city: Boston

first: Nikolaos

last: Tsopoulidis

address: 185 Cambridge Street, CPZN 4100

institute: MGH Molecular Biology

summary: Most mammalian genes contain multiple polyadenylation signals, yielding mRNA-isoforms with different 3’UTR ends via alternative polyadenylation (APA). While APA can profoundly impact protein levels, its physiological roles remain elusive. Here, we show that the APA regulator Nudt21 is essential for tissue regeneration by maintaining proliferative stem and progenitor cells. Leveraging a Nudt21-titratable system, we show that APA modulation impacts stem/progenitor cell function in a dose-dependent manner. Intermediate levels elicit a differentiation arrest owing to the 3’UTR-shortening of chromatin-associated mRNAs that escape miRNA regulation. By contrast, complete Nudt21 loss disrupts stem cell self-renewal by shortening the 3’UTRs of mRNAs encoding for essential multiprotein complexes, including the nuclear pore, leading to their degradation. Critically, deletion of the alternative 3’UTR of Nucleoporin-160 recapitulates defects observed with Nudt21 loss. Our findings uncover a previously unrecognized dual role for APA in tissue maintenance, by modulating differentiation-associated gene expression and preserving multiprotein complexes essential for proliferation.

overall_design:
RNA-seq timecourse for Nudt21 KO and Nudt21 Hypomorph esophageal basal cells:
RNA-seq was performed for Nudt21 KO (d0, d2, d4, d6) and Nudt21 Hypomorph (d4, d6) in triplicate. Day 0 are cells that were treated with ETOH instead of 4OHT, thus they retain the floxed Nudt21 allel

PAS-seq for Nudt21 KO and Nudt21 Hypomorph esophageal basal cells:
PAS-seq was performed for Control, Nudt21 KO (d4) and Nudt21 Hypomorph (d4) in triplicate. Control samples  were treated with ETOH instead of 4OHT, thus they retain the floxed Nudt21 allel

Small-RNA-seq for Control and Nudt21 KO esophageal basal cells:
small-RNA-seq was performed for Control and Nudt21 KO (d4) in triplicate. Control samples  were treated with ETOH instead of 4OHT, thus they retain the floxed Nudt21 allel

first: Konrad

last: Hochedlinger


title: Inhibition of ADSS2-mediated de novo AMP biosynthesis resensitizes acute myeloid leukemia to BH3 mimetics

status: Public on Nov 21 2025

city: Monrovia

first: Ling

last: Li

state: CA

address: 1218 S 5TH AVE, MONROVIA

department: Hem Malignancies Trans Sci

country: USA

institute: City of Hope National Medical Center

type: Expression profiling by high throughput sequencing

summary: De novo purine synthesis is required to promote tumor growth; however, its role in therapy resistance remains elusive. Here, through a dynamic BH3-priming based CRISPR-Cas9 screen, we found that deletion of ADSS2, which encodes for an enzyme functioning in de novo AMP synthesis, re-sensitizes drug resistant acute myeloid leukemia (AML) cells to BH3 mimetics. Single-cell sequencing and metabolomics analyses reveal that high ADSS2 activity in leukemia samples including those with TP53 aberrations inversely correlates with venetoclax responsiveness. Further, we developed anADSS2 antagonist, exhibiting synergism with BH3 mimetics in preclinical AML models. Mechanistically, sensitization to BH3 mimetics mediated by ADSS targeting was associated with downregulated AMPK activity, which governs mitochondrial homeostasis. AMPK activity in resistant cells promotes mitophagy to eliminate damaged mitochondria upon BH3 mimetics treatment. These data demonstrate that AMP synthesis governs venetoclax resistance, and that combining ADSS targeting with BH3 mimetic treatment could represent a promising approach against AML.

overall_design: P1-R cells with WT or ADSS2-KO were collected for analysis.

first: Xin

last: He

first: Wei

last: Chen


title: AAV Assembled Capsids Are Produced in Cells Blocked fromFrom Cell Cycle Progression

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

summary:
Adeno-associated virus (AAV) is a promising delivery system for gene therapy. However, current
manufacturing of AAV suffers from very low yields compared to other biotherapeutics. The AAV
dose per patient ranges between 1011and 1015 viral genomes (vg), requiring an average of 10 to 30 L
production/dose. As a consequence, production costs are prohibitive for most indications. Our
recent studies revealed that only 10% of the HEK293 cells that have received the AAV encoding DNA
produce assembled AAV capsids. This observation prompts the question: Why would cells that have
been successfully transfected, be unable to produce AAV. To answer this question, we undertook a
detailed study to characterize the two sub-populations from the same transfection, the cells that
were making assembled capsids and those that were not. We found that the two populations had
distinct cell cycle profiles, with a block in cell cycle progression characterizing the producer
population. RNA-seq analysis of the two populations reveals differences in the molecular pathways
impacted and provides a basis for making changes to improve productivity.

overall_design: 11 RNA samples were used for RNA sequencing. All RNA extractions were performed on paraformaldehyde-fixed and antibody-stained cells. 2 RNA samples were isolated from un-transfected, fixed and stained 293SF cells, 3 from mock-transfected, fixed and stained cells and 6 from cells that were sorted into 2 populations after transfection, fixing and staining,  one producing virus and the other not, after transfection, fixing and staining.

first: Alaka

last: Mullick

first: Audrey

last: Morasse

first: Melanie

last: Leclerc


title: Rebalancing Viral and Immune Damage versus Tissue Repair Prevents Death from Lethal Influenza Infection

city: Port Saint Lucie

first: Emily

last: Speranza

state: FL

address: 9801 SW Discovery Wy

department: Florida Research and Innovation Center

institute: Cleveland Clinic Lerner Research Institute

summary: Maintaining tissue function while eliminating pathogen-infected cells is a fundamental challenge in host defense. Studies of acute viral respiratory diseases such as influenza and COVID-19 have emphasized the key role of innate inflammatory damage survival on outcome, yet other than high dose steroids, a wide variety of immunomodulatory drugs have only modest positive effects. Here we tested more than 50 immunomodulatory regimes in a mouse model of lethal influenza infection, with only the previously reported early depletion of neutrophils showing efficacy. This suggests that the infected host passes an early tipping point in which reduction of further innate immune damage alone cannot rescue adequate physiological tissue function. To re-balance the system around this tipping point, we investigated whether late in infection, partial limitation of viral spread using oseltamivir (Tamiflu) together with enhancement of epithelial repair by blockade of interferon signaling or limitation of further epithelial cell loss mediated by cytotoxic CD8+ T cells would rescue infected animals. These treatments rescued a large fraction of infected animals through the two anticipated mechanisms. These findings provide new insight into the importance of repair processes and the timing of adaptive immune responses in survival from influenza infections.

overall_design: 8 to 12 week old C57Bl/6J mice were inoculated with the PR8 version of H1N1 influenza virus or PBS along (controls). Animals were then treated with PBS (controls), Tamiflu, Tamiflu and anti-IFNAR, or Tamiflu and anti-CD8a. Right inferior lung lobes were collected at 4,6,8, and 12 days post infection for RNA extraction and sequencing.

first: Hiroshi

last: Ichise

first: Federica

last: La Russa

first: Tibor

middle: Z

last: Veres

first: Colin

middle: J

last: Chu

first: Anita

last: Gola

first: Ronald

middle: N

last: Germain


title: Asymmetric surface disposition of β-helix protein YjbI controls bimodal antibiotic susceptibilities

city: Würzburg

first: Manuel

last: Velasco Gomariz

address: Josef-Schneider-Straße 2/D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

summary: While cytoplasmic pentapeptide repeat proteins (PRPs) protect DNA gyrase from cytotoxic quinolones, the function of secreted (s)PRPs remains unknown. We show that a YjbI-type sPRP regulates antibiotic sensitivity, bimodally for small or large molecules, from the Caulobacter crescentus outer membrane (OM). YjbI silences two converging envelope stress pathways that globally reprogram the OM proteome via TonB-dependent receptors (TBDRs), periplasmic proteases and AcrAB-NodT, a multidrug efflux pump whose induction by small molecules and antibiotics is lethal to yjbI mutant cells. Loss of YjbI also confers sensitivity to vancomycin and bacitracin, two large peptidoglycan-targeting and zinc-binding antibiotics that permeate the OM via the uncharacterized TBDR BugA and orthologs. Zinc stress triggers YjbI’s rapid proteolytic removal and transcriptionally activates BugA, other TBDRs, and ultimately replenishes YjbI. Molecular dynamics simulations and reactive thiol-probing imply an asymmetric surface disposition of YjbI, explaining the differential accessibility of its conserved cysteine pairs that flank the quadrilateral β-helix.

overall_design: Transcriptomic of Caulobacter NA100 wild-type (KFS-6) & Caulobacter NA100 Δyjbl (PV20792) in the absence/presence on 80 µM ZnSo4. Cells were growing in PYE medium at 30°C until they reached OD660=0.4. 80 µM of ZnSO4 or mock was added to the cells and after 30´ samples were collected for RNAprep

first: Kathrin

middle: S

last: Fröhlich

first: J

last: Costrafolaz

first: P

middle: H

last: Viollier


title: Gene expression profiles of nasal epithelium in long COVID

city: Amsterdam

first: Anke-Hilse

last: Maitland-van der Zee

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

summary:
The nasal epithelium(NE) is the primary site of infection for SARS-CoV-2, however little is known about its role in long COVID(LC). Therefore, this study aimed to investigate its biological profiles to unravel pathophysiological mechanisms of LC.
Medical data and NE were collected from LC patients at 3-6 and 12-18 months post-COVID. Transcriptomes were explored using hierarchical clustering to identify transcriptomic and cellular clusters. Patients with and without pulmonary radiological abnormalities(PRA) were compared using a supervised approach. CRISPR-Cas9 gene-editing was used for functional validation.
Transcriptomic (n=2) and cellular (n=2) clusters of NE were identified and related to inflammation and ciliogenesis (padj<0.05). In patients with PRA, SMURF1 was significantly upregulated. SMURF1-/- mutant NE cells showed significantly decreased inflammatory cytokine production upon viral stimulation. Concluding, inflammatory profiles of NE were found in LC. This study shows the need to further assess and validate SMURF1 for the disease management of LC.

