title: Endothelial exosomes remodel chromatin accessibility and superenhancer in cancer cells to promote liver metastatic colonization

city: Guangzhou

first: bei

last: Jin

address: Jinsui street

institute: Zhongshan Ophthalmic Center

summary: Liver-organotropic metastasis occurs in cancers such as uveal melanoma (UM) and pancreatic ductal adenocarcinoma (PDAC) and is a leading cause of mortality at the terminal stage. Colonization is a rate-limiting and converging step in the metastatic cascade. The drivers underlying liver colonization have largely remained elusive. In this report, we hypothesized that pioneer transcription factors (TFs) increase chromatin accessibility and SE remodeling, which subsequently promote colonization-associated cellular features (e.g., proliferation, survival, cancer stem cells (CSCs), motility) by driving the transcription of the respective SE-associated genes. We tested this hypothesis and discovered that the pioneer TF KLF4 promoted chromatin accessibility and SE remodeling by ATAC-seq and ChIP-seq. Chromatin accessibility and SE remodeling significantly increased the transcription of the SE-associated genes MCL-1 and RASGRP3, which consequently promoted proliferation, motility, and metastasis. Furthermore, the upregulation of KLF4 expression in UM cells was promoted by RN7SL2-containing exosomes from surrounding endothelial cells. Analysis of clinical datasets revealed that the overexpression of RIG-I, STAT1, KLF4 and RASGRP3 was individually correlated with shorter metastasis-free survival or overall survival in patients with UM and PDAC. In conclusion, the identification of the exoRN7SL2-STAT1-KLF4-SEs-RASGRP3 signaling axis may help elucidate metastatic colonization through interactions between tumor cells and the endothelial niche and may yield novel and viable therapeutic targets.

overall_design: RNA-seq：These data constitute two independent RNA-seq datasets (DATA-Mel270 RNA-seq and DATA-5pppExoRNA-Seq). 1) Mel270 cells were treated with THZ1 at 0, 62.5, and 250 nM for 6 h prior to RNA extraction and sequencing. 2) RNA extraceted from HUVEC exosomes was treated with terminator 5’-Phosphate-Dependent Exonuclease (Epicenter, Madsion, WI) to degrade 5’-monophosphate RNA in exosomal RNA, and subsequently treated with 5’ polyphosphatase (Epicenter, Madsion, WI) to convert 5’ppp to 5’p, yielding specifically ligated RNA adaptor P5_RNA to RNAs that originally have 5’ppp. ChIP-seq： 1) Mel270-luc-GFP cells were cocultured without or with HUVEC cells for 4 days.Mel270-Luc-GFP cells were subsequently sorted by GFP-based flow cytometry and then subjected to ChIP-seq analysis with an anti-H3K27ac antibody. 2) Mel270 cells were stably expressing lentiviral scramble or shRNA against KLF4, and subsequently subjected to ChIP-seq with anti-H3K27ac. 3) The parental Mel270-Luc subline, the Mel270-HM3 sublines (Subline#1, Subline#11 and Subline#15) were subjected to ChIP-seq with anti-H3K27ac.  ATAC-seq: 1) CFPAC-1 cells were transduced with constucts encoding pTSB-Vector or pTSB-KLF4 and subsequently subjected to ATAC-seq. 2) CFPAC-1 cells stably expressing lentivial scramble, or two different fragments of shRNA targeting KLF4 (shKLF4#1 or shKLF4#2) were subjected to ATAC-seq.

first: Jin

last: Bei

first: Liu

last: Shenglan

first: Huang

last: Hongke

first: Yang

last: Luo

first: Wei

last: Dong

first: Dai

last: Wei

first: Zhou

last: Jingfeng

first: Wang

last: Yun

first: Zhang

last: Ping

first: Ye

last: Qianyun

first: Pan

last: Jingxuan


title: PD-1 regulates latent effector differentiation of thymic cytotoxic CD8+ T cells

status: Public on May 01 2026

city: Rochester

first: Haidong

state: MN

address: 200 First Street SW

country: USA

institute: Mayo Clinic

summary: Durable T cell immunity against cancer depends on the continual replenishment of effector CD8⁺ T cells. Thymic output has been associated with favorable prognosis in cancer patients across a range of ages, suggesting that the thymus is an important source for replenishing T cells capable of controlling cancer progression. However, whether CD8⁺ T cells acquire effector potential within the thymus, and how thymic output of effector CD8⁺ T cells contribute to peripheral tumor immunity, remain unclear. In this study, we discover that thymic single-positive (SP) CD8⁺ T cells undergo latent effector differentiation following thymic selection, but this process is subject to PD-1 regulation. We further demonstrate that PD-1 limits the contribution of thymic output of CD8⁺ T cells in shaping the TCR repertoire within the tumor tissues for tumor immunosurveillance. Although PD-1 inhibition facilitates the expansion of effector CD8⁺ T cells in the periphery, these cells gradually lose antitumor activity within tumors due to accelerated exhaustion in the absence of PD-1. Thus, while latent effector differentiation of thymic CD8⁺ T cells enable a rapid response to malignant cells in the periphery, PD-1 restrains this process to prevent overt or terminal effector differentiation, which could compromise balanced and durable peripheral immunity.

overall_design: Selected tissue sections from four patients with muscle-invasive bladder cancer were evaluated to define regions of interest (ROIs) enriched for NKG7⁺ and NKG7⁻ CD8⁺ T cells. ROIs containing NKG7⁺ CD8⁺ T cells and ROIs containing NKG7⁻ CD8⁺ T cells were subsequently profiled using spatial transcriptomics.

first: Zhiming

last: Mao

first: Ying

last: Li


title: Conserved replication strategies facilitate the cross-species

city: Bochum

first: Eike

last: Steinmann

address: Universitätsstraße 150

department: Molecular and Medical Virology

country: Germany

institute: Ruhr University

type: Expression profiling by high throughput sequencing

summary: A significant number of pandemics, endemics and even sporadic outbreaks trace back to zoonotic spillovers of emerging RNA viruses.  Especially, zoonotic infections with the distantly related hepatitis E virus (HEV, species Paslahepevirus balayani) from various animal origins, such as pigs, deer, wild boar, rabbits and camelids, are well-documented and account for 20 million acute hepatitis cases each year. The detection of HEV RNA in rats surrounding pig farms suggest that they serve as an additional reservoir and source of zoonotic HEV infection. Moreover, the rising number of zoonotic spillover events with the distantly related rat hepatitis E virus (ratHEV, species Rocahepevirus ratti) underscores the urgent need to elucidate the role of rats as a reservoir for HEV infection and in the transmission dynamics of viruses within the family Hepeviridae. Herein, we introduce a novel HEV reverse zoonosis model based on the infection of rat liver cells, which supports completion of the entire HEV replication cycle. RNA sequencing analyses unraveled distinct host responses to HEV infection characterized by minimal activation of innate immune responses. Importantly, host-directed antivirals targeting entry factors previously identified in human host cells effectively restricted HEV infection in rat liver cells. Furthermore, human-specific genomic rearrangements conferred increased fitness across human and rat hepatoma cells. In conclusion, our study indicates conserved viral replication mechanisms of HEV between rats and humans, providing valuable insights into the molecular mechanisms of zoonotic spillover across species.

overall_design: total RNA-seq of untreated primary rat hepatocytes of 3 donors of Wistar Han rats (species Rattus norvegicus forma domestica) and two passages of untreated McA-RH7777 rat hepatoma cells. Further samples were analyzed of McA-RH7777 cells inoculated with HEV 3 (strain Kernow-C1/p6 and 83-2-27) and DMSO, NIT008 or Baricitinib treated  or uninfected.


title: NuRD-Enabled CTCF-TET Crosstalk Orchestrates Epigenome Reprogramming and Genome Architecture

status: Public on May 02 2026

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

country: China

institute: City University of Hong Kong

type: Methylation profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Escherichia coli
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: PD-1 regulates latent effector differentiation of thymic cytotoxic CD8+ T cells [scRNA-Seq]

overall_design: Isolated thymic CD8+ T cells and splenic CD8+ T cells at baseline from Pdcd1fl/fl and Pdcd1 cKO mice were performed single cell RNA sequencing. CD8+ tumor infiltrating lymphocytes were isolated from B16-OVA at day 12 post tumor injection in Pdcd1fl/fl and Pdcd1 cKO mice and analysed by single cell RNA sequencing.


title: Epigenomic profiling of H3K9me3 and H3K27ac across melanoma cell lines with different mutational backgrounds

city: Suzhou

first: Gongjie

last: Wu

address: Renai Road

institute: Xi'an Jiaotong-Liverpool University

summary: Melanoma is a genetically and phenotypically heterogeneous cancer, and changes in chromatin state have been implicated in melanoma progression, phenotypic plasticity, and tumor behavior. To investigate the epigenetic landscape associated with melanoma aggressiveness and mutational background, we performed ChIP-seq for the active chromatin mark H3K27ac and the repressive chromatin mark H3K9me3 in five human melanoma cell lines: SK-Mel-19, SK-Mel-29, SK-Mel-103, UACC-62, and UACC-257. These cell lines represent melanomas with different degrees of aggressiveness and distinct mutation profiles. Our analysis revealed differential patterns of H3K27ac across the cell lines, suggesting that enhancer-associated chromatin states are linked to mutation-dependent transcriptional regulation in melanoma.

overall_design: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) was performed in five human melanoma cell lines: SK-Mel-19, SK-Mel-29, SK-Mel-103, UACC-62, and UACC-257. For each cell line, ChIP was carried out using antibodies against H3K27ac and H3K9me3 to profile active and repressive chromatin regions, respectively. The selected cell lines differ in aggressiveness and harbor distinct melanoma-associated mutations, enabling comparative analysis of mutation-dependent chromatin patterns. Sequencing data were generated to identify genome-wide enrichment profiles of these histone marks and to compare epigenomic differences among the melanoma cell lines.

first: Ferdinand

last: Kappes


title: Bulk RNA-seq data from the nucleus accumbens of female and male prairie voles

city: Boulder

first: Mary

middle: Ann

last: Allen

state: Co

address: UCB 596  JSCBB

department: BioFrontiers

institute: University of Colorado

summary: Relationships are shaped by reciprocal interaction and feedback between individuals, where one individual acts, and the other interprets their actions to respond in turn. As relationships mature, pairs share common goals, improve their ability to work together, and experience coordinated emotions. However, the neural underpinnings responsible for this unique, pair-specific experience remain largely unexplored. Here, we examined the transcriptional landscape of the nucleus accumbens (NAc), a brain region extensively implicated in social bonding, in socially monogamous prairie voles in long-term peer or mating-based relationships.

overall_design: Prairie voles were paired with ar mate (opposite-sex) partner for a certain amount of times. Some pairs were paired for  two weeks (bondedpaired), some were paired for two weeks and subsequently isolated for 4 weeks, and some where paired for 6 weeks. Brain tissue was frozen at -80C and later the nucleus accumbens was dissected from each brain separately.

middle: A

first: Zoe

last: Donaldson


title: Airway immune signatures of protection and disease progression in recent human tuberculosis household contacts [bulk RNA-seq]

