title: Immune-Epithelial Interactions and Tissue Remodeling in the Inflammatory Respiratory Nasal Tract [scRNA-seq]

first: Guanrui

last: Liao

summary: Chronic rhinosinusitis (CRS) is a common inflammatory disease of the nasal cavity and sinuses that affects millions of individuals worldwide. The complex pathophysiology of CRS remains poorly understood, with emerging evidence implicating diverse immune and epithelial cell types in the disease process. We employed single-cell RNA sequencing (scRNA-seq) in dissociated tissues to investigate the cellular and molecular heterogeneity of CRS with and without nasal polyps.

overall_design: Samples from patients with CRS with and without nasal polyps and healthy controls were collected and analyzed using single-cell RNA sequencing (scRNA-seq).

first: Jayakar

last: Nayak


title: CIRCADIAN MODULATION OF NEUTROPHIL FUNCTION DETERMINES CEREBRAL PERFUSION AND STROKE OUTCOME

status: Public on Nov 12 2025

city: Madrid

first: María

middle: Ángeles

last: Moro

address: C. de Melchor Fernández Almagro, 3

department: Cardiovascular Risk Factors and Brain Health

country: Spain

institute: CNIC

type: Expression profiling by high throughput sequencing

summary: Stroke is a leading cause of mortality and disability, driven by complex and time-dependent mechanisms that aggravate ischemic damage. Recent evidence indicates that infarct volumes fluctuate according to diurnal oscillations, both in mice and humans, with worse outcomes during the inactive phase of their circadian cycle. Here, we show that neutrophils are responsible for these circadian variations. By depleting neutrophils or blocking their circadian clock, differences in infarct volumes were abolished, suggesting that both the number of neutrophils and their circadian phenotype contribute to ischemic damage. Mechanistically, these differences were linked to the collateral circulation: cerebral blood flow measurements at different times after ischemia showed differential perfusion in the ipsilesional area. We found that, during the inactive mouse phase, neutrophil extracellular traps (NETs), were markedly elevated, coinciding with a reduction in ipsilesional blood flow, a higher percentage of intravascular neutrophils, and an increase in infarct volumes compared with the active phase. These findings underscore a crucial role of neutrophils, their circadian dynamics, and NET release as key drivers of ischemic damage, suggesting novel personalized therapeutic strategies based on circadian rhythms for the treatment of stroke.

overall_design: To elucidate whether circadian rhythms affect the transcriptional landscape of neutrophil heterogeneity during stroke in mice, we conducted single-cell RNA sequencing of DAPI-CD11b+Ly6G+ cells obtained from ischemic brain of mice under different conditions.

first: Sandra

last: Vazquez-Reyes

middle: I

last: Cuartero

first: Alicia

last: García-Culebras

middle: A


title: Bovine Formative Embryonic Stem Cell Plasticity in Embryonic and Extraembryonic Differentiation [ bulk RNA-seq]

status: Public on Nov 13 2025

city: Storrs

first: Yue

last: Su

address: 1390 Storrs Road

country: USA

institute: University of Connecticut

summary: Bovine embryonic stem cells (bESCs) can greatly enhance understanding of bovine embryonic development and applications for disease-resistance, biomedical and zoonotic pre-clinical models. However, formative bESCs with distinct morphology and complete differentiation capacity are still unreported. We document here the generation of bESCs which are pluripotent both in vitro and in vivo, and efficiently converted into neural progenitor cells (NPCs) and primordial germ cell-like cells (PGCLCs) by direct differentiation. These cells exhibited distinct metabolic features from human and mouse ESCs and early embryos. Formative bESCs contributed to a wide range of cell types within embryonic and extraembryonic tissues after aggregating with mouse and bovine embryos. The establishment of bovine formative ESCs with dual developmental plasticity represents a milestone for agricultural biotechnology and decoding the underlying mechanism of bona fide bovine pluripotency.

overall_design: To investigate the pluripotency of our bESCs, we performed RNA-seq of 6 formative bESC lines.

first: Ruifeng

last: Zhao

first: Yifei

last: Fang

first: Guangsheng

last: Li

first: Liangliang

last: Jin

first: Jiaxi

last: Liu

first: Jiaqi

last: Zhu

first: Neha

last: Mishra

first: Deborah

last: Kaback

first: Siu

middle: P

last: Yee

first: Chuzhao

last: Lei

first: Jingyue

middle: E

last: Duan

first: Xiuchun

middle: C

last: Tian

first: Young

last: Tang


title: The Function of Tetrameric MADS-box Transcription Factors in Floral Fate Determination [RNA-seq]

city: Berlin

first: Manuel

last: Neumann

address: Philippstr. 13

country: Germany

institute: HU Berlin

summary: MADS-domain transcription factors (TF) are critical in determining floral cell fate and floral organ identities. However, their function molecular mechanisms are still poorly understood. Here, we show that effective DNA-binding in closed chromatin and target gene regulation of APETALA1 (AP1), a  key floral MADS-box TF requires tetramerisation, indicating the fundamental role of tetrameric MADS-box TFs in floral cell fate programming.

overall_design:
ChIP-seq, ATAC-seq and RNA-seq datasets were generated with seedling tissues at different time points (2, 8, 24 and 48 hours) after dexamethasone induction. In addition, mock-treated seedlings were collected at different time points as a control. Two biological replicates were generated for each time point.
Please note that each processed data file was generated from both replicates and is linked to the corresponding *r1 sample records.

first: Kerstin

last: Kaufmann

first: Xiaocai

last: Xu


title: Effect of elastin insufficiency on gene expression in cultured human aortic smooth muscle cells

city: New Haven

first: Junichi

last: Saito

state: CT

address: 300 George Street, 7th Floor

department: Internal Medicine

institute: Yale University

summary: Defective elastin induces aortic smooth muscle cell hyperproliferation. To elucidate gene expression changes with elastin insufficiency, bulk RNA-seq was performed on  cultured human aortic smooth muscle cells treated with siRNA targeting elastin.

overall_design: Cultured human aortic smooth muscle cells were treated with scrambled RNA or siRNA-targeting elastin. Total RNA was extracted 72 hours after siRNA transfection and subjected to bulk RNA-seq.

first: Jui

middle: M

last: Dave

first: Daniel

last: Greif


title: Bovine Formative Embryonic Stem Cell Plasticity in Embryonic and Extraembryonic Differentiation [scRNA-seq]

first: Yue

last: Su

overall_design: scRNA seq data of D25 bESC-incorporated bovine chimeric embryos.

first: Ruifeng

last: Zhao

first: Yifei

last: Fang

first: Guangsheng

last: Li


title: The Function of Tetrameric MADS-box Transcription Factors in Floral Fate Determination [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design:
ChIP-seq, ATAC-seq and RNA-seq datasets were generated with seedling tissues at different time points (2, 8, 24 and 48 hours) after dexamethasone induction. In addition, mock-treated seedlings were collected at different time points as a control. Two biological replicates were generated for each time point.
Please note that each processed data file was generated from all replicates and is linked to the corresponding *r1 sample records.


title: The Splicing Factor PTBP1 Interacts with RUNX1 and is Required for Leukemia Cell Survival [Long Read]

status: Public on Nov 11 2025

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

summary: Runt-related Transcription Factor 1 (RUNX1) is essential for definitive hematopoiesis and is among the most frequently mutated genes in leukemia. Previous work from our lab demonstrated that Histone Deacetylase 1 (HDAC1), a known RUNX1 partner, is unexpectedly required for active transcription suggesting a non-histone role for HDAC1 regulating components of the RUNX1 complex. Here, we use proteomics, genomics, and long-read transcriptomics to identify novel RUNX1 interacting partners and decipher their role in gene regulation and RNA splicing in leukemia cells. We demonstrate that Polypyrimidine Tract Binding Protein 1 (PTBP1) interacts with RUNX1 in an HDAC1-dependent manner. Chromatin profiling revealed extensive genome-wide overlap in sites occupied by RUNX1 and PTBP1, with significant enrichment at promoters of actively transcribed genes. Loss of PTBP1 in AML cells led to widespread alterations in RNA splicing and decreased expression of genes whose promoters are bound by both factors, including metabolic genes. In agreement with these findings, we found that loss of PTBP1 reduced glycolysis and glucose uptake and ultimately caused cell death. Based on our data, we propose that the interaction between RUNX1 and PTBP1 facilitates expression of metabolic proteins essential for leukemia cell growth and survival.

overall_design: Long-read RNA-seq of MOLM-13 cells with PTBP1 shRNA knockdown and control, treated with doxycycline for 9 days

first: Arjun

last: Dhir

first: Alexander

last: Ethell

first: Riley

last: Watkins

first: Calvin

last: Lam

first: Kevin

last: Tur-Rodriguez

first: Jimmie

last: Persinger

first: Kasidy

middle: K

last: Dobish

first: Sipra

last: Panda

first: Shannon

last: Buckley

first: Samantha

last: Swenson

first: Sandipan

last: Brahma

first: Katherine

last: Hyde


title: The Function of Tetrameric MADS-box Transcription Factors in Floral Fate Determination [ATAC-seq]

first: Manuel

last: Neumann

first: Kerstin

last: Kaufmann

first: Xiaocai

last: Xu


title: Single-Cell Mapping Reveals Age-Related Alterations in Periosteal Progenitor Cells and Immune Microenvironment Impairing Bone Regeneration

city: Shanghai

first: Lei

last: Zhao

state: Shanghai

address: 500 Zhennan Road

country: China

institute: Tongji University

summary: Aging profoundly impacts bone homeostasis and regeneration, yet the cellular and molecular mechanisms underlying periosteal aging remain poorly understood. Using single-cell RNA sequencing, we profiled the periosteum of 3-, 9-, and 18-month-old mice, revealing age-related shifts in progenitor, neutrophil, and macrophage subpopulations. Aging reduced mesenchymal cell populations and impaired osteogenic potential, disrupting periosteal homeostasis. Periosteal progenitor subsets exhibited distinct aging trajectories: Dpt⁺ fibrous-layer cells undergoing early senescence, while Postn⁺ progenitors showed osteogenic decline. Aging also shifted immune profiles, increasing inflammatory Cd38hi macrophages and dysfunctional Nlrp3hi neutrophils, further disrupting bone homeostasis. Notably, aged progenitor cells upregulated CSF1 and CXCL signaling, driving macrophage and neutrophil infiltration, exacerbating bone loss. Our findings provide a comprehensive periosteal aging atlas, highlighting disrupted progenitor-immune crosstalk as a key driver of bone homeostasis imbalance and impaired regeneration, offering potential therapeutic targets for age-related bone disorders.

overall_design: Long bones were harvested from wild-type C57BL/6 J mice across three age groups: 3 months, 9 months, and 18 months, with six males per group (Aniphe Biolaboratory Inc.). The acquisition protocol was as follows: following cervical dislocation for euthanasia, the animals were sterilized by external application of 75% ethanol. The lower limbs were then aseptically dissected, and the overlying skin, muscles, fat, and other soft tissues were meticulously removed. The intact femur and tibia were subsequently isolated for further processing.