overall_design: To understand molecular underpinning of long COVID we analyzed the nasal epithelial transcriptomes of long COVID patients at 3-6 months and 12-18 months post-infection

first: Nadia

last: Baalbaki

first: Jelle

middle: M

last: Blankestijn

first: Samuel

middle: W

last: Kazer

first: Mahmoud

middle: I

last: Abdel-Aziz

first: Harm

last: Bogaard

first: Merel

middle: E

last: Cornelissen

first: Cornelis

last: van Drunen

first: Daniëlle

last: van Egmond

first: Esther

last: de Groot

first: Jaclyn

last: Long

last: Nossent

first: Jose

last: Ordovas-Montanes

first: Korneliusz

last: Golebski


title: Spatial transcriptomics to dissect molecular signature of cardiac fibroblasts in experimental autoimmune myocarditis

city: Kraków

first: Monika

middle: Marta

last: Stefanska

state: malopolska

address: Medical College, Wielicka 265

department: Department of Clinical Immunology

country: Poland

institute: Jagiellonian University

summary: Myocarditis is a severe inflammatory cardiac disease that can progress to dilated cardiomyopathy and heart failure. Experimental autoimmune myocarditis (EAM) represents an animal model of acute myocarditis, which is followed by the development of post-inflammatory cardiac fibrosis and systolic dysfunction. In this model, cardiac inflammation is characterized by the massive influx of myeloid infiltrates and is paralleled by the activation of extracellular matrix-producing cardiac fibroblasts. 6–8-week-old BALB/c mice were immunized with αMyHC peptide together with Complete Freunds’ Adjuvant to induce EAM. Heart tissues were isolated, embedded in OTC, sectioned into 10 µm-thick fragments, and placed on a 10x Genomics Visium Gene Expression Slide. Single-cell spatial libraries were prepared using 10x Genomics Visium protocols, and the sequencing was performed using Illumina Chemistry. Single-cell RNA sequencing data was analyzed using RStudio software. In our analysis, we included three biological time points: a healthy heart (d0), acute myocarditis (d19). Following sequencing, we analyzed 3789 spots under the tissue. We identified the main cell populations present in the mouse heart, including fibroblasts, immune cells, endothelial cells, smooth muscle cells, and cardiomyocytes. Subset analysis on cardiac fibroblasts resulted in the presence of four different subsets (FB1–FB6). Subset FB3 has a myofibroblastic signature defined by the expression of, among others, Acta2, Postn, Vim, Col1a1 and Col3a1. This subset is transiently present at d19 of EAM. Spatial analysis of infiltrating immune cells characterized by the expression of, e.g., Ly6c1 and Lyz2 resulted in the presence of five subsets (INF1–INF5). The INF4 subset is present only at acute myocarditis phase (d19) and is spatiotemporally colocalized with the myofibroblastic subset(FB3). Our data indicate that myofibroblasts and infiltrating immune cells colocalize within the tissue during acute phase of myocarditis. This may indicate active molecular interplay between inflammatory cells and cardiac fibroblasts.

overall_design: Spatial transcriptomic data of mouse heart at different stages of experimental autoimmune myocarditis.  6-8-week-old BALB/c mice were immunized with αMyHC peptide together with Complete Freunds’ Adjuvant to induce EAM. Heart tissues were isolated, embedded in OTC, sectioned into 10 µm-thick fragments, and placed on a 10x Genomics Visium Gene Expression Slide. Single-cell spatial libraries were prepared using 10x Genomics Visium protocols, and the sequencing was performed using Illumina Chemistry. Single-cell RNA sequencing data was analyzed using RStudio software.

first: Katarzyna

last: Sarad

first: Marta

last: Kot

first: Martyna

last: Strzelec

first: Daria

last: Krzysztofik


title: Non-reciprocal callosal projections and input gradients underlie interhemispheric communication in binocular visual cortex

status: Public on Nov 20 2025

first: Elisabetta

last: Furlanis

address: Longwood avenue

institute: Harvard Medical School

summary: How the brain combines information received independently by the two hemispheres is not fully understood. Here we describe a non-reciprocal circuit for interhemispheric communication in mouse binocular visual cortex via anatomically segregated neuronal populations. Callosal projecting neurons (CPNs) received only weak or no callosal input, whereas callosal receiving neurons (CRNs) made only weak or no callosal projections. Both populations received direct input from the thalamus. At the cellular level, CRNs had reduced excitability compared to non-CRNs (putative CPNs) due to elevated Kv1 potassium channel expression (encoded by the KCNA2 gene), with excitability of CRNs correlated with the magnitude of callosal input. Functionally, CRNs were predominately binocular, with binocularity correlated with callosal input, whereas non-CRNs (putative CPNs) were predominately monocular. In summary, we find that non-reciprocal callosal projections between CPNs and CRNs together with differences in excitability shaped by callosal input underlie interhemispheric communication in binocular visual cortex.

overall_design: RNA-seq profiling of virally labeled and FAC-sorted callosal projecting (CPN) and callosal receiving (CRN) neurons from the mouse binocula visula cortex


title: Single-cell RNA sequencing of circulating 41BBzeta CART19 cells in mice treated with gavage of water or beta-hydroxybutyrate

city: Philadelphia

first: Marco

last: Ruella

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Single-cell gene expression of circulating 41BBzeta CART19 cells isolated from lymphoma-bearing NSG mice treated with daily oral gavage of water or beta-hydroxybutyrate. Cells were captured and processed using 10X 3' GEX Reagent Kit v2

overall_design: Single cell RNA sequencing of circulating CAR T cells. In vivo design for single cell RNA-sequencing (scRNA-seq) on circulating CART19 cells: First, NSG mice were inoculated subcutaneously with 5e6 CD19⁺ OCI-Ly18 cells and gavaged daily with oral beta-hydroxybutyrate, or. BHB (80mg per mouse, Ketone-IQ from HVMN) or vehicle (water). On day 0 post-implantation, mice received a curative dose of 5e6 human CART19 cells. Peripheral blood T cells were purified on day 17 following infusion, (n = 7 mice per arm), pooled amongst groups, and prepared for 3′ scRNA-seq (10X Genomics).

first: Shan

last: Liu

first: Puneeth

last: Guruprasad

first: Maayan

last: Levy


title: GPR25 promotes the formation of lung and liver tissue-resident memory CD8+ T cells

city: LA JOLLA, SAN DIEGO

first: Pandurangan

last: Vijayanand

state: CALIFORNIA

address: 9420 ATHENA CIRCLE

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

summary: Tissue-resident memory (TRM) CD8+ T cells are key players that orchestrate protective anti-viral and anti-tumor immune responses. The molecules that support their development and function are not fully defined. Here, we report on the regulation and function of an orphan G-protein coupled receptor, GPR25 that is expressed at higher levels in TRM cells. TGF-b, a key cytokine involved in the development to TRM cells, induces the expression of GPR25 in CD8+ T cells, and TRM-associated cis-regulatory elements in the GPR25 locus show binding of SMAD1, key transcription factors downstream of TGF-b signaling. By using Gpr25-deficient T cells in an LCMV infection model, we show that Gpr25 acts in a cell-intrinsic manner to promote the development of both primary and secondary TRM cells in the liver. Gpr25 deficiency in T cells also impairs their capacity to develop into CD69+CD103+ TRM cells in the lungs as well as to control lung metastasis in a tumor challenge model. Single-cell transcriptomic analysis of Gpr25-deficient memory T cells and TRM cells showed potential defects in restraining the ZEB2-S1PR5 pathway that drives tissue egress and in supporting a stem-like memory program as opposed to effector differentiation. Our findings support the concept that modulating Gpr25 function may be an attractive therapeutic option to boost the magnitude and quality of TRM responses generated in the context of infection and cancer.

overall_design: CD45.1.2 Gpr25 WT and CD45.2 Gpr25 KO OT-I cells were mixed in a 1:1 ratio and adoptively transferred at 1 x 10^6 total cells per recipient CD45.1 mouse. Mice were then infected with LCMV-OVA. Thirty days after infection, liver and lung tissues were detached and CD8+ T cells (or CD69+ CD8+ T cells) were isolated by FACS sorting.

first: Sungjun

last: Park

first: Han

last: Feng

first: Jae

last: Woo Shin

first: Francisco

last: Castañeda-Castro

first: Benjamin

last: Schmiedel

first: Changlu

first: Michael

middle: R

last: Jackson

first: Christian

last: Ottensmeier


title: Mouse DNA methylation atlas using Infinium Mouse Methylation Beadchips [EPIC array profiling]

first: Wanding

last: Zhou

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

type: Methylation profiling by genome tiling array

summary: Design, annotation, and technical and biological validation of the MouseMethylation Beadchips (MM285) platform. Application of the mouse array for tissue and tumor epigenetics, comparative epigenomics, genomic imprinting, epigenetic inhibitors, PDX assessment, backcross tracing, and epigenetic clocks. The mouse data were deposited in GSE184410.

sample_organism:
Homo sapiens
Mus musculus

overall_design: 37 samples, mixing human blood with mouse spleen and adipocyte (fat) cell DNA at different ratios. The mixed DNA is then subject to EPIC array profiling before being used to infer mouse DNA in patient derived xenograph models.

first: Zhou

last: Wanding

first: Hui

last: Shen

first: Peter

last: Laird


title: Loss of vitamin C biosynthesis protects from the pathology of a parasitic infection

city: Shanghai

first: Gongwen

last: Chen

address: 220 Handan Road

country: China

institute: Fudan University

summary: The ability to synthesize essential molecules is sometimes lost in evolution. A classic example is ascorbate (Vitamin C), which is synthesized in most animals by L-Gulonolactone Oxidase (GULO), an enzyme lost multiple independent times in animal evolution. This event is thought to be evolutionarily neutral, however, GULO-deficient animals including humans need to obtain ascorbate from their diet and are prone to ascorbate deficiency and scurvy. We therefore hypothesized that this disadvantage of GULO loss is offset by physiological benefits. Here we show that ascorbate deficiency benefits mice infected with schistosome parasites, which cause schistosomiasis, a debilitating parasitic disease that afflicts 250 million people. Schistosoma mansoni worms required host ascorbate to produce eggs in vivo. Consequently, ascorbate-deficient mice were protected from schistosomiasis pathologies and transmission. Intermittent ascorbate deficiency protected Gulo-deficient mice from both scurvy and schistosomiasis mortality. The effects of ascorbate on schistosome reproduction were mediated by ascorbate-dependent histone demethylation which promoted vitellocyte development in female schistosomes. We propose that vitamin deficiencies are not always detrimental but can protect animals from pathogens which need to obtain vitamins from their host.

overall_design: RNA-seq profiling of virgin female Schistosoma mansoni after 10-day in vitro culture with Vitamin C treatment versus an untreated control.


title: A gene expression atlas of a juvenile nervous system.

city: Nashville

first: David

last: Miller III

state: Tennessee

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: Although the fundamental architecture of metazoan nervous systems is typically generated in the embryo, substantial numbers of neurons are added during post-natal development as existing neurons also expand in size and undergo additional differentiation. To reveal the underlying molecular determinants of post-embryonic neurogenesis and maturation, we have produced gene expression profiles of all neuron types and their progenitors in the first larval stage (L1) of C. elegans. Comparisons of the L1 profile to the embryo and to the later L4 larval stage identified thousands of differentially expressed genes across individual neurons throughout the nervous system. Key neuropeptide signaling networks, for example, are remodeled during larval development. Gene regulatory network analysis revealed potential transcription factors driving the temporal changes in gene expression across the nervous system, including a likely broad role of the heterochronic gene lin-14. We utilized available connectomic data of juvenile animals in combination with our neuron-specific atlas to identify potential molecular determinants of membrane contact and synaptic connectivity. These expression data are available through a user-friendly interface at CeNGEN.org for independent investigations of the maturation, connectivity and function of a developing nervous system.