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: The local early immune factors dictating whether individuals who have been infected with Mycobacterium tuberculosis remain healthy or progress to active TB have not been defined. We interrogated the airway immune response at single cell resolution in bronchoalveolar lavage (BAL) from PET-CT characterised recent TB household contacts, who either controlled the infection or progressed to TB disease, as well as of active TB patients at diagnosis. Single cell RNA-sequencing revealed type I IFN-dependent and -independent neutrophil signatures in BAL from active TB patients and TB progressors. We report an inverse relationship between airway neutrophils and T cells, with T cells showing signatures of exhaustion, cytotoxicity and cell death in progressors and active TB patients with a neutrophil dominated airway profile. Conversely, we identified T cell signatures of protection in non-progressor contacts dominated by genes related to regulation, quiescence and a stem-like profile. Both the signature of TB progression and the stem-like T cell signature of non-progressors from human airways were recapitulated in scRNA-seq data from non-human primate (NHP) granulomas, associated with disease or immune protection, respectively. Our findings from early human airway responses in TB contacts reveal genes, pathways and cell states that may dictate infection outcome and inform strategies for developing effective host-directed therapies and vaccines.

overall_design: Bulk and single-cell RNAseq of bronchoalveolar lavage from human cohort of tuberculosis patients and their household contacts.

first: William

middle: J

last: Branchett

first: Jee-Whang

last: Kim

first: Jessica

last: Shields

first: Anver

last: Kamil

first: Jo

last: Lee

first: Ismail

last: Novsarka

first: Hubert

last: Slawinski

first: Katalin

last: Wilkinson

first: Robert

first: Raman

last: Verma

first: Pranabashis

last: Haldar

first: Anne

last: O'Garra


title: Paternal morphine exposure enhances morphine self-administration and induces region-specific neural adaptations in reward-related brain regions of male offspring

city: Philadelphia

first: Dana

last: Zeid

state: PA

address: 1701 North 13th St

institute: Temple University

summary: BACKGROUND: A growing body of preclinical studies report that parental exposures can impact the behavior and physiology of offspring. Despite the prevalence of opioid exposure throughout human populations, little is known about the impact of paternal (male-line) opioid use on progeny; METHODS: Adult male rats self-administered morphine or saline for 60 days. These sires were then bred to drug-naïve dams to produce first-generation (F1) offspring. Morphine, cocaine, and nicotine self-administration were evaluated in adult F1 progeny. Molecular correlates of addiction-like behaviors in reward-related brain regions were also measured in a cohort of drug-naïve F1 offspring; RESULTS: Male offspring bred from morphine-exposed sires exhibited a dose-dependent increase in morphine self-administration and increased motivation to earn morphine infusions under a progressive ratio schedule of reinforcement. This phenotype was drug-specific, as self-administration of cocaine, nicotine, and sucrose were not altered by paternal morphine history. Accompanying these behavioral changes, increased mu-opioid receptor expression was observed in the ventral tegmental area (VTA), but not the nucleus accumbens (NAc), of male F1 offspring bred from morphine-exposed sires. RNA sequencing further revealed broad transcriptomic alterations to the F1 NAc and VTA transcriptomes; CONCLUSIONS: Paternal morphine exposure increased morphine addiction-like behavioral vulnerability in male progeny. This phenotype may be driven by adaptations to brain regions that modulate reward processing.

overall_design: RNA-seq on rat brain tissue punches from two brain regions: nucleus accumbens (NAC) & ventral tegmental area (VTA). Brain regions were analyzed separately. For each brain region, the experimental groups were: SAL-sired (fathers exposed to saline) and MOR-sired (fathers exposed to morphine). Brain tissue was from F1 (first generation) male rats sired by fathers who were allowed to self-administer morphine OR saline for 60 days. Effects of father's drug exposure between SAL-sired and MOR-sired F1 brain tissue were studied.

first: Andre

last: Toussaint

first: Alexandra

last: Ellis

first: Angela

last: Bongiovanni

first: Drew

last: Peterson

first: Charlotte

last: Bavley

first: Reza

last: Karbalaei

first: Hannah

last: Mayberry

first: Shivam

last: Bhakta

first: Carmen

last: Dressler

first: Caesar

last: Imperio

first: Genesis

last: Rosiles

first: Yandres

last: Cintron

first: John

last: Maurer

first: Heath

last: Schmidt

first: Chongguang

last: Chen

first: Kathryn

last: Bland

first: Lee-Yuan

last: Liu-Chen

first: Mathieu

last: Wimmer


title: Single-nucleus profiling reveals that cardiomyocyte loss and inflammation drive microenvironment remodeling in early-stage PKP2-deficient ARVC

city: Shanghai

first: Yuze

last: Wang

address: Shanghai Minhang District Dongchuan Road No. 800

institute: Shanghai Jiao Tong University

summary: Here we use a cardiomyocyte-specific Pkp2 knockout mouse model and single-nucleus RNA sequencing (snRNA-seq), delineated the early cellular landscape of the disease.

overall_design: The entire heart was collected at 2 weeks post tamoxifen injection for cell isolation. Each biological sample was generated by pooling hearts from two mice (one male and one female). Each pooled sample was subsequently used for nuclei isolation, library preparation, and sequencing.

first: Tingting

last: Liu


title: Reprogramming engineered autologous T cells to overcome resistance in Merkel cell carcinoma [TCR-Seq]

city: Seattle

first: Aude

last: Chapuis

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

summary: Immune checkpoint inhibitors (CPIs) have transformed Merkel cell carcinoma (MCC) outcomes, but most patients with MCC develop resistance. We identified TCRMCC1, a highly-avid, HLA-A*02:01-restricted T cell receptor (TCR) targeting the Merkel Cell Polyoma Virus (MCPyV) oncoprotein LTAg15–23. Seven patients with CPI-refractory metastatic MCPyV+ MCC received TCRMCC1-transduced cells (TTCR-MCC1)  following lymphodepleting chemotherapy or HLA-enhancing interventions (radiation or IFNg-1b [Actimmune®]), with concurrent CPIs (NCT03747484). TTCR-MCC1 trafficked to tumor sites and expressed a gene expression profile compatible with T cell activation, with tumor regression observed in two patients. However, therapeutic activity was limited by HLA class I silencing, a common mechanism of immune escape in MCC. In one patient, delayed tumor regression coincided with endogenous effector immune activation and restoration of MCC HLA expression, implying robust local responses could reverse HLA silencing. To overcome this barrier, we engineered CD4 and CD8 TTCR-MCC1 to co-express CD8ab and a CD200R-CD28 switch receptor, enabling CD4 T cell engagement and T cell co-stimulation. These modifications enhanced tumor infiltration, increased HLA expression, and improved control of HLAlow MCC in vivo in mice. These findings support the feasibility of TCR-engineered cell therapy for MCPyV+ MCC and provide a blueprint for overcoming immune evasion via targeted localized enhancement of antigen presentation.

overall_design: Single-cell T cell receptor sequencing (scTCR-seq) of PBMCs and tumor-infiltrating T cells from MCC patients. TCR libraries were generated using 10x Genomics Chromium Single Cell V(D)J Reagent Kits to capture paired TCR alpha and beta chains for analysis of T cell clonality and repertoire diversity within tumors.

first: Yuta

last: Asano

first: Cheng-Jung

last: Sung

first: Francesco

last: Mazziotta

first: Bo

last: Lee

first: Lauren

last: Martin

first: Philip

middle: D

last: Greenberg

middle: G


title: Effect of docosahexaenoic acid priming of human adipose-tissue mesenchymal stromal cells used to produce secretome for regenerative applications in spinal cord injury

city: Braga

first: Jonas

last: Campos

state: Minho

address: Campus de Gualtar, Universidade do Minho

department: School of Medicine

country: Portugal

institute: ICVS - Life and Health Sciences Research Institute

summary: Bulk mRNAsec analysis was performed on human adipose-tissue mesenchymal stromal cells (ASCs) cultured in vitro after 72 hours of exposure to the omega-3 lipid docosahexaenoic acid. It was found that this lipid treatment promoted broad and specific transcriptional changes associated with metabolic and stress response pathways.

overall_design: At P6, cells from three individual donors were seeded into T25 flasks and were cultured for DHA priming with 40micromolar concentration. At 72 h post DHA treatment, total RNA was extracted for bulk mRNA sequencing. Briefly, mRNA was isolated using the miRNeasy Micro kit (Qiagen) according to manufacturer’s instructions. RNA quality and integrity was assessed both by Nanodrop and Bioanalyzer 2100 and only samples with 260/280 and 260/230 absorbance ratio 1,8-2 and RIN>8,5 were sequenced. RNA-sequencing was performed by Novogene Company, Ltd. Sequence library (mRNA with polyA enrichment) was prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (New England Biolabs) and sequenced on an Illumina NovaSeq using a paired‐end 150bp system (6Gb per sample). Raw data was subjected to quality control to remove adapters contamination, reads containing N>10% and reads Qscore of over 50% bases below 5. Alignment to the reference genome was performed with HISAT2. The distribution of gene expression levels, FPKM, and heat-maps with correlation coefficients were compared. Differential expression analysis was performed using the DESeq2 package in R. To unravel biological functions or pathways significantly associated with differentially expressed genes (DEGs), functional enrichments were calculated using clusterProfiler software (GO enrichment and KEGG). Functional enrichments were also calculated via gene set enrichment analysis (GSEA; v4.0). P values in dot-plots and GSEA analysis are given after Benjamini and Hochberg correction for multiple comparisons.


title: Cytotoxic Tissue-Resident NK Cells Infiltrate and Control Solid Epithelial Tumor Growth [CITE-Seq]

status: Public on May 04 2026

city: STANFORD

first: Imran

middle: Ahammad

last: Mohammad

state: CA

address: lokey stem cell research building, 2165, 265 Campus Drive, Palo Alto, CA 94305

department: OHNS

institute: Stanford University

summary: Human tissue-resident natural killer (trNK) cells – broadly defined by markers of tissue-residency, such as CD49a (integrin alpha1, ITGA1) and CD103 (integrin alpha E, ITGAE) – are increasingly recognized for their immunoregulatory role in host control of infection, malignancy, and autoimmunity. Although the importance of transforming growth factor beta (TGFβ) in trNK cell differentiation has been demonstrated, the context in which the differentiation of CD49a+CD103+ trNK cells occurs can result in either an immunosuppressive phenotype or a highly cytotoxic one. To understand this dichotomy better, we utilized a multiomics approach to molecularly characterize these cells and identified a highly cytotoxic trNK (ctrNK) cell phenotype, characterized by the expression of CD39.

overall_design: CITE seq: CTRL, HNSCC-induced, and TGF-β induced NK cells were collected and stained with Fixable Viability Dye eFluor 780 (eBioscience; Cat# 65-0865-18). Human TruStain FcX (BioLegend) was used for Fc blocking for 15 minutes at 4°C. NK cell surface proteins were stained using TotalSeq B oligonucleotide-labeled antibodies (0.5 µg of each in 50 µL, BioLegend) targeting CD56, CD16, CD49a, CD103, and CD39. Cell hashing with hashtag oligonucleotides (HTO) was performed for multiplexing different conditions. After antibody incubation for 25 minutes at 4°C, cells were washed once to remove unbound antibodies.

middle: B

last: Sunwoo

first: Jennifer

last: Foltz


title: R-loop landscapes in the developing human brain are linked to neural differentiation and cell type-specific transcription [prenatal brain DRIP-seq]

city: New York

first: Elizabeth

last: LaMarca

state: NY

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: Here, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show that R-loops are abundant in the progenitor-rich germinal matrix, with preferential formation at promoters slated for upregulated expression at later stages of differentiation, including numerous neurodevelopmental risk genes. RNase H1-mediated contraction of the genomic R-loop space in neural progenitors shifted differentiation toward the neuronal lineage and was associated with transcriptomic alterations and defective functional and structural neuronal connectivity in vivo and in vitro. Therefore, we conclude that R-loops are important for fine-tuning differentiation-sensitive gene expression programs of neural progenitor cells.

overall_design:
DNA/RNA-Immunoprecipiation Sequencing (DRIP-seq) from hiPSC-derived neurons transduced with an RNase H1-overexpression construct or a catalytically-inactive RNase H1-D145N mutant construct or a blue fluorescent protein (BFP) lentiviral backbone control. Data were collected from independent cultures from 2 donors.  DRIP-seq bigwigs, and DRIP-seq peak data are provided. Additionally included are DRIP-seq bigwigs and peak files from human second trimester prenatal brain (17-21 gestational weeks. Germinal matrix n = 3 and cortical plate n = 3).
Submitters state that raw FASTQs are not provided due to patient privacy concerns (as the samples are prenatal autopsy samples).