first: Chao

last: Wu


title: Altered thymopoiesis in thymoma is associated with defects in negative selection machinery and decreased Treg abundance

city: Paris

first: Alexandre

last: Lanau

address: 26 rue d'Ulm

department: Unité 830

country: France

institute: Institut Curie

summary: Thymomas are rare thymic epithelial tumors harboring a high but variable proportion of lymphocytes without obvious function. Auto-immunity is present in one third of patients at diagnosis. Herein, we performed a phenotypic, scRNAseq, and spatial analysis of both the T cells and tumoral cells. All stages of T cell development -from immature to mature- were present in the tumor suggesting active thymopoiesis in thymoma. However, multiple approaches suggest a maturation blockade at the DN-DP stages. In the mature T cell compartment, the frequency of Tregs was strongly decreased. Notably according to scRNAseq, the transcriptome of tumoral Thymic Epithelial Cells (tTEC) was most similar to that of non-tumoral medullary TEC but the expression of key molecules involved in positive and negative selection was defective. Multiplexed Immunohistochemical Consecutive Staining evidenced a loss of the cortex-medulla zoning in thymoma which may be related to a decrease expression of T cell targeted chemokines by tTEC. Altogether, these results suggest that the thymopoiesis present in thymoma is abnormal and may provide the grounds for the prevalent auto-immunity observed in this disease.

overall_design: Either tumor cells (CD45- Epcam+) or thymocytes (T cells selection kit milteny) were isolated. Thymocytes were sequenced using 10x 5’scRNA-seq paird with scTCR-seq kit. Tumor cells were sequenced using 10X 3’ scRNA-seq kit.

first: Clemence

last: Basse

first: Joshua

middle: J

last: Waterfall

first: Olivier

last: Lantz

first: Nicolas

last: Girard


title: The Splicing Factor PTBP1 Interacts with RUNX1 and is Required for Leukemia Cell Survival [CUT&Tag]

first: Jordan

last: Rowley

overall_design: CUT&Tag of RUNX1 and PTBP1 and CUT&RUN of H3K27me3, with IgG controls, in MOLM-13 cells

first: Arjun

last: Dhir

first: Alexander

last: Ethell

first: Riley

last: Watkins

first: Calvin

last: Lam

first: Kevin

last: Tur-Rodriguez

first: Jimmie

last: Persinger


title: A human iPSC-based neural spheroid platform for modeling glioblastoma infiltration using high-content imaging

city: London

first: Victoria

last: Tsang

state: Select a State

address: Charterhouse Square Campus

department: Translational Medicine and Therapeutics

country: United Kingdom

institute: Queen Mary University of London

summary: Glioblastoma is the most aggressive adult brain tumor, characterized by resistance to therapy and high recurrence due to diffuse infiltration. To mimic glioblastoma migration, we developed a physiologically relevant co-culture model, combining patient-derived glioblastoma cell lines with cortical-like neural spheroids differentiated from human induced pluripotent stem cells. Using high-content imaging, we demonstrate that GBM1 and GBM20 cell lines migrate directionally along axons toward neural spheroids in live imaging assays and infiltrate spheroids extensively in endpoint assays, unlike non-cancerous neural stem cells. A proof-of-principle drug screen identified PF-573228 (FAK inhibitor) and Motixafortide (CXCR4 inhibitor) as potent suppressors of GBM1 and GBM20 infiltration, respectively. Bulk RNA sequencing revealed gene expression profiles correlating with invasive behavior and drug sensitivity. This platform offers a valuable model for studying glioblastoma infiltration along axons and provides proof-of-principle that migration can serve as a measurable and actionable phenotype to screen therapeutic vulnerabilities in glioblastoma.

overall_design: Bulk RNA sequencing of patient-derived glioblastoma cell lines GBM1 and GBM20. Each line was snap-frozen as pellets containing 1 × 10^⁶ cells. Replicates included GBM1A and GBM1B for the GBM1 line, and GBM20A and GBM20B for the GBM20 line.

middle: S

first: Federica

last: Riccio

first: Hannah

last: Nudds

first: Jason

middle: D

last: Coombes

first: Heiko

last: Wurdak

first: Harry

last: Bulstrode

first: Ivo

last: Lieberam

first: Davide

last: Danovi

first: Aimee

last: Wilson


title: Simultaneous Targeting of KRAS and CDK4 Synergistically Induces Durable Growth Arrest in Pancreatic Cancer Cells [AsPC-1_RNA_Seq]

city: Göttingen

first: Maj-Britt

last: Paulsohn

address: Justus-von-Liebig-Weg 11

department: Department of Molecular Oncology

institute: University Medical Center Göttingen

summary: We show that the KRAS-G12D inhibitor MRTX1133 synergizes with the CDK4/6 inhibitor Palbociclib to eliminate pancreatic ductal adenocarcinoma (PDAC) cells (AsPC-1) harboring KRAS-G12D mutations. This synergy was especially pronounced following drug washout, indicating a durable cellular response. Mechanistically, the combinations induced sustained cell cycle arrest.

overall_design: RNA-Sequencing of AsPC-1 cells treated for 24 h with DMSO, Palbociclib (5 µM), MRTX1133 (0.5 µM) or the combination.

first: Matthias

last: Dobbelstein


title: PITX2 dosage-dependent pacemaker cell state changes underlie sinus node dysfunction and atrial arrhythmia-susceptibility

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: Reduced spatiotemporal transcription factor levels have been shown to affect traits, organism development and disease predisposition. Here, we investigated the impact of physiologically relevant increases in transcription factor dosage, which has remained largely unexplored. Patients with genomic deletions far upstream of PITX2 present with sinus node dysfunction (SND) and atrial fibrillation. We show that delB mice, which recapitulate the deletion-driven arrhythmia in patients, ectopically express PITX2 in sinus node pacemaker cardiomyocytes (PCs) in a highly heterogeneous pattern from early embryonic development onwards. During development, delB sinus nodes form subdomains of mildly affected PC and strongly affected PCs that have lost their PC identity and switched towards an atrial cardiomyocyte-like state in a PITX2 dosage-dependent manner. Compared to heterozygous delB mice, homozygous delB mice have more PITX2+ PCs that express on average more PITX2, form proportionally larger subdomains of strongly affected PCs and have much more severe SND and atrial arrhythmia susceptibility. Ectopic expression of PITX2 in human induced pluripotent stem cell-derived PCs resulted in PITX2 dosage-dependent transcriptional changes reminiscent of those observed in the sinus node subdomains of delB mice. These results show that genetically driven ectopic expression of PITX2 in PCs causes SND and increased susceptibility for atrial arrhythmias, illustrating how spatiotemporally-defined increases in transcription factor dosage translates into developmental defects and disease predisposition.

overall_design: iPSC-derived cariomyocytes were transduced with AAV6 virus to express PITX2c or mcherry (control). Cells were detached and used for 10X Genomics Chromium Single Cell RNA seq.

first: L

last: van der Maarel

first: M

middle: R

last: Mungroo

first: O

last: Mulleners

last: Rivaud

first: F

middle: H

last: Tiel Groenesteege

last: Fokkert

first: C

last: de Gier-de Vries

first: K

last: van Duijvenboden

first: B

last: Jensen

first: H

last: Devalla

first: V


title: Plagl1 and Lrrc58 control mammalian body size by triggering target-directed microRNA degradation of miR-322 and miR-503 [RNA-seq]

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: Precise control of microRNA (miRNA) expression is critical for normal development. An important mechanism of miRNA regulation is target-directed microRNA degradation (TDMD), a pathway in which the binding of miRNAs to specialized trigger RNAs induces ubiquitylation and decay of associated Argonaute (AGO) proteins by the ZSWIM8 ubiquitin ligase. ZSWIM8-deficient mice exhibit reduced body size, cardiopulmonary and neurodevelopmental defects, and perinatal lethality. Despite widespread dysregulation of miRNAs in these animals, the vast majority of presumptive trigger RNAs that induce decay of ZSWIM8-regulated miRNAs remain undefined. Here, using AGO crosslinking and sequencing of hybrids (AGO-CLASH), a high-throughput method for identifying miRNA binding sites, we report the identification of Plagl1 as a trigger for TDMD of miR-322-5p, and Lrrc58 and Malat1 as TDMD triggers for miR-503-5p in mouse embryonic fibroblasts (MEFs). In mice, deletion of the miR-322-5p and miR-503-5p trigger sites in the Plagl1 and Lrrc58 3' UTRs, respectively, abrogated TDMD of these miRNAs and resulted in miR-322/503-dependent embryonic growth restriction, recapitulating a key feature of the Zswim8—/— phenotype. Thus, these results demonstrate that the transcripts encoding Plagl1 and Lrrc58 regulate mammalian body size by inducing degradation of miR-322-5p and miR-503-5p and provide a valuable resource for identification of additional TDMD triggers.

overall_design: RNA seq on total RNA from mouse tissues from wildtype and trigger site KO mice at E18.5

first: Collette

last: LaVigne

first: Jaeil

last: Han

first: He

last: Zhang

first: Sihoon

last: Cho

first: Minseon

last: Kim

first: Komal

last: Sethia

first: Bret M

last: Evers

first: Asha

last: Acharya

first: Tsung-Cheng

last: Chang

middle: T


title: DUX4-induced HSATII RNA accumulation drives protein aggregation impacting RNA processing pathways

city: Seattle

first: Stephen

last: Tapscott

state: Washington

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

summary: RNA-driven protein aggregation leads to cellular dysregulation by sequestering regulatory proteins, disrupting normal cellular processes, and contributing to the development of diseases and tumorigenesis. Here, we show that double homeobox 4 (DUX4), an early embryonic transcription factor and causative gene of facioscapulohumeral muscular dystrophy (FSHD), induces the accumulation of stable intranuclear RNAs, including nucleolar-associated RNA and human satellite II (HSATII) repeat RNA. Stable intranuclear RNAs drive protein aggregation in DUX4-expressing muscle cells. Specifically, HSATII RNA sequesters m6A and m5C RNA methylation factors. Furthermore, HSATII-YBX1 ribonucleoprotein (RNP) complex formation is mediated by HSATII RNA accumulation, NSUN2 activity and RNA methylation. YBX-1 specifically associates with HSATII double-stranded RNA. Aberrant HSATII-RNP complexes affect key RNA processing pathways, including mRNA splicing. Differential splicing of genes mediated by HSATII-RNP complexes are associated with pathways known to be dysregulated by DUX4 expression. These findings highlight the broader influence of DUX4 on nuclear RNA dynamics and suggest that HSATII RNA could be a critical mediator of RNA processing regulation in DUX4-expressing cells. Understanding the impact of HSATII-RNP formation on RNA processing pathways provides valuable insight into the molecular mechanisms underlying FSHD.

overall_design: RNA sequencing from MB135 iDUX4ca inducible DUX4 myoblasts treated with either HSATII or control gapmers.

