title: A wound-responsive transcription factor, OsWRKY53 dictates downstream wound responses upon OsPep2 perception [ChIP-seq]

first: Shivaprasad

last: Padubidri V.

summary: OsWRKY53 responded to both wounding and wound-derived peptide, OsPep2 treatment. We have performed ChIP-seq experiments to determine the contribution of OsWRKY53 to both wounding as well as OsPep2 treatment.

overall_design: Plants expressing GFP tagged WRKY under native promoter was used for all the experiments. Peptide treatment was administered to the six-week-old leaf strips. 1 µM was used for treatment. The leaf strips were collect according to the time point and crosslinked before freezing. The frozen samples were ground and used for further experiments.

first: P

last: Shivaprasad

first: C

middle: Y

last: Harshith


title: Cut&Tag profiling of NR1D1 in primary mouse vascular smooth muscle cells with or without vasostatin-2 stimulation

status: Public on Sep 01 2025

city: Shanghai

first: Jingmeng

last: Liu

address: No. 197, Ruijin 2nd Road, Huangpu District, Shanghai

department: Department of Cardiovascular Medicine

country: China

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: NR1D1 (also known as Rev-erbα) is a nuclear receptor involved in circadian rhythm and metabolic regulation. Its role in vascular biology is not fully understood. We performed CUT&Tag (Cleavage Under Targets and Tagmentation) to investigate the genome-wide binding profile of the transcription factor NR1D1 in primary vascular smooth muscle cells (VSMCs) isolated from mice. Two experimental conditions were included: cells treated with vasostatin-2 and untreated controls. The goal of this study was to identify potential transcriptional regulatory targets of NR1D1 under basal and vasostatin-2-stimulated conditions. CUT&Tag was carried out using a specific antibody against NR1D1, and sequencing was performed on the Illumina NovaSeq 6000 platform.

overall_design: CUT&Tag was performed using an NR1D1 antibody in primary mouse vascular smooth muscle cells with or without vasostatin-2 treatment to investigate differential chromatin binding under stimulated and control conditions.

first: Qiujing

last: Chen

first: Rosalinda

last: Madonna

first: Yang

last: Dai

first: Lin

last: Lu

first: Raffaele

last: De Caterina


title: Effect of vasostatin-2 treatment on gene expression in mouse femoral arteries following wire injury

type: Expression profiling by high throughput sequencing

summary: Neointimal hyperplasia is a major pathological process underlying restenosis following vascular injury. Vasostatin-2, a bioactive peptide derived from chromogranin A, has been implicated in vascular protection, but its mechanism remains unclear. To investigate the molecular basis through which vasostatin-2 modulates vascular remodeling, we performed transcriptomic profiling using RNA sequencing in a mouse model of femoral artery wire injury. Mice underwent wire-induced endothelial denudation of the femoral artery and immediately received perivascular treatment with either vasostatin-2 or saline. At 3 days post-injury, the injured femoral arteries were harvested for RNA-seq analysis to examine the impact of vasostatin-2 treatment on gene expression changes associated with vascular injury and neointima formation. This dataset provides insight into the transcriptional programs regulated by vasostatin-2 during the early phase of vascular injury and may reveal therapeutic targets for preventing restenosis.

overall_design: RNA sequencing was performed on mouse femoral arteries 3 days post-wire injury, following perivascular treatment with either vasostatin-2 or saline, with three biological replicates per group, to examine gene expression changes associated with vascular injury and neointima formation.


title: Gene expression profile at single cell level from skin of WT and Tsk mice

city: los angeles

first: Sandra

last: Orsulic

state: california

address: 10833 Le conte ave

department: OBGYN

country: USA

institute: UCLA

summary: Patients with systemic sclerosis have a significantly increased incidence of developing various solid malignancies within a few years of systemic sclerosis onset but the mechanism of tumor promotion is not well understood. The tight skin (TSK) mouse has been a valuable model for investigating systemic sclerosis-related pathologies due to increased extracellular matrix deposition, fibrosis in connective tissues, and altered immune cell activation. Despite the role of extracellular matrix and fibrosis in cancer progression, the potential of the TSK mouse as a model for cancer studies is unexplored. Our RNA sequencing analysis of adult dorsal skin samples from TSK and wild-type (WT) mice revealed a notable enrichment for genes typically associated with cancer aggressiveness and desmoplasia. To investigate the impact of the altered microenvironment in TSK mice on cancer progression, we compared the tumor-forming capabilities in TSK mice and WT mice using a syngeneic mouse model of ovarian cancer. TSK mice exhibited larger and more invasive subcutaneous and intraperitoneal tumors in comparison to WT controls, suggesting the role of the microenvironment in promoting cancer progression. Single-cell RNA sequencing analysis of tumors in TSK and WT mice revealed a higher neutrophil-to-lymphocyte ratio, and an enrichment in profibrotic subpopulations of myofibroblasts and macrophages in TSK mice.

overall_design: To better understand the differences in cell populations in TSK and WT mice (i.e. subtypes of fibroblasts and specific functional subsets of immune cells), we conducted single-cell RNA sequencing analysis of skin isolated from TSK and WT mice.

first: Orsulic

last: Sandra

first: Recouvreux

last: Maria Sol


title: Selective Intestinal Decontamination Mitigates Binge Alcohol-Induced Cardiovascular Dysfunction via Reduced Anandamide Production

city: Rockville

first: Qiaoping

last: Yuan

state: MD

address: 5625 Fishers Lane, Suite 3S32

institute: NIAAA

summary: Binge drinking contributes to a rising number of emergency room visits in the United States. Our previous work demonstrated that binge drinking impairs cardiac performance and exerts complex hemodynamic alterations through activation of the endocannabinoid–CB1 receptor (CB1R) signaling pathway. Anandamide, an endogenous CB1R agonist, is produced in response to stimuli such as endotoxin challenge and oxidative stress; however, the effect of binge drinking on myocardial anandamide production and subsequent CB1R-mediated cardiodepression remains unclear. Here, we studied the impact of endotoxins derived from intestinal Gram-negative bacteria on myocardial anandamide formation and CB1R-dependent cardiac dysfunction following acute alcohol intoxication. Using a mouse model of binge drinking (5 g/kg orally), we observed a reduced rate of mesenteric microcirculation concurrent with elevated circulating endotoxin levels. Selective intestinal decontamination significantly lowered circulating endotoxin levels, coinciding with reduced cardiac anandamide levels at 3 hours post-binge. These changes were paralleled with improved left ventricular performance, vascular tone, and reduced myocardial oxidative stress. Moreover, cardiac RNA sequencing revealed marked alterations in gene expression following alcohol gavage that were absent in mice with prior selective intestinal decontamination. These findings provide novel mechanistic insights that highlight the crucial role of intestinal Gram-negative bacteria in modulating cardiac anandamide production after binge drinking, thereby exacerbating cardiovascular function and blood redistribution. Cardiac tissues were homogenized in Trizol (Invitrogen, Carlsbad, CA, USA), and total RNA was isolated with a Direct-zol RNA Miniprep Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s instructions. RNA concentrations were determined using a NanoDrop 2000 Spectrophotometer (Thermo Scientific). AmpliSeq libraries were prepared using the Ion AmpliSeq™ Library Kit Plus (Thermo Fisher Scientific, 4488990) per the manufacturer’s instructions. Library quality was determined using the Agilent High Sensitivity DNA Kit (Agilent Technologies, 5067-4626), and library concentrations were quantified using the Ion Library TaqMan™ Quantitation Kit (Life Technologies, 4468802), per manufacturer’s instructions. Barcoded AmpliSeq libraries were loaded on the sequencing chips using the Ion 540TM Chip Kit (ThermoFisher, A27766) and Ion Chef™ Instrument. Libraries were sequenced on the Ion Torrent S5 Sequencing System via the Ion Torrent 540-OT2 kit (ThermoFisher, A27753). 8 to 9 libraries were loaded per sequencing chip, and 2 sequencing ships were loaded and sequenced at a time. An average of 8.5 million counts per sample were sequenced. Alignment and gene expression count were performed using Ion Torrent AmpliSeq RNA Plugin v0.5.4.0 (Thermo Fisher) using mm10 genome.

overall_design: In the first set of experiments, mice were exposed to a single alcohol gavage at a dose of 5g/kg body weight following overnight fasting . As for the control group, mice were administered saline similarly. Intestinal microcirculation, morphology, and levels of systemic circulating endotoxins were evaluated at different time points following alcohol gavage. In the second cohort, mice were treated orally with a mixture of antibiotics (Sigma-Aldrich, St. Louis, MO, USA)  before alcohol gavage to selectively eliminate intestinal Gram-negative flora, as previously described, with minor modifications.20,21 Briefly, mice were randomly assigned to control or antibiotic treatment groups, where they either received water or non-absorbable antibiotics (neomycin, polymyxin-B, and nystatin; 200 mg/kg, 150 mg/kg, and 1 mg/kg, respectively) for a 14-day pre-treatment period prior to alcohol gavage. After selective intestinal decontamination, mice were exposed to alcohol, as described above. Endpoints were collected 3 hours after alcohol gavage.

first: Sarah

last: Cohen

first: Meagan

last: Donovan

first: Davin

last: Gardner

first: Danielle

last: Sambo

first: Resat

last: Cinar

first: David

last: Goldman

first: Jason

first: Pal

last: Pacher

first: Janos

last: Paloczi


title: Differential cell survival outcomes in response to diverse amino acid stress

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

country: Germany

institute: Max-Planck-Institute for biochemistry

summary: Amino acid (AA) detection is fundamental for cellular function, balancing translation demands, biochemical pathways, and signaling networks. While the GCN2 and mTORC1 pathways are known to regulate AA sensing, the global cellular response to AA deprivation remains poorly understood, particularly in non-transformed cells, which may exhibit distinct adaptive strategies compared to cancer cells. Here we employed murine pluripotent embryonic stem (ES) cells as a model system to dissect cellular responses to AA stress. Using multi-omics analyses over an extended time course, we examined the effects of arginine (Arg) and leucine (Leu) deprivation, uncovering extensive yet non-lethal proteomic, phosphoproteomic, transcriptomic, and metabolomic adaptations, including increased lysosome production. We found that Arg or Leu starvation induces reversible cell cycle exit, promoting a quiescent state that enhances resistance to cytotoxic stressors. By contrast, cysteine (Cys) and threonine (Thr) deprivation led to cell death via distinct pathways: ferroptosis for Cys starvation, while Thr deprivation triggered a previously uncharacterized form of cell death, which could be entirely suppressed by methionine (Met) co-starvation, mTOR or translational inhibition. These findings suggest that ES cells implement specialized survival strategies in response to different AA limitations, highlighting their ability to reprogram cellular biochemistry under nutrient stress.

overall_design: mRNA sequencing of Wild-type and GCN2-deficient E14 mouse embryonic stem cells after 3h of arginine or leucine starvation. Each starvation group were compared with the control group

first: Russier

last: Marion

first: Yeroslviz

last: Assa

first: Murray

last: Peter J.


title: APOE4 to APOE2 allelic switching in mice improves Alzheimer’s disease-related metabolic signatures, neuropathology and cognition

city: Lexington

first: Jessica

middle: L.

