title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML. [ChIP-Seq 2]

status: Public on Feb 27 2026

city: Mainz

first: Aarón

last: Gallego Crespo

state: Rhineland-palatinate

address: Langenbeckstraße 1

department: III. Medical Department

institute: University Medical Center of the Johannes Gutenberg University

summary: The lysine acetyltransferase (KAT) activity of p300/CREBBP has traditionally been linked to transcriptional activation. This has been attributed largely to acetylation of histone residues such as H3K27ac, a defining hallmark of active regulatory elements. Here we show that, in acute myeloid leukemia (AML), inhibition of p300/CREBBP catalysis can paradoxically increase transcription. We combined time-resolved dynamics of nascent and total transcription with chromatin binding dynamics of p300/CREBBP and their associated TFs/co-regulators (inferred from chromatin pull-down proteomics, acetyl-proteomics and motif enrichment) to uncover mechanisms of transcriptional rewiring after p300/CREBBP catalytic inhibition. In parallel, we dissected the functional contribution of individual p300/CREBBP acetyl-interactome members to KAT inhibition using genome-wide CRISPR-Cas9 dropout and focused Perturb-seq screens. Together, these approaches revealed that KAT inhibition paradoxically retains p300/CREBBP and promotes cooperative TF assembly and increased H3K27 acetylation at a subset of regulatory elements. The effect was most pronounced at IRF motif-enriched loci, including interferon-stimulated genes (ISGs), where KAT inhibition triggered p300/CREBBP accumulation and enhanced combinatorial TF binding, enabling recruitment of the ISG activator STAT1. Consequently, ISG loci were converted into transcriptionally active states that induced cell-cycle arrest, differentiation and apoptosis. Therapeutically, combining KAT inhibition with interferon-alpha augmented ISG expression, synergistically drove AML cell death in vitro and significantly extended survival in both AML xenografts and murine models. These findings refine our understanding of p300/CREBBP KAT activity, demonstrating that cooperative TF assembly can reconfigure p300/CREBBP-containing complexes under catalytic inhibition to induce transcription, with translational implications for reprogramming interferon-driven programs through catalytic inhibition in AML and beyond.

overall_design: ChIP-Seq performed on multiple transcription factors and co-regulators associated with p300/CREBBP in two monocytic leukemia cell lines (MOLM-13 and OCI-AML3) under two conditions (DMSO control and 24h of A-485 treatment)

first: Markus

last: Meyerhöfer

first: Yawen

last: Zhou

last: Gallego-Crespo

first: Malte

last: Behrendt


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML. [Perturb-Seq]

country: Germany

overall_design: Cells were transduced with a targeted sgRNA library (186 sgRNAs). After selection cells were treated with either A-485 or DMSO. Cell Fixation performed directly 24 hours after treatment. Subsequent barcoding performed with Kits from ParseBiosciences (Mini/Mega v3) plus CRISPR Detect.

first: Viral

last: Shah

first: Daniel

last: Sasca


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML. [CRISPR-Screens]

overall_design: Dropout Screens using either Inobrodib or A-485, Treatment performed for 48 Hours, total screen duration 14 days


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
The lysine acetyltransferase (KAT) activity of p300/CREBBP has traditionally been linked to transcriptional activation. This has been attributed largely to acetylation of histone residues such as H3K27ac, a defining hallmark of active regulatory elements. Here we show that, in acute myeloid leukemia (AML), inhibition of p300/CREBBP catalysis can paradoxically increase transcription. We combined time-resolved dynamics of nascent and total transcription with chromatin binding dynamics of p300/CREBBP and their associated TFs/co-regulators (inferred from chromatin pull-down proteomics, acetyl-proteomics and motif enrichment) to uncover mechanisms of transcriptional rewiring after p300/CREBBP catalytic inhibition. In parallel, we dissected the functional contribution of individual p300/CREBBP acetyl-interactome members to KAT inhibition using genome-wide CRISPR-Cas9 dropout and focused Perturb-seq screens. Together, these approaches revealed that KAT inhibition paradoxically retains p300/CREBBP and promotes cooperative TF assembly and increased H3K27 acetylation at a subset of regulatory elements. The effect was most pronounced at IRF motif-enriched loci, including interferon-stimulated genes (ISGs), where KAT inhibition triggered p300/CREBBP accumulation and enhanced combinatorial TF binding, enabling recruitment of the ISG activator STAT1. Consequently, ISG loci were converted into transcriptionally active states that induced cell-cycle arrest, differentiation and apoptosis. Therapeutically, combining KAT inhibition with interferon-alpha augmented ISG expression, synergistically drove AML cell death in vitro and significantly extended survival in both AML xenografts and murine models. These findings refine our understanding of p300/CREBBP KAT activity, demonstrating that cooperative TF assembly can reconfigure p300/CREBBP-containing complexes under catalytic inhibition to induce transcription, with translational implications for reprogramming interferon-driven programs through catalytic inhibition in AML and beyond.
This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

last: Zhow


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML. [ChIP-seq]


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML. [RNA-seq]

overall_design: RNA-Seq performed in two monocytic leukemia cell lines (MOLM-13 and OCI-AML3) under three conditions (DMSO control, 24h of A-485 treatment and 24h of Inobrodib treatment (bromodomain inhibition of p300/CREBBP).


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML. [PRO-Seq]

overall_design: PRO-Seq performed in monocytic leukemia cell line MOLM-13 in DMSO controls and after 12h of A-485 treatment


title: Lisinopril Activates BI1 to Reprogram Lipid Metabolism and Restore Autophagy in ALS

city: Changchun

first: Hanlan

last: Yin

state: Jilin

address: 2699, Qianjin street

country: China

institute: Jilin University

summary:
Background
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder. Abnormal lipid metabolism represents a critical pathogenic determinant and key therapeutic target in ALS. Bax inhibitor 1 (BI1), an endoplasmic reticulum membrane protein, is downregulated in ALS and exhibits neuroprotective properties. However, due to incomplete understanding of its metabolic regulatory mechanisms, targeting BI1 for ALS therapy remains an area requiring further investigation.
Methods
Skeletal muscles from ALS mice pre- and post-BI1 treatment underwent transcriptomic analysis to identify BI1-regulated target genes and signaling pathways. Subsequently, we performed a structure-based virtual screening of FDA-approved compounds to identify potential BI1 activators. Lisinopril was selected as a lead candidate, and its effects were validated in SOD1G93A-transfected NSC34 cells and an ALS mouse model. Mechanistic studies explored its impact on autophagy regulation, lipid metabolism, and TGF-β1signaling pathways.
Results
Lisinopril upregulated BI1 protein expression, stabilizing mitochondrial membrane potential and conferring resistance to SOD1G93A-induced apoptosis. Concurrently, it regulated TGF-β1/PI3K/AKT/mTOR-dependent autophagy, maintained neuromuscular junction (NMJ) integrity, and reshaped triglyceride/sphingolipid/glycerophospholipid metabolism to attenuate spinal cord pathology in ALS mice, promoting energy metabolism shift toward glucose oxidation. Additionally, lisinopril inhibited the TGF-β1/Smad2/3 pathway to alleviate muscle fibrosis, downregulate Acp5/FN expression, and reduce type I collagen deposition.
Conclusions
Our study elucidated the molecular mechanism by which BI1 remodels lipid metabolism via the TGF-β1 pathway to influence ALS pathogenesis. These findings provided the first evidence that pharmacological activation of BI1 suppresses TGF-β1 expression and modulates triglyceride/sphingolipid/glycerophospholipid metabolism, thereby ameliorating ALS-related pathological phenotypes. Notably, repurposing lisinopril (an FDA-approved drug for hypertension) held promise for ALS therapy.

overall_design: Skeletal muscle tissue samples (100 mg) from ALS CON, and ALS BI1 mice were homogenized in TRIzol reagent for total RNA extraction, with RNA quality verified using an Agilent 2100 Bioanalyzer. Pooled libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads, with base calling and demultiplexing performed using CASAVA software.

first: Zhichao

last: Ren

first: Yan

last: Zhang

first: Yuxiang

last: Wang

first: Yiyang

last: Sun

first: Fuqiang

first: Linlin

last: Zeng


title: Inhibition of p300/CREBBP catalytic activity drives context-dependent transcriptional activation in AML. [SLAM-Seq]

overall_design: SLAM-Seq performed in monocytic leukemia cell line MOLM-13 at three timepoints (2h, 12h and 24h). At each timepoint, the cells were studied under four conditions (DMSO control, A-485 treatment, Inobrodib treatment (bromodomain inhbitor for p300/CREBBP) and dCBP-1 treatment (p300/CREBBP degradation).


title: Dosage compensation defects due to roX RNA deletion are rescued by recalibration of X/autosome stoichiometry [ChIP-seq]

status: Public on Feb 26 2026

city: Planegg-Martinsried

first: Fotios

last: Gkountromichos

address: Großhaderner Strasse 9

department: Molecular Biology

institute: Biomedical Center, Ludwig-Maximilians-Universität München

summary: Metazoa evolved regulatory networks to balance the expression of their sex chromosomes. In Drosophila, males have a single gene-rich X chromosome, whereas females have two. Balanced X/autosome expression is essential for viability, and in male flies is achieved by activation of genes on the X through the male-specific-lethal (MSL) dosage compensation complex (DCC). This ribonucleoprotein assembly contains long, non-coding roX RNAs. To dissect the functional requirements of roX in a cell-based system, we deleted the roX2 gene in male S2 cells and selected two independent lines lacking detectable roX RNA. In the absence of roX, the remaining MSL protein complex was unable to associate with known or newly identified binding sites and thus failed to activate transcription. Surprisingly, the X/autosome expression ratio appeared nevertheless compensated. Cytogenetic and genomic analyses revealed that both roX-deficient cell populations had acquired additional X chromosomes. Apparently, chromosome gains due to mis-segregation made up for the loss of DCC-mediated dosage compensation. Interestingly, ectopic expression of full-length roX2, but not of shortened derivatives, fully restored DCC binding and normalized the karyotype. These findings illustrate that X chromosome dosage compensation is critical for viability even in cultured cells and provide a striking example of rapid evolution under stringent selection.

overall_design: ChIP-seq of MSL2 and H4K16ac in wild-type and roX2-KO Drosophila Schneider S2 cells.

first: George

last: Yankson

first: Muhunden

last: Jayakrishnan

first: Aline

last: Campos Sparr

first: Marisa

last: Müller

first: Patrick

last: Heun

first: Peter

middle: B

last: Becker


title: An InDel Genomic Variant within a Bifunctional Super-Enhancer for LINC00636 and CD47 Regulation in Breast Cancer [RNA-seq]

city: San Francisco

first: Carolina

last: Di Benedetto

state: CA

address: 2340 Sutter Street, S371

country: USA

institute: University of California, San Francisco

summary: Highly accessible genomic super-enhancers often upregulate tumor-promoting genes in cancer, yet the role of genomic variation within them remains unclear. We identified a bifunctional super-enhancer that regulates the expression of cancer-promoting genes LINC00636 and CD47 in breast cancer. Our study revealed that a common germline insertion variant within the super-enhancer is associated with better progression-free survival in breast cancer patients and reduced chromatin accessibility at the super-enhancer locus. By deleting the insertion allele in breast cancer cells, we observed increased chromatin accessibility, leading to upregulation of LINC00636 and CD47, delayed cell death, and reduced infiltration of CD80+ pro-inflammatory macrophages—events that promote tumor growth. The absence of the insertion also activated a protumoral transcriptional program through LINC00636 overexpression. Our findings highlight an insertion/deletion variant that fine-tunes the regulatory function of a bifunctional super-enhancer and suggest a protective role for the insertion in breast cancer.

