title: Oncohistone H3.3K27M-driven CREB5/ID1 Axis Mediates the Malignant Cell States of Diffuse Intrinsic Pontine Glioma (DIPG) [ATAC-seq]

overall_design:
To investigate the DNA accessibility impact of CREB5. The ATAC-seq experiments were conducted in WT, CREB5 KD DIPG17 cells.
To investigate the DNA accessibility impact of ABBV-075, the ATAC-seq experiments were conducted in DIPG17 cells treated with DMSO and ABBV-075.


title: Oncohistone H3.3K27M-driven CREB5/ID1 Axis Mediates the Malignant Cell States of Diffuse Intrinsic Pontine Glioma (DIPG) [CUT&Tag]

status: Public on Feb 03 2025

city: Beijing

first: Qiaoran

last: Xi

address: Haidian District

department: School of Life Sciences

country: China

institute: Tsinghua University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Diffuse intrinsic pontine glioma (DIPG), an exceptionally lethal pediatric cancer with limited treatment options, is characterized by relentless proliferation and differentiation arrest, primarily influenced by H3K27M oncohistones. This study unveils that ID1 activation occurs independently of BMP signaling in H3.3K27M/ACVR1WT DIPG subtype. ID1 inhibition promotes cell differentiation and apoptosis in DIPG. Additionally, we discover the intricate regulation of ID1 tied to the lineage-specific transcription factor CREB5—an oncogenic contributor hindering differentiation in the H3.3K27M subtype of DIPG. The SWI/SNF complex is identified as a co-regulator of CREB5, further promoting tumorigenesis. Intriguingly, H3.3K27M oncohistones act as a trigger for CREB5 overexpression, facilitating the formation of super-enhancer promoter loops. Moreover, our research highlights the potent anti-tumor effect of ABBV-075 in treating DIPG. In essence, this study elucidates the oncohistone-driven H3.3K27M/CREB5/ID1 axis, providing insights into the malignant cellular state within a DIPG subtype and offering potential therapeutic avenues for this devastating pediatric cancer.

overall_design: The CUT&Tag experiments were conducted in WT, CREB5 KD, H3.3K27M KD DIPG17 cells and WT, H3.3K27M OE PPC cells. The markers performed by CUT&Tag methods in DIPG/PPC cells included CREB5, H3.3K27M, BRG1, H3K9me2, H3K27ac, and H3K27me3.

first: Wei

last: Zhou


title: NLRP3-mediated glutaminolysis regulates microglia in Alzheimer’s disease [ATAC-seq]

city: La Jolla

first: Johannes

last: Schlachetzki

address: 9500 Gilman Drive

country: USA

institute: UCSD

summary: Activation of the NLRP3 inflammasome has been implicated in the pathogenesis of Alzheimer’s disease (AD), via the characterised release of IL-1β and ASC specks. However, whether NLRP3 was involved in pathways beyond this remained unknown. Here we show that loss of NLRP3 influences glutamine/glutamate-related metabolism and increases expression of microglial Slc1a3, which was associated with enhanced mitochondrial and metabolic activity. The generation of α-ketoglutarate during this process impacted cellular function including more significant clearance of Aβ peptides, epigenetic and gene transcription changes. This pathway is conserved between murine and human cells. Critically, we can mimic this effect pharmacologically using NLRP3-specific inhibitors, but only with chronic NLRP3 inhibition. Together, these data demonstrates a new role for NLRP3, where it can modulate mitochondrial and metabolic function, with important downstream consequences for the progression of AD.

overall_design: ATAC-seq of wild type (C57BL/6N genetic background) and Cias1-knockout mice (named Nlrp3-/-; Millennium Pharmaceuticals)

first: Róisín

last: McManus

first: Christopher

last: Glass

first: Eicke

last: Latz

first: Michael

last: Heneka


title: Isoform Usage as a Distinct Regulatory Layer Driving Nutrient-Responsive Metabolic Adaptation (Monkey-Pacbio)

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

type: Expression profiling by high throughput sequencing

summary: This study outlines the landscape of isoform usage modulations across major metabolic organs in both mice and monkeys, spanning diverse metabolic states. Our in-depth analysis identify numerous isoform-usage events, intricately influenced by nutrient challenges and largely independent of gene expression regulation. When analysing splicing factor-binding motifs in nutrient-regulated events, HuR emerges as the predominant orchestrator of the isoform network in adipocytes.

overall_design: Monkey full-length Pacbio data to provide more complete transcript information in various tissues.

first: Chaoqun

last: Cai

middle: W

last: Teo

first: Kai

middle: S

last: Chin

first: Li

last: Qiang

first: Dan

last: Xu

first: Lei

last: Sun


title: Profiling of chromatin features during naive to formative ESC differentiation [CUT&Tag]

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

department: Urology

institute: UCSF

summary: We performed CUT&Tag for various chromatin features during the naive to formative ESC differentiation.

overall_design:
Two replicates derived from independent cultures were collected per chromatin feature and cellular state (naive and formative)
Please note that *merged.cpm.bw was generated from both rep1 and rep2 samples, and is linked to the corresponding rep1 sample records.

first: Deniz

last: Goekbuget

first: Ryan

last: Boileau


title: Profiling replication timing in WT, MLL3KO and MLL3/4dKO cells during naive to formative ESC differentiation [Bio-Repli-seq]

summary: We performed BioRepli-seq for WT, MLL3KO and MLL3/4dKO ESCs the naive to formative ESC differentiation.

overall_design: Three replicates derived from independent cultures were collected per genotype and cell state (naive and formative)


title: Isoform Usage as a Distinct Regulatory Layer Driving Nutrient-Responsive Metabolic Adaptation

summary: Transcriptome modulation is essential for metabolic adaptation to nutrient environments. However, the role of isoform usage, a crucial transcriptome component, is not yet fully understood. This study outlines the landscape of isoform usage modulations across major metabolic organs in both mice and monkeys, spanning diverse metabolic states. Our in-depth analysis identifies numerous isoform-usage events, intricately influenced by nutrient challenges and largely independent of gene expression regulation. Comparative analyses of mice and monkeys highlight hundreds of conserved isoform events that exhibit consistent responses to nutrient challenges across species and correlate with human metabolic traits. When analysing splicing factor-binding motifs in nutrient-regulated events, HuR emerges as the predominant orchestrator of the isoform network in adipocytes, which is validated using an adipose tissue-specific knockout and an Ap2-promoter-driven transgenic mouse model. In summary, our results offer a comprehensive perspective on isoform usage in metabolic regulation, setting a platform for future functional inquiries.

sample_organism:
Macaca fascicularis
Mus musculus

platform_organism:
Macaca fascicularis
Mus musculus

overall_design: Refer to individual Series


title: Brain pericytes and perivascular fibroblasts are stromal progenitors with dual functions in cerebrovascular regeneration after stroke

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

country: Germany

institute: University Medicine Greifswald

summary: Functional revascularization is key to stroke recovery and requires remodelling of blood vessels, around which is located the brain’s only stromal compartment. Stromal progenitor cells (SPC) form a functional grouping of cells critical for tissue regeneration following injury in many organs, yet their identity in the brain remains elusive despite implications in neovascularization and scar formation. Here we show that the perivascular niche of brain SPCs includes pericytes, venular smooth muscle cells and a distinct population of perivascular fibroblasts, that together help regenerate the cerebral microvasculature following stroke. The ischemic injury triggers amplification of pericytes and perivascular fibroblasts in the infarct region where they associate with endothelial cells inside a reactive astrocyte border. Fate-tracking of Hic1+ SPCs uncovers a transient functional and transcriptional phenotype of stroke-activated pericytes and perivascular fibroblasts, where both populations remain segregated, displaying dichotomous angiogenic and fibrogenic profiles. In the adult brain, pericytes and perivascular fibroblasts are therefore distinct subpopulations of stromal progenitors that coordinate revascularization and scar formation after injury.

overall_design: BioProject accession: PRJNA608615; SRA Study accession (temporary): SUB6996815

first: Louis

middle: P

last: Bernier

first: Jasmin

middle: K

last: Hefendehl

first: Wilder

middle: R

last: Scott

first: Lin Wei

last: Tung

first: Coral-Ann

last: Lewis

first: Hesham

last: Soliman

first: Lasse

last: Dissing-Olesen

first: Jan

last: Hofmann

first: David

last: Guo

first: Murphy

last: DeMegilo

first: Fabio

middle: M

last: Rossi

middle: T

last: Underhill

first: Brian

middle: A

last: MacVicar


title: A key role of PIEZO2 mechanosensitive ion channel in adipose sensory innervation [bulk RNA-seq]

status: Public on Feb 02 2025

first: Yu

last: Wang

address: 10550 N. Torrey Pines Rd.

institute: Scripps Research

summary: Compared to the well-established functions of sympathetic innervation, the role of sensory afferents in adipose tissues remains less understood. Recent work revealed the anatomical and physiological significance of adipose sensory innervation; however, its molecular underpinning remains unclear. Here, using organ-targeted single-cell RNA sequencing, we identified the mechanoreceptor PIEZO2 as one of the most prevalent receptors in fat-innervating dorsal root ganglia (DRG) neurons. Selective PIEZO2 deletion in fat-innervating neurons led to molecular alternations in adipose tissue similar to DRG ablation. Conversely, a gain-of-function PIEZO2 mutant shifted the adipose phenotypes in the opposite direction. These results indicate that PIEZO2 plays a major role in the sensory regulation of adipose tissues. This discovery opens new avenues for exploring mechanosensation in organs not traditionally considered mechanically active, such as the adipose tissues, and therefore sheds light on the broader significance of mechanosensation in regulating organ function and homeostasis.

overall_design: A unilateral retrograde AAV injection expressing Cre was administered into the iWAT of PIEZO2f/f or PIEZO2GOF f/f male mice to knock out PIEZO2 or express the PIEZO2 GOF mutant in fat-innervating DRGs. Mice were then maintained on a chow or high-fat diet (HFD) for three weeks before tissue harvesting.

first: Yunxiao

last: Zhang

first: Verina

middle: H

last: Leung

first: Saba

last: Heydari Seradj

first: Li

last: Ye

first: Ardem

last: Patapoutian


title: ATF3 regulates hepatic ApoA4 upon metabolic stress

city: Baltimore

first: Michael

last: Wolfgang

state: MD

address: 855 N. Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: Johns Hopkins University School of Medicine

summary: The liver plays essential roles in maintaining systemic glucolipid homeostasis under ever changing metabolic stressors.  Metabolic dysregulation can lead to both adaptive and maladaptive changes that impact systemic physiology.  Here we examined disparate genetic and environmental metabolic stressors and identified Apolipoprotein A4 (ApoA4) as a circulating protein upregulated in liver-specific knockouts for Carnitine Palmitoyltransferase 2 and Pyruvate Carboxylase. We found this upregulation to be exacerbated by fasting and high fat or ketogenic diets.  Unique among these models was a concomitant increase in Activating Transcription Factor 3 (Atf3).  Liver-specific overexpression of Atf3 resulted in increased ApoA4 expression in a sex-dependent manner.  To understand the requirement of Atf3 to metabolic stress, we generated liver-specific Atf3, Cpt2 double knockout mice.  These experiments demonstrated the requirement for Atf3 in the induction of ApoA4 mRNA, ApoA4 protein, and serum triglycerides that were also sex dependent.  These experiments reveal the roles of hepatic Atf3 and ApoA4 in response to metabolic stress in vivo.