overall_design: Neurons were isolated from L1 stage hermaphrodite Caenorhabditis elegans using Fluroescence-activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Seth

last: Taylor

first: Claire

last: Olson

first: Lidia

last: Ripoll-Sanchez

first: Giulio

last: Valperga

first: Rebecca

last: McWhirter

first: S. Talmage

last: Barney

first: Alexander

last: Atkinson

first: Sidharth

last: Goel

first: Alexis

last: Weinreb

first: Andrew

last: Hardin

last: Rolfson

first: Jacob

last: Pattee

first: G. Robert

last: Aguilar

first: Daniel

last: Merritt

first: Matthew

last: Eroglu

first: Maryam

last: Majeed

first: Ethan

last: Grungvig

last: Child

first: Isabel

last: Beets

first: Petra

last: Vertes

first: William

last: Schafer

first: Erdem

last: Varol

first: Marc

last: Hammarlund

first: Oliver

last: Hobert


title: Simultaneous measurement of intrinsic promoter and enhancer potential reveals principles of functional duality and regulatory reciprocity

city: Ithaca

first: Haiyuan

last: Yu

state: New York

address: 237 Tower Road

department: Department of Computational Biology, Weill Institute for Cell and Molecular Biology

institute: Cornell University

summary: Accumulating evidence indicates that both promoters and enhancers are capable of exerting promoter and enhancer functions; however, the relationship between these two activities within individual elements and the determinants of this dual functionality remain poorly understood. We developed a massively parallel dual reporter assay that enables simultaneous assessment of the intrinsic promoter and enhancer potential exerted by the same sequence. Parallel quantification for thousands of elements reveals that canonical human promoters and enhancers can act as both promoters and enhancers under the same contexts, and that promoter activity may be necessary but not sufficient for enhancer function. Perturbations to element transcription factor binding motifs lead to disruptions in both activities, implicating a shared syntax for the two regulatory functions. Combinations of elements with different minimal promoters reveal reciprocal activity modulation, which, together with a strong correlation between promoter and enhancer functions, imply a bidirectional feedback loop to sustain environments of high transcriptional activity. Finally, we validate this reciprocity and correlation in situ using CRISPR activation at the human β-globin locus. Our approach reveals that the functional convergence between promoters and enhancers arises from a shared regulatory logic and sequence syntax, advancing a unified model for regulatory element biology.

overall_design: Quantitative Unifying Assay for Simultaneously Active Regulatory Regions by sequencing (QUASARR-seq), a massively parallel dual-reporter assay that simultaneously measures the intrinsic promoter and enhancer activities exerted by the same DNA sequence.

first: Mauricio

last: Paramo

first: John

middle: T

last: Lis


title: ClpC1-targeting peptide natural products differentially dysregulate the proteome of Mycobacterium tuberculosis.

city: Camperdown

last: Hesselson

state: NSW

address: Bldg 93, RPA Hospital, Missenden Rd

country: Australia

institute: Centenary Institute

summary: Targeting the protein quality control system in Mycobacterium tuberculosis offers a powerful and largely untapped opportunity for antibiotic development. The ClpC1:ClpP1P2 protease is an essential component of the system and is involved in both regulatory and stress-related protein degradation. Several non-ribosomal peptide natural product families have been discovered, including ecumicin, ilamycins (also called rufomycins) and cyclomarins, which bind to the ClpC1 chaperone component of the system and possess potent antimycobacterial activity. This has led to significant interest in these molecules, and the ClpC1:ClpP1P2 system more generally, as a bona fide target for the development of new tuberculosis drugs. In this study, we apply a systematic and multi-layered approach combining quantitative proteomics, bioinformatics, transcriptomic profiling, CRISPRi gene knockdown, and targeted biochemical and biophysical assays to dissect the mechanisms of ecumicin, ilamycin, and cyclomarin in clinically relevant Mycobacterium tuberculosis. Strikingly, despite exhibiting similar binding modes to ClpC1, each natural product elicits distinct substrate-specific effects on protein-degradation. We further show that derivatives of ilamycin and ecumicin engage the stress-response chaperones ClpC2 and Hsp20 respectively, albeit with varied sequestration capacity. Together our data reveal that these natural products dysregulate ClpC1 substrate recognition and perturb stress response chaperones in distinct ways, highlighting opportunities to target multiple nodes of protein quality control for the development of next generation antimycobacterials.

overall_design: Exponentially growing Mtb H37Rv cultures were treated with MIC90 Ecu* (1) and incubated for a further 48 h at 37 C. The Mtb cells were then centrifuged at 3725 g for 10 min to pellet bacteria. Pellets were resuspended with 1 mL TRIzol and transferred to a 2 mL O-ring tube with acid-washed glass beads. To disrupt the mycobacterial cell envelope, cells were subjected to six cycles of bead beating (20 s at 4600 rpm and 40 s on ice) with a (Biopec products) mini beadbeater. Samples were then clarified at 18000 g for 1 min. After a short room temp incubation chloroform was added to each sample and samples were inverted by hand for 15 seconds and incubated at room temperature for 3 min. Samples were then centrifuged at 12000 g for 15 min at 4 C. The upper aqueous phase containing RNA was collected. RNA was purified from the aqueous phase with the Isolate II RNA micro kit. Libraries were prepared using the (Illumina) Total RNA library kit with Ribo-Zero Plus chemistry for rRNA depletion and sequenced on an (Illumina) NovaSeq 6000 platform to generate 150 bp paired-end reads (>65 million pairs per sample).

middle: K

last: Barter

first: Max

last: Bedding

first: Julia

last: Leodolter

first: Joshua

last: Maxwell

first: Paige

last: Hawkins

first: Maxwell

last: Stevens

middle: B

last: McNeil

last: Jowsey

first: Trixie

last: Wang

first: Diana

last: Quan

first: Sabryna

last: Junker

first: Manuela

last: Flórido

first: Gregory

last: Cook

first: Tim

last: Clausen

first: Warwick

last: Britton

first: Mark

last: Larance

first: Richard

last: Payne


title: NNMT overexpression promotes tubular senescence and fibrosis in human chronic kidney disease (NNMT inhibition and SAM supplementation in TEC cells)

first: Alessandra

last: Tammaro

state: AZ

address: Meibergdreef 05

department: Department of pathology

institute: Amsterdam University Medical Center

summary: Renal tubular epithelial cells (TECs) are increasingly recognized as the central locus of chronic kidney disease and renal fibrosis. Here, we used conditionally immortalized TECs (expressing SV40 large T antigen at permissive conditions, 33°C with IFNγ, and behaving like normal primary cultures after 7 days in restrictive conditions, 37°C without IFNγ), stimulated with TGFβ to mimic the senescent and pro-fibrotic phenotypic shift of TECs during kidney disease. TGFβ stimulation and co-treatment with either the small-molecule NNMT inhibitor 5-amino-1-methylquinolinium iodide (NNMTi) or S-adenosyl methionine (SAM) altered the DNA methylation profile of the cells.

overall_design: 11 samples, 3 replicates (except 2 for TGFβ + SAM), 4 conditions. Control, TGFβ 10 ng/mL, TGFβ + NNMTi (5-amino-1-methylquinolinium) 50 µM, TGFβ + S-adenosyl methionine (SAM) 0.5mM. Cells treated for 48h.

first: Lucie

last: Chanvillard

first: Hildo

middle: C

last: Lantermans

first: Christopher

last: Wall

first: Jonathan

last: Thevenet

first: Loes

last: Butter

first: Loic

last: Tauzin

first: Nike

last: Claessen

first: Stefan

last: Christen

first: Giulia

last: Lizzo

first: Sonia

last: Karaz

first: José

middle: L

last: Sanchez-Garcia

first: Sylviane

last: Métairon

first: Valentina

last: Ferro

first: Sofia

last: Moco

first: Daniel

last: Raalte

first: Joris

last: Roelofs

first: Matthew

last: Sanders

first: Jerom

last: Feige

first: Vincenzo

last: Sorrentino


title: NBL1 Correlates with Renal Phenotypes in Mouse Models of Kidney Disease, but is not Causal: Male Nbl1 HET or WT Mice Treated with Cisplatin or PBS

city: Bar Harbor

first: Courtney

last: Willey

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

summary: Background: Increased concentrations of neuroblastoma suppressor of tumorgenicity 1 (NBL1) in the blood have been associated with disease progression in diabetic kidney disease and IgA nephropathy. However, it is unclear whether NBL1 is a causal factor for kidney disease and what is driving these increased concentrations in the blood. Methods: We tested causality of NBL1 by knocking out Nbl1 in two different mouse models of kidney disease (X-linked Alport Syndrome (XLAS) and low-dose cisplatin treatment) and performed a genetic analysis for the drivers of NBL1 concentrations in two independent cohorts of genetically diverse (DO) mice with X-linked Alport Syndrome (DO-XLAS). Results: Significant correlations were found between NBL1 concentrations in the blood and both GFR and ACR in DO-XLAS mice. However, XLAS mice with only one functional Nbl1 allele and reduced NBL1 concentrations had similar GFR and ACR compared to Nbl1 wildtype animals. Similarly, there was no difference between animals with one or two functional Nbl1 alleles after chronic low-dose cisplatin treatment. Genetic analysis of NBL1 concentrations in our DO-XLAS cohorts identified associations with loci on Chromosomes 4 and 17, with Clcnka, and MHC2 as potential candidates. Conclusion: Increased NBL1 in blood is a marker for different forms of kidney disease but is not a causal factor.

overall_design: Male Nbl1 HET or WT mice treated with Cisplatin or PBS (Control) for 4 consecutive weeks starting at 8 weeks of age (all mice are on the B6 background). Bulk RNA-seq of kidneys collected 3 days post treatment at 11-weeks of age.

first: Rei

last: Bufi

first: Harsphpreet

last: Chandok

first: Ron

last: Korstanje


title: Gene expression and chromatin accessibility in human embryonic stem cells with partial deletion of PDHB during DE differentiation [ChIP-seq]

status: Public on Nov 24 2025

city: WuHan

first: liming

last: meng

address: No. 115, Donghu Road

institute: WuHan university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We established a PDHB heterozygous cell line in human embryonic stem cell HUES8. Then we performed definitive endoderm (DE) differentiation using both WT and PDHB partial deletion cell lines, and assessed gene expression and chromatin accessibility changes during this process by RNA-seq and ATAC-seq. Differentially expressed genes and regions with altered chromatin accessibility showed that in the PDHB-deleted cell line, the efficiency of endoderm differentiation was significantly inhibited. This alteration primarily occurred through changes in chromatin accessibility at BAF complex binding sites on DNA, which is a major ATP-dependent chromatin remodeling complex. And we also detected the SMAD2/3 binging by ChIP-seq.

overall_design: We performed the DE differentiation in WT and PDHB partial deletion cells. The DE differentiation medium was based on DMEM and supplemented with 100 ng/mL Activin A, 1x penicillin/streptomycin, and 0.2% bovine serum albumin. After the differentiation, we performed the RNA-seq and ATAC-seq in both cells. Besides that, we performed the SMAD2/3 ChIP-seq in WT cells. Detection was carried out after 3 days of induction using the same system.

first: Liming

last: Meng

first: Jie

last: Yang

first: Wei

last: Jiang


title: Identification of UVB-induced TREM-1 positive tolerogenic DCs and TREM-1 signaling as a target in prevention of UVB-induced immune suppression and skin carcinogenesis

city: Birmingham

first: Hui

last: Xu

state: AL

address: VH566B 1670 University Blvd.

department: Dermatology

institute: The University of Alabama at Birmingham

summary: Ultraviolet-B (UVB) light was used to irradiate the back skin of C57BL/6 mice. Skin tissues were collected and gene differential expression analysis was performed using the nanostring nCounter Mouse PanCancer Immune Profiling Panel.

overall_design: The back skin of Wild type C57BL/6 mice was shaved and irradiated for 4 consecutive days with 200 mJ/cm2 of UVB light. The skin tissues were collected 24h after last UVB exposure and nanostring immune profiling was performed. C57BL/6 non irradiated mice were used as controls.