last: Funnell

state: Kentucky

address: 392 Chase Pl

department: Physiology

institute: University of Kentucky

summary: Compared to individuals carrying two copies of the ε4 allele of Apolipoprotein E (APOE), ε2 homozygotes have a ~99% reduction in late-onset Alzheimer’s disease (AD) risk. Here, we developed a transgenic mice model  which allows for an inducible ‘switch’ between risk and protective alleles (APOE4s2). Gene expression and proteomic analyses confirm that APOE4s2 mice synthesize E4 at baseline and E2 after tamoxifen administration. A whole-body allelic switch results in a metabolic profile resembling E2/E2 humans and drives AD-relevant alterations in the lipidome and single-cell transcriptome, particularly in astrocytes.

overall_design: To examine how switching from APOE4 to APOE2 globally influences cell-type specific changes to the brain transcriptome, we performed scRNAseq on whole brain tissue from 6-month-old APOE4s2G mice, Cre-negative APOE4s2 controls, and age- and sex-matched E2-TR and E4-TR mice. The APOE4s2G mice (E4 switched to E2 expression in all cell types) were switched one month prior to brain tissue isolation and single cell transcriptomic analysis.

first: Lesley

middle: R

last: Golden

first: Dahlia

middle: S

last: Siano

first: Isaiah

middle: O

last: Stephens

first: Steven

middle: M

last: MacLean

first: Kai

last: Saito

first: Georgia

middle: L

last: Nolt

first: Akhil

middle: V

last: Pallerla

first: Sangderk

last: Lee

first: Cathryn

last: Smith

first: Jing

last: Chen

first: Haining

last: Zhu

first: Clairity

last: Voy

first: Callie

last: Whitus

first: Gabriela

last: Hernandez

first: Brandon

middle: C

last: Farmer

first: Kumar

last: Pandya

first: Dale

last: Cowley

first: Shannon

last: Macauley

first: Scott

last: Gordon

first: Josh

last: Morganti

first: Lance

middle: A

last: Johnson


title: Differential gene expression in canine prostate cancer vs benign prostate hyperplasia tissue. [NanoString]

city: Wrocław

first: Maciej

last: Zacharski

state: dolnoslaskie

address: Norwida, 31

department: Department of Biochemistry and Molecular Biology

country: Poland

institute: Wroclaw University of Environmental and Life Sciences

summary: Despite its low incidence, the aggressive nature and high metastatic potential of canine prostate cancer (PC) make it a serious problem in veterinary medicine. However, knowledge of the molecular mechanisms and regulatory networks underlying the development and progression of canine PC is still limited.  We used RNAseq to identify diffentially expressed genes between PC (n=2) and benign prostate hyperplasia (BPH, n=3) samples. Based on these results, we chose 26 genes for validation on a larger patient cohorts. We used Nanosting nCounter technology for the comparative analysis of gene expression profiles in PC (n=14) and BPH (n=7) tissue samples. Finally the results for voltage-dependent calcium channel α2δ1 subunit were validated using Western blotting and immunohistochemistry.

overall_design: 14 samples of RNA from canine prostate cancer tissue were included as a PC group and 7 samples of  RNA from benign prostate hyperplasia tissue were included as a BPH group.

last: Ugorski

first: Przemysław

last: Prządka

first: Stanisław

last: Dzimira

first: Sonja

last: Skevin

first: Iwona

last: Sidorkiewicz

first: Bartłomiej

last: Liszka

first: Piotr

last: Skrzypczak

first: Filip

last: Van Nieuwerburgh

first: Adam

last: Krętowski

first: Alicja

last: Tomaszek


title: HDAC2-Mediated Recruitment of METTL3 to Chromatin Regulates Human Embryonic Stem Cell Differentiation

city: WuHan

first: Jie

last: Yang

state: Hubei Province

address: Donghu Road, No. 115

department: Medical Research Insitiute

institute: WuHan university

summary: N6-methyladenosine (m6A) methylation and its methyltransferase METTL3 are crucial for maintaining pluripotency and regulating stem cell differentiation. In this study, we demonstrate that METTL3 directly interacts with the histone deacetylase HDAC2. Notably, knockout of HDAC2 reduces METTL3 binding to chromatin, leading to a downregulation of m6A modifications on HDAC2 target genes, which were associated with stem cell lineage differentiation. Conversely, deletion of METTL3 does not affect HDAC2 expression or histone acetylation levels. Disrupting the interaction between HDAC2 and METTL3, either by knocking out HDAC2 or METTL3, significantly impairs differentiation of human embryonic stem cells (hESCs). Additionally, we observe a marked decrease in the RNA stability and translation of genes in which m6A levels were downregulated. Mechanistically, HDAC2 recruits METTL3 to regulate the m6A levels of its target genes, and these changes in m6A modification subsequently influence RNA stability and translation, ultimately contributing to hESC differentiation. Our findings identify a novel interactor of METTL3 and elucidate the functional and mechanistic roles of the HDAC2-METTL3 interaction axis in hESCs.

overall_design: We performed RNA-seq and m6A-seq in wildtype, METTL3-KO, and HDAC2-KO hESCs, while ChIP-seq were conducted in wildtype and HDAC2-KO hESCs.

first: Wei

last: Jiang


title: Multiple FGFR1 mutations modulate tumorigenic mechanisms in glioneuronal tumors.

city: L'Hospitalet de Llobregat

first: Jacopo

last: Boni

state: Barcelona

address: Avinguda de la Granvia de l’Hospitalet, 199

department: Hereditary Cancer

country: Spain

institute: IDIBELL

summary: FGFR1 genetic alterations are associated with human diseases, including brain tumors. We reported multiple FGFR1 mutations in familial and sporadic cases of low-grade glioneuronal tumors, suggesting intrinsic mechanisms of selective pressure toward FGFR1 multiple events arising in the context of a quiet genome. To decipher the molecular mechanisms triggered by multiple FGFR1 mutations, we have mapped the proximal interactome of wild-type, single- and double-mutant FGFR1 proteins through a BioID-MS approach. Our data reveals novel oncogenic functionality for the two hotspots N546K and K656E, linked to evasion of lysosomal degradation. We identified a modulatory role played by the susceptibility variant R661P, which hampers the oncogenic potential of both hotspot mutations by rescuing receptor degradation and reducing N546K affinity for the downstream effector PLCγ. The R661P variant alone abolished the self-renewal capacity of oligodendroglioma cells and showed downregulation of genes involved in neurodevelopment and neuro-glial cell fate decisions, both aspects overcome in the double mutants. This study sheds light on the oncogenic effects associated with FGFR1 alterations and their recurrence in low-mutation burden and therapy naïve tumors.

overall_design: RNA-seq profiling of Parental and CRISPR-edited (FGFR1-mutant) HOG cell lines.

first: Barbara

last: Rivera

first: Míriam

last: Fernández


title: Ageing-driven molecular and functional changes in the bovine endometrium

city: Jouy-en-Josas

first: Mariam

last: Raliou

address: Allée de Vilvert

department: PHASE

country: France

institute: INRAE

summary: Understanding how ageing impacts endometrial function is crucial for preserving fertility in older females. While ageing-related cellular dysfunction and inflammation are observed in the bovine uterus, its effects on endometrial physiology remain unclear. Using an experimental model of young (4-7 years) and old (13-15 years) cloned female cattle, we assessed the effect of ageing on the endometrium through transcriptome profiling and responses of cultured endometrial cells to interferon tau (IFNT) and of cultured endometrial explants to LPS. Progesterone profiles were similar between young and old females. Transcriptomic analysis of endometrial biopsies on day 15 of the estrous cycle identified 859 differentially expressed genes (DEG; p ≤ 0.05, |FC| ≥ 1.5), among which 402 DEG were over-expressed and 457 DEG were under-expresssed in old females. These DEG are linked to immune, inflammatory, metabolic, and cell organization pathways and networks. RT-qPCR validation of selected candidate DEG revealed an increased expression of COL4A3, CPA3, IGFBP1, IGFBP2, RSAD2, SCARA5, and SERPINA14 in young females. In vitro stimulation with IFNT of primary uterine glandular epithelial and stromal cells revealed that glandular epithelial cells exhibit a greater sensitivity to IFNT than stromal cells, both in old and young females. Glandular epithelial cells derived from old females exhibit a weaker response to IFNT, in terms of the number of differentially expressed genes, compared to those from young females. The effect of LPS treatment on cytokine concentrations was lightly more pronounced in young females than in old females, with LPS leading to a significant increase in the concentration of IL-1α, IL-1β, IL-6 and IL-10 in young females. By altering the transcriptomic profile of the endometrium and its capacity to respond to both the embryo's signal and inflammatory factors, we propose that age may be a key factor underlying uterine-related reproductive failures. Further experiments are required to confirm this hypothesis.

overall_design: Total RNA was extracted from  12 endometrial biopsies taken on Day 15 of estrous  cycle from 4 young females (jc), 4 old females (vc) and 4 contemporary cow (CP). Transcriptional profiling was performed  was performed using a custom bovine slide consisting of 61,325 nucleotides (including 23,926 unique transcripts) as described previously (Carvalho et al., 2017). Ninety-seven percent of the transcripts present on the slide were transcripts from the bovine genome Bos Bos taurus (taxid:9913) annotated by Ensembl (http://www.ensembl.org/Bos_taurus/Info/Index). abelling was carried out with the fluorochrome Cyanine 3 (Cy-3) using the One-Color Low Input Quick Amp Labelling kit (Agilent Technologies) as described above (Carvalho et al., 2017).

first: Olivier

last: Sandra

first: Catherine

last: Archilla

first: Marine

last: Denis

first: Doulaye

last: Dembélé

first: Audrey

last: Houpe

first: Veronique

last: Duranthon


title: Global but not myeloid lineage-directed Girk3 deletion increases bone mass in female mice

city: Madison

first: Samantha

last: Weaver

state: WI

address: 2015 Linden Drive

institute: University of Wisconsin-Madison

summary: Germline and osteoblast-directed deletion of G protein-gated inwardly rectifying K+ channel 3 (Girk3) was recently shown to increase bone mass after 18 weeks of age in male mice. Here, we show that germline Girk3 deletion also increases trabecular and cortical bone mass and increases the mechanical strength of the femur in female mice after 18 weeks of age. Unlike male mice, however, osteoblast-directed Girk3 deletion using 2.3kb-Col1a1-Cre does not increase bone mass in adult female mice. To discover mechanisms underlying high bone mass in female Girk3-/- mice, bulk RNA-sequencing was performed on 2-day-old calvarial bone, revealing lower expression of proinflammatory cytokines such as IL-1β and IL-6 in Girk3-/- mice. Accordingly, cytokines and chemokines are largely suppressed in the circulation of adult Girk3-/- mice compared to WT littermates. The cytokines GM-CSF, IL-1β, IL-2, and IL-9 are reduced in the serum of both male and female Girk3-/- mice, while eotaxin, IFNg, and MIP-1a are sexually dimorphic. Histomorphometry reveals that osteoclast activity is modestly reduced in Girk3-/- bone, which is supported by in vitro osteoclast resorption assays. However, deletion of Girk3 in myeloid-lineage cells with LysM-Cre is not sufficient to recapitulate high bone mass in either male or female mice. Moreover, female Girk3-/- mice are not protected from ovariectomy-induced bone loss. Finally, unbiased screening of monocyte populations in the bone marrow via cytometry by time-of-flight revealed no differences in immune cell abundances due to global Girk3 deletion. Taken together, while Girk3 regulates inflammatory cytokine expression in the bone and serum, deletion of Girk3 in myeloid-lineage cells does not affect bone mass.

