title: Pooled single-cell screening in colorectal cancer identifies transcriptional modules of clinical relevance unlocked by oncogenes

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite Universitätsmedizin Berlin

summary:
While oncogenic mutations shape colorectal cancer biology and therapy response, their prognostic value remains low. Cluster-based classification of patient cancer transcriptomes has shown greater promise for prognosis, yet these systems do not account for the roles of oncogenes in establishing cancer phenotypes. Here, we create and validate a prognostic classifier for colorectal cancer based on transcriptional programs induced by oncogenes.
To systematically investigate oncogenic drivers, we employed a barcoded library of colorectal cancer-associated oncogene variants across a panel of genetically diverse colorectal cancer cell lines. We profiled the transcriptomes of over 100,000 transgenic cells and used machine learning to define transcriptional modules capturing key functional traits.
Our analysis revealed heterogeneity on the cell-to-cell level and context-dependent gene expression patterns induced by oncogenes. We identified overarching gene expression modules reflecting core oncogenic processes, including cancer cell plasticity, inflammatory response, replicative stress, and epithelial-to-mesenchymal transition. These modules enabled a functional classification that linked oncogenic signalling states to distinct transcriptional profiles. We demonstrated their prognostic value by stratifying clinical colorectal cancer cohorts into high- and low-risk groups. Although partially correlated with established clinical parameters, the modules provided additional prognostic information, improving survival prediction and therapy stratification beyond existing classification systems.
In summary, our study establishes a framework that connects oncogenic mutations to core transcriptional modules. By integrating experimental models with clinical data, we provide a resource for investigating colorectal cancer progression and oncogene-specific vulnerabilities, facilitating future research and precision oncology.

overall_design: We cultured Caco-2-et, HT-29-et, RKO-et, SW480-et and HCT 116 cells transfected with pooled viral oncogenes. Four day post infection, we harvested cells, FACS sorted them and subjected cells to scRNA-seq.

first: Viola

last: Hollek

first: Francisca

last: Böhning

first: Markus

last: Morkel


title: Targeting intrinsically disordered nuclear protein 1 (NUPR1) with single-domain antibodies alleviates triple-negative breast cancer (TNBC) progression in vivo

status: Public on Jan 12 2026

city: 杭州市

first: 宣儒

last: 陈

state: 浙江省

address: 杭州师范大学仓前校区慎12-205

country: China

institute: 杭州师范大学

type: Expression profiling by high throughput sequencing

summary: Triple-negative breast cancer (TNBC) is a highly aggressive subtype that currently lacks effective targeted therapies. Transcriptional co-regulator nuclear protein 1 (NUPR1) has been identified as a key stress-adaptive protein that promotes tumor progression and therapy-induced resistance. In this study, we developed a robust high-throughput platform integrating in situ proximity ligation assay followed by DNA sequencing (isPLA-seq), NanoBiT assays, and C-degron degradation validation to screen for functional single-domain antibodies (sdAbs) targeting NUPR1. Consequently, sdAb#07.81 emerged as a lead candidate, demonstrating strong binding affinity and the ability to degrade endogenous NUPR1 in TNBC cells. Functional assays confirmed that sdAb#07.81 suppressed TNBC cell growth and induced senescence in vitro. In vivo validation using a 4T1 cell-derived mouse model further established its therapeutic efficacy, with significant reductions in tumor size, NUPR1 expression, and cell proliferation. These findings highlight sdAb#07.81 as a promising therapeutic agent and validate the platform’s effectiveness for addressing intracellular targets like NUPR1. This work underscores the potential of sdAbs as a cancer therapeutics and provides a foundation for advancing sdAb#07.81 into preclinical and clinical development to address the critical unmet needs of TNBC treatment.

overall_design: RNA-seq profiling of wildtype 4T1 cells and treatment sdAb (sdAb-Con and sdAb#07.81; 0.5μg/ml) at 24 h and 48 h.

first: Zhuo

middle: T

last: Wang

first: Min

first: Ru

middle: X

last: Chen

first: Yuan

middle: R

last: Yin

first: Tao

middle: J

last: Xu

middle: Y

last: Sun

first: Ling

middle: A

last: Wu

first: Zhe

last: Liu

first: Yi

middle: Z

last: Ma


title: Uncovering a Key Metabolic Role of the GATA1 N-Terminus in Red Blood Cell Development [CUT&Run]

city: Memphis

first: Rashid

last: Mehmood

state: Tennessee

address: 324 NIGHT SAIL DR N APT 112, UNIT # 04-112

department: Hematology

country: USA

institute: St Jude Children's Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mutations in GATA1 that result in skipping of exon 2, which encodes the N-terminus, are associated with the myeloid leukemia of Down syndrome and Diamond-Blackfan anemia (DBA). To elucidate the molecular functions of the N-terminus, we employed single-cell RNA sequencing (scRNA-seq) of fetal liver cells derived from Gata1 mutant embryos that express the GATA1 short (GATA1s) isoform in place of full-length GATA1 (GATA1FL). scRNA-seq highlighted defects in erythropoiesis and revealed that the absence of the N-terminus resulted in elevated expression of genes involved in glycolysis, such as the rate-limiting pyruvate kinase PKM. To elucidate the regulation of the PKM gene, we performed precision nuclear run-on sequencing and cleavage under targets and release using nuclease on erythroid cells following acute deletion of GATA1 and determined that PKM is a direct target of GATA1. Mechanistically, we found that substitution of GATA1FL with GATA1s led to increased glycolysis in erythroid progenitor cells but did not affect oxidative phosphorylation. We further discovered that the expression of PKM is significantly elevated in DBA patients with RPS19 mutations, consistent with a role for GATA1 regulation of glycolysis in erythropoiesis. Together, these findings reveal that GATA1 controls not just heme metabolism, but also glycolysis.

overall_design: Occupancy profiling was conducted on HUDEP1 clones expressing either the full-length GATA1 (GATA1FL) or the short isoform (GATA1s_1D5 and GATA1s_1KI9) under expansion or differentiation (on day 4 or 24-hour differentiation) conditions, utilizing the CUT&RUN method.

first: Te

last: Ling

first: John

last: D. Crispino


title: Discovery of a global translation activator in Pseudomonas aeruginosa [CLIP-Seq]

city: Boston

first: Simon

last: Dove

state: Massachusetts

address: Boston Childrens Hospital, 300 Longwood Avenue EN761.1

department: Infectious Diseases

institute: Boston Children's Hospital

summary: We identified PhaF as an RNA binding protein in Pseudomonas aeruginosa. In order to identify the different target transcripts of PhaF, we carried out the CLIP (Crosslinking and immunoprecipitation) and CLAP-Seq (Covalent linkage affinity purification) approaches, which utilizes UV irradiation to crosslink PhaF with the transcripts that are in close vicinity to it. For CLIP-Seq experiments, we used the Pseudomonas aeruginosa PAO1 strain along with a derivative of PAO1 that harbors a C-terminal VSVG tag on PhaF. In order to determine the importance of the C-terminal domain (CTD) of PhaF on RNA binding, we used PAO1ΔphaF strains carrying plasmids that express a C-terminal VSVG tagged version of PhaF-CTD (pPhaF-CTD-V), along with a control strain that carries the same plasmid (pPhaF-CTD) but without the VSVG tag. For CLAP-Seq experiments, we used the Pseudomonas aeruginosa PAO1 strain along with a derivative of PAO1 that harbors a C-terminal Halo tag on PhaF. All the strains were subjected to UV irradiation, lysed, immunoprecipitated using either anti-VSVG-antibody coated beads or Magne Halo tagged beads. Following immunoprecipitation, the RNAs were purified. We also purified Total (Tot) RNA (samples collected before immunoprecipitation) from the PAO1 strains harboring the C-terminal VSVG tag on PhaF. The purified RNA samples were converted to cDNA libraries, which were subsequently sequenced using the Illumina NextSeq. The sequences were mapped to the genome to identify the target transcripts. In a separate series of experiments we also carried out RNA-Seq to identify the genes that are differentially regulated using Pseudomonas aeruginosa PAO1 and PAO1ΔphaF strains. The isolated RNA was sent to SeqCenter (Pittsburgh, PA) and the sequences obtained were mapped to the genome and DESeq analysis was performed.

overall_design: Strains used for CLIP-Seq were PAO1 and a derivative of PAO1 that harbors a C-terminal VSVG tag on PhaF along with PAO1 ΔphaF strains carrying plasmids that express a C-terminal VSVG tagged version of PhaF-CTD (pPhaF-CTD-V), and a control strain that carries the same plasmid (pPhaF-CTD) but without the VSVG tag. For CLAP-Seq we used PAO1 strain along with a derivative of PAO1 that harbors a C-terminal Halo tag on PhaF. In both CLIP-Seq and CLAP-Seq experiments, LB grown overnight cultures were back-diluted to an OD600 of 0.01. The strains were grown with aeration at 37°C to an OD600 of 2.0. For expressing the CTD of PhaF (either pPhaF-CTD or pPhaF-CTD-V, cloned in the pPSV38 plasmid background), 2mM IPTG was added to the culture to induce expression along with 30 μg/ml of Gentamicin.

first: Pallabi

last: Basu


title: Uncovering a Key Metabolic Role of the GATA1 N-Terminus in Red Blood Cell Development

overall_design: Expression libraries were constructed according to the Chromium 10X single cell 5′ reagent protocol, from total fetal liver.Single-cell transcriptional profiling using the 10x Genomics platform was performed on total fetal liver cells isolated from four E13.5 male Gata1s embryos and three wild-type littermate control embryos.


title: Urokinase plasminogen activator receptor (uPAR) attenuates allergen-induced eosinophil migration and airway hyperresponsiveness through distinct mechanisms

city: RTP

first: Brian

middle: Nicholas

last: Papas

address: 111 TW Alexander Drive

department: DIR

institute: NIEHS

summary: Allergic asthma is a widespread disease of the airway stemming from the actions of multiple cell types, including eosinophils and epithelial cells. The urokinase plasminogen activator receptor (uPAR) is a membrane bound protein that can contribute to the activation and mobilization of leukocytes and is present at increased levels in asthmatics. However, its role in allergic asthma remains poorly understood. Here, we have used multiple mouse strains and different models of allergic asthma to study the function of uPAR in allergic airway inflammation (AHR). Plaur, the gene encoding uPAR, was rapidly induced following allergic sensitization through the airway, and again following subsequent allergen challenge. Plaur-deficient mice displayed both increased numbers of eosinophils and heightened AHR in multiple models of allergic asthma. Mice selectively lacking Plaur in eosinophils also had more robust eosinophilia than did WT mice, and eosinophils lacking Plaur displayed increased activity in an ex-vivo assay of chemokine-dependent migration. However, those mice did not have increased AHR compared with WT mice. Conversely, although mice selectively lacking Plaur in lung epithelial cells did not have increased inflammation compared with WT mice, they displayed heightened AHR. These findings suggest that uPAR controls both airway inflammation and AHR, but through distinct mechanisms. Targeting uPAR might have therapeutic potential for treating inflammation and AHR in asthma.

overall_design: 8 C57B6/J (WT) mice and 8 Plaur–/– mice were sensitized on days 0 and 7 with LPS/OVA, and then subsequently challenged to aerosolized OVA on day 14.