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

first: Atsushi

last: Saito

first: Amara

last: Plaza-Jennings

first: Sergio

last: Espeso-Gil

first: Allyse

last: Hellmich

first: Michael

last: Fernando

first: Benham

last: Javidfar

first: Will

last: Liao

first: Molly

last: Estill

first: Kayla

last: Townsley

first: Anna

last: Florio

first: James

middle: E

last: Ethridge

first: Catherine

last: Do

first: Benjamin

last: Tycko

first: Li

last: Shen

last: Kamiya

first: Nadejda

middle: M

last: Tsankova

first: Kristen

last: Brennand

first: Schahram

last: Akbarian


title: Reprogramming engineered autologous T cells to overcome resistance in Merkel cell carcinoma [Xenium]

first: Aude

last: Chapuis

overall_design: Xenium in situ gene expression profiling was performed on formalin-fixed paraffin-embedded (FFPE) tumor sections from MCC patients using a 480-gene custom panel. This dataset provides spatial localization of tumor and immune cell populations in the tumor microenvironment.

first: Francesco

last: Mazziotta

first: Bo

last: Lee

first: Lauren

last: Martin

first: Evan

middle: W

last: Newell

last: Elz

first: Daniel

last: Chen

first: Yapeng

last: Su

first: Philip

last: Greenberg


title: The HSF2-HSP110 Axis Promotes Genome Stability by Supporting RNA Polymerase II Dependent Transcription and DNA Repair Gene Expression [PRO-Seq]

city: Augusta

first: Nahid

middle: F

last: Mivechi

state: GA

department: Georgia Cancer Center

institute: Augusta University

summary: The precise regulation of RNA polymerase II (RNAPII) is essential for transcriptional fidelity and genome stability. Here, we identify a previously unrecognized genotoxic stressresponsive transcriptional axis composed of Heat Shock Factor 2 (HSF2) and its client chaperone HSP110, which is activated by ionizing radiation (IR). Loss of HSF2 or HSP110 leads to increased DNA damage and heightened IR sensitivity. Mechanistically, the HSF2-HSP110 axis safeguards genome stability by sustaining RNAPII processivity and its C-terminal domain (CTD) phosphorylation, particularly at serine 7 (S7). Disruption of this axis leads to transcriptional dysregulation, altered pre-mRNA splicing, increased transcription-replication conflict, and downregulation of DNA damage response genes, resulting in DNA damage. In vivo, loss of HSF2 accelerates IR-induced lymphomagenesis by impairing transcriptional regulation, specifically inhibiting DNA repair gene expression. These findings define the HSF2-HSP110 axis as an essential transcriptional mechanism in the genotoxic stress response and reveal a therapeutic vulnerability that could be exploited to sensitize tumors to genotoxic therapies.

overall_design: Parental and sgHSF2 K562 cells (in duplicates) were rinsed with ice-cold PBS and werepermeabilized using buffer containing 10mM Tris-HCl pH 8.0, 10% glycerol, 250mM sucrose,5mM MgCl2, 1mM EGTA, 10mM KCl 0.1 % (v/v) Igepal CA-630, 0.05 % (v/v) Tween-20.0.5mM DTT and SUPERase IN (0.2ml/ml). Subsequent steps were performed in the NascentTranscriptomics Core at Harvard University (Garrido-Martin et al., 2018).

first: Xiongjie

last: Jin

first: Caixia

last: Xi

first: Bhaumik

last: Pandya

first: Junfeng

last: Pang

first: Binnur

last: Eroglu

first: Demetrius

last: Moskophidis


title: STAT1 expression in myeloid cells restrains murine norovirus-induced hepatitis and fibrosis

city: Vancouver

first: Lisa

middle: C

last: Osborne

state: BC

address: 3507-2350 Health Sciences Mall

department: Microbiology & Immunology

country: Canada

institute: University of British Columbia

summary: Rare cases of non-hepatotropic virus (NHV) infection in humans can cause severe hepatitis and even acute liver failure. Clinically relevant animal models of NHV-induced hepatitis are limited, contributing to the incomplete understanding of pathological mechanisms. Murine norovirus (MNV) elicits hepatosplenomegaly in mice lacking the antiviral immune effector Signal Transducer and Activator of Transcription-1 (STAT1), providing a model to investigate mechanisms of NHV-induced hepatic pathology. STAT1-sufficient and -deficient (Stat1Het, Stat1KO) littermates infected intravenously (i.v.) with MNV strain CR6 were assessed for hepatic inflammation and viral burden. Cell types and molecular pathways associated with hepatic pathology in CR6-infected Stat1KO mice were identified by flow cytometry and RNAseq of liver tissue. The relative importance of hematopoietic vs non-hematopoietic expression of STAT1 in restricting CR6 replication and maintaining tissue homeostasis was assessed in bone marrow chimeras. MNV CR6 Stat1KO mice developed severe hepatitis with patchy hepatocellular necrosis and localized enrichment of CR6-infected myeloid cells, particularly macrophages. Gene set enrichment analysis (GSEA) of hepatic biopsies isolated from CR6-infected Stat1KO mice suggested dysregulated myeloid cell activation and indicated similarities between murine and human hepatic pathologies. STAT1 expression in hematopoietic cells was protective against hepatic viral dissemination, but hematopoietic STAT1-deficiency permitted persistent hepatic MNV infection, facilitating dysregulated myeloid cell activation and hepatic fibrosis. These results demonstrate that the role of STAT1 extends beyond restricting MNV dissemination and suggest that STAT1-dependent regulation of myeloid cell activation prevents acute hepatic necroinflammation and secondary fibrosis. This model of MNV-induced hepatitis may prove valuable in elucidating mechanisms of rare clinical complications.

overall_design: RNA-seq profiling of liver biopsies following murine norovirus strain CR6 infection (day 5 post-infection).

first: A

last: Sharon

first: Madilyn

last: Portas


title: Airway immune signatures of protection and disease progression in recent human tuberculosis household contacts

first: Probir

last: Chakravarty

overall_design: Single-cell RNAseq of bronchoalveolar lavage from human cohort of tuberculosis patients and their household contacts.

first: William

last: Branchett

first: Jee-Whang

last: Kim

first: Jessica

last: Shields

first: Anver

last: Kamil

first: Jo

last: Lee

first: Ismail

last: Novsarka

first: Hubert

last: Slawinski

first: Katalin

last: Wilkinson

first: Robert

first: Raman

last: Verma

first: Pranabashis

last: Haldar

first: Anne

last: O'Garra


title: Reprogramming engineered autologous T cells to overcome resistance in Merkel cell carcinoma [scRNA-seq]

first: Aude

last: Chapuis

overall_design: Single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) and tumor biopsies from Merkel cell carcinoma (MCC) patients. Cells were processed with 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits v2 to profile transcriptomic heterogeneity across immune and tumor populations.

first: Yuta

last: Asano

first: Cheng-Jung

last: Sung

first: Francesco

last: Mazziotta

first: Bo

first: Lauren

last: Martin

first: Philip

last: Greenberg


title: Effect of interferon-gamma stimulation on the transcriptome of RANKL/M-CSF-induced osteoclasts

city: Hangzhou

first: Yani

last: Chen

state: Zhejiang

address: No. 268, Kaixuan Rd.

institute: Zhejiang University

summary: Interferon-gamma (IFN-γ) is a pleiotropic cytokine with context-dependent effects on bone homeostasis, capable of both inhibiting and promoting osteoclastogenesis depending on the cellular milieu and stage of differentiation. To delineate the direct transcriptional consequences of IFN-γ exposure during terminal osteoclast differentiation, we performed RNA sequencing on RANKL/M-CSF-induced osteoclasts treated with or without IFN-γ. Differential expression analysis identified a suite of IFN-γ-responsive genes and revealed significant perturbation of pathways governing osteoclast fusion and bone resorption. Notably, we identified Lipocalin-2 (Lcn2) as a key downstream effector whose expression is robustly induced by IFN-γ. These data elucidate the molecular mechanisms by which IFN-γ translates immune signals into pro-osteoclastogenic instructions, highlighting a specific transcriptional program that enhances osteoclast differentiation and may contribute to inflammatory bone loss.

overall_design: RNA-seq profiling of RANKL/M-CSF-induced primary osteoclasts derived from wildtype C57BL/6 mice, treated with or without interferon-gamma (IFN-γ) during differentiation.


title: The differentiation of myeloid progenitors is effected by cascading waves of coordinated gene expression that remodel cellular physiology in a characteristic sequence [RNA-seq]

city: Grand Forks

first: Manu

last: Manu

state: ND

address: 10 Cornell Street, Stop 9019

department: Biology

institute: University of North Dakota

summary: The differentiation of hematopoietic progenitors into specialized types requires the transmittal of information from a few external or internal regulators to the thousands of genes that produce a cell type's characteristic phenotypes.  While the main signaling pathways, transcription factors, and the genes eliciting the terminal phenotypes are known, how information flows from a few regulators to thousands of genes to change the state of the cell remains to be fleshed out. To profile this information transfer process, we sampled the differentiation of the PUER myeloid cell line into macrophages and neutrophils at 27 time points over seven days.  There is extensive transient regulation; the number of transcripts modulated in time is twice the number differentially expressed between endpoints.  Differentiation is marked by two sharp transitions, at ~8h and ~80h, when transcriptomic state changes suddenly. We utilized non-negative matrix factorization to identify behaviors, characteristic temporal patterns of gene expression, and to classify transcripts by behavior. Only 10 distinct behaviors are sufficient to recapitulate the expression of ~36,000 transcripts with high fidelity. Gene expression in most of the behaviors occurs in pulses of varying initiation times and durations. This implies that information transfer during differentiation occurs in cascading waves of gene expression culminating in the permanent turning on of certain genes after ~80h. Each behavior is enriched in specific biological processes, so that physiological remodeling proceeds in a characteristic order---signal transduction, translation and mRNA processing, metabolism, and, ultimately, myeloid phenotypic processes. The sharp transition at 8h corresponds to the completion of transcriptional and translational remodeling and the initiation of metabolic remodeling; the one at 80h corresponds to the elicitation of myeloid phenotypes. Our analysis shows that differentiation relies upon a series of transient, rapid, and complex gene regulatory events and highlights the importance of profiling it at a high temporal resolution.