overall_design: Calvaria were isolated from 2- to 3-day-old WT (n=4) and Girk3-/- (n=4) female mice. The calvaria were isolated, washed with PBS, then snap frozen. Calvaria were homogenized in Trizol, then total RNA was extracted and sent for bulk RNA Sequencing.


title: Stem cell-based approach to identify regulatory TFs during mammalian cell differentiation

city: New York

first: Esteban

middle: O.

last: Mazzoni

state: NY

address: 430 East 29th Street 4th floor

department: Department of Cell Biology

institute: NYU Grossman School of Medicine

summary: Cell differentiation is controlled by transcription factors (TFs). However, we still do not fully understand which TFs are needed for even one mammalian differentiation pathway. To address this, we developed a detailed and integrated method. This method combines pluripotent stem cell differentiation in the lab, single-cell transcriptomics, and a CRISPR-based TF loss-of-function screen. Using this approach, we identified all the TFs required for spinal motor neuron (MN) differentiation in mice and their requirement in human MN differentiation. Our transcriptomic analysis revealed that while over 1,300 TFs are transcribed during ventral spinal cord differentiation, only 55 have annotated functions in the literature. The screen identified 232 TFs and other transcription-regulating genes essential for the progression of ventral spinal cord differentiation, including 116 TFs specifically required for MN differentiation. This approach led to three critical observations. First, the motor neuron progenitor (pMN) stage is a regulatory hub that correlates with a reduction in cell potential. Second, a secondary screen in human ventral spinal cord differentiation revealed a greater degree of conservation j between mouse pMNs and the human-specific ventral MN progenitors (vpMNs). This finding was unexpected, as the conservation was anticipated to be with the canonical human pMN stage. Third, the screen underscored the importance of the numerous and yet understudied ZF TFs controlling mammalian cell differentiation. In summary, we present a universal, unbiased strategy for studying TFs in mammalian differentiation, comparable to methodologies used in simpler organisms. This approach enhances our understanding of MN differentiation and provides a practical framework to identify all TFs required for any differentiation trajectory that can be recapitulated in vitro, offering many applications in various fields of developmental biology.

overall_design: Mouse ES cell line E14 Tg2a was differentiated with retinoid acid and smoothened agonist as embryoid bodies into ventral spinal cord. Cells were sampled at day 0, 2, 3, 4, 5, and 6 of differentiation and cryopreserved until proceeded with single-cell sequencing.

first: Yingzhen

last: Pei


title: Gene expression profile at single cell level of syngeneic breast tumors from WT and Tsk mice

first: Sandra

last: Orsulic

overall_design: To better understand the differences in cell populations in TSK and WT mice (i.e. subtypes of fibroblasts and specific functional subsets of immune cells), we conducted single-cell RNA sequencing analysis of tumors isolated from TSK and WT mice after injection of 1x10^6 EO771 cells (syngeneic breast cancer cell line)

first: Maria Sol

last: Recouvreux


title: Single-cell multi-omics analysis identifies metabolism-linked epigenetic reprogramming as a driver of therapy-resistant medulloblastoma

city: Aurora

first: Bethany

last: Veo

state: CO

department: Pediatrics-Heme/Onc

institute: University of Colorado Anschutz Medical Campus

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

overall_design: Refer to individual Series


title: Single-cell multi-omics analysis identifies metabolism-linked epigenetic reprogramming as a driver of therapy-resistant medulloblastoma [PDX Multiome]

summary: We perform scMultiomic sequencing on matched patient primary and recurrent tumors. We identify a unique population of cells that is metabolically and epigenetically altered. We recapitulate this population of cells in in vivo radiation resistant models. Disruption of this population with wtIDH1 inhibitors suppresses growth and re-sensitizes cells to irradiation.

overall_design: We isolated nuclei from PDX411 xenograft MB tumors according to 10xGenomics protocol for cyropreserved tissue. Human cells were isolated using the miltenyi mouse cell depletion kit.  Nuclei were then isolated using the 10x genomica protocol and submitted for scMultiomic sequencing.

first: Bethany L

first: Dong

last: Wang

first: John

last: DeSisto

first: Angela

last: Pierce

first: Rajeev

last: Vibhakar


title: Single-cell multi-omics analysis identifies metabolism-linked epigenetic reprogramming as a driver of therapy-resistant medulloblastoma [ATAC_seq]

overall_design: senisitive and IR esistant D458 cells were treated with an IDH1i (IDH305 or GSK321) for 48hrs. 50,000 cells were then isolated for ATAC assay and library sequencing


title: scRNA-seq analysis of Cd45+ cells isolated from MC38 tumors inoculated in p53+/-, Lck-Cre and p53fl7KQ/-, Lck-Cre mice

city: Beijing

first: Donglai

address: #5 Dong Dan San Tiao

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Tumor-infiltrating T cells are critically involved in modulating immunological responses within the tumor microenvironment (TME). We employed single-cell RNA sequencing (scRNA-seq) analysis to determine T cell-intrinsic p53-mediated regulation of antitumor immunity.

overall_design: Cd45+ leukocytes isolated from MC38 tumors inoculated into p53+/-, Lck-Cre and p53fl7KQ/-, Lck-Cre mice, respectively, were collected by fluorescence-activated cell sorting (FACS) with the PE-conjugated Cd45 antibody and subjected to scRNA-seq analysis.

first: Xiaojun

last: Yan

first: Wenbin

last: Xu

first: Han

last: Yao

first: Zhen

last: Wu

first: Jingyuan

last: Ning

first: Shidong

last: Zhao

first: Yajing

last: Liu

first: Meng

last: Zhang

first: Dongkui

first: Zhanlong

last: Shen

first: Wei

last: Gu


title: Systems biology mapping of rBCG-LTAK63-induced protection against tuberculosis reveals the significance of autophagy and circadian rhythm regulation by cAMP

city: São Paulo

first: Luciana

middle: Cezar de Cerqueira

last: Leite

state: SP

address: Avenida Vital Brasil, 1500

department: Desenvolvimento de Vacinas

country: Brazil

institute: Instituto Butantan

summary: Using systems biology and RNA sequencing data from lung cells, we investigated the immune mechanisms of protection induced by this vaccine in mice, both after immunization and following challenge. The RNA-seq data were analyzed using IPA (Ingenuity Pathways Analysis), CEMiTools (modular co-expression analysis). The RNA-seq derived results were analysed through correlation with immune response and disease outcomes, such as bacillary load, pathology score (infiltrated cell number, inflammatory area, and functional area).

overall_design:
Bulk RNA-seq applyed to comprehensively study the impact of rBCG-LTAK63 vaccination in mice at various time points before and after Mtb exposure, aiming to understand how these alterations influence lung immune response and contribute to TB protection.
Babl/c mice were immunized and lungs and lymph nodes were collected, for RNA-seq, at 7, 90 after immunization.  At 90 days after immunization, animals that left were challenged with 500 CFU of Mycobacterium tuberculosis H37Rv, via intranasal instilation.At 97 and 120 days post immunization (7 days and 30 days post challenge), the lungs were collected, RNA sequencing. Eight samples were sequenced in each timepoints. Two saline controls were included (one in 7 dpi and other in 90 dpi). The infection control group, were included at 7dpc and 30 dpc.

first: Lázaro

last: Marques-Neto

first: Monalisa

last: Trentini

first: Ana Carolina

last: Moreno

first: Silas

middle: F

last: Eto

last: Carvalho

first: Murilo

last: Amaral

first: André

middle: G

last: Martins

middle: N

last: Gonçalves

first: Ana Marisa

last: Chudzinki-Tavassi

first: Alex

middle: I

last: Kanno

first: Aldo

last: Tagliabue

first: Diana

last: Boraschi

first: Sergio

last: Verjovski-Almeida

first: Helder

last: Nakaya

first: Leonardo

middle: P

last: Farias

first: Pablo

last: Ramos


title: Illumina SBS sequencing and DNBSEQ perform similarly for single-cell transcriptomics

city: Edinburgh

first: Nadine

last: Bestard-Cuche

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

summary: High-throughput single-cell RNA sequencing (scRNA-seq) workflows produce libraries that demand extensive sequencing. However, standard next-generation sequencing (NGS) methods remain expensive, contributing to the high running costs of single-cell experiments and often negatively affecting the sample numbers and statistical strength of such projects. In recent years, a plethora of new sequencing technologies have become available to researchers through several manufacturers, often providing lower-cost alternatives to standard NGS. In this study, we compared data generated from scRNA-seq libraries sequenced with both standard Illumina sequencing by synthesis (Illumina SBS) and MGI’s DNA nanoball sequencing (DNBSEQ). Our findings reveal similar overall performance using both technologies. DNBSEQ exhibited mildly superior sequence quality compared to Illumina SBS, as evidenced by higher Phred scores, lower read duplication rates, and a greater number of genes mapping to the reference genome. Yet, these improvements did not translate into meaningful differences in single-cell analysis parameters of our experiments, including detection of additional genes within cells, gene expression saturation levels, and numbers of identified cells, with both technologies demonstrating equally robust performance in these aspects. The data produced by both sequencing platforms also produced comparable analytical outcomes for single-cell analysis. No significant difference in the annotation of cells into different cell types was observed and the same top genes were differentially expressed between populations and experimental conditions. Overall, our data demonstrate that alternative technologies can be applied to sequence scRNA-seq libraries, generating virtually undiscernible results compared to standard methods, and providing cost-effective alternatives.

overall_design: brain tissue harvests and dissociations were performed at a consistent time of day for all 8 mice, with processing of mice of different genotypes being mixed to reduce batch effects. Tissues were rapidly processed without perfusion, and thalami were dissected from both hemisphere and processed. We generated brain single-cell suspensions using the Adult Brain Dissociation Kit (130-107-677, Miltenyi Biotec). Cell sorting was conducted to exclude doublets, erythrocytes, and debris. Post-sorting viability confirmation was performed, and single cells were processed using the Chromium Single Cell Platform. Illumina-compatible libraries generated using the 10X Genomics 3’ V3.1 workflow were converted for MGI sequencing using the PCR-based MGI Easy Universal Library Conversion kit (App-A) following the manufacturer’s instructions. The kit adds a 5’phosphate modification to the 10X library to enable circularisation and subsequent DNA Nanoball generation as part of the DNBSEQ sequencing process. 50 ng inputs were used and 5 cycles of PCR, to avoid the possibility of introducing errors through PCR. The libraries were sequenced on an MGI DNBSEQ-T7 instrument with an E1 flow cell. The sequencing consisted of 28 cycles for Read1, 90 cycles for Read2 and 10 cycles for the barcode indexes.


