Plus (Illumina) platform.

first: Huang

last: Tzu-Ting


title: Reporter-gene-assisted small molecule inhibitor screening of heterochromatin boundary maintenance in Plasmodium falciparum

city: Nijmegen

first: Jonas

last: Gockel

email: jonas-gockel@web.de, jonas.gockel@ru.nl

address: Geert Grooteplein-Zuid 8

country: Netherlands

institute: Radboud University

summary: Phenotypic variation between malaria parasites is one of the major contributors to the pathogens success and is enabled by differences in chromatin organisation. Epigenetic changes, especially in chromatin structure, are largely responsible for differential expression of genes involved in antigenic variation as well as transmission between the human host and mosquito vector. Genes contributing to phenotypic variability are often located close to the boundaries between densely-packed heterochromatin and transcriptionally active, loosely packed euchromatin. Heterochromatin occupancy at these loci is variable and the primary source of heterogeneity between parasite strains/clones. Despite the central importance of heterochromatin in parasite biology, mechanisms on how heterochromatin domains are organised are not yet understood.In order to identify small molecular inhibitors influencing maintenance of heterochromatin boundaries, parasites were genetically modified by GFP tagging of a euchromatic gene close to a heterochromatin domain and a control gene within euchromatin was marked with tdTomato to ensure proper parasites staging. In this Heterochromatin Spreading Sensor (HSS) line heterochromatin spreading is expected to suppress reporter gene expression and would lead to the loss of the GFP signal while tdTomato signal remain unaltered. Using this system we tested the effects of two different small molecule inhibitor libraries (in total ~300 epigenetic and kinase inhibitors) on reporter gene expression utilising a high-content imaging system, and identified eleven compounds with an effect on GFP expression levels. Nine of these compounds are histone demethylase or methyltransferase inhibitors and their effects on heterochromatin occupancy levels were assessed by Cleavage under Target & Tagmentation (CUT&Tag).

overall_design: Parasites were grown in the presence of inhibitor compounds identified by microscopy. Parasites were harvested and HP1-CUT&Tag was performed.

first: Till

last: Voss

first: Richard

last: Bartfai


title: MondoA mediates transcriptional coordination between the MYC network and the integrated stress response in pancreatic ductal adenocarcinoma [CUT&Run]

city: Seattle

first: Brian

last: Freie

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: MYC amplification contributes to poor survival and outcome in pancreatic ductal adenocarcinoma (PDAC). Here we show that in PDAC cell lines with amplified MYC, MondoA is required for viability, facilitating proliferation while suppressing apoptosis in vitro and in vivo. Transcriptional and genomic profiling demonstrates that loss of MondoA leads to altered expression of direct MondoA targets as well as MYC target genes and is accompanied by shifts in genomic occupancy of MYC, MNT, and the MondoA paralog ChREBP.  This altered genomic binding by MYC network members is associated with transcriptional perturbation of multiple metabolic and stress pathways, as well as global changes in N6-methyladenosine modification (m6A) of mRNA. MondoA inhibition disrupts coordination between MYC network members and the integrated stress response (ISR) resulting in decreased translation of ATF4 mRNA, discordant target gene regulation of shared targets of MYC and ATF4, and ultimately, apoptosis. Re-establishing ATF4 protein expression rescues the diminished viability due to loss of MondoA expression or activity, providing direct evidence of a link between deregulated MYC and the transcriptional machinery of the ISR. Lastly, we find that small-molecule inhibition of MondoA is lethal in a subset of PDAC cell lines, including patient-derived organoids, suggesting that the ability to target MYC via chemical inhibition of MondoA transcriptional activity may have broad efficacy.

overall_design: PSN1 PDAC cells were treated with siRNA or the drug SBI-477 to inhibit MondoA, and occupation of genomic DNA by MondoA, MYC, MNT, and ChREBP were determined by CUT&RUN analysis. The differential occupation of these genes are correlated with RNAseq data.

first: Erin

last: Ramsey

first: Stephanie

last: Dobersch

first: Nan-Hyung

last: Hong

first: Xiaoying

last: Wu

first: Sita

last: Kugel

middle: N

last: Eisenman

first: Patrick

last: Carroll


title: MondoA mediates transcriptional coordination between the MYC network and the integrated stress response in pancreatic ductal adenocarcinoma [RNA-Seq]

overall_design: PSN1 PDAC cells were treated with siRNA or the drug SBI-477 to inhibit MondoA, and RNA was extracted and sequenced to quantitate the transcriptional changes that occur compared to cells treated with control conditions.