first: Carlos

middle: A

last: Mier-Aguilar

first: Mohammad

last: Asif Sherwani

first: Yuko

last: Tsuruta

first: Noha

last: Abdelsamad

first: David

last: Crossman

first: Sejong

last: Bae

first: Andrzej

last: Slominski

first: Craig

last: Elmets

first: Nabiha

last: Yusuf


title: Effect of PLK3 inhibitors treatment on the global transcriptome of resting CD4+ T Cells [miRNA-Seq]

city: Shenyang

first: Li

last: Zhao

address: Nanjing north street

department: Key Laboratory of AIDS Immunology of National Health and Family Planning Commission

institute: The First Affiliated Hospital of China Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: The persistence of HIV-1 reservoirs in resting CD4⁺ T cells despite the administration of antiretroviral therapy (ART) remains a major barrier to achieving a cure. In this research, we identified polo-like kinase 3 (PLK3) as a host antiviral factor able to suppress HIV-1 translation by targeting rare host tRNAs—specifically, tRNA-Ile-TAT and tRNA-Leu-TAA—in resting CD4⁺ T cells.The inhibition of PLK3 increases the production of viral proteins, including gp120 and Gag, in active reservoirs without cellular stimulation, thereby rendering infected cells vulnerable to CAR-T–mediated clearance.Together, these findings provide evidence that PLK3 is a key host regulator of HIV-1 translation in resting CD4⁺ T cells as well as a potential therapeutic target for reservoir eradication that may lead to a functional cure.

overall_design: RNA-seg profiling of CD4+T cells treated with DMSO, GW843682X, TAK-960, NMS-P937 at 24h and 48h.

first: Ruolin

last: Wang

first: Xiaofan

last: Luo


title: Effect of PLK3 inhibitors treatment on the global transcriptome of resting CD4+ T Cells [RNA-Seq]


title: Refined cellular activity expression signatures provide a targeted framework to quantify phenotypic intra-tumour heterogeneity in single-cell data IV

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

country: France

institute: Cancer Research Centre of Lyon

summary: Single cell RNA-seq (scRNA-seq) nowadays allows deeper insight into cellular biology at both the individual and population level. Measuring cell-to-cell variations in the population can furthermore help quantify phenotypic heterogeneity in populations in which cell states and identities deviate from healthy expectations. Cellular activities quantifiable using gene set enrichment analyses can provide useful grounds to quantify phenotypic heterogeneity, but the specificity and adequacy of existing molecular signatures scRNA-seq data is still insufficient. Here we induced 6 activities in vitro, for which we refined existing expression signatures to enhance specificity and detection: epithelial-mesenchymal transition (EMT), DNA repair, responses to interferons α and γ (IFNα and IFNγ, respectively), glycolysis, oxidative phosphorylation (OxPhos).

overall_design: human Mammary Epithelial Cells (hMEC) were cultured in vitro in three different media: neutral (negative control) ; glycolysis-inducing ; oxidative-phosphorylation-inducing. scRNA-seq analyses were performed after 12 weeks of culture in their specific media, cells cultured in each of the three conditions.

first: Lauriane

last: Muller


title: Refined cellular activity expression signatures provide a targeted framework to quantify phenotypic intra-tumour heterogeneity in single-cell data I

overall_design: MCF10A cells were cultured in vitro and analyzed in three different conditions: 4 days after EMT induction mediated by TGFb addition to the medium (EMT); 4h post DNA repair induction by irradiation at 4Gy (DNArepair) ; untreated (Control).


title: Refined cellular activity expression signatures provide a targeted framework to quantify phenotypic intra-tumour heterogeneity in single-cell data II

overall_design: MCF10A cells were cultured in vitro and analyzed at 1, 2, 3, 4 and 5 days after EMT induction mediated by TGFb addition to the medium (EMT). A negative "not-induced" control was also perform without addition of TGFb to the medium.


title: Refined cellular activity expression signatures provide a targeted framework to quantify phenotypic intra-tumour heterogeneity in single-cell data III

overall_design: MDA-MB-468 cells were cultured in vitro. IFNa response was induced by adding IFNa to the medium and analyzed 4 hours after. IFNg response was induced by adding IFNg to the medium and analyzed 18 hours after. Control cells were not exposed to either IFN.


title: FluPRINT Study: Characterisation of the Immune and Transcriptional Response to LAIV

city: Boston

first: Adriana

last: Tomic

address: 650 Albany St.

institute: Boston University

summary: The development of universal influenza vaccines requires eliciting durable T stem cell-like memory (TSCM) responses, yet the baseline determinants governing TSCM expansion remain undefined. Here, using multi-omic systems immunology in a pediatric cohort immunized with live attenuated influenza vaccine (LAIV), we identify a pre-existing state of innate antiviral readiness as the master determinant of vaccine-mediated TSCM induction. This submission contains the baseline (Visit 1) whole-blood transcriptional profiles of 19 healthy children (ages 4-6) prior to vaccination.

overall_design: Whole blood samples were collected from healthy children (4-6 years old) at baseline (Visit 1) prior to administration of the live attenuated influenza vaccine (LAIV). Total RNA was extracted and sequenced to identify pre-existing transcriptional signatures associated with subsequent vaccine responses.

first: Ivan


title: Integrated sudden origin of complex N2-fixing cells upon global oxygenation

city: Wuhan

first: Yali

address: NO.152 Luoyu Road

department: School of Life Sciences

institute: Central China Normal University

summary: Origin of a novel organ or specialized cell can be considered as a process by which the underlying gene regulatory network (GRN) was organized. Large changes in this process could be caused by co-option of functional modules to novel locations or re-wiring of the regulatory networks, through alterations in cis-regulatory elements and recruitment of new regulatory factors. Here, we show the role of an evolutionary coordinator in the integrated sudden origin of complex N2-fixing cells in multicellular cyanobacteria, called heterocysts, during the Neoproterozoic Oxygenation Event (NOE). We employed ChIP-seq and a synthetic Anabaena transcription system in Escherichia coli to systematically analyze the gene regulatory relationships. The GRN of heterocyst differentiation (het-GRN) and the ancestral primitive GRN were successfully reconstructed.

overall_design: ChIP-seq of HetZ in wild type and mutant strains (hetZ4-201 and DhetP) of Nostoc sp. PCC 7120 at 8 h after nitrogen stepdown.

first: Xi

last: Hu

first: Xudong


title: The conserved SEN1 DNA/RNA helicase has multiple functions during yeast meiosis

city: Stony Brook

first: Ed

last: Luk

state: NY

address: 100 Nicolls Rd, Life Sciences Building

department: Biochemistry and Cell Biology

institute: Stony Brook University

summary: DNA:RNA hybrids are unusual structures found throughout the genomes of many species, including yeast and mammals. While DNA:RNA hybrids may promote various cellular functions, persistent hybrids lead to double strand breaks, resulting in genomic instability. DNA:RNA hybrid formation and removal are therefore highly regulated, including by enzymes that either degrade or unwind RNA from the hybrid. Meiosis is the specialized cell division that creates haploid gametes for sexual reproduction. Previous work in yeast and mammals showed that elimination of DNA:RNA hybrids by RNase H facilitates meiotic recombination. This work demonstrates that the conserved Sen1 DNA/RNA helicase functions during three temporally distinct processes during yeast meiosis. First, SEN1 allows meiosis-specific genes to be expressed at the proper time to allow entry into meiosis. Second, SEN1 prevents the accumulation of hybrids during premeiotic DNA replication. Third, SEN1 promotes the repair of programmed meiotic double strand breaks that are necessary to form crossovers between homologous chromosomes to allow their proper segregation at the first meiotic division. Given the evolutionary conservation of Sen1 with its mammalian counterpart, Senataxin, studies of Sen1 function in yeast are likely to be informative about the regulation of DNA:RNA hybrids during humans as well.

overall_design: To investigate how SEN1 contributes to the regulation of IME1, nanopore direct RNA sequencing (dRNA-seq) was performed on coding and non-coding transcripts isolated from SEN1 and sen1-md cells in Spo medium. dRNA-seq requires that each transcript has a 3’ poly(A) tail to which a sequencing adapter and motor protein that threads the RNA through a pore can be ligated. Non-coding RNAs—particularly those that fail to terminate properly in the absence of the Nrd1-Nab3-Sen1 (NNS) complex lack poly(A) tails and therefore would be underrepresented. To capture these transcripts, poly(A) tails are added in vitro. However the high abundance of the four ribosomal RNAs (rRNAs) (25S, 18S, 5.8S and 5S) in total RNA preparations would swamp out this reaction and so must be removed prior to polyadenylation. The four rRNAs were depleted from total RNA isolated from SEN1 and sen1-md cells by hybridization to the combined biotinylated anti-sense transcripts for each rRNA, followed by streptavidin-based removal. The resulting rRNA-depleted RNA was then polyadenylated in vitro using E. coli poly(A) polymerase prior to nanopore library preparation. Two biological replicates were performed for SEN1 and sen1-md strains after two hours in Spo medium, yielding ~6-7 million uniquely aligned reads per replicate to the S. cerevisiae SK1 genome.

first: Robert

last: Gaglione

first: Leonidas

last: Pierrakeas

first: Lihong

last: Wan

first: Jonathan

last: Caradonna

first: Amy

last: MacQueen

first: Nancy

last: Hollingsworth


title: The impact of Tat expression on the host transcriptome landscape as the cells transit through the successive phases of the latency cycle

city: Bengaluru

first: Ranga

last: Udaykumar

state: Karnataka

address: Jakkur post

department: Molecular Biology and Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

summary: We hypothesized that Tat may exert opposing effects on viral gene expression depending on its PTMs. Furthermore, we propose that Tat can actively regulate the expression of host factors responsible for these PTMs, thereby influencing the establishment of latency. To investigate this, we define a latency cycle, capturing the distinct stages of cellular transition through the OFF-ON-OFF phases of viral gene expression. Jurkat cells were infected with a dual-reporter viral construct co-expressing a short-lived d2EGFP and a long-lived mScarlet fluorescent protein fused to Tat. The extended half-life of the Tat-mScarlet fusion enabled us to track and stabilize Tat expression even during the LTR-OFF state, providing a means to assess differential host gene expression. In the defined latency cycle, prior to stimulation, infected cells were dual-negative for both reporters (DN: GFP⁻ RFP⁻), indicative of a latent state. Upon activation of the LTR, cells transitioned to a dual-positive phase (DP: GFP⁺ RFP⁺), followed by a single-positive phase (SP: GFP⁻ RFP⁺), and eventually returned to the DN phase. These subsets correspond to distinct stages in the latency cycle: latent, transcriptionally active, early latent, and latent, respectively. We developed a doxycycline-inducible system to selectively activate the viral LTR, without stimulating the host cells. Upon doxycycline treatment, diTat is expressed, providing a controlled, pulse-like activation of the viral LTR and enabling the establishment of a latency cycle. The distinct phases of the latency cycle were sorted, and a transcriptomic analysis was conducted.

overall_design: Samples are as follows: Day 0: P1 – DN (GFP⁻ RFP⁻), representing the latent pre-induction state Day 3: P2 – DP (GFP⁺ RFP⁺), active transcription phase; and P3 – SP (GFP⁻ RFP⁺), early latent cells Control: rtTA3 (cells expressing rtTA3 protein), and diTat (cells with Tet-ON-Tat system)

first: Chhavi

last: Saini

first: Mani

last: Shanmugansenthil


title: Bulk RNA-Seq  of head and neck squamous cell carcinomas

city: Houston

first: Yu

middle: Leo

last: Lei

state: TX

address: 1901 East Rd

department: Head and Neck Surgery

institute: The University of Texas M.D. Anderson Cancer Center

summary: To substantiate the physiological relevance of the glutamine-BATF2 pathway, we performed bulk RNA-Seq on 15 HNSCC specimens. Then, we performed a correlation analysis between BATF2-IFN-I pathway genes and glutamine metabolism markers.