first: Gregory

middle: S

last: Whitehead

first: Keiko

last: Nakano

first: Christina

middle: L

last: Wilkinson

first: Antonio

middle: M

last: Patterson

first: Sandeep

last: Upadhyay

first: Abdull

last: Massri

first: Artiom

last: Gruzdev

first: Manas

last: Ray

first: Hideki

first: Donald

middle: N

last: Cook


title: Discovery of a global translation activator in Pseudomonas aeruginosa [RNA-seq]

overall_design: Strains used for RNA-Seq were Pseudomonas aeruginosa PAO1 and PAO1 ΔphaF strains carrying the empty vector pPSV38 (pEV). LB grown overnight cultures were back-diluted to an OD600 of 0.01. The strains were grown with aeration at 37°C to an OD600 of 2.0. 2mM IPTG was added along with 30 μg/ml of Gentamicin.


title: Molecular effects of glucose on MIR503HG-regulated genes in triple-negative breast cancer

city: El Paso

first: Enrique

middle: Ivan

last: Ramos

state: Texas

address: 5001 El Paso Dr.

department: Molecular and Translational Medicine

institute: Texas Tech University Health Sciences Center El Paso

summary: Triple-negative breast cancer (TNBC) is the msot aggressive breast cancer subtype, characterized by the lack of key hormone receptors on tumor cells. As there are limited treatment options for these patients, it is important to further investigate this disease to better understand its mechanisms. In this study, we used an integrated genomics approach to examine the impact of glucose on genes regulated by long non-coding RNA (lncRNA) MIR503HG, which has been known to play an assortment of roles across different cancers. Our RNA-seq analysis of MIR503HG-overexpressing TNBC cells exposed to diverse glucose conditions revealed significant differences in regulation of genes associated with key biological processes. Analysis of gene subsets specific to various glucose environments identified clinical outcomes for breast cancer patients across different molecular subtypes. Our results suggest lncRNA MIR503HG could potentially be a therapeutic target in the treatment of TNBC.

overall_design: RNA-seq profiling of MDA-MB-157 cells with 4 h induced overexpression of MIR503HG (GFP as the control), and co-treated with varying glucose concentrations (1, 5, or 15 g/L).

first: Victoria

last: Reid

first: Barbara

last: Yang

middle: I

first: Shrikanth

last: Gadad


title: A High-Resolution Map Predicts Lineage and Birth Order Underlying Neuronal Identity

city: Oxford

first: Aaron

middle: Munro

last: Allen

address: Tinsley Building, Mansfield Road

department: DPAG

country: United Kingdom

institute: University of Oxford

summary: We have used single-cell RNA-sequencing to profile dissected central brains from female and male adult Drosophila melanogaster.

overall_design: Virgin female and male flies were collected and stored individually until the age of 5 days post-eclosion at 25°C prior to dissection. Two female replicates and two male replicates were processed with 20 brains each. The flies were transgenically expressing GFP under the control of the gene doublesex.

first: Stephen

middle: F

last: Goodwin


title: Urokinase plasminogen activator receptor (uPAR) attenuates allergen-induced eosinophil migration and airway hyperresponsiveness through distinct mechanisms [CD45+]

first: Brian


title: WNT7 orchestrates myofibroblast heterogeneity to induce desmoplasia

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

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

overall_design: Refer to individual Series


title: NF-κB-dependent redistribution of the GR cistrome recruits GR to inflammatory gene loci and correlates with reduced repression by glucocorticoid [GR_IkBaDN_ChIPseq]

city: Calgary

first: Alex

last: Gao

state: Alberta

address: 3330 Hospital Dr NW

department: Physiology and Pharmacology

country: Canada

institute: University of Calgary

summary: While ligand-activated glucocorticoid receptor (GR) binds DNA to activate transcription, glucocorticoids, including budesonide, reduce inflammatory gene expression, yet recruit GR to many such gene loci. In epithelial cells, the inflammatory cytokine, interleukin-1β (IL1B), activates NF-κB to induce gene expression and co-treatment with budesonide produces nanoscale GR-RELA nuclear co-localization. Such co-stimulation orchestrated reciprocal genome-wide redistribution of GR and RELA binding regions (GBRs and RBRs, respectively) relative to each mono-treatment to produce widespread GBR RBR overlap. This correlated with increased RNA polymerase-2 presence and required NF-κB for GR cistrome remodeling. Mapping transcription start sites to the nearest GBR or RBR both revealed associations with upregulated, but not repressed, genes. Importantly, RBR proximity to budesonide upregulated genes and GBR proximity to IL1B-upregulated genes correlated with attenuated repression on co-treatment. As this occurred on a background of glucocorticoid-induced repression, GR presence at specific IL1B-induced gene loci may reduce, or protect, from an otherwise prevalent glucocorticoid induced repression.

overall_design: To understand the impact of NF-κB on GR cistrome redistribution, A549 cells were infected with Ad-GFP (control), or Ad-IκBαΔN (NF-κB inhibitor) before no treatment, or treatment with IL1B, budesonide, or both for 1h. ChIP was performed using GR and RELA antibodies, and sequenced using Illumina NovaSeq 6000..

first: Mahmoud

last: Mostafa

first: Robert

last: Newton

first: Amandah

last: Necker-Brown


title: TWIST1 drives endothelial-to-mesenchymal-transition to stabilize atherosclerotic plaques [AEBP1 RNA-Seq]

city: London

first: Paul

last: Evans

address: Charterhouse square

institute: QMUL

summary: The effect of AEBP1 and PELP1 deletion was studied in human aortic endothelial cells exposed to atheroprone WSS, using the orbital system.

overall_design: Human aortic endothelial cells (HAoECs) were seeded onto gelatin-coated six-well plates and transfected with AEBP1 siRNA (siAEBP1), PELP1 siRNA (siPELP1), or scrambled control siRNA (sictrl) using the Lipofectamine RNAiMAX transfection system. After a six-hour incubation, the media was replaced, and cells were exposed to flow on an orbital shaker for 72 hours. Cells subjected to disturbed flow in the center of the well were scratched, and total RNA was extracted and analyzed via bulk RNA sequencing.

first: Mannekomba

last: Diagbouga

first: Mark

last: Dunning

first: Blanca

last: Tardajos Ayllon


title: Inducing ferroptosis to impede metastasis by inhibiting the calcium channel TRPC6

city: Worcester

first: Junhui

last: Li

state: MA

address: 364 Plantation St

institute: University of Massachusetts Medical School

summary: TRPC6 (transient receptor potential cation channel 6) contributes to the ability of breast cancer cells to persist after chemotherapy.  Here, we investigated a potential function of TRPC6 in enabling breast cancer cells to resist stimuli that induce ferroptosis.   A minority population of quiescent cells was isolated from triple-negative breast cancer (TNBC) cell lines using a p27 reporter.  These p27+ cells exhibited increased TRPC6 expression and resistance to ferroptosis compared to the p27- proliferating population.  The p27+ cells were also more metastatic than the p27- cells supporting the hypothesis that metastasis requires the ability of cells to evade ferroptosis. In pursuit of the mechanism involved, we discovered that the ability of TRPC6 to repress c-Myc is essential because repression of c-Myc sustains levels of glutathione that are sufficient to impede ferroptosis. Importantly, treatment of TNBC cells with a TRPC6 inhibitor reduced metastasis significantly, an effect that was mitigated by liproxstatin-1 treatment. These results support the hypothesis that a sub-population of TNBC cells characterized by TRPC6 expression has the potential to form metastases by evading ferroptosis.

overall_design: RNA-seq profiling of CAL-51 cells sorted based on p27 expression following transfection with a p27-mVenus reporter plasmid.

first: Boris

last: Dimitrov

first: Hira

last: Goel

first: Ayush

last: Kumar

first: Emmet

last: Karner

first: Arthur

last: Mercurio


title: Development, validation, and clinical utility of a novel methylation classifier for recurrence risk prediction in meningiomas [dataset 2]

city: Chicago

first: Drew

last: Duckett

state: IL

address: 541 N Fairbanks Ct, 8th Floor

department: Pathology

institute: Northwestern Medicine

type: Methylation profiling by genome tiling array

summary: Meningiomas are common intracranial tumors with complex behavior that can be difficult to predict. Historically, morphology has been used to predict tumor aggressiveness and risk of recurrence but has limitations as a prognostic tool. Recent work has shown the value of DNA methylation, transcriptomic, and copy number data for identifying groups of tumors which have distinct biological signatures and predicting recurrence risk. Here, we describe development, clinical validation, and implementation of a methylation classifier based on k-means clustering for prognostic stratification of meningiomas. Previously published work has validated the concept of meningioma prognostic stratification through DNA methylation data, but our system is unique in that it is the first clinically validated classifier which identifies risk groups based exclusively on DNA methylation signatures. This work has the potential to improve diagnostic workup, recurrence risk prediction, and clinical management of meningiomas.

overall_design: 217 meningioma tumors used in the clinical training and validation of a meningioma risk machine learning classifier using methylation profiling

first: Lucas

last: Santana-Santos

first: Matthew

last: McCord

first: Vanessa

last: Smith

first: MB

last: Lopes

last: Youngblood

first: Stephen

last: Magill

first: James

last: Chandler

first: Rimas

last: Lucas

first: Ditte

last: Primdahl

first: Roger

last: Stupp

first: Rudolph

last: Castellani

first: Craig

last: Horbinski

first: Daniel

last: Brat

first: Lawrence

last: Jennings

first: Madina

last: Sukhanova

first: Pouya

last: Jamshidi


title: TWIST1 drives endothelial-to-mesenchymal-transition to stabilize atherosclerotic plaques [Twist1 RNA-Seq]

first: Paul

last: Evans

summary: The effect of TWIST1 deletion was studied in human aortic endothelial cells exposed to atheroprone or atheroprotective wall shear stress.

overall_design: Human aortic endothelial cells (HAoECs) were seeded Ibidi slides I 0.4 coated with gelatin and transfected with a TWIST1 siRNA (siT1) or a scrambled siRNA (control, siNT) using the Lipofectamine RNAiMAX transfection system. After a 6 hour incubation, media was replaced and cells were exposed to different flow patterns using the Ibidi flow system for 72 hours. The different flow conditions were: High laminar shear stress (HSS; 13 dynes/cm²), low laminar shear stress (LSS; 4 dynes/cm²) and low oscillatory shear stress (LOSS; ±4 dynes/cm², 0.5 Hz). Total RNA from HAoECs was extracted and analysed using bulk RNA sequencing.

first: Mannekomba

last: Diagbouga

first: Mark

last: Dunning

first: Blanca

last: Tardajos Ayllon


title: Development, validation, and clinical utility of a novel methylation classifier for recurrence risk prediction in meningiomas

first: Drew

last: Duckett


title: TWIST1 drives endothelial-to-mesenchymal-transition to stabilize atherosclerotic plaques