overall_design: RNA-seq on whole livers was performed to investigate differentially regulated genes between 24hr fasted livers of Atf3;Cpt2 liver-specific DKO mice, Cpt2 liver-specific knockout mice, and control mice. Liver-specific knockouts were generated by crossing floxed lines to and albumin-Cre transgenic mouse line.

first: Jasmine

last: Encarnacion


title: Traffic Jam activates the Flamenco piRNA cluster locus and the Piwi pathway to ensure transposon silencing and Drosophila fertility

city: BOSTON

first: NELSON

middle: C

last: LAU

state: MA

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Flamenco (Flam) is the most prominent piRNA cluster locus expressed in Drosophila ovarian follicle cells, and it is required for female fertility to silence gypsy/mdg4 transposons. To determine how Flam is regulated, we used promoter-bashing reporter assays in OSS cells to uncover novel enhancer sequences within the first exons of Flam. We confirmed the enhancer sequence relevance in vivo with new Drosophila Flam deletion mutants of these regions that compromised Flam piRNA expression and lowered female fertility from activated transposons. Our proteomic analysis of proteins associated with these enhancer sequences discovered the transcription factor Traffic Jam (TJ). Tj knockdowns in OSS cells caused a decrease in Flam transcripts, Flam piRNAs, and multiple Piwi pathway genes. A TJ ChIP-seq analysis from whole flies and OSS cells confirmed TJ binding exactly at the enhancer that was deleted in the new Flam mutant as well as at multiple Piwi pathway gene enhancers. Interestingly, TJ also bound the Long Terminal Repeats of transposons that had decreased expression after Tj knockdowns in OSS cells. Our study reveals the integral role TJ plays in the on-going arms race between selfish transposons and their suppression by the host Piwi pathway and the Flam piRNA cluster locus.

overall_design: Small RNAs and total RNAs were sampled from Drosophila mutant strains where we generated new deletions in the Flamenco promoter region.  We also sequenced small RNAs and long RNAs from Drosophila OSS cells that were treated with siRNAs to knockdown Piwi, TJ and Ci genes.  Lastly, we performed ChIP-seq against the TJ transcription factor from crosslinked OSS cells, and we performed Cut&Run on the histone marks H3K9me3 and H3K4me3 from OSS cells after siRNA knockdown of siTJ and siPiwi.

first: Austin

last: Rivera

first: Jou-Hsuan

last: Lee

first: Shruti

last: Gupta

first: Linda

last: Yang

first: Raghuveera

last: Goel

first: Joseph

last: Zaia

first: Nelson

last: Lau


title: RNA-Seq profiles of pancreatic adenocarcinoma PANC-1 and osteosarcoma U2OS cells with Pin1 knocking down

city: Chengdu

first: Ying

last: Tong

state: Sichuan

address: 29 Wangjiang Road

department: College of life science

institute: Sichuan University

summary: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) mediates conformational conversion of protein substrates to trigger the modulation of protein phosphorylation status. Pin1 was knockdown in the pancreatic adenocarcinoma cell PANC-1 and osteosarcoma cell U2OS. The expression profiles of them were compared to explore the key features regulated by Pin1.

overall_design: The protein levels of Pin1 were knocked down in PANC-1 and U2OS cells with three biological replicates. RNAs were sequenced on an Illumina Novaseq platform. Transcriptomic profilings were compared to analyze the differentially expressed genes.

first: Yuanyuan

last: Dong

first: Juan

last: Long

first: Jiaxing


city: New York

first: Alexander

last: Nectow

state: New York

address: 630 W 168th St., Physicians and Surgeons

department: Medicine

institute: Columbia University

summary: Hunger is a fundamental drive, evolutionarily hard-wired to ensure that an animal has sufficient energy to survive and reproduce. Just as important as knowing when to eat is for an animal to know when not to eat. Here, using spatially resolved, single cell translational phenotyping and ensemble-level molecular profiling, we characterize a small population of neuropeptidergic neurons in the brainstem’s dorsal raphe nucleus (DRN) and describe how they regulate appetite. Together, this work identifies a likely conserved cellular mechanism that transforms diverse neurohumoral signals into a key behavioral output.

overall_design: Molecular profiling of brainstem peptidergic neurons using viral TRAP (vTRAP) in tandem with high-throughput RNA sequencing.

first: Srikanta

last: Chowdhury


title: Pharmacological Modulation of BMAL1 Alters Circadian Dynamics and the Macrophage Immune Response

city: Oxford

first: Laura

last: Bailey

address: Radcliffe Department of Medicine

department: Oxford Centre for Diabetes, Endocrinology and Metabolism

country: United Kingdom

institute: University of Oxford

summary: The master transcription factor BMAL1-CLOCK is crucial for orchestrating rhythmic gene expression and governing circadian rhythms.  Pharmacological manipulation of this central circadian regulator requires accessible protein cavities and selective compounds. By targeting BMAL1 through a resident cavity in its PAS-B domain, we demonstrate that the small-molecule Core Circadian Modulator (CCM) penetrates and substantially expands this pocket. Biochemical and cellular analyses validate CCM's target engagement selectivity, enabling direct access to BMAL1's transcriptional activities. CCM induces dose-dependent changes in PER2-Luc macrophage oscillations and selectively modifies expression patterns of circadian controlled genes. In activated macrophages, CCM modulates BMAL1-CLOCK controlled inflammatory and phagocytic pathways to promote their downregulation.  Our findings demonstrate the feasibility of directly targeting BMAL1-CLOCK as a strategy for circadian regulation and targeting circadian-regulated processes

overall_design: To investigate the specificity and effects of pharmacological manipulation of Bmal1, bone-marrow derived macrophages from both myeloid cell specific Bmal1-KO mice and littermate controls were treated with CCM. The effect of inflammation was monitored: this was done under both basal and stimulated conditions.

first: David

last: Ray


title: TOP2A inhibition and its cellular effects related to cell cycle checkpoint adaptation pathway

status: Public on Feb 01 2025

city: Darmstadt

first: Maria

last: Arroyo Lopez

state: Hessen

address: Schnittspahnstr.

department: Biology

institute: Technical University of Darmstadt

summary: In this study, we investigate the G2 checkpoint activated by chromosome entanglements, the so-called Decatenation Checkpoint (DC), which can be activated by TOP2A catalytic inhibition. Specifically, we focus on the spontaneous ability of cells to bypass or override this checkpoint, referred to as checkpoint adaptation. Some factors involved in adapting to this checkpoint are p53 and MCPH1. Using cellular models depleted of p53 or both p53 and MCPH1 in hTERT-RPE1 cells, we analyzed cell cycle dynamics and adaptation, segregation defects, apoptosis rate, and transcriptional changes related to prolonged exposure to TOP2A inhibitors. Our findings reveal that cell cycle dynamics are altered in MCPH1-depleted cells compared to control cells. We found that MCPH1 depletion can restore the robustness of the DC in a p53-negative background. Furthermore, this research highlights the differential effects of TOP2A poisons and catalytic inhibitors on cellular outcomes and transcriptional profiles. By examining the different mechanisms of TOP2A inhibition and their impact on cellular processes, this study contributes to a deeper understanding of the regulation and physiological implications of the DC and checkpoint adaptation in non-carcinogenic cell lines.

overall_design: Human hTERT RPE-1 cells WT and MCPH1 KO were subjected to different treatments: untreated (NT) (control, only DMSO), or ICRF193 (catalytic TOP2A inhibition). 12 hours treatments. Total RNA was extracted and used for library preparation. The same samples were subjected to cell cycle profiling by FACs.

last: Arroyo

first: Maria Angeles

last: Fernandez-Mimbrera

first: Elena

last: Gollini

first: Anna

last: Esteve-Codina

first: Antonio

last: Sanchez

first: Juan Alberto

last: Marchal Ortega


title: Isoform Usage as a Distinct Regulatory Layer Driving Nutrient-Responsive Metabolic Adaptation (RIP-seq)

first: Jia

last: Li

overall_design: RNA Immunoprecipitation Sequencing (RIP-seq) of Elavl1(HuR) in adipocyte cell under different nutrient conditions

first: Chaoqun

last: Cai

first: Wei

last: Teo

first: Kai

last: Chin

first: Yadanar

last: Naing

first: Shengren

last: Song

first: Franklin

last: Nelson

first: Li

last: Qiang

first: Dan

last: Xu

first: Lei

last: Sun


title: Isoform Usage as a Distinct Regulatory Layer Driving Nutrient-Responsive Metabolic Adaptation (RNA-seq)

overall_design: RNA-seq data reveals HuR as a pivotal regulator in meatabolic controls


title: Fibroblast-derived osteoglycin promotes alveolar epithelial cell repair

city: Groningen

first: Reinoud

last: Gosens

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

country: Netherlands

institute: University of Groningen

summary: There is an increasing need for pharmacological treatments that target defective epithelial repair in chronic diseases, such as chronic obstructive pulmonary disease. The mesenchymal niche plays a major regulatory role in guiding epithelial progenitor cell activation during repair. We persuaded that the secreted factors involved in this interaction hold potential as drug targets. In this study, we utilized a proteomics-guided drug discovery strategy, leveraging the secretome of lung fibroblasts, to uncover drug targets affecting epithelial progenitor behavior. Using lung organoids, we identified several ligands with regenerative potential, of which the matrix protein osteoglycin (OGN) surprisingly had the most profound effect. RNA sequencing revealed that OGN promoted alveolar epithelial type II cell differentiation, whilst increasing reactive oxygen species detoxification, reducing senescence, and enhancing growth factor-mediated fibroblast- epithelial crosstalk. In accordance with this OGN protein expression was reduced in damaged lung tissue of COPD patients and in smoke-exposed mice. Additionally, we found an active fragment of OGN comprising the leucine-rich repeat regions 4-7 to have comparable regenerative potential in regulating lung organoid formation. The active fragment of OGN ameliorated elastase-induced lung injury in precision-cut lung slices (PCLS) and improved lung function in mice. These findings identify lung fibroblast-derived OGN as a matrix protein supporting alveolar epithelial growth and its active fragment as a promising therapeutic target for epithelial cell repair in individuals with accelerated tissue damage.

overall_design: Mouse lung organoids (primary EpCAM+ cells co-cultured with CCL206 fibroblasts) were used to study epithelial growth and differentiation. Organoids exposed to recombinant OGN (10 ug/ml), MRC5-derived extracellular vesicles (EVs) and MRC5-derived soluble factors (SFs) for 72 hours were resorted into EpCAM+ and CCL206 fractions, and subjected to RNA-sequencing.

first: Luke

last: van der Koog

first: Henderik

last: Frijlink

first: Anika

last: Nagelkerke


title: Anaerobic respiration of host-derived methionine sulfoxide protects intracellular Salmonella from the phagocyte NADPH oxidase

city: Aurora

first: Andrés

last: Vázquez-Torres

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

summary: We report the changes in transcriptional landscape that occur under anaerobic conditions in the absence of a DMSO reductase in Salmonella enterica subsp. enterica serovar Typhimurium strain 14028s. By comparing the transcriptome of the parental, wild-type Salmonella to the transcriptome of a ∆dmsABC strain, we identified that there was a significant upregulation of SPI-2 genes in the ∆dmsABC strain.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: Salmonella strains (parental, wild-type and a ∆dmsABC strain) grown aerobically overnight in LB broth at 37°C were diluted to ~2 x 10^8 cells/ml in MOPS-CAA and cultured anaerobically for 6 h at 37°C. Cultures were then pelleted and total RNA was extracted.