title: Gene expression profile at single cell level of syngeneic melanoma tumors from WT and Tsk mice

first: Sandra

last: Orsulic

overall_design: To better understand the differences in cell populations in TSK and WT mice (i.e. subtypes of fibroblasts and specific functional subsets of immune cells), we conducted single-cell RNA sequencing analysis of tumors isolated from TSK and WT mice after injection of 1x10^6 B16-m10 cells (syngeneic melanoma cancer cell line)

first: Maria Sol

last: Recouvreux


title: Large B-cell lymphoma imprints a dysfunctional immune phenotype that persists years after treatment

city: Erlangen

first: Giulia

last: Benintende

address: Ulmenweg 18

institute: Universitaetsklinikum Erlangen Medizinische Klinik 5

summary: Comprehensive study of the immune fingerprint of lymphoma and immunotherapy on DLBCL survivors

overall_design: MDSCs and activated CD4 T cells were sorted and their RNA was sequenced

first: Richard

last: Pelzl

first: Fabian

last: Müller


city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

institute: INRAE / IRHS

summary: RNAseq from seeds of tomato cultivars microtom (uTom), Criollo (Cr) and Stupicke (St) treated with 48h osmopriming (PEG 8000, -1 MPa) with MeJA 2mM or water control. Seeds were dried for 2 days prior to RNA extraction.

first: Lukasz

last: Tarkowski


title: TNF Superfamily Member 14 Drives Post-Influenza Depletion of Alveolar  Macrophages Enabling Secondary Pneumococcal Pneumonia

city: Bad Nauheim

first: Noah

last: Knoppik

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max-Planck-Institute for Heart and Lung Research

summary: Secondary bacterial infection, often caused by Streptococcus pneumoniae (Spn), is one of the most frequent and severe complications of influenza A virus (IAV)-induced pneumonia. Phenotyping of the pulmonary innate immune landscape after IAV infection revealed a significant depletion of the tissue-resident alveolar macrophage (TR-AM) population at day 7, which was associated with increased susceptibility to Spn outgrowth. To elucidate the molecular mechanisms underlying TR-AM depletion, and to define putative targets for treatment, we combined single-cell transcriptomics and cell-specific PCR profiling in an unbiased manner, using in vivo models of IAV infection and IAV/Spn co-infection. The TNF superfamily 14 (TNFSF14) ligand-receptor axis was revealed as the driving force behind post-influenza TR-AM death during the early infection phase, enabling the transition to pneumococcal pneumonia, while intrapulmonary transfer of genetically modified TR-AMs and antibody-mediated neutralization of specific pathway components alleviated disease severity. With a mainly neutrophilic expression and a high abundance in the bronchoalveolar fluid (BALF) of patients with severe virus-induced ARDS, TNFSF14 emerged as a novel determinant of virus-driven lung injury. Targeting the TNFSF14-mediated intercellular communication network in the virus-infected lung can, therefore, improve host defense, minimizing the risk of subsequent bacterial pneumonia, and ameliorating disease outcome.

overall_design: To identify the main leukocyte  source of the TNFSF14 ligand upon IAV pneumonia, 500,000 live leukocytes (gated as Sytox- CD45+) from the homogenized single-cell lung suspensions of IAV-infected mice on day 3 (ext303) and 7 post infection (pi) (ext294) were flow-sorted into FACS tubes containing 0.35μL 0.04% BSA/PBS-/-. Following viability control, 10,000 cells were loaded onto Chromium Chip  B (10X Genomics). Gel beads in emulsion (GEM) generation, cDNA synthesis and amplification, and library preparation were performed with the Chromium Single Cell 3’ Reagent Kit v3.1 (10X Genomics), as per the manufacturer’s protocol. Indexed libraries were sequenced on an Illumina NextSeq2000. Prior to analysis, reads were aligned against the mouse genome (GRCm38.p6) and quantified using StarSolo  (https://github.com/alexdobin/STAR). Analysis was conducted with the Scanpy  software (https://github.com/theislab/scanpy). After quality filtering, raw cell counts  were normalized to the median count over all cells and transformed into log space for  variance stabilization. Principal component analysis (PCA) identified 14 and 11 components on days 3 and 7 pi, respectively. Uniform Manifold Approximation and 609 Projection (UMAP) embedding was created to identify cell type clusters through Leiden  clustering. Doublet analysis was conducted on day 7 using Scrublet  (https://github.com/swolock/scrublet), leading to the removal of a doublet cluster (118  cells).

first: Christina

last: Malainou

first: Christin

last: Peteranderl

first: Maximiliano

last: Ferrero

first: Ana

last: Vazquez-Armendariz

first: Ioannis

last: Alexopoulos

first: Julian

last: Better

first: Mohammad

last: Estiri

first: Hendrik

last: Schultheis

first: Judith

last: Hoppe

first: Maria-Luisa

last: del Rio

first: Jose

last: Rodriguez-Barbosa

first: Klaus

last: Pfeffer

first: Stefan

last: Günther

first: Mario

last: Looso

first: Achim

middle: D

last: Gruber

first: Istvan

last: Vadasz

first: Ulrich

last: Matt

first: Susanne

last: Herold


title: Productive mRNA chromatin escape is promoted by PRMT5 activity - Cytoplasm Nucleoplasm Chromatin Fractions

city: Bronx

first: David

last: Shechter

state: New York

address: 1300 Morris Park Ave

department: Biochemistry

institute: Albert Einstein College of Medicine

summary: Protein Arginine Methyltransferase 5 (PRMT5) regulates RNA splicing and transcription by symmetric dimethylation of arginine residues (Rme2s/SDMA) in many RNA binding proteins. However, the mechanism by which PRMT5 couples splicing to transcriptional output is unknown. Here, we demonstrate that a major function of PRMT5 activity is to promote chromatin escape of a novel, large class of mRNAs that we term Genomically Retained Incompletely Processed Polyadenylated Transcripts (GRIPPs). Using nascent and total transcriptomics, spike-in controlled fractionated cell transcriptomics, and total and fractionated cell proteomics, we show that PRMT5 inhibition and knockdown of the PRMT5 SNRP (Sm protein) adapter protein pICln (CLNS1A) —but not type I PRMT inhibition—leads to gross detention of mRNA, SNRPB, and SNRPD3 proteins on chromatin. Compared to most transcripts, these chromatin-trapped polyadenylated RNA transcripts have more introns, are spliced slower, and are enriched in detained introns. Using a combination of PRMT5 inhibition and inducible isogenic wildtype and arginine-mutant SNRPB, we show that arginine methylation of these snRNPs is critical for mediating their homeostatic chromatin and RNA interactions. Overall, we conclude that a major role for PRMT5 is in controlling transcript processing and splicing completion to promote chromatin escape and subsequent nuclear export.

overall_design: To measure subcellular transcriptomic consequences of PRMT5 inhibition by GSK591, A549 cell chromatin, nucleoplasm, and cytoplasmic fractions were subjected to directional mRNA-seq with Drosophila melanogaster S2 cell (5%) spike-in normalization controls

first: Joseph

last: DeAngelo


title: TDP-43 binds to RNA G-quadruplex structure and regulates mRNA stability and translation

city: Hong Kong

first: Feng

last: Yang

address: Room 503, 5/F, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital

department: Chemical Pathology

institute: The Chinese University of Hong Kong

summary: TDP-43 is a hallmark protein associated with neurodegenerative diseases. Recent studies revealed TDP-43 as an RNA G-quadruplex (rG4) binding protein, impacting mRNA transport and function. However, our understanding on the interaction between TDP-43 and RNA secondary structure remains poorly understood. Additionally, reports on specific rG4 targets regulated by TDP-43 are limited. Herein, we show that TDP-43 exhibits a preference for binding to the rG4 structure under K+ condition by a high-throughput RNA Bind-n-Seq method. Besides, we find that loss of TDP-43 contributes to a decrease in mRNA structure in the transcriptome by using the newly developed SHALiPE-seq technology. By analyzing the SHALiPE-seq data of TDP-43 binding sites, we further demonstrate that the reduction in structural complexity is likely due to the loss of TDP-43 binding to the RNA targets, especially in the 3'UTR. Importantly, our transcript-specific investigation reveals that TDP-43 binds to a novel rG4 structure in the 3'UTR of SLC1A5 mRNA, promoting the mRNA stability and translation. Our findings not only offer new insights into the role of TDP-43 in regulating RNA structure such as rG4, but also contribute to a better understanding of its broader functions and provide potential targets for therapeutic strategies in TDP43-related diseases.

overall_design: SHALiPE-seq of Ctrl HK293T and TDP-43 knockdown HEK293T cell line

first: Chun

middle: K

last: Kwok

first: Huating

last: Wang

first: Jieyu

last: Zhao

first: Yuwei

last: Zhang


title: TDP-43 binds to RNA G-quadruplex structure and regulates mRNA stability and translation [RBNS]

overall_design: To investigate the binding specificity of TDP-43 and the effect of TDP-43 on target RNA structures, we conducted RNA Bind-n-Seq (RBNS) using TDP-43 protein.

first: Chun-Kit


title: Mapping the FOXA1 Interactome in ER+ Breast Cancer Cells using Proximity Labeling Reveals Novel Interactions with the Orphan Nuclear Receptor NR2C2

city: San Juan

first: Hector

last: Franco

state: Puerto Rico

address: 2nd Floor Centro Medico- Office #275

institute: University of Puerto Rico Comprehensive Cancer Center

summary: FOXA1 is a pioneer transcription factor essential for chromatin accessibility and transcriptional regulation in hormone-driven cancers. In breast cancer, FOXA1 plays a central role in facilitating nuclear receptor binding, reprogramming enhancer landscapes, and promoting transcriptional changes associated with therapy resistance. While FOXA1’s function has been primarily studied in the context of estrogen receptor-α (ER), its broader protein interaction network remains incompletely defined. Here, we systematically map FOXA1-interacting proteins in ER-positive breast cancer cells using proximity-dependent biotin labeling (miniTurbo) combined with quantitative LC-MS/MS proteomics. We engineered MCF-7 cell lines stably expressing miniTurbo-tagged FOXA1 at either the N-terminus or C-terminus to ensure comprehensive coverage of interaction interfaces. This approach recovered known FOXA1 partners, including AR, MLL3, YAP1, and GATA3, and identified 157 previously unreported FOXA1 interactors. Notably, 42 of these novel partners, including NR2C2, were significantly associated with poor relapse-free survival in ER+ breast cancer patients. To demonstrate the utility of this resource, we characterized the FOXA1-NR2C2 interaction in depth. Integrating ChIP-seq and RNA-seq, we show that FOXA1 and NR2C2 co-occupy a subset of genomic regions and drive co-regulated transcriptional programs involved in tumor progression. Our study reveals an expanded FOXA1 interactome and new insights into its functional network in breast cancer, providing candidate proteins for further exploration as biomarkers or therapeutic targets.

overall_design: To interogate the genome-wide binding profile of NR2C2 in ER+ breast cancer cells and to determine whether FOXA1 acts as a pioneer factor for NR2C2 binding, we compared control MCF-7 cells (untreated) to MCF-7 cells treated with 40 nM siRNA against FOXA1 for 48 hours. After confirming FOXA1 protein depletion, biological duplicates of controls and siFOXA1 were submitted to Active Motif (AM). AM performed ChIP-seq using 40 ug chromatin and the NR2C2 antibody ab109301 (Abcam).