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Stem cell-derived human glutamatergic neurons with pathogenic KCNQ2 variants display hyperactive bursting phenotypes

city: Toronto

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

institute: The Hospital for Sick Children

summary: Pathogenic variants in the KCNQ2 gene, which encodes a potassium channel subunit, are associated with neonatal seizures, epileptic encephalopathy, intellectual disability, and autism. Although the consequences of disrupted KCNQ2 channel function have been studied in the past, the detailed molecular mechanisms underlying the development of neurological phenotypes remain unclear, and neuronal models of specific patient variants are lacking. We generated patient-specific induced pluripotent stem cells (iPSCs) from fibroblasts from three individuals with distinct KCNQ2 pathogenic variants. We corrected the KCNQ2 variants using CRISPR-Cas9 editing to create isogenic controls and differentiated these iPSCs into glutamatergic neurons to study the effects of each variant on neuronal function. The three KCNQ2 variants were: 1) KCNQ2 c.875_877delTCCinsCCT, L292_L293delinsPF, 2) KCNQ2 c.766G>T, G256W, and 3) KCNQ2 c.821C>T, T274M. Our data revealed longer neurite outgrowth in two patient lines (T274M and G256W). Transcriptional profiling showed that all three KCNQ2 lines had increased expression of genes involved in synaptic transmission/signaling, cell adhesion, and GTPase signal transduction. Functional analyses of neuronal networks revealed increased burst duration in all three KCNQ2 lines compared with their isogenic controls. Furthermore, neurons from the L292_L293delinsPF and T274M lines displayed increased network connectivity associated with increased density of synaptic markers. Finally, we detected hyperexcitable neuronal networks in the G256W line with electrical stimulation of the neural networks on a high-density microelectrode array, and this phenotype was rescued with retigabine. These disease-related phenotypes for each of the KCNQ2 pathogenic variants can be used for drug screening to identify treatment options for the patients.

overall_design: RNAseq profile of 30-day old differentiated glutamatergic neuron samples from 3 isogenic human induced pluripotent stem cell lines with 5-7 replicates per sample.

first: Maria

last: Sundberg

first: Carole

last: Shum

first: Erika

last: Norabuena

first: Nina

last: Makhortova

first: Cidi

last: Chen

first: Lucy

last: Yu

first: Emma

last: Wightman

first: Kristina

last: Kim

first: Yeon

last: Han

first: Jennifer

last: Howe

first: Elizabeth

middle: D

last: Buttermore

first: Mustafa

last: Sahin


title: ATRX loss couples genome instability at a G-rich repeat to dysregulation of human alpha-globin expression [scRNA-seq]

first: Yuqi

last: Shen

state: Oxfordshiore

address: MRC WIMM, University of Oxford

department: Radcliffe Department of Medicine

summary: Germline mutations in the chromatin remodelling protein ATRX cause a severe developmental disorder associated with α-thalassemia. In addition, ATRX is amongst the twenty genes most frequently mutated in cancer. How ATRX mutations alter gene expression remains unclear. Using the α-globin locus as a model, here we show that ATRX deficiency downregulates α-globin in a subset of cells exhibiting DNA damage. A G-rich repeat at the α-globin locus serves as a potential site of G-quadruplex formation and DNA damage. ATRX binds this repeat co-transcriptionally, and its loss increases R-loop accumulation at this site, leading to local DNA damage and transcriptional disruption in cis. Deletion of this repeat abolishes this effect, while targeted DNA damage reinstates it. These findings reveal a mechanism linking ATRX’s role in genome stability to transcriptional regulation, and uncover a molecular basis of human genetic disease mediated by a long-range G-rich repeat.

overall_design: ATRX was knocked out using CRISPR-Cas9 in CD34+ haematopoietic stem cells (HSCs) derived from healthy donors. These cells were then differentiated into erythroid cells and analysed for gene expression using single-cell RNA sequencing (Smart-seq2).

first: Sean

last: Wen


title: scRNA-seq of total CD45+ aortic cells  with cell Hashing

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

overall_design: We performed single-cell RNA-seq analysis with cell hashing of total viable CD45+ cells isolated from the aorta of B6.Ldlr-/- mice transplanted with BM or BMT and fed a WD for 8 weeks

first: Ivana

last: Jorgacevic

first: Haroon

last: Shaikh

first: Sarah

last: Schäfer

first: Alma

last: Zernecke

first: Andreas

last: Beilhack

first: Antoine-Emmanuel

last: Saliba

first: Clément

last: Cochain


title: Dual Mechanisms of Supporting Cell Regeneration in the Neonatal Mouse Cochlea

city: Stanford

first: Alan

last: Cheng

state: CA

address: 240 Pasteur Drive

institute: Stanford University

summary: Cochlear supporting cells are critical for proper hearing function and regeneration of hair cells, which are responsible for perceiving sound in the inner ear. In the neonatal mouse cochlea, when supporting cells are ablated, they can regenerate through progenitor cells in the cochlea. Here, we show through single cell RNA sequencing and in vivo fate mapping, that upon supporting cell ablation in the neonatal cochlea, inner phalangeal cells regenerate through two independent mechanisms; one which requires proliferation and the other by which transdifferentiation (i.e. regeneration without mitotic division) of cochlear progenitor cells occurs. These dual mechanisms are spatially distinct where transdifferentiation occurs in all three turns of the cochlea, while proliferation-induced regeneration occurs exclusively in the apical and middle turns. Inhibiting proliferation using aphidicolin, slightly decreased the number of regenerated IPhCs in the apex middle turns, but not the base, after damage. We also observed a medial to lateral transition in the compartmentalization of the GER after supporting cell damage, suggesting de-differentiation of these domains. Overall, our study reveals GER cells as supporting cell progenitors that undergo dual mechanisms of regeneration (mitotic and non-mitotic). Additionally, we uncover transcriptomic changes after supporting cell damage in the neonatal mouse cochlea that could be used as gene targets in therapies for hearing loss.

overall_design: Whole cochlea from postnatal days (P) 4, P5, P6 and P7 Ki67CreERT/+;Lgr5DTR/+;Rosa26RtdTomato/+ (damage) and Ki67CreERT/+;Rosa26RtdTomato/+ (control) mice were dissociated in biological duplicate for single cell RNA-sequencing. Cells were processed using 10X Genomics Chromium Single Cell 3' Reagents v3.1. After sequencing, Cell Ranger was used for read mapping and quantification, followed by further analysis using Seurat.

first: Julia

last: Abitbol

first: Maggie

last: Matern

middle: G


title: Thrombospondin-4 regulates apoptosis of vascular smooth muscle cells after artery transplanted into vein

city: Beijing

first: Fei

last: Xu

address: Room 421, Building 5

institute: Beihang University

summary: In the context of coronary artery bypass grafting (CABG), mechanical factors are pivotal;   however, the molecular underpinnings of vascular atrophy and remodeling subsequent to arterial transplantation into a venous hemodynamic milieu remain enigmatic.   Consequently, this study employed the vascular anastomosis wheel technique to graft the common carotid artery of New Zealand white rabbits into the external jugular vein, thereby establishing an innovative animal model of arterial mechanical unloading. The efficacy of the animal model was ascertained through ultrasound imaging. Immunohistochemical methodologies, transmission electron microscopy, and TUNEL staining were utilized to delineate alterations in vascular morphology. Advanced techniques such as gene transcriptomic analysis, proteomic profiling, iPathway guide (IPG) analysis, gene overexpression/silenced, flow cytometry, and stretch testing were applied to elucidate the potential molecular mechanisms. Comparative analysis between the arterial graft and the control group revealed the successful preparation of the mechanical unloading animal model in vitro. Morphological examination of the arterial vessels indicated that atrophy under venous flow mechanics is predominantly attributed to the apoptosis of vascular smooth muscle cells (VSMCs). Genomic and proteomic analyses revealed that thrombospondin-4 (THBS4) plays a pivotal role in vascular remodeling. IPG analysis suggested that THBS4 may modulate VSMCs apoptosis via the focal adhesion pathway. THBS4 gene overexpression/silence experiments and flow cytometry demonstrated the regulation of VSMCs apoptosis by THBS4. Furthermore, it was established that low stretch tension facilitates the expression of THBS4 and VSMCs apoptosis, thereby confirming the relationship between THBS4 and VSMCs apoptosis. This study was the first to introduce gene transcriptomics and proteomics into the arterial mechanical unloading animal model and the first to demonstrate the role of THBS4 in promoting VSMCs apoptosis. Consequently, THBS4 emerges as a promising therapeutic target for the prevention of intimal hyperplasia post-vascular transplantation in vascular surgery.

overall_design: RNA-seq analysis was performed at 14 and 30 days after surgery in the control group (the artery of the contralateral group without operation) and the experimental group (the artery transplated into vein), respectively

first: Xiaoling

last: Jia

first: Shoudong

last: Chai

first: Haifeng

last: Liu

first: Yubo

last: Fan


title: Development, validation, and clinical utility of a novel methylation classifier for recurrence risk prediction in meningiomas [dataset 1]

first: Drew

last: Duckett

first: Lucas

last: Santana-Santos

first: Matthew

last: McCord

first: Vanessa

last: Smith

first: MB

last: Lopes

first: Mark

last: Youngblood

first: Stephen

last: Magill

first: James

last: Chandler

first: Rimas

last: Lucas

first: Ditte

last: Primdahl

first: Roger

last: Stupp

first: Rudolph

last: Castellani

first: Craig

last: Horbinski

first: Daniel

last: Brat

first: Lawrence

middle: J

last: Jennings

first: Madina

last: Sukhanova

first: Pouya

last: Jamshidi


title: LncRNA WEE1-AS coordinates oxidative fatty acid metabolism through the activation of mitochondrial Cdk1/Cyclin B1

city: Seoul

first: Haena

last: Choi

address: , Gwanak_1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly prevalent with life-threatening complications, underscoring the need for new therapeutic targets. In this study, we identified a novel long non-coding RNA (lncRNA), WEE1-AS, which is transcribed from the antisense strand of the Wee1 gene locus. Hepatic WEE1-AS was expressed in a spatiotemporal manner in response to a high-fat diet challenge. Functionally, WEE1-AS enhanced mitochondrial fatty acid oxidation by activating the Cdk1/Cyclin B1 complex through two mechanisms. First, it suppressed the transcription of the Wee1 gene by preventing access to the transcriptional machinery. Second, WEE1-AS bound and stabilized the Cyclin B1 protein by suppressing ubiquitin/proteasome-mediated degradation. Notably, treatment with the Wee1 inhibitor Adavosertib ameliorated MASLD symptoms by improving mitochondrial function in the liver. Furthermore, we identified a human homolog, lnc106435.1, which improved mitochondrial function, suggesting that targeting lnc106435.1 could be a valuable therapeutic strategy for managing MASLD.

overall_design: to investigate the function of lnc RNA Wee1-AS in the regulation of cell cyle and metabolic process in the C57BL/6 mice liver, we overexpressed the Wee1-AS in the liver by injecting AAV-Wee1-AS through retro-orbital injection to high-fat diet fed mice.  We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 liver samples at one time points.  comparative gene expression profiling analysis of RNA-seq data for mouse liver samples (HFD with AAV-GFP, HFD with AAV-Wee1-AS)

first: Hyeon-Ji

last: Kim

first: Cheolhee

last: Jeong

first: Sang-Heon

last: Lee

first: Mi-Ock


title: ATRX loss couples genome instability at a G-rich repeat to dysregulation of human alpha-globin expression [ChIP-seq]

first: Yuqi

last: Shen

overall_design: To determine ATRX binding pattern during erythroid differentiation, the immortalised erythroid progenitor cell line HUDEP-2 were differentiated and samples from different differentiation stages were collected for ATRX ChIP-seq.


title: Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine clinical biopsies of lymphoid cancers