first: Ju

last: Kim

first: Alyssa

last: Margolis


title: ChIP-seq of trascription factors after SMARCA2/4 degrader treatment

city: South San Francisco

first: Tomasz

last: Włodarczyk

state: California

address: 1 DNA Way

institute: Genentech

summary: Transcription factors (TFs) and transcriptional coregulators represent an emerging and exciting class of targets. By quantifying target gene modulation, gene regulatory networks (GRNs) delineate disease biology and evaluate pharmacological agents targeting these regulators. However, none of the existing methods are explicitly designed to measure the effects of perturbations in which TF expression is decoupled from its activity. We present Epiregulon, a method that constructs GRNs from single-cell ATAC and RNA data for accurate prediction of TF activity. Our weight estimation, based on co-occurrence of TF expression and chromatin accessibility, avoids erroneous inflation of TF activity as seen with TF expression only approaches. Furthermore, our utilization of ChIP-seq data expands inference to include transcriptional coregulators lacking defined motifs. Our extensive network of regulators facilitates identification of cell-state specific interaction partners. Using Epiregulon, we uncover divergent cell fate transitions of prostate cancer cells driven by NKX2-1 and GATA6 expression. We accurately predicted the effects of AR inhibition across various drug modalities. Finally, Epiregulon was able to infer the context-dependent activity of a chromatin remodeler lacking a defined motif sequence and recapitulate the unique etiologies of prostate cancer. By mapping out the network of key regulators across a multitude of perturbations, Epiregulon can accelerate the discovery of new therapeutics targeting transcription factors.

overall_design: MDA-PCa-2b and DU145 were treated with DMSO or 100 uM SMARCA2_4.1 (a SMARCA2/4 degrader) for 24 hours. SMARCA4, AR, FOXA1 were profiled by ChIP-seq  in MDA-PCa-2b cells while SMARCA4, FOSL1 and TEAD1 were profiled by ChIP-seq in DU145 cells

first: Xiaosai

last: Yao

first: Xiaofen

last: Ye

first: Minyi

last: Shi


title: Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

city: Boston

first: Martha

middle: L.

last: Bulyk

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics

institute: Brigham and Women's Hospital

summary: Transcription factors (TFs) control gene expression by interacting with DNA and cofactors to regulate transcription. Human TF genes produce multiple protein isoforms with altered DNA binding domains, effector domains, and other protein regions. The global extent to which this results in functional differences between TF isoforms of the same gene remains unknown. Here, we systematically tested 693 isoforms of 246 TF genes, assessing DNA binding, protein binding, transcriptional activation, subcellular localization, and condensate formation. Compared to the reference isoform, two-thirds of alternative TF isoforms exhibit differences in their molecular activities, which often cannot be predicted from sequence alone. We observed two primary categories of alternative TF isoforms: “rewirers” and “negative regulators”, both of which are associated with differentiation and cancer. Our results support a model wherein the relative expression levels of and interactions between TF isoforms add an understudied layer of complexity to gene regulatory networks, demonstrating the importance of isoform-aware characterization of TF functions and providing a rich resource for further studies.

overall_design: 5 full-length TF isoforms belonging to 2 TF genes were assayed by protein binding microarrays (PBM) as part of the above work.

first: Kaia

last: Mattioli

first: Elisabeth

last: Rothman

first: Sabrina

last: Phanor

first: Sachi

last: Inukai

first: Anisa

last: Prasad

middle: L


title: A Novel Microglia-Specific Transcriptional Signatures Correlates with Behavioural Deficits in Neuropsychiatric Lupus (NP-SLE)

city: Chicago

first: Deborah

last: Winter

state: IL

address: 240 E. Huron Street, M300

institute: Northwestern University

summary: Systemic lupus erythematosus (SLE) can present with neuropsychiatric manifestations, collectively termed NP-SLE. This study identifies a microglia-specific transcriptional signature in mouse models of NP-SLE. Through RNA-seq analysis of microglia and brain-infiltrating macrophages, we uncover an 18-gene 'NP-SLE signature' and its correlation with behavioral deficits. We also observe enrichment of genes associated with disease-associated microglia (DAM), which have been implicated in neurodegenerative diseases. These findings suggest a critical role for microglia-intrinsic mechanisms in the onset of NP-SLE and provide new insights into the cellular and molecular pathways driving this disease.

overall_design: Bulk RNA sequencing was performed on microglia and macrophages isolated by fluorescence-activated cell sorting (FACS) from brains of wild-type (WT - Casp8flox) and Caspase-8 Removed CD11c-specific Overactive MyD88 (CReCOM - CD11cCre Casp8flox) mice at young (5-6 months) and old (11-12 months) time points.

first: Carla M.

last: Cuda

first: Deborah R.


title: Unique CD8+ T Cell Priming by Antigen Presenting Plasmacytoid Dendritic Cells Compared to Conventional Dendritic Cells

city: Aarhus

first: Juan Luis

last: Garcia-Rodriguez

address: Høegh-Guldbergs Gade 10

department: Biomedicine

country: Denmark

institute: Aarhus University

summary: Plasmacytoid dendritic cells (pDCs) play a crucial role in orchestrating immune responses, especially against viral infections, and have traditionally been well recognized for their ability to produce type I and type III interferons. However, recent discoveries reveal pDCs to be heterogeneous with more complex functions that include antigen uptake, processing, and presentation. We investigated the antigen cross-presentation ability of pDCs and their role in CD8+ T cell priming, a subject of ongoing debate. Utilizing a novel culturing system of CD8+ T cells and autologous pDCs derived from human blood circulating CD34+ hematopoietic stem and progenitor cells (cHSPCs), we demonstrate that pDCs can efficiently prime CD8+ T cells through cross-presentation, thereby contributing to their expansion and cytotoxic activity. The pDCs’ antigen presentation ability is comparable to that of monocyte-derived dendritic cells (moDCs), which are traditionally known for their efficient antigen presentation capacity. Bioinformatic analysis of the primed CD8+ T cells to uncover their transcriptomic profile following priming by pDCs versus moDCs, revealed distinct genetic signatures, indicating that pDCs prime CD8+ T cells differently than cDCs. These findings challenge the traditional view of pDCs as mere IFN-producing cells, highlighting their significant role in antigen presentation and T cell activation.

overall_design: CD8+ T cells sorted after co-cultured with cHSPC-pDCs and moDCs stimulated with TLR7 or TLR4 agonist, respectively, and subsequently incubated with or without antigen

first: Renée

last: van der Sluis

first: Martin

last: Jakobsen


title: Acquired resistance to immunotherapy by physical barriers with cancer cell–expressing collagens in non–small cell lung cancer

city: Chengdu, Cihna

first: Xaingyu

last: Pan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

summary: Drug resistance is the principal challenge of cancer therapies, including recently developed immunotherapy. More and more popular use of immunotherapy, especially treatments with immune checkpoint inhibitors (ICIs), witnesses explosively increasing cases of both primary and acquired immunotherapy resistance. While primary resistance has been extensively studied, mechanisms underlying acquired resistance of immunotherapy are less understood. Here we reported that tumor cells could develop acquired resistance to ICI treatment through self-built collagen-containing physical barriers in non-small cell lung cancer (NSCLC). We found that tumor cells expressed high levels of multiple collagen genes, including COL3A1 and COL6A1, and were fully covered with collagen fibers. COL3A1 formed a castle-like structure of a cluster of tumor cells and prevented the infiltration of T cells, while COL6A1 seemed to be an armor-like structure of each tumor cell and protected them from attack by cytotoxic T cells. Genetic or pharmaceutic disruption of these collagens, by warfarin, a commonly used medicine, significantly reversed the acquired resistance. Thus, our data reveal an unprecedented tumor cell-intrinsic mechanism, mediated by collagen-containing physical barriers, of acquired immunotherapy resistance, which immediately suggests a treatment option for patients.

overall_design: sc-RNAseq in immunotherapy- sensitive+veh (n=2), sensitive+anti-PD1 (n=2), resistant+veh (n=2), resistant+anti-PD1 (n=2), resistant dKO+veh (n=2), resistant dKO+anti-PD1 (n=2), resistant + anti-PD1+veh (n=1) and resistant + anti-PD1+warfarin (n=1) mouse NSCLC groups.

first: Manli

last: Wang

first: Xiangyu

first: Yu

last: Liu

first: Chong

last: Chen


overall_design: Bulk RNAseq in mouse normal lung organoids, NSCLC organoids, immunotherapy-sensitive and resistant NSCLC organoids.


title: STING activation improves T-cell-engaging immunotherapy of acute myeloid leukemia

city: Munich

first: Marion

last: Subklewe

address: Feodor-Lynen Straße 25

institute: LMU - Gene Center Munich

summary: T-cell recruiting bispecific antibodies (BsAbs) are in clinical development for relapsed/refractory acute myeloid leukemia (AML). Despite promising response rates, early clinical trials have failed to demonstrate durable responses. Here we investigated whether activation of the innate immune system through stimulator of interferon genes (STING) can enhance target-cell killing by a BsAb targeting CD33 (CD33 BiTE® molecule). Indeed, we show that cytotoxicity against AML mediated by the CD33 BiTE molecule AMG 330 can be greatly enhanced when combined with the STING agonist 2',3'-cyclic GMP–AMP (cGAMP). We used invitro cytotoxicity assays, immunoblotting, transcriptomic analyses, and extensive CRISPR–Cas9 knockout experiments to investigate the enhancing effect of cGAMP on the cytotoxicity of AMG330 against AML. Mechanistically, activated T cells prime target AML cells to STING activation through their effector cytokines interferon-gamma (IFNγ) and tumor necrosis factor (TNF), leading to increased production of typeI interferons and induction of interferon-stimulated genes. This feeds back to the T cells, leading to a further increase in effector cytokines and an overall cytotoxic T-cell phenotype, contributing to the beneficial effect of cGAMP in enhancing AMG330-mediated lysis. As such, we establish a key role for IFNγ in AMG 330-mediated cytotoxicity against AML cells, as well as in rendering AML cells responsive to STING agonism. Here, we propose to improve the efficacy of CD33-targeting BsAbs by combining them with a STING agonist.

overall_design: HL-60 and human T cells from three different healthy donors were co-cultured for 8 h in the presence of AMG 330 ± cGAMP, and separated by FACS before subjecting them to RNA-sequencing. Dataset shows gene expression data for T cells across all conditions (cBiTE, cBiTE+cGAMP, AMG330, AMG330+cGAMP) and donors for every mapped gene following demultiplexing, mapping, filtering, normalization across conditions and variance-stabilizing-transformation by zUMIs and in R

first: Andreas

last: Linder

first: Daniel

last: Nixdorf

first: Ignazio

last: Piseddu

first: TengTeng

last: Xu

first: Gunnar

last: Kuut

first: Rebekka

last: Endres

first: Veit

last: Bücklein

first: Johann

last: de Graaff

first: Thomas

last: Carell

first: Roman

last: Kischel

last: Hornung


title: A key role of PIEZO2 mechanosensitive ion channel in adipose sensory innervation [scRNA-seq]

city: La Jolla

overall_design: To identify the sensory neuron cell types innervating adipose tissues, DRGs were dissected from male mice that received CTB488 injections into iWAT and CTB647 injections into eWAT. DRGs from spinal levels T10 to L6 were collected, dissociated, and subjected to FACS sorting to isolate 488+, 647+, and double-negative populations. Sorted cells were processed using the 10x Genomics platform, with samples pooled from 16 mice.