overall_design: Time series of RNA-seq during the differentiation of a mouse cell-line, PUER, into macrophages and neutrophils. RNA-seq was performed in triplicate over a course of 168h following tamoxofin (OHT) treatment. After sampling undifferentiated PUER cells (IL3-OHT 0h), cells were sampled every hour for the first four hours (1-4h), every 4 hours for the first 24h (8-24h), and every eight hours until 168h (32-168h) during both macrophage (IL3) and neutrophil (GCSF) differentiation.

first: Andrea

last: Repele

first: Joanna

last: Handzlik

first: Nimasha

last: Samarawickrama

first: Trevor

last: Long

first: Sunil

last: Nooti

first: Veena

last: Potluri

first: Yen Lee

last: Loh


title: The Transcription Factor TCF21 is Necessary for Adoption of Cell Fates by Foxd1+ Stromal Progenitors during Kidney Development

city: Chcago

first: Gal

last: Finier

state: IL

address: 225 E. Chciago Ave

department: Peditrics

institute: Northwestern University

summary: The stromal compartment of the developing kidney arises from Foxd1-expressing progenitors and gives rise to diverse cell types essential for nephrogenesis, including the renal stroma, capsule, mesangial cells, renin cells, pericytes, and vascular smooth muscle cells (VSMCs). However, the molecular mechanisms guiding their fate specification remain incompletely defined. Here, we identify the basic helix-loop-helix transcription factor Tcf21 as a critical determinant of stromal cell identity during kidney development. We performed single-cell RNA sequencing (scRNA-seq) on Foxd1-lineage cells isolated from embryonic day 14.5 (E14.5) Tcf21 conditional knockout (Tcf21-cKO) Foxd1Cre/+;Rosa26mTmG;Tcf21f/f and control kidneys, revealing seven transcriptionally distinct stromal subpopulations. Loss of Tcf21 resulted in marked depletion of Medullary/Perivascular stroma, Collecting duct associated stroma, Proliferating stroma, and Nephrogenic zone associated subpopulations, confirmed by immunostaining, which revealed severe constriction of medullary and collecting duct stromal spaces. Additionally, we identified a novel cluster unique to Tcf21-cKO kidneys, characterized by high expression of Endomucin (Emcn). These cells spanned pseudotime trajectories and were distributed broadly across the mutant kidney. These findings were corroborated by E14.5 single-cell ATAC sequencing (scATAC-seq), which confirmed altered chromatin accessibility in Tcf21-deficient stroma. To assess the persistence and downstream impact of these defects, we performed bulk and scRNA-seq at E18.5, revealing sustained expansion of Emcn+ cells with pro-fibrotic and perivascular transcriptional programs. Histological analyses at 2 months demonstrated lasting architectural disruption, interstitial fibrosis, and impaired renal function in Tcf21-cKO mice. Our results identify Tcf21 as a key regulator of stromal progenitor fate and establish a developmental origin for fibrotic remodeling and kidney dysfunction.

overall_design:
E14.5 scRNA-seq: Single cells representing Foxd1+ progenitors and their progeny were purified from E14.5 mouse kidneys by fluorescence-activated cell sorting (FACS). scRNA-seq libraries were prepared using the 10x Genomics platform. Samples with same genotype/sex were pooled to produce four groups: Control Female (n=2 embryos), Control Male (n=4 embryos), Mutant Female (n=3 embryos), Mutant Male (n=1 embryo).
E18.5 scRNA-seq: Single cells representing Foxd1+ progenitors and their progeny were purified from E18.5 mouse kidneys by fluorescence-activated cell sorting (FACS). scRNA-seq libraries were prepared using the 10x Genomics platform. Samples with same genotype/sex were pooled to produce four groups: Control Female (n=2 embryos), Control Male (n=2 embryos), Mutant Female (n=2 embryos), Mutant Male (n=1 embryos).
E14.5 scATAC-seq: Single nuclei representing Foxd1+ progenitors and their progeny were purified from E18.5 mouse kidneys by fluorescence-activated cell sorting (FACS). scATAC-seq libraries were prepared using the 10x Genomics platform. Samples with same genotype were pooled to produce two groups: Control Male (n=4 embryos), Mutant Male (n=4 embryos)
E18.5 bulk RNA-seq: RNA was extracted and profiled in whole kidney lysates at E18.5 (n=2 control embryos and n=2 mutant embryos, all males).

last: Finer

first: George

middle: S

last: Yacu

first: Mohammad

last: Khan

first: Yalu

last: Zhou

first: Gaurav

last: Gadhvi

first: Sarah

last: Ward

first: Mohammed

last: Sayed

first: R

last: Gomez

first: Maria Luisa

last: Sequeira-Lopez

first: Joo-Seop

last: Park

first: Hee-Woong

last: Lim

first: Susan

last: Quaggin

first: Deborah

middle: R

last: Winter


title: A ceramide synthase is important for filamentous fungal biofilm morphology and antifungal drug susceptibility

city: Hanover

first: Charles

last: Puerner

state: NH

address: 1 Rope Ferry Rd

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth College

summary: The complex structure of the biofilm generates microenvironments which impact the fitness of the biofilm community as a whole. Contributions to fitness include the development of emergent properties resulting in the recalcitrance to external stressors such as environmental stress or drug stress in the context of a pathogen. The biofilm developed by the filamentous fungal pathogen Aspergillus fumigatus develops zones of low oxygen which contribute to a reduction in antifungal drug susceptibility, however the mechanisms driving this have remained elusive. Here we have utilized a transcriptomic approach to probe the biofilm structure in comparison to a planktonic lifestyle to identify unique biofilm transcriptional patterns. Importantly we utilized two phenotypically diverse strains. From this analysis we have identified biofilm specific gene co-expression networks as well as a ceramide synthase, designated barA, with a striking increase in transcript abundance specifically in the biofilm. Null mutants for barA in two strain backgrounds display altered biofilm morphology with some strain specific differences but interestingly do not impact virulence. Importantly we find the BarA ceramide synthase has a role in regulating susceptibility to classes of ergosterol targeting antifungal drugs. In the absence of barA, treatment with voriconazole leads to significant cellular damage in the form of lysis. Through this we have identified a novel mechanism driving antifungal drug resistance in the biofilm of filamentous fungal pathogen.

overall_design: RNAseq profiling of A. fumigatus strains AF293 and CEA10 submerged biofilm and planktonic tissue harvested at 18--hours of development in four biological replicates. Planktonic tissue was with and without exposure to 0.2% oxygen for 30-minutes.

first: Owen

last: Wilkins

first: Robert

last: Cramer


title: Bulk RNA sequencing of total lung cells from  Atg14f/f and Atg14f/f-LysM-cre mice.

city: Beijing

first: Siwei

last: Feng

address: No.30,Shuangqing street

institute: Siwei Feng

summary: Host responses to infection are determined by how well primed the innate immune system is to respond on first exposure to an invader. Here, we describe innate immune priming prior to infection that conferred resistance to respiratory pathogens. The lung innate immune priming for early response to infection occurred via functional reprogramming of innate immune cells independently of either the microbiome or adaptive immunity. In normal animals, priming was suppressed by autophagy in alveolar macrophages, rendering animals susceptible to infection. Mice lacking autophagy in myeloid cells demonstrated swifter and more efficient innate immune clearance of Staphylococcus aureus infection while minimizing lung damage and inflammation. Enhancing the primed state of innate immunity by blocking autophagy also protected against influenza A virus. Inhibition of autophagy primed innate immunity in the lung by triggering elevated IL-1α expression in autophagy-deficient alveolar macrophages, which enhanced IL-1R/MyD88 signaling in neutrophils. Transiently introducing IL-1α or inhibiting autophagy conferred broad spectrum protection in mice against bacterial and viral pathogens. Ultimately, parallel to trained innate immunity induced by prior microbial exposure, priming of innate immunity by inhibition of autophagy is a robust and broad spectrum resistance mechanism, providing an attractive strategy to fine-tuning immune responses to combat important respiratory infections

overall_design: Lung cells from Atg14f/f and Atg14f/f-LysM-cre mice. Cells pooled from 4 mice each, age 8-10 wks


title: A single-cell and spatial atlas of prostate cancer reveals the combinatorial nature of gene modules underlying lineage plasticity and metastasis

city: San Francisco

first: Hanbing

last: Song

address: 513 Parnassus Ave, HSE

department: Department of Medicine

institute: UCSF

summary: Prostate cancer encompasses a spectrum of disease states driven by complex cellular heterogeneity. To delineate the transcriptional programs underlying lineage plasticity and metastasis, we constructed a comprehensive single-cell atlas of 128 patients, spanning localized, castration-resistant, and metastatic disease. Lineage plasticity was prevalent in localized disease, with subsets of tumor cells adopting distinct basal-like and club-like states. Luminal-like cancer cells also displayed extensive lineage infidelity, defined not by a binary loss of identity but by the combinatorial erosion of luminal gene modules associated with higher grade and stage. In the metastatic setting, gene program association analysis (GPAS) identified a broad induction of cell-cycle gene modules across organ sites as well as an induction of organ-specific gene modules, including osteomimetic signaling in bone, neuro-migratory genes in brain, and erythroid-like transitions in liver. Neuroendocrine prostate cancers (NEPCs) were not monolithic but defined by combinations of NE-associated gene modules including a novel HES6 program. Notably, these modules were detected at intermediate levels in localized samples, suggesting molecular plasticity precedes histological transformation. We also developed a refined NE signature that could distinguish NEPC tumors more accurately than previously published signatures. Within the tumor microenvironment (TME), we observed an elevation of pro-inflammatory Th17 T-cells in African American patients and identified a rare Schwann cell population. Finally, we present PCformer, a transformer-based foundation model trained on >500,000 cells to automate cell-state classification. Together, this comprehensive atlas demonstrates the complex nature of gene modules underlying lineage infidelity and plasticity in cancer cells and highlights distinct immune and stromal populations within the tumor ecosystem.

overall_design: 36 localized prostate cancer patients and 2 metastatic prostate cancer patients (one liver metastatic and one sphenoid metastatic) enrolled in this study.

last: Hsu

first: Julia

middle: H

last: Pham

first: Yih-An

last: Chen

first: Hannah

last: Weinstein

first: Matthew

last: Cooperberg

first: Nancy

last: Greenland

first: Franklin

last: Huang


title: Effect of BHLHE40 silencing using short-hair pin RNA on CD34+ cells isolated from human cord blood, during TGF-B1 depedent Langerhans cell differentiation

city: Graz

first: Sally

last: Connolly

state: Steiermark

address: Otto Loewi Forschungszentrum - Immunologie und Pathophysiologie Medizinische Universität Graz Heinrichstraße 31a A-8010 Graz

country: Austria

summary: Langerhans cells (LCs) are resident antigen presenting cells of the epidermis whose differentiation, immature state and tissue residency critically depend on transforming growth factor–β1 (TGF-β1) signaling. Although several downstream transcriptional regulators of TGF-β1 have been identified, how LC epithelial identity and homeostasis are transcriptionally stabilized remains incompletely understood.Human CD34⁺ hematopoietic progenitors were differentiated into LCs or monocyte-derived cells in vitro using cytokine-defined conditions, combined with lentiviral knockdown or ectopic expression of BHLHE40. Bulk-RNA seq of shBHLHE40 cells reveals blunted induction of TGF-β1 responsive genes.