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

department: Department of Pathology

institute: University of Michigan Medical School

summary: We performed Hi-C retrospectively on archival formalin-fixed paraffin embedded (FFPE) tissue biopsies of lymphoid cancers to explore the utility of Hi-C for comprehensively identifying enhancer-hijacking oncogene rearrangements in routine clinical samples. Our data shows that FFPE-compatible Hi-C retains state-specific topological features of tumor cells at gene loci associated with germinal center B cell or plasma cell state and comprehensively detects rearrangements genome-wide with high concordance against prior clinical testing. Hi-C additionally reveals enhancer-promoter interactions consistent with enhancer-hijacking across rearrangement breakpoints at recurrent, uncommon, and diversely-rearranging loci, and provides topological information to support the interpretation of these events that is not provided by alternative routine clinical assays such as FISH.

overall_design:
Genome-wide chromatin conformation capture (Hi-C) performed on formalin-fixed paraffin-embedded tissue specimens of lymphoid cancers from patients

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

first: Jamin

last: Wu

first: Alec

last: Chu

first: Jang

last: Cho

first: Misha

last: Movahed-Ezazi

first: Kristyn

last: Galbraith

first: Camila

last: Fang

first: Yiying

last: Yang

first: Chanel

last: Schroff

first: Kristin

last: Sikkink

first: Michelle

last: Perez-Arreola

first: Logan

last: Van Meter

first: Savanna

last: Gemus

first: Jon-Matthew

last: Belton

first: Xue

last: Song

first: Aishwarya

last: Gurumurthy

first: Hong

last: Xiao

first: Valentina

last: Nardi

first: Abner

last: Louissant Jr.

first: Raju

middle: K

last: Pillai

first: Joo

middle: Y

first: Dennis

last: Shasha

first: Aristotelis

last: Tsirigos

first: Anamarija

last: Perry

first: Noah

last: Brown

first: Tatyana

last: Gindin

first: Lina

last: Shao

first: Marcin

middle: P

last: Cieslik

first: Minji

first: Anthony

last: Schmitt

first: Matija

last: Snuderl


title: Strongly regulated “super-target” transcription factors exert an outsized influence in microRNA-regulated networks

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

summary: To elucidate the role of microRNAs (miRNAs), it is essential to identify their direct post-transcriptional targets. However, identifying the most functionally significant targets is challenging due to factors such as the inherent limitations of predictive algorithms, the abundance of RNA interactions detected in co-precipitation studies, and the prevalence of non-productive targeting caused by weak interactions or unfavorable stoichiometries. We introduce the concept of 'super-targets'—genes whose regulation disproportionately drives miRNA functionality by virtue of both strong targeting and the critical role of the gene itself, such as a transcription factor whose disruption has broad downstream effects. A prime example is the reciprocal regulation between the miR-200 family and ZEB transcription factors, which governs the epithelial-mesenchymal status of cells. To assess the impact of such 'super-targeting,' we developed a system that isolates ZEB regulation from all other miR-200 activities. This approach reveals a complex network of transcriptional and post-transcriptional regulation, where miR-200’s ability to maintain an epithelial phenotype and suppress cell migration is fully dependent on the repression of ZEB1 and ZEB2, though other effects are ZEB-independent. Our findings suggest that a significant portion of miRNA regulatory impact may result from the potent targeting of a few key genes, highlighting that indirect transcriptional effects are a fundamental mechanism of miRNA function and likely more impactful than numerous modestly-regulated direct targets that otherwise dominate the publication landscape.

overall_design: RNA-seq profiling of wild-type MDA-MB-231 cells and their derivatives with DOX-inducible ZEB1 and ZEB2 expression constructs (lacking 3'UTRs and thus, insensitive to miR-200 mediated repression).  miR-200c or control miRNAs were co-transfected.

middle: A

first: Julie

last: Bracken

first: Laura

last: Sourdin

first: Gregory

last: Goodall

first: Cameron


title: Single cell transcriptome sequencing of hemocytes of mud crab (Scylla paramamosain) before and after WSSV infection

city: NanChang

first: 航

last: 胡

address: No. 999, Xue Fu Road

institute: 生命科学学院本部

summary: We used the BDA DNBelabC4 platform to conduct single-cell RNA transcriptome sequencing on hemocytes before and after infection with WSSV, and to study the changes in hemocytes composition and antiviral mechanism of a crustacean virus infection represented by mud crab. The blood cells, or hemocytes, of the mud crab (Scylla paramamosain) play crucial roles in its innate immune system.  These cells are involved in various immune responses, including phagocytosis, encapsulation, and the production of antimicrobial peptides.  The hemocytes can be isolated and characterized using techniques such as flow cytometry, which helps in understanding their functions and interactions within the crab's immune system. White Spot Syndrome Virus (WSSV) is a highly contagious and lethal virus that primarily infects crustaceans, particularly shrimp and crabs.  It is an enveloped double-stranded DNA virus, typically oval-shaped, measuring about 320nm in length and 100nm in width, making it one of the largest known viruses.  WSSV is the causative agent of White Spot Syndrome, a disease that has caused significant economic losses in the aquaculture industry.

overall_design: 10^7 WSSV were injected into the joint of the third appendage of mud crab. After 20 hours, the hemlymph of mud crab was extracted, and the precipitation cells were centrifuged after 1:1 mixing with citric acid anticoagulant, and single-cell RNA sequencing was performed to study the changes of cell types of hemocytes infected with WSSV and screen cells with antiviral function.

first: Hu

last: Hang


title: Beta cell-derived cholecystokinin drives obesity-associated pancreatic adenocarcinoma development

city: New Haven

first: Mandar

middle: Deepak

last: Muzumdar

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: Pancreatic endocrine-exocrine crosstalk plays a key role in normal physiology and disease and can be altered by host metabolic states, such as obesity. Classically, endocrine islet beta (β) cell secretion of insulin is thought to promote the development of obesity-associated pancreatic adenocarcinoma (PDAC), an exocrine cell-derived tumor. Here, we show that β cell expression of the peptide hormone cholecystokinin (CCK) is necessary and sufficient for obesity-associated PDAC progression in mice and that CCK expression – rather than insulin – correlates strongly with enhanced tumorigenesis. Single-cell RNA-sequencing, in silico latent-space archetypal and trajectory analysis, and experimental lineage tracing in vivo reveal that obesity induces the expansion of postnatal immature β cells, which adapt to express CCK via stress-responsive JNK/cJun signaling. Finally, obesity perturbs CCK-dependent peri-islet exocrine cell transcriptional states and enhances islet-proximal tumor formation. These results define endocrine-exocrine CCK signaling as a bona fide driver of obesity-associated PDAC development and uncover new avenues to target the endocrine pancreas to subvert exocrine tumorigenesis.

overall_design: RNA-seq profiling of pancreata isolated from 12-week old C57BL6/J mice with lean wild-type (WT) mice, obese leptin-deficient (Lep(ob/ob), aka OB) mice, or leptin-deficient (OB) mice treated 6 weeks with CCK-receptor antagonists (CCKR-I, proglumide or lorglumide) drinking water (versus control water), beginning at 6 weeks of age. All mice on standard ad libitum chow diet.

first: Jeremy

middle: B

last: Jacox

first: Christian

middle: R

last: Ruiz


title: Cytosolic transport of citrate protects pancreatic cancer from ferroptosis under nutrient stress.

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

summary: Pancreatic cancer is a deadly disease as the long-term overall survival rate is only 12%, indicating that there is no effective therapeutic approach available to the patients. Recent studies link the conditions in the pancreatic tumor microenvironment to the aggressive phenotype of the disease and drug resistance. The pancreatic tumor microenvironment is poorly perfused, which limits the nutrients and oxygen availability for tumor cells. We and others have demonstrated that cancer cells rewire their metabolism to adapt to harsh conditions present in the tumor microenvironment of pancreatic cancer. A better understanding of metabolic dependencies may assist in developing targeted therapies. Our results demonstrate that cytosolic transport of citrate via a transporter, SLC25A1, confers a survival advantage to pancreatic cancer cells by protecting them against ferroptosis, an iron-dependent cell death mechanism, under nutrient withdrawal. Additionally, targeting the transporter via a small molecule inhibitor of SLC25A1 prevents the growth of subcutaneous pancreatic xenograft tumors in animals. Any therapeutic advance in the area of pancreatic cancer beyond conventional chemotherapy would significantly improve lives and outcomes.

overall_design: RNA-seq profiling of SLC25A1, ACLY, and ACO1 gene knock-down in MiaPaCa-2 cells.

first: Ali

last: Vaziri-Gohar


title: ComBO: A combined human bone and lympho-myeloid bone marrow organoid for pre-clinical modelling of haematopoietic disorders

first: Yuqi

last: Shen

summary: We developed a new combined human bone and lympho-myeloid bone marrow organoid (comBO) model using human induced pluripotent stem cells (hiPSCs). To characterise this model, we employed 10x single-cell RNA sequencing (scRNA-seq) to analyze cell composition and cell-cell interactions. Additionally, we engrafted the comBOs with cells derived from healthy donors or multiple myeloma patients and performed scRNA-seq to explore its potential for disease modeling.

overall_design: Two approaches were used to generate the comBO model: bulk hydrogel and granular gel. scRNA-seq was applied to both versions for comparative analysis. Subsequently, the fragmented gel method was used to generate comBO organoids engrafted with cells from one healthy donor and three multiple myeloma patients. scRNA-seq was then performed to identify differences in cell composition and interactions across these conditions.

first: Antonio

last: Rodriguez-Romera

first: Kristian

last: Gurashi

first: Samuel

last: Kemble

first: Charlotte

last: Smith

first: Abdullah

middle: O

last: Khan


title: The LncRNA 3222401L13Rik Is Upregulated in Aging Astrocytes and Regulates Neuronal Support Function Through Interaction with Npas3 [young]

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: Aging is linked to a decline in cognitive functions and significantly increases the risk of neurodegenerative diseases. While molecular changes in all central nervous system (CNS) cell types contribute to aging-related cognitive decline, the mechanisms driving disease development or offering protection remain poorly understood. Long non-coding RNAs (lncRNAs) have emerged as key regulators of cellular functions and gene expression, yet their roles in aging, particularly within glial cells, are not well characterized. In this study, we investigated lncRNA expression profiles in non-neuronal cells from aged mice. We identified 3222401L13Rik, a previously unstudied lncRNA enriched in glial cells, as being specifically upregulated in astrocytes during aging. Knockdown of 3222401L13Rik in primary astrocytes revealed its critical role in regulating genes essential for neuronal support and synapse organization. This function was also conserved in human iPSC-derived astrocytes. Additionally, we found that 3222401L13Rik mediates its cellular effects through interaction with the transcription factor Neuronal PAS Domain Protein 3 (Npas3), and that overexpression of Npas3 effectively rescued the functional deficits observed in astrocytes lacking 3222401L13Rik. Our findings suggest that upregulation of 3222401L13Rik in aging astrocytes acts as a compensatory mechanism to enhance neuronal and synaptic support, potentially delaying the onset of molecular and structural changes in both astrocytes and neurons. Strategies to boost 3222401L13Rik expression earlier in life may help mitigate age-associated loss of neuronal plasticity.