overall_design: Insertion-deleted MCF7 clones: RNA-seq was performed in parental MCF7 cells or in the clones M11 (MCF7Δ#1) and M46 (MCF7Δ#2), in which the germline insertion variant rs58296163 was deleted by CRISPR. This insertion variant is located within a core element of a bifuntional super-enhancer for the regulation of LINC00636 and CD47 gene expression. Two biological replicates per condition were used. LINC00636 overexpression in MCF7: RNA-seq was performed in LINC00636-overexpressing MCF7 cells. LINC00636 overexpression was carried out using CRISPR activation and two different sgRNAs (sgRNA1 or sgRNA2) targeting LINC00636-TSS or scramble sgRNA as control. Three biological replicates per condition were used.

first: Paola

last: Betancur


title: Dosage compensation defects due to roX RNA deletion are rescued by recalibration of X/autosome stoichiometry

overall_design: CUT&RUN of MSL2 and H4K16ac in wild-type and roX2-KO Drosophila Schneider S2 cells.

last: Muller


title: MAPK/ERK signaling regulates H3K9me3 heterochromatin reorganization to confer mesendoderm developmental competence

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: During gastrulation, dynamic interplay among cell signaling pathways dictates cell fate decisions. While extensive studies have elucidated their critical roles in morphological regulation, how these signals orchestrate the epigenome to confer developmental competence remains unclear. In this study, we demonstrate that H3K9me3-marked facultative heterochromatin domains undergo global reorganization during differentiation of human pluripotent stem cells (hPSCs) into mesendoderm (ME) and definitive endoderm (DE), which arise through epithelial-mesenchymal transition (EMT), but not into early neural ectoderm (NE), which retains epithelial state. We identify the MAPK/ERK pathway, acting downstream of FGF signaling, as a key mediator of this reorganization within a critical temporal window during hPSC-to-ME differentiation. Mechanistically, phosphorylated-ERK is enriched across chromatin domains spanning key developmental gene loci and exhibits a reciprocal genomic pattern with H3K9me3, which becomes ectopically accumulated upon MAPK/ERK inhibition. Furthermore, using CRISPRi-mediated perturbation of H3K9me3 methyltransferases, we reveal that proper establishment of H3K9me3 domains plays a dual role in repressing off-target genes and enabling robust activation of lineage-specific programs. Collectively, our findings reveal a previously unrecognized role for MAPK/ERK signaling in reorganizing the H3K9me3 landscape to confer developmental competence, providing mechanistic insight into how signaling pathways shape the epigenetic landscape during development.

overall_design: RNA-seq data of human pluripotent stem cell (hPSC)-derived neuroectoderm (NE),  mesendoderm (ME), and definitive endoderm (DE), with or without 1 µM MEK/ERK inhibitor (PD0325901) treatment, as well as H3K9me3 methyltransferase-CRISPRi (MTase-TKD) condition.

first: Satoshi

last: Matsui

first: Samuel

last: Sampson

first: Makiko

last: Iwafuchi


title: An InDel Genomic Variant within a Bifunctional Super-Enhancer for LINC00636 and CD47 Regulation in Breast Cancer  [ATAC-seq]

overall_design: ATAC-seq was performed in parental MCF7 cells or in the clones M11 (MCF7Δ#1) and M46 (MCF7Δ#2), in which the germline insertion variant rs58296163 was deleted by CRISPR. This insertion variant is located within a core element of a bifuntional super-enhancer for the regulation of LINC00636 and CD47 gene expression. Samples were processed in duplicates.


overall_design: ChIP-seq data of H3K9me3 and P-ERK in human pluripotent stem cells (hPSCs), neuroectoderm (NE), mesendoderm (ME), and definitive endoderm (DE), with or without 1 µM MEK/ERK inhibitor (PD0325901) treatment.

first: Gerardo

last: Mirizio

first: Marissa

last: Granitto


title: Mapping early PRC2 nucleation sites upon Suz12 reintroduction reveals features of de novo Polycomb recruitment

status: Public on Feb 25 2026

city: Mexico City

first: Víctor

middle: Julián

last: Valdés

state: Mexico City

address: Circuito Exterior s/n, Ciudad Universitaria

department: Departamento de Biología Celular y Desarrollo

country: Mexico

institute: Instituto de Fisiología Celular (IFC), Universidad Nacional Autónoma de México (UNAM)

summary: Polycomb domains safeguard cell identity by maintaining lineage-specific chromatin states enriched in repressive histone modifications preserving the epigenetic memory of each cell lineage. While Polycomb Repressive Complex 2 (PRC2) can re-establish its occupancy after perturbation, the mechanisms that guide de novo Poly-comb recruitment remain unclear. To address this, we engineered an auxin-inducible degradation system to reversibly deplete and reintroduce the endogenous PRC2 core subunit Suz12 in mouse embryonic stem cells (mESCs). Genome-wide profiling at early recovery time point revealed PRC2 nucleation sites, characterized by rapid Suz12 and H3K27me3 re-accumulation and signal strength.

overall_design:
ChIP-seq of Suz12 (GFP antibody) and H3K27me3 in mouse embryonic stem cells (mESCs) with an Auxin Inducible Degradation (AID) system of the Suz12 core subunit of PRC2. Experimental conditions include Control, Auxin and Reintroduction samples. For each condition, two biological replicates were conducted.
ChIP-seq of H2AK119ub1 in mouse embryonic stem cells (mESCs) with an Auxin Inducible Degradation (AID) system of the Suz12 core subunit of PRC2. Experimental conditions include Control, Auxin and Reintroduction samples. For each condition, two biological replicates were conducted.

first: Itzel

middle: A

last: Hernández-Romero

first: Carlos

last: Peralta-Alvarez

first: Victor

middle: J

last: Valdes


title: A role for ETV1 and endothelial cell-derived extracellular vesicle microRNAs in priming fibroblast response to vesicle-bound FGF2

city: Chicago

first: Heidi

last: Yuan

address: 801 S Paulina St

institute: University of Illinois Chicago

type: Non-coding RNA profiling by high throughput sequencing

summary: Communication between various cell types following wounding is paramount for proper healing and regeneration of injured tissue. Endothelial cells and fibroblasts are critical cellular players involved in cutaneous wound repair, yet their communication mechanisms are not well understood. It has previously been shown that extracellular vesicles derived from endothelial cells (ECEVs) induce dermal fibroblasts to express a gene signature correlated with FGF2-mediated cancer associated fibroblast (CAF) activation, under the control of transcription factor ETV1. In this report, we utilize loss-of-function studies to define the mechanistic role of ETV1 in conferring this ECEV-induced transcriptomic shift and functional change in fibroblasts. Additionally, we identify highly expressed ECEV microRNAs and examine their potential contribution to the ECEV mechanism through downstream gene modulation. In summary, we describe a plausible mechanism by which both ETV1 and top ECEV microRNAs promote a genotypic and phenotypic shift in dermal fibroblasts that have taken up ECEVs.

overall_design: Small RNA sequencing of extracellular vesicles isolated from primary human dermal microvascular endothelial cells (ECEVs) using a PEG-based isolation reagent.

first: Chen

last: Han

first: Lin

last: Chen

first: Sriram

last: Ravindran

first: Luisa

last: DiPietro


title: Unraveling age-related cellular and molecular changes associated with vestibular hair cells

city: Omaha

first: David

middle: Z

last: He

state: NE

address: 2500 California Plaza

department: Biomedical Science

institute: Creighton University

summary: The cochlear and vestibular sensory epithelia contain four types of hair cells (HCs) for detecting sound and head motion respectively. In the current study, we comprehensively assessed the molecular changes associated with vestibular HCs with aging to identify age-related marker genes for age-related vestibular dysfunction and performed a comparative analysis with cochlear aging to assess the aging patterns in the two organs of the inner ear.

overall_design: HCs from cochlear and vestibular sensory organs were isolated from 22-month-old CBA/J mice. cDNA library was constructed using the 10x Genomics Chromium Single Cell 3’ V3.1 dual index kit. Seven mice were used for each biological replicate. Six and four biological replicates were prepared for cochlear sensory epithelium and vestibular sensory epithelia respectively. Illumina NextSeq 6000 sequencer was used for sequencing.

first: Samadhi

last: Kulasooriya

first: Huizhan

last: Liu


title: RNA-seq analysis of liquid-induced suspended animation (LISA) in C. elegans

status: Public on Feb 24 2026

first: Junqiang

state: CA - California

address: 555 Mission Bay Blvd South

summary: To elucidate the molecular landscape associated with liquid-induced suspended animation (LISA) in C. elegans, we performed transcriptomic profiling of animals subjected to high-density isosmotic liquid conditions. Wild-type N2 animals were maintained at 20 °C. To induce LISA, synchronized L4 larvae were incubated under static high-density liquid conditions (“standing” treatment) for 12 hours, while control animals were maintained under standard plate culture conditions prior to collection.  At the time of sample collection, animals were washed off NGM plates using M9 buffer, collected into 1.5 mL microcentrifuge tubes, and homogenized using a tissue disruptor. Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (RC112-01, Vazyme) according to the manufacturer’s instructions. RNA concentration and purity were measured using a NanoDrop spectrophotometer, and RNA integrity was assessed by agarose gel electrophoresis. For each sample, 1 µg of total RNA was used for library preparation and sequencing. Three  biological replicates were included for each condition.  Transcriptomic analysis revealed robust induction of stress-responsive genes during LISA. Notably, members of the small heat shock protein family, particularly the hsp-16 gene cluster, were among the most strongly upregulated transcripts. This induction was sharply confined to the genomic hsp-16 cluster without affecting adjacent genes. These findings define a distinct LISA-associated transcriptional state characterized by coordinated stress-responsive gene expression, consistent with a dormant yet physiologically primed condition.

overall_design: For standing treatment, synchronized L4 larvae were either subjected to standing 12 hours or maintained under control conditions prior to collection.

first: Dengke

last: Ma


title: Impact of vitamin D deficiency on defective endometrial decidualization and the repressive role of VDR in the epigenomic network [CUT&Run]

city: Durham

first: MyeongJin

last: Yi

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: The identification of the factors regulating female reproduction is critical to understanding how the environment and nutrition impact female fertility and reproductive health. Vitamin D and its cognate receptor, VDR, are recognized for their role in calcium homeostasis; however, their broader impact on female reproduction remains underexplored. Here, we demonstrate that vitamin D and VDR are involved in the hormonal induction of uterine stromal cell differentiation, known as decidualization. Mice fed a vitamin D-deficient diet displayed an impaired hormonally induced decidual response. In a human endometrial stromal cell line, T-HESC, VDR decreases during decidualization. siRNA knockdown of VDR in T-HESC enhanced decidualization, while overexpression of VDR inhibited decidualization. Chromatin accessibility and histone modification analyses revealed that VDR functions as a chromatin regulator, restricting accessibility and maintaining transcriptional repression in specific genomic regions. Transcriptomic analyses confirmed that VDR broadly modulates gene expression, with most ligand-mediated effects dependent on its presence. These findings identify VDR as a key regulator of transcriptional and chromatin landscapes in endometrial stromal cells, offering novel insights into vitamin D signaling in reproduction. This study highlights the potential of targeting vitamin D pathways to treat uterine disorders associated with impaired decidualization.