first: Rosemary

last: Plagens

first: Shen

last: Li

first: Christine

last: Mills

first: Laura

middle: E

last: Herring

first: Carla

last: Rodriguez Tirado

first: Natalia

last: Maldonado-Vazquez

first: Julie

last: Dutil

first: Ingrid

last: Montes-Rodriguez


title: Single-cell multi-omics analysis identifies metabolism-linked epigenetic reprogramming as a driver of therapy-resistant medulloblastoma [scRNA-seq]

first: Bethany

last: Veo

overall_design: D458 xenograft tumors were harvested from the cerebellum of mice. Tumors were chopped with razor blades and dissociated in RPMI media. Live cell suspensions were flow sorted based on green fluorescent protein (GFP) expression on a MoFlo XDP-Flex (Beckman Coulter) and 2,000/L GFP+ cells were submitted to the University of Colorado Genomics core for scRNA sequencing with the Chromium X. N=6

first: Bethany L

first: Dong

first: John

last: DeSisto

first: Angela

last: Pierce

first: Rajeev

last: Vibhakar


title: Single-cell Sequencing of ABCA4-Mutant Human Retinal Organoids Reveals Organoids Application in Modeling Inherited Retinal Diseases

city: HOUSTON

first: Rui

last: Chen

state: Texas

address: One Baylor Plaza, Taub Building, 8th floor, room T836

department: Department of Molecular and Human Genetics

institute: Baylor College of Medicine

summary: In the studies of Inherited Retinal Diseases (IRDs), the knockout of traditional animal models like mice often fails to accurately replicate human phenotypes due to genetic and anatomical differences. Human retinal organoids (ROs) derived from stem cells have emerged as promising developmental models in retinal studies to delineate cell growth, but their ability to represent the characteristics of late-onset IRDs remains unclear. This study aims to validate ROs as a disease model for Stargardt's Disease (STGD) caused by Abca4 mutations. Using single-cell RNA sequencing, ROs from 2 STGD patients were compared with unaffected ROs at two developmental stages on both the cellular and transcriptomic levels. The results from gene-level comparisons show promising evidence that ROs successfully capture the underlying molecular variations between patient and control samples even at the early developmental stage, providing the potential of applying ROs to facilitate the study of IRDs and late-onset neurodegenerative diseases.

overall_design: 4 samples were cone-enriched human retinal organoids derived from the iPSC of Stardgart's Disease patients harboring ABCA4 gene mutation and 2 samples were cone-enriched human retinal organoids derived from the iPSC of healthy, unaffected individuals

first: Yourong

last: Bao

first: Anna

last: Matynia

first: Xinye

last: Qian

first: Xuesen

last: Cheng

first: Yumei


title: E2F Deregulation Compromises ER homeostasis by Attenuating IRE1 Activity

city: Montréal

first: Nam Sung

last: Moon

state: Quebec

address: 1205 Docteur Penfield Avenue, N3/17

department: Biology

country: Canada

institute: McGill University

summary: The E2F family of transcription factors is an essential regulator of the cell cycle across all metazoan and is often deregulated in cancer. While their primary function is in cell cycle control, E2Fs also influence various cellular processes, such as apoptosis and metabolism. Previous studies in mice have shown that E2F deregulation particularly affect exocrine tissues such as the salivary gland and pancrease. However, the mechanisms behind exocrine cell sensitivity to E2F loss remain inadequately explored. Our lab recently discovered a novel alternatively spliced isoform of Drosophila de2f1, de2f1b, with an additional 16 amino acids than the canonical isoform of de2f1, de2f1a. de2f1b mutants have defects in development of polyploid tissues such as larval salivary glands (SG).  Interestingly, SGs of de2f1b mutant shows DNA damage, accumulate cytoplasmic DNA and activation of immune response. This RNA-seq study is to create a gene expression profile of the de2f1b SGs to get a comprehensive understanding of the effects of de2f1b mutation in exocrine tissues.

overall_design: RNA-seq analysis of salivary glands from third instar wandering larvae of de2f1b mutant using w1118 as control. All fly strains were maintained in standard cornmeal medium at 25°C and 50% humidity.

first: Das

last: Arghya

first: Fan

last: Yiting

first: Li

last: Yining

first: Moon

last: Nam-Sung


title: Depletion of ribosome biogenesis factors in NPM1-mutant acute myeloid leukemia: Insights into direct consequences of the mutation and implications for treatment

city: Cambridge

first: Muxin

last: Gu

email: muxingu@gmail.com, mg445@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

institute: University of Cambridge

summary: Mutations in the NPM1 gene are found in more than 30% of acute myeloid leukemia (AML) cases. The mutations disrupt a nucleolar localization signal (NoLS) and create a novel nuclear export signal (NES), leading to cytoplasmic displacement of the protein (NPM1c). NPM1c mutations prime hematopoietic progenitors to leukemic transformation, but their precise molecular consequences remain elusive. Here, we first examined the effects of isolated NPM1c mutations on the global proteome of pre-leukemic hematopoietic progenitors using a conditional knock-in Npm1cA/+ mouse model. We discovered a significant depletion of many factors involved in the ribosome biogenesis pathway which, importantly, persists in NPM1-mutant AML patients. Next, we found that pre-leukemic Npm1cA/+ cells display higher sensitivity to Actinomycin D (ActD) and other RNA pol I inhibitors when compared to wild-type Npm1+/+ cells. Combination treatment with ActD and Venetoclax inhibited the growth and colony forming ability of pre-leukemic and leukemic NPM1c+ cells and low-dose ActD treatment was able to re-sensitize resistant NPM1c+ cells to Venetoclax. Finally, by contrasting our findings with data from CRISPR drop-out screens, we identified and validated TSR3, a ribosome maturation factor of the 40S ribosomal subunit whose knock-out preferentially inhibited the proliferation of NPM1c+ AML cells by activating a p53-dependent response.  Similar to low-dose ActD treatment, TSR3 depletion could partially restore sensitivity to Venetoclax in therapy-resistant NPM1c+ AML models.

overall_design: We compared ranscriptomic data of gRNA transduced cells (gTSR3) against the control (gControl) in NPM1c+ cell lines

first: Aristi

last: Damaskou

first: Rachael

last: Wilson

first: Malgorzata

last: Gozdecka

first: Maria

last: Eleftheriou

first: Eliza

last: Yankova

first: Justyna

last: Rak

first: George

middle: S

last: Vassiliou


title: Bisphenol TMC disturbs mitochondrial activity and biogenesis, reducing lifespan and healthspan in the nematode Caenorhabditis elegans

city: Jinju

first: Ho Jeong

last: Lee

address: 17 Jeigok-gil

country: South Korea

institute: Korea institute of toxicology (KIT)

summary: This study underscores the urgency of comprehensively assessing the safety and impact of BPTMC, given its widespread use in various consumer goods and the potential risks it may pose to human health and the environment.

overall_design: We analyzed RNA-sequencing in the BPTMC group compared to the control group. Control: DMSO / Test: 1 mM BPTMC (exposed to Caenorhabditis elegans)

first: M

middle: J

last: Hyun

first: H


title: Somatic hypermutation patterns in immunoglobulin variable regions are dictated by a motif-specific sequence grammar and motif position

city: London

first: Rushad

last: Pavri

address: Guy's Campus, Great Maze Pond, SE1 9RT

department: Peter Gorer Department of Immunobiology

institute: King’s College London

summary: Somatic hypermutation (SHM) of immunoglobulin variable (V) regions by activation-induced deaminase (AID) is essential for the maturation of protective antibodies. AID preferentially mutates cytosines within WRCH motifs (W=A/T, R=A/G, H=A/C/T), yet WRCH motifs show large but reproducible variations in mutation frequency, highlighting a crucial role for sequence-intrinsic mechanisms (a sequence grammar) in determining mutational outcomes and, therefore, in antibody maturation. Here, we demonstrate that the same sequence context can exert significantly varying effects on the mutability of different WRCH motifs. Furthermore, targeting of SHM to the template and non-template cytosines in palindromic AGCT motifs can be differentially regulated by sequence contexts. Additionally, we provide evidence that the location of a motif within the V region can have a significant impact on its mutability. Therefore, discrete V region mutation patterns arise from a combination of a motif-specific sequence grammar and motif position.

overall_design: Examination of mutations in immunoglobulin variable region using MutPE-seq

first: Bianca

last: Bartl

first: Ursula

last: E. Schoeberl

first: Johanna

last: Fitz

first: Renan

last: Valieris

first: Benjamin

last: Gundinger

first: Israel

last: Tojal da Silva


title: DNA methylation contributes to plant acclimation to naturally fluctuating light

city: Birmingham

first: Robyn

last: Emmerson

address: Edgbaston

institute: University of Birmingham

type: Methylation profiling by high throughput sequencing

summary:
Plants in the natural environment experience continuous dynamic changes in light intensity. Here, we exposed Arabidopsis thaliana plants to naturally fluctuating light regimes alongside traditional square light regimes such as those often found in control environment growth chambers. The physiological response was highly consistent across experiments in sibling plants, indicating the possibility of an epigenetic mechanism, leading us to investigated differences in DNA methylation.
Our results identified a large number of changes in DNA methylation patterns between fluctuating light acclimated plants and square light acclimated plants, demonstrating natural fluctuations in light impacts plant epigenetic mechanisms. Most importantly, there are more differences in DNA methylation patterns between different light pattern regimes than between different light intensities. These differences in DNA methylation were accompanied by significant changes in gene expression, some of which correlated with altered DNA methylation. One of these genes, MCCA, was found to significantly impact photosynthetic efficiency when knocked out.  Thousands of transposable elements copies were differentially methylated between light regimes. Interestingly, up to 30% of these TEs are linked to nearby differentially expressed genes. Our data suggests DNA methylation plays a role in acclimation to natural light which may directly regulate gene expression and impact transposable element activation.

overall_design:
WGBS: 4 samples (1 replicate per light regime) consisting of a pool of 6 leaves from individual plants
RNAseq: 12 samples (3 per light regime), each is an independent replicate


title: Single-cell multi-omics analysis identifies metabolism-linked epigenetic reprogramming as a driver of therapy-resistant medulloblastoma [Multiome]

first: Bethany

last: Veo

overall_design: We isolated nuclei from matched primary and recurrent group 3 and group 4 MB tumors according to 10xGenomics protocol for cyropreserved tissue. Nuclei were submitted for scMultiomic sequencing.

first: Bethany L

first: Dong

last: Wang

first: John

last: DeSisto

first: Angela

last: Pierce

first: Rajeev

last: Vibhakar


title: Single-cell multi-omics analysis identifies metabolism-linked epigenetic reprogramming as a driver of therapy-resistant medulloblastoma [CUT&RUN]

overall_design: senisitive and IR esistant D458 cells were treated with an IDH1i (IDH305 or GSK321) for 48hrs. 500,000 cells were then isolated for Cut and Run and library sequencing


title: Next-generation breast organoids capture human organogenesis with high-resolution live imaging

city: Boston

first: Charlotte

last: Kuperwasser

state: MA

address: 136 Harrison Ave

institute: Tufts University School of Medicine

summary: Organoids have emerged as a powerful tool for modeling tissue growth and diseases. In this study, we introduce a groundbreaking organotypic culture technique that replicates the morphology, scale, and heterogeneity of human breast tissue, and includes a mesenchymal-like stromal component. A standout feature of this approach is the use of long-term live imaging at high temporal resolution to directly observe stem cell dynamics during organogenesis, from single cells to mature organ tissue. The system is adaptable for high throughput applications and allows for genetic manipulation of the cells. Real-time imaging of ex-vivo tissue formation reveals a non-canonical process of ductal-lobular morphogenesis and branching, and de-novo generation of a supportive stroma. Incorporating patient-derived single cells from multiple donors offers an enhanced representation of the spectrum of individual responses and the impacts of distinct exposures. While developed for breast tissue, the principles of this technology can serve as a model for the development of similar systems in other tissues, where organoids do not merely reproduce the tissue, but where their regeneration can also be observed and studied.  In addition, this model provides a quantitative experimental system to study mechanisms of embryogenesis, development, and tissue organization where biomechanics plays an important role.