overall_design: To identify lncRNAs that are deregulated during aging, we isolated the hippocampal CA1 region of 3-  and 16-month-old mice. We isolated neuronal and glial nuclei by performing FACS sorting for NeuN, isolated RNA, generated libraries and performed total RNA sequencing

first: Sophie

last: Schroeder

first: M. Sadman

last: Sakib


title: Uridine Metabolism as a Targetable Metabolic 'Achilles' Heel' for chemo-resistant B-ALL

first: Yuxuan

last: Liu

state: California

address: 265 Campus Drive

department: Pediatrics

summary: Relapse continues to limit survival for patients with B-cell acute lymphoblastic leukemia (B-ALL). Previous studies have independently implicated activation of B-cell developmental signaling pathways and increased glucose consumption with chemo-resistance and relapse risk. Here, we connect these observations, demonstrating that B-ALL cells with active signaling, defined by high expression of phosphorylated ribosomal protein S6 (“pS6+ cells”), are metabolically unique and glucose dependent. Metabolic flux and carbon tracing confirms pS6+ cells to be highly glycolytic and notably sensitive to glucose deprivation, relying on glucose for de novo nucleotide synthesis. Uridine, but not purines or pyrimidines, rescues pS6+ cells from glucose deprivation, demonstrating uridine to be essential for their survival. Active signaling in pS6+ cells drives uridine production through activating phosphorylation of carbamoyl phosphate synthetase (CAD), the enzyme catalyzing the initial steps of uridine synthesis. Inhibition of signaling abolishes glucose dependency and CAD phosphorylation in pS6+ cells. Primary pS6+ cells demonstrate high expression of uridine synthesis proteins, including dihydroorotate dehydrogenase (DHODH), the rate-limiting catalyst of de novo uridine synthesis. Gene expression demonstrates that increased expression of DHODH is associated with relapse and inferior event-free survival after chemotherapy. Further, the majority of B-ALL genomic subtypes demonstrate activity of DHODH. Inhibiting DHODH using BAY2402232 effectively kills pS6+ cells in vitro with its IC50 correlated with the strength of pS6 signaling across 14 B-ALL cell lines and patient-derived xenografts (PDX). In vivo DHODH inhibition prolongs survival and decreases leukemia burden in pS6+ B-ALL cell line and PDX models. These findings link active signaling to uridine dependency in B-ALL cells and associate this with risk of relapse. Targeting uridine synthesis through DHODH inhibition offers a promising therapeutic strategy for chemo-resistant B-ALL as a novel therapeutic approach for relapsed disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sorted pre-B cell in comparing pS6+ and pS6- patients.

first: Jolanda

last: Sarno

first: Pablo

last: Domizi

first: Kara

last: Davis


title: Functional gene regulatory networks and broad applications of the human expandable pancreatic progenitor-islet system [snATAC-seq]

city: Hangzhou

first: Saiyong

last: Zhu

state: Zhejiang

address: 866 Yuhangtang Rd.

department: Life Sciences Institute

institute: Zhejiang University

summary: Investigating the precise gene regulatory programs directing pancreatic differentiation provides insights into the mechanisms of pancreatic development and diabetes progression. Here, we performed integrated single-cell multi-omic analyses of the expandable pancreatic progenitor (ePP)-islet system. We defined the dynamic transcriptomic and chromatin landscapes of pancreatic differentiation, inferred the sophisticated gene regulatory networks (GRNs) that govern ePP self-renewal, endocrine specification and islet function, and identified the essential roles and interesting mechanisms of the NKX2.2-CLEC16A/endosomal pathway axis during cell-fate transitions. We have obtained interesting observations that are human specific not observed in mouse models (e.g., CLEC16A-related diabetes mechanisms), and further took advantage of the ePP-islet system to identify pharmacological rescuers. Notably, this study highlights the ePP-islet system as a very powerful platform for uncovering the molecular mechanisms of cell fate decision and rich information for further optimizing the differentiation process. With further optimization and better understanding, the ePP-islet system will undoubtedly have very broad applications, including disease modeling, drug discovery, and regenerative medicine.

overall_design: For snATAC-seq experiments, ePP-WT, EP-WT, WT-R7d5 cells were collected. [snATAC-seq]

first: Xiaojie

last: Ma

first: Guo

last: Chen

first: Liling

last: Jiang


title: Comparative transcriptomic analysis of CD83+ly75+GCB cells in wild type and Gls B knockout models

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

summary: This study aims to characterize the transcriptome in wild type and Gls B KO CD83+ly75+GCB cells, and find the potential mechanism of the Gls B KO CD83+ly75+GCB cells。

overall_design: CD83+ly75+GCB cells from 4 wild type mice and 4 Gls B KO mice.

first: Xiaoming

last: Wang

first: Jingjing

first: Yuliang


title: Genome-wide maps of H3K27me3 modification in wild type and Gls CD19cre B KO  or Efnb1 ai3 B KO or Kdm6b OE  CD83+ly75+GCB cells

summary: This study aims to characterize the H3K27me3 modification in wild type and Gls CD19cre B KO  or Efnb1 ai3 B KO or Kdm6b OE   CD83+ly75+GCB cells, and find the potential mechanism of the Gls CD19cre B KO  or Efnb1 ai3 B KO or Kdm6b OE   CD83+ly75+GCB cells。

overall_design: CD83+ly75+GCB cells from 2 wild type mice , 1 CD19cre B KO mice, 2 EV mice, 2 Kdm6b overexpression mice, 1 Efnb1cre ai3 B KO mice.


title: Comparative transcriptomic analysis of  germinal center B cells between DN subcluster and DP subcluster.

summary: This study aims to characterize the transcriptome between DP subcluster and DN subcluster of  germinal center B cells, and find the differential mechanism between DP subcluster and DN subcluster of  germinal center B cells。

overall_design: Germinal center B cells from 3 wild type mice, each wild type mice with both DN subcluster and DP subcluster.


title: Functional gene regulatory networks and broad applications of the human expandable pancreatic progenitor-islet system [scRNA-Seq]

overall_design: For scRNA-seq experiments, ePP-WT, EP-WT, WT-R7d5 cells and WT/C16-KO cells at R6d8 were collected.


title: Cellular and transcriptional trajectories of adult neural fate specification in a sea anemone

first: Heather

last: Marlow

address: 920 E 58th Street

department: Organismal Biology and Anatomy

institute: University of Chicago

summary: We investigated the cellular and transcriptional trajectories of adult neurogenesis in the sea anemone Nematostella vectensis through single-cell transcriptome analysis of Elav>KikGR+, FoxL2>KikGR+, SoxC>KikGR+ body wall with mesenteries (no oral region) adult samples.

overall_design: Adult sea anemones (Nematostella vectensis) with a transgenic photoconvertible reporter (either Elav>KikGR, SoxC>KikGR, or FoxL2>KikGR) were photoconverted. At 2, 4 or 7 days post-photoconversion, animals were amputated below the pharynx and the body wall with mesenteries region was dissociated into single cells, KikGR+ cells were sorted using Fluorescence-Activated Flow Cytometry (FACS) into individual wells of 384-well plates. Single cell RNA-Seq libraries were generated with the MARS-Seq protocol (one scRNA-Seq library for each half-plate). Each sample here is one of 84 half-plate scRNA-Seq library.

first: Flora

last: Plessier


title: Functional gene regulatory networks and broad applications of the human expandable pancreatic progenitor-islet system [RNA-Seq]

overall_design: For RNA-seq experiments, WT/C16-KO cells and WT/N2-KO cells at R6d8 were collected.


title: Transcriptomic analysis of RNA (mRNA/ lncRNA/ circRNA) expression and epitranscriptomic profiling of N4-acetylcytidine-related RNA (mRNA/ lncRNA/ circRNA) acetylation in renal cortex from mice with ischemia reperfusion injury

city: guangzhou

first: peng

last: wang

address: 1838 North Guangzhou Avenue

institute: Southern Medical University

summary: N4-acetylation of cytidine (ac4C) in RNA are crucial for regulating the expression level and promoting the translate efficiency of mRNA. However, epitranscriptomic profiling of ac4C-related RNA (mRNA/ lncRNA/ circRNA) acetylation in renal cortex are largely unknown. Therefore, we profiled the transcriptome-wide ac4C modification in mRNA/ lncRNA/ circRNA in renal cortex from either ischemia reperfusion-acute kidney injury (I/R-AKI) mouse or Sham-operated mouse. At the same time, the expression levels of mRNA/ lncRNA/ circRNA were also evaluated by the sequencing experiment in input group. Therefore, this is an experiment for quantifying both the expression levels and the ac4C modification alterations in mRNA/ lncRNA/ circRNA within renal cortex from I/R-AKI mouse.

overall_design: To quantify both the expression levels and the ac4C modification alterations in mRNA/ lncRNA/ circRNA within renal cortex from I/R-AKI mouse (n=3) or  Sham-operated mice (n=3).

first: Peng

first: Tongtong


title: single cell analysis from prostates from PTEN(i)pe-/- and PTEN/VDR(i)pe-/-

first: Gilles

last: Laverny

address: 1 rue Laurent fries

country: France

institute: IGBMC

summary: Prostate cancer (PCa)-related deaths highly corelate with its metastatic spread due to limited efficiency of current therapies. In addition, the cases of de novo metastatic hormone-naïve prostate cancer (mHNPC) are increasing, highlighting the urgent need to identify novel biomarkers and treatment strategies for PCa spread. The impact of vitamin D receptor (VDR) signaling on prostate tumorigenesis remains unknown despite several epidemiologic studies suggesting its preventive role. Here, the consequences of VDR loss in prostatic epithelial cells (PECs) are studied using a relevant mouse model of PCa, Pten(i)pe−/− mice. We show that loss of VDR promotes oxidative stress in prostatic neoplasia that in turn enhances PECs proliferation. Moreover, VDR-loss leads to higher CXCL5 secretion by PTEN-deficient PECs, enhancing immunosuppressive neutrophils infiltration in prostates. Additionally, our data highlight elevated circulating neutrophil levels as a biomarker for PTEN-deficient PCa dissemination to the liver, and show the efficiency of targeting neutrophil chemotaxis to limit cancer spread. Overall, this work demonstrates how vitamin D signaling slows down PTEN-loss driven tumorigenesis and suggests new therapeutic and diagnostic strategies for mHNPC.

overall_design: 2 samples were analyzed, and prepared from dissociated prostates

first: Kateryna

last: LEN

last: LAVERNY


title: Study of vitamin D signaling pathways during the initiation of prostate cancer

summary: To determine the mechanism underlying the role of VDR in prostatic epitheliales cells during prostate cancer, bulk RNA- sequencing will be performed on sorted luminal cells from PTEN(i)pe-/- and PTEN/VDR(i)pe-/- mouse 1M-3M AGI.

overall_design: Total RNA was isolated from FACS-isolated luminal cells using TRI Reagent (Molecular Research Center, Inc.) and RNeasy Kits (Qiagen). cDNA libraries were generated from 600 ng RNA with an integrity number > 8 using the Stranded mRNA-seq Lib Prep Kit (Illumina), according to the manufacturer’s instructions, quantified and checked for quality using capillary electrophoresis. Fifty base pair single-read sequencing was performed on a NextSeq 2000 (Illumina) following the manufacturer’s instructions. Reads preprocessing steps were performed using cutadapt 1.10, reads were mapped onto the mm10 assembly of Mus musculus genome using STAR version 2.5.3a. Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1, with annotations from Ensembl version 108 and “union” mode. Only non-ambiguously assigned reads were retained for further analyses.