overall_design:
Bulk RNA-seq was performed on fresh tumor tissues from 15 oral cancer patients, with duplicate samples sequenced for each patient. Here are total 30 samples and  samples 31 is the replacement of samples 10. >>>Raw data for human samples not available due to patient privacy concerns<<<

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

first: James

last: Moon

first: Steven

last: Chinn

first: Greg

last: Wolf

first: Yuying

last: Xie

first: Arash

last: Yunesi

first: Xingwu

last: Zhou

first: Wang

last: Gong


title: PNPLA3-I148M genetic variant rewires lipid metabolism to drive programmed cell death in human hepatocytes

city: Pittsburgh

first: Soto

middle: Gutierrez

last: Alejandro

address: 200 Lothrop St.

department: Department of Pathology

institute: University of Pittsburgh

summary: Genetic variants in lipid metabolism influence the risk of developing metabolic dysfunction-associated steatotic liver disease (MASLD), cirrhosis, and end-stage liver disease (ESLD). The mechanisms by which these variants drive disease are poorly understood. Because of the PNPLA3-I148M variant's strong correlation with all stages of the MASLD spectrum and the lack of tractable therapeutic targets, we sought to understand its impact on cellular function and liver metabolism. Primary human hepatocytes (HAH) and iPSC-derived hepatocytes (iHeps) from healthy individuals possessing the PNPLA3-I148M mutation were characterized for changes in lipid metabolism, cellular stress, and survival. Using lipidomics, metabolomics, stable isotope tracing, and flux propensity analysis, we created a comprehensive metabolic profile of the changes associated with the PNPLA3-I148M variant. Functional analysis showed that the presence of the PNPLA3-I148M variant increased endoplasmic reticulum stress, mitochondrial dysfunction, and peroxisomal β-oxidation, ultimately leading to cell death via ferroptosis. Nutritional interventions, ferroptosis-specific inhibitors, and genetic approaches modulating GPX4 activity in PNPLA3-I148M HAH and iHeps decreased programmed cell death. Our findings indicate that therapies targeting ferroptosis in patients carrying the PNPLA3-I148M variant could affect the development of MASLD and ESLD and highlight the utility of iPSC-based models for the study of genetic contributions to hepatic disorders.

overall_design: RNA-Seq profiling of isolated primary human hepatocytes carrying the SNP PNPLA3-I148M as compared to the WT

first: Rodrigo

last: Florentino

first: Olamide

last: Animasahun

first: Nils

last: Haep

first: Minal

last: Nenwani

first: Kehinde

middle: O

last: Omoloja

first: Leyla

last: Altay

first: Abhinav

last: Achreja

first: Kazutoyo

last: Morita

first: Takashi

last: Motomura

first: Ricardo

last: Diaz-Aragon

first: Lanuza

last: Faccioli

first: Yiyue

last: Sun

first: Zhenghao

last: Liu

first: Zhiping

last: Hu

first: Bo

last: Yang

first: Fulei

last: Wuchu

first: Ajay

last: Shankaran

first: Miya

last: Paserba

first: Annalisa

last: Baratta

first: Shohrat

last: Arazov

first: Zehra

last: Kocas-Kilicarslan

first: Noah

last: Meurs

first: Jaideep

last: Behari

first: Edgar

last: Tafaleng

last: Franks

first: Alina

last: Ostrowska

first: Takahiro

last: Tomiyama

first: Kyohei

last: Yugawa

first: Akinari

last: Morinaga

first: Zi

last: Wang

first: Kazuki

last: Takeishi

first: Dillon

last: Gavlock

first: Mark

last: Miedel

first: D.

last: Taylor

first: Ira

middle: J

last: Fox

first: Tomoharu

last: Yoshizumi

first: Deepak

last: Nagrath

first: Alejandro

last: Soto-Gutierrez


title: Hyperosmotic stress induces a large-scale rewiring of 3D chromatin interactions [Cut & Tag]

city: Chapel Hill

first: John Patrick

last: Flores

state: NC

address: 104 Manning Dr

institute: UNC Chapel Hill

summary: Cells rapidly adapt to hyperosmotic stress through coordinated molecular responses. To determine how three-dimensional (3D) chromatin structure contributes to this process, we profiled chromatin interactions, architectural protein occupancy, and transcriptional dynamics in human cells exposed to sorbitol-induced hyperosmotic stress. We performed time-resolved Hi-C to measure stress-induced remodeling of chromatin loops and domains, CUT&Tag to quantify CTCF, RAD21, YAP1, and H3K27ac occupancy at loop anchors, and RNA-seq to capture stress-responsive transcriptional programs. These data reveal global loss of pre-existing chromatin contacts and concurrent formation of de novo, transient loops enriched for retained CTCF and cohesin, as well as transcriptional responses that are temporally layered and largely decoupled from loop remodeling. This dataset provides a resource for investigating how nuclear architecture and transcriptional regulation respond to hyperosmotic stress.

overall_design: eGFP-YAP HEK293 cells were serum-starved for 1 hour and then exposed to 200 mM sorbitol to induce hyperosmotic stress. Chromatin organization was profiled by in situ Hi-C at eight time points (0 min, 10 min, 30 min, 1 h, 3 h, 6 h, 12 h, and 24 h) to capture the formation, loss, and recovery of chromatin interactions. To assess the generality of chromatin remodeling, additional Hi-C experiments were performed in HEK293 wild-type and HCT116 cells with and without 1 hour of sorbitol treatment. Transcriptional responses were measured by stranded RNA-seq across a time course (0 h, 1 h, 3 h, 6 h, 9 h, 12 h, and 24 h). To quantiy changes in architectural protein occupancy, CUT&Tag for CTCF and RAD21 was performed in untreated and 1-hour sorbitol-treated HEK293 cells.

first: JP

first: Andrea A.

last: Perreault

first: Zack

last: Drum

first: Chenxi

last: Xu

first: Doris

last: Cruz Alonso

first: Gelila

last: Petros

first: Yijia

last: Wu

first: Ivana Y.

last: Quiroga-Barber

first: Isha

last: Sahasrabudhe

first: Justin

last: Demmerle

first: Gang Greg

first: Danfeng

last: Cai

first: Douglas

last: Phanstiel


title: A transcriptomic atlas of astrocyte heterogeneity across space and time in mouse and marmoset

city: Cambridge

first: Margaret

last: Schroeder

state: MA

address: 77 Massachusetts Avenue

department: Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

summary: How astrocyte regionalization unfolds over development is not fully understood. We used single-nucleus RNA sequencing to characterize the molecular diversity of brain cells across six developmental stages and four brain regions in the mouse and marmoset brain. Our analysis revealed striking regional heterogeneity among astrocytes, particularly between telencephalic and diencephalic regions in both species. Most of the region patterning was private to astrocytes and not shared with neurons or other glial types. Though astrocytes were already regionally patterned in late embryonic stages, this region-specific astrocyte gene expression signature changed significantly over postnatal development, and its composition suggests that regional astrocytes further specialize postnatally to support their local neuronal circuits. Across mouse and marmoset, we found hundreds of species differentially expressed genes and divergence in the expression of astrocytic region- and age-differentially expressed genes. Finally, we used expansion microscopy to show that astrocyte morphology is also regionally specialized.

sample_organism:
Callithrix jacchus
Mus musculus

platform_organism:
Callithrix jacchus
Mus musculus

overall_design: We used 10x Genomics Chromium v3 single-nucleus RNA sequencing to characterize the molecular diversity of brain cells across six developmental stages (from late fetal to aged adult) and four brain regions (prefrontal cortex, motor cortex, striatum, and thalamus) in the mouse and marmoset brain. Each developmental time point and region combination (except for aged mouse) has 2-3 biological replicate donors. Nuclei are NOT enriched (e.g., FACS sorted) for any particular population and contain neurons, glia, and vasculature populations.

first: Margaret E

first: Fenna M.

last: Krienen

first: Guoping

last: Feng


title: Neuroendocrine control of planarian regeneration(RNAi scRNA-seq)

city: Shanghai

first: Yuxiaofei

last: Wang

address: 320 Yue-Yang Road

institute: University of Chinese academy of sciences

summary: Effective tissue regeneration requires cells to perceive the surrounding context and make internal state adaptations that enable context-dependent fate changes in time and space, but the mechanisms underlying this complex process remain unclear. Here, transcriptom sequencing was used for study neuroendocrine control of planarian regneration

overall_design: Examine single-cell gene expression profiles on 3dpa planarian tail fragments after EGFP RNAi(control), nsf RNAi and scg5 RNAi.

first: Yue

last: Chen

first: An

last: Zeng


title: Sensitive direct detection of cancer antigens enabled by user-defined peptide libraries

first: Catherine

state: Massachusetts

address: 415 Main Street-Rm

institute: Broad Institute of MIT and Harvard - Cambridge, MA

summary: Data dependent mass spectrometry (MS) is routinely used to identify HLA-bound peptides but it can have limitations in sensitivity and reproducibility. We introduce Pepyrus, a method that uses E. coli to generate large-scale user-defined peptide libraries that can be utilized to improve the confidence in identification of HLA-bound peptides, including lowly abundant neoantigens. Using a Pepyrus peptide library paired with an HLA-specific data independent acquisition (DIA) MS strategy, we recovered >75% of the expected sequences per single injection for libraries of >10,000 peptides. Pepyrus peptide libraries also enabled the identification of 0.1 fmol spiked-in peptides in a complex background. Application of Pepyrus to create personalized peptide libraries facilitated the identification of clinically relevant HLA antigens from melanoma and renal cell carcinoma patient derived cell lines, several of which were previously undetected. Pepyrus customization enables rapid creation of patient- or disease-specific peptide libraries facilitating the confident identification of rare HLA peptides from immunopeptidomics data and the generation of large training datasets to improve spectrum, retention time, and IM prediction tools.

overall_design: Replicates of pepyrus libraries encoding 10,000 peptides were amplified upstream of the peptide coding sequence and subjected to next generation sequencing.

first: Kasidet

last: Manakongtreecheep

first: Claudia

last: Ctortecka

first: Luis

last: Correa-Medero


title: SAM-synthase specific effects on metabolism and mitochondria underlie resistance to heat stress in C. elegans

city: Worcester

first: Amy

last: Walker

address: 373 Plantation Street

institute: UMass Medical School

summary: S-adenosylmethionine (SAM), produced by SAM synthases, is critical for various cellular regulatory pathways and the synthesis of diverse metabolites. Studies have often equated the effects of knocking down one synthase with broader SAM-dependent outcomes such as histone methylation or phosphatidylcholine (PC) production. However, many organisms express multiple synthase genes including humans and Caenorhabditis elegans. Evidence in C. elegans, which possesses an expanded family of SAM synthases, suggest that the enzymatic source of SAM impacts its function. For instance, loss of sams-1 leads to enhanced heat shock survival and increased lifespan, whereas reducing sams-4 adversely affects heat stress survival. Here, we reveal that loss of sams-1 exerts age-dependent effects on nuclear-encoded mitochondrial gene expression, mitochondrial metabolites, and mitophagy. Notably, we find that that SAMS-1 exerts synthase-specific effects on PC production. We propose a mechanistic framework wherein the reduced SAM from SAMS-1 acts through PC to impact mitochondrial fission and mitophagy, thereby enhancing survival during heat stress. This study highlights multifaceted roles of SAM across metabolic pathways and synthase-specific SAM functions.