overall_design:
Experimental Design: 2 Different Experiments
Experiment 1. Identification of cistromic changes in human endometrial stromal cells by the receptor (VDR) and the ligand (1,25(OH)2D3).
There are 8 groups, and 24 samples in total. All libraries were prepared from the human endometrial stromal cell line (T-HESC).
1) Control lentiviral GFP vector transduced T-HESCs treated with vehicle and precipitated with VDR antibody, n=3
2) Control lentiviral GFP vector transduced T-HESCs treated with vehicle and precipitated with IgG, n=3
3) Control lentiviral GFP vector transduced T-HESCs treated with 1,25(OH)2D3 and precipitated with VDR antibody, n=3
4) Lentiviral VDR plasmid transduced T-HESCs treated with 1,25(OH)2D3 and precipitated with IgG, n=3
5) Lentiviral VDR plasmid transduced T-HESCs treated with vehicle and precipitated with VDR antibody, n=3
6) Lentiviral VDR plasmid transduced T-HESCs treated with vehicle and precipitated with IgG, n=3
7) Lentiviral VDR plasmid transduced T-HESCs treated with 1,25(OH)2D3 and precipitated with VDR antibody, n=3
8) Lentiviral VDR plasmid transduced T-HESCs treated with 1,25(OH)2D3 and precipitated with IgG, n=3
Experiment 2.  Impact of VDR and 1,25(OH)2D3 on histone modifications
There are 8 groups, and 24 samples in total. All libraries were prepared from the human endometrial stromal cell line (T-HESC).
1) Non-targeting pooled siRNA-transfected T-HESCs and precipitated with H3K4me3, n=3
2) Non-targeting pooled siRNA-transfected T-HESCs and precipitated with H3K27me3, n=3
3) Non-targeting pooled siRNA-transfected T-HESCs and precipitated with H3K27ac, n=3
4) Non-targeting pooled siRNA-transfected T-HESCs and precipitated with IgG, n=3
5) VDR siRNA-transfected T-HESCs and precipitated with H3K4me3, n=3
6) VDR siRNA-transfected T-HESCs and precipitated with H3K27me3, n=3
7) VDR siRNA-transfected T-HESCs and precipitated with H3K27ac, n=3
8) VDR siRNA-transfected T-HESCs and precipitated with IgG, n=3
Data Analysis Strategy: Dr. Austin Bell-Hensley, Dr. Tianyuan Wang, and Dr. Abdull Massri from the informatics group supported Dr. MyeongJin Yi with the analysis.
1) Remove adaptor 2) QC with trim-galore 3) Map the pair-end reads 4) Count reads mapped to chrM 5) Remove duplicated reads 6) Remove unmapped reads 7) Remove reads mapped to chrM 8) Prepare SAM file based on trimmed 9bp reads 9) Random sampling to the same depth 10) Compare between different groups

first: Skylar

last: Montague Redecke

first: Tianyuan

last: Wang

first: Austin

last: Bell-Hensley

first: Abdull

last: Massri

first: Francesco

last: DeMayo


title: Divergent clonal evolution and tumor microenvironment remodeling shape gastric cancer peritoneal metastasis

status: Public on Feb 23 2026

city: Seongnam-si

first: Clementine

last: Charton

state: Gyeonggi-do

address: 82 Gumi-ro-173-beon-gil Bundang-gu

country: South Korea

institute: Seoul National University Bundang Hospital

summary: Gastric cancer peritoneal metastasis (GCPM) is a distinct clinical entity with a poor prognosis, characterized by aggressive features and limited treatment options. Understanding its molecular biology is critical for developing effective therapies. We performed whole genome and transcriptome sequencing on GCPM samples and paired primary gastric cancer (GC) tissues from 14 and 26 patients, respectively. Our analysis revealed substantial intra-patient heterogeneity between GCPM and primary tumors at both genetic and functional levels. Inter-patient variability was observed in mutational overlaps, with some signatures unique to either GCPM or primary tumors. Tumor evolution analysis suggested divergent clonal evolution, with distinct clones specific to GCPM or primary tumors in most patients. The tumor microenvironment (TME) was poorly conserved between primary GC and GCPM, with desert-type primary tumors often transitioning to immune-enriched TMEs in metastases. These findings suggest that immunotherapy resistance in GCPM may arise from factors beyond intrinsic TME characteristics, such as limited drug delivery due to the peritoneal-plasma barrier. Collectively, our results highlight significant molecular and TME heterogeneity between GCPM and primary tumors, emphasizing the need for GCPM-specific stratification and innovative treatment strategies to improve outcomes.

overall_design: RNAseq profiling of 26 advanced gastric cancer patients, including 18 primary GC tumors, 26 GC peritoneal seeding tumors (GCPM), 6 Normal adjacent to the tumor, 2 omentum metastatic tumors and 2 lymph node metastatic tumors; paired primary-metastatic tumors were available for 20 patients

first: So Hyun

last: Kang

first: Stephanie

middle: S

last: Kim

first: Young Suk

last: Park

first: Sang-Hoon

last: Ahn

first: Yun-Suhk

last: Suh

first: Nak Jung

last: Kwon

first: Kyoung Un

first: Jieun

last: Lee

first: Jinho

first: Hyung-Ho


title: Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria

city: Cambridge

first: Jennifer

last: Cascino

state: MA

address: 31 Ames Street

department: Biology

institute: Massachusetts Institute of Technology

summary: Cyanobacteria are the most abundant phototrophs and hold potential as a carbon-negative platform for bioengineering applications. However, these efforts have been hampered by limited mechanistic understanding of their gene expression, including transcription termination. Unlike most bacteria, cyanobacteria lack the transcription termination factor Rho, raising the speculation that all transcription ends with intrinsic terminators. Here we show that most transcription units (TUs) in Synechococcus elongatus PCC 7942 are not terminated by known termination pathways. Although many TUs (52%) have unique, well-defined 3' ends, only a small fraction have features that resemble canonical intrinsic terminators (30%). The noncanonical 3' ends (22%) broadly lacked strong secondary structure, leaving it unclear how these ends are protected against 3'-5' exonucleolytic decay, but a dinucleotide motif was observed. Furthermore, many TUs (46%) have diverse positions of mRNA 3' ends, suggesting a potentially diffuse termination signal. Finally, we provide evidence that the transcription-repair coupling factor Mfd reduces transcriptional readthrough at the well-defined 3' ends, suggesting that Mfd-dependent termination may be prevalent in this species. Together, our work reveals unique end architectures of the cyanobacterial transcriptome and suggests that undescribed transcription termination mechanisms are active in the phylum.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Rend-seq mapping of transcription unit architectures including RNA 3' ends at single-nucleotide resolution in the wild-type (WT) freshwater cyanobacterium Synechococcus elongatus PCC 7942 and a mutant deleted for the transcription-repair coupling factor Mfd (Mfd_KO). Rend-seq libraries for two technical replicates of WT (cells collected from the same flask) and two biological replicates of Mfd_KO (separate flasks) were prepared.

first: K. Julia

last: Dierksheide

first: Gene-Wei

last: Li


title: Single-nucleus RNA Sequencing of Kidney and Brain Samples from Young WT and Klotho KO Male Mice

city: Boston

first: Alexander

last: Tyshkovskiy

state: Massachusetts

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital, Harvard Medical School

summary: This dataset includes single-nucleus gene expression profiles from kidney and cerebral cortex samples of a young male C57BL/6J mouse with α-klotho gene knockout, along with the age-matched wild-type control. This short-lived model was used to validate transcriptomic clocks and to comprehensively characterize the molecular hallmarks of mortality associated with this genetic modification.

overall_design: Young (8-week-old) male wildtype (WT) and α-klotho knockout (Klotho KO) C57BL/6J mice. 4 biological replicates: 1 kidney and 1 brain sample per genotype.

first: Tomoko

last: Kasahara

first: Yoshiyasu

last: Tongu

first: Takaaki

last: Abe

first: Vadim

middle: N

last: Gladyshev


title: RNA Sequencing of Kidney and Skeletal Muscle Samples from Young WT and Klotho KO Male Mice

summary: This dataset includes gene expression profiles from kidney and skeletal muscle samples of young male C57BL/6J mice with α-klotho gene knockout, along with age-matched wild-type controls. This short-lived model was used to validate transcriptomic clocks and to comprehensively characterize the molecular hallmarks of mortality associated with this genetic modification.

overall_design: Young (8-week-old) male wildtype (WT) and α-klotho knockout (Klotho KO) C57BL/6J mice. 24 biological replicates: 6 kidney and 6 skeletal (gastrocnemius) muscle samples per genotype.


title: Tim-3 Agonist Restrains ILC2 Function and Attenuates Airway Hyperreactivity via NLK Pathway

status: Public on Feb 22 2026

city: Los Angeles

first: Yoshihiro

last: Sakano

address: 1450 Biggy street

department: Molecular Microbiology & Immunology

institute: Unversity of Southern California

summary: Allergic asthma is driven by type 2 inflammation involving cytokines such as IL-4, IL-5, and IL-13, with group 2 innate lymphoid cells (ILC2s) playing a key pathogenic role. Here, we identify T cell immunoglobulin and mucin domain-containing protein 3 (Tim-3) as a negative regulator of ILC2 function. Tim-3 expression was upregulated in activated pulmonary ILC2s, and engagement with Tim-3 agonists inhibited ILC2 activation, proliferation, and type 2 cytokine production via the NLK signaling pathway and suppression of mitochondrial metabolism. In vivo, Tim-3 agonists alleviated airway hyperreactivity (AHR) and inflammation in both IL-33- and Alternaria alternata-induced AHR models, while ILC2-specific Tim-3 deletion exacerbated AHR. These results were confirmed in human ILC2s and humanized mice, supporting the translational relevance. Our findings establish Tim-3 as an inhibitory checkpoint for ILC2s and suggest its potential as a therapeutic target in allergic asthma and other ILC2-mediated diseases.

overall_design: mRNA profiles of mouse lung ILC2s which were cultured with isotype control or Tim3 agonist,  from CB57BL/6 mice were generated by deep sequencing, in duplicates, using a NextSeq 500.


title: Whole-Genome Bisulfite Sequencing (WGBS) Analysis of Tail Tip Tissues from F2 Generation Mice

status: Public on Mar 08 2026

city: Guangzhou

first: Qi

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

department: Developmental biology

institute: Southern Medical University

type: Methylation profiling by high throughput sequencing

summary: Here, we include data on the transmission of DNA methylation patterns to the F2 generation, which are derived from F1 progeny sired by either in vivo or O-Torgs-derived  spermatids.