first: Yunxiao

last: Zhang

first: Verina

last: H. Leung

first: Saba

last: Heydari Seradj

first: Li

last: Ye

first: Ardem

last: Patapoutian


title: ChIP-seq data processing and relative and quantitative signal normalization for Saccharomyces cerevisiae

city: Seattle

first: Toshio

last: Tsukiyama

address: 1100 Fairview Ave N

institute: Fred Hutch Cancer Center

summary: Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) is a widely used technique for genome-wide analyses of protein-DNA interactions. This protocol provides a guide to ChIP-seq data processing in Saccharomyces cerevisiae, with a focus on signal normalization to address data biases and enable meaningful comparisons within and between samples. Designed for researchers with minimal bioinformatics experience, it includes practical overviews and refers to scripting examples for key tasks, such as configuring computational environments, trimming and aligning reads, processing alignments, and visualizing signals. This protocol employs the sans-spike-in method for quantitative ChIP-seq (siQ-ChIP) and normalized coverage for absolute and relative comparisons of ChIP-seq data, respectively. While spike-in normalization, which is  semiquantitative, is addressed for context, siQ-ChIP and normalized coverage are recommended as mathematically rigorous and reliable alternatives.

overall_design: S. cerevisiae ChIP-seq profiling of Hho1 and Hmo1 was performed in two independently derived strains (biological replicates; Hho1: yTT6336 and yTT6337; Hmo1: yTT7750 and yTT7751), with samples collected at three distinct cell cycle stages: G1, G2/M, and quiescence (Q). The HHO1 and HMO1 genes were separately tagged with a 3xFLAG epitope, including flexible linkers (2L-3FLAG), generating HHO1-2L-3FLAG and HMO1-2L-3FLAG strains. As there is no indication that the tag compromises the function of either Hho1 or Hmo1, these strains are labeled "WT" (wild type) in file names. Spike-in chromatin from Schizosaccharomyces pombe was incorporated into the immunoprecipitation reactions to facilitate normalization; the S. pombe spike-in strain (Sphc821) contains abp1-3FLAG.

first: Kris

middle: G

last: Alavattam

first: Bradley

last: Dickson

first: Rina

last: Hirano

first: Rachel

last: Dell


title: Physiological stress drives the emergence of a Salmonella subpopulation through ribosomal RNA regulation

city: Rehovot

first: Roi

last: Avraham

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

summary: Bacteria undergo cycles of growth and starvation, to which they must adapt swiftly. One important strategy for adjusting growth rates relies on ribosomal levels. While high ribosomal levels are required for fast growth, their dynamics during starvation remain unclear. Here, we analyzed ribosomal RNA (rRNA) content of individual Salmonella cells using Fluorescence In-Situ Hybridization (rRNA-FISH), and measured during nutrient limitation a dramatic decrease in rRNA numbers only in a subpopulation, resulting in a bimodal distribution of cells with high and low rRNA content. During nutritional upshifts the two subpopulations were associated with distinct phenotypes. Using a transposon screen coupled with rRNA-FISH, we identified two mutants, DksA and RNase I, acting on rRNA transcription shutdown and degradation, that abolished the formation of the subpopulation with low rRNA content. Our work identifies a bacterial mechanism for regulation of ribosomal bimodality that may be beneficial for population survival during starvation.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: To identify the genetic factors driving ribosomal bimodality and the formation of 16Shigh and 16Slow subpopulations, we generated a saturated genome-wide library of S.Tm mutants via random Tn5 transposition. We grew the transposon mutant library in LB medium to the transition phase, stained for 16S rRNA-FISH and analyzed by flow cytometry. 16Shigh and 16Slow subpopulations were separately sorted and analyzed by Transposon insertion site sequencing (TIS).

first: Camilla

last: Ciolli Mattioli

first: Kfir

last: Eisner

first: Aviel

last: Rosenbaum

first: Mengyu

last: Wang

first: Andre'

last: Rivalta

first: Ariel

last: Amir

first: Ido

last: Golding


title: Effects of GABP knockdown on the transcriptome of macaque fibroblast cells

city: Nagoya

first: Junfeng

last: Chen

state: 23 - 愛知県

address: Nagoya University

country: Japan

institute: Nagoya University

summary: We identified a total of 2,058 GABP-regulated genes (1,067 up-regulated and 991 down-regulated genes in the GABP knockdown cells) with the threshold of Padj < 0.05 and Fold change > 1.5.

overall_design: To investigate the regulations of GABP of macaque transcriptome, we examined the effects of siRNA knockdown of GABPA and GABPB1 in the macaque fibroblast cells.

first: Takashi

last: Yoshimura


title: Endocrine islet beta-cell subtypes with differential function are derived from biochemically distinct embryonic endocrine islet progenitors that are regulated by maternal nutrients

city: Nashville

first: Guoqiang

last: Gu

state: TN

address: 2213 Garland Avenue

department: Cell and Developmental Biology

institute: Vanderbilt University

type: Methylation profiling by high throughput sequencing

summary: Endocrine islet beta cells comprise heterogenous cell subsets. Yet the origin, stability, and physiological significance of these subsets remain largely unknown. Using combinatorial cell lineage tracing, scRNA-seq, and DNA methylation analysis, we show here that embryonic islet progenitors with differential gene expression and DNA methylation produce stable beta-cell subtypes of different function and viability in adult mice. Differentially expressed genes, including the Myt transcription factors, voltage-gated channels, and Ca2+-sensor synaptotagmins, contribute to the functional differences of these subtypes. Maternal overnutrition, a major diabetes risk factor, reduces the proportion of endocrine progenitors of the better-functionality beta-cell subtype. Intriguingly, the gene signature that defines mouse beta-cell subtypes can reliably divide human cells into two populations, with the proportion of better-functionality beta cells reduced in diabetic donors. These results establish that some beta-cell subtypes are determined via DNA methylation in embryonic islet progenitors, which is regulated by diabetes-causing maternal factors. The implication is that modulating DNA methylation in islet progenitors can be explored to improve beta-cell function in the prevention and therapy of diabetes.

overall_design: Mice with a genotype of Myt1cCre; Ngn3nCre; Ai9 (MNA) will be derived via routine crossing.  This allows the activation of islet progenitors that co-express Ngn3 and Myt1 to be labeled with tdTomato permanently. When MNA mice were at postnatal day 2 (P2) and 2-months, they will be used for islet isolation. Islets were then washed with Ca2+/Mg2+ free HBSS and dissociated into single cells (~3-5 minutes). They were then used for InDrop RNAseq.

first: Verda

last: Agan

first: Emily

last: Hodges

first: Yanwen

last: Xu

first: Ruiying

last: Hu


title: Expression of lymphoid enhancer-binding factor 1 in cancer-associated fibroblasts mediates tumor growth and transdifferentiation toward squamous cell carcinoma in human breast cancer

city: Tokyo

first: Takehiro

last: Yasukawa

address: 2-1-1 Hongo, Bunkyo-ku

institute: Juntendo University

summary: Cancer-associated fibroblasts (CAFs) play a significant role in human breast cancer as a major stromal component. While their role in promoting cancer proliferation and malignancy through interaction with cancer cells in the tumor microenvironment is known, the exact mechanisms behind this interaction are not fully understood. Our study reveals that lymphoid enhancer-binding factor 1 (LEF1), a central transcription factor for Wnt/β-catenin signaling, is expressed in experimentally generated tumor-promoting CAFs (exp-CAFs) as well as in CAFs from breast cancer patients, particularly those with a poor prognosis. Notably, LEF1-expressing CAFs are prevalent in the stroma of squamous cell carcinoma (SCC), an aggressive metaplastic breast cancer subtype with a limited understanding of its development. To investigate the functional importance of LEF1 expression in CAFs, we depleted LEF1 in the exp-CAFs and subcutaneously implanted them along with breast ductal carcinoma MCF10DCIS.com cells into immunodeficient mice. Depleting LEF1 resulted in reduced xenograft tumor growth, accompanied by decreased cancer-cell proliferation and angiogenesis in the tumors. Additionally, we observed a significant reduction in the expression of SCC markers p40 (ΔNp63) and cytokeratin 5/6 in the xenograft tumors when LEF1 was depleted in the exp-CAFs. Furthermore, we identified 13 genes, none of which are established downstream genes of the Wnt/β-catenin pathway, that exhibit expression patterns similar to LFE1 in our cultured fibroblasts. In summary, our findings suggest that LEF1 expression contributes to the tumor-promoting abilities of breast CAFs and that LEF1-expressing CAFs may drive transdifferentiation toward SCC, possibly through a pathway independent of the canonical Wnt/β-catenin signaling.

overall_design: Comparison of RNA expression between 544 cells with shCtrl and those with LEF1-targeting shRNAs (shLEF1-1, -3, and -9)

first: Hiroya

last: Okazaki

first: Akira

last: Orimo


title: Spatial transcriptomics on treatment-naïve pancreatic ductal adenocarcinoma (PDAC) patients

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

summary: To investigate the spatial distribution of different cell types within the tumor microenvironment in PDAC, we performed Visium spatial transcriptomics (10X Genomics) on FFPE samples from five treatment-naïve PDAC patient tissues.

overall_design: Visium spatial transcriptomics (10X Genomics) was performed on FFPE tissues following the Visium Spatial Gene Expression protocol (CG000407). Sequencing was conducted on a NextSeq 2000 (Illumina).

first: Jimin

last: Min

first: Kimal

middle: I

last: Rajapakshe

first: Guangsheng

last: Pei

first: Paola

last: Guerrero

first: Linghua


title: Mapping the Genetic Interaction Network of PARP inhibitor Response

city: Princeton

first: Jia

last: Ling

state: NJ

address: Carl Icahn Laboratory, South Drive

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: Genetic interactions have long informed our understanding of the coordinated proteins and pathways that respond to DNA damage in mammalian cells, but systematic interrogation of the genetic network underlying this system has yet to be achieved. Towards this goal, we measured 147,153 pairwise interactions among genes implicated in PARP inhibitor (PARPi) response with and without exposure to PARPi. By applying an analytical framework we defined differential genetic interactions at scale, identified novel interactions belonging to different interaction categories, and revealed PARP1-trapping as a common mode of sensitization of PARPi across genetic backgrounds. We uncovered  the minimally characterized gene, AUNIP, while not essential for genome stability under normal conditions, plays a key role in repairing PARPi induced DNA damage together with FA pathway genes and is antagonized by the BRCA1-A complex. Our work thus establishes a foundation for mapping differential genetic interactions in mammalian cells and provides a comprehensive resource for future studies of DNA repair and PARP inhibitors.