overall_design: Lysis of young adult C. elegans was performed in 0.5% SDS, 5% β-ME, 10 mM EDTA, 10 mM Tris-HCl ph7.4, 0.5 mg/ml Proteinase K, before purification of RNA by TRI-Reagent (Sigma). cDNA was produced with Transcriptor First-strand cDNA kits (Roche), and RT-PCR was performed using Kappa SYBR Green 2X Mastermix. RNA for sequencing was purified using RNAeasy columns (Qiagen). RNA sequencing (including library construction was performed by BGI (Hong Kong). Reads were analyzed through the NextFlow analysis platform (https://github.com/DanHUMassMed/RNA-Seq-Nextflow), using DeSeq2 to identify differentially expressed genes. Gene set enrichment was performed using WormCat (http://www.wormcat.com).

first: Athena

last: Munden

first: Dominique

middle: S

last: Lui

first: Daniel

middle: P

last: Higgins

first: Matthew

last: Fanelli

first: Thien-Kim

last: Ngyuen

first: Maria

last: Ericsson

first: Adwait

last: Godbole

first: Jessica

last: Spinelli

first: John

last: Haley

first: Caroline

last: Lewis

last: Promislow

first: Benjamin

last: Harrison

last: Raftery

first: Danijel

last: Djukovic

first: Dana

last: Miller


title: Lineage-specific enhancer insertions regulate Prdm14 to drive the rapid transition from naïve to formative pluripotency in rodents

city: Sanda

first: Yoshiyuki

last: Seki

state: hyogo

address: 1, Gakuen Uegahara

department: School of Biological and Environmental Sciences

country: Japan

institute: Kwansei Gakuin University

summary: The network of transcription factors is dynamically reorganized during the transition from naïve to formative pluripotency. In mice, Prdm14 is expressed in naïve pluripotent cells but rapidly downregulated upon exit from the naïve state. In contrast, PRDM14 expression persists throughout pluripotency transitions in non-rodent mammals, including pigs and humans. Here, we investigate the molecular mechanisms underlying the rodent-specific expression of Prdm14. Using CRISPR/Cas9-mediated deletions, we demonstrated that OCT4 and TFCP2L1 recognition sequences within Muroidea-specific cis-regulatory elements located downstream of Prdm14 are essential for its transcriptional upregulation required for the upregulation of Prdm14 in naive embryonic stem cells (ESCs). Loss of these enhancers suppresses Pramel7 induction and impairs degradation of UHRF1, thereby attenuating global DNA demethylation under 2iL conditions. Moreover, deletion of PRDM14-binding motifs in Muroidea-specific enhancers disrupts its negative feedback loop, resulting in delayed transition from the naïve to formative pluripotent state.

overall_design: RNA-seq experiments of WT, Cis KO of Prdm14, Prdm14-overexpressing embryonic stem cells


title: Oncogenic KRAS/ERK/JUNB signaling suppresses differentiation regulator GATA6 in pancreatic cancer

city: Singapore

first: David

last: Virshup

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

summary: GATA6 is a master regulator of differentiation in the pancreas and its expression levels determine the two main molecular subtypes of pancreatic cancer. High GATA6 contributes to the “classical” pancreatic cancer subtype, which is associated with a higher degree of tumor differentiation and better disease prognosis. However, why GATA6 expression varies across pancreatic cancers and what regulate GATA6 expression remain elusive. Here we report that the oncogenic KRAS-activated ERK signaling suppresses GATA6 transcription in pancreatic cancers. GATA6 mRNA levels inversely correlated with KRAS/ERK activity in pancreatic tumors. A genome-wide CRISPR screen in a GATA6-EGFP reporter knockin cell line identified JUNB as the ERK-regulated transcriptional repressor for GATA6. Active ERK stabilizes JUNB protein while KRAS/ERK inhibition led to ubiquitin-independent proteasomal degradation of JUNB and increased transcription of GATA6. Up-regulation of GATA6 enhanced chemosensitivity of pancreatic cancer cells and KRAS/ERK inhibitors synergized with chemotherapy in a GATA6-dependent manner. Our study identifies how oncogenic KRAS/ERK signaling suppresses GATA6 to cause dedifferentiation in pancreatic cancer. Combining KRAS/ERK inhibitors with standard-of-care chemotherapies could be a promising therapeutic strategy for treating pancreatic cancers.

overall_design: To explore the genome occupancy of JUNB in pancreatic cancer and how MEK/ERK inhibition affects JUNB’s genome occupancy, we performed Cut&Run assays with anti-JUNB antibody or IgG control in HPAF-II cells treated with or without the MEK inhibitor trametinib, followed by next-generation sequencing (Cut&Run-seq).

first: Zheng

last: Zhong


title: CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire

city: East Lansing

first: Yu

last: Zhang

state: MI

address: 567 Wilson Rd, Biomedical and Physical Sciences Building, Rm 5176

department: Microbiology, Genetics and Immunology

institute: Michigan State University

summary: Dynamic genome folding is important for V(D)J recombination at the immunoglobulin kappa (Igk) locus, which recombines Jk and Vk gene segments across a 3.2 Mb region in both deletional and inversional orientations. Chromatin loop extrusion and diffusion are considered two key mechanisms underlying Igk folding, but how they coordinate remains unclear. Here we show that CTCF is a key regulator coupling loop extrusion and diffusion during Igk V-J rearrangement, promoting recombination in both orientations across long genomic distances. Mechanistically, the CTCF N-terminus promotes long-range loop extrusion that facilitates distal Vk usage by stabilizing cohesin against WAPL release, and also forms loop barriers enabling chromatin diffusion for inversional Vk joining. In CTCF N-terminal-deficient B cells, defects in inversional Vk joining are not restored by WAPL depletion but are instead largely rescued by a dCas9-blockade targeted to the Vk-Jk intergenic region, mimicking the CTCF barrier. Our findings thus highlight how CTCF coordinates distinct genome-folding mechanisms through its dual roles in cohesin stabilization and extrusion barrier formation to ensure the generation of a diverse Igk repertoire.

overall_design: We performed PRO-Seq in WT and CTCF N-terminal mutant v-Abl transformed pro-B cells to study the molecular basis of CTCF's role in Igk recombination


title: Bioinformatics differential expression analysis of the effect of cannabidiol in chronic myeloid leukemia cell line

city: Sofia

first: Petar

middle: Petrov

last: Donchev

address: "Akademic Georgi Bonchev" building 26

department: Immunology

country: Bulgaria

institute: Stephan Angeloff Institute of Microbiology

summary: Chronic myeloid leukemia (CML) is the first clonal myeloproliferative disorder of the pluripotent stem cell to be associated with a specific genetic abnormality, the Philadelphia chromosome, bearing the BCR-ABL1 fusion oncogene. First treatment option for control of the chronic phase of CML are the tyrosine kinase inhibitors (TKIs), though alternative treatments are necessary for resistant cases. Cannabidiol (CBD), one of the major constituents of hemp oil exerts a broad range of pharmacological effects in various malignancies, yet its molecular mechanisms in leukemia remain unclear. In the present study, Imatinib-sensitive K-562S cells were subjected to CBD treatment (IC50: 17.69 μM) for 4 and 12 hours, followed by RNA sequencing to identify differentially expressed genes (DEGs). The consecutive transcriptomic profiling revealed 3518 DEGs at 12 hours and 3433 DEGs at 4 hours of treatment, showing significant modulation of metallothionein-regulated oxidative stress responses (MT1, MT2, SLC30A2), p53-mediated apoptosis (TP53TG3, DDIT4, BBC3, CHAC1, NOXA1, DAPK2), alteration in immune signaling pathways, including type I interferon activation, PI3K-Akt-mTOR and Toll-like receptor signaling, crucial in leukemia progression, as well as shifts in lipid metabolism and mitochondrial homeostasis.  The results presented in this study invigorate the considerable potential of CBD to induce broad transcriptional and signaling alterations, related to immune modulation, apoptosis, and metabolic processes in K-562S cells. These findings provide new insights in the therapeutic potential of CBD and lay the groundwork for further investigation into its precision applications in hematological malignancies.

overall_design: RNA-seq profiling was performed on wild-type K562 cells under three conditions: untreated control, treatment with cannabidiol (CBD) for 4 hours, and treatment with CBD for 12 hours.


title: Disruption of the Fgfr1-Fgf23-Phosphate Axis and Targeted Therapy in a Murine Model of Osteoglophonic Dysplasia

city: Rockville

first: Carlos

middle: Raul

last: Ferreira

state: Maryland

address: 10 Center Drive, Building 10, Room 2-5142

institute: NICHD

summary: Osteoglophonic Dysplasia (OGD) is an autosomal dominant skeletal dysplasia characterized by impaired bone growth resulting in short stature, severe craniofacial abnormalities, and in some patients FGF23-mediated hypophosphatemia. It is caused by gain-of-function variants in FGFR1, particularly in or near the transmembrane domain of the receptor. We used CRISPR to knock-in the Fgfr1 p.N330I variant in mice, chosen based on its association with FGF23 excess. Skeletal phenotyping of this Fgfr1+/N330I model demonstrated markedly small body weight, nasoanal length, shortened long bones, and craniosynostosis, all hallmarks of the human disease. Mutant mice exhibited profound microarchitectural changes in cortical bone and severe disorganization of the growth plate and articular cartilage, driven by decreased cell proliferation and increased apoptosis in skeletal tissues. Other than the osteochondrodysplasia, we noted dramatic increases in plasma FGF23 and hypophosphatemia, driven by upregulated Fgf23 mRNA expression and protein levels in bone, with consequent undermineralization. An in vivo ossicle assay allowed longitudinal evaluation of mineral metabolism. We attempted to modulate the signaling pathway by repurposing an inhibitor of the overactive receptor, infigratinib, resulting in partial restoration of length in treated mutant mice. These data offer insights into the pathogenesis of OGD and open avenues for potential targeted therapeutic strategies.

overall_design: Trancriptomics of RNA extracted from femurs collected from 3- or 4-week-old mice (5  Fgfr1+/N330I mice and 5 WT littermate controls).

first: Giuliana

last: Ascone


title: Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming [ES_H3K9ac_ChIP-seq]

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Spatiotemporal changes in the nuclear lamina and cell metabolism shape cell fate, yet their interplay is poorly understood. Here, we show that nuclear lamina dynamics regulate cysteine catabolic flux, crucial for proper stem cell fate and longevity. Lamin A/C loss in naïve pluripotent stem cells upregulates CTH and CBS enzyme expression, promoting de novo cysteine synthesis. Increased cysteine flux into acetyl-CoA fosters histone H3K9 and H3K27 acetylation, triggering a transition from naïve to primed pluripotency and abnormal cell fate. Conversely, gain-of-function mutation of lamin A/C, associated with premature aging, reduces CTH and CBS levels. This reroutes the cysteine catabolic flux and alters the balance between H3K9 acetylation and methylation, crucially impacting germ layer formation and genome stability. Importantly, modulation of cysteine metabolism rescues the abnormal cell fate, DNA damage repair defects, and the senescent phenotype upon lamin A/C mutation, highlighting the potential of modulating cell metabolism to mitigate epigenetic diseases.

overall_design: PLKO_LmnaKO，LmnaKO_shCbs and LmnaKO_shCth Nkx2-5-GFP mES cell lines were cultured on feeder condition in DMEM high glucose supplemented with 15% FCS and 1000 U/ml LIF. ESCs  were harvested to perform for H3K9ac ChIP-seq.