title: Bruton's tyrosine kinase inhibitors rescue neuronal impairment caused by B cell-mediated lymphotoxin-α release

city: Mainz

first: Neuroimmunology

last: Mainz

address: Langenbeckstr. 1

department: Neurology

institute: University Medical Center of the Johannes Gutenberg University Mainz

summary: Although B cell depletion slows disability accrual in people with multiple sclerosis (pwMS), the role of B cells in MS-associated neuronal injury remains elusive. B cells release cytokines such as lymphotoxin-α (LTα), and this proinflammatory protein is also present in the cerebrospinal fluid (CSF) and meninges of pwMS. B cell-specific ablation of LTα alleviates disease severity in a preclinical model of MS. To further study the impact of B cell-derived cytokines on neuronal function, we performed patch-clamp recordings on human iPSC-derived neurons. Coculture with proinflammatory human B cells led to depolarization and aberrant firing. Pretreatment of proinflammatory B cells with a Bruton's tyrosine kinase inhibitor (BTKi), reported in patients to beneficially affect disability progression even in the absence of inflammatory relapse activity, prevented neuronal impairment and inhibited LTα release from B cells. Blocking LTα, tumor necrosis factor receptor 1 (TNFR1), or receptor-interacting protein kinase 1 or 3 also prevented neuronal impairment, but blocking TNFα or LTβ had no such effect. Neuronal impairment was reversible by BTKi or blockage of LTα, and this reversibility was dependent on the activity of acid sphingomyelinase. In pwMS, LTα correlated with elevated neurofilament light chain (NfL) abundance in CSF, and anti-CD20 B cell-depletion therapy led to a reduction in circulating LTα, supporting the role of B cells as a regulator for LTα. These findings highlight the negative impact of B cell-derived LTα on neurons and suggest potential treatment avenues for MS-associated neuronal injury.

overall_design: human B cells were isolated from PBMCs and treated with BTKi (Evobrutinib, 1µM)or vehicle during their 3d stimulation before cells were detached and RNA was isolated

first: Paul

last: Götz

first: Nesrin

last: Sharif

first: Nicholas

last: Hanuscheck

first: Josef

last: Shin

first: Frauke

last: Zipp


title: Systemic Role of the IbmiR168-3p-IbKTN80 Module in Jasmonate Biosynthesis Pathway in Sweet Potato After Wounding

city: Taipei 106319

first: Shih-Tong

last: Jeng

state: Taipei

address: No. 1, Sec. 4, Roosevelt Rd.

department: Institute of Plant Biology

country: Taiwan

institute: National Taiwan University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) control their target genes by RNA cleavage or translation inhibition. The regulation of miRNA in the local leaves of plants after wounding has been studied, but its systemic effect is less understood. In this study, wounding-induced miR168-3p in the systemic leaves of sweet potato (Ipomoea batatas cv. Tainung 57) was analyzed. Bioinformatics analysis indicated that the target gene of miR168-3p is IbKTN80, which encodes the katanin p80 subunit. Their relationship was confirmed by agroinfiltration with transient expression of primary miR168 and IbKTN80 transcript. Transgenic sweet potatoes overexpressing and silencing miR168-3p further confirmed that IbKTN80 was the target gene of miR168-3p. Moreover, IbKTN80 is homologous to AtKTN80.2, and the expression of IbKTN80 could recover the functional defectiveness of the AtKTN80.2 in Arabidopsis treated with abscisic acid. IbKTN80, similar to AtKTN80.2, regulated MYC2, which is involved in the jasmonate (JA) signaling and biosynthesis. Conclusively, wounding induced the systemic generation of miR168-3p, which repressed the expression of IbKTN80. The miR168-3p-IbKTN80 module was involved in JA regulation and may participate in the signal transduction of systemic effect.

overall_design: RNA-seq and sRNA-seq profiling of systemic leaves from wounded and non-wounded Ipomoea batatas cv. Tainung 57.

first: Yi-Ching

last: Chiu

first: Cheng-Chung

last: Huang

first: Yu-Chi

last: King


title: Urolithin A rewires inter-organellar communication via calcium signaling to promote mitophagy and longevity

city: Athens

first: Konstantinos

last: Palikaras

address: Mikras Asias 75

department: Physiology

country: Greece

institute: Medical School, National and Kapodistrian University of Athens

summary: Mitochondrial dysfunction and mitophagy deregulation are hallmark features of aging and age-related pathologies. Urolithin A (UA), a potent mitophagy inducer, is known to confer neuroprotection, maintain muscle integrity, and extend healthspan and lifespan across diverse species. Nonetheless, the molecular mechanisms underlying UA-mediated mitophagy remain largely unknown. Here, we demonstrate that UA treatment modulates cytosolic calcium levels, which are essential for initiating robust mitophagy in both neurons and muscles. Transcriptomic and proteomic analyses reveal that UA facilitates the reorganization of inter-organellar communication between endoplasmic reticulum (ER), lysosomes and mitochondria; processes that are highly dependent on calcium signaling. Our findings suggest that UA induces calcium release from the ER and enhances lysosomal activity, while downstream uptake of released calcium from mitochondria, ultimately leads to mitochondrial fission and the successful execution of mitophagy. Consistently, calcium chelation abolishes UA-induced mitophagy, leading to impaired muscle function and diminishes lifespan extension, underscoring the critical role of calcium dynamics. We further found that UA-induced calcium elevation triggers mitochondrial biogenesis through the activation of UNC-43/CaMKII and SKN-1/Nrf2; these pathways are also critical for healthspan and lifespan extension. In human cells, UA supplementation not only induces mitophagy but also enhances mitochondrial metabolism and prevents stress-induced senescence in a calcium-dependent manner. Ultimately, our findings uncover the mechanistic insights of UA-mediated geroprotection and underscore the central role of calcium dynamics in orchestrating the crosstalk and functional wiring of different cellular compartments, thereby sustaining energy homeostasis and overall organismal physiology.

overall_design: Four age-synchronized populations of wild type (N2) C. elegans, treated with 50μM of Urolithin A from the L4 stage until day 4 of adulthood, were harvested independently and each was processed as an individual sample. Four additional populations were harvested in the absence of Urolithin A and were used as control samples. Total RNA was extrected from each sample and used for library preparation and RNAseq analysis to obtain gene expression profiles of Urolithin A-treated vs control animals.

first: Borbolis

last: Fivos

first: He

last: Haijun

first: Palikaras

last: Konstantinos


overall_design: cultured human iPSC derived neuons were treated with BTKi (Evobrutinib, 1µM) or vehicle for 24h before cells were detached and RNA was isolated


title: TWIST1 drives endothelial-to-mesenchymal-transition to stabilize atherosclerotic plaques [single cell RNA-seq]

city: London

last: Evans

address: Charterhouse square

institute: QMUL

summary: Single cell RNA sequencing (scRNA-seq) was used to analyse the diversity of ECs in the atherosclerotic mouse aorta, as well as the effect of endothelial-specific Twist1 deletion on aortic endothelial cells in mice exposed to a high fat diet.

overall_design: 8-10 week old mice were given a high fat diet for 8 weeks. Aftes this, they were injected with tamoxifen for 5 consecutive days to induce gene deletion, and they were fed a high fat diet for 6 weeks longer. The aorta from Twist1 EC-KO mice and  Twist1 EC-WT mice was dissected and digested. Single endothelial cells were isolated by Fluorescence-activated cell sorting (FACS), selecting CD45-, CD31+ and Topro3- cells. Cells were analyzed using scRNAseq.

first: Mark

last: Dunning

first: Blanca

last: Tardajos Ayllón


title: Functional characterisation of tumour suppressor PDCD4 reveals a previously undisclosed role in the control of cell adhesion

city: Cambridge

first: Veronica

last: Dezi

address: Tennis Ct Rd

department: MRC Toxicology Unit

institute: University of Cambridge

summary: PDCD4 is a multifunctional RNA binding protein which has tumour suppressor function. To more fully understand how dysregulation of this protein contributes to carcinogenesis we have carried out a comprehensive analysis of the role of PDCD4 in RNA metabolism in untransformed epithelial cells. We show that PDCD4 predominantly localises in the nucleus, where it interacts with proteins involved in a range of different RNA metabolic processes. We find that PDCD4 knockdown is associated with significant changes in either the expression or splicing of a number of transcripts, although it appears to have an indirect role in splicing. We identified the RNA targets of PDCD4 using iCLIP and observed an enrichment in binding to transcripts encoding cell adhesion and structural proteins. Consistent with these data, we show that PDCD4 acts as a general regulator of cell adhesion, which in a tumour setting would increase the metastatic potential of cells, and demonstrate that the nuclear localisation of PDCD4 is crucial in this process. Overall, the information obtained in untransformed cells provides new perspective for the role of PDCD4 as a tumour suppressor.

overall_design: We knocked down PDCD4 with 10nM siRNAs for 48 hours (siPDCD4) and compared the effects on gene expression to control cells (siCT)


title: single-cell RNAseq of transferred B1-8 antigen-specific B cells from 8-week-old C57BL/6J mice

first: Yuchao

last: Jing

summary: The aim of this study is to characterize the accurate cell cluster of  transferred B1-8 antigen-specific B cells.

overall_design: 0.4×10e6 transferred B1-8 antigen-specific B cells were sorted from NP-OVA immunized C57BL/6J mice for single cell RNAsequencing.

first: Xiaoming

last: Wang

first: Jingjing

last: Chen

first: Yuliang


summary:
PDCD4 is a multifunctional RNA binding protein which has tumour suppressor function. To more fully understand how dysregulation of this protein contributes to carcinogenesis we have carried out a comprehensive analysis of the role of PDCD4 in RNA metabolism in
untransformed epithelial cells. We show that PDCD4 predominantly localises in the nucleus, where it interacts with proteins involved in a range of different RNA metabolic processes. We find that PDCD4 knockdown is associated with significant changes in either the expression or splicing of a number of transcripts, although it appears to have an indirect role in splicing. We identified the RNA targets of PDCD4 using iCLIP and observed an enrichment in binding to transcripts encoding cell adhesion and structural proteins. Consistent with these data, we show that PDCD4 acts as a general regulator of cell adhesion, which in a tumour setting would increase the metastatic potential of cells, and demonstrate that the nuclear localisation of PDCD4 is crucial in this process. Overall, the information obtained in untransformed cells provides new perspective for the role of PDCD4 as a tumour suppressor.

overall_design: We performed iCLIP and compared the RNAs bound to PDCD4 to those attached to the IgG control


title: Genome-wide maps of H3K27me3 and H3K4me3 modification in different subclusters of  B cells

summary: This study aims to characterize the H3K27me3 and H3K4me3 modification in different subclusters  B cells.

overall_design: Different subclusters of  B cells in one wild type mice, one part for H3K4me3, the other part for H3K27me3.


title: Renal tubular VMP1 protects against acute kidney injury via facilitating autophagic flux

city: nanjing

first: yang

last: wenwen

address: No. 163 Xianlin Avenue, Qixia District, Nanjing

institute: life science school of nanjing university,china

summary: Acute kidney injury (AKI) is intricately linked to autophagy. Our study investigates the pivotal role of the autophagy-associated protein VMP1 in the pathogenesis and progression of AKI.