first: Sean

last: Bennett

first: Tessa

last: Arends


title: Supplementation with short-chain fatty acids and a prebiotic improves clinical outcome in Parkinson’s disease: A randomized double-blind prospective study [RNA-Seq]

city: Ramat Gan

first: Nissan

last: Yissachar

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University

summary: Background: Parkinson’s disease is associated with a dysbiotic, proinflammatory gut microbiome, disruptions to intestinal barrier functions, and immunological imbalance. Microbiota-produced short-chain fatty acids, such as propionic and butyric acid promote gut barrier integrity and immune regulation, but their impact on Parkinson’s disease pathology remains mostly unknown .Methods: In a randomized double-blind prospective study, 72 people with Parkinson’s disease received propionic and butyric acid and/or the prebiotic fiber 2′-fucosyllactose supplementation over 6 months in combination with existing Parkinson’s disease-specific therapy. Patients underwent complete neurological assessment and provided blood and stool samples before as well as 3 and 6 months after supplementation. Results: We observed improvement in motor and nonmotor symptoms, in addition to modulation of peripheral immunity and improved mitochondrial respiration in immunocytes. Postintervention microbiota remodeled inflammatory and barrier-related gene sets in gut organ cultures and improved in vitro barrier functions. Treatment response was associated with microbiome composition, distinct patterns of colonic transcription and permeability ex vivo. Multiobjective analysis revealed immune parameters associated with an optimal response to supplementation. Conclusion: Short-chain fatty acids ameliorate clinical symptoms in Parkinson’s disease patients and modulate intestinal and peripheral immunity.

overall_design: Colon organ cultures were infused with microbiota samples collected from PD patients at baseline and 6 months postintervention (n=8, all intervention groups included) or with sterile medium as an internal control.

first: Tobias

last: Hegelmaier

first: Alexander

last: Duscha

first: Christiane

last: Desel

first: Sabrina

last: Fuchs

first: Michal

last: Shapira

first: Sivan

last: Amidror

first: Qihao

last: Shan

first: Gabriele

last: Stangl

first: Frank

last: Hirche

first: Stefan

last: Kempa

first: András

last: Maifeld

first: Lisa-Marie

last: Würtele

first: Jana

last: Peplinski

first: Diana

last: Jauk

first: Gitali

last: Naim

first: Nuphar

last: Shidlovsky

first: Adva

last: Cohen

first: Yifat

last: Bennet

first: Lisa

last: Paschold

first: Claudia

last: Dumitru

first: Ute

last: Obermüller-Jevic

first: Svein-Olaf

last: Hustvedt

first: Nina

last: Timmesfeld

first: Ralf

last: Gold

first: Antonia

last: Zapf

first: Mascha

last: Binder

first: Ibrahim

last: Sandalcioglu

first: Sanaz

last: Mostaghim

first: Horst

last: Przuntek

first: Eran

last: Segal

first: Aiden

last: Haghikia


title: Blocking 6PGD restricts immunosuppression driven by the innate immune response in cancer

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: The pentose phosphate pathway (PPP) has always been relegated to the background of cellular metabolism, but our research identifies its unique and provocative influence on cell function, specifically in myeloid-derived suppressor cells (MDSCs). We’ve uncovered that 6-phosphogluconate dehydrogenase (6PGD), a rate limiting enzyme in this pathway, is not just a metabolic enzyme but a crucial determinant of MDSC behavior. While the IL-6/STAT3 axis propels 6PGD activity, it also empowers MDSCs to exert their immune-suppressive prowess. When we disrupt 6PGD – either through genetic knockout or pharmacological inhibition – an astonishing transformation occurs. The accumulation of 6-phosphogluconate (6PG) sets off a cascade involving JNK1-IRS-1 interaction and PI3K-AKT-pDRP1 signaling pathway, triggering mitochondrial fragmentation and dismantling oxidative phosphorylation (OXPHOS). This change in metabolism doesn’t just disrupt MDSC function; it transforms it stimulatory, leading to a strong anti-tumor response and making anti-PD1 therapies much more effective. Our results suggest we need to completely rethink the role of the PPP in cell function, with 6PGD emerging as a key target that could change the future of cancer immunotherapy.

overall_design: CD45+ cells were isolated Pgdfl/fl LysmCre (KO) and Pgdfl/fl (WT) AT3 tumor bearing mice and their transcriptomics profile was evaluated by single cell RNA sequencing (scRNA-seq).

first: Saeed

last: Daneshmandi

first: Eduardo

last: Gomez

first: Hemn

last: Mohammadpour


title: CDK4/6 and SHP2 mediate BRAF/MEK inhibitor resistance in Class 2 and 3 BRAF mutant cancers

city: Montreal

first: April

last: Rose

address: 3755 chem. de la côte ste Catherine

department: Lady Davis Institute

country: Canada

institute: McGill University

summary: Class 2 and 3 non-V600E BRAF mutations are oncogenic drivers in many cancer types.  Currently, there are no established targeted therapies with proven efficacy for cancers with non-V600E BRAF mutations. We developed the investigator-initiated, Phase II BEAVER clinical trial (NCT03839342) to evaluate the efficacy of BRAF and MEK inhibitors in patients with non-V600E BRAF mutations. The best objective response rate was 14% (3/21). By analyzing genomic data from patient tumors, circulating tumor DNA (ctDNA), patient-derived xenograft (PDX) models generated from enrolled patients, and Class 2 & 3 BRAF mutant cell lines, we discovered MAPK-dependent and independent mechanisms of resistance to BRAF/MEK inhibition. These mechanisms included the acquisition of new mutations in NRAS, MAP2K1, RAF1, and RB in ctDNA at the time of disease progression. CDK4/6 and SHP2 were identified as mediators of intrinsic resistance to BRAF/MEK inhibition in Class 2 & 3 BRAF mutant tumors. Therapeutic strategies combining CDK4/6 or SHP2 inhibitors with BRAF/MEK inhibitors were more effective than BRAF/MEK inhibitors alone in these cancers. https://doi.org/10.1038/s41467-025-68076-7

overall_design: RNA-seq profiling of PDX tumours at experimental endpoint treated with either Vehicle, Binimetinib+Encorafenib, Palbociclib, TNO155, Binimetinib+Encorafenib+Palbociclib, or Binimetinib+Encorafenib+TNO155. RNA-seq profiling of Non-V600 BRAF mutant cancer cell lines treated with DMSO or Binimetinib+Encorafenib for 24 hours.

first: Jennifer

last: Maxwell

first: Emmanuelle

last: Rousselle

first: Chantel

last: Mukonoweshuro

first: Islam

last: Elkholi

first: Melody

last: Riaud

first: Marco

last: Biondini

first: Erica

last: Cianfarano

first: Isabel

last: Soria-Bretones

first: Chantal

last: Tobin

first: Meghan

last: McGuire

first: Ian

last: King

first: Tong

last: Zhang

first: Trevor

last: Pugh

first: Zaid

last: Kamil

first: Marcus

last: Butler

first: Frances

last: Shepherd

first: Natasha

last: Leighl

first: Albiruni

last: Razak

first: Aaron

last: Hansen

first: Sam

last: Saibil

first: Philippe

last: Bedard

first: Peter

last: Siegel

first: Lillian

middle: L

last: Siu

first: David

middle: W

last: Cescon

first: Anna

last: Spreafico


title: Plagl1 and Lrrc58 control mammalian body size by triggering target-directed microRNA degradation of miR-322 and miR-503 [AGO-CLASH]

first: Joshua

last: Mendell

overall_design: AGO CLASH was performed from UV cross-linked mouse brain and lung and sequencing library was prepared for illumina sequencing

first: Collette

last: LaVigne

first: Jaeil

last: Han

first: He

first: Sihoon

last: Cho

first: Minseon

last: Kim

first: Komal

last: Sethia

first: Bret M

last: Evers

first: Asha

last: Acharya

first: Tsung-Cheng

last: Chang


title: TOWARDS THE GENERATION OF A LASER CAPTURE MICRODISSECTION-BASED HUMAN ANAGEN HAIR FOLLICLE TRANSCRIPTOME ATLAS

city: Muenster

first: Markus

last: Fehrholz

address: Mendelstr. 17

institute: Monasterium Laboratory GmbH

summary: While this is available for murine HFs, systematic characterization of the transcriptome of specific human hair follicle (HF) compartments remains a major unmet challenge in human hair research. Here, we have aimed to initiate the generation of such an atlas to reveal HF compartment-specific transcriptome. We performed laser capture microdissection (LCM) on 8 selected compartments, i.e. bulge outer root sheath (ORS), suprabulbar ORS, inner root sheath (IRS), precortical hair matrix (HM), germinative HM, dermal papilla (DP), the lower dermal cup (DC), and the connective tissue sheath (CTS), of human anagen VI scalp HFs, and analysed these by RNA-seq. Principal component analysis (PCA) was used to validate the distinctness of the microdissected compartments. Biological replicates were clearly separated by HF compartments and a high degree of similarity of the distinct transcriptional profiles of each examined compartment was seen. Afterwards, we matched well-known signature genes to the correct HF compartments. For example, VCAN (versican) and ALPL (alkaline phosphatase) were correctly expressed in the DP, the lower DC, and suprabulbar CTS, while TCHH (trichohyalin) was solely found in the proximal IRS, and KRT85 (Keratin 85) and KRT31 (Keratin 31) were almost exclusively expressed in the precortical HM. These transcriptomic data were used to generate an easily accessible database for identifying and defining compartment-specific gene expression profiles, which can be ultimately made publicly accessible (“hair follicle MONasterium InteraCtive atlas – hairMONic”). This human HF transcriptomic map and the associated interactive database will support the identification of HF compartment-specific signature genes, and facilitates the development of compartment-specific, therapeutic interventions for the management of human HF disorders.

overall_design: We utilized laser capture microdissection (LCM)-based RNA-Seq from 8 defined HF compartments - bulge outer root sheath (bORS), suprabulbar ORS (sbORS), inner root sheath (IRS), germinative hair matrix (gHM), precortical HM (pcHM), dermal papilla (DP), lower dermal cup (DC), and connective tissue sheath (CTS) – of occipital scalp terminal anagen VI HFs from 7-10 male and female donors undergoing hair transplantation, followed by RNA-Seq analysis of 3-5 HFs per donor.

first: Lisa

last: Epping

first: Ilaria

last: Piccini

first: Ludovica

last: Timperi

first: Xiaolin

last: Li

first: Francisco

last: Jimenez

first: Daniela

last: Pinto

first: Ralf

last: Paus

first: Marta

last: Bertolini


title: Effect of elastin-deficiency on gene expression in murine aortic smooth muscle cells at embryonic day 15.5

first: Junichi

last: Saito

summary: Defective elastin induces aortic smooth muscle cell hyperproliferation. As elastin is expressed from embryonic day 14 in the murine aorta, we utilized bulk RNA-seq to reveal molecular differences between Eln(+/+) and Eln(-/-) aortic smooth muscle cells at  embryonic day 15.5.

overall_design: Acta2-GFP, Eln(+/-) mice were bred with each other and embryos were collected at embryonic day 15.5. Aorta was isolated from Acta2-GFP embryos carrying Eln(+/+) or Eln(-/-). After digestion with collagenase enzyme mixtures, GFP+, CD31-, DAPI- smooth muscle cells were sorted by FACS and incubated with RNA lysis buffer. Extracted RNA was subjected to bulk RNA-seq.