first: Julio

last: Cordero

first: Yinuo

last: Wang


title: Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming [ES_RNA_seq_G609G_LA_EXP2]

summary: Spatiotemporal changes in the nuclear lamina and cell metabolism shape cell fate, yet their interplay is poorly understood. Here, we identify lamin A/C as a key regulator of cysteine catabolic flux essential for proper cell fate and longevity. Its loss in naïve mouse pluripotent stem cells leads to upregulation of the cysteine generating and catabolizing enzymes, cystathionine γ-lyase (CTH) and cystathionine β-synthase (CBS), thereby promoting de novo cysteine synthesis. Increased cysteine flux into acetyl-CoA fosters histone H3K9 and H3K27 acetylation, triggering a transition from naïve to primed pluripotency and abnormal cell fate and function. Conversely, the toxic gain-of-function mutation of Lmna, encoding lamin A/C and associated with premature aging, reduces CTH and CBS levels. This reroutes cysteine catabolic flux and alters the balance between H3K9 acetylation and methylation, crucially impacting germ layer formation and genome stability. Importantly, modulation of Cth and Cbs rescues the abnormal cell fate and function, restores the DNA damage repair capacity, and alleviates the senescent phenotype caused by lamin A/C mutations, highlighting the potential of modulating cell metabolism to mitigate epigenetic diseases.

overall_design: RNA-seq of Lmna+/+, LmnaG609G/+,, LmnaG609G/G609G as well as CBS-OE-LmnaG609G/G609G embryonic stem cells

first: Haoije

last: Shi


title: Transcriptomic changes in uteri collected from 6-week-old Tcf21f/f and Tcf21d/d mice

city: Beijing

first: Jie

last: Li

address: No.8 Xishiku Street, Xicheng District, Beijing

institute: Peking University First Hospital

summary: We performed transcriptomic profiling to investigate the potential mechanisms underlying the impaired endometrial stromal development in Tcf21-deficient uteri.

overall_design: We performed RNA sequencing on uterine tissues collected from 6-week-old, body weight–matched Tcf21^f/f^ (control) and Tcf21^d/d^ (conditional knockout) female mice (n = 3 per group). The goal was to investigate the potential downstream target genes regulated by TCF21 involved in uterine development. Each sample represents an individual biological replicate. No treatment was applied prior to tissue collection. Control and experimental samples were processed simultaneously to minimise batch effects.

first: Jingwen

last: Zhu

first: Qing

last: Xue


title: Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming [ES_RNA_seq_G609G_LA_EXP1]


title: Zymomonas mobilis oxidative stress transcriptomics

city: Madison

first: Kevin

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: Zymomonas mobilis is an important bioenergy organism that has potential to produce biofuels, including ethanol, in high volumes. Here we examined the response of Zymomonas mobilis to various oxidative stresses using genome-scale transcriptomics data. We first examined the transcrpit abundance in WT aerobic growth compared to aerobic grown in paraquat, which forms superoxide. Under anaerobic growth conditions we compared WT Zymomonas mobilis with strains grown in media lacking iron as well as strains lacking iron that were treated with the iron chelator DIP before collection. Finally we examined transcript abundance in cells lacking ZMO_0422 (Rrf2 family transcription factor homolog) and ZMO_1411 (Fur homolog) grown under anaerobic conditions.

sample_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: Transcriptomic analysis of WT, a deletion of ZMO_0422, and a deletion of ZMO_1411 in Zymomonas mobilis ZM4 under aerobic and anaerobic growth conditions along with various oxidative stresses:  Paraquate addition, No Iron, and hydrogen peroxide addition.

first: Isabel

last: Askenasy

first: Kevin S

first: Patricia J

last: Kiley


title: Single-cell RNA-seq analysis of cervical lymph nodes from mice intradermally infected with Mycobacterium tuberculosis

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

summary: In mice, establishment of a contained and persistent yet non-pathogenic infection with Mtb ("contained Mtb infection", CMTB) rapidly and durably reduces tuberculosis disease burden after re-exposure through aerosol challenge. The bacteria are introduced by intradermal inoculation into the ear and are contained in the corresponsing cervical lymph node. Protection is associated with elevated activation of alveolar macrophages, the first cells that respond to inhaled Mtb, and accelerated recruitment of Mtb-specific T cells to the lung parenchyma. This study used single-cell RNA-seq to compare the cellularity and transcriptional profiles of innate immune cells in the cervical lymph node of naive mice and mice with CMTB.

overall_design: Mice were left untreated or inoculated with Mtb (strain H37Rv) to establish contained Mtb infection. 8 weeks later, the cervical lymph nodes were harvested and analyzed by single-cell RNA-seq.

first: Johannes

last: Nemeth

first: Katharina

last: Kusejko

first: Cédric

last: Dollé

first: Edoardo

last: Sarti

first: Dat

last: Mai

first: Ana

middle: N

last: Jahn

first: Dong

last: Liu

first: Gregory

last: Olson

first: Alan

middle: H

last: Diercks


title: Transcriptomic analysis of ZMO_0422 in Zymomonas mobilis

summary: Deletion of the IscR homolog ZMO_0422 was performed in Zymomonas mobilis to investigate the role of Fe-S cluster biogenesis in Zymomonas. Here we perform genome-wide transcirptomics study to examine transcript chagnes in delta-ZMO_0422 compared to WT Zymomonas mobilis under both aerobic and anaerobic growth conditions.

platform_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: Transcriptomic analysis of WT and a deletion of ZMO_0422 of Zymomonas mobilis ZM4 under aerobic and anaerobic growth conditions.

first: Patricia


title: Fibrotic Liver-Derived Organoids Provide a Physiologically Relevant Model of Liver Fibrosis

city: Seoul

first: Jiyoung

last: Heo

address: Gwanak-ro 1

country: South Korea

institute: Seoul National University

summary: We have performed a comparison of gene expression profiles between in vitro and in vivo liver fibrosis organoid models to assess their resemblance to in vivo fibrotic liver tissue and to evaluate the therapeutic effects of Sargassum japonica (S. japonica) on liver fibrosis.

overall_design: Liver organoids were generated from either healthy or carbon tetrachloride-induced fibrotic mouse liver tissue. Organoids were treated with Sargassum japonica, and total RNA was extracted for transcriptomic profiling to assess fibrosis-related gene expression changes.

first: Kyung-Rok

last: Yu


title: The contribution of Arpc5 for gene expression in intestinal macrophages

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: Patients with loss-of-function mutations in the ARPC5 subunit of the Arp2/3 complex develop inflammation and immunodeficiency after birth, leading to early mortality.  However, the mechanistic basis for these phenotypes remains obscure.  Our work demonstrate that loss of Arpc5 in the murine hematopoietic system causes early-onset intestinal inflammation.  This condition is initiated by microbiota breaching the ileal mucosa, leading to local and systemic inflammation.  Macrophage infiltrate into the ileum, but in the absence of Arpc5 fail to restrict microbial invasion.  So, we wanted to investigate the Arpc5 contribution for intestinal macrophages expression.

overall_design: intestinal content from control and mutant mice was extracted, FACS sorted and sequenced for analysis. The intestines were divided in small intestine and colon. Small intestines were subdivided in intraepithelial and lamina propria phases.

first: Michael

last: Way

first: Luiz

last: Vasconcellos

first: Shaina

last: Huang

first: Emanuele

last: Libertini


title: Sequential DC-intrinsic Lymphotoxin Beta Receptor and Retinoic Acid Receptor signals regulate cDC2 fates

city: New York

first: Chrysothemis

last: Brown

state: New York

department: Immuno-Oncology Program

institute: Memorial Sloan Kettering Cancer Center

summary: Type II conventional dendritic cells (cDC2) are functionally and phenotypically heterogenous. Previous work identified two major cDC2 subsets (cDC2A and cDC2B) and a transcriptionally related monocytic DC3 subset; however, the underlying microenvironmental cues governing their distinct differentiation pathways remain unclear. Here we delineate cDC2 lineage relationships, and the sequential signals required for cDC2A specification and maintenance. We show that T-bet+ cDC2A, arising from a Clec9a+ DC progenitor, express the retinol receptor RBPR2, require cell-intrinsic retinoic acid (RA) signaling for their maintenance in the spleen and mesenteric lymph nodes, and depend on intrinsic RA receptor signaling to sustain downstream Notch signals. Prior to their expression of T-bet, splenic cDC require cell-intrinsic Lymphotoxin beta receptor (LTbR) which is needed to reduce F-actin content and prevents the escape of cDC2 to the blood. We propose a novel mechanism whereby splenic cDC2-intrinsic LTbR signaling anchors cDC2 within the spleen so that they may access macromolecules such as retinol to promote cDC2A development.

overall_design: scRNA-seq (gene expression and HTOs) of YFP+ and YFP– CD45+Lin–MHCII+ cells from spleen and mLN of Tbx21RFP-creERT2_Clec9a-cre/cre_R26-YFP (Clec9a fate-mapping) mice, pooled from 4 biological replicates.

first: Logan

last: Fisher

first: Anushka

last: Yadav


title: Targeted editing of histone H3K27 trimethylation elucidates its significance in photoperiodic control of flowering

city: Xianyang

first: Jingyun

last: Lu

state: Shanxi

address: No. 22, Xinong Road

institute: Northwest A&F University

summary: Epigenetic modifications play essential roles in regulating gene expression, yet establishing direct causality between specific modifications and transcriptional outcomes remains challenging. In this study, we employed a CRISPR/dCas9-SunTag system to specifically reduce H3K27me3 levels at the FLOWERING LOCUS T (FT) gene in Arabidopsis thaliana. Targeting a truncated version of the H3K27 demethylase REF6 lacking its DNA-binding zinc fingers (REF6ΔZnF) to the FT locus effectively decreased local H3K27me3, enhanced FT transcription, and led to early flowering phenotypes, particularly under non-inductive short-day (SD) conditions. Chromatin immunoprecipitation confirmed the site-specific reduction of H3K27me3, with minimal genome-wide changes. Under long-day (LD) conditions, H3K27me3 levels at FT oscillated diurnally, coinciding with FT induction at dusk, while in SD conditions, H3K27me3 remained stable, contributing to FT repression. Our results provide direct evidence that H3K27me3 represses FT transcription under non-inductive conditions and demonstrate the utility of epigenetic editing for fine-tuning gene expression and developmental traits in plants

overall_design: Examination of H3K27me3 enrichment in wild-type and transgenic seedlings

first: Danhua

last: Jiang


title: Diabetes exacerbates destructive inflammation by activating the CD137L-CD137 axis in dendritic and gd T-cells

city: Philadelphia

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

summary: Periodontal disease, a bacterial infection affecting a large percentage of the world's population, is an important risk factor for several systemic diseases and is significantly worsened by diabetes. To investigate how diabetes exacerbates the inflammatory response to bacteria in this disease, we combined insights from murine and human studies. Through single-cell RNA sequencing, we identified a compelling hyperglycemia-driven molecular pathway: the upregulation of CD137L in dendritic cells and increased expression of its receptor, CD137, in γδ T-cells. The CD137L-CD137 axis emerged as a pivotal mediator of diabetes-induced inflammatory tissue destruction. Antibody-mediated inhibition of CD137L markedly reduced the diabetes-driven bone loss, neutrophil recruitment, expansion of γδ T-cells, and excessive infiltration by IL17A+ cells.