overall_design: Whole-Genome Bisulfite Sequencing (WGBS) Analysis of  tail tip tissues from F2 generation mice.

first: Xiaoyang

last: Zhao

first: Fang

last: Luo

first: Kai

last: Miao

first: Cong

last: Wan


title: RNA Sequencing of Liver Samples from UM-HET3 Mice Exposed to Various Compounds from the ITP Study

summary: This dataset contains liver gene expression profiles of aged UM-HET3 male and female mice subjected to long-term treatment with various compounds from ITP studies, along with age-matched and young control mice of the same strain. It is part of a broader dataset used to identify gene expression signatures of aging, mortality, and lifespan, as well as to develop rodent and multi-species transcriptomic clocks of chronological age and expected mortality.

overall_design: Male and female UM-HET3 mice were treated with various compounds in food as part of the ITP program until sacrifice at 22 months. Canagliflozin group: 7 biological replicates per sex; other compounds: 3 biological replicates per sex; old (22-month-old) control group: 24 biological replicates per sex; young (4-6-month-old) control group: 6 biological replicates per sex.


title: Reconstitution of spermatogenesis and continuous generation of functional haploid germ cells in mouse testicular organoids

summary: Testicular organoids that support spermatogenesis and generate functional haploid germ cells are still lacking. Here, we developed a formation-differentiation culture approach to generate optimized testicular organoids (O-Torgs) derived from neonatal mouse primary testicular cells. These O-Torgs could essentially recapitulate the seminiferous tubule morphogenesis, Sertoli cell maturation and testosterone secretion. Importantly, O-Torgs not only support spermatogenesis but also sustain proliferative undifferentiated spermatogonia and continuous generation of functional haploid cells for up to three months, with offspring derived from these haploid cells displaying normal growth and reproductive capability to F2 generation. Mechanistically, we found that the formation stage enhanced the reconstruction of tubule-like structures and subsequent spermatogenesis by providing a more conducive extracellular matrix niche. Finally, O-Torgs were proved to be effective in modeling male infertility and drug screening, with BTT-3033 acting as a potential drug in protecting busulfan-mediated germ cell loss. Overall, our work establishes a strategy to obtain functional testicular organoids, offering promising avenues for male infertility modeling and drug discovery.

overall_design: scRNA - seq profiling of testicular organoids cultured with the traditional system and optimized system at Day6 and Day40


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

status: Public on Feb 20 2026

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

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

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

first: Ali

last: Khadim

first: Mahsa

last: Zabihi

first: Elie

last: El Agha


title: SF3B1 Phosphorylation Prompts U2AF2 Dissociation for Widespread Control of Pre-mRNA Splicing

status: Public on Mar 06 2026

city: Rochester

first: Clara

last: Kielkopf

state: New York

address: 601 Elmwood Ave

department: Biochemistry & Biophysics

institute: University of Rochester

summary: Reversible pre-mRNA splicing factor phosphorylation is a well-documented feature of spliceosome assembly, activation, and disassembly, yet its functional and mechanistic roles are still emerging. SF3B1, a core spliceosome subunit, is extensively phosphorylated before the first catalytic step of pre-mRNA splicing. Intriguingly, most SF3B1 phosphorylation sites surround its binding sites for U2AF2, an early-stage pre-mRNA splicing factor. Here, we discovered that SF3B1 phosphorylation significantly decreases its association with U2AF2. We determined three crystal structures revealing electrostatic repulsion between an acidic U2AF2 alpha helix and the negatively charged phosphoryl group of SF3B1. Variants with amino acid substitutions that prevent or mimic SF3B1 phosphorylation perturbed thousands of splice sites, primarily those marked by uridine-rich splice site signals recognized by U2AF2. Collectively, our findings demonstrate a widespread but previously unrecognized role for SF3B1 phosphorylation as a gateway for U2AF2 dissociation so that pre-mRNA splicing can proceed.

overall_design: RNA-seq of SF3B1 knockdown and rescue with wildtype or TP-substituted derivatives (AP or EP) SF3B1 constructs as well as OTS964 treatment in HEK 293T cells.

first: Christopher

middle: L

last: Kirchhoff

first: Hannah

middle: R

last: Powell

first: Justin

middle: W

last: Galardi

first: Sarah

last: Loerch

first: Mary

last: Pulvino

first: Jermaine

last: Jenkins

first: Paul

last: Boutz


title: Single nucleus RNA-seq of  mouse kidney throughout postnatal development.

status: Public on Feb 19 2026

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

summary: We sought to characterize transcriptomic changes in cells of the Loop of Henle throughout posnatal developed.

overall_design: Nuclei were obtained from digestion of kidneys from which the cortex had been grossly removed and analyzed with snRNA-seq.

first: Jane N.

last: Warshaw

first: Denise K.

last: Marciano


title: YAP activation reverses aging-related visual dysfunction caused by impaired cell-matrix adhesion

city: Ulsan

first: Hyo Kyung

last: Lee

address: UNIST-gil 50

department: Biomedical engineering

institute: UNIST

summary: Cellular senescence of retinal pigment epithelium (RPE) cells is a major contributor to age-related visual decline, particularly in the pathology of age-related macular degeneration (AMD). While genome-wide association studies (GWAS) have advanced our understanding of the genetic factors underlying AMD, the molecular mechanisms driving RPE senescence remain poorly understood. In this study, we performed single-cell RNA sequencing (scRNA-seq) on RPE cells from young and old mice, uncovering a close relationship between dysregulated genes involved in cell-matrix adhesion and RPE senescence. Using hydrogel systems to manipulate integrin-mediated cell-matrix adhesion, we demonstrated that impaired adhesion can induce cellular senescence in RPE cells. Mechanistically, we identified the mechanotransducer Yes-associated protein (YAP) as a key protector against RPE senescence. Notably, YAP activation alone was sufficient to trigger stem cell transcriptional programs and reverse aging phenotypes in senescent RPE cells. Furthermore, treatment with TRULI, a small-molecule YAP activator, significantly restored visual function in both an AMD mouse model and naturally aged mice. Our findings highlight the integrin-YAP mechanotransduction pathway as a fundamental mechanism preventing RPE senescence, positioning YAP activation as a promising strategy to reverse RPE aging and restore visual function.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
For scRNA-seq, young and old mice were sacrificed to dissociate cells from the RPE. Their eyes were immediately enucleated and the anterior eye cups were subsequently dissected. After carefully removing the retina, RPE cells were dissociated following the manufacturer’s instruction for the papain dissociation system (Worthington).
To analyze transcriptome profiles of three human ARPE19 cell line samples, ARPE19 cells expressing control vectors were cultured either on plastic or 1.5 kPa, and cells with overexpression of YAP-HA were cultured on 1.5 kPa.
For mouse samples, old mice treated either with or without TRULI were sacrificed for RNA extraction, and their eyes were immediately enucleated.

first: Gyuri

last: Kim

first: Chanok

last: Son

first: Yujeong

last: Oh

first: Jae-Byoung

last: Chae

first: Chul-Woo

last: Park

first: Chaekyu

first: Ja-Hyoung

last: Ryu

first: Semin

first: Jiwon

last: Jang

first: Hyewon

last: Chung


title: Target discrimination and PAM profiling of the Thermotoga maritima type I-B CRISPR system

city: Baltimore

first: Charles

last: Lenihan

state: MD

address: 8 S Durham St

institute: Johns Hopkins University

summary: Type I-B CRISPR-Cas systems represent the most abundant CRISPR subtype in nature and have emerged as powerful tools for endogenous genome editing in diverse prokaryotes. Here we reconstitute and characterize the type I-B1 system from the thermophile Thermotoga maritima (Tma) using purified components. We demonstrate that Tma Cascade requires standalone Cas11 expression, as the cryptic internal translation start site within cas8b1 is non-functional in E. coli. The reconstituted system exhibits canonical type I function including RNA-guided DNA binding, PAM-dependent target discrimination, Cas3-mediated degradation, and seed region interrogation spanning seven PAM-proximal nucleotides. Using next-generation sequencing-based PAM library screens, we define a YYD consensus PAM (Y = C/T; D = G/A/T) with strong discrimination against the array repeat-adjacent sequence (AAC). Comprehensive PAM profiling reveals context-dependent tolerance for non-consensus sequences and identifies numerous intermediate-activity PAMs that may function in priming. Comparison with other characterized type I-B systems reveals correlation between Cas8b variant and position -3 specificity, conserved pyrimidine preference at position -2, and variability at position -1. This work establishes a thermostable type I-B platform for biotechnological applications and provides insights into evolutionary mechanisms balancing PAM promiscuity with self-discrimination in the most abundant CRISPR-Cas subtype.

overall_design: In vitro characterization of the PAM preferences of a purified CRISPR-Cas system. Assaying target binding by Cascade, as well as target degradation by Cascade and Cas3.

first: John

last: Mallon

first: Sowmyaa

last: Shridhar

first: Scott

last: Bailey


title: Clonal dynamics reveal cancer resistance arises from adaptive programs [RNA-Seq]

status: Public on Feb 18 2026

city: Philadelphia

first: Yeqing

last: Chen

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

summary: Most advanced cancers initially respond to targeted therapies but eventually relapse1. Rather than acquiring new mutations, resistance is driven by drug-tolerant persister cells (DTP) that enter a reversible drug-refractory state and sustain minimal residual disease2. Here, we developed MeRLin, a high-resolution barcoding platform combining single-cell RNA sequencing, RNA fluorescence in situ hybridization, and computational analyses to track clonal and transcriptional dynamics of melanoma cells during targeted therapy. Clonal tracking reveals that dominant resistant clones arise from minor pre-treatment subpopulations. The pre-treatment melanoma populations diversify into phenotypically distinct DTP subpopulations, marked by stress-like, lipid metabolism, PI3K signaling, and extracellular matrix remodeling programs associated with adaptive resistance. Spatial transcriptomics revealed the co-localization of lipid metabolism and PI3K signaling programs near the tumor boundaries, and a complex network of autocrine and paracrine interactions among DTP subpopulations. Using barcoded RNA fluorescence in situ hybridization, we identified a dominant persister subpopulation in resistant tumors marked by SLC2A1 expression. Thus, MeRLin provides a robust framework to dissect melanoma heterogeneity and uncover vulnerabilities in persister populations to improve long-term treatment efficacy.

overall_design: WM4237-1 cells were spinfected with a lentiviral barcode library in the presence of polybrene (8 μg/mL). mNeptune2.5-positive cells were sorted by flow cytometry to ensure a multiplicity of infection (MOI) below 40%. Barcoded cells were then expanded and split into replicate populations, with one aliquot preserved as the original control. Replicates of barcoded WM4237-1 cells were subcutaneously injected into immunodeficient mice and monitored for tumor growth. Upon establishment, tumors were treated with BRAFi/MEKi, and samples were collected longitudinally throughout treatment until relapse.