overall_design: The GI library of dual-sgRNA expression constructs were cloned and transduced into a well-validated K562 CRISPRi cell line, with or without exposure to niraparib, collecting cells at the beginning of the screen (T0, day of drug treatment) and after ten days of growth (reference or PARPi endpoints). Expression cassettes were isolated and sequenced from each sample to generate counts for each sgRNA pair, from which three metrics of phenotype scores were calculated: reference growth phenotypes (γ), growth phenotypes after PARPi exposure (τ), and PARPi sensitization phenotypes (ρ). Genetic interaction scores and differential genetic interactions were derived from those measurements.

first: Danny

last: Simpson

first: Yangwode

last: Jing

first: Britt

last: Adamson


title: Khdc3 Regulates Metabolism Across Generations in a DNA-Independent Manner

status: Public on Jan 31 2025

first: Matthew

last: Smith-Raska

address: 1300 York Ave.

department: Pediatrics

institute: Weill Cornell Medicine

summary: Genetic variants can alter the profile of heritable molecules such as small RNAs in sperm and oocytes, and in this manner ancestral genetic variants can have a significant effect on offspring phenotypes even if they are not themselves inherited.  Here we show that wild type female mice descended from ancestors with a mutation in the mammalian germ cell gene Khdc3 have hepatic metabolic defects that persist over multiple generations.  We find that genetically wild type females descended from Khdc3 mutants have transcriptional dysregulation of critical hepatic metabolic genes, which persist over multiple generations and pass through both female and male lineages.  This was associated with dysregulation of hepatically-metabolized molecules in the blood of these wild type mice with mutational ancestry.  The oocytes of Khdc3-null females, as well as their wild type descendants, had dysregulation of multiple small RNAs, suggesting that these epigenetic changes in the gametes transmit the phenotype between generations.  Our results demonstrate that ancestral mutation in Khdc3 can produce transgenerational inherited phenotypes, potentially indefinitely.

overall_design: Comparison of hepatic transcriptomes in genetically wild type female mice descended from a  Khdc3-null maternal grandmother (F2 outcross) with wild type female mice with all wild type ancestors (WT).

first: Liana

last: Senaldi


title: Investigate the effect of cardiomyocyte-specific deletion of Trbp in transaortic constriction model in mice

city: Los Angeles

first: Yao Wei

last: Lu

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

summary: Cardiac remodeling in response to disease or tissue damage severely impairs heart function. Therefore, the description of the molecular mechanisms responsible is essential for the development of effective therapies. Trbp (Tarbp2) is a multi-functional RNA-binding protein (RBP) that is essential during heart development but its role in the adult heart and cardiac remodeling are unknown. We generated inducible conditional knockout mice to delete Trbp from cardiomyocytes in young adults (Trbp-cKOs). While Trbp-cKO mice did not display a detectable phenotype, under stress conditions induced by transverse aortic constriction (TAC) pressure overload, they rapidly developed severe heart failure; this was associated with maladaptive cardiac remodeling and increased interstitial fibrosis.

overall_design: Trbp-flox/flox (Trbp-fl/fl) mice were generated as previously described. The alpha-MHC-MerCreMer (αMHC-MCM) transgenic mice were purchased from the Jackson Lab and bred with Trbp-fl/fl mice to obtain Trbp-fl/fl-MCM mice. Tamoxifen (TAM) (30mg/kg) was injected once daily for 5 days by intraperitoneal injection into 4-week-old male Trbp-fl/fl-MCM mice to obtain Trbp cardiomyocyte-specific inducible knockout mice (Trbp-cKO). Corn oil was injected as vehicle control into 4-week-old male Trbp-fl/fl-MCM mice. Trbp-fl/fl male mice were also injected with Tamoxifen (30mg/kg for five consecutive days) to control for the potential side effects of Tamoxifen.

first: Bo

last: Pan

first: Da-Zhi

last: Wang


title: Cancer cells avoid ferroptosis induced by immune cells via fatty acid binding proteins [RNA-seq]

city: Houston

first: Qi

state: TX

address: 7007 Bertner Ave

institute: UT MD Anderson Cancer Center

summary: Abstract Background Cancer creates an immunosuppressive environment that hampers immune responses, allowing tumors to grow and resist therapy. One way the immune system fights back is by inducing ferroptosis, a type of cell death, in tumor cells through CD8+ T cells. This involves lipid peroxidation and enzymes like lysophosphatidylcholine acyltransferase 3 (Lpcat3), which makes cells more prone to ferroptosis. However, the mechanisms by which cancer cells avoid immunotherapy-mediated ferroptosis are unclear. Our study reveals how cancer cells evade ferroptosis and anti-tumor immunity through the upregulation of fatty acid-binding protein 7 (Fabp7).  Methods To explore how cancer cells resist immune cell-mediated ferroptosis, we used a comprehensive range of techniques. We worked with cell lines including PD1-sensitive, PD1-resistant, B16F10, and QPP7 glioblastoma cells, and conducted in vivo studies in syngeneic 129 Sv/Ev, C57BL/6, and conditional knockout mice with Rora deletion specifically in CD8+ T cells, Cd8 cre;Rorafl mice. Methods included mass spectrometry-based lipidomics, targeted lipidomics, Oil Red O staining, Seahorse analysis, quantitative PCR, immunohistochemistry, PPARγ transcription factor assays, ChIP-seq, untargeted lipidomic analysis, ROS assay, ex vivo co-culture of CD8+ T cells with cancer cells, ATAC-seq, RNA-seq, Western blotting, co-immunoprecipitation assay, flow cytometry and Imaging Mass Cytometry.  Results PD1-resistant tumors upregulate Fabp7, driving protective metabolic changes that shield cells from ferroptosis and evade anti-tumor immunity. Fabp7 decreases the transcription of ferroptosis-inducing genes like Lpcat3 and increases the transcription of ferroptosis-protective genes such as Bmal1 through epigenetic reprogramming. Lipidomic profiling revealed that Fabp7 increases triglycerides and monounsaturated fatty acids (MUFAs), which impede lipid peroxidation and ROS generation. Fabp7 also improves mitochondrial function and fatty acid oxidation (FAO), enhancing cancer cell survival. Furthermore, cancer cells increase Fabp7 expression in CD8+ T cells, disrupting circadian clock gene expression and triggering apoptosis through p53 stabilization. Clinical trial data revealed that higher FABP7 expression correlates with poorer overall survival and progression-free survival in patients undergoing immunotherapy.  Conclusions Our study uncovers a novel mechanism by which cancer cells evade immune-mediated ferroptosis through Fabp7 upregulation. This protein reprograms lipid metabolism and disrupts circadian regulation in immune cells, promoting tumor survival and resistance to immunotherapy. Targeting Fabp7 could enhance immunotherapy effectiveness by re-sensitizing resistant tumors to ferroptosis.

overall_design: identify differentially expressed genes in T cells co-cultured with Res_ctrl and Res_ShFabp7 cells

first: Maria Angelica

last: Cortez


title: Ruxolitinib mediated paradox JAK2 hyperphosphorylation is due to the protection of activation loop phosphotyrosines from phosphatases

city: Lübeck

first: Yamil

middle: Abdala

last: Maluje

state: Schleswig- Holstein

address: Ratzeburger Allee 160

department: Institute of Experimental Dermatology

institute: University of Luebeck

summary: Ruxolinitib was approved by the FDA for the treatment of JAK2-V617F positive myelofibrosis. Unexpectedly, treatment of JAK2-V617F expressing cells with ruxolitinib causes paradoxical hyperphosphorylation of JAK2 at Tyr1007/1008 sites. The mechanism of ruxolitinib-induced JAK2 hyperphosphorylation is not well understood. A ruxolitinib-resistant JAK2 variant (V617F+L983F) and a JAK2-V617F kinase dead mutant (JAK2-V617F+K882R) did not show paradox hyperphosphorylation after ruxolitinib treatment indicating that ruxolitinib-mediated JAK2 hyperphosphorylation is mediated by a JAK2 intrinsic mechanism. Native immunocomplexes of JAK2-V617F with an antibody against pTyr1007/1008 could be blocked by the presence of ruxolitinib, although JAK2-V617F was hyperphosphorylated at these sites, suggesting that in the presence of ruxolitinib the JAK2 activation loop is buried within the kinase domain. This stabilization of the activation loop conformation results in the protection of pTyr1007/1008 sites from phosphatases. When JAK2 is in an inhibited conformationally restricted state, the phosphate group of Tyr1007 and Tyr1008 forms an intermolecular interaction with Arg975 and Lys999, respectively. Mutation of Arg975 and Lys999 to Ala reduced the phosphorylation at both Tyr1007/1008 residues, and importantly, ruxolitinib treatment did not lead to JAK2 hyperphosphorylation in these variants. Hyperphosphorylated JAK2 is hyperactive after ruxolitinib dissociation and activates STAT5 target genes PIM2, ID1, and MPL. Our results suggest a novel mode of kinase regulation by modulating kinase activity through conformational changes induced by ruxolitinib.

overall_design:
To identify the functional significance of ruxolitinib-mediated hyperphosphorylation of JAK2-V617F, we performed RNA-seq analysis on Ba/F3 cells treated with vehicle control and ruxolitinib for 6 hours. We also performed RNA-seq analysis on Ba/F3 cells expressing JAK2-V617F treated with CHZ868 for 6 hours compared to vehicle treatment.
We then performed RNA-seq analysis on Ba/F3 cells stably expressing the JAK2-V617F with one hour treatment with 1μm ruxolitinib and ruxolitinib washed out by three times PBS wash and maintained in the presence of RPMI with 10%FBS, 1%pen/stre for 6 hours. We also performed RNA-seq analysis on Ba/F3 cells stably expressing the JAK2-V617F with one hour treatment of 1μm CHZ868 and washed out CHZ868 by three times PBS wash and maintained in the presence of RPMI with 10%FBS, 1%pen/stre for 6 hours.
We compare the gene sets that are significantly up-regulated only in ruxolitinib wash compared to CHZ868 washout samples to identify the target genes that are due to JAK2 hyperphosphorylation in the presence of ruxolitinib.

first: Sivahari

last: Gorantla

first: Lorenz

last: Oelschlager

first: Gerin

last: Prince

first: Jasmin

last: Osius

first: Suresh

last: Babu Kolluri

first: Anke

last: Fähnrich

first: Hauke

last: Busch

first: Timo

last: Gemoll

first: Stephanie

last: Fliedner

first: Justus

last: Duyster

first: Nikolas

last: von Bubnoff


title: Human gastric cancer cell line; RNA-seq analysis of SNU-16 clones cells

city: Suzuka

first: Kazuki

last: Kanayama

state: Mie

address: 1001-1 Kishioka

institute: Suzuka University of Medical Science

summary: Chromosomal instability in gastric cancer cells is associated with the amplification of oncogenes that encode receptor tyrosine kinases (RTKs), such as HER2 and FGFR2; such gene amplification varies from cell to cell and manifests as genetic heterogeneity within tumours. The intratumoural genetic heterogeneity of RTK gene amplification causes heterogeneity in RTK protein expression, which has been suggested to be associated with therapeutic resistance to RTK inhibitors; however, the underlying mechanism is not fully understood. Here, we show that extrachromosomal DNA (ecDNA) causes intratumoural genetic heterogeneity in RTKs and drug resistance due to diverse dynamic changes. We analysed the dynamics of FGFR2 and MYC ecDNA in a gastric cancer cell line after single-cell cloning. Similar to those in parental cells, the copy numbers of FGFR2 and MYC in subclones differed significantly between cells, indicating intraclonal genetic heterogeneity. Furthermore, the ecDNA composition differed between subclones, which affected FGFR2 protein expression and drug sensitivity. Interestingly, clone cells that were resistant to the FGFR2 inhibitor AZD4547 presented diverse changes in ecDNA, including chimeric ecDNA, large ecDNA and increased ecDNA numbers; these changes were associated with high expression and rephosphorylation of FGFR2. Conversely, when resistant clone cells were cultured under conditions that excluded AZD4547, the ecDNA status became similar to that of the original clone cells, and the inhibitory effect on cell growth was restored. Our results show that dynamic quantitative and qualitative changes in ecDNA can drive the intratumoural genetic heterogeneity of RTKs and resistance to RTK inhibitors.