first: Eunate

last: Gallardo-Vara

first: Rolando

last: Garcia Milian

first: Daniel

last: Greif


title: A circadian checkpoint relocates neutrophils to minimize injury

first: Alejandra

last: Aroca-Crevillén

address: C/ Melchor Fernández Almagro 3

institute: Spanish National Center for Cardiovascular Research Carlos III (CNIC)

summary: Inflammation-driven injury, a significant source of morbidity and mortality worldwide, is largely mediated by the cytotoxic activity of neutrophils, which extend the initial lesion and jeopardize organ function. Intriguingly, inflammatory injury naturally declines at specific times of day, suggesting that circadian mechanisms exist that mitigate the destructive activity of neutrophils and protect the host. Here, we show that the periods of diurnal protection coincide with peaks in plasma CXCL12, a chemokine that inhibits a neutrophil-intrinsic circadian clock by signaling through CXCR4. Genetic deletion of this clock, or a hyperactive form of CXCR4, prevented the diurnal spikes of injury, and treatment with a synthetic CXCR4 agonist conferred protection from myocardial and vascular occlusion. In tissues, this protection was mediated by repositioning neutrophils in the wound core, thus sparing neighboring host cells from death. Thus, a circadian neutrophil checkpoint protects from exuberant inflammatory injury and can be activated to protect the host.

overall_design: To elucidate the transcriptional landscape of leukocyte heterogeneity during myocardial infarction in mice, we conducted single-cell RNA sequencing of DAPI-CD45+, DAPI-CD45-CD31+ and DAPI-CD45-CD31-PDGFRa+ cells obtained from control and infarcted heart of mice under different conditions. These conditions included vehicle-treated and ATI2341 treated mice, to elucidate the effect of a CXCR4 agonist (ATI2341) in leukocytes and other cell populations after an inflammatory insult such as myocardial infarction (45 min occlusion, 24h of reperfusion). Basal condition was also included as a control.

last: Aroca-Crevllén

first: Jon

last: Sicilia

first: Andrea

last: Rubio-Ponce

first: Andrés

last: Hidalgo


title: ZKSCAN3 promotes ovarian cancer cell proliferation through upregulating HSPB1

city: Wuhan

first: suli

last: LV

address: Wuhan, Hubei, China

institute: Huazhong University of Science and Technology

summary: Ovarian cancer has the worst prognosis in major gynecological cancers. Current therapies includes platinum, taxol, angiogenesis inhibitor, PARP inhibitor. However, most ovarian cancer patients develop resistance. Identification of more pro-tumor factors in ovarian cancer may shed insight into ovarian cancer biology and therapy. In this study, we find ZKSCAN3, a zinc-finger transcription factor is overexpressed in ovarian cancer. We show ZKSCAN3 promotes ovarian cancer cell proliferation. Through RNA-sequencing and ChIP-sequencing, HSPB1 is identified as a target gene of ZKSCAN3. HSPB1 expression is significantly decreased by suppressing ZKSCAN3. Suppressing HSPB1 expression inhibits ovarian cancer cell proliferation as well. In contrast, expressing exogenous HSPB1 partially rescues the cell proliferation in ZKSCAN3 knock-down cells. Collectively, our study uncovers a functional ZKSCAN3-HSPB1 axis that promotes ovarian cancer cell proliferation.

overall_design: To examine the effect on transcriptome by ZKSCAN3, we performed ChIP-Seq and RNA-Seq to identify ZKSCAN3 directly-regulated genes. For ChIP-Seq, we stably expressed HA-ZKSCAN3 in Hey ovarian cancer cells. HA antibody was used for Chromatin IP. ChIP DNA was analyzed with Next generation sequencing. For RNA-Seq, Hey cells were transduced with lentiviruses expressing ZKSCAN3-shRNA or control sequences. Total RNA was extracted for RNA-Seq.

first: Tanjing

last: Song

first: Lidong

last: Sun

first: Suli

last: Lv


title: PITX2 dosage-dependent pacemaker cell state changes underlie sinus node dysfunction and atrial arrhythmia-susceptibility III

first: Vincent

last: Christoffels

overall_design: Wild-type (n=3), delB/+ (n=3) and delB/delB (n=3) adult hearts were analysed using spatial transcriptomics. Regions of interest were segmented based on HCN4 and TNNI3 expression, including the TNNI3+ right atrium (RA), HCN4+ wild-type sinus node, and delB/delB HCN4-high and HCN4-low sinus node.

first: L

last: van der Maarel

first: M

last: Mungroo

first: O

last: Mulleners

last: Rivaud

first: F

last: Tiel Groenesteege

last: Fokkert

first: C

last: de Gier-de Vries

first: K

last: van Duijvenboden

first: B

last: Jensen

first: H

last: Devalla

first: V


title: Discovery of novel circular RNAs through integration of short- and long-read RNA sequencing

city: St. Louis

first: Christopher

last: Maher

state: Missouri

address: 1 Brookings Dr

institute: Washington University in St. Louis

summary: Circular RNAs (circRNAs) are associated with crucial hallmarks of tumorigenesis. Select circRNAs contain circular open reading frames (cORFs) and impact tumorigenesis through encoded small peptides. However, current circRNA detection approaches bias towards using short-read RNA-seq for detecting circRNA backsplice junctions (BSJs) without reliably reconstructing complete circRNA sequences, inhibiting accurate cORF prediction. To address these challenges, we performed long-read sequencing to enrich for full-length circRNAs that could serve as a guide for short-read alignment. This approach “rescued” circRNAs eluding existing tools focused on circRNA detection from short reads and enabled the development of an open-source bioinformatics workflow that characterizes and rescues circRNAs by integrating short- and long-read RNA-seq: CHRIS (CHaracterizing CircRNAs by Integrative Sequencing). Application of the approach to colorectal cancer (CRC) cell lines and patient samples revealed 6,445 non-canonical isoforms of known circRNAs of which 69 were altered during cancer metastasis. Validation experiments in CRC cell lines confirmed endogenous expression of 11 high-confidence circRNAs rescued by CHRIS. Next, proteogenomic analysis using 67,326 circRNAs detected by CHRIS and mass spectrometry data from 261 CRC patients from Clinical Proteomic Tumor Analysis Consortium (CPTAC) identified 6,848 peptides encoded by circRNAs, including 994 only detectable with long-read integration and 914 potential neoantigens. Overall, this research develops an approach that can facilitate circRNA detection and provide valuable resources for future circRNA tumor biology research.

overall_design: Integrative analysis using both short-read and long-read RNA-seq to profile novel circRNAs in CRC cell lines and patient samples

first: Sidi

last: Zhao

first: Amy

last: Ly

first: Ryan

last: Fields


title: Polycomb-dependent breakdown of the intestinal barrier in aging Drosophila

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

summary: Aging compromises gut integrity, yet the chromatin changes driving this decline remain unclear. Polycomb mediated repression is essential for developmental silencing, but becomes dysregulated with age. Using single-cell chromatin profiling of the Drosophila intestine, we find that intestinal cell types have distinct repressed landscapes, and that enterocytes — not stem cells — undergo the most significant chromatin shifts in older animals. Aged enterocytes aberrantly repress genes essential for transmembrane transport and chitin metabolism, contributing to gut barrier decline. In contrast, stem cells exhibit increased proliferation, linked to hypertranscription of S-phase histone genes and to activation of JAK-STAT signalling pathways. These findings suggest that aberrant Polycomb repression in old differentiated cells is an example of antagonistic pleiotropy aging animals.

overall_design: We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.

first: Sarah

last: Leichter

first: Kami

last: Ahmad

first: Steven


title: Transcriptomic Regulation Driven by TCF12 Isoform Switching

city: Chicago

first: Xiao

last: Song

state: IL

address: 303 E Superior St, Lurie 6-250

department: Neurology

institute: Northwestern University Feinberg School of Medicine

summary: TCF12 is a member of the basic helix–loop–helix (bHLH) transcription factor family, which functions through homo- or heterodimerization with other bHLH proteins to regulate gene expression during development. We identified an alternative splicing event at exon 15 (E15) of TCF12 that differs among glioma cell states, with E15 more frequently included in NPC- and OPC-like states, but less included in MES- and AC-like states. To investigate the biological function of this isoform switch, we employed a dCasRx-RBM25/gRNA system to promote E15 inclusion in a patient-derived glioma stem-like cells (GSC1478) and performed RNA-seq to profile transcriptomic changes.

overall_design: RNA-seq profiling of GSC1478 cells treated with dCasRx-RBM25 only, dCasRx-RBM25 with control gRNA, or gRNA-I16 and I19 that induce TCF12 E15 inclusion.

first: Shi-Yuan

last: Cheng


title: PITX2 dosage-dependent pacemaker cell state changes underlie sinus node dysfunction and atrial arrhythmia-susceptibility I

first: Vincent

last: Christoffels

overall_design: Wild-type (n=3) and delB/delB (n=6) fetal (E17.5) hearts were analysed using spatial transcriptomics. Regions of interest were segmented based on HCN4 and TNNI3 expression, including the TNNI3+ right atrium (RA), HCN4+ wild-type sinus node, and delB/delB HCN4-high and HCN4-low sinus node.

first: L

last: van der Maarel

first: M

last: Mungroo

first: O

last: Mulleners


title: Comparative Eye Transcriptome Atlas

city: Aarhus C

first: Christian

last: Damsgaard

address: C F Møllers Alle 3

department: Department of Biology

country: Denmark

institute: Aarhus University

summary: The Comparative Eye Transcriptome Atlas provides transcriptomic resources to study retinal evolution and physiology across non-mammalian vertebrates. We profiled retinas from four species using two complementary high-throughput approaches. Eight 10x Genomics Visium spatial transcriptomics datasets were generated from Anolis carolinensis (n = 2), Taeniopygia guttata (n = 4), Columba livia (n = 1), and Gallus gallus (n = 1), capturing spatially resolved gene expression with matched histology images. In parallel, six 10x Genomics Chromium Single Cell 3′ RNA-seq datasets were obtained from zebra finch (T. guttata) retinas to resolve cell-type–specific transcriptomes. Raw sequencing data (FASTQ) and processed outputs from SpaceRanger (Visium) and CellRanger (Chromium) are provided. Downstream integrated and annotated datasets can be explored interactively at https://linlab.au.dk/Damsgaard_lab/CETA/ and full Seurat objects are available on request.

sample_organism:
Columba livia
Gallus gallus
Anolis carolinensis
Taeniopygia guttata

overall_design: Retinas were dissected from healthy adult animals of four species: the green anole (Anolis carolinensis; n = 2), zebra finch (Taeniopygia guttata; n = 4 for Visium, n = 6 for Chromium), rock pigeon (Columba livia; n = 1), and chicken (Gallus gallus; n = 1). For spatial transcriptomics, retinas were cryosectioned and processed with the 10x Genomics Visium Spatial Gene Expression kit v1 (55 µm spot resolution) and imaged at 20× magnification before library preparation. For single-cell transcriptomics, retinas from zebra finches were dissociated and processed with the 10x Genomics Chromium Single Cell 3′ v3 workflow. All libraries were sequenced on an Illumina HiSeq 4000 using paired-end 2 × 150 bp reads. Raw data were processed with SpaceRanger 3.1.1 (Visium) and CellRanger 7.1.0 (Chromium) against the following reference genomes: AnoCar3.1 (A. carolinensis), TaeGut1 (T. guttata), Cliv_2.1 (C. livia), and GRCg7b (G. gallus). The processed data deposited here are the standard filtered outputs of these pipelines without additional ambient RNA removal, doublet removal, or downstream QC filtering.