first: Haiyin

last: Li

first: Jessica

last: Kaster

first: Maggie

last: Dunne

first: Min

last: Xiao

first: Ling

first: Monzy

last: Thomas

first: Nazifa

last: Promi

first: Dylan

last: Fingerman

first: Gregory

last: Brown

first: Xingyue

last: Zhu

first: Meenhard

last: Herlyn


title: Single nucleus transcriptomics to study sex differences during murine E. coli pyelonephritis

first: Ashlee

middle: M

last: Earl

address: 415 Main Street

department: Infectious Disease and Microbiome Program

institute: Broad Institute

summary: This project employs models of urinary tract infection (UTI) in female, androgen-exposed female, and male mice to determine molecular mechanisms by which host androgen exposure promotes Escherichia coli pyelonephritis as well as renal scarring, a common sequela of upper-tract UTI. Our prior findings indicated that the influence of sex, including androgen exposure, on these common bacterial infections is more complex than previously appreciated. Specifically, male sex was associated with increased risk for chronic cystitis and high-titer pyelonephritis, as well as formation of renal abscesses. These snRNA-seq experiments were designed to interrogate the fundamental sex differences impacting the host-pathogen interaction and cellular responses in E. coli pyelonephritis, thereby influencing pathogenicity and outcome of infection.

overall_design: single nucleus RNA-seq investigation of male, female, and androgen-explosed female C3H/HeN mice in a model of urinary tract infection (UTI).

first: Teri

last: Hreha

first: Abigail

last: Manson

first: Christina

last: Collins

first: Haojia

last: Wu

first: Christophe

last: Georgescu

first: Benjamin

last: Humphreys

first: David

last: Hunstad


title: Inhibition of the non-lysosomal glucosylceramidase GBA2 accounts for the efficacy of sinbaglustat in a murine model of Sandhoff disease

city: Allschwil

first: Pijus

last: Brazauskas

address: Hegenheimermattweg 91

country: Switzerland

institute: Idorsia Pharmaceuticals

summary: Sinbaglustat is a small molecule under investigation as a treatment for lysosomal storage disorders. It inhibits two enzymes involved in glycosphingolipid (GSL) metabolism, the non-lysosomal glucosylceramidase (GBA2) and, with a lower affinity, glucosylceramide synthase (GCS). High  doses of structurally related dual GBA2/GCS inhibitors such as miglustat, and pure GCS inhibitors have shown efficacy in a transgenic mouse model (Hexb-/-) of Sandhoff disease, aGM2 gangliosidosis. Whether the inhibition of GBA2 alone confers protection is unknown. We first assessed the functional profile of sinbaglustat relating to GBA2 and GCS inhibition in cellular models and wild-type (WT) mice. Then we investigated sinbaglustat’s potential efficacy in preventing disease manifestation in Hexb-/- mice upon chronic treatment with two dose levels (30 and 300 mg/kg/day), aimed at predominant inhibition of GBA2 or GBA2 and GCS. Non-treated WT mice served as controls. Sinbaglustat inhibited GBA2 more potently than GCS in GM2 gangliosidosis patient-derived fibroblasts and primary mouse neurons. The dual inhibition profile was also reflected in a dose-dependent, bell-shaped modulation of glucosylceramide, the substrate of GBA2 and product of GCS  , in wild-type mouse brain. At the two sinbaglustat dose levels that we tested in Hexb-/- mice, glucosylceramide levels in cerebral cortex were elevated, indicating GBA2 target engagement. Only the high 300 mg/kg/day dose reduced in addition the levels of various other GSLs compared to Hexb-/- untreated mice, demonstrating GCS target engagement in the central nervous system. In the liver and plasma, sinbaglustat dose-dependently decreased many GSLs including hexosaminidase A substrates. Sinbaglustat partially reversed the increase in mRNA expression of several neuroinflammation-related genes in the hippocampus of Hexb-/- mice. Sinbaglustat treatment at both dose levels delayed the age at which Hexb-/- mice started to develop motor impairments by about 2-4 weeks. The 30 mg/kg/day dose increased median survival of Hexb-/- mice by approximately 13.5%, the 300 mg/kg/day dose by approximately 18%.  The study indicates that sinbaglustat could represent a viable treatment option for GM2 gangliosidosis if data from the mouse model translate to human. Importantly, our data also reveal that GBA2 inhibition in the central nervous system is largely responsible for sinbaglustat’s therapeutic effect in Hexb/- mice.

overall_design: RNAseq of the hippocampus of Hexb/- mice (hexβtm1R1p) and WT littermates treated with singablustat from week 4 to week 15 at either 30 mg/kg/day, for primary inhibition of GBA2, or 300 mg/kg/day, for inhibition of both GBA2 and GCS. Untreated Hexb /- and untreated WT mice served as comparator and control.

first: Michel

last: Steiner

first: Kostantin

last: Dobrenis

first: Catherine

last: Vaillant

first: Jesper

last: Ryge

first: Bérengère

last: Renault

first: Richard

last: Welford


title: Microglia Mitochondria Support Neuronal Maturation via Metabolic and Transcriptional Reprogramming in Human 3D In Vitro Brain Model

status: Public on Feb 16 2026

city: Cincinnati

first: Volha

last: Liaudanskaya

address: 3159 Eden Ave.

department: Biomedical Engineering

institute: University of Cincinnati

summary: Autism Spectrum Disorder (ASD) is a neurodevelopmental condition characterized by disrupted neuronal circuit maturation. Emerging evidence implicates microglial function and mitochondrial regulation as contributors to ASD-associated biology, yet the mechanisms linking these processes to neuronal development remain poorly defined. Neuronal maturation requires tightly coordinated metabolic and transcriptional remodeling, in which mitochondria play a central role in regulating the developmental tempo and metabolic identity, while microglia modulate neuronal synaptic network maturation; however, whether microglia influence neuronal development through direct mitochondrial contributions remains unknown. Here, using a 3D human in vitro brain model, we show that microglial mitochondria can act as transferable cues that promote metabolic, mitochondria-dynamic, and transcriptional aspects of neuronal maturation. Neurons treated with microglial mitochondria exhibited enhanced oxidative metabolism, improved mitochondrial dynamics, and activation of gene programs associated with nervous system development and neurogenesis. These effects were accompanied by increased expression of dendritic maturation markers, supporting the view that transferred mitochondria can contribute to the regulation of neuronal state. However, full structural and synaptic maturation required the combined action of microglia-derived mitochondria and secreted signaling factors. Together, this study identified microglial mitochondrial transfer as a contributor to neuronal maturation with potential relevance to developmental trajectories disrupted in ASD.

overall_design: RNA-seq profiling of NM (Neurons and Microglia co-cultures), NTr (microglia mitochondria-treated neurons), and NUnTr (untreated neurons). (N refers to mt-DsRed2 Induced Human Neural Stem Cells (hiNSCs) and M refers to -mt-EBFP2 HMC3 Microglia Cell Line )

first: Sydney

middle: P

last: Sterben

first: Charitha

middle: C

last: Anamala

first: Sahan

last: Kansakar

first: Vaishnavi

last: Koduri


title: Deep Cellular and Spatial Profiling of the Mouse Spinal Cord Reveals Sex-Specific Neuron Types and the Ascending Projection Neuron Repertoire

first: Allan-Hermann

last: Pool

state: TX

address: 6000 Harry Hines Blvd

department: Department of Neuroscience, Peter O'Donnell Brain Institute, Department of Anesthesia and Pain Management

institute: University of Texas Southwestern Medical Center

summary: Spinal cord gives rise to central somatosensation and orchestrates autonomic and motor control. How its cellular diversity achieves physiological functions across sex and along its longitudinal axis and links spinal cord to higher order brain centers remains poorly understood. Here we used retrograde viral tracing with spatial transcriptomics and multiomic profiling of >750k mouse spinal cord neurons to define its output logic and functional cellular repertoire. We identified 70 spinal projection neuron classes that link the spinal cord to hind-, mid-, and forebrain centers implicated in itch, touch, and pain revealing the output wiring logic of the spinal cord. Furthermore, we characterized >500 anatomically and transcriptomically distinct neuron types that revealed extensive (~50%) rostro-caudal cellular specialization as well as first sex specific neuron classes in the spinal cord.  Finally, we assembled a neuron-class-to-phenotype map of the structure based on genetically defined interventions. As a result, we deliver an anatomically and functionally annotated cellular atlas of the complete adult mouse spinal cord to guide future interrogation of the organ.

overall_design: Cervical, thoracic, lumbar and sacral spinal cords were harvested from adult (p56) C57Bl6J male and female mice. Nuclei were extracted and NeuN+ neuronal nuclei were isolated with FACS sorting. Resulting neuronal suspensions were profiled with Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kits from 10x Genomics. Altogether 3 biological replicates were acquired from all four spinal cord regions with three technical replicates each.

first: Liliana

last: Cano Gomez

first: Helen

last: Poldsam


title: RNA-seq of Human nasopharyngeal carcinoma cells in BALF2-LR and BALF2-HR overexpress group

status: Public on Feb 17 2026

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

summary: To investigate the biological function of EBV BALF2-HR in NPC pathogenesis, we constructed overexpression vectors for BALF2-HR and BALF2-LR (used as a control) and transfected them into the EBV-negative NPC cell line HK1 [Fig. S1D]. Differential gene expression analysis, conducted using RNA sequencing (RNA-seq)


title: Heat stress triggers nuclear invagination and spatial compartmentalization of protein metabolism

status: Public on Mar 03 2026

city: guagnzhou

first: tang

last: guorun

address: xingang

institute: Sun Yat-sen University

summary: Heat stress is a common challenge for cells, causing multiple types of cellular damage while triggering complex stress responses, including the classical heat shock response. However, the subcellular coordination of these stress responses remains poorly understood. In this study, we identify reversible nuclear morphological changes under heat stress, characterized by kidney-shaped invaginations. These nuclear invaginations are associated with intermediate filament collapse and the regional clustering of organelles. Through immunofluorescence imaging and proteomic analysis, we further reveal that nuclear invagination region function as "protein metabolism hotspots", where both protein translation and degradation are enhanced. Moreover, this compartmentalization is not only essential for cellular adaptation and recovery from heat stress but also correlates with the differential heat tolerance across cell lines. Our findings highlight a previously unappreciated mechanism by which cells spatially reorganize protein metabolism to optimize stress responses, providing new insights into heat stress adaptation.

overall_design: RNA-seq profling of HEK293T cells under three conditions: untreated wild-type, heat shock treatment (43°C for 1 hour), and recovery after heat shock (37°C for 1, 6, 18 hours)

first: Zhihao

last: Zhang

first: Yuantao

last: Qiu

first: Yifeng

last: Huang

first: Yelin

last: Lan

first: Yuli

last: Zhao

first: Fu

last: Wu

first: Chenlong

last: Wang

first: Guorun

last: Tang

first: Jingyun

last: Ji

first: Zhang

first: Guanzheng

last: Luo


title: Cuproptosis and disulfidptosis converge to empower PD-L1 checkpoint therapy via Cadict-induced PD-L1 translation

status: Public on Mar 01 2026

first: Shaoqing

address: No. 58, Zhongshan 2nd Road, Guangzhou

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: To elucidate the mechanism by which Cadict and Cu-Cys exert cytotoxic effects on colorectal cancer cells, we performed transcriptome analysis using RNA-seq to investigate the signaling pathways affected by Cadict and Cu-Cys.