overall_design: RNA-seq profiling of SNU-16 clone D7, clone D7 after 72 h of treatment with AZD4547 and clone D7-R#0.

first: Hiroshi

last: Imai

first: Chise

last: Matsuda

first: Eri

last: Usugi

first: Yoshifumi

last: S Hirokawa

first: Masatoshi

last: Watanabe


title: Clonal cell states link gastroesophageal junction tissues, metaplasia, and cancer [Spatial transcriptomics]

city: Philadelphia

first: Sydney

last: Shaffer

state: PA

address: 421 Curie Boulevard

department: Penn Medicine

institute: University of Pennsylvania

summary: Barrett's esophagus is a common type of metaplasia and a precursor of esophageal adenocarcinoma. However, the cell states and lineage connections underlying the origin, maintenance, and progression of Barrett’s esophagus have not been resolved in humans. Here, we performed single-cell lineage tracing and transcriptional profiling of patient cells isolated from metaplastic and healthy tissue. Our analysis unexpectedly revealed that the squamous esophagus and gastric cardia contained cells belonging to common lineages that also included transitional basal progenitor cells; both esophageal and gastric tissues were also related to Barrett's esophagus. Barrett’s esophagus biopsies consisted of multiple clones, with lineages that contained all progenitor and differentiated cell types. In contrast, precancerous dysplastic lesions were initiated by the expansion of a single molecularly aberrant Barrett’s esophagus clone. Together, these findings provide a comprehensive view of the cell dynamics of Barrett's esophagus, linking cell states along the disease trajectory, from its origin to cancer.

overall_design: Performed single-cell lineage tracing and transcriptional profiling of patient cells isolated from metaplastic and healthy tissue.

first: Rodrigo

last: Gier

first: Raúl

last: Reyes Hueros

first: Jiazhen

last: Rong

first: Maureen

last: DeMarshall

last: Bracht

first: Tatiana

last: Karakasheva

first: Amanda

middle: B

last: Muir

first: Gary

last: Falk

first: Nancy

last: Zhang


title: Cancer cells avoid ferroptosis induced by immune cells via fatty acid binding proteins

first: Qi

last: Wang

summary: Cancer creates an immunosuppressive environment that hampers immune responses, allowing tumors to grow and resist therapy. One way the immune system fights back is by inducing ferroptosis, a type of cell death, in tumor cells through CD8+ T cells. This involves lipid peroxidation and enzymes like lysophosphatidylcholine acyltransferase 3 (Lpcat3), which makes cells more prone to ferroptosis. However, the mechanisms by which cancer cells avoid immunotherapy-mediated ferroptosis are unclear. Our study reveals how cancer cells evade ferroptosis and anti-tumor immunity through the upregulation of fatty acid-binding protein 7 (Fabp7).    Methods  To explore how cancer cells resist immune cell-mediated ferroptosis, we used a comprehensive range of techniques. We worked with cell lines including PD1-sensitive, PD1-resistant, B16F10, and QPP7 glioblastoma cells, and conducted in vivo studies in syngeneic 129 Sv/Ev, C57BL/6, and conditional knockout mice with Rora deletion specifically in CD8+ T cells, Cd8 cre;Rorafl mice. Methods included mass spectrometry-based lipidomics, targeted lipidomics, Oil Red O staining, Seahorse analysis, quantitative PCR, immunohistochemistry, PPARγ transcription factor assays, ChIP-seq, untargeted lipidomic analysis, ROS assay, ex vivo co-culture of CD8+ T cells with cancer cells, ATAC-seq, RNA-seq, Western blotting, co-immunoprecipitation assay, flow cytometry and Imaging Mass Cytometry.    Results  PD1-resistant tumors upregulate Fabp7, driving protective metabolic changes that shield cells from ferroptosis and evade anti-tumor immunity. Fabp7 decreases the transcription of ferroptosis-inducing genes like Lpcat3 and increases the transcription of ferroptosis-protective genes such as Bmal1 through epigenetic reprogramming. Lipidomic profiling revealed that Fabp7 increases triglycerides and monounsaturated fatty acids (MUFAs), which impede lipid peroxidation and ROS generation. Fabp7 also improves mitochondrial function and fatty acid oxidation (FAO), enhancing cancer cell survival. Furthermore, cancer cells increase Fabp7 expression in CD8+ T cells, disrupting circadian clock gene expression and triggering apoptosis through p53 stabilization. Clinical trial data revealed that higher FABP7 expression correlates with poorer overall survival and progression-free survival in patients undergoing immunotherapy.    Conclusions  Our study uncovers a novel mechanism by which cancer cells evade immune-mediated ferroptosis through Fabp7 upregulation. This protein reprograms lipid metabolism and disrupts circadian regulation in immune cells, promoting tumor survival and resistance to immunotherapy. Targeting Fabp7 could enhance immunotherapy effectiveness by re-sensitizing resistant tumors to ferroptosis.

overall_design: This study investigates the effects of anti-PD-1 treatment on 344SQ parental (Sen) and anti-PD-1 resistant (Res) tumor cells in vivo. Tumors were treated with either anti-PD-1 or control IgG, and RNA expression profiles were analyzed from four experimental groups.

first: Wang

last: Xiaohong

first: Liu

last: Changgong

last: Xiuping

first: Welsh

last: James

last: Qi

first: Freitas-Cortez

last: MA


title: Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [CTCF-HiChIP-seq]

city: Hershey

first: Suming

last: Huang

address: 500 University Dr.

institute: Penn State College of Medicine

summary: We found NUP98 fusions activate Hoxb-associated lncRNA, HoxBlinc that occupies homeotic/oncogenic topologically associated domain (TAD) boundaries in malignant hematopoiesis. Aberration of HoxBlinc led to recruitment of MLL1 complex and reorganization of homeotic/oncogenicTADs that enhanced chromatin accessibilities and aberrantly activated homeotic/hematopoietic oncogenes defined by Hoxblinc chromatin occupancies in NUP98-PHF23 related murine leukemia cells. Eliminated HoxBlinc in NUP98 fusion-driven leukemic cells resulted in loss of Hoxblinc binding, TAD integrity, recruitment of MLL complex, and MLL driven H3K4me3 and chromatin accessibility within the HoxBlinc defined domain in a CTCF independent manner, leading to inhibiting homeotic/leukemic oncogenes and mitigating NUP98 fusion-driven leukemia in xenografted mouse models. Moreover, overexpression of HoxBlinc in mouse bone marrow hematopoietic compartment developed multiple leukemia resembling NUP98-PHF23 knock-in mice via enhancing HoxBlinc binding and TAD formation to transcriptionally expanding HS/PC and myeloid/lymphoid subpopulations leading to leukemogenesis. Our studies reveal a CTCF independent role of HoxBlinc in leukemic TAD organization and oncogenic gene regulatory networks in NUP98-fusion related leukemia.

overall_design: We have finished the RNA-seq, ATAC-seq, ChIP-seq, ChIRP-seq, HiC-seq, HiChIP-seq for WT and HoxBlinc KO in NUP98-PHF23 related leukemia cell lines and HoxBlinc Transgenic mice bone marrow cells to investigate HoxBlinc function in leukemogenesis. LK cells (Lin- Kit+) and LSK cells (Lin- Sca1+ Kit+) were sorted by FACS from the bone marrow of WT and HoxBlinc transgenic mice for single cell-RNA seq. We also used primary AML patient samples harboring NUP98-HOXA9 fusion for bulk RNA-seq.

first: Karina

last: Hamamoto


title: Resolution of SARS-CoV-2 infection in human lung tissues is driven by CD163+ inflammatory monocytes

city: Galveston

first: Jacquelyn

last: Turcinovic

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

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

overall_design: Refer to individual Series


title: Incomplete repair causes permanent defects in renal medullary structure and function after reversal of urinary obstruction

first: Mark

last: de Caestecker

address: 1161 21st Avenue South

institute: Vanderbilt University Medical Center

summary: Urinary obstruction causes injury to the renal papilla and leads to defects in the ability to concentrate urine which predisposes to progressive kidney injury. However, the regenerative capacity of the papilla after reversal of obstruction is poorly understood. To address this, we developed a mouse model of reversible urinary obstruction which is characterized by extensive papillary injury, followed by a robust regeneration response and complete histological recovery over a 3-month period. However, these mice have a pronounced defect in urinary concentrating capacity. We now show that this is due to permanent changes in the composition, organization, and transcriptional signatures of epithelial, endothelial, and interstitial cell lineages in the papilla. There are persistent inflammatory responses that are also seen in patients with renal stone disease but are associated with cell-specific adaptive responses to the increasingly hypoxic environment of the papilla after reversal of obstruction. Taken together, our analysis of a new model of reversible urinary obstruction reveals that partial repair leads to permanent changes in the structure and function of all of the major cellular compartments in the papilla that include both shared and distinct responses to different types of renal papillary injury in humans and mice.

overall_design: Papillae were dissected at two times points of injury (d28, d84 after R-UUO) and from healthy controls. We pooled 3-4 papilla per sample, and included 4 replicate samples (each with 3-4 papilae per sample) from healthy controls, 4 samples from D28, and 2 samples from D84 after RUUO

first: Vanichapol

last: Thitinee

first: Gonzalez

last: Alex

first: Delgado

last: Rachel

first: Brewer

last: Maya

first: Clouthier

last: Kelly

first: Menshikh

last: Anna

first: Synyder

last: William

first: Rahman

last: Teebro

first: Sander

last: Veronika

first: Yang

last: Haichun

first: Davidson

last: Alan

first: de Caestecker

last: Mark


title: RNA sequencing of HaCaT cells exposed to TNF-α/IFN-γ

city: hangzhou

first: zhiqi

last: xie

address: huzhou street 51

institute: Hangzhou city university

summary: Keratinocytes are one of the major sources of chemokines in skin tissue. Therefore, we used keratinocytes HaCaT exposed to TNF-α/IFN-γ  (10 ng/ml) to construct to establish an in vitro AD model. RNA from the control group and AD model group were performed RNA sequencing and KEGG analysis. The results showed that lots of cytokine-cytokine receptor pathways of HaCaT cells were activated in the AD model. Further analysis showed that chemokine expression was significantly up-regulated in the model group

overall_design: mRNA profiles of HaCaT cells treated with or without TNF-α/IFN-γ  (10 ng/ml) for 48h, n=3

first: Jinjin

last: Shao


title: MFRP in the retina is a molecular hub that organizes the apical membrane of RPE cells by engaging in interactions with specific protein and lipid molecules

city: Irvine

first: Aleksander

last: Tworak

state: CA

address: 837 Health Sciences Rd

department: Ophthalmology

institute: University of California Irvine

summary: Membrane frizzled-related protein (MFRP) is an integral membrane protein present in the retinal pigment epithelium (RPE) and is essential for ocular development and the physiology of the retina. Mutations in MFRP are associated with autosomal recessive non-syndromic nanophthalmos, leading to severe hyperopia and early-onset retinitis pigmentosa. While several preclinical gene augmentation and gene editing trials hold promise for future therapies aimed at stopping degeneration and restoring retinal function, the molecular mechanisms underlying MFRP biology remain largely undefined. Here, we studied the biochemical properties of MFRP and the molecular consequences of its loss in a mouse model. Using transcriptomic and lipidomic approaches, we observed that DHA accumulation constitutes a primary defect in the MFRP-deficient RPE. In biochemical assays, we showed that MFRP undergoes extensive glycosylation and preferentially binds several classes of lipids, including phosphatidylserine and phosphatidylinositol 4-phosphate, as well as several other transmembrane proteins, notably adiponectin receptor 1 (ADIPOR1) and inward rectifier potassium channel 13 (KCNJ13). Moreover, MFRP determines ADIPOR1 and KCNJ13 subcellular localization in the RPE in vivo. This feature is affected upon MFRP deficiency and can be restored by gene therapy approaches. Overall, our observations suggest that MFRP constitutes an important interaction hub within the apical membrane of RPE cells, essential for protein trafficking and subcellular localization within the RPE and lipid homeostasis within the entire retina.