overall_design: Primary human breast epithelial single cells were grown in a next generation ECM hydrogel for 19 days and analyzed using scRNA-seq

first: Nicole

last: Traugh

first: Gat

last: Rauner


title: Breast cancer remodels lymphatics in sentinel lymph nodes

city: Turku

first: Sirpa

last: Jalkanen

address: Tykistökatu 6a

department: Medical Microbiology and Immunology

country: Finland

institute: Univeristy of Turku

summary: In this study we investigated the effects of breast cancer cell conditioned media on human lymphatic endothlial cells. For this, we cultured the three different breast cancer cell lines MDA-MB-231, MCF-7 and T47D in endothelial cell media and transferred this conditioned media to primary, lymph-node derived human lymphatic endothelial cells. These cells were then collected and RNA-sequencing was performed from them.

overall_design: We cultured three human breast cancer cells lines (MDA-MB-231, MCF-7 and T47D) in Endothelial Cell Media for 1 day and transferred their conditioned media to human lymph node derived lymphatic endothelial cells. These cells were then incubated for two days before collection.

first: Dominik

last: Eichin

first: Akira

last: Takeda

first: Diana

last: Lehotina

first: Maki

last: Uenaka

first: Meri

last: Leppänen

first: Kati

last: Elima

first: Tapio

last: Lönnberg

first: Pia

last: Boström

first: Ilkka

last: Kiskivuo

first: Maija

last: Hollmen


title: SANT domain-containing proteins modulate gene transcription and negatively regulate plant thermotolerance by coordinating histone H3KAc and Khib modifications

city: Shenzhen

first: Xishi

last: Zhou

address: No 7, Pengfei Road

institute: Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences

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

overall_design: Refer to individual Series


title: Productive mRNA chromatin escape is promoted by PRMT5 activity - mRNA Seq PRMT5 pICln RIOK1 CoPR5 kd

first: David

last: Shechter

overall_design:
To measure transcriptomic consequences of PRMT5 cofactor knockdowns, CRISPRi knockdown with dCas9-KRAB-MeCP2 was performed. Two guide RNAs (gRNA) per target were made and mRNA-seq was performed with poly-A capture non-directional library preparation and PE150 reads (9GB total data, roughly 30M PE reads per sample)
Raw data was mapped to hg38 using STAR in the nf-core/rnaseq pipeline and length-normalized counts called by salmon. DESeq2 was then used for differential abundance of the knockdown vs sgScr (scrambled guideRNA) control

first: Joseph

last: DeAngelo


state: South-West Finland

address: Tykistökatu 6A

department: Institute of Biomedicine

institute: University of Turku

summary: Cancer metastasis into sentinel lymph nodes (LNs) is a crucial determinant of patient mortality. While it is recognized that tumor-induced lymphangiogenesis facilitates metastasis into LNs in murine models, the tumor-induced alterations in human lymphatic vessels remain obscure. Here we utilized single-cell RNA-seq to profile lymphatic endothelial cell (LEC) subsets in paired metastatic and non-metastatic LNs obtained from breast cancer patients. Tumor metastasis leads to a decrease in inflammatory LEC subsets such as subcapsular sinus LECs, while inducing increase of immunosuppressive CD200+ LECs. Matrix Gla protein (MGP) was the most upregulated gene in metastatic LN LECs, and its expression on LECs was VEGF and TGF-b dependent. Silencing MGP in LECs revealed that MGP promotes cancer cell adhesion to LECs. Thus, breast cancer cell metastasis into LNs remodels LEC subsets in human LNs and escalates MGP expression, which potentially facilitates the  dissemination of cancer cells through lymphatics.

overall_design: Droplet-based single-cell RNA sequencing (scRNAseq) of human CD45- CD31+ PDPN+ cells in the metastatic and non-metastatic LNs from breast cancer patients. ScRNAseq was performed using 10X Genomics Single Cell 3' solution, according to manufacture's instructions. Libraries were sequenced on HiSeq3000.


title: CPOP1 is the key heme synthesis enzyme required for nodule microenvironment control and successful symbiotic nitrogen fixation in Lotus japonicus

city: Beijing

first: Yufang

last: Tian

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: Heme is utilized as the cofactor of diverse proteins and plays critical roles in different redox reactions. The fixation active nodules of legumes are abundant with heme-containing leghemoglobin to buffer the oxygen concentration. Symbiotic rhizobia could also synthesize heme, and employ heme for efficient respiration and iron uptake regulation. However, the role and regulation of host-controlled heme production during symbiotic nitrogen fixation have not been directly investigated and experimentally proved. Here, we identified the coproporphyrinogen III oxidase plastid related 1 (CPOP1) as a key regulator of symbiotic heme synthesis enzyme in Lotus japonicus. CPOP1 is specifically highly expressed in nitrogen-fixing nodules, and knocking out CPOP1 alone causes leaf etiolation and dwarfism which could be fully recovered by the exogenous application of nitrogen source, indicating nitrogen fixation defect. The cpop1 mutant shows significantly increased nodule oxygen level and decreased nitrogen fixation activity compared to the wild type (WT). Moreover, cell division and related gene expression of bacteroids are also affected upon CPOP1 knockout. We conclude that CPOP1 is essential for the microaerophilic environment control of infected cells and the activation of rhizobial nitrogenase required for symbiotic nitrogen fixation, through host-regulated nodule heme synthesis.

overall_design: In order to reveal core pathways in CPOP1-regulated symbiotic nitrogen fixation, we designed the transcriptome analysis between WT and cpop1 nodules at 10 DPI (young root nodule) and 21 DPI (mature root nodule).


title: Non-cell autonomous tumor suppression by fatty liver disease

city: Leuven

first: Georg

last: Halder

address: Herestraat 49

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB-KU Leuven


title: Activation of a nongenetic AHR-ELMSAN1 axis optimizes BET-targeting therapy and suppresses leukemia stem cells in preclinical models

first: xinyue

last: zhou

state: Alabama

address: WTI 510G 1824 6th Ave S

department: hematology and oncology

institute: university of alabama at birmingham


title: SANT domain-containing proteins modulate gene transcription and negatively regulate plant thermotolerance by coordinating histone H3KAc and Khib modifications [RNA-seq]

summary: Histone post-translational modifications (PTMs), such as acetylation and recently identified lysine 2-hydroxyisobutyrylation (Khib), act as active epigenomic marks in plants. SANT domain-containing proteins (SANT1/2/3/4), derived from PIF/Harbinger transposases, form a novel complex with histone deacetylase 6 (HDA6) to regulate gene expression via histone deacetylation. However, whether SANT1/2/3/4 coordinate different types of PTMs to regulate transcription and mediate responses to specific stresses in plants remain unclear. Here, in addition to modulating histone deacetylation, we found that SANT1/2/3/4 proteins acted like HDA6 or HDA9, in regulating the removal of histone Khib. H3KAc and histone Khib coordinated by SANT1/2/3/4 act in concert to regulate gene expression, with H3KAc playing a predominant role and Khib acting complementarily to H3KAc. SANT1/2/3/4 mutation significantly increased the expression of heat-inducible genes with concurrent change of H3KAc levels under normal and heat stress conditions, resulting in enhanced thermotolerance. Interestingly, hda6 mutant plants exhibited a reduced thermotolerance, suggesting that SANT1/2/3/4 negatively regulate plant thermotolerance independently of HDA6. This study revealed the critical roles of Harbinger transposon-derived SANT domain-containing proteins in transcriptional regulation by coordinating different types of histone PTMs and in the regulation of plant thermotolerance.

overall_design: To obtain further insights into the role of SANT1/2/3/4-mediated transcriptional regulation in response to high temperature, we performed RNA-seq on triplicate wild type (Col-0), sant-null and hda6 seedlings grown under normal condition (22 ℃) or exposed to 37 ℃ for 1 h. Total RNA was extracted from 7-day-old Arabidopsis seedlings growing on 1/2 MS medium plates with and without  37 ℃ treatment using TRIzol reagent (Invitrogen). mRNA-seq libraries were built according to the manufacturer’s protocol (NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)) and paired-end sequenced on an Illumina NovaSeq 6000 platform.

first: Cuijun

last: Zhang


title: snRNAseq of bCat-Kras tumors in normal and NASH diet

summary: Current models of hepatocellular tumorigenesis propose that the chronic injury and inflammation in NASH are mutagenic and growth promoting which can eventually lead to HCC. However, contrary to this model, here we show that NASH suppresses the early development of liver cancers in mice. We found that NASH did not hinder the malignant reprogramming of oncogene expressing hepatocytes but suppressed their clonal expansion and led to their elimination. This elimination was not caused by a direct effect of NASH on malignant cells but due to the stimulation of cell competition in tumor-surrounding hepatocytes. Mechanistically, NASH activated the Hippo pathway effectors Yap and Taz in hepatocytes, which elevated their cellular fitness. Thus, deletion of Yap/Taz in tumor-surrounding hepatocytes abolished the elimination of tumor cells by NASH, while experimental hyperactivation of Yap in malignant cells protected them from NASH-induced elimination

overall_design: To understand how NASH affects βCat-KRas expressing hepatocytes, we analyzed their transcriptional profiles by single nucleus RNA-sequencing (snRNA-seq). We injected βCat-KRas plasmids together with a plasmid expressing H2B-GFP into normal and NASH diet fed mice and purified transfected nuclei by FACS after 4 weeks.

first: Weronika

last: Kowalczyk

first: Ana

last: Algeró-Nadal

first: Hasse

last: Mol

first: Elena

last: Zoppolato

first: Leticia

last: Sansores


title: Characterizing and controlling CRISPR repair outcomes in nondividing human cells

status: Public on Aug 31 2025

city: San Francisco

first: Gokul

middle: Nathan

last: Ramadoss

state: California

address: 1200 Mariposa St

institute: UCSF

summary: Genome editing is poised to revolutionize treatment of genetic diseases, but poor understanding and control of DNA repair outcomes hinders its therapeutic potential. DNA repair is especially understudied in nondividing cells like neurons, limiting the efficiency and precision of genome editing in many clinically relevant tissues. To address this, we used induced pluripotent stem cells (iPSCs) and iPSC-derived neurons to examine how postmitotic human neurons repair Cas9-induced DNA damage. We showed that CRISPR editing outcomes differ dramatically in neurons compared to genetically identical dividing cells. Neurons also took far longer to fully resolve this damage, and upregulated non-canonical DNA repair factors in the process. Manipulating this response with chemical or genetic perturbations allowed us to direct DNA repair toward desired editing outcomes: in nondividing human neurons, cardiomyocytes, and primary T cells. By studying DNA repair in clinically relevant cells, we uncovered unforeseen challenges and opportunities for precise therapeutic editing.

overall_design: To determine how postmitotic neurons respond to Cas9-VLP treatment, we conducted bulk RNAseq on human iPSC-derived neurons (NGN2), before and after treatment with various types of VLPs and controls.