overall_design: 48 hours after HK2 cells were transfected with FLAG-VMP1 plasmid, RIP (RNA immunoprecipitation) was performed using Flag antibody magnetic beads, and the extracted RNA was sequenced by transcriptome.The protocol of RIP:To perform an RNA Binding Protein Immunoprecipitation (RIP) assay, first lyse cells in a buffer containing protease and RNase inhibitors. Pre-clear the lysate with protein A or G beads, then add specific antibodies against the target RNA-binding protein and incubate overnight at 4°C. After incubation, add the beads again and continue to incubate for several hours to allow binding. Wash the beads extensively to remove non-specific interactions, and then elute the bound RNA. Finally, extract and analyze the RNA using methods such as RT-qPCR or RNA sequencing to identify the associated RNA species.

first: Wenwen

last: Yang

first: Fenglian

last: Zhou


title: Comparative transcriptomic analysis of  germinal center B cells between DN subcluster and DP subcluster

overall_design: Germinal center B cells from 4 wild type mice, each wild type mice with both DN subcluster and DP subcluster.


title: RNA Editing for the Treatment of Alpha-1 Antitrypsin Deficiency

first: Jigar

last: Desai

address: 733 Concord Avenue

institute: Wave Life Science

summary: Alpha-1 antitrypsin deficiency (AATD) is both a gain- and loss-of-function disease that impacts the liver and lung.1 Most severe cases result from a homozygous missense mutation in the SERPINA1 gene (Z mutation). While current therapies and those in development may ameliorate lung or liver disease, few are designed to address both.1 We have developed SERPINA1-994, a N-Acetylgalactosamine-conjugated chemically modified oligonucleotide that elicits adenine-to-inosine RNA editing using endogenous adenosine deaminases acting on RNA enzymes, to correct SERPINA1 Z transcripts. We show that SERPINA1-994 edits 50% of the Z transcript in hepatocytes of NSG-PiZ mice, which increases total serum AAT levels and induces the production of wild-type protein. SERPINA1-994 addresses loss of AAT function in lung by increasing the neutrophil elastase inhibition capacity of mouse serum and gain-of-function in liver by decreasing protein aggregation, decreasing inflammation and correcting gene expression patterns. SERPINA1-994 relies on a clinically proven delivery technology and directs highly specific RNA rather than DNA editing, so there is no risk for permanent off-target effects. Overall, these data suggest that SERPINA1-994 changes a ZZ homozygous state, which is associated with a high risk for AATD, to a low-risk MZ-like phenotype.

overall_design: NSG-PiZ mice, a model for AATD that expresses the human SERPINA1 Z transgene, were treated with AIMERs to restore WT SERPINA1. Mutant mice were treated with AIMER to correct mutation and the resulting transcriptome was examined to observe both AIMER editing as well the restoration of a healthier mouse transcriptome after AIMER editing

first: Prashant

last: Monian

first: Chikdu

last: Shivalila

first: Genliang

last: Lu

first: Keith

last: Bowman

first: Marissa

last: Bylsma

first: Michael

last: Byrne

first: Megan

last: Cannon

first: Alyse

last: Faraone

first: Frank

last: Favaloro

first: Anamitra

last: Ghosh

first: Jack

last: Godfrey

first: Nidia

last: Hernandez

first: Olivia

last: Huth

first: Naoki

last: Iwamoto

first: Tomomi

last: Kawamoto

first: Jayakanthan

last: Kumarasamy

first: Pachamuthu

last: Kandasamy

first: Anthony

last: Lamattina

first: Muriel

last: Lemaitre

first: Amber

last: Lindsey

first: Fangjun

last: Liu

first: Richard

last: Looby

first: Khoa

last: Luu

first: Jake

last: Metterville

first: Ik-Hyeon

last: Paik

first: Qianli

last: Pan

first: Erin

last: Purcell-Estabrook

first: Jeanette

last: Rheinhardt

first: Mamoru

last: Shimizu

first: Kuldeep

last: Singh

first: Stephany

last: Standley

first: Carina

last: Thomas

first: Snehlata

last: Tripathi

first: Hailin

first: Ryan

last: Yordanoff

first: Yuan

last: Yin

first: Hui

last: Yu

first: Cynthia

last: Caracta

first: Padma

last: Narayanan

first: Paloma

middle: H

last: Giangrande

first: Chandra

last: Vargeese


title: Comparative transcriptomic analysis of pre-plasma germinal center B cells in wild type and Kdm6b B knockout models

first: Yuchao

last: Jing

summary: This study aims to characterize the transcriptome in wild type and Kdm6b B KO pre-Plasma germinal center B cells, and find the potential mechanism of the Kdm6b B KO pre-Plasma germinal center B cells。

overall_design: Pre-Plasma germinal center B cells from 6 wild type mice and 6 Kdm6b B KO mice.

first: Xiaoming

last: Wang

first: Jingjing

last: Chen

first: Yuliang


title: Assessment of the molecular consequences associated with loss of dysferlin expression in hiPSC-derived muscle cells from LGMD R2 patients.

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

summary: LGMD R2 is a rare genetic disorder characterized by progressive proximal muscle weakness and wasting caused by a recessive loss of function of dysferlin, a transmembrane protein controlling plasma membrane repair in skeletal muscles. Despite major advances in biotherapies in recent years, there is currently no curative treatment available for LGMD R2, or dysferlinopathies in general. This failure can be explained in part by our lack of understanding of the functions performed by dysferlin within the muscle fiber. Indeed, despite the identification of dysferlin's role in membrane repair, intracellular vesicular trafficking or calcium homeostasis, we do not know which of these functions or combination of functions is most involved in the pathophysiological development of dysferlinopathies. It also seems highly likely that other dysferlin functions have yet to be discovered. In this aim, we generated hiPSC-derived skeletal muscle model and investigated the molecular consequences associated with loss of dysferlin expression by performing a comparative gene expression profiling between control and LGMD R2 myotubes.

overall_design: 6 samples were analyzed with 3 replicates per condition: 3 WT hiPSC-derived myotubes (control) 3 Limb-Girdle Muscular Dystrophy type R2 (LGMD R2) hiPSC-derived myotubes

first: Céline

last: Bruge

first: Xavier

last: Nissan

first: Margot

last: Jarrige

last: Polveche


title: Genome-wide maps of H3K27me3 modification in wild type and Kdm6b B KO pre-Plasma germinal center B cells.

summary: This study aims to characterize the H3K27me3 modification in wild type and Kdm6b B KO pre-Plasma germinal center B cells, and find the potential mechanism of the Kdm6b B KO pre-Plasma germinal center B cells。

overall_design: Pre-Plasma germinal center B cells from 2 wild type mice and 2 Kdm6b B KO mice.


title: RNA sequencing of hnRNPA1 knockdown in HeLa cells

city: Wuhan

first: Lan

last: Lin

address: 299 Bayi Road, Wuchang District

department: School of Life Sciences

institute: Wuhan University

summary: shRNA knockdown against hnRNPA1 in HeLa cells followed by RNA-seq.

overall_design: We performed  hnRNP A1 knockdown in HeLa cells and analyzed alternative splicing patterns by high-throughput RNA sequencing


title: Gene expression analysis of corneal endothelial cells in iridocorneal endothelial syndrome

city: Beijing

first: Jiaxin

last: Zhang

address: No.49 Garden North Road

department: Ophthalmology

institute: Peking University Third Hospital

summary: Iridocorneal endothelial (ICE) syndrome is a rare ocular disease affecting the anterior segment, characterized by progressive deterioration leading to significant complications, including corneal endothelial compensation and secondary glaucoma. The unclear etiology of this syndrome limits clinical management to symptomatic interventions. The abnormality of corneal endothelial cells (ICE cells) in patients with ICE syndrome is considered the initial step of this disease. This study endeavors to elucidate the transcriptomic profiles of ICE cells utilizing smart-seq2 single-cell RNA sequencing techniques.

overall_design: The Descemet's membrane from both patients with ICE syndrome and donors was harvested, tissue dissociated, and cells were retrieved under a microscope using a pipette. In each technical replicate, 1-5 cells were selected.

first: Jing

last: Hong


title: Analysis of three-dimensional enhancer network regulated by CTCF in CD4+ T cells [in situ Hi-C]

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

institute: Yonsei University College of Medicine

summary:
Purpose: We aim to analyze genome-wide changes in RNA expression, histone modifications, chromatin structure, and 3D genome organization in CD4+ T cells following CTCF depletion.
Conclusions: CTCF controls gene expression via 3D enhancer network in CD4+ T cells

overall_design: in situ Hi-C analysis for CTCF-WT and CTCF-KO CD4+ T cells with biological replicates

first: Eun-Chong

last: Lee

first: Woong-Jae

last: Jung

first: Sugyung


title: HEB factors restrain proliferation and effector gene programming in stem cell-like memory CD8 T cells

city: Toronto

first: Michael

last: Geuenich

address: 600 University Ave

institute: Lunenfeld Tanenbaum Research Institute

summary: Stem cell-like memory CD8 T cells are essential for maintaining long-term immunological memory. These cells arise directly downstream of TCR signaling during the primary immune response and persist by self-renewal. To understand how these cells are generated, we examined the role of HEB factors in memory T cell differentiation using HEB-deficient mice. In memory-polarizing cultures, CD8 T cells from HEB-deficient mice exhibited enhanced proliferation and accelerated memory T cell differentiation. Transcriptomic analysis revealed aberrant upregulation of immune response genes and decreased expression of genes promoting stem-ness in HEB-deficient cells. HEB-deficient mice also exhibited more abundant short-lived effector cells in response to a viral infection. However, these perturbations were not observed at later time points, and stem-like memory T cells were more abundant after infection in HEB-deficient mice. Consequently, manipulating HEB activity in T cell expansion cultures could hold significant promise for improving the effectiveness of immunotherapy.

overall_design: To investigate the role of HEB in CD8 T cell differentiation, WT and HEB cKO CD8+ naïve, stem-cell like memory (SCM), central memory (CM), and effector/effector memory (EM) T cells were generated in vitro with CD3/CD28 stimulation + IL-7 & IL-15 for 2 days and rested for one. Cells were then sorted and RNA was extracted for downstream sequencing with two biological duplicates per cell type pooled from independent experiments.

first: Joanne

last: Leung

first: Michele

last: Anderson

first: Kieran

last: Campbell


title: Analysis of three-dimensional enhancer network regulated by CTCF in CD4+ T cells [RNA-seq]

overall_design: RNA-seq analysis for CTCF-WT and CTCF-KO CD4+ T cells with biological replicates


title: Analysis of three-dimensional enhancer network regulated by CTCF in CD4+ T cells [ChIP-seq]

overall_design: ChIP-seq analysis for CTCF-WT and CTCF-KO CD4+ T cells with biological replicates


title: RNA sequencing of C. auris and C. albicans under different conditions

city: Shanghai

first: Wanxing

last: Xu

address: 227 South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Candida auris, listed as the “urgent antimicrobial resistance threat” by the CDC in 2023, is an emerging human fungal pathogen. It has resulted in several outbreaks in hospitals and other healthcare facilities which are associated with high mortality rates, ranging from 30 to 60% due to its extensive multidrug resistance to all three classes of antifungal agents (azoles, polyenes, and echinocandins). However, there is limited evidence on its virulence, pathogenicity determinants, and complex host-pathogen interactions4. Understanding the pathogenic mechanism is an important step toward rapidly addressing the new threats posed by C. auris. Here we performed a global transcriptomic analyses in the context of 32 stress conditions to explore the stress-response of C. auris. C. albicans was used for comparison.