overall_design: RNA-seq profiling of shCTRL and shBHLHE40 transduced CD34+ cells  at 0 hours and 24 hours post-culturee with TGF-β1 to promote Langerhans cell differentiation

first: Hebert

last: Strobl


title: Targeting Y593-phosphorylated DDX5 triggers mitochondrial dysfunction and synergizes with BCL2 inhibition in acute myeloid leukemia

city: Boston

first: WEI

last: NI

state: MA

address: 450 Brookline Ave, Bldg MA-0543

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Acute myeloid leukemia (AML) remains a lethal malignancy with limited therapeutic durability. DEAD-box RNA helicase 5 (DDX5) is highly expressed in AML and associated with poor outcome, yet its mechanistic role and therapeutic tractability are incompletely defined. Here, we identify phosphorylation at tyrosine 593 (Y593) of DDX5 as a therapeutic vulnerability in AML. We show that DDX5 is constitutively phosphorylated at Y593 in AML cells independent of Src or c-Abl activity. While genetic depletion of DDX5 suppresses AML growth, phosphorylation-deficient Y593F knock-in mutants show that Y593 phosphorylation is dispensable for baseline proliferation but is required to maintain mitochondrial integrity and define the BCL-2 family–controlled apoptotic threshold. Targeting Y593-phosphorylated DDX5 with the small-molecule RX-5902 destabilizes β-catenin and, more importantly, triggers acute mitochondrial dysfunction characterized by impaired oxidative phosphorylation, permeabilizes mitochondrial outer membranes, and increases BCL-2 dependence. Accordingly, inhibition of Y593-phosphorylated DDX5 represents a mitochondrial sensitizer that creates vulnerability to BCL-2 blockade. Consistent with this mechanism, RX-5902 strongly synergizes with venetoclax across AML cell lines, primary patient samples, and xenograft models. Together, these findings establish Y593-phosphorylated DDX5 as an actionable regulator of mitochondrial apoptotic priming in AML and support combined targeting of DDX5 and BCL-2 as a rational therapeutic strategy.

overall_design: RNA-seq profiling of MOLM-14 cells transduced with control shRNA (shControl) or DDX5-targeting shRNA (shDDX5). Cells were collected 96 hours post lentiviral infection. Biological replicates (n = 3 per condition) were included.                                                                      RNA-seq profiling of MOLM-14 cells treated with DMSO (0.1%) or RX-5902 (100 nM) for 6 hours. Biological replicates (n = 3 per condition) were included.

first: Wei

last: Ni

first: James

last: Griffin


title: R-loop landscapes in the developing human brain are linked to neural differentiation and cell type-specific transcription [RNA-seq]

first: Elizabeth

last: LaMarca

overall_design: RNA-seq files from hiPSC-derived neurons transduced with an RNase H1-overexpression construct or a catalytically-inactive RNase H1-D145N mutant construct or a blue fluorescent protein (BFP) lentiviral backbone control. Data were collected from independent cultures from 2 donors. Raw FASTQs and an RNA count matrix are provided.

first: Atsushi

last: Saito

first: Amara

last: Plaza-Jennings

first: Sergio

last: Espeso-Gil

first: Allyse

last: Hellmich

first: Michael

last: Fernando

first: Benham

last: Javidfar

first: Will

last: Liao

first: Molly

last: Estill

first: Kayla

last: Townsley

first: Anna

last: Florio

last: Ethridge

first: Catherine

last: Do

first: Benjamin

last: Tycko

first: Li

last: Shen

last: Kamiya

first: Nadejda

last: Tsankova

first: Kristen

last: Brennand

first: Schahram

last: Akbarian


title: R-loop landscapes in the developing human brain are linked to neural differentiation and cell type-specific transcription [hiPSC-derived neuron DRIP-seq]

first: Elizabeth

last: LaMarca

overall_design: DNA/RNA-Immunoprecipiation Sequencing (DRIP-seq) from hiPSC-derived neurons transduced with an RNase H1-overexpression construct or a catalytically-inactive RNase H1-D145N mutant construct or a blue fluorescent protein (BFP) lentiviral backbone control. Data were collected from independent cultures from 2 donors. Raw FASTQs, DRIP-seq bigwigs, and DRIP-seq peak data are provided. Additionally included are DRIP-seq bigwigs and peak files from human second trimester prenatal brain (17-21 gestational weeks. Germinal matrix n = 3 and cortical plate n = 3).

last: Saito

last: Plaza-Jennings

first: James


title: Spatial Transcriptomics Analysis of inflamed versus healthy Dental Pulps

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

summary: Diagnostic protocols in endodontics rely heavily on subjective pain assessments and sensibility testing, which often fail to reflect the true histopathological and molecular state of the pulp. This limitation can result in misdiagnosis of reversible pulpitis as irreversible, leading to unnecessary devitalization of teeth that might otherwise respond to vital pulp therapy (VPT). Improved understanding of pulp biology is essential to refine case selection and enhance VPT outcomes. We aim to investigate the transcriptomic profiles of pulpitis, identify inflammation subtypes, and improve classification beyond the traditional reversible/irreversible framework. Methods: Spatial transcriptomics (Visium-CytAssist-V2) was used to analyze four dental pulp tissues. Cell deconvolution and differential gene expression analyses were performed to characterize transcriptomic signatures of healthy pulp (HL), reversible pulpitis (RP), and irreversible pulpitis (IP), with specific attention to coronal regions adjacent to carious lesions.

overall_design: To evaluate the inflammatory profile of several degrees of dental pulpitis beyond clinical diagnosis, we analysed dental pulp samples by spatial transcriptomics. Our samples were one healthy pulp, one clinically diagnosed reversible pulpitis and two clinically diagnosed irreversible pulpitis.

first: Samer

last: Zaky

first: Giueseppe

last: Intini

first: Charles

last: Sfeir

first: Renato

last: Silva


title: Single-cell RNA sequencing data indicate that CD40 promots macrophage efferocytosis following myocardial infarction.

city: 任何人

first: canbiao

last: wang

state: State

address: wenlan ,nanjing jiangsu

institute: nanjing normal university

summary: CD40 expressed on the macrophage membrane is recognized as one of the characteristic biomarkers for their inflammatory phenotype. We demonstrated that macrophage CD40 functionally promotes post-myocardial infarction (MI) repair. To elucidate the role of CD40 in the post-MI repair process, we dissected infarct and border zones from the hearts of wild-type (WT) and CD40 knockout (KO) mice at 3 days post-MI. Mononuclear macrophages (CD45⁺CD11b⁺CD64⁺) were isolated via flow cytometry and subjected to single-cell RNA sequencing analysis. This study establishes that CD40 plays a critical role in macrophage efferocytosis. Furthermore, analysis of scRNA-seq data led to the identification of developmental precursor cells of repair-phenotype macrophages.

overall_design: At 3 days post-MI, mononuclear macrophages (CD45⁺CD11b⁺CD64⁺) were isolated from the infarct and border zones of hearts from WT and CD40 KO mice, and subjected to single-cell RNA sequencing using the 10× Genomics platform.

first: Linlin

last: Zhang

first: Canbiao

last: Wang

first: Longjiang


title: RNA-seq analysis of human corneal epithelial cells under hyperosmotic stress modeling dry eye disease

city: Nanjing

first: Yun

last: Tang

address: 321 Zhongshan Road

institute: Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University

summary: We performed RNA-seq to investigate the transcriptomic changes in human corneal epithelial cells (HCECs) under hyperosmotic stress mimicking dry eye disease (DED).

overall_design: Comparison of gene expression profiles between control HCECs and HCECs treated with hyperosmotic medium (90 mM NaCl) for 24 hours. Three biological replicates per group.


title: Dynamin 2 regulates mitochondrial mitotic fission in pulmonary hypertension

city: Kingston

first: Stephen

last: Archer

address: 94 Stuart Street

institute: Queen's University

summary: Dynamin-related protein 1 (DRP1) mediates mitochondrial fission and permits rapid cell cycle progression in hyperproliferative cells by coordinating nuclear and mitochondrial division, a process called mitotic fission. However, DRP1 alone appears insufficient to complete fission and the link between fission and cell cycle progression is unknown.We hypothesize Dynamin 2 (DNM2) interacts with DRP1 to complete mitochondrial fission and regulate cell cycle progression. We show that DNM2 is upregulated in pulmonary arterial smooth muscle cells in human and rodent pulmonary arterial hypertension (PAH PASMC), contributing to disease pathophysiology.

overall_design: We want to study the transcriptomic changes after silencing DNM2 in PAH PASMCs.

first: Ashish

last: Das Gupta

first: Kuang-Hueih

last: Chen

first: Danchen

last: Wu

first: Siddhartha

last: Yerramili

first: Patricia

last: Lima

first: Ashley

last: Martin

first: Rachel

last: Bentley

first: Benjamin

last: Ott

first: Tanvi

last: Nandani

first: Jeff

last: Mewburn

first: Lian

last: Tian

first: Ruaa

last: Al-Qazazi

first: Issac

last: Emon

first: Pierce

last: Colman

first: Lindsay

last: Jefferson

first: Curtis

last: Noordhof

first: Oliver

last: Jones

last: Hindmarch


title: Pervasive Enhanced Transcription in Inflammatory Breast Cancer Tumors and PBMCs Impacts RNA Splicing and Intronic RNAs in Plasma

city: Austin

first: Alan

last: Lambowitz

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

summary: Inflammatory breast cancer (IBC), the most aggressive and lethal breast cancer subtype, lacks unequivocal genomic differences or robust biomarkers that differentiate it from non-IBC. Here, Thermostable Group II Intron Reverse Transcriptase sequencing of RNA samples revealed myriad differences in tumors, PBMCs, and plasma that distinguished IBC from non-IBC patients and healthy donors across all tested non-IBC subtypes. By mapping reads to genome and transcriptome reference sequences and quantitating intron-to-exon read depth ratios, we developed methods for parallel analysis of transcriptional and post-transcriptional gene regulation. This analysis identified numerous protein-coding genes in IBC patient tumors and PBMCs with high intron-to-exon read depths, suggesting rate-limiting RNA splicing that negatively impacts mRNA production. Mirroring gene expression differences in tumors and PBMCs, over-represented protein-coding gene RNAs in IBC patient plasma were largely intron RNA fragments, while those in non-IBC patient and healthy donor plasma were largely mRNA fragments. Our findings provide new insights into IBC and should enable monitoring disease progression by liquid biopsy.

overall_design: Thermostable Group II Intron Reverse Transcriptase sequencing (TGIRT-seq) of RNA samples in tumors, PBMCs, and plasma collected from inflammatory breast cancer (IBC) and breast cancer (non-IBC) patients and healthy donors across all tested non-IBC subtypes.

first: Dennis

last: Wylie

first: Xiaoping

last: Wang

first: Jun

last: Yao

first: Hengyi

last: Xu

first: Elizabeth

last: Ferrick-Kiddie

first: Toshiaki

last: Iwase

first: Savitri

last: Krishnamurthy

first: Naoto

middle: T

last: Ueno


title: Efferocytosis and other corpse clearance transfers metal micronutrients to engulfing macrophages triggering a metallothionein response necessary to preserve mitochondrial function

city: Denver

first: Alexandra

last: McCubbrey

state: CO

address: 1400 Jackson St

institute: National Jewish Health

summary: In the human body, billions of cells die each day during normal turnover, infection, and tissue damage. Macrophages are critical for engulfing and clearing dead cells to maintain health. It is increasingly appreciated that this process requires rapid degradation the corpse metabolic load to maintain normal macrophage functions and mount appropriate immune responses. To understand conserved reprogramming associated with successful corpse engulfment, this study compares RNA-sequencing on three different macrophage populations in mice to understand conserved programming downstream of apoptotic cell engulfment in vitro and in vivo. Pathway analysis identifies enrichment of conserved pathways related to metabolite handling in all three engulfing macrophage populations, including pathways related to metal ion homeostasis. Our study identifies metals as part of the corpse-derived metabolic load transferred to macrophages. We demonstrate a conserved role of macrophage metallothionein (MT) gene upregulation in the management of cell-derived metals transferred during engulfment of apoptotic corpses, necrotic corpses, or live cells. Mechanistically, MTs facilitate prompt control of free zinc released during corpse degradation in the phagolysosome. MTs are necessary for macrophages to enhance oxidative phosphorylation in response to apoptotic cell engulfment, connecting control of corpse-derived metals to macrophage metabolic response. Collectively, these findings identify metals as micronutrients transferred from corpses to engulfing macrophages during efferocytosis and other corpse clearance and demonstrate an important role for metallothioneins in processing corpse-associated metals to preserve macrophage functions.