first: Rudra

last: Bose

first: Manasi

last: Kumar

first: Martin

last: Kampmann

first: Bruce

middle: R

last: Conklin


title: SANT domain-containing proteins modulate gene transcription and negatively regulate plant thermotolerance by coordinating histone H3KAc and Khib modifications [ChIP-seq]

first: Xishi

last: Zhou

overall_design: Two biological replicates of 12-day-old wild-type(Col-0), san-null, hda6 and hda9 seedlings growing on 1/2 MS medium plates were used for histone Khib ChIP-seq experiment. We used anti-Khib antibody (PTM-802, PTM Bio-labs, Hangzhou, China). Each replicate contained two dataset: ChIP and input (to avoid background interference).


title: Characterization of CD63+ adult liver stem cells and downstream lineages

city: Shanghai

first: Kunshan

address: 389 Xincun Rd.

department: Tongji Hospital

institute: Tongji University

summary: Understanding the liver stem cells (LSCs) holds great promise for new insights into liver diseases and liver regeneration. By employing single-cell RNA-seq technology, we examined transcriptome features of distinct Krt19 lineage-tracing cell types isolated from Krt19CreERT; Rosa26R-GFP reporter mouse livers, and identified adult LSCs, as well as their downstream hepatocytes and cholangiocytes. Importantly, we discovered a novel cell surface LSCs marker, CD63, as well as CD56, which distinguished active and quiescent LSCs. Furthermore, we confirmed that CD63+CD56- quiescent LSCs could be activated by a combined action of VEGF and bFGF, and subsequently underwent terminal differentiation. These findings define an authentic adult liver stem cells compartment and highlight its contribution to liver homeostasis during pathophysiologic processes.

overall_design: Liver cells of the Krt19CreERT;Rosa26R-GFP or CD63CreERT2;Rosa26-TdTomato mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence of GFP or Tomato(Cherry) signal and analyzed using scRNAseq.

first: Fei

last: Chen

first: Siguang

last: Li

first: Yiping

last: Hu


title: Spatial transcriptomics of the distal lung bronchioles unravel the mechanisms underlying epithelial desquamation in idiopathic pulmonary fibrosis (IPF)

city: New Haven

first: Rolando

last: Garcia-Milian

state: CT

address: 333 Cedar St

department: CWML

institute: Yale University

summary: One histopathological hallmark seen in end-stage IPF within the distal bronchioles is epithelial desquamation, a process in which the epithelial cells detach from their basement membrane. We performed spatial transcriptomics to profile the distal bronchiolar epithelium of the IPF lung and compared it to healthy lung bronchiolar epithelium. Our analysis has revealed crucial pathways leading to epithelial desquamation.

overall_design: The Nanostring GeoMx spatial transcriptomics platform was utilized to isolate the transcriptome from our regions of interest (ROI). Eight ROIs from ciliated regions of distal bronchiolar epithelium from IPF patients and three ROIs from patients with no pulmonary history were analyzed.

first: Rachana

last: Chandran

first: Brigitte

last: Gomperts


title: Identification of a spinal circuit for skilled locomotion

city: Berlin

first: Niccolò

last: Zampieri

address: Robert-Rössle-Straße 10

institute: MDC

summary: Neural circuits in the spinal cord have a critical role in integrating sensory information and descending commands to coordinate body movements. Defining the functional diversity of spinal neurons is therefore essential for understanding the mechanisms underlying motor control. In this study, by combining anatomical, molecular, and functional analyses in mice, we identified and characterized a subtype of ascending spinal neurons belonging to the V0g family. We found that V0g ascending neurons are integrated in lumbar sensorimotor circuits and their function is specifically required for the execution of precise limb movements necessary for skilled locomotion. This work advances our understanding of the functional organization of V0 neurons and highlights a previously unappreciated role in adjusting body movements to the more demanding needs of skilled locomotor tasks

overall_design: Rabies retrograde tracing was used to label with a fluorecent protein the nuclei of ascending and descending mouse spinal neurons reciprocally connecting the lumbar and cervical enlargements. Nuclei were isolated via fluorescence-activated nucleus sorting and analysed using sn-RNA-seq.

first: Elisa

last: Toscano

first: Aristotelis

last: Misios

first: Elijah

last: Lowenstein

first: Carmen

last: Birchmeier


title: Identification of an autoantibody promoting the development of Sjögren's Syndrome-like sialadenitis

city: Shinjuku-ku

first: Mana

last: Iizuka

address: 35 Shinanomachi

country: Japan

institute: Keio University School of Medicine

summary: We identified an autoantibody (IgGr22) directly involved in the development of sialadenitis. IgGr22 was found to promote the proliferation of pathogenic T cells. IgGr22 specifically recognized double-stranded RNA (dsRNA) and induced the activation of dendritic cells, thereby enhancing the expression of IFN signature and inflammatory genes.

overall_design: CD45+ cells were isolated from the salivary glands of Rag-/- mice transferred with pathogenic CD4+ T cells and recombinant autoantibody (IgGr22) related to Sjögren's syndrome using fluorescence-activated cell sorting (FACS).


title: NASH time course

first: Georg

last: Halder

overall_design: We purified hepatocytes from control mice (ND = normal diet) and mice that were fed a NASH diet for different lengths of time and determined their gene expression profile by RNA sequencing.

first: Weronika

last: Kowalczyk

first: Ana

last: Algeró-Nadal

first: Hasse

last: Mol

first: Elena

last: Zoppolato

first: Leticia

last: Sansores


title: Single-cell analysis of human thymus and peripheral blood unveils the dynamics of T-cell development and aging.

city: Chengdu

first: Yujun

last: Deng

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

institute: Sichuan University

summary: Age-related thymic involution is the hallmark of immune aging, leading to susceptibility to cancers and emerging pathogens such as SARS-Cov2 in the elderly. However, the precise mechanisms underlying the thymic involution and the effect on compromised peripheral T-cell function is unknown. Here by scRNA-seq and TCR-seq, we captured and analyzed cells in the thymus and peripheral blood from the young and elderly. Collectively, our data constitute the first detailed single-cell analysis of ageing-related human thymic involution and T-cell homeostasis in peripheral, providing the insights into human immune aging and potential strategies to rejuvenate the involuted thymus and compromised T-cell immunity.

overall_design: Human thymus and peripheral blood samples in different age groups were obtained from patients undergoing cardiac surgery following protocol approved by the Ethics Committee of the West China Hospital, Sichuan University. Fresh peripheral blood from supercentenarians was also obtained following the protocol approved by the Ethics Committee of the West China Hospital Sichuan University. Informed consent was obtained from all donors.

first: Hongbo


title: Primitive macrophages enable long-term vascularization of human heart-on-a-chip platforms

city: Toronto

first: Shira

last: Landau

state: ON

address: 170 College St.,, MB317

institute: University of Toronto

summary: The intricate anatomical structure and high cellular density of the myocardium significantly complicate the bioengineering of vascular networks within cardiac tissues, creating challenges in establishing a perfusable and stable vasculature within these tissues. Emerging evidence from murine in vivo studies underscores the significant role of resident cardiac macrophages in facilitating cardiac regeneration post-injury, specifically their role in enhancing angiogenesis processes. Here, for the first time, we integrate human pluripotent stem cell derived macrophages, resembling primitive yolk-sac derived macrophages, within human in vitro vascularized heart-on-chip platforms.  The incorporation of primitive macrophages had a profound impact on the long term functionality of microvascularized cardiac tissue, particularly in enabling formation of perusable vasculature with a stable barrier function. These effects were contingent on physical cell-cell interactions and significantly diminished in transwell culture. The inclusion of primitive macrophages mitigated tissue cytotoxicity and curtailed the release of cell-free mitochondrial-DNA, underscoring their indispensable role for bioengineered human cardiac tissues. Furthermore, their incorporation upregulated the secretion of pro-angiogenic, matrix remodeling and cardioprotective cytokines such as MMP-12, MMP-2, Angiopoietin-like 1, NRG-3, SIGIRR and Adiponectin. RNA sequencing disclosed upregulation of cardiac maturation (TTNI3, SCN5A, MYL2,  and RYR2), and endothelial cells genes (PDGF-B, PECAM-1 and CDH5) indicating a decrease in endothelial cells death. Collectively, our results offer valuable insights into the integral role of primitive macrophages in directing long-term functional vascularization of cardiac tissues, paving the way for novel therapeutic strategies and advancing heart-on-a-chip systems.

overall_design: To understand reciprocal interactions in our multicellular system, we performed single nucleus RNA sequencing (snRNA-seq) on three groups: 1) macrophage suspensions, 2) tissues comprising EC/DPSC/CM, and 3) tissues comprising of EC/DPSC/CM/MΦs. Our overall goal was to assess how macrophages transcriptionally change due to other cells present in cardiac tissue, and further, to dissect intercellular communication and downstream pathways induced in ECs, cardiomyocytes and stromal cells driven by the presence of macrophages.

first: Yimu

last: Zhao

first: Gregory

last: Kent

first: Sargol

last: Okhovatian

first: Rick

last: Lu

first: Chuan

last: Liu

first: Sarah

last: Shawky

first: Karl

middle: T

last: Wagner

first: Krisco

last: Cheung

first: Homaira

last: Hamidzada

first: Daniel

last: Vosoughi

first: Erika

last: Beroncal

first: Ian

last: Fernandes

first: Carolyn

middle: L

last: Cummins

last: Andreazza

first: Gordon

middle: M

last: Keller

first: Slava

last: Epelman

first: Milica

last: Radisic


title: Effects of methylphenidate ingestion in male mice on the brains of their grandchildren.

city: Shinagawa-ku

first: Ryota

last: Nakano

state: Tokyo

address: Hatanodai 1-5-8

department: Showa University Graduate School of Pharmacy

institute: Showa university

summary: Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental disorder widely observed from childhood to adulthood, with methylphenidate (MPH) used as the first-line treatment. Recent evidence suggests that the preconception paternal environment can affect offspring health, potentially extending to multiple generations. In our previous study, we reported that MPH administration to sires induced decreased anxiety-related behaviors and memory impairment in the F1 generation. To extend these findings and examine the range of transgenerational effects, this study investigated the impact of preconception male MPH exposure on brain gene expression in the F2 generation.

overall_design: Comparative gene expression profiling analysis of the cerebral cortex RNA-seq data from 6-week-old F2 offspring derived from male mice administered with methylphenidate or saline.

first: Yoshitaka

last: Yamazaki

first: Masahiro

last: Hosonuma


title: Organoid modeling reveals the tumorigenic potential of the alveolar progenitor cell state

first: Carle

middle: F.

last: Kim

address: 300 Longwood Avenue

institute: Boston Children's Hospital

summary: The goal of this study was to investigate the transcriptional and epigenetic changes after the onset of KrasG12D and P53 Loss in Alveolar type 2 (AT2) cells using organoid model. Single cell Multi-omic sequencing were performed on 7 days tumor organoids which were derived from induced AT2 cells.