first: Lin

last: Lin


title: Gastric Bypass Elicits Persistent Gut Adaptation and Unique Diabetes Remission-Related Metabolic Gene Regulation

city: Boston

first: Margaret

last: Stefater-Richards

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: Abstract: Objective: We have previously shown that early intestinal adaptation precedes and relates to metabolic improvement in humans after Roux-en-Y gastric bypass surgery (RYGB). We hypothesized that intestinal adaptation would persist at the one-year postoperative timepoint, and that gene expression (GE) signatures would relate to Type 2 diabetes (T2D) remission, providing insight into potential mechanisms for intestinally-mediated metabolic improvement after RYGB. Methods: We determined GE by RNA-seq in jejunum (Roux limb, RL) collected from 28 patients before and 12 months after RYGB. Results: Global GE from paired baseline and 1-year jejunal samples did not separate according to clinical phenotype (T2D remission, sustained weight loss). In general, GE was consistent with persistent RL remodeling, and microvilli were elongated by 39%. Remodeling was not attenuated in patients with lack of diabetes remission or with weight regain. Patients with diabetes remission demonstrated greater jejunal activation of lipogenesis-related pathways driven by RXR, LXR and SREBP. Conclusions: RL adaptation is a key feature of RYGB in all patients, likely reflecting the dramatic alterations to gastrointestinal anatomy, but jejunal lipogenesis appears to be more strongly activated in those patients with diabetes remission. Further study is needed to understand whether these pathways may drive metabolic remission after RYGB.

overall_design: We determined GE by RNA-seq in jejunum (Roux limb, RL) collected from 28 patients before and 12 months after RYGB. "B," Baseline samples; "P," postoperative samples. "D" indicates sample from patient with diabetes and "C" indicates sample from patient without diabetes.


title: Cell-cycle-dependent repression of histone gene transcription by histone H4

summary: In all eukaryotes DNA replication is coupled to histone synthesis to coordinate chromatin packaging of the genome. Canonical histone genes coalesce in the nucleus into the Histone Locus Body (HLB), where gene transcription and 3’ mRNA processing occurs. Both histone gene transcription and mRNA stability are reduced when DNA replication is inhibited, implying that the Histone Locus Body senses the rate of DNA synthesis. In Drosophila melanogaster, the S-phase-induced histone genes are repeated in an ~100 copy repeat unit array, whereas in humans, these histone genes are scattered. In both organisms these genes coalesce into Histone Locus Bodies.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: We used a transgenic histone gene reporter and RNAi in Drosophila to identify canonical H4 histone as a unique repressor of histone synthesis during the G2 phase in germline primary spermatocytes.

first: Matt

last: Wooten

first: Brittany

middle: N

last: Takushi

first: Velinda

last: Vidaurre

first: Xin

last: Chen


title: METTL3 safeguards cell identity and epigenome of human trophoblast stem cells

city: Tianjin

first: Chunxiao

state: Tianjin

address: Xuefu Road

department: College of Life Science

institute: Nankai University

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is the most prevalent mRNA modification with diverse regulatory functions in mammalian cells. However, its significance in the human trophoblast lineage and human placenta development remains largely unexplored. Here, we found that in human pregnancy, METTL3 and METTL14, the primary enzymes responsible for m6A deposition, specifically mark cytotrophoblast cells in the human placenta. By utilizing a METTL3 inducible knockout (iKO) system, we demonstrated the essential role of METTL3 in generating human trophoblast stem cells (hTSCs) from human expanded potential stem cells (hESPCs). Furthermore, METTL3 is critical for the self-renewal ability and cellular identity in the established hTSCs. Mechanistically, METTL3-dependent m6A modification regulates histone modifiers such as EP300 and EZH2 to maintain the epigenetic homeostasis of hTSCs. The depletion of METTL3 in hTSCs results in epigenetic dysregulation, leading to activation of inflammation and premature senescence, which are associated with the preeclampsia phenotype. Notably, our findings from in vitro model show that inhibiting EP300 could efficiently rescue the preeclampsia signature at the transcriptomic level. These results underscore the critical roles of METTL3-dependent m6A RNA methylation in human placentation and the development of placental diseases.

overall_design: we performed RNA sequencing (RNA-seq) to analyze global gene expression profiles in P0, P2 and P3 hTSCs using two independent cell lines. We performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) to analyze m6A modification profiles in P0 and P2 hTSCs. We performed RNA stability analysis, in which we introduced Actinomycin D to transiently suppress global transcription then performed RNA-seq experiments at different time points to evaluate the transcription dynamics in P0 and P2 hTSCs. we conducted CUT&Tag for H3K27ac, H3K27me3, H3K9me3, H3K4me1 and JUND, as well as ATAC-seq for chromatin accessibility in P0 and P3 hTSCs.

first: Haifeng

last: Fu


title: CDK4/6 Inhibitor, Palbociclib, overcomes Venetoclax resistance mechanisms and outperforms single agents in Acute Myeloid Leukemia [RNA-Seq]

city: Portland

first: Daniel

last: Bottomly

address: 3181 S.W. Sam Jackson Park Rd.

institute: Oregon Health and Science University

summary: Venetoclax (ven) combined with the hypomethylating agent azacytidine (aza) is a widely used therapy for Acute Myeloid Leukemia (AML), however, most patients develop resistance. Using RNASeq, we identified loss of Ikaros (IKZF1) as a potential resistance mechanism to ven+palbo. Examination of cells with IKZF1-loss revealed upregulation of the receptor, AXL, with concordant AXL inhibitor sensitivity in AML tumors harboring IKZF1 mutations.  This work suggests that the combination of ven+palbo is a potential novel therapy for AML for potential subpopulations that may benefit the most from this treatment, as well as targeting translation as a means to overcome ven resistance.

overall_design: Using RNA-Seq, we compared three OCI-AML2 cell lines with a IKZF1 knock-out to three others with a non-targeting control  to identify differentially expressed genes associated with loss of IKZF1.

first: Melissa

last: Stewart

first: Jessica

last: Gibbs

first: Andy

last: Kaempf

first: Jeffrey

last: Tyner


title: PITX2 dosage-dependent pacemaker cell state changes underlie sinus node dysfunction and atrial arrhythmia-susceptibility II

first: Vincent

last: Christoffels

summary: Reduced spatiotemporal transcription factor levels have been shown to affect traits, organism development and disease predisposition. Here, we investigated the impact of physiologically relevant increases in transcription factor dosage, which has remained largely unexplored. Patients with genomic deletions far upstream of PITX2 present with sinus node dysfunction (SND) and atrial fibrillation. We show that delB mice, which recapitulate the deletion-driven arrhythmia in patients, ectopically express PITX2 in sinus node pacemaker cardiomyocytes (PCs) in a highly heterogeneous pattern from early embryonic development onwards. During development, delB sinus nodes form subdomains of mildly affected PC and strongly affected PCs that have lost their PC identity and switched towards an atrial cardiomyocyte-like state in a PITX2 dosage-dependent manner. Compared to heterozygous delB mice, homozygous delB mice have more PITX2+ PCs that express on average more PITX2, form proportionally larger subdomains of strongly affected PCs and have much more severe SND and atrial arrhythmia susceptibility. Ectopic expression of PITX2 in human induced pluripotent stem cell-derived PCs resulted in PITX2 dosage-dependent transcriptional changes reminiscent of those observed in the sinus node subdomains of delB mice. These results show that genetically driven ectopic expression of PITX2 in PCs causes SND and increased susceptibility for atrial arrhythmias, illustrating how spatiotemporally-defined increases in transcription factor dosage translates into developmental defects and disease predisposition.

overall_design: Wild-type (n=3), delB/+ (n=6), delB/delB (n=3) fetal (E17.5) hearts were analysed using spatial transcriptomics. Regions of interest were segmented based on HCN4 and TNNI3 expression, including the TNNI3+ right atrium (RA), HCN4+ wild-type sinus node, and delB/+ and delB/delB HCN4-high and HCN4-low sinus node.

first: L

last: Rivaud

first: F

last: Tiel Groenesteege

last: Fokkert

first: C

last: de Gier-de Vries

first: K

last: van Duijvenboden

first: B

last: Jensen

first: H

last: Devalla

first: V


title: Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment

status: Public on Nov 10 2025

city: New York

first: Nicholas

last: Tolman

department: Ophthalmology

institute: Columbia University

summary: Since the trabecular meshwork (TM) is central to intraocular pressure (IOP) regulation and glaucoma, a deeper understanding of its genomic landscape is needed. We present a multimodal, single-cell resolution analysis of mouse limbal cells (includes TM). In total, we sequenced 9,394 wild-type TM cell transcriptomes. We discovered three TM cell subtypes with characteristic signature genes validated by immunofluorescence on tissue sections and whole-mounts. The subtypes are robust, being detected in datasets for two diverse mouse strains and in independent data from two institutions. Results show compartmentalized enrichment of critical pathways in specific TM cell subtypes. Distinctive signatures include increased expression of genes responsible for 1) extracellular matrix structure and metabolism (TM1 subtype), 2) secreted ligand signaling to support Schlemm’s canal cells (TM2), and 3) contractile and mitochondrial/metabolic activity (TM3). ATAC-sequencing data identified active transcription factors in TM cells, including LMX1B. Mutations in LMX1B cause high IOP and glaucoma. LMX1B is emerging as a key transcription factor for normal mitochondrial function and its expression is much higher in TM3 cells than other limbal cells. To understand the role of LMX1B in TM function and glaucoma, we single-cell sequenced limbal cells from Lmx1bV265D/+ mutant mice (2,491 TM cells). In V265D/+ mice, TM3 cells were uniquely affected by pronounced mitochondrial pathway changes. Mitochondria in TM cells of V265D/+ mice are swollen with a reduced cristae area, further supporting a role for mitochondrial dysfunction in the initiation of IOP elevation in these mice. Importantly, treatment with vitamin B3 (nicotinamide), to enhance mitochondrial function and metabolic resilience, significantly protected Lmx1b mutant mice from IOP elevation.

overall_design: All sequencing data were obtained from mouse ocular limbal strips, a portion of the anterior eye. Briefly, the posterior eye was removed by cutting between the limbus and sclera, followed by removal of the lens. A small circular incision was then made in the anterior cornea to excise the central one-third of the corneal area. Only limbal tissues were collected. In total, six samples were generated: five by single-cell RNA sequencing (scRNA-seq) and one by single-nucleus RNA and ATAC sequencing (multiome). Three samples were from 2-month-old C57BL/6J mice and sequenced at Columbia University (two scRNA-seq and one multiome). One sample was from 3-month-old C57BL/6J mice and sequenced at Duke University. Two samples were from 2-month-old C57BL/6J mice carrying the Lmx1b^V265D mutation and sequenced at Columbia University. Each sample consisted of limbal strips pooled from eight eyes for a single sequencing run. Columbia samples included both sexes, whereas the Duke sample consisted only of male mice.