overall_design: RNA-seq profiling of murine peritoneal macrophages comparing corpse-engulfing, non-engulfing, and unexposed groups.

first: Hope

last: Chatwin

first: Shannon

last: McManus

first: Brian

last: Vestal

first: Kelsey

last: Anderson

first: Stephanie

last: Bersie

first: Angela

first: Joel

last: Douglas

first: Zekiel

last: Haney

first: Fan

last: Jia

first: Daniel

last: Stephenson

first: Jack

last: Congel

first: Katherine

last: Hisert

first: Kara

last: Mould

middle: L


title: Paradoxical Oncogenic Effects of Hepatic Brca1 through Modulating Bhmt

city: To

first: Martha

last: Ghebreselassie

address: 10-601D, Princess Margaret Cancer Research Tower 101 College Park

institute: University of Toronto

summary: Using 10x Genomics single nuclear RNA sequencing (snRNA-seq)  to characterize differences between mice with and with Brca1 specifically in the liver, after carcinogen exposure. Hepatocellular carcinoma (HCC) is among the most common and deadly cancers worldwide and HCC-associated cases and deaths are projected to increase. Recently, tumor suppressor gene Breast cancer susceptibility  gene 1 (BRCA1) was implicated in liver tumor development, yet its mechanisitc role remains unclear. We found that hepatic Brca1 deficiency in mice paradoxically protected against carcinogen induced liver tumor development. Using snRNAseq, we sought to characterize differences in non-tumor liver tissue to determine the underlying mechanism driving liver tumor protection.

overall_design: Mice received liver carcinogen diethylnitrosamine (DEN; 25mg/kg) at 14 days old and were sacrificed at 12 months of age. Non-tumor liver tissue was procured and used for snRNA-seq.

first: Minna

last: Woo


title: Gene expression profile of Siglec F+ alveolar macrophages  under conditions of liver regeneration after 70% resection.

city: Moscow

first: Polina

last: Vishnyakova

address: Oparina 4

country: Russia

institute: National Medical Research Center for Obstetrics, Gynecology and Perinatology

summary:
The aim of the work was to study the expression profile of Siglec F+ alveolar macrophages  under conditions of liver regeneration after 70% resection.
We used microarrays for comparison of Siglec F+ alveolar macrophages  in intact mice and in mice under conditions of liver regeneration after 70% resection.

overall_design: Male c57 Black mice were hepactomized. Alveolar macrophages were sorted with magnetic beads with anti-Siglec F antiboby in 1,3 and 7 days after liver resection and in control group

first: Maria

last: Kuznetsova


title: Restoration of impaired lysosomal function mitigates drusen-like deposits formation and cell death in Malattia Leventinese

city: Sakyo-ku

first: Yumi

last: Inoue

state: Kyoto

address: 54 Shogoin Kawaramachi

country: Japan

institute: Kyoto University

summary: Malattia Leventinese (MAL) is an inherited macular degeneration disorder characterized by retinal drusen formation in adolescence, leading to vision loss. A mutation in the fibulin-3 gene (EFEMP1) causes MAL; however, the mechanisms underlying disease onset and drusen formation remain unclear. In this study, we generated induced pluripotent stem cell-derived retinal pigment epithelial (iPSC-RPE) cells from a patient with MAL to investigate disease mechanisms and potential therapies. MAL iPSC-RPE exhibited fibulin-3 and apolipoprotein E (ApoE) aggregation, increased endoplasmic reticulum stress, and enhanced apoptosis. Long-term culture with photoreceptor outer segments led to drusen-like deposits containing ApoE, complement components, collagen IV accumulation, and matrix metalloproteinase-2 (MMP2) activation. Untargeted lipid analysis revealed increased hexosylceramide and bis-monoacylglycerophosphate levels in MAL iPSC-RPE cells. A key pathological feature was lysosomal dysfunction associated with altered regulation of lysosomal gene programs, including reduced transcription factor EB transcript levels. Treatment with trehalose, a lysosome-modulating compound, increased lysosomal content and function, reducing drusen-like deposits formation, inhibiting MMP2 activation, and suppressing apoptosis. This study highlighted lysosomal dysfunction as a contributor to RPE damage, drusen-like deposits accumulation, and extracellular matrix degradation. Pharmacological restoration of lysosomal function alleviated these defects, suggesting therapeutic potential for MAL and other drusen-related diseases, including age-related macular degeneration.

overall_design: RNA seq profiling of NOR and MAL iPSC-RPE cells. Cells were cultured for 4weeks, followed by an additional 4weeks of incubation in the presence or absence of POS.

first: Hanako

middle: O

last: Ikeda

first: Masayuki

last: Hata

first: Yuto

last: Iida

first: Keiko

last: Okamoto-Furuta

first: Isao

last: Asaka

first: Makoto

last: Arita

first: Akitaka

last: Tsujikawa


title: The HSF2-HSP110 Axis Promotes Genome Stability by Supporting RNA Polymerase II Dependent Transcription and DNA Repair Gene Expression [CUT&Run]

city: Augusta

first: Nahid

last: Mivechi

institute: Augusta University

summary: The precise regulation of RNA polymerase II (RNAPII) is essential for transcriptional fidelity and genome stability. Here, we identify a previously unrecognized genotoxic stressresponsive transcriptional axis composed of Heat Shock Factor 2 (HSF2) and its client chaperone HSP110, which is activated by ionizing radiation (IR). Loss of HSF2 or HSP110 leads to increased DNA damage and heightened IR sensitivity. Mechanistically, the HSF2-HSP110 axis safeguards genome stability by sustaining RNAPII processivity and its C-terminal domain (CTD) phosphorylation, particularly at serine 7 (S7). Disruption of this axis leads to transcriptional dysregulation, altered pre-mRNA splicing, increased transcription-replication conflict, and downregulation of DNA damage response genes, resulting in DNA damage. In vivo, loss of HSF2 accelerates IR-induced lymphomagenesis by impairing transcriptional regulation, specifically inhibiting DNA repair gene expression. These findings define the HSF2-HSP110 axis as an essential transcriptional mechanism in the genotoxic stress response and reveal a therapeutic vulnerability that could be exploited to sensitize tumors to genotoxic therapies.

overall_design: CUT&RUN analyses using an RNAPII antibody in parental and sgHSF2 K562 cells, either untreated or exposed to IR, followed by 2- or 4-hour recovery periods

first: Xiongjie

last: Jin

first: Caixia

last: Xi

first: Bhaumik

last: Pandya

first: Junfeng

last: Pang

first: Binnur

last: Eroglu

first: Demetrius

last: Moskophidis


title: Limonoid DDK restores mitochondrial redox homeostasis to alleviate metabolic dysfunction-associated steatohepatitis via promoting SDHA deacetylation and SDH complex activity

first: Mingyu

last: Sun

address: Chunhua Subdistrict,Jiangning District

institute: China Pharmaceutical University

summary: Mitochondrial dysfunction and redox imbalance are key drivers of metabolic dysfunction-associated steatohepatitis (MASH), yet therapeutic strategies targeting mitochondrial respiratory integrity remain limited. We identified succinate dehydrogenase subunit A (SDHA) as a direct functional target of the natural limonoid compound DDK. Using CETSA coupled with mass spectrometry (MS) and bio-layer interferometry (BLI), we demonstrate that DDK directly binds SDHA. The mitochondrial-protecting and oxidative phosphorylation (OXPHOS)-recovering effects of limonoid compound DDK were abolished in SDHA-deficient hepatocytes, suggesting that SDHA is indispensable for DDK’s bioactivity. SDH activity decreased in the liver tissues of MASH murine models, while SDHA knockdown in hepatocytes further aggravated impaired OXPHOS activity and mitochondrial dysfunction. Mechanistically, DDK promoted complex II (SDH) assembly and enzymatic activity by reducing pathological acetylation of SDHA at lysine 335. Site-specific mutation of K335 abrogated DDK-induced enhancement of complex II assembly and mitochondrial respiration, demonstrating that SDHA deacetylation is required for its therapeutic efficacy. To conclude, our findings uncover an SDHA acetylation–complex II assembly axis as a therapeutic strategy in MASH, offering evidence that DDK may be a new therapeutic option for MASH treatment.

overall_design: To investigate how small molecule DDK protects MASH , we conducted RNA sequencing (RNA-seq) on the livers from 3 DDK-treated mice and 3 vehicle-treated control mice under HFHC feeding conditions.

first: Yingrong

last: Leng

first: Ying

last: Zheng

first: Yanqiu

last: Zhang

first: Yuqiong

last: Song

first: Xin

last: Li

first: Lingyi

last: Kong

first: Hao


title: R-loop landscapes in the developing human brain are linked to neural differentiation and cell type-specific transcription [scRNA-seq]

city: New York

first: Elizabeth

last: LaMarca

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: Here, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show that R-loops are abundant in the progenitor-rich germinal matrix, with preferential formation at promoters slated for upregulated expression at later stages of differentiation, including numerous neurodevelopmental risk genes. RNase H1-mediated contraction of the genomic R-loop space in neural progenitors shifted differentiation toward the neuronal lineage and was associated with transcriptomic alterations and defective functional and structural neuronal connectivity in vivo and in vitro. Therefore, we conclude that R-loops are important for fine-tuning differentiation-sensitive gene expression programs of neural progenitor cells.

overall_design: scRNA-seq files from hiPSC-derived neurons transduced with an RNase H1-overexpression construct or a blue fluorescent protein (BFP) lentiviral backbone control. Data were collected from independent cultures from 2 donors. Samples were multiplexed using hashtag oligonucleotides (HTOs) and sequenced as a single pooled GEX and HTO library. Raw FASTQs, HTO hastags, and processed files (barcodes, features, matrix) are provided, along with sample-level metadata.

middle: A

first: Atsushi

last: Saito

first: Amara

last: Plaza-Jennings

first: Sergio

last: Espeso-Gil

first: Allyse

last: Hellmich

first: Michael

last: Fernando

first: Benham

last: Javidfar

first: Will

last: Liao

first: Molly

last: Estill

first: Kayla

last: Townsley

first: Anna

last: Florio

first: James

last: Ethridge

first: Catherine

last: Do

first: Benjamin

last: Tycko

first: Li

last: Shen

last: Kamiya

first: Nadejda

last: Tsankova

first: Kristen

last: Brennand

first: Schahram

last: Akbarian


title: Transcriptome analysis of Aohog1 in nematode-trapping fungus Arthrobotrys oligospora

city: kunming

first: Si

last: Chen

address: Yunnan university 2th hubei road,wuhuaqu

institute: yunnan university

summary: Transcriptomic analysis revealed that differentially expressed genes in the absence of Aohog1 were involved in  carbohydrate metabolism, amino acid metabolism, lipid metabolism, transport and catabolism, energy metabolism, and translation.