overall_design: AT2 cells were isolated from KrasLSL-G12D/WT; P53flox/flox; Rosa26LSL-eYFP (KPY) mice using well established surface marker (CD31-/CD45-/Epcam+/Sca1-). The freshly sorted AT2 cells were induced with Adenovirus containing Cre recombinase. Then, the induced AT2 cells were co-cultured with lung stromal cells at air-liquid interface for deriving tumor organoids. After 7 days culture, the organoids were digested into single cells and FACS sorted YFP+ epithelial cells.  scMulti-omic sequencing was performed using the 10X genomics platform (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit, PN-1000285)

first: J

last: Li

first: C


title: The Effect of Epstein Barr Virus Latency on Cellular DNA Methylation Profile of DiffuseLarge B Cell Lymphoma

status: Public on Aug 30 2025

city: Burlington

first: Ashley

middle: Keller

last: Volaric

state: Vermont

address: 111 Colchester Avenue

department: Pathology and Laboratory Medicine

institute: University of Vermont Larner College of Medicine

summary: Epstein-Barr virus (EBV) is implicated in the pathogenesis of different B-cell lymphomas and lymphoproliferative disorders, including diffuse large B-cell lymphoma (DLBCL) arising in immunodeficiency settings. Despite its clinical significance, the mechanisms of EBV-mediated lymphomagenesis across different disease subtypes remains poorly understood. Global DNA methylation profiling can provide insight into tumor heterogeneity and disease mechanisms. To further characterize the underlying biology of EBV(+) DLBCL, we performed a global methylome analysis of a cohort of EBV(+)/(-) DLBCL. Illumina MethylationEPIC array data were generated from a curated set of DLBCL tissue samples (n=43) from a rural patient population with defined EBV status and immunodeficiency background. Differential methylation analyses were conducted using linear mixed models to identify significant methylation changes associated with EBV status. Principle component analysis (PCA) and probe-level comparisons revealed a distinct, globally hypermethylated DNA methylome in EBV(+) DLBCL compared to EBV(-) cases, and an overall hypomethylated profile in all DLBCL relative to control tissues. We identified a total of 117,334 differentially methylated probes mapping to 1,557 cancer-associated genes in EBV(+) versus EBV(-) DLBCL, and 330,872 probes mapping to 4,230 cancer-associated genes in all DLBCL versus controls. Pathway enrichment analysis highlighted distinct biological processes in EBV(+) DLBCL, including P53 feedback loops (hypermethylated genes) and MAPK signaling (hypomethylated genes). These findings demonstrated that EBV(+) DLBCL is epigenetically distinct from EBV(-) disease, with alterations that may contribute to clinical heterogeneity and potentially serve as biomarkers for disease classification and therapeutic targeting.

overall_design: We profiled the human cellular DNA methylation states of EBV-mediated diffuse large B-cell lymphomas (DLBCL) from our institution (UVM) utilizing the Illumina/Infinium MethylationEPIC array (v2.0), targeting ~935k CpG sites. Tumor cellular DNA was extracted from formalin-fixed, parrafin-embedded tissue blocks of patients samples of DLBCL. We analyzed a total of 43 patient samples following QC protocols (differential methylation values, p<0.05), which resulted in a total of 9 EBV(+) DLBCL, 22 EBV(-) DLBCL, and 12 control tissue (including EBV(+)/(-) reactive lymphoid proliferations and lymphoproliferative disorders of the lymph node and tonsil).

first: Volaric

last: Ashley K.

first: Barrantes-Reynolds

last: Ramiro

first: Sahakyan

last: Karine

first: Fedoriw

last: Yuri

first: Frietze

last: Seth


title: Dectin-1 Stimulation Promotes a Distinct Inflammatory Signature in the Setting of HIV infection and Aging

first: Heidi

last: Zapata

address: 300 Cedar St

summary: Dectin-1 is an innate immune receptor that recognizes and binds β-1,3/1,6 glucans on fungi. We evaluated Dectin-1 function in myeloid cells in a cohort of HIV-positive and HIV-negative young and older adults. Stimulation of monocytes with β-D-glucans induced a pro-inflammatory phenotype in monocytes of HIV-infected individuals that was characterized by increased levels of IL-12, TNF-α, and IL-6, with some age-associated cytokine increases also noted. Dendritic cells showed a striking HIV-associated increase in IFN-α production. These increases in cytokine production paralleled increases in Dectin-1 surface expression in both monocytes and dendritic cells that were noted with both HIV and aging. Differential gene expression analysis showed that HIV-positive older adults had a distinct gene signature compared to other cohorts characterized by a robust TNF-α and coagulation response (increased at baseline), a persistent IFN-α and IFN-γ response, and an activated dendritic cell signature/M1 macrophage signature upon Dectin-1 stimulation. Dectin-1 stimulation induced a strong upregulation of MTORC1 signaling in all cohorts, although increased in the HIV-Older cohort (stimulation and baseline). Overall, our study demonstrates that the HIV Aging population has a distinct immune signature in response to Dectin-1 stimulation. This signature may contribute to the pro-inflammatory environment that is associated with HIV and Aging.

overall_design: Expression profile of WGP stimulated CD14+CD16+ monocytes in the setting of HIV infection and aging

first: Archit

last: Kumar

first: Jiawei

last: Wang

first: Haowen

last: Zhou

first: Chris

last: Radcliffe

first: Brent

last: Vander Wyk

first: Heather

last: Allore

first: Sui

last: Tsang

first: Lydia

last: Barakat

first: Subhasis

last: Mohanty

first: Hongyu

last: Zhao

first: Albert

middle: C

last: Shaw


title: USP20 promotes T-ALL evolution by deubiquitinating modified HIF1A

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary:
T-cell acute lymphoblastic leukemia (T-ALL) is a highly aggressive hematologic malignancy. The potential of investigating USP20 holds promise for more targeted therapies and better outcomes. Knocking down USP20 led to decreased T-ALL cell survival and growth both in vitro and in vivo, similar to using the USP20 inhibitor GSK2643943A.
To explore USP20-dependent gene regulation,
RNA-seq analysis was conducted and the differently expressed genes were revealed in the USP20-knockdown J.gamma1 cells in comparison to control group.
Cleavage Under Targets and Tagmentation (CUT&Tag) showed the co-localization of USP20 with HIF1a on chromatin in J.gamma1 cells.

overall_design:
mRNA profiles of J.gamma1 cells transfected with control shRNA (sh-NC) or sh-USP20 were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

CUT&Tag using antibody against USP20 and HIF1a in J.gamma1 cells.

first: Ling

last: Xu

first: Jun

last: Lu

first: Jian

last: Pan


title: Sclerotic GvHD and Scleroderma Share Dysregulated Gene Expression that is Ameliorated by EREG Therapeutic Antibody

status: Public on Aug 29 2025

first: Ian

last: Odell

address: 330 Cedar St. LMP-5040

department: Dermatology

summary: Immune driven fibrotic skin diseases including scleroderma/systemic sclerosis (SSc) and chronic graft-versus-host-disease (cGvHD) cause skin stiffening that has major impact on patient quality of life and associated patient mortality. Therapies to improve sclerotic skin resulting from these diseases are largely ineffective. We previously showed that EREG, a DC3 dendritic cell-derived EGFR ligand, is elevated in the skin and lung of patients with SSc and required for maintenance of skin fibrosis. Here, we developed a fully human anti-EREG neutralizing antibody that has both high affinity and specificity. We found this therapeutic antibody to be functional and safe in vivo using human EREG knock-in mice. To understand the antifibrotic mechanism of targeting EREG, we aligned skin single-cell transcriptomic profiles of SSc, morphea (localized scleroderma) and SclGvHD with disease biomarkers. EREG expression in the skin was elevated in all three fibrotic diseases and a driver of TNC production by myofibroblasts in all three fibrotic diseases. TNC is a pro-inflammatory extracellular glycoprotein that functions as an endogenous TLR4 ligand which induces expression of TLR4 target genes CCL2 and IL6. Examination of skin explants from patients with active SclGvHD treated with anti-EREG therapeutic antibody by spatial transcriptomics demonstrated upregulation of matrix degradation by increased MMP and decreased TIMP1 expression. Protein measurements showed reduced secretion of EREG targets TNC, CCL2, and TIMP1 in all patients, and type I collagen and FN1 in 3/4 patients. Thus, sclerotic skin treated with the anti-EREG therapeutic antibody reduced inflammatory and fibrosis biomarkers associated with EGFR and TLR4 signaling.

overall_design: Skin biopsies from 3 patients with sclerotic graft-vs-host disease analyzed using 10x genomics platform


title: Transcriptomic data of inhibition of CDK12 in GBM12 cell line by SR-4835 treatment

city: new york city

first: Jeongyeon

last: Mun

institute: Columbia University Irving Medical Center

summary: This dataset contains transcriptomic profiles of the human glioblastoma cell line GBM12 following treatment with SR-4835, a selective CDK12 inhibitor. GBM12 cells were treated with SR-4835 or vehicle control for 24 hours, and total RNA was extracted for RNA sequencing. The study aims to elucidate transcriptional changes associated with CDK12 inhibition in glioblastoma and to identify downstream targets or pathways affected by SR-4835.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for GBM12 cells with DMSO (Condition1) or SR-4835 (Condition2) .

first: Jeong-Yeon

first: Markus

last: Siegelin


title: Vascular endothelial-specific loss of TGF-beta signaling as a model for choroidal neovascularization and central nervous system vascular inflammation

status: Public on Aug 28 2025

city: Baltimore

first: Amir

last: Rattner

state: MD - Maryland

address: 725 North Wolfe St.

institute: Johns Hopkins University

summary: In mice, postnatal endothelial cell (EC)-specific knockout of the genes coding for Transforming Growth Factor-Beta Receptor (TGFBR)1 and/or TGFBR2 eliminates TGF-beta signaling in vascular ECs and leads to distinctive central nervous system (CNS) vascular phenotypes. Knockout mice exhibit (1) reduced,intra-retinal vascularization, (2) choroidal neovascularization with occasional anastomoses connecting choroidal and intraretinal vasculatures, (3) infiltration of diverse immune cells into the retina, including macrophages, T-cells, B-cells, NK cells, and dendritic cells, (4) a close physical association between immune cells and retinal vasculature, (5) a pro-inflammatory transcriptional state in CNS ECs, with increased ICAM1 immunoreactivity, and (6) increased Smooth Muscle Actin immunostaining in CNS pericytes. Comparisons of the retinal phenotype with two other genetic models of retinal hypovascularization – loss of Norrin/Fzd4 signaling and loss of VEGF signaling – shows that the immune cell infiltrate is greatest with loss of TGF-beta signaling, more modest with loss of Norrin/Fzd4 signaling, and undetectable with loss of VEGF signaling. The phenotypes caused by loss of TGF-beta signaling in ECs recapitulate some of the cardinal features of retinal and neurologic diseases associated with vascular inflammation. These observations suggest that therapies that promote TGF-beta-dependent anti-inflammatory responses in ECs could represent a promising strategy for disease modulation.

overall_design: The role of TGF-beta signaling in retinal and brain vascular development has been studied with CreER/LoxP conditional KO mice. Retinas and enriched brain endothelial cells from young adult mice with early postnatal EC-specific loss of Tgfbr1 or Tgfbr2 [VEcadCreER;Tgfbr1CKO/- or VEcadCreER;Tgfbr2CKO/- mice treated with 4- hydroxy-tamoxifen (4HT) between postnatal day (P)3 and P5] were analyzed by single nuclei RNA sequencing.

first: Yanshu

last: Wang

first: Zhongming

last: Li

first: Philip

last: Smallwood

first: Jeremy

last: Nathans