overall_design: Total RNAs from MC38 cells were extracted with TRIzol reagent and sequenced on the Illumina Novaseq 6000 sequencing instrument (BGI, China). There were three experimental groups (CTL vs Cu-Cys vs Cadict) with 3 replicates for each.


title: A covalent fragment screen identifies ferroptosis induced by GPX4 inhibition as a vulnerability of senescent cells [PC3]

status: Public on Feb 15 2026

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: NOT PROVIDED; REQUESTED

overall_design: These samples come from an in vivo experiment performed with PC3 xenografts prostate tumor model. We have 4 different experimental groups: vehicle (V), RSL3 (R), Palbociclib (P) and palvociclib+RSL3 (P+R).

first: Mariantonietta

last: D'Ambrosio

first: Jesus

last: Gil

first: Sanjay

last: Khadayate


title: Alterations of splicing and gene expression in DMSO or 4OHT treated-IMR90 ER:HRAS G12V cells upon knockdown of SF3B1 and RBM39

summary: The goal of this study was to analyse changes of splicing and gene expression induced in IMR90 Control and IMR90 RAS (HRASG12V) cells upon knockdown of splicing factors SF3B1 and RBM39

overall_design: Comparative analysis of splicing and gene expression changes in DMSO-treated IMR90 ER:RAS (control) and 4OHT-induced IMR90 ER:RAS cells following the knockdown of SF3B1 and RBM39 by siRNA (siSF3B1 and siRBM39) compared to non-targeting siRNA (siNT).

first: Laura

last: Bousset

first: Marian

last: Dore

first: Ivan

last: Andrew

first: Ka Lok

last: Choi

first: Laurence

last: Game

first: Alexandre

last: da Silva Alfonso

first: Rita

last: Borges da Silva

first: Nuno

last: Barbosa Morais


title: Alterations of splicing and gene expression in IMR90 Control cells and IMR90 RAS cells upon knockdown of SF3B1.

summary: The goal of this study was to analyse changes of splicing and gene expression induced in IMR90 Control and IMR90 RAS (HRASG12V) cells upon knockdown of splicing factor SF3B1.

overall_design: Comparative analysis of splicing and gene expression changes in IMR90 control and IMR90 RAS cells induced by knockdown of SF3B1 by siRNA (siSF3B1) compared to non-targeting siRNA (siNT).

first: Wagner

last: Verena

first: Gil

last: Jesus

first: Khadayate

last: Sanjay

first: Ascensao

middle: F

last: Mariana

first: Barbosa

last: Nuno


title: Transcriptomics of different forms of senescence

first: LMS

last: Bioinformatics Core

summary: The goal of this study was to compare the transcriptomics of different forms of senescence with each other and to normal growing and quiescent IMR90 cells.Senescence was induced in IMR90 cells by different stimuli. Therapy-induced senescence was induced by treatment with doxorubicin, irradiation, etoposide and palbociclib. Oncogene-induced senescence was induced by addition of tamoxifen (4OHT) to IMR90 ER:RAS cells.

overall_design: 8 samples in total, 4 replicates each: IMR90 growing, IMR90 quiescent, IMR90 senescent (doxrubicin), IMR90 senescent (irradiation), IMR90 senescent (palbociclib), IMR90 senescent (etoposide), IMR90 ER:RAS non-induced (growing), IMR90 ER:RAS induced (Ras-induced senescence)

first: Verena

last: Wagner

first: Gopuraja

last: Dharmalingam


title: A covalent fragment screen identifies ferroptosis induced by GPX4 inhibition as a vulnerability of senescent cells

summary: We report the analysis of RNA sequencing aimed at understanding senescence induction in SK-MEL103 cells.

overall_design: SK-MEL103 cells were treated for 6 days with DMSO, Etopodise and Tozasertib.

first: Mariantonietta

last: D'Ambrosio

first: Jesus

last: Gil

first: Sanjay

last: Khadayate


title: PKM2 lactylation promotes colorectal cancer vasculogenic mimicry and resistance to bevacizumab treatment by facilitating FOSL1 super-enhancer formation [RNA-Seq]

status: Public on Feb 14 2026

first: Weihao

last: Li

address: 651 Dongfeng Road east

institute: Sun yat-sen university cancer center

summary: Despite the clinical utility of bevacizumab in advanced colorectal cancer (CRC), resistance remains a major challenge. Here, we unveiled a lactate-mediated mechanism driving vasculogenic mimicry (VM) and bevacizumab resistance through PKM2 lactylation. PKM2 lactylation at K206 by AARS1 promoted PKM2 nuclear translocation and interaction with FOSL1. PKM2 binding facilitated FOSL1-dependent super-enhancer formation and target gene transcription, which contributed to CRC cell VM. Genetic or pharmacological inhibition of PKM2 lactylation disrupted VM and synergized with bevacizumab in patient-derived pre-clinical models, significantly improving therapeutic efficacy. Together, this study reveals lactylation as a metabolic switch linking cancer glycolytic reprogramming to transcriptional rewiring and proposes targeting PKM2 lactylation to enhance the anti-tumor activity of bevacizumab in CRC.

overall_design: RNA-seq profiling of PKM2 wildtype (WT) HCT116 cells and their PKM2 K206R mutant cells.

first: Jianhong

last: Peng

first: Jiahua

last: He

first: Zhizhong

last: Pan

first: Chi

last: Zhou

first: Junzhong

last: Lin


title: PKM2 lactylation promotes colorectal cancer vasculogenic mimicry and resistance to bevacizumab treatment by facilitating FOSL1 super-enhancer formation [CUT&Tag]

overall_design: CUT&Tag sequencing of anti-H3K27ac in PKM2 wildtype (WT) HCT116 cells and their PKM2 K206R mutant cells; CUT&Tag sequencing of anti-FOSL1 and PKM2 in PKM2 WT HCT116 cells


title: PKM2 lactylation promotes colorectal cancer vasculogenic mimicry and resistance to bevacizumab treatment by facilitating FOSL1 super-enhancer formation [ATAC-seq]

overall_design: ATAC-seq of anti-H3K27ac in PKM2 wildtype (WT) HCT116 cells and their PKM2 K206R mutant cells


title: Targeting tumor-specific T cells with LAG3-directed interleukin-2 prevents T cell exhaustion and reinvigorates antitumor immunity

status: Public on Feb 28 2026

city: Beijing

first: Xiaohong

last: Yu

state: 北京

address: Yard 28,Science Park Road

institute: Changping Laboratory

summary: LAG3 is a critical inhibitory receptor that is highly enriched on exhausted T cells within the tumor microenvironment (TME), where it functions as a key driver of T cell exhaustion-an archetypal barrier to robust antitumor immunity. In a colon cancer model, we identified that LAG3+CD8+ tumor-infiltrating lymphocytes (TILs) constitute the predominant tumor-specific T cells but exhibit defective IL2 signaling. To address whether exogenous IL2 replenishment unpins their dysfunction, we engineered LAG3-LaIL2 (low-affinity IL2), a fusion protein delivering IL2 selectively to LAG3+CD8+ TILs. LAG3-LaIL2 expanded pre-exhausted tumor-specific CD8+ T cells, reprogrammed their exhaustion trajectory toward an intermediate effector state, and prevented terminal exhaustion, leading to tumor regression and prolonged survival in mice. Mechanistically, LAG3-LaIL2 restored IL2R-JAK3-STAT5 signaling by upregulating the high-affinity IL2 receptor subunit CD122, thereby rejuvenating TIL functionality. Furthermore, LAG3-LaIL2 amplified tumor-specific effector and memory T cells in draining lymph nodes, enabling systemic antitumor immunity against distal tumors and preventing tumor recurrence. Collectively, our findings validate LAG3-LaIL2 as a precision immunotherapeutic agent that specifically targets exhausted TILs, concomitantly enhancing therapeutic efficacy and safety by restricting IL2 exposure to non-target cells. This strategy provides a translatable approach to overcoming T cell exhaustion in solid tumors, offering a promising avenue to improve clinical outcomes for cancer patients

overall_design: MC38 tumors were isolated at day 15 post-5 days treatment. Tumor tissues were minced and digested with MACS tumor dissociation kit (Miltenyi Biotec) according to the manufacturer’s instruction. Following mechanical dissociation, cells were stained with anti-CD3 antibodies and sorted by BD FACSAria. scRNA-seq was conducted using the Chromium Next GEM Single Cell 3’ Kit (10x Genomics). All subsequent steps were performed according to the manufacturer’s protocol. The resulting libraries were purified and sequenced on a NextSeq sequencing system (Illumina).

first: Huiping

last: Liao


title: Mouse models of Alazami syndrome reveal a developmental window of vulnerability in the hippocampal dentate gyrus to transcriptional dysregulation

city: Chengdu

first: T

last: Q

state: Sichuan Province

address: No.17, Section 3, Renmin South Road

institute: West China Second University Hospital

summary: Enhanced P-TEFb activity is thought to promote cell proliferation by increasing the transcriptional output of RNA polymerase II, and normally most cellular P-TEFb is inhibited by 7SK snRNP containing LARP7 and HEXIM1.  Paradoxically, instead of causing overgrowth syndromes, loss-of-function mutations of LARP7 are linked to Alazami syndrome, a human neurodevelopmental disorder characterized by growth restriction and cognitive impairment.  Here, we generate genetically engineered mouse models to investigate the etiology underlying Larp7 deficiency.  Conditional knockout of either Larp7 or Hexim1 in the brain results in similar developmental defects as in human patients.  Notably, the size and the function of the hippocampal dentate gyrus are markedly reduced.  Multi-omics analyses and functional assays reveal that a heightened P-TEFb activity enhances the self-renewal transcriptional programs in Emx1+ neural progenitor cells to limit neurogenesis at the neonatal stage, resulting in dentate gyrus hypoplasia.  These results demonstrate that dysregulated subtissular stem cell dynamics reconcile increased P-TEFb activity and cell proliferation with reduced organismal sizes.  Because neonatal and adult dentate gyrus neurogenesis are highly alike, clinical-grade P-TEFb inhibitors, originally developed for treating cancer, may present a translational opportunity to ameliorate the adverse effects of several medical conditions on dentate gyrus size and function.

overall_design: To identify differentially regulated pathways during neurosphere differentiation, RNA-seq profiling of wild-type and larp7 knockout neurosphere after 2 days differentiation.   ATAC-seq profiling of wild-type and larp7 knockout neurosphere.  CUT&Tag of RNA polymerase II, Pol II-Ser2 and Pol II-Ser5 in wild-type and larp7 knockout neurosphere. Single-cell RNA-seq was used to analyze cell compositions and functional states of the dentate gyrus, obtained from micro-dissected wild-type, Larp7f/f;Emx1-Cre, and Larp7f/f;nestin-Cre mutant mice at P7, respectively.  To obtain enough materials, 3-4 dentate gyri from littermates were combined for each genotype.