sample_organism:
Candida albicans
Candidozyma auris

platform_organism:
Candida albicans
Candidozyma auris

overall_design: RNA sequencing profiles of C. auris (BJCA001) and C. albicans (SC5314), including wildtype, knockout and stress stimulation type

first: Chaoyue

first: Xiaoqing


title: LINC00862 Inhibits Hepatocellular Carcinoma via a RBM47-mediated Positive Feedback Loop

city: Weifang

first: Yingying

last: Jiang

state: Shandong

address: 7166 Baotong west Road

institute: Weifang Medical University

summary: Hepatocellular carcinoma (HCC) continues to claim a significant number of lives worldwide, yet the molecular drivers behind its progression remain elusive. Despite the annotation of thousands of long non-coding RNAs (lncRNAs) as transcriptional products, their specific roles in suppressing HCC remain poorly understood. Here, we have uncovered LINC00862, a lncRNA that exhibits pronounced downregulation in HCC tissues and whose expression levels linked positively to favorable HCC outcomes, as a function of tumor stage and size. Through in-depth functional assays, we have established the formidable anti-tumor effects of LINC00862 on HCC processes such as proliferation, invasion, metastasis, and growth in both in vitro and in vivo settings. Mechanistically, our detailed RNA sequencing and quantitative proteomics analyses revealed that LINC00862's downstream target effector in HCC cells is RBM47. Our further experimentation strongly supports RBM47 as a central mediator of LINC00862's profound tumor-suppressive effects. Furthermore, we discovered the critical role of Hoogsteen pairing in LINC00862's ability to bind to the RBM47 promoter and recruit CHD5 as a transcription factor, promoting RBM47 transcriptional upregulation in HCC cells. It is intriguing to note that we also discovered that RBM47 is able to act as a transcription factor, positively regulating LINC00862 expression. Our identification of a positive feedback loop involving LINC00862 and RBM47 expands our comprehension of the intricate regulatory network that shapes HCC pathogenesis. LINC00862 represents a promising molecular marker for HCC diagnosis and therapeutics.

overall_design: Our study involved the overexpression of LINC00862 in HCCLM3 cells and the analysis of changes in RNA molecules and pathways using RNA sequencing, which allowed us to identify putative targets and pathways modulated by LINC00862.

first: Tao

last: Guo


title: Analysis of three-dimensional enhancer network regulated by CTCF in CD4+ T cells [PRO-seq]

overall_design: PRO-seq analysis for CTCF-WT and CTCF-KO CD4+ T cells with biological replicates


title: Analysis of three-dimensional enhancer network regulated by CTCF in CD4+ T cells

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

overall_design: Refer to individual Series


title: Effects of isoliensinine on gene expression in  Jurkat cells

first: Po

last: Hu

address: 138 Xianlin Rd

institute: Nanjing University of Chinese Medicine

summary: To investigate the effects of isoliensinine (IsoL) on gene expression in Jurkat cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the Jurkat cells treated with  20 μmol/L isoliensinine for 12 h.

first: Yang

last: Pan

first: Xiao

last: Ge

first: Guoxiang

last: Rui


title: single-cell RNAseq of splenic germinal center B cells from 8-week-old C57BL/6J mice

first: jingjing

last: chen

address: 101 Longmian Road

institute: Nanjing Medical University

summary: The aim of this study is to characterize the accurate cell cluster of germinal center B cells

overall_design: 0.4×10e6 germinal center B cells were sorted from SRBC immunized C57BL/6J mice  for single cell RNAsequencing.

first: Jingjing

last: Chen

first: Xiaoming

last: Wang


title: Molecular characterization of glioblatoma tissue samples

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: Patient-derived glioblastoma tissues were collected from discarded specimens obtained from GBM patients undergoing surgery at UT Health San Antonio under an IRB approved biorepository. The specimens were collected in accordance with the Declaration of Helsinki and approved by the Institutional Review Board (or Ethics Committee) of UT Health San Antonio. Patients provided informed consent for surgery and use of their tissues for research.The RNA was isolated and utilized for RNA-seq analysis. These GBM tissues were subtyped based on established TCGA gene expression-based molecular classifications.

overall_design: Patient-derived glioblastoma tissues were obtained from GBM patients undergoing surgery at UT Health San Antonio under an IRB approved biorepository. Total RNA from tissues was isolated using RNeasy mini kit according to the manufacturer's instructions (Qiagen, Valencia, CA).  Illumina TruSeq RNA Sample Preparation was performed following the manufacturer's protocol. Samples were run on an Illumina HiSeq 3000. The combined raw reads were aligned to UCSC hg19, and genes were annotated by Tophat. Genes were annotated and quantified by the HTSeq-DESeq pipeline.

first: Salvador

last: Alejo

first: Yidong

first: Gangadhara

last: Sareddy


title: Pyruvate carboxylase promotes glycolysis and progression of endometriosis by activating the AKT pathway

status: Public on Jan 11 2026

city: Hangzhou

first: Yongfeng

last: Wu

state: Zhejiang Province

address: No. 261 Huansha Road

institute: Hangzhou First People's Hospital

summary: Pyruvate carboxylase (PC) is a key metabolic enzyme, and its role in endometriosis progression remains unclear. This study aimed to investigate whether PC promotes endometriosis progression and explore its underlying mechanisms. Immunohistochemical analysis was used to detect PC expression in patient tissues; PC was knocked down or overexpressed in immortalized human endometriotic stromal cells (ihESCs) to assess proliferation (colony formation, EdU assay) and migration (Transwell assay) changes. Quasi-targeted metabolomics and RNA sequencing were applied to explore the effects of PC knockdown on downstream metabolism and pathways, and Western blotting was used to detect related protein changes. Additionally, an allogeneic endometriosis model in C57BL/6J female mice with AAV9-mediated PC overexpression was established to verify PC's in vivo effect. Results showed that PC expression was significantly upregulated in endometriosis patients; in vitro and in vivo experiments confirmed PC promotes endometriosis progression. Quasi-targeted metabolomics revealed PC enhances ihESCs glycolysis, while RNA sequencing and western blotting identified PC activates the PI3K-AKT pathway. Further studies with AKT agonist (SC79) and inhibitor (AZD5363) demonstrated PC promotes endometriosis glycolysis and progression via the AKT pathway. Moreover, PC inhibitors ZY-444 and octyl gallate inhibited ihESCs proliferation and migration, and ZY-444 suppressed endometriotic lesion growth in mice.

overall_design: IhESCs from the siPC and NC groups were subjected to RNA-seq, with three biological replicates per group.

first: Jinyi

last: Tong


title: Analysis of three-dimensional enhancer network regulated by CTCF in CD4+ T cells [HiChIP]

first: Hyoung-Pyo

last: Kim

overall_design: HiChIP-seq analysis for CTCF-WT and CTCF-KO CD4+ T cells with biological replicates

first: Eun-Chong

last: Lee

first: Woong-Jae

last: Jung

first: Sugyung


title: Transcriptional network controlled by Candida albicans treated by otilonium bromide (OB)

city: Taipei city

first: Li-Hang

last: Hsu

state: Taiwan (R.O.C)

address: No. 1, Sec. 4, Roosevelt Rd

department: Plant Pathology and Microbiology

institute: National Taiwan University

summary: To investigate potential target of otilonium bromide in C. albicans, we conducted the RNA-sequencing and found 145 genes with significantly different gene expressions (DGEs), which represented equal to or more than 2 fold-change in gene expression. Among these genes, there were 109 genes showing up-regulated in C. albicans treated with 0.5 μg/mL OB, and the other 36 were down-regulated. Main functions of these genes included oxidoreductase activity, heme binding and tetrapyrrole binding, and all functions analyzed from gene ontology indicated metal ion might play a critical role in otilonium bromide-mediated gene regulation.

overall_design: Total mRNAs extracted from C. albicans wild-type SC5314 treated or untreated with OB were analyzed using RNA sequencing.

first: Ying-Lien


title: Single-cell resolution drug effects on renin-angiotensin-aldosterone blockade in ZSF1 rat diabetic kidney disease

city: Berlin

first: Michael

middle: S

last: Balzer

address: Charitéplatz 1

department: Dpt. of Nephrology and Medical Intensive Care

institute: Charité - Universitätsmedizin Berlin

summary: Diabetic kidney disease (DKD) is the leading cause of renal failure worldwide. Overactivation of the renin angiotensin-aldosterone system (RAAS) is associated with detrimental outcomes in DKD patients. RAAS inhibitors such as enalapril have been used for decades as antiproteinuric, antihypertensive, and kidney protective agents. Still, the exact cell type of action and the main drivers of drug action are elusive. Here, we leverage state-of-the-art single-cell transcriptomics in the ZSF1 obese rat to elucidate potential target cells and driver molecules exerting enalapril drug effects. We report previously unknown injury cell states of the distal nephron, describe cathepsin D (Ctsd) as an important regulator of enalapril effects, and reveal Trem2+ residential macrophages as top receivers of distal nephron cell-cell communication. Finally, we show that our findings translate to humans and demonstrate that enalapril-associated gene signatures allow stratification of human kidney samples by disease-relevant outcome measures such as kidney function and fibrosis.

overall_design: Single cells were isolated from ZSF1 rat kidneys. N=4 Lean, n=4 Obese, n=3 Obese+enalapril

first: Jianfu

last: Zhou

first: Amin

last: Abedini

first: Ziyuan

last: Ma

first: Yanjuan

last: Hou

first: Tejaswini

last: Yadav

first: Manuel

last: Grundmann

first: Mira

last: Pavkovic

first: Katalin

last: Susztak


title: Gene expression of Sargassum micracanthum extracts on human deraml fibroblast cells

city: Gwangju

first: Hyeongwoo

last: Choi

address: 77, Yongbong-ro, Buk-gu

country: Afghanistan

institute: Chonnam National University

summary: Sargassum micracanthum, a brown macroalga rich in bioactive metabolites, has been widely recognized for its pharmacological potential. However, its role in collagen production and extracellular matrix (ECM) remodeling for skin regeneration remains largely unexplored. Therefore, this study examined the effects of S. micracanthum ethanolic extract on collagen-related pathways in human dermal fibroblasts (HDFs) through RNA sequencing and in vitro analysis. A total of 657 differentially expressed genes were identified, including 15 associated with collagen synthesis. Notably, COL4A1, COL4A2, COL5A3, and COL18A1 were significantly upregulated in the extract-treated group. Gene ontology analysis revealed enrichment in collagen-related terms, while WikiPathway analysis indicated upregulation of growth-factor-related pathways, which are crucial for cell proliferation, ECM remodeling, and tissue regeneration. In vitro experiments demonstrated a dose-dependent increase in collagen production, with a significant enhancement observed at 100 μg/mL (p < 0.05). These findings demonstrate the potential applicability of S. micracanthum in skin regeneration and biomedical therapies.

overall_design: RNA-seq profiling of S. micracanthum extract treatment group and control group.

first: Tae-Hee

first: Dong-Joo

last: Park

first: Se-Chang

first: Bonggi

first: Hyen-Woo

first: Won-Kyo