overall_design: Examination of differential genes in the WT, ΔAohog1 mutant strains and prediction of multiple cytological processes that may affect trap formation in Arthrobotrys oligospora.

first: Jin-kui

last: Yang


title: PD-1 regulates latent effector differentiation of thymic cytotoxic CD8+ T cells [TCR-Seq]

city: Rochester

first: Haidong

last: Dong

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: Durable T cell immunity against cancer depends on the continual replenishment of effector CD8⁺ T cells. Thymic output has been associated with favorable prognosis in cancer patients across a range of ages, suggesting that the thymus is an important source for replenishing T cells capable of controlling cancer progression. However, whether CD8⁺ T cells acquire effector potential within the thymus, and how thymic output of effector CD8⁺ T cells contribute to peripheral tumor immunity, remain unclear. In this study, we discover that thymic single-positive (SP) CD8⁺ T cells undergo latent effector differentiation following thymic selection, but this process is subject to PD-1 regulation. We further demonstrate that PD-1 limits the contribution of thymic output of CD8⁺ T cells in shaping the TCR repertoire within the tumor tissues for tumor immunosurveillance. Although PD-1 inhibition facilitates the expansion of effector CD8⁺ T cells in the periphery, these cells gradually lose antitumor activity within tumors due to accelerated exhaustion in the absence of PD-1. Thus, while latent effector differentiation of thymic CD8⁺ T cells enable a rapid response to malignant cells in the periphery, PD-1 restrains this process to prevent overt or terminal effector differentiation, which could compromise balanced and durable peripheral immunity.

overall_design: In this cohort of TCR sequencing, thymic and splenic CD8+ T cells at baseline as well as thymic and tumor-infiltrating CD8+ T cells isolated from B16-OVA-bearing, and B16-F10-bearing Pdcd1fl/fl and Pdcd1 cKO mice were isolated and analysed for clonotype information.

first: Zhiming

last: Mao

first: Ying

last: Li


title: Failure of Early B Cell Tolerance and possible BCR Signaling Dysregulation Underlie NF155-Mediated Autoimmune Nodopathies

city: New Haven, CT

first: Bhaskar

last: Roy

state: CT

address: 15 York Street

department: Neurology

institute: Yale University School of Medicine

summary: Autoimmune nodopathies (AINs) are rare acquired autoimmune neuropathies with distinct clinical features and circulating autoantibodies, often of the immunoglobulin G4 (IgG4) subclass, targeting proteins at the node of Ranvier. Defects in B-cell tolerance checkpoints have been implicated in several autoimmune diseases, including MuSK-positive myasthenia gravis (MG), another IgG4 autoantibody-mediated disease. Here, we investigated whether tolerance defects exist in neurofascin-155-mediated AIN (NF155-AIN), using a well-established assay, by generating recombinant antibodies from new emigrant (NE) and mature naïve (MN) B cells from three NF155-AIN patients, and tested them for polyreactivity and autoreactivity. Additionally, we analyzed the transcriptome of peripheral blood mononuclear cells with a special focus on naïve B cells and CD4+ T cells at the single-cell level, along with characterization of cell-cell interactions. NF155-AIN patients have an elevated frequency of polyreactive B cells in the NE (37.4% compared to 9.7% in healthy controls (HCs), p = 0.03) and MN (31.5% compared to 10.5% in HCs, p = 0.03) compartments, consistent with a breach in early B cell tolerance checkpoints. In this unbiased exploratory transcriptomics analysis, we observed potentially abnormal B cell receptor (BCR) signaling characterized by low CD79B, CSK, BLNK, and BTK expression, and possible impaired CD4+ T cell regulatory function. Moreover, comparison with chronic inflammatory demyelinating polyneuropathy (CIDP), a related autoimmune neuropathy, suggested that these differences are specific to NF155-AIN. A breach in early B cell tolerance checkpoints, with defective BCR signaling, and disrupted T cell-B cell interactions in NF155-AIN, may contribute to the development of pathogenic autoreactivity.

overall_design: For this project we used PBMC samples after dead-cell removal. Some samples were enriched for B cells. The samples were hashtagged using HTOs, and then demultiplexed using Seurat. We have used the standard Seurat pipeline for the analysis. Cell annotation was done using Azimuth, and for some specific cell types manual annotation was performed.

first: Kevin

last: O'Connor

first: Luis

last: Querol

first: Richard

middle: J

last: Nowak

first: Zhenjiang

last: Wang

first: Daniel

last: Joo


title: The differentiation of myeloid progenitors is effected by cascading waves of coordinated gene expression that remodel cellular physiology in a characteristic sequence [CUT&RUN]

city: Grand Forks

first: Manu

last: Manu

address: 10 Cornell Street, Stop 9019

institute: University of North Dakota

summary: The differentiation of hematopoietic progenitors into specialized types requires the transmittal of information from a few external or internal regulators to the thousands of genes that produce a cell type's characteristic phenotypes.  While the main signaling pathways, transcription factors, and the genes eliciting the terminal phenotypes are known, how information flows from a few regulators to thousands of genes to change the state of the cell remains to be fleshed out. To profile this information transfer process, we sampled the differentiation of the PUER myeloid cell line into macrophages and neutrophils at 27 time points over seven days.  There is extensive transient regulation; the number of transcripts modulated in time is twice the number differentially expressed between endpoints.  Differentiation is marked by two sharp transitions, at ~8h and ~80h, when transcriptomic state changes suddenly. We utilized non-negative matrix factorization to identify behaviors, characteristic temporal patterns of gene expression, and to classify transcripts by behavior. Only 10 distinct behaviors are sufficient to recapitulate the expression of ~36,000 transcripts with high fidelity. Gene expression in most of the behaviors occurs in pulses of varying initiation times and durations. This implies that information transfer during differentiation occurs in cascading waves of gene expression culminating in the permanent turning on of certain genes after ~80h. Each behavior is enriched in specific biological processes, so that physiological remodeling proceeds in a characteristic order---signal transduction, translation and mRNA processing, metabolism, and, ultimately, myeloid phenotypic processes. The sharp transition at 8h corresponds to the completion of transcriptional and translational remodeling and the initiation of metabolic remodeling; the one at 80h corresponds to the elicitation of myeloid phenotypes. Our analysis shows that differentiation relies upon a series of transient, rapid, and complex gene regulatory events and highlights the importance of profiling it at a high temporal resolution.

overall_design: CUT&RUN during the differentiation of a mouse cell-line, PUER, into macrophages. CUT&RUN was performed on undifferentiated PUER cells and 48 hrs after tamoxifen (OHT) treatment using PU.1, H3K4me3, and IgG antibodies.

first: Andrea

last: Repele

first: Joanna

last: Handzlik

first: Nimasha

last: Samarawickrama

first: Trevor

last: Long

first: Sunil

last: Nooti

first: Veena

last: Potluri

first: Yen Lee

last: Loh


title: CD109 is dynamically expressed in endothelial and endocardial subpopulations during heart development, modulates endothelial cell behavior in vitro, but is not required for cardiovascular morphogenesis

status: Public on May 03 2026

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: CD109 encodes a GPI-linked glycoprotein that acts as a signaling modulator in the TGF-β pathway. CD109 has emerged in several genome-wide association studies as linked to coronary artery disease, myocardial infarction, and angina pectoris. Heterozygous loss-of-function mutations in CD109 have also been reported in patients with congenital heart defects, suggesting potential developmental relevance, though CD109 has never been investigated in the context of cardiovascular development. We previously identified Cd109 upregulation in murine atrioventricular valves undergoing myxomatous degeneration following a reduction of epicardial-derived cells. Here, we characterize Cd109 expression in the murine cardiovascular system and assess its function during development using in vitro and in vivo approaches. We found that Cd109 is strongly expressed in the endothelium of the coronary vasculature and in an endocardial-derived subpopulation in the atrioventricular valves. This expression persists through key stages in cardiovascular development. Western blotting and immunostaining confirm endothelial expression in heart and lung tissues. siRNA knockdown of CD109 in primary human endothelial cells led to dysregulation of vascular development pathways and decreased tube formation capacity. We generated Tie2Cre;Cd109fl/fl mice, eliminating Cd109 expression from heart and lung tissues without overt morphological consequences. Together, these results establish Cd109 as a useful marker of coronary vasculature in the heart and indicate that endothelial lineage-specific deletion of Cd109 does not cause gross morphological defects during cardiac development. The transcriptional and functional changes observed in endothelial cells in vitro suggest that additional studies will be necessary to define contexts in which Cd109 influences vascular biology.

overall_design: RNA-seq profiling of Human Umbilical Vein Endothelial Cells (HUVECs) 72h after transfection with siRNA targeting CD109 or transfection with a scramble control.

first: Andrew

last: Harvey

first: Andy

last: Wessels


title: Transient epigenetic changes promote cardiomyocyte differentiation of the subcutaneous adipose stromal vascular fraction

city: Kanazawa

first: Shinichiro

last: Takashima

address: 13-1 Takara-machi

department: Cardiovascular Medicine

institute: Kanazawa University

summary: Introduction: The subcutaneous adipose-tissue-derived stromal vascular fraction (Sa-SVF) contains stem/progenitor cells that rarely transdifferentiate into beating cardiomyocytes. Previously, we developed a culture protocol in which adult murine inguinal Sa-SVF cells reproducibly transdifferentiate into beating cardiomyocyte-like cells (beating CMs) without any specific induction in the primary culture. However, the mechanism underlying the differentiation of the Sa-SVF toward the cardiac lineage is unclear. Methods: To identify a key regulator of cardiac differentiation, we investigated sequential changes in global gene expression profiles of Sa-SVF cells during primary culture. Sa-SVF cells were isolated from adult murine inguinal subcutaneous fat pads and cultured using our beating CM induction method. At six time points during primary culture, total RNA was extracted and subjected to RNA-sequencing and quantitative polymerase chain reaction analysis. Results: Beating CMs appeared on day 14. Of 14,574 prefiltered genes, 749 showed significant expression changes (153 upregulated and 596 downregulated, > 2-fold) between days 7 and 14, coinciding with the appearance of beating CMs. Gene ontology analysis highlighted histone deacetylase (HDAC)-associated genes, expression of which was transiently suppressed during the period when cardiac sarcomere-related genes and the transcription factor Mef2c were upregulated. Treatment with an HDAC inhibitor increased cardiac troponin T expression on day 28. Furthermore, treatment of Mef2c-transduced Sa-SVF cells with an HDAC inhibitor markedly augmented cardiac troponin T expression (18-fold vs. control). Conclusions: We identified transient epigenetic modulation—particularly suppression of class II HDACs—as a key driver of Sa-SVF transdifferentiation into cardiomyocytes. These findings provide a mechanistic basis and a potential combinational strategy to enhance SVF-based cardiac regenerative approaches.