overall_design: RNA-seq profiling of RPE cells from 1 mo wt and retinal degeneration 6 (rd6) mice

first: Krzysztof

last: Palczewski


title: Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [ChIRP-seq]

first: Suming

last: Huang

overall_design: We have finished the RNA-seq, ATAC-seq, ChIP-seq, ChIRP-seq, HiC-seq for WT and HoxBlinc KO in NUP98-PHF23 related leukemia cell lines and HoxBlinc Transgenic mice bone marrow cells to investigate HoxBlinc function in leukemogenesis. LK cells (Lin- Kit+) and LSK cells (Lin- Sca1+ Kit+) were sorted by FACS from the bone marrow of WT and HoxBlinc transgenic mice for single cell-RNA seq. We also used primary AML patient samples harboring NUP98-HOXA9 fusion for bulk RNA-seq.

first: Karina

last: Hamamoto


title: Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [CUT&Run]


title: Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [scRNA-Seq]

first: Huacheng

last: Luo


title: Oligodendroglial precursors orchestrate immune cellular network instigating multiple sclerosis

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

summary: The immunomodulatory cellular network that triggers early inflammation and demyelination, the key steps in multiple sclerosis (MS) pathogenesis remains poorly characterized. Here, we demonstrate that overactivation of the Wnt pathway promotes pathological transformation of oligodendrocyte precursor cells (OPCs) to replicate pathological OPCs in human MS. In mouse experimental autoimmune encephalomyelitis (EAE), pathological OPCs attract CD4+ T-helper 1 (Th1) cells into the spinal cord and the brain through CC-chemokine ligand 4 (CCL4). Th1 cells cooperate with OPCs inducing subpopulation of cytotoxic macrophages that execute early demyelination. Simultaneously, Th1 cells and cytotoxic macrophages upregulate Wnt signaling and CCL4 expression in OPCs, thus exerting positive feedback onto the OPC-immune cascade and establishing a vicious cycle propagating EAE pathogenesis. Breaking this cascade by targeting CCL4 reduces immune cell infiltration, alleviates demyelination, and attenuates EAE severity. Our findings demonstrate a closely coordinated network of OPCs and immune cells therefore providing an alternative insight into MS pathophysiology

overall_design:
To investigate the transcriptomic change in APC knockout oligodendrocyte precursor cells (OPCs) compared to the wild type, OPCs were isolated from Olig2-Cre:Apc-fl/fl mice and their Apc-fl/fl littermate (as wild type control) by immunopanning, cultured with PDGFAA-supplemented media for 3 days, and collected for RNA sequencing.
To investigate the transcriptomic signature of infiltrated cytotoxic macrophage and Th1 in the EAE model, EAE model was established in the Pdgfra-CreER:Apc-fl/fl mice; on day 18 post induction, the spinal cords of the mice were collected, digested, and the resulting single cell suspension was subjected to FACS; the CD11b+Gr-1+NK1.1+ cytotoxic macrophages and the CD4+ Th1 cells were isolated by FACS, and subjected to RNA-sequencing
================================================
On April 28, 2025 the raw files for samples GSM7823493,GSM7823495-GSM7823498 were replaced. Raw data are not available for sample GSM7823494

first: Qi

last: Wang

first: Jianqin

last: Niu


title: Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [Hi-C]


title: Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [RNA-Seq]

summary: We found NUP98 fusions activate Hoxb-associated lncRNA, HoxBlinc that occupies and regulates homeotic/oncogenic topologically associated domain (TAD) in malignant hematopoiesis. Aberration of HoxBlinc led to recruitment of MLL1 complex , altered chromatin landscape (both H3K4me3 and chromatin accessibility), and HOX/homeotic gene activatiion in NUP98-PHF23 fusion driven leukemia and HoxBlinc -Tg models. Conversely, eliminated HoxBlinc in NUP98 fusion-driven leukemic cells resulted in loss of Hoxblinc binding, TAD integrity, recruitment of MLL complex, and MLL driven H3K4me3 and chromatin accessibility within the HoxBlinc defined domain in a CTCF independent manner, leading to inhibiting homeotic/leukemic oncogenes and mitigating NUP98 fusion-driven leukemia in xenografted mouse models. Thus, our studies revealed a CTCF independent role of HoxBlinc in leukemic TAD organization and oncogenic gene regulatory networks in NUP98-fusion related leukemia.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We performed the RNA-seq, ATAC-seq, ChIP-seq, ChIRP-seq, HiC-seq for WT and HoxBlinc KO in NUP98-PHF23 related leukemia cell lines and HoxBlinc Transgenic mice bone marrow cells to investigate HoxBlinc function in leukemogenesis. LK cells (Lin- Kit+) and LSK cells (Lin- Sca1+ Kit+) were sorted by FACS from the bone marrow of WT and HoxBlinc transgenic mice for single cell-RNA seq. We also used primary AML patient samples harboring NUP98-HOXA9 fusion for bulk RNA-seq.


title: Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [ATAC-Seq]


title: Bi-directional neuro-immune communication regulates host defense against helminth infection

city: Hangzhou

first: Heping

last: Xu

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

summary: Emerging studies reveal that neuropeptides play critical role in regulating anti-helminth immune responses, hinting at the potential of intrinsic enteric neurons (iENs) in orchestrating intestinal immunity. However, whether and how the iENs get activated during infection, and whether they engage in a bi-directional communication with the immune cells, remain poorly defined. Here we show that iENs became activated in response to helminth infection. Single-nucleus RNA sequencing of the iENs revealed significant alterations in gene expression in IL-13R+ intrinsic primary afferent neurons (IPANs), including the upregulation of the neuropeptide -CGRP. Using genetic mouse models, we demonstrated that both group 2 innate lymphoid cells (ILC2s) and neuronal IL-13R signaling are indispensable for optimal iEN activation, which subsequently inhibit ILC2 responses and anti-helminth immunity. Together, these results reveal a previously unrecognized bi-directional neuro-immune crosstalk in the intestine.

overall_design: Baf53-cre Sun1-GFP (CTL) mice or Baf53-cre Il13ra1 flox Sun1-GFP (CKO) mice were injected subcutaneously with 500 third-stage larvae (L3) Nippostrongylus brasiliensis (N. brasiliensis)  in 250 μl PBS. Muscularis externa were harvested on day 5 after the infection for nucleus isolation and fluorescence-activated cell sorting (FACS). Then the flow-sorted GFP+ nuclei were pooled for gene expression library and Feature Barcode library construction via using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10×Genomics).

first: Yingsheng

first: Shaorui

last: Liu


title: Seasonal transcriptome atlas of 80 neural and peripheral tissues of male and female non-human primate Macaca mulatta

first: Junfeng

last: Chen

address: Nagoya University

institute: Nagoya University

summary: Rhythms of life on earth are shaped by the seasons. Accordingly, various physiological functions such as hormonal secretion, metabolism, growth, immune function, and reproduction show profound seasonal changes in animals including humans. Morbidity in humans due to cardiovascular disease, influenza, and psychiatric diseases is also seasonally regulated and peaks in winter. However, their underlying molecular bases remain unknown. Non-human primates (NHPs) represent the nearest-to-human alternative and are crucial to understand human physiology and diseases. In this study, we identifed genes that showed seasonal oscillations in the expressions for each of the 80 tissues, including 30 brain regions and 50 peripheral tissues collected every 2 months from male and female NHP rhesus macaques (Macaca mulatta) that were kept under seminatural outdoor conditions. In addition, the seasonal transcriptome partterns can be checked in our web database entitled “Non-Human Primate Seasonal Transcriptome Atlas (NHPSTA)”. The overall study contributes to our understanding of the molecular basis for seasonally regulated physiological mechanisms and provides potential biomarkers and targets for developing novel therapeutic intervention for seasonally regulated diseases.

overall_design: Transcriptome analysis of 80 tissues, including 30 brain regions and 50 peripheral tissues collected every 2 months from male and female NHP rhesus macaques (Macaca mulatta) that were kept under seminatural outdoor conditions.

first: Takashi

last: Yoshimura


title: Human gastric cancer cell line; CGH array analysis of SNU-16 parental and clones cells

first: Kazuki

last: Kanayama

overall_design: Control vs. SNU-16 parental cells, Control vs. SNU-16 clone D7 cells, Control vs. SNU-16 clone E8 cells, Control vs. SNU-16 resitant clone D7 cells, SNU-16 parental cells vs. SNU-16 clone D7 cells, SNU-16 parental cells vs. SNU-16 clone E8, SNU-16 parental cells vs. SNU-16 resistant clone D7 cells. Biological replicates: Control vs. samples 1 replicate, SNU-16 parental cells vs. samples 1 replicate.

first: Hiroshi

last: Imai

first: Chise

last: Matsuda

first: Eri

last: Usugi

first: Yoshifumi

last: Hirokawa

first: Masatoshi

last: Watanabe


title: Gene expession profiles of p16high and p16low stromal cells in PDAC tumor microenvironment

city: Minato City, Tokyo

first: Teh-Wei

address: 4 Chome-6-1 Shirokanedai

institute: IMSUT

summary: We used scRNA-seq analysis to investigate the characteristics and communication of p16high cancer stromal cells in the tumor microenvironment.

overall_design: We conducted the p16CreERT2-tdTomato mice combined with allograft model of PDAC to study the function of p16high stromal cells in tumor microenvironment. The tdTomato-positive and negative stromal cells were collected through FACS and processed for library preparation.