overall_design:
Wild-type mice were CD11CCre-/- mice, which are on a mixed C57B6 - FVB background. Type-I diabetes mellitus was induced in mice using streptozotocin. Bacterial induced inflammation for two weeks, waiting period was two weeks. Cells were isolated from the gingiva, pooled from 3 mice per group with negative selection of dead cells (DAPI+), endothelial cells (CD31+), RBC (Ter-119+)and positive selection of CD45+ cells with 20% enrichment of CD11c+CD45+ cells by FACS sorting. 10,000 FACS sorted cells were loaded per lane of a 10x Genomics Chromium instrument for scRNA-seq analysis

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first: Xin

first: Min

middle: V

first: Rahul

last: Debnath

first: Hamideh

last: Afzali

first: Yongwon

last: Choi

first: Su

last: Kim

first: Kang

middle: I

last: Ko

first: Dana

last: Graves


title: Endothelial CEPT1 Promotes Angiogenesis Through PPAR𝝰 and VEGF-A Signaling

city: Saint Louis

first: Mohamed

middle: Adel

last: Zayed

email: zayedlab@wustl.edu, zayedm@wustl.edu

state: MO

address: 4940 Children’s place

department: Surgery

institute: Washington University School of Medicine

summary: Cept1 is essential for de novo phopholipogenesis and is impacted by diabetes. We previously demonstrated that conditional knockdown of Cept1 in the endothelium leads to reduced tissue recovery. Therefore, we hypothesized that Cept1 may also be sufficient in promoting post-ischemic angiogenesis and recovery in the setting of diabetes. We have employed a single cell sequencing approach using 10x Genomics scRNAseq to study the role of Cept1 overexpression in mice aortic tissue.

overall_design: An endothelial cell (EC)-specific Cept1 overexpression mouse model was developed (Cept1fl/flCre+) in adult C57BL6 mice. Murine aortas were harvested, for single-cell RNA sequencing (scRNA-seq). Transcriptional profiling of Cept1fl/fl Cre− and Cept1fl/fl Cre+ mouse whole aortas was performed using droplet-based massively parallel 10X genomic single-cell RNA sequencing (scRNA-seq) 3’ v3.

first: Tariq

last: Khan

first: Rodrigo

last: Meade

first: Santiago

last: Elizondo Benedetto

first: Larisa

last: Belaygorod

first: Omar

last: Saffaf

first: Brigida

last: Rusconi

first: Fong-Fu

last: Hsu

first: Sangeeta

last: Adak

first: Batool

last: Arif

last: Zaghloul

first: Tiandao

last: Li

first: Bo

last: Zhang

first: Clay

middle: F

last: Semenkovich


title: Blocking the transfer of damaged mitochondria from cancer cells to RGS5+ MYL9+ CAFs reduces persistent tolerance to TKIs in EGFR-mutant lung cancer

city: Nanjing

first: Siwei

last: Wang

state: Jiangsu

address: No. 42, Baiziting

department: Thoracic Surgery

institute: Jiangsu Cancer Hospital

summary: Eliminating drug-tolerant persister (DTP) cells remain a significant challenge in overcoming resistance to tyrosine kinase inhibitors (TKIs) in EGFR-mutant lung adenocarcinoma. Utilizing single-cell RNA sequencing, we identify a novel RGS5+MYL9+ cancer associated fibroblasts (CAFs) subset. This subset is linked to TKI resistance and correlates with poorer prognosis. The RGS5+MYL9+ CAFs are spatially positioned close to DTP cells, a proximity facilitated by CCL11 recruitment from DTP cells. TKIs induced mitochondria ROS activates Rho GTPase 1 (Miro1) and RhoA of tumor cells, subsequently promoting the formation of tunneling nanotube connections with neighboring RGS5+MYL9+ CAFs. These CAFs play a protective role for DTP cells, aiding in the transfer of damaged mitochondria from tumor cells through these nanotubes. By employing the Rho kinase inhibitor Fasudil to block this transfer of damaged mitochondria, we observed a significant reduction in persistent tolerance to Osimertinib in a xenograft mouse model. Our study highlights the critical role of RGS5+MYL9+ CAFs in mediating resistance to EGFR-TKIs and suggests potential therapeutic strategies for overcoming this challenge.

overall_design: Single-cell RNA sequencing was performed on tumor tissues from patients with EGFR-mutant lung adenocarcinoma, and bulk RNA sequencing was conducted on parental 827 cells, TKI-induced DTP 827 cells, and DTP 827 cells co-cultured with distinct CAF populations.

first: Rong

last: Yin

first: Tongyan

last: Liu

first: Shiyin

last: Huang

first: Zhitong

first: Jianyu


title: Hyperosmotic stress induces a large-scale rewiring of 3D chromatin interactions [RNA-Seq]

city: Chapel Hill

first: John Patrick

last: Flores

address: 104 Manning Dr

institute: UNC Chapel Hill

summary: Cells rapidly adapt to hyperosmotic stress through coordinated molecular responses. To determine how three-dimensional (3D) chromatin structure contributes to this process, we profiled chromatin interactions, architectural protein occupancy, and transcriptional dynamics in human cells exposed to sorbitol-induced hyperosmotic stress. We performed time-resolved Hi-C to measure stress-induced remodeling of chromatin loops and domains, CUT&Tag to quantify CTCF, RAD21, YAP1, and H3K27ac occupancy at loop anchors, and RNA-seq to capture stress-responsive transcriptional programs. These data reveal global loss of pre-existing chromatin contacts and concurrent formation of de novo, transient loops enriched for retained CTCF and cohesin, as well as transcriptional responses that are temporally layered and largely decoupled from loop remodeling. This dataset provides a resource for investigating how nuclear architecture and transcriptional regulation respond to hyperosmotic stress.

overall_design: HEK293 eGFP-YAP cells were serum-starved for 1 hour and then exposed to 200 mM sorbitol to induce hyperosmotic stress. Chromatin organization was profiled by in situ Hi-C at eight time points (0 min, 10 min, 30 min, 1 h, 3 h, 6 h, 12 h, and 24 h) to capture the formation, loss, and recovery of chromatin interactions. To assess the generality of chromatin remodeling, additional Hi-C experiments were performed in HEK293 wild-type and HCT116 cells with and without 1 hour of sorbitol treatment. Transcriptional responses were measured by stranded RNA-seq across a time course (0 h, 1 h, 3 h, 6 h, 9 h, 12 h, and 24 h). To quantiy changes in architectural protein occupancy, CUT&Tag for CTCF and RAD21 was performed in untreated and 1-hour sorbitol-treated HEK293 cells.

first: JP

first: Andrea A.

last: Perreault

first: Zack

last: Drum

first: Chenxi

last: Xu

first: Doris

last: Cruz Alonso

first: Gelila

last: Petros

first: Yijia

last: Wu

first: Ivana Y.

last: Quiroga-Barber

first: Isha

last: Sahasrabudhe

first: Justin

last: Demmerle

first: Gang Greg

first: Danfeng

last: Cai

first: Douglas

last: Phanstiel


title: Synergistic Inhibition of CHK1 and MUS81 to target replicative stress in high-risk neuroblastoma

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

summary: Neuroblastoma (NB) is a pediatric tumor marked by genetic heterogeneity and frequent chromosomal alterations, including MYCN amplification and 17q gain, both linked to poor prognosis. These alterations affect key genes involved in transcriptional regulation and DNA damage response (DDR). NB cells experience high replicative stress (RS), making them particularly sensitive to DDR inhibition. Through integrative bioinformatics, genes such as EME1, RAD51C, and FANCJ on 17q were identified as critical in RS regulation. Targeting the downstream endonuclease MUS81, especially in combination with CHK1 inhibition, produced synergistic anti-tumor effects. This combination offers a promising strategy to exploit RS vulnerability in high-risk NB.

overall_design: RNA-sequencing of high dose Dyngo4a and combination drugging of Dyngo4a and prexasertib in IMR-32 neuroblastoma cell lines.

first: Elien

last: Hilgert

first: Fien

last: Martens

first: Suzanne

last: Vanhauwaert

first: Christophe

last: Vanneste

first: Frank

last: Speleman

first: Lisa

last: Depestel

first: Kaat

last: Durinck


title: The Aging Microenvironment is a Determinant of Immune Exclusion and Metastatic Fate in Pancreatic Cancer

city: La Jolla

first: Cosimo

last: Commisso

state: CA

address: 10901 N. Torrey Pines Road

department: Cancer Metabolism and Microenvironment Program

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Aging is a critical yet understudied determinant in pancreatic ductal adenocarcinoma (PDAC). Despite a strong epidemiological association with age, conventional PDAC preclinical models fail to capture the histopathological and stromal complexities that emerge in older organisms. Using an age-relevant syngeneic orthotopic model, we demonstrate that organismal aging accelerates PDAC progression and metastasis. Through transcriptomic profiling, we identify a conserved extracellular matrix gene signature enriched in cancer-associated fibroblasts (CAFs) from aged tumors, consistent with an augmented fibrotic landscape that supports immunosuppression, metastatic tropism, and poor prognosis. To directly test the functional impact of stromal aging, we employed heterochronic co-implantation models, revealing that revitalizing the aged tumor stroma with young CAFs restores immune infiltration and attenuates metastasis in older hosts. Conversely, aged CAFs, while immunosuppressive, fail to enhance metastasis in young hosts, suggesting that a youthful microenvironment exerts dominant regulatory control over disease progression. These findings demonstrate that stromal age is a critical modulator of both immune exclusion and metastatic behavior in PDAC. Importantly, our work establishes a new conceptual framework for understanding how aging shapes the tumor microenvironment in PDAC and opens a fertile avenue of investigation into age-specific stromal regulation. Moreover, this work raises compelling questions about the underlying molecular mechanisms—questions now accessible through our models—and lays the foundation for future efforts to therapeutically target stromal aging in PDAC.

overall_design: Transcriptomic profiling using bulk RNA sequencing of tumors harvested from young and old mice

first: Priyanka

last: Gupta


title: Pfkfb1 Selectively Identifies Macrophages Harboring Intracellular Growing Bacteria

city: shang hai

first: Li

last: Fan

address: song jiang qu

institute: Shanghai jiao tong university

summary: Through releasing virulence molecules into host cells, intracellular bacteria interfere with host cellular functions and grow in the cells that engulf them. To ensure survival and virulence, these pathogens also manipulate host factors, but this process is not fully understood. In this study, we investigated the host molecular mechanisms required for intracellular bacterial growth in macrophages using Salmonella typhimurium (Salmonella) infection model and bacterial division reporter system. Upon Salmonella infection, Protein Phosphatase 6 (Pp6) was significantly reduced in macrophages containing growing bacteria. Conditional knockout of Pp6 increased host susceptibility to Salmonella-mediated killing, which was attributed to the poor resistance in Pp6-deficient macrophages. MicroRNA-31 (miR-31) was identified as a negative regulator of Pp6, and its conditional deletion promoted Salmonella clearance. Moreover, a yeast two-hybrid screening identified 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (Pfkfb1), a key metabolic regulator, as a substrate of Pp6. Pp6-deficient macrophages exhibited elevated Pfkfb1 expression. Furthermore, we found that macrophages containing growing Salmonella exclusively exhibited high Pfkfb1 expression. Pfkfb1 deletion reduced bacterial growth, likely due to increased NO levels, while also downregulating arginase-1 (Arg-1) expression and impairing arginine biosynthesis and metabolism in macrophages. Together, we investigated the role of Pp6-Pfkfb1 axis in orchestrating host metabolic adaptions and intracellular bacterial survival, which may provide therapeutic targets for infectious diseases against intracellular multidrug-resistant bacteria.

overall_design: RNAseq profiling of WT  and Pfkfb1-/- BMDMs to explore the mechanistic basis

first: Yang

last: Sun