overall_design: Bilateral inguinal subcutaneous adipose tissues without lymph nodes, weighing approximately 500 mg, were obtained from female C57BL/6J mice (age 8–12 weeks). The Sa-SVF cells were isolated as described previously. Briefly, the tissues were digested using a Tumor Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany) in serum-free Dulbecco’s modified Eagle’s medium (DMEM)/F-12 (Thermo Fisher Scientific, Waltham, MA, USA) for 30 min at 37°C using gentleMACS (Miltenyi Biotec). The digested tissue was thoroughly pipetted approximately 10 times in DMEM supplemented with 10% fetal bovine serum (FBS) (F7524, Sigma-Aldrich, St. Louis, MO, USA), filtered through a 100-μm nylon mesh, and then centrifuged at 400× g for 5 min. After washing with DMEM/F-12 with FBS and centrifugation, the cell pellet was resuspended in BD Pharm Lyse Lysing Buffer (BD Biosciences, Franklin Lakes, NJ, USA) and incubated for 5 min to lyse red blood cells. After a further round of centrifugation, the cell pellet was filtered through a 35-μm mesh and centrifuged at 400× g for 5 min; then, the Sa-SVF cells were resuspended in culture medium. Sa-SVF cells were counted using a TC20 automated cell counter (Bio-Rad Laboratories, Hercules, CA, USA) and seeded on a standard uncoated tissue culture plate (Nunc) (Thermo Fisher Scientific) in minimal growth medium (GM) consisting of Iscove’s Modified Dulbecco’s Medium (IMDM; I3390, Sigma-Aldrich), 10% fetal bovine serum (FBS), 2 mmol/L L-glutamine (Wako, Osaka, Japan), 100 units/mL penicillin, 100 μg/mL streptomycin, and 0.1 mmol/L 2-mercaptoethanol (StemSure) (Wako) at 5000 live cells/cm2, and then cultured under standard conditions (37°C with 5% CO2). To examine temporal changes in gene expression, we performed RNA-Seq analysis of Sa-SVF cell groups, from which total RNA was collected at days 0, 3, 7, 14, 21, and 28 of primary culture. Additionally, the Sa-SVF cell group at day 28 was also passaged and cultured for 28 days to collect total RNA as the P1 SaSVF group.

first: Yusuke

last: Shinjo

first: Soichiro

last: Usui

first: Masayuki

last: Takamura


title: Transcriptome profiling of USP40-silenced mouse podocytes

city: Shinagawa-ku

first: Kunio

last: Kawanishi

state: Tokyo

address: 1-5-8 Hatanodai

institute: Showa Medical University

summary: USP40 is a deubiquitinating enzyme implicated in podocyte cytoskeletal organization and cellular homeostasis. To investigate the transcriptional consequences of USP40 depletion, conditionally immortalized mouse podocytes were transfected with two independent USP40-targeting siRNAs (siRNA#1 and siRNA#2) or a non-targeting control siRNA. Three independent biological replicates were prepared for each condition. Total RNA was extracted 48 hours after transfection, followed by poly(A)+ RNA enrichment and strand-specific library preparation. Paired-end RNA sequencing (2 × 36 bp) was performed on an Illumina NextSeq 500 platform, generating two FASTQ files (R1 and R2) per sample. Sequence reads were aligned to the Mus musculus reference genome (GRCm39), and gene-level raw read counts were generated. Differential expression analysis was conducted using DESeq2, and genes with adjusted p-value < 0.1 and |log2 fold change| > 0.3 were considered differentially expressed. To ensure biological robustness, downstream analyses focused on genes commonly altered in both independent siRNA-mediated knockdowns. This dataset provides insight into USP40-dependent transcriptional reprogramming toward an injury-prone, cytoskeleton-remodeling state in podocytes.

overall_design: Immortalized mouse podocytes were transfected with either control siRNA (NC) or two independent USP40-targeting siRNAs (s105625: siRNA#1; s105626: siRNA#2). Each condition was prepared in biological triplicate (n = 3 per group), resulting in nine independent RNA-seq libraries. RNA was isolated 48 hours after transfection. Poly(A)+ RNA was enriched and used for strand-specific library construction. Libraries were sequenced in paired-end mode (2 × 36 bp) on an Illumina NextSeq 500 platform. Raw reads were processed and aligned to the Mus musculus genome (GRCm39), and gene-level count matrices were generated for downstream analysis.

first: Naoki

last: Mikami

first: Kunimasa

last: Yan


title: Multi-omic analysis reveals molecular subtypes with distinct immunological phenotypes in SLE [EM-Seq]

city: Indianapolis

first: Helen

last: Masson

address: 893 S Delaware St.

institute: Eli Lilly and Company

summary: Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease characterized by variability in clinical manifestations and underlying molecular mechanisms. To investigate this heterogeneity, we performed integrative multi-omic profiling—including epigenomic (EM-seq), transcriptomic (RNA-seq), and proteomic (Olink) analyses—on whole blood samples from over 700 SLE patients enrolled in two Phase III clinical trials. Using this approach, we identified three stable molecular endotypes of SLE, providing a framework for understanding disease subtypes and informing precision medicine strategies.

overall_design: EM-seq epigenomic profiling was performed on whole blood samples from patients with systemic lupus erythematosus (SLE) enrolled in two Phase III clinical trials: BRAVE-I (NCT03616912) and BRAVE-II (NCT03616964), as well as from 84 healthy control subjects.

first: David

last: Gemperline

first: Christoph

last: Preuss

first: Ernst

last: Dow


title: Bulk RNA sequencing study of iGCB day3 cells to investigate differences between Eif3e cg1cre knockout B cells and control  B cells

city: xiamen

first: Lianghua

last: Lin

state: Fujian

address: Xiang An Nan Lu 4221

institute: 生命科学学院

summary: To obtain a larger number of Eif3e-deficient B cells induced by cg1cre, we utilized an in vitro germinal center B cell (iGCB) culture system. By day 3 of culture, we harvested abundant YFP+ Eif32-deficient B cells and their corresponding control cells. RNA-seq comparison revealed that Eif3e-deficient B cells upregulated some co-stimulatory molecules, including Cd80 and Icam1. GO enrichment analysis showed that upregulated genes were primarily associated with ribosome-related pathways, while downregulated genes were mainly enriched in lipid metabolism. The upregulation of co-stimulatory molecules may confer Eif3e-deficient B cells with the capacity to promote CD4+ T cell activation.

overall_design: Three biological replicates each for cKO and control groups were included, with naïve B cells derived from individual mice. The cells were cultured for 3 days with 40LB cells irradiated at 120 Gy in 1640 complete medium supplemented with IL-4. YFP+ cells (indicating cg1cre expression) were sorted for RNA-seq analysis.

first: Pengda

last: Chen

first: Jiazhen

last: Wang

first: Xinyong


title: Effect of CST3 knockout on gene expression in THP-1-derived macrophages

city: Changzhou

first: Jie

last: Zhao

state: Jiangsu

address: No.68 Gehu Road

institute: The Third Affiliated Hospital of Nanjing Medical University

summary: To systematically investigate the biological role of CST3 in macrophages, we performed RNA-seq on THP-1-derived macrophages from wildtype (CST3+/+) and CST3 knockout (CST3-/-) backgrounds. Comparative transcriptomic analysis revealed differential expression of genes involved in inflammatory response upon CST3 loss. These findings provide a comprehensive resource for understanding the molecular mechanisms by which CST3 regulates macrophage phenotype and function, with potential implications for inflammatory diseases and immune modulation.

overall_design: RNA-seq profiling of THP-1-derived macrophages from wildtype (CST3+/+) and CST3 knockout (CST3-/-) genotypes, with three biological replicates per genotype.


title: Multi-omic analysis reveals molecular subtypes with distinct immunological phenotypes in SLE [RNA-Seq]

overall_design: RNA-seq transcriptomic profiling was performed on whole blood samples from patients with systemic lupus erythematosus (SLE) enrolled in two Phase III clinical trials: BRAVE-I (NCT03616912) and BRAVE-II (NCT03616964), as well as from 84 healthy control subjects.

first: James

last: Scherschel


title: Single-cell sequencing study of splenocytes and YFP+ B cells to investigate differences between Eif3e cg1cre knockout mice and control mice

summary: To gain insights into the cellular mechanisms underlying the lymphoproliferative disorder developed in cKO mice, we performed single cell RNA-seq (scRNA-seq) analysis of YFP+ and total splenocytes from cKO and control mice at the age of 2 months, when lymphocyte activation and proliferation had not yet become obvious.Through our study, we found that Eif3e-deficient B cells are impaired in their development into GCB and PC, becoming blocked at the pre-GCB stage. Additionally, all B cells exhibited high expression of MHC-II. Among CD4+ T cells, the TFH cell population was significantly expanded in cKO mice and showed high expression of IL4. Based on the early-stage phenotype of this mouse model, we hypothesize that Eif3e-deficient B cells promote IL4 expression in CD4+ T cells, which in turn stimulates upregulation of MHC-II on all B cells. The increased MHC-II further enhances CD4+ T cell activation, forming a positive feedback loop.

overall_design: For each batch, spleens from 2-3 cKO or control mice (2 months old) were pooled. Single-cell sequencing was then performed on sorted total splenocytes and YFP+ cells.

first: Chao

last: Huang

first: Yunjie

last: Zhang


title: Combined DNA and RNA profiling refines prognostic stratification independent of therapeutic actionability in cholangiocarcinoma

city: Montpellier

first: Simon

last: Cabello-Aguilar

address: Avenue du doyen Gaston Giraud

country: France

institute: CHU Montpellier

summary: Background Cholangiocarcinoma (CCA) exhibits marked biological heterogeneity. While genomic profiling identifies targetable alterations such as FGFR2 fusions and IDH1 mutations, transcriptomic analyses reveal distinct immune, proliferative and mesenchymal profiles. How these genomic and transcriptomic features jointly influence clinical outcomes remains unclear. Methods We performed integrated DNA and RNA profiling in 62 patients with intrahepatic and extrahepatic CCA treated at a single tertiary center. Targeted DNA sequencing assessed single-nucleotide variants, copy-number alterations, and microsatellite instability. Extended RNA sequencing evaluated gene fusions and pathway-level transcriptomic subtypes. Associations with progression-free survival (PFS) and overall survival (OS) were examined. Results Among 58 DNA-profiled tumors, the most frequent alterations were TP53 (43.1%) and KRAS (29.3%), followed by IDH1 (10.3%, restricted to intrahepatic CCA). Actionable alterations (IDH1, FGFR2 fusions, ERBB2 amplification, microsatellite instability-high) were detected in 25% of cases and associated with longer overall survival (67.5 vs 20.8 months; p=0.0004), consistent with benefit from matched therapies rather than intrinsic tumor biology. RNA profiling identified five transcriptomic subtypes: Immune (21%), Proliferative (18%), Mesenchymal (42%), Immune-Proliferative (8%), and Unclassified (11%). KRAS-TP53 co-mutation was the strongest adverse prognostic factor (38.1 vs 13.2 months; p=0.0004). The Mesenchymal subtype was associated with shorter PFS (5.9 vs 17.9 months; p=0.045) in patients treated with chemotherapy ± immunotherapy but did not significantly affect OS. Conclusions Integrated genomic and transcriptomic profiling refines prognostic stratification in cholangiocarcinoma independent of therapeutic actionability. KRAS-TP53 co-mutation and the Mesenchymal transcriptomic subtype represent independent high-risk markers detectable on routine FFPE tissue. These features complement actionable alterations and may inform patient selection and clinical trial design.

overall_design: Targeted RNA-seq

first: Julie

last: Vendrell

first: Inès

last: Dalmon

first: Jacques

last: Colinge

first: Eric

last: Assenat

first: Jérôme

last: Solassol