first: Robert


title: Macrophage-glia interactions regulate immune-damage to enteric neurons during West Nile virus infection [3]

city: St Louis

first: Fang

middle: R

last: Zhao

state: MO

institute: Washington University in St Louis

summary: Functional gastrointestinal (GI) tract disorders affect a substantial proportion of the global population and are often preceded by intestinal infections that cause injury to enteric neurons and glia through unrestrained immune responses. However, the mechanisms that limit infection-induced inflammation and protect the enteric nervous system remain poorly understood. Here, we investigated neuron-glia-macrophage interactions after West Nile virus (WNV) infection, a model neurotropic virus that causes GI tract dysmotility via injury of enteric neurons through a T cell-mediated cytolytic mechanism. In response to WNV infection, resident muscularis macrophages upregulate antiviral, proinflammatory, and immunomodulatory genes. However, pharmacological depletion of resident macrophages did not affect viral burden in the GI tract, but rather reshaped the enteric glial response to WNV, resulting in excessive production of T cell and neutrophil chemoattractants. This amplified recruitment of immune cells worsened enteric neuronal injury. Together, our findings identify resident muscularis macrophages as key regulators of glia-driven inflammation during enteric viral infection and reveal their role in protecting enteric neurons from immune-mediated damage.

overall_design: Translating ribosomal affinity purification (TRAP) of the muscularis externa of West Nile virus (WNV)  Plp1CreER;NuTRAP mice treated with either anti-CSF1R (to deplete resident macrophages) or isotype control antibody  was performed at 6 days post infection to identify factors regulating response of enteric glia in distal part of small intestine to WNV in the absence of resident macrophages. Isolated immunopreciptated ribosome-bound mRNA from enteric glia was used for high-throughput sequencing.

first: Hana

last: Janova

first: Ali

last: Akgul

first: Meredith

last: Schatz

first: Daniel

last: Alligood

first: David

last: Alvarado

first: Larissa

middle: B

last: Thackray

first: Thaddeus

middle: S

last: Stappenbeck

first: Michael

last: Diamond


title: Macrophage-glia interactions regulate immune-damage to enteric neurons during West Nile virus infection [4]


title: Macrophage-glia interactions regulate immune-damage to enteric neurons during West Nile virus infection [2]

overall_design: Translating ribosomal affinity purification (TRAP) of the muscularis externa of West Nile virus (WNV) and mock-infected Plp1CreER;NuTRAP mice was performed at 6 days post infection to identify factors regulating response of enteric glia in distal part of small intestine to WNV. Isolated immunopreciptated ribosome-bound mRNA from enteric glia was used for high-throughput sequencing.


title: The microRNA profiles of extracellular vesicles (EVs) from  sympathetic neurons.

city: Tokyo

first: Takaaki

last: Tamura

address: 6-7-1 Nishishinjuku, Shinjyuku-ku

institute: Tokyo Medical University

summary: Emerging evidence suggests that the autonomic nervous system contributes to tumor progression, but the molecular basis of nerve–tumor communication remains unclear. Here, we performed NGS analysis to investigate the microRNA (miRNA) profiles within EVs from sympathetic neurons.

overall_design: To investigate the EV contents derived from sympathetic neurons, we prepared EVs from  differentiated PC12 cells (dPC12 cells). As controls  EVs from undiffrentiated PC12 cells (uPC12 cells) were prepared.PC12 differentiation was induced in the presence of NGF. EVs were isolated from culture supernatant using ultracentrifugation.

first: Marta

last: Prieto-Vila

first: Takahiro

last: Ochiya


title: Macrophage-glia interactions regulate immune-damage to enteric neurons during West Nile virus infection [1]

overall_design: Sorting of resident macrophages from the muscularis externa of West Nile virus (WNV) and mock-infected CX3CR1CreER;YFP mice was performed at 6 days post infection to identify factors regulating response of resident muscularis macrophages in distal part of small intestine to WNV. Isolated  mRNA from resident muscularis macrophages was used for high-throughput sequencing.


title: The gene expression profiles of breast cancer (BCa) cells treated with sympathetic nerve-derived extracelllar vesicles (SNEVs).

summary: Emerging evidence suggests that the autonomic nervous system contributes to tumor progression, but the molecular basis of nerve–tumor communication remains unclear. Here, we performed NGS analysis to investigate the characteristics of BCa cells treated with SNEVs.

overall_design: To investigate the impact of SNEVs on the molecular characteristics of BCa cells, we checked gene expressions in rat BCa cell line RMT1 cells treated with EVs from differentiated PC12 cells (dPC12 cells). As controls RMT1 cells treated with EVs from undiffrentiated PC12 cells (uPC12 cells) and PBS were prepared. PC12 cell differentiation was induced in the presece of NGF.