title: Antiviral and anti-inflammatory effects of Tabamide A derivative, TA25, against human rhinovirus and multiple zoonotic viruses in vitro and in silico

status: Public on Feb 11 2026

city: Chuncheon

first: Bohyeon

last: Kim

state: Gangwon-do

address: Department of Microbiology, College of Medicine Hallym  University 1, Hallimdaehak-gil, Chuncheon-si 24252, Gangwon-  do, Republic of Korea

department: Department of Microbiology

institute: College of Medicine, Hallym University

summary: Human rhinovirus (HRV), first isolated in 1956, belongs to the family Picornaviridae. HRV causes mild cold and severe respiratory disease. To date, no FDA-approved antiviral or anti-inflammatory drugs are available. TA25 is a phenolic amide derivative extracted from Nicotiana tabacum. To investigate the potential candidate for antiviral therapeutics, we evaluated the antiviral potency of TA25 for HRV and multiple zoonotic viruses. The antiviral and anti-inflammatory effects were evaluated using RT-qPCR and RNA-seq. Strand-specific RT-qPCR was performed to measure genomic and anti-genomic RNA expression after TA25 treatment. In addition, an AI-based docking test was conducted to investigate the binding affinity of TA25 with viral proteins. TA25 induced significant reduction in viral replication and suppressed the expression of pro-inflammatory genes. Inhibition of viral replication by TA25 treatment was confirmed by strand-specific RT-qPCR. TA25 showed broad-spectrum antiviral activity against multiple viruses, including HRV-1A, ZIKV, DENV, VACV, and IBV. Using AI-driven structure-based docking analysis, TA25 showed strongest binding affinity with HRV 2B protein. This study demonstrates that TA25 confers the broad antiviral and anti-inflammatory activity against HRV and multiple zoonotic viruses. These findings provide valuable insights into antiviral strategies of TA25 for a promising therapeutic candidate in response to emerging RNA and DNA viruses.

overall_design: Innate immune and pro-inflammatory genes expression profiling analysis of total RNA-seq data from HeLa, HRV-infected HeLa or HRV-infected and 30 μM of TA25-treated HeLa cells. Samples were colleted at 48 hpi.

first: Altanzul

last: Bat Ulzii

first: Taehun

last: Lim

first: Jin Woo

first: Wonkyun Ronny

last: Im

first: Shivani

last: Rajoriya

first: Augustine

last: Natasha

first: Divya

last: Misra

first: Hennisa

last: Hennisa

first: Na Young

last: Kwag

first: Daewoon

last: Yoon

first: Gyunghee

last: Jo

first: Young Bin

last: Park

first: Jinkyu

first: Jeong Tae

last: Lee

first: Sung Ho

last: Jeon

first: Won-Keun


title: An epigenetic switch in vascular phenotype augments anti-tumor immunity [scRNA-seq]

status: Public on Feb 13 2026

city: Charlottesville

first: Andrew

last: Dudley

state: VA

address: 1340 Jefferson Park Avenue

department: Dept. of Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

summary: The abnormal tumor vasculature can present a barrier to the infiltration of anti-tumor immune cells, which impairs immune surveillance and response to immunotherapy. Here, we show that targeting the epigenetic factor DNA  methyltransferase 1 in endothelial cells (ECs) results in reduced angiogenesis while imparting profound changes to the tumor immune microenvironment (TIME), including increased proportions of CD4+ memory T-cells and NK cells. Depleting CD4+ T-cells, or blocking lymphocyte egress from the lymph nodes with FTY720, rescues tumor growth in mice with conditional deletion of Dnmt1 in ECs (Dnmt1iECKO) and dramatically shortens overall survival, whereas NK cells are dispensable. Tumors implanted in Dnmt1iECKO mice show reduced vascular branching, elevated expression of Vcam1, increased vessel-associated T-cells, and a shift in vascular specification including increased proportions of immune-permissive post-capillary venules (PCVs) and interferon-stimulated ECs (IFN_x0002_ECs). Deleting Dnmt1 in EC cultures strikingly potentiates responses to combinations of IFNg and TNFa and, notably, up-regulates important T-cell co-stimulatory molecules for memory CD4+ T-cells, including Icosl, Cd40, and Tnfsf4. Finally, immune checkpoint blockade (ICB) administered to Dnmt1iECKO mice with experimental melanoma lung metastasis reduces tumor burden, with some mice showing tumor eradication. Our findings identify endothelial Dnmt1 as a key regulator of vascular-mediated anti-tumor immunity, providing a rationale for integrating epigenetic modulation of the vasculature with cancer immunotherapy regimens.

overall_design:
Tumor Endothelial Cell (TEC) Isolation and Sorting
YUMMER1.7 tumors (~1 cm³) from three control mice and three Dnmt1iECKO mice were harvested, and tumors within each sample were pooled to obtain sufficient EC numbers. Samples were collected in ice-cold low-glucose DMEM (LG-DMEM), washed thoroughly, and minced into fragments <5 mm under sterile conditions. Tissue fragments were transferred to GentleMACS C tubes containing a digestion mix of collagenase II (2 mg/mL, Worthington LS004176), dispase (2.5 U/mL, Worthington LS02104), and DNase I (1 mg/mL, Worthington LS002006). Tumors were digested at 37 °C for 3045 min with agitation (120 rpm) and processed on a GentleMACS Dissociator using program m_imptumor_02 to achieve single-cell suspensions. Digested samples were passed through 100µm strainers, washed with FACS buffer (PBS + 0.5% BSA + 2 mM EDTA), and centrifuged at 1200 rpm for 5 min. Red blood cell lysis was performed using 1× Pharm Lyse B. Cell suspensions were first incubated with Live-or-Dye viability dye (Biotium 32002), followed by Fc block (Miltenyi 130-092-575) for 10 min on ice. Cells were then stained with PE-conjugated CD31 (BD 553373) and APC_x0002_conjugated CD45 (BD 559864) for 30 min on ice.Live CD31⁺CD45⁻ tumor endothelial cells (TECs) were sorted on an Influx cell sorter (Becton Dickinson) into LG-DMEM supplemented with 10% FBS, washed, and resuspended in PBS + 0.04% BSA. Final cell suspensions were adjusted to 500700 cells/µL with >85% viability. Sorted TECs were immediately used for 10x Genomics Chromium Single Cell 3’ v3 library preparation according to the manufacturer’s protocol.
Single-cell RNA-seq Library Preparation and Sequencing
Sorted cells were processed using the 10x Genomics Chromium Single Cell 3′ Gene Expression kit (GEM-X v4) following the manufacturer’s protocol. Libraries were prepared targeting ~10,000 cells per sample and sequenced on an Illumina NextSeq 2000 using the P2 XLEAP-SBS 100-cycle kit (paired-end) at a depth of 20,00025,000 reads per cell.

first: Dae Joong

first: Mitchell

last: McGinty

first: Swetha

last: Anandh

first: Caroline

last: Riedstra

first: Yuvraj

last: Sethi

first: Melanie

last: Rutkowski


title: An epigenetic switch in vascular phenotype augments anti-tumor immunity [bulkRNA-seq]

overall_design: Bulk rnaSequencing: Mouse lung ECs were seeded at 1×105 cells/mL in 6-well plates and cultured overnight at 37 °C in a humidified 5% CO2 incubator. The next day, cells were transfected with either control siRNA or DNMT1-targeting siRNA (BLOCK-iT oligos; Invitrogen) using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in Opti-MEM I Reduced Serum Medium for 4 h, following the manufacturer’s instructions. A BLOCK-iT Alexa Fluor Red fluorescent oligo (Invitrogen) was used in parallel wells to monitor transfection efficiency. After 4 hrs, the transfection medium was replaced with growth medium containing 20% serum, and the cells were cultured for 24 hrs at 37 °C, humidified 5% CO₂. A second siRNA transfection was performed 24 h later to reinforce the knockdown. Cells were then treated with TNFa (10 ng/mL) or IFNg (1,000 U/mL) for 16 hrs. Total RNA was isolated using a column-based RNA extraction kit (Zymo Research) according to the manufacturer’s instructions. Libraries were prepared and sequenced by Novogene for bulk RNA-seq analysis. Experiments were performed with n = 4 biological replicates per condition.

last: Kim


title: A reversible broad-spectrum antiviral targets the human V-ATPase VO domain

city: Vancouver

first: Diana

last: Bautista-Sánchez

state: British Columbia

address: 2350 Health Sciences Mall

department: Microbiology & Immunology

country: Canada

institute: University of British Columbia

summary: Increasing threats of viral disease underscore the urgent need for broad-spectrum antiviral drugs (BSADs). Host proteins utilized by human pathogenic viruses are key BSAD targets. The vacuolar-type H⁺-ATPase (V-ATPase) has been identified as a proviral factor for most pH-dependent enveloped viruses classified as pandemic threats. We report here the discovery of cladoniamide A (CA)—a V-ATPase inhibitor with single-digit nanomolar antiviral activity and a high selectivity index (SI: 103-104) against human enveloped viruses [e.g., SARS-CoV-2 variants, influenza A viruses (H1N1, H5N1), respiratory syncytial virus, dengue serotypes 1–4, and Zika virus]. Transcriptome profiling, pH estimation assays, and V-ATPase bioassays indicate that CA interferes with V-ATPase-dependent acidification of the host endolysosomal network thus preventing viral entry. Using pseudoviruses derived from five pathogenic virus families, we confirmed that CA is a BSAD acting as an entry inhibitor. CryoEM revealed that CA inhibits the V-ATPase rotary motor by occupying unique binding sites in the membrane-embedded Vo motor. Importantly, intranasal CA treatment in mice infected with influenza A H1N1 significantly reduced viral load in the lung by four log orders. Together, these findings pave the way for developing next-generation BSADs targeted at unique druggable pockets that enable the reversible pharmacological modulation of the human V-ATPase.

overall_design: To investigate the cellular mechanism of cladoniamide A (CA), we performed RNA-sequencing on Calu-3 cells pretreated for 3 h with the natural compounds [CA (250 nM), cladoniamide D (CD, 250 nM), bafilomycin A (BafA1, 100 nM), and DMSO (0.1%)] and collected at the designated time points (3, 6, 12, and 24 h post-treatment).

first: Jimena

last: Pérez-Vargas

first: Rebecca

last: Oot

first: Connor

last: Thompson

first: David

middle: E

last: Williams

first: Lianne

last: Presley

first: Danielle

middle: G

last: Gordon

first: Annika

last: Schulz

first: Kassidy

last: Knight

first: Siobhan

last: Ennis

last: Scheibner

first: Nidhi

last: Kaushik

first: Syan

last: Olver

first: Guang

last: Gao

first: Jun Bae

first: Ivan

last: Villanueva

first: Kéryanne

last: Gagnon

first: Luka

last: Kramptert

first: Steven

last: McArthur

first: Alexander

last: Nowakowski

first: Claire

last: Brown

first: Leon

middle: H

last: Chew

first: Erin

last: Knock

first: Brian

last: Hetrick

first: Sandra

last: Diederich

first: Soung-Hun

last: Roh

first: Masahiro

last: Nikura

first: Bryce

last: Warner

first: Stephan

last: Wilkens

first: Raymond

last: Andersen

first: François

last: Jean


title: Nucleolar migration regulates meiotic sex chromosome inactivation via phase separation during mammalian spermatogenesis