first: Revathi

last: Balasubramanian

first: Taibo

last: Li

first: Guorong


title: Single cell-RNA datasets from cell lines and dissociated mouse and maize tissues

city: Tainan

first: Po-Min

last: Chiang

state: TAIWAN

address: No. 35, Xiaodong Road,, Rm. 7068

department: Institute of Clinical Medicine

country: Taiwan

institute: National Cheng Kung University

summary: A generally applicable method to profile RNA from single cells and nulclei with high sensitivity and throughput is desirable.To demonstrate the potential, cells and nuclei from different sources and species were acquired and profiled.

sample_organism:
Zea mays
Homo sapiens
Mus musculus

platform_organism:
Zea mays
Homo sapiens
Mus musculus

overall_design: Human and mouse cell lines were used to benchmark gene detection sensitivity against other platforms or as spike-ins to demonstrate minimal multiplet formation in the same experiments. Tissues from mouse and maize were directly lysed to collect nuclei, demonstrating the method's applicability to complex multicellular structures.

first: Ya-Wen

last: Hsueh


title: Multiscale profiling of tyrosine kinase inhibitor cardiotoxicity reveals mechanosensitive ion channel PIEZO1 as cardioprotective

city: Palo Alto

first: Yu

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

institute: Stanford University

summary: Tyrosine kinase inhibitors (TKIs) have improved cancer outcomes but are limited by cardiovascular toxicity, most notably hypertension and heart failure. The underlying mechanisms remain poorly understood, hindering the development of protective strategies. Here, we investigated the role of endothelial mechanotransduction in mediating vascular and cardiac injury caused by the VEGFR-targeting TKI sunitinib. Using patient-specific induced pluripotent stem cell-derived endothelial cells (iPSC-ECs) and a mouse model of TKI-induced hypertension, we identified downregulation of PIEZO1, a mechanically activated ion channel, as a central driver of endothelial dysfunction. Restoring PIEZO1 expression, either pharmacologically with Yoda1, a selective agonist, or through inducible overexpression in iPSC-ECs, reversed sunitinib-induced endothelial dysfunction and mitigated its hypertensive effects, providing both mechanistic and genetic validation of PIEZO1’s protective role against vascular toxicity. In mice, Yoda1 co-treatment prevented the long-term cardiac dysfunction observed following sunitinib exposure, and normalized elevations in circulating cardiac stress biomarkers. Single-nuclei multiomic profiling of mouse hearts revealed that sunitinib exposure activated chromatin remodeling and fibrogenic programs, which were reversed with PIEZO1 activation. Human engineered cardiac organoids further demonstrated that sunitinib impaired cardiomyocyte function only in the presence of endothelial cells, confirming a role for disrupted endothelial-cardiomyocyte crosstalk in TKI cardiotoxicity. Together, these findings identify endothelial PIEZO1 as a critical mediator of TKI-induced hypertension and cardiac dysfunction and highlight PIEZO1 activation as a potential therapeutic strategy for protecting cardiovascular health during cancer therapy.

overall_design: scRNA-seq of vacular tissues collected from mice treated with vehicle, sunitinib, and sunitinib + Yoda1

first: Nazish

last: Sayed


title: Multiscale profiling of tyrosine kinase inhibitor cardiotoxicity reveals mechanosensitive ion channel PIEZO1 as cardioprotective [snMultiome]

overall_design: snMultiome of heart tissues collected from mice treated with vehicle, sunitinib, and sunitinib + Yoda1


title: An in vivo and in vitro spatiotemporal atlas of human fetal midbrain development

city: London

first: George

middle: Thomas

last: Hall

address: Zayed Centre for Research, 20 Guilford Street

department: UCL Great Ormond Street Institute of Child Health

institute: University College London

summary: The dopaminergic system has key roles in human physiology and is implicated in a broad range of neurological and neuropsychiatric conditions that are increasingly investigated using induced pluripotent stem cell-derived midbrain models. To determine the similarity of such models to human systems, we undertook single cell and spatial profiling of first and second trimester fetal midbrain and compared it to in vitro midbrain models. Our initial histological analysis of second trimester fetal midbrain revealed structural complexity already similar to that of adult tissue, although this similarity did not fully extend to transcriptional activity. Moreover, we show that in vitro models recapitulate the transcriptional activity of late first trimester fetal midbrain, while 3D models replicate the spatial organization and cellular microenvironments of first and second trimester fetal midbrain. Understanding the extent of human tissue recapitulation in midbrain laboratory models is essential to justify their use as biological proxies.

overall_design:
For spatial transcriptomics data:
Fetal midbrain samples from four timepoints were profiled with spatial transcriptomics.  Each sample had three biological replicates. Four spatial transcriptomics capture areas (each containing six organoids) were also profiled.
The fetal samples are:
PC_AGE_1_REP_1
PC_AGE_1_REP_2
PC_AGE_1_REP_3
PC_AGE_2_REP_1
PC_AGE_2_REP_2
PC_AGE_2_REP_3
PC_AGE_3_REP_1
PC_AGE_3_REP_2
PC_AGE_3_REP_3
PC_AGE_4_REP_1
PC_AGE_4_REP_2
PC_AGE_4_REP_3
The organoid samples are:
OCT_BLOCK_1
OCT_BLOCK_2
OCT_BLOCK_3
OCT_BLOCK_4
For single-cell transcriptomics data:
In vitro 2D and 3D organoids (both iPSC-derived samples) were profiled throughout neuronal differentiation, along with fetal midbrain from first and second trimester. For 2D models, samples from 2 donors (2 controls) were collected at days 40 and 70 of differentiation. For 3D models, samples from 4 donors (2 controls, 2 patients, one patient-corrected line) were collected at days 40, 70 and 120 of differentiation. Fetal midbrain samples were collected at post-conceptional weeks 10, 12, 16 and 20. To reduce the batch effects between donors, individual donors were pooled at the time of sequencing. The biological samples described below correspond to 10x libraries (samples processes through the same GEM well).
The 2D and 3D models are:
mid_organoids8644112
mid_organoids8644113
mid_organoids8644114
mid_organoids8643920
mid_organoids8643921
mid_organoids8643922
mid_organoids8644016
mid_organoids8644017
mid_organoids8644018
The fetal samples are:
F10121620_A
F10121620_B
F10121620_C
F10121620_D

first: Pau

last: Puigdevall Costa


title: CDK4/6 Inhibitor, Palbociclib, overcomes Venetoclax resistance mechanisms and outperforms single agents in Acute Myeloid Leukemia [CRISPR Screen]

first: Daniel

last: Bottomly

summary: Venetoclax (ven) combined with the hypomethylating agent azacytidine (aza) is a widely used therapy for Acute Myeloid Leukemia (AML), however, most patients develop resistance. A genome-wide CRISPR screen showed that loss of genes involved in translation conferred sensitivity to ven but not ven+palbo. Accordingly, we show that increased translation occurs after AML cells are challenged with ven, and ven+palbo blocks this increase. We also found that loss of BAX, which leads to ven resistance, was overcome by combination with CDK4/6 inhibitors. Conversely, loss of RB1, a known mechanism of resistance to CDK4/6 inhibitors, was mitigated by ven+palbo. This work suggests that the combination of ven+palbo is a potential novel therapy for AML for potential subpopulations that may benefit the most from this treatment, as well as targeting translation as a means to overcome ven resistance.

overall_design: Using a genome-wide CRISPR screen on OCI-AML2 cells, we performed comparisons of sgRNA read counts between DMSO and venetoclax, palbociclib as well as their combination at Day 0 and 21.  Genes that were significantly depleted (enriched) relative to DMSO controls were deemed candidates for enhancing drug sensitivity (resistance).

first: Melissa

last: Stewart

first: Jessica

last: Gibbs

first: Shannon

last: McWeeney

first: Jeffrey

last: Tyner


title: The effect of HSD17B1 inactivating mutation in adult mouse ovary gene expression

city: Turku

first: Matti

last: Poutanen

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

summary: We compared the mRNA expression in ovaries of female mice with an inactivating Ser143Ala mutation of HSD17B1 (HSD17B1-KI) and wild-type (WT) littermates. We aimed to identify the possible differences in gene expression patterns due to the disruption of estrogen biosynthesis caused by the lack of HSD17B1 activity.

overall_design: Ovaries were collected from 6-month-old HSD17B1-KI and WT females during the estrus phase of the estrous cycle.

first: Arttu

last: Junnila

first: Nataliia

last: Petruk

first: Hanna

last: Heikelä

first: Guillermo

last: Martinez-Nieto


title: The origin of hepatocellular carcinoma is regulated by metabolic zonation [Single Nuclear Genotyping]

city: Dallas

first: Hao

last: Zhu

address: 5323 Harry Hines Blvd

institute: UTSW

type: Genome variation profiling by high throughput sequencing

summary: The origin of cancer is poorly understood because premalignant cells are rarely followed in their native environments. While the spatial compartmentalization of metabolic functions is critical for proper liver function, it is unknown if cancers arise from some zones but not others, and if there are metabolic determinants of cancer risk. Zone-specific, mosaic introduction of Ctnnb1 and Arid2 mutations, commonly co-mutated genes in hepatocellular carcinoma (HCC), showed that position and metabolic context determine clone fates. Ctnnb1/Arid2-driven cancers were much more likely to arise in zone 3. The zone 3 genes Gstm2 and Gstm3 were required for efficient HCC initiation, in part through inhibition of ferroptosis. In the liver, the zonal determinants of HCC development can reveal metabolic vulnerabilities of cancer.

overall_design: Genetic mouse models with zone-specific CreER were given tamoxifen at P28 to induce zone-specific tumor drivers and euthanized at 5 months post-tamoxifen prior to tumor formation

first: Jason

last: Guo

first: Benjamin

last: Kroger


title: The origin of hepatocellular carcinoma is regulated by metabolic zonation [RNA-seq]

overall_design: Genetic mouse models with zone-specific CreER were given tamoxifen at P28 to induce zone-specific tumor drivers and followed for 6-12 months post-tamoxifen for tumor formation. WT C57/BL6 mice used for controls were treated with AAV-Cre and were maintained on normal chow diet for up to 12 months.

first: Yunguan

last: Wang

first: Yi

last: Han

first: Tao


title: Reconstructing Epigenomic Dynamics through a Single-Cell Multi-Epigenome Data Integration Framework

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

summary: Transcriptional regulation arises from the dynamic and combinatorial actions of multiple regulatory factors on genomic DNA. Although many epigenomic regulators have been identified, the precise order in which these factors accumulate at individual gene loci to activate transcription remains unclear. Here we show a single-cell data integration framework that infers the binding order of multiple chromatin factors at single-cell resolution. Central to this framework is sci-mtChIL-seq, a scalable single-cell method that simultaneously profiles genome-wide binding of RNA polymerase II (RNAPII) and diverse epigenomic regulators. By defining transcriptional states through RNAPII occupancy and integrating multiple sci-mtChIL-seq datasets, we systematically link the combinatorial patterns of transcription factor binding, histone modifications and chromatin remodeling. This framework reveals the temporal coordination among chromatin factors during transcriptional activation, providing a powerful approach to uncover context-dependent epigenomic dynamics and the principles of gene regulation in complex cellular systems.