first: Yue

last: Zhang

first: Makoto

last: Nakanishi


title: Neural ensembles that encode nocifensive mechanical and heat pain in mouse spinal cord

city: Solna

first: Patrik

last: Ernfors

address: Biomedicum, Solnavägen 9

department: MBB/Molneuro

country: Sweden

institute: Karolinska Institutet

summary: Pain is an unpleasant experience caused by intense heat or mechanical force. How the spinal cord neural circuits attribute differences in quality of noxious information such as the psychophysically distinct modalities remain unknown. By means of genetic capture, activity manipulation and scRNA sequencing, we identified distinct neural ensembles in the spinal cord encoding mechanical and heat pain. Re-activation or silencing these ensembles potentiated or stopped, respectively, affective but not reflex behaviour without altering pain behaviour to cross stimuli modality. Within ensembles, excitatory neurons encoded quality and a single molecular type of polymodal Gal+ inhibitory neuron type gated affective pain regardless of modality. Following peripheral nerve injury there was a marked circuit-wide molecular perturbation associated with inflammation and the ensembles failed to respect noxious information quality and to resolve allodynia and hypersensitivity in mice. Our results reveal the existence of a spinal representation of cutaneous noxious heat and mechanical stimuli which forms the neural basis of the affective qualities of acute pain perception and that these are under the control of feedforward inhibition by a shared inhibitory neuron type.

overall_design: Mouse spinal cord cells isolated and analyzed using scRNA-seq

first: Mingdong

first: Jussi

last: Kupari

first: Jie

first: Yizhou

last: Hu

first: Kajsa

last: Magnusson

first: Laura

last: Calvo-Enrique

first: Dmitry

last: Usoskin

first: Gioele

last: Albisetti

first: Andrew

middle: D

last: Leavitt

first: Fan

first: Hanns

last: Ulrich Zeilhofer

first: Tomas

last: Hökfelt

first: Malin

last: Lagerström


title: Transcriptome investigation shed light into the role of volatile organic compounds in the growth inhibition of Xanthomonas species

city: Campinas

first: Joaquim

last: Martins Junior

state: SP

address: Rua Giuseppe Maximo Scolfaro 10000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

summary: X. albilineans is one of the most important phytobacteria species which affect sugarcane production. Volatile organic compounds (VOCs) produced by microorganisms may have a noteworthy role in the control of plant diseases. Thus, this study investigated VOC-producing soil bacteria with an antagonistic effect against X. albilineans and evaluated the molecular mechanisms of growth inhibition trigged by the volatile dimethyl disulfide (DMDS). The comparative transcriptomic data of X. albilineans treated with DMDS showed that several metabolic pathways are up-regulated, such as two-component system, flagellar assembly, chemotaxis and bacterial secretion system. Interesting, although the ethanol used as DMDS solvent did not inhibit X. albilineans growth, it triggers a similar gene up-regulation and somehow, the phytopathogen can deal with this harmful compound better than DMDS.

overall_design: Study of the effect of bacterial volatiles on the transcriptome of Xanthomonas albilineans. The RNA-seq experiment was carried out using 3 replicates of X. albilienans treated with the volatile dimethyl disulfide (DMDS), 4 replicates of  X. albilienans treated ethanol (VOC-solvent) and 4 replicates in the control condition (X. albilineans only).

first: Luciane

middle: F

last: Coerini

first: Aline

last: Mulato

last: Martins-Junior

first: Gabriela

last: Persinoti

first: Juliana

middle: V

last: Oliveira


title: Deletion of an evolutionary conserved TAD boundary leads to changes in gene expression, histology and function in mouse testis.

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

summary: Spermatogenesis is a complex process that can be disrupted by genetic and epigenetic changes, potentially leading to male infertility. Recent research has rapidly increased the number of protein coding mutations causally linked to impaired spermatogenesis in humans and mice. However, the role of non-coding mutations remains largely unexplored. As a case study to evaluate the effects of non-coding mutations on spermatogenesis, we first identified an evolutionarily conserved topologically associated domain (TAD) boundary near two genes with important roles in mammalian testis function: Dmrtb1 and Lrp8 . We then used CRISPR-Cas9 to generate a mouse line where 26kb of the boundary was removed including a strong and evolutionarily conserved CTCF binding site. ChIP-seq and Hi-C experiments confirmed the removal of the CTCF site and a resulting increase in the DNA-DNA interactions across the domain boundary. Mutant mice displayed significant changes in testis gene expression, abnormal testis histology, a 35% drop in the estimated efficiency of spermatogenesis and a 28% decrease in daily sperm production compared to littermate controls. Despite these quantitative changes in testis function, mutant mice show no significant changes in fertility. This suggests that non-coding deletions affecting testis gene regulation may have smaller effects on fertility compared to coding mutations of the same genes. Our results demonstrate that disruption of a TAD boundary can have a negative impact on sperm production and highlight the importance of considering non-coding mutations in the analysis of patients with male infertility.

overall_design: We used CRISPR-Cas9 to delete a TAD boundary in mice. Consequences of the deletion were investigated using RNA-seq, ChIP-seq and Capture HiC on testis from three replicataes per genotype.

first: Jake

last: VanCampen

first: Lucia

last: Carbone


title: Single-cell analysis of lung epithelial cells reveals age and cell population-specific responses to SARS-CoV-2 infection in ciliated cells

city: Rochester

first: Raven

middle: M.

last: Osborn

address: 601 Elmwood Ave

department: Microbiology

institute: University of Rochester School of Medicine and Dentistry

summary: In this study, we characterized cell type and age-specific responses to SARS-CoV-2 from primary lung epithelial cells cultured on an air-liquid interface.

overall_design: Gene expression profiling analysis of scRNA-seq data of primary lung epithelial cells from donors of different age groups cultured on air-liquid interface for 4-5 weeks before infected with SARS-CoV-2.  Samples were collected 48 hours post infection.

first: Christopher

middle: S

last: Anderson

first: Justin

last: Leach

first: ChinYi

last: Chu

first: Stephen

last: Dewhurst

first: Thomas

middle: J

last: Mariani

first: Juilee

last: Thakar


title: Notch3 is an asymmetric gene and a modifier of heart looping defects in Nodal mouse mutants

city: Paris

first: Sigolène

middle: M

last: Meilhac

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine, Institut Pasteur

summary: The TGFb secreted factor NODAL is a major left determinant required for the asymmetric morphogenesis of visceral organs, including the heart. Yet, when this signalling is absent, shape asymmetry, for example of the embryonic heart loop, is not fully abrogated, indicating that there are other factors regulating left-right patterning. Here, we used a tailored transcriptomic approach to screen for genes asymmetrically expressed in the field of heart progenitors. We thus identify Notch3 as a novel left-enriched gene and validate, by quantitative in situ hybridization, its transient asymmetry in the lateral plate mesoderm and node crown, overlapping with Nodal. In mutant embryos, we analysed the regulatory hierarchy and demonstrate that Nodal in the lateral plate mesoderm amplifies Notch3 asymmetric expression. The function of Notch3 was uncovered in an allelic series of mutants. In single neonate mutants, we observe that Notch3 is required with partial penetrance for ventricle thickness, septation and aortic valve, in addition to its known role in coronary arteries. In compound mutants, we reveal that Notch3 acts as a genetic modifier of heart looping direction and shape defects in Nodal mutants. Whereas Notch3 was previously mainly associated with the CADASIL syndrome, our observations in the mouse and a human cohort support a novel role in congenital heart defects and laterality defects.

overall_design: Bulk transcriptomic analysis of paired left and right heart fields at E8.5f  in control C57bl6/J male mouse embryos.

first: Tobias

last: Bønnelykke

first: Emeline

last: Perthame

first: Mélanie

last: Parisot

first: Mohammed

last: Zarhrate

first: Christine

last: Bole-Feysot

first: Nicolas

last: Cagnard

first: Audrey

last: Desgrange


title: Loss of ATG7 in Microglia Impairs UPR, Triggers Ferroptosis and Weakens Amyloid Pathology Control [bulk RNA-seq]

status: Public on Jan 30 2025

city: St Louis

first: Zhangying

last: Cai

state: MO

address: 425 S Euclid Ave

institute: Washington University in St. Louis

summary: Microglia impact brain development, homeostasis, and pathology. One important microglial function in Alzheimer’s Disease (AD) is to contain proteotoxic amyloid β (Aβ) plaques. Recent studies reported the involvement of autophagy-related (ATG) proteins in this process. Here we found that microglia-specific deletion of Atg7 in an AD mouse model impaired microglia coverage of Aβ plaques, increasing plaque diffusion and neurotoxicity. Single-cell RNA sequencing, biochemical and immunofluorescence analyses revealed that Atg7 deficiency reduces unfolded protein response (UPR) while increasing oxidative stress. Cellular assays demonstrated that these changes lead to lipoperoxidation and ferroptosis of microglia. In aged mice without Aβ build-up, UPR reduction and increase oxidative damage induced by Atg7 deletion did not impact microglia numbers. We conclude that reduced UPR and increased oxidative stress in Atg7-deficient microglia lead to ferroptosis when exposed to proteotoxic stress from Aβ plaques. However, these microglia can still manage misfolded protein accumulation as they age.

overall_design: Bulk RNA sequencing of FACS-sorted microglia from 20-month-old Atg7-flox Cx3cr1-CreERT2 mice and Atg7-flox littermate controls

first: Shoutang

last: Wang

first: Marco

last: Colonna


title: Loss of ATG7 in Microglia Impairs UPR, Triggers Ferroptosis and Weakens Amyloid Pathology Control [scRNA-seq]

overall_design: scRNA-seq of FACS-sorted microglia from 5-month-old mice of 4 genotypes: WT (Atg7-flox), KO (Atg7-flox; Cx3cr1-CreERT2), 5xFAD WT (Atg7-flox; 5xFAD), and 5xFAD KO (Atg7-flox; Cx3cr1-CreERT2; 5xFAD).


title: ATOH8 confers the vulnerability of tumor cells to ferroptosis by repressing SCD expression [ChIP-Seq]

city: shanghai

first: Huixiang

last: Xiao

state: shanghai

address: pujian road 160

institute: shanghai jiaotong university

summary: Ferroptosis, a non-apoptotic programmed cell death triggered by excessive iron-dependent lipid peroxidation, plays a pivotal role in tumor progression. Significant progress has been made in elucidating the role of transcription factors in the regulation of ferroptosis. Nevertheless, the identification of the key transcription factor responsible for inducing ferroptosis remains elusive. In this study, we discovered that ATOH8 is upregulated in prostate cancer cells treated with the ferroptosis inducer. Overexpression of ATOH8 increased the vulnerability of prostate cancer to ferroptosis, while ATOH8 deletion promotes ferroptosis evasion. Mechanistically, ATOH8 suppresses the transcription of SCD, reducing the synthesis of monounsaturated fatty acids that confer resistance to ferroptosis. Additionally, ATOH8 works in conjunction with the E protein E47 to form a transcriptional repression complex that inhibits SCD transcription. Furthermore, we discovered that EZH2 epigenetically suppresses the expression of ATOH8 through DNA methylation and H3K27 methylation. Interestingly, EZH2 was found to be downregulated in ferroptosis, resulting in an upregulation of ATOH8. Pharmacological inhibition of EZH2 combined with ferroptosis inducer significantly suppresses prostate cancer growth in vitro and in vivo. Together, our findings unveil that EZH2-mediated ATOH8 downregulation promotes ferroptosis evasion and suggest that pharmacological manipulation of EZH2 and ATOH8 is a promising therapeutic strategy for prostate cancer.

overall_design: ChIP-seq for ATOH8 or TCF3 in DU145 cells.

first: Huan

last: Hou

first: Xinxing

last: Du

first: Wenyun

last: Guo