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

summary: During spermatogenesis, the unsynapsed XY chromosomes undergo meiotic sex chromosome inactivation (MSCI) and form a heterochromatic XY body. Defects in MSCI lead to meiotic arrest and male infertility. Although DNA damage response (DDR) factors are established as key initiators of MSCI, how transcriptional silencing is subsequently achieved remains elusive. Here, we identify the nucleolar components NPM1, SENP3, and rRNA as essential downstream effectors of DDR signaling in MSCI. During pachytene, these components migrate to and transiently cover the XY body during MSCI establishment, before becoming restricted to a corner of the XY body. Genetic deletion of Npm1 or Senp3, or inhibition of rRNA transcription severely impairs MSCI. Mechanistically, SENP3-mediated deSUMOylation of NPM1 promotes its interaction with rRNA, enabling liquid-liquid phase separation, via which they exclude Pol II from the XY body. Together, these data reveal a previously unrecognized role of nucleolar components in the transcriptional regulation of MSCI in mammalian spermatogenesis.

overall_design: Small scale in situ high throughput chromatin conformation capture (sisHi-C) or RNA-seq for WT and mutant zygotene, pachytene, or diplotene spermatocytes

first: Wei

last: Xie


title: DNA Methylation in the Placenta and Maternal Socioeconomic Status: The SPAH Study

status: Public on Feb 10 2026

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

type: Methylation profiling by genome tiling array

summary:
Background: Disparities in socioeconomic status have been associated with adverse pregnancy outcomes, including preterm birth and fetal growth restriction. As the barrier between maternal exposures and the fetus, the placenta has been proposed to play a role in the mechanisms leading to poor health outcomes seen with socioeconomic disadvantage. We hypothesized that exposure to lower SES during pregnancy may lead to altered placental DNA methylation (DNAme) that is in turn associated with other pregnancy outcomes.
Methods: Placental samples from the Stress, Pregnancy, and Health Study (SPAH) study (n=493) were processed for DNAme analysis using the Illumina Infinium MethylationEPIC BeadChip array. Linear modelling was used to assess whether placental DNAme was associated with Socioeconomic Position, Financial Resources, and/or Disadvantage.
Results: At FDR <0.05 and |∆β| >0.05, we observed only 2 CpGs associated with Socioeconomic Position after correcting for gestational age and ancestry, while at a less stringent |∆β| >0.02 threshold there were 77 and 22 CpG associations with Socioeconomic Position and Disadvantage respectively. However, these changes seemed to be explained by genetic variation influencing DNAme in combination with population stratification by socioeconomic status. We did observe associations between socioeconomic status and DNAme-inferred cell composition and epigenetic age acceleration, with intrinsic (p=0.047) and extrinsic (p=0.050) age acceleration being slightly accelerated with lower levels of Socioeconomic Position. Financial Resources and Disadvantage SES trended in the same direction as Social Position, with lower socioeconomic status seen with higher levels of age acceleration, though not reaching significance. No meaningful associations in sex stratified analyses were identified, although XX placentas showed higher cytotrophoblast:syncytiotrophoblast ratio than XY placentas (p=0.00013).
Conclusions: Our results emphasize the importance in placental studies involving diverse cohorts to account for genetic variation in order to avoid false findings. This study also demonstrates the challenges with elucidating mechanisms underlying socioeconomic associated outcomes, given the complex nature of correlated variables. Further investigation is required to elucidate whether epigenetic age acceleration is an adverse effect of exposure to prenatal maternal stress associated with socioeconomic disparities, or alternatively, if placental epigenetic aging is a potential healthy adaption to pregnancy complications that increase the risk of preterm delivery.

overall_design:
The SPAH study was initially focused on understanding the social and lifestyle factors that affect birthing parents’ and infants’ health during pregnancy (https://sites.northwestern.edu/spah/). We aimed to identify placental DNAme associated with socio economic status using DNAme data from 493 unique human chorionic villi samples profiled with the Infinium MethylationEPIC v1.0 array in Evanston, Illinois, USA.

***************************************************************
IDAT files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable SNP genotyping data for open access.
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first: Ella

middle: O

last: Beraldo

first: Hannah

middle: I

last: Illing

first: Ann

last: Borders

first: Linda

last: Ernst

first: Alexa

last: Freedman

first: Lauren

last: Keenan-Devlin

first: Amy

last: Inkster

first: Jungwon

last: Kim

first: Maria

last: Penaherrera

first: Gregory

last: Miller


title: Islet versus enterochromaffin lineage allocation of hPSC-derived pancreatic progenitors can be modulated at both pre-progenitor and post-progenitor stages

city: Toronto

middle: Cristina

last: Nostro

address: 101 College Street

institute: McEwen Stem Cell Institute

summary: Little is known about the molecular mechanisms that underlie the allocation of human pluripotent stem cell-derived pancreatic progenitors (hPSC-PPs) into specific endocrine lineages. By systematically interrogating the components of pancreatic differentiation media, we identify methods to reliably generate hPSC-PPs with high-grade NKX6-1 expression, but find that this alone has a minimal effect on modulating the endocrine composition of hPSC-derived islets. We then test the effect of altering the signaling cues provided after progenitor specification and find that the BMP and FGF/MEK pathways can be manipulated to shift hPSC-PPs between islet and non-islet endocrine lineages. We further find that the method of hPSC-PP specification integrates with these later cues in a way that can be leveraged to selectively increase the frequencies of specific islet lineages or enterochromaffin (EC)-like cells. Using a model of disrupted murine islet development that gives rise to pancreatic EC-like cells, we identify prolonged NEUROG3 expression as a conserved feature associated with both human and murine pancreatic EC-like cell differentiation. In addition to expanding our understanding of pancreatic endocrine lineage allocation, these findings provide some of the first tools to fine-tune composition of hPSC-derived islets for research and therapeutic applications.

overall_design: Day 13 human pluripotent stem cell-derived pancreatic progenitors with enhanced NKX6-1 expression were differentiated towards either islet or EC lineages. At day 26, cells were dissociated, viability-sorted, and fixed. 24 hours later, they were sent for fixed RNA profiling.

first: Paraish

last: Misra


title: Selective targeting of type II tRNAs underlies SLFN14-mediated translational repression and its dysregulation by thrombocytopenia-linked mutations

status: Public on Feb 09 2026

city: Ithaca

first: Saori

last: Uematsu

address: 526 Campus Road, Cornell University

department: Division of Nutritional Sciences

institute: Cornell University

summary: Schlafens (SLFNs) are interferon-inducible proteins with emerging roles in RNA metabolism and antiviral defense. SLFN14 is a ribosome-associated endoribonuclease whose pathogenic variants cause an autosomal dominant form of inherited thrombocytopenia (IT), yet the molecular basis of this disorder has remained unclear. Here, we show that SLFN14 represses global protein synthesis and viral replication primarily through selective cleavage of type II tRNAs. Using cell lines engineered to express SLFN14 variants, we demonstrate that thrombocytopenia-linked mutations alter RNA substrate specificity, enhancing degradation of type II tRNAs while diminishing rRNA cleavage. This shift in substrate preference increases ribosome stalling at codons decoded by type II tRNAs, leading to global translational arrest, stress signalling, and ultimately cell death. The heightened degradation of type II tRNAs by SLFN14 mutants provides a mechanistic explanation for the translational defects and impaired megakaryocyte maturation observed in SLFN14-associated IT. Our findings suggest that type II tRNA targeting is a conserved regulatory strategy within the SLFN family and identify enhanced tRNA cleavage and the resulting impaired translation as the central pathogenic processes driven by thrombocytopenia-linked SLFN14 mutations.

overall_design: Ribo-seq from HEK293T cells expressing SLFN14 variants treated with Dox at different timepoints (0 and 24 h).


title: Integrative transcriptomic analysis uncovers the miRNA-centric regulation of Japanese encephalitis virus infection in porcine trophoblast cells [RNA-Seq]

city: Yangzhou

first: Juan

last: Yang

address: 大学南路88号

department: College of Veterinary Medicine

institute: Yangzhou University

summary: To characterize porcine placental miRNAs, we performed small RNA-seq experiments using porcine placental tissues and the porcine placental trophoblast cell line pTr. To investigate the intracellular responses of pTr cells following JEV infection, RNA-seq and small RNA-seq experiments were conducted on pTr cells with or without JEV infection.

overall_design: We collected placental samples from first - parity naturally delivered Duroc gilts, pTr cell samples under normal culture conditions, and pTr cell samples at 24 and 48 hours post - infection with JEV as well as non - infected samples. Two replicates per sample were used for RNA-seq and small RNA-seq experiments.

first: Jiayao

last: Jiang

first: Jiajia

last: Gong

first: Shuai

last: Chen

first: Ming-an

last: Sun


title: Ontogeny-independent expression of LPCAT2 in granuloma macrophages during experimental visceral leishmaniasis [scRNA-seq]

city: York

first: Paul

last: Kaye

state: North Yorkshire

address: University of York, Heslington

institute: Hull York Medical School, University of York

summary: Granulomas are organized inflammatory lesions that form in response to persistent stimuli such as infections. Murine infection with Leishmania donovani results in the formation of granulomas around infected Kupffer cells in the liver and serves as a well-defined model of immune granuloma formation. The formation and resolution of granulomatous inflammation requires dynamic shifts in immune cell activation states, imposing significant metabolic demands. As mediators of energy homeostasis and cell signaling, lipids and lipid metabolism play a key role in regulating immune cell function during inflammation and the response to infection. However, the extent to which alterations in lipids are spatially linked to altered immune cell transcription has yet to be resolved. In this study, we performed a multimodal imaging analysis combining MALDI mass spectrometry, spatial and single cell transcriptomics, proteomics of flow-sorted macrophages and histopathology of L. donovani induced hepatic granulomas. Using this spatially-integrated approach, we identified LPCAT2-mediated membrane re-modelling of myeloid cells as a novel feature of these granulomas. Our study provides new insights into local immunometabolic changes associated with granuloma formation and macrophage activation.

overall_design: Adult female C57BL/6J mice were maintained and bred at the University of York, UK. The mice were housed in ventilated cages under specified pathogen-free conditions with access to food and water ad libitum. Identification of the mouse colony was confirmed through genetic profiling of microsatellite markers, verifying C57BL/6J genetic background with minor variations at 3 markers. Healthy (6-8 week old females) were infected intravenously with 3x107 amastigotes of the Ethiopian LV9 strain of Leishmania donovani to establish visceral infection. At 28 days post-infection, mice were euthanized by CO2 inhalation followed by cervical dislocation according to Home Office regulations. Livers were harvested after euthanization and the major lobe cut and snap-frozen in liquid nitrogen while bathed in isopenane and then kept in -80 degrees until used. The remaining liver was harvested in 2% fetal calf serum (FCS) in 1x PBS and immediately processed into a single cell-suspension. Age-matched uninfected female mice from the same colony were used as baseline controls for liver tissue. For single-cell RNA seq 6 infected mice were run as individual samples selected from 2 independent experiments and the 2 naive samples were each pooled from 3x uninfected mice.

first: Shoumit

last: Dey

first: Jian-Hua

last: Cao

first: Benjamin

last: Balluff

first: Nidhi

first: Lesley

last: Gilbert

first: Sally

last: James

first: Adam

middle: A

last: Dowle

first: Grant

last: Calder

first: Peter

last: O'Toole

first: Ron

last: Heeren