overall_design: Sci-mtChIL-seq for H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3, H3K36me3, H3.1/3.2, and RNA PolII in SP2 cells and sci-mtChIL-seq for RNA PolII-H3K4me3, RNA PolII-H3K27me3 and RNA PolII-MyoD in embryo and for RNA PolII-H3K4me3, RNA PolII-H3K27me3, RNA PolII-MyoD, RNA PolII-H3K27ac, RNA PolII-Brg1 and RNA PolII-Myog in  NIH3T3 cells.

first: Takeru

last: Fujii

first: Akihito

last: Harada


title: Somatic deficiency of human E3 ubiquitin ligase CBL in leukocytes  Impairs B cell but not T cell development and function

first: Anna-Lena

last: Neehus

address: 1 Blackfan Circle

summary: The casitas B lineage lymphoma (CBL) proto-oncogene promotes positive selection and antigen responses in murine T lymphocytes by ubiquitinating ZAP70. However, CBL and CBL-B are redundant for ubiquitination of SYK and regulation of B cell receptor (BCR) signaling in murine B cells. We studied lymphocyte development, maturation and function in patients with somatic homozygosity for CBL loss-of-function variants in leukocytes. Surprisingly, human CBL is largely redundant for the development and function of human T cells. Conversely, CBL is critical for B cell development and function. Patients with somatic, hematopoietic CBL deficiency have a 10-fold increase in transitional B cells during childhood and are susceptible to bacterial infections. CBL deficiency impairs B cell maturation in a cell-intrinsic manner through reduced apoptosis and dysregulated BCR signaling, thereby reducing the proportions and numbers of memory B cells. Overall, our findings demonstrate that CBL deficiency has two major effects on human B cells. First, B-cell development in the bone marrow is altered at the immature stage, resulting in enhanced survival and differentiation of autoreactive B cell clones and impaired B cell tolerance, manifested as the production of autoantibodies. Second, the generation of antigen-specific B cells is impaired, thereby disrupting the establishment of adaptive immune memory. Thus, our study reveals the critical role of human CBL in B cells and its redundancy in T cells.

overall_design: Umbilical cord blood CD34+ hematopoietic stem and progenitor cells were edited at the AAVS1 safe harbor locus (n=2), the CBL locus (in frame exon 8 deletion; n =2) or base edited use ABEm8 at the PIK3CD locus (n=1) to generate the p.C416R gain-of-function variant. To initiate B cell differentiation, the edited CD34+ cells were co-cultured with MS-5 stroma cells in the presence of IL-7. At day 21 of co-culture (day 24 post editing), the cells were collected from the MS5, sorted for CD19+CD10+CD20dim and subsequently rested for 12 hours in RPMI+10%FBS. RNA was extracted from each sample in duplicates using the Total RNA Purification Micro Kit (Norgen, #35300) according to the manufacturer’s instructions. All samples were treated with DNase I to remove residual genomic DNA.

first: Vijay

middle: G

last: Sankaran


title: Effect of Aiolos on virtual memory T cell differentiation and function

city: Columbus

first: Ken

last: Oestreich

state: Ohio

address: 460 W 12th Ave, Biomedical Research Tower

department: Microbial Infection and Immunity

institute: The Ohio State University College of Medicine

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

overall_design: Refer to individual Series


title: The origin of hepatocellular carcinoma is regulated by metabolic zonation [Xenium]

overall_design: Genetic mouse models with zone-specific CreER were given tamoxifen at P28 to induce zone-specific tumor drivers and livers were collected one month later. One mouse each from our zone 1 and zone 3 tumor models were collected and compared to a wild type mouse of the same age.

first: Boyuan

last: Li


title: FSP1 and histone deacetylases suppress cancer persister cell ferroptosis

city: La Jolla

first: August

last: Williams

address: 9500 Gilman Dr.

department: Dermatology

institute: UC San Diego

summary: Cancer persister cells which survive oncogene targeted therapies are sensitized to ferroptosis but mechanistic understanding of this vulnerability remains limited. Here, we found that while levels of iron, glutathione and various ferroptosis suppressing enzymes vary among persister cell types, ferroptosis suppressor protein 1 (FSP1) is downregulated in multiple persister cell types and persister cells which survive glutathione peroxidase 4 (GPX4) inhibition rely upon residual FSP1 to survive. Furthermore, persister cells which survive GPX4 inhibition downregulate oxidative phosphorylation, a key source of mitochondrial reactive oxygen species which are required for persister cell ferroptosis. We also found that persister cell treatment with histone deacetylase inhibitors induce reactive oxygen species and sensitize multiple persister cell types to GPX4 inhibition. Together, these findings reveal that FSP1 and histone deacetylases suppress persister cell ferroptosis.

overall_design: Single cell RNA sequencing of PC9 cells with 10X Genomics. PC9 lung cancer cells were untreated (parental) or treated with 100 nM erlotinib for 10 days to derive persister cells. Additionally, parental and persister cells were both separately treated with 1 µM GPX4 inhibitor, RSL3, for 24 hours; or with 7.5 nM HDAC inhibitor, panobinostat, for 48 hours.

middle: F

first: Matthew

last: Hangauer


title: In toto imaging reveals intravascular proliferation promotes transmigration of daughter cells during brain invasion of Cryptococcus neoformans

city: Shanghai

first: Donglei

last: Sun

address: 800 Dongchuan RD. Minhang District

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

summary: Cryptococcus neoformans causes lethal cryptococcal meningoencephalitis. Although the mechanism of blood-brain barrier (BBB) transmigration has been widely studied, the predominant route remains unclear due to technical limitations. Here, we developed a whole-organ imaging workflow, termed fTRACE, that enables in toto visualization of individual fungal cells within host tissue. Further labeling of host counterparts revealed in situ host-pathogen interaction in detail. We utilized fTRACE to address the major route of fungal brain invasion and found C. neoformans can proliferate intravascularly within capillaries prior to BBB transmigration. Notably, by distinguishing mother and daughter cells in vivo, we discovered that daughter cells, rather than mother cells, predominantly transmigrate via the paracellular route. We also identified key factors supporting fungal proliferation in serum as mimicry of intravascular environment. RNA sequencing revealed that serum-growing fungi exhibit a markedly altered gene expression profile. In particular, de novo purine biosynthesis is essential for serum and intravascular proliferation. A fluorescent strain deficient in purine synthesis allowed us to trace the fate of non-proliferating fungi during prolonged brain infection. Unlike inert polystyrene beads, fungal cells showed significantly reduced wash-away events from capillaries - a process enhanced by VEGFR inhibition. For those fungi remain in the brain, the majority remained trapped in capillaries, while a smaller portion was able to induced local capillary pruning. Angiophagy, presumably by transcellular pathway, was detectible but at a low frequency. Collectively, this study not only elucidates the major route of brain invasion by C. neoformans, but also set a paradigm for studying host pathogen interactions using in toto imaging approach.

overall_design: RNA-seq profiling of C. neoformans grown in mouse serum versus rich medium(Sabouraud dextrose broth) for 12 hours.


title: Differential activity of transcription factors and neuronal effectors during the development of pikeperch brain

city: České Budějovice

first: Radka

last: Symonova

address: Branisovska 1645/31a

department: Department of Applied Informatics

country: Czech Republic

institute: Faculty of Science, University of South Bohemia

summary: Juvenile pikeperch (Sander lucioperca) undergo several ontogenetic shifts whose timing determines the survival of their first winter. The shift from a planktivorous phenotype to a more active predatory (piscivorous) behavior is accompanied by moving from pelagic to demersal habitat with much more stimuli and hence by potential brain functional reorganizations. During two consecutive years, we collected planktivores and piscivores, with different body sizes between the years recording distinct stages relative to the shift and analyzed their whole-brain transcriptomes framed by detailed ecological knowledge. The differential gene transcription analysis identified a distinct non-overlapping group of transcription factors (TFs) significantly upregulated in each phenotype: TFs upregulated in planktivores correspond to initial establishment of brain regions and overall architecture; TFs upregulated in piscivores correspond to the refinement of neuronal populations and the formation of specific neuronal circuits. The planktivorous phenotype independently of body size was characterized by interconnected activity of two TFs, fosab and junba. Gene set enrichment revealed extracellular matrix and collagen-related Gene Ontology terms in piscivores from both years. A highly increased activity of solute carrier (Slc) transporters was identified in the smaller-bodied piscivorous phenotype (20 members of 12 Slc families). The overall count of Slc genes transcribed in pikeperch brain was 334, which is higher than known for humans (287). The neurotranscriptomics results reflected differences in body size and matched with ecological data and survival rates. The multidimensional brain regulome indicated that the intra-phenotypic body size difference can translate into the specific gene activity of the brain in juvenile pikeperch. The period of transition to piscivory appears to be an important ontogenetic step accompanied by increased specific transcription activity.

overall_design: RNA-seq profiling of juveinle pikeperch brains of planktivorous (N) and piscivorous (L/C) phenotypes during 2 consequtive seasons 2022-2023


title: Age-dependent immune responses and resident cell dynamics in young mice following pneumonia [RNA-Seq]

city: Philadelphia

first: Sylvia

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

summary: A developmental murine model of pneumonia was used to investigate how lower respiratory tract E. coli infections differentially affects lung immune responses and cell behavior in young mice (neonates; PND5 and juveniles; PND12). Acutely, juveniles recover more quickly than neonates, but alveolar simplification occurred in both groups 6-8 weeks post-infection. Single-cell RNA sequencing revealed transient inflammatory responses in neutrophils, macrophages, and fibroblasts at 48 h post infection in both age groups with a partial return to baseline by 96h. The highly proliferative neonatal alveolar type 2 (AT2) cells showed a modest decrease at 48h post infection, whereas the quiescent juvenile AT2 cells exhibited a proliferative response only post-infection. Neonatal PDGFRα+ fibroblasts had higher expression of inflammatory genes post infection than juveniles and in vitro stimulation of PDGFRα+ fibroblasts with LPS-exposed primary macrophages alone, induced expression of the inflammatory marker SAA3. We conclude that early-life pneumonia alters lung homeostasis in an age-differential manner, potentially affecting lung structure and function in adulthood.

overall_design: Sorted AT2 cells or fibroblasts from the lungs of mice infected with E. coli or PBS (controls) at the neonatal (PND5) or juvenile (PND12) time-points were collected for bulk RNA-seq.

last: Singer

first: Sharon

middle: A

last: McGrath-Morrow


title: Effect of Aiolos on virtual memory T cell differentiation and function [RNA-Seq]

summary: Virtual memory CD8+ T (TVM) cells provide rapid bystander protection during an infection despite their antigen naivety. In addition, these cells are also capable of antigen-specific response, making them an intriguing part of both the host innate and adaptive immune repertoire. While the innate and adaptive capabilities of these cells have been well characterized, much remains to be defined regarding the mechanisms governing their differentiation and function. Here, we investigate the role of the Ikaros zinc-finger (IkZF) transcription factor Aiolos in regulating CD8+ TVM generation and function. Using bulk RNA-sequencing and Assay for Transposase-Accessible Chromatin (ATAC)-sequencing, we identify differences in gene expression as well as accessibility profiles of key TVM effectors and regulators in TVM cells isolated from the spleen of control (wild-type) and Aiolos-deficient (Ikzf3-/-) mice. These studies will provide mechanistic insight into the regulation of TVM differentiation and function by Aiolos.

overall_design: RNA-sequencing of TVM cells isolated from the spleen of specific pathogen free WT and Aiolos-deficient mice.Also included is naïve WT CD8+ T cells from the spleen of unifected mice.

first: Srijana

last: Pokhrel


title: Age-dependent immune responses and resident cell dynamics in young mice following pneumonia

overall_design: Unsorted cells from the lungs of multiple C57Bl/6 WT mice aspirated at either PND5 (neonatal) or PND12 (juvenile) with either PBS, E. coli, or room air and sacrificed at either 48hr or 96hr post-aspiration were loaded into independent lanes of a 10X Chromium GEX 3’ v3 microfluidics chip for 3’-biased scRNA-seq.

first: Benjamin


title: Versatile molecular tools enabling customizable DNA methylation editing in plants [BiSulfite-seq]

first: Li

last: He

address: No. 3888 Chenhua Road

department: Shanghai Center for Plant Stress Biology

institute: CAS Center for Excellence in Molecular Plant Science (CEMPS)

summary: Tools to edit DNA methylation in a targeted manner are vital for clarifying the causal relationships between DNA methylation and its function, as well as for plant breeding and gene therapy; non-specific tools that induce genome-wide DNA methylation changes are valuable for the creation of novel epialleles and performing large-scale screens. Here, by constructing dCas9 fusions to a panel of effectors and cofactors, we uncovered a range of tools for editing DNA methylation, including five tools for DNA methylation and six tools for DNA demethylation. Our tools show diversity of performance in terms of specificity and efficiency, offering either the capacity to target editing DNA methylation or the ability to edit DNA methylation at the genome-wide level. Remarkably, DNA methylation edited by these tools was inherited in the absence of transgene. These versatile tools pave the way for diverse applications in DNA methylation editing and hold promise for advancing plant epigenetic breeding.

overall_design: 127 WGBS

first: Yao

last: Yao

first: Jian-Kang

last: Zhu


title: Axon Regeneration and Functional Recovery from Spinal Cord Injury is Enhanced by Allele-Specific ApoE Neuronal Action through Lrp8

city: New Haven

first: Stephen

last: Strittmatter.

state: Connecticut

address: 295 Congress Ave, BCMM Rm433

institute: Yale University

summary: Adult CNS trauma frequently causes neuronal disconnection and persistent deficits due to failed axon regeneration. While model system screening has identified candidate neural repair genes, ApoE – LRP8 signaling is unique in being implicated clinically. Here, we show that cortical axon regeneration requires LRP8 and is modified by APOE variants. ApoE2-expressing mice show reparative corticospinal and raphespinal axon growth with greater motor function than controls after spinal cord injury. Distinct from ApoE in other settings, there is no change in inflammation or scarring. After axotomy, ApoE exerts allele_x0002_specific effects on LRP8 localization and signaling in cortical neurons. APOE alleles regulate synaptic organization gene expression by cortical neurons after injury, with little effect on glial gene expression. AAV-mediated overexpression of ApoE2 in mice after spinal trauma increased locomotor recovery and reparative axon growth. Thus, a role for ApoE – LRP8 signaling is supported by preclinical and clinical observations, providing a potential site for intervention.

overall_design: Age-matched adult (12-13 weeks) female mice of ApoE2 or ApoE4 genotype were subjected to a thoracic dorsal-over hemisection (injured) or shame (control) surgery.  All animals received subcutaneous injections of 100 mg/kg ampicillin and 0.1 mg/kg Buprenex twice daily for the first 2 d after surgery and additional injections later as necessary. Eleven days post-surgery, the motor cortices of both SCI-injured and control mice were dissected and processed for single nuclei isolation and RNA sequencing for comparative transcriptomic expression profile analysis.

first: Ramakrishnan

last: Kannan

first: Xingxing

last: Wang

first: LaShae

last: Nicholson

first: Nancy

last: Lin

first: Elisa

last: Howard

first: Atrayee

last: Basu

first: Ines

last: Ingabire

first: Yuichi

last: Sekine

last: Strittmatter


title: Versatile molecular tools enabling customizable DNA methylation editing in plants [ATAC-seq]

overall_design: 1 ATAC-seq


title: Tumor immunity following radiopharmaceutical + checkpoint blockade varies with treatment sequence, radioisotope, and tumor immunogenicity

city: Madison

first: Zachary

last: Morris

address: 1111 Highland Avenue

institute: University of Wisconsin

summary: Radiopharmaceutical therapy (RPT) enhances tumor response to immune checkpoint inhibitors (ICI) in preclinical models, but the effects of different radioisotopes have not been compared. To evaluate mechanisms of response to RPT+ICI, we used NM600, an alkylphosphocholine selectively taken up by most tumors. Effects of 90Y-, 177Lu-, and 225Ac-NM600 + ICIs were compared in syngeneic murine models, B78 melanoma (poorly immunogenic) and MC38 colorectal cancer (immunogenic). 90Y-/177Lu-/or 225Ac-NM600 delivering 2 Gy mean tumor dose promoted tumor regression and improved survival when combined with ICIs in syngeneic mice bearing B78 or MC38 tumors. Regardless of the administered isotope, this combination was optimized with early ICI administration (days -3/0/3) relative to day 1 RPT. 90Y-NM600+ICI produced the greatest anti-tumor response for MC38, whereas high linear energy transfer (LET) alpha particle radiation from 225Ac-NM600+ICI was most effective against poorly immunogenic B78 tumors. Flow cytometry and single cell RNA and T cell receptor (TCR) sequencing illuminated distinct mechanisms of 90Y- or 177Lu-NM600 in promoting expansion of existing adaptive immunity and of 225Ac-NM600 in promoting immune priming when combined with ICI. Antitumor immune response can be achieved with appropriate application of α- or β- emitting RPT in combination with ICIs in diverse murine tumor models.

overall_design: B78 melanoma tumor-bearing mice received either 2 Gy 90Y-, 177Lu-, 225AcNM600 or EBRT on day 1 + ICI (anti-CTLA4 and anti-PD-L1) on days -3/0/3 or ICI alone. Tumors were harvested on day 15, dissociated, and immune cells were isolated by Ficoll density gradient centrifugation for single cell RNA sequencing analysis. All samples had viability > 90%, and were resuspended at a concentration of 1.2 *106 cells/mL in RPMI-1640 for single-cell RNA sequencing.


title: Endothelial cells in sepsis - batch 2

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

summary: Differentially expressed genes were identified in lung endothelial cells of CLP-treated mice compared to sham-treated controls and after treatment with sitagliptin. Sitagliptin strongly reduced the inflamatory response.

overall_design: Sepsis was induced in mice by CLP (Cecal Ligation Puncture). Some mice were treated with sitagliptin. Endothelial cells from the lungs of CLP-treated, CLP plus sitagliptin, sham-treated and untreated mice were isolated and subjected to RNAseq analysis. Analysis was done in two batches, this is batch 2.

first: Nana-Maria

last: Wagner

first: Laura

last: Brabenec

first: Katharina

middle: E

last: Hellenthal


title: Comprehensive long-read transcriptomic analysis reveals multi-level transcriptional alterations mediated by miR-214-3p dysregulation in gastric cancer cells

status: Public on Nov 09 2025

city: Yinchuan

first: ruijuan

last: Xin

state: Ningxia

address: Zhengyuan South Street

institute: People's Hospital of Ningxia

summary: Long-length sequencing has been widely used in cancer-related research for exploring transcriptome variations in human cancer in recent years. miR-214-3p, a microRNA, has been reported to have abnormal expression and play important regulation roles in diverse cancers. However, information about the genome-wide targets and action mechanisms of miR-214-3p in cancer cells is still limited. Here, long-read sequencing were performed to character the transcriptome variations after disturbing the expression of miR-214-3p in AGS cells, a gastric cancer cell line. The results showed that both miR-214-3p overexpression (OE) and suppression (KD) extensively increased or decreased expression level of a number of genes involved in apoptotic process and transcription at transcript level and gene level. In particular, both miR-214-3p KD and OE could increase or decrease on the expression levels of some target genes at the same direction. Moreover, miR-214-3p broadly regulated the alternative splicing of hundreds of genes with functions of cell division, cellular senescence and transcription regulation. In addition, the changes in the expression level of miR-214-3p can cause changes in the alternative polyadenylation and 3UTR lengths of the transcript. Taken together, these results indicated that miR-214-3p could mediate apoptosis by diverse modes in AGS cells, which adds to the understanding of the critical role of miR-214-3p in cancer cancer.

overall_design: Using Oxford Nanopore Technology (ONT)-based long-read sequencing, we investigated the effects of miR-214-3p overexpression (OE) and knockdown (KD) to elucidate the functional role of miR-214-3p in AGS cells

first: Ruijuan

first: Xiaoqin

last: Ma

first: Min

last: Niu

first: Qian

last: Hao

first: Hongliang

last: Li

first: Shengjuan

last: Hu


title: N1-Methylpseudouridine Directly Modulates Translation Dynamics

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

institute: Weizmann Institute

summary: The remarkable effectiveness of mRNA vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted synthetic mRNA as a promising technology. A critical feature of this approach is the incorporation of the modified ribonucleotide N1-methylpseudouridine (m¹Ψ), which enhances antigen expression while reducing immunogenicity. However, a comprehensive understanding of how this modification influences translation remains incomplete. Here, we analyze translation at sub-codon resolution using ribosome profiling and demonstrate that m¹Ψ increases ribosome density on synthetic mRNAs. This elevated ribosome load, together with the correlated increase in protein production, occurs independently of intrinsic cellular immunity or eIF2α phosphorylation. Our data reveal that m¹Ψ directly slows ribosome elongation in specific sequence contexts while concurrently enhancing translation initiation. Cryo-electron microscopy shows that m¹Ψ-modified mRNAs alter interactions within the ribosome decoding center, providing a mechanistic basis for slowed elongation dynamics. Furthermore, by introducing synonymous mutations that disrupt modification-mediated changes in elongation, we show that the m¹Ψ-dependent effect on protein output can be modulated, and that its impact is strongest in mRNAs containing non-optimal codons with uridines at the wobble position. Together, these findings demonstrate that m¹Ψ directly modulates translation elongation and initiation, thereby enhancing translational capacity and increasing protein output from synthetic mRNAs in defined sequence contexts.

overall_design: All experiments involved comparing in vitro transcripts (IVTs) synthesized with standard UTP to the same IVTs synthesized with either Ψ or m¹Ψ substitutions at all uridine positions. Two specific IVTs were studied in detail: SARS-CoV-2 and luciferase (in two different nucleotide sequence variants). For these IVTs, we performed RNA-seq, Ribo-seq, and, in the case of luciferase, also a chase experiment.  In addition, we generated a library of luciferase-encoding sequences with varying uridine content. For this library, we performed polysome profiling, followed by sequencing of five gradient fractions as well as the total RNA.

first: Batsheva

last: Rozman

first: Karin

last: Broennimann

first: Aharon

last: Nachshon

first: Tamar

last: Arazi


title: Effect of Aiolos on virtual memory T cell differentiation and function [ATAC-Seq]

first: Ken

last: Oestreich

overall_design: ATAC-sequencing of TVM cells isolated from the spleen of specific pathogen free WT and Aiolos-deficient mice.

first: Srijana

last: Pokhrel