title: 5ɑ-Dihydrotestosterone Upregulates Interferon Signaling in Osteoclast Differentiation During Inflammatory State

city: Rochester

first: Kiana

middle: Lee

last: Chen

state: New York

address: 601 Elmwood Avenue

institute: University of Rochester Medical Center

summary: Rheumatoid arthritis (RA) is characterized by chronic inflammatory erosions and a more prevalent disease in females. In RA, the differentiation of osteoclast precursor cells (OCPs) into bone-resorbing osteoclasts is stimulated by the inflammatory environment, causing significant erosive disease. Notably, androgen, the dominant sex hormone in males, is protective against this inflammation-driven bone loss. To investigate how androgen regulates osteoclastogenesis in an inflammatory state, bone marrow-derived cells were treated with or without androgen in a TNF-mediated osteoclast culture. 5ɑ-dihydrotestosterone (DHT)-treated and vehicle-treated cells were collected, analyzed, and compared with single-cell RNA-sequencing which determined differences in cell populations, gene expression, functional gene ontology, and differentiation.

overall_design: Bone marrow derived cells from a C57BL/6 male mouse were treated with either DHT or vehicle control and grown in an inflammatory osteoclast cell culture system. Cells were collected after 24 hours with RANKL and hTNFɑ stimulation and analyzed with single-cell RNA-sequencing.

first: Michael

last: Christof

first: Gulzada

last: Kulzhanova

first: Chia-Lung

first: Homaira

last: Rahimi


title: Sex determines the Natural Killer cell-mediated immunity against Pancreatic Cancer.

status: Public on Mar 17 2026

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

type: Expression profiling by high throughput sequencing

summary: Pancreatic ductal adenocarcinoma ranks among the most aggressive malignancies and exhibits a higher prevalence and poorer prognosis in male patients. Natural killer cells play a critical role in tumor immunosurveillance by directly recognizing and eliminating tumor cells.  It is well established that females generally mount stronger immune responses than males. The present study aims to answer the question of whether sex has an influence on the NK cell-mediated anti-tumor function in PDAC. To validate our in vitro findings in a physiological context, we employed a syngeneic allograft mouse model.

overall_design: We investigate the in vitro killing efficacy of primary male and female mouse Nk cells on an established PDAC cell line via flow cytometry, RNA sequencing, and live cell imaging. To validate our in vitro findings in a physiological context, we employed a syngeneic allograft mouse model.

first: Arlt

last: Elise

first: Bley

last: Nadine

first: Misiak

last: Danny


title: Excitatory cortical neurons from CDKL5 deficiency disorder patient-derived organoids show early hyperexcitability not identified in neurogenin2 induced neurons [RNA-Seq]

city: Boston

first: Madison

middle: Rose

last: Glass

state: MA

address: 3 Blackfan St

department: Neurobiology

country: USA

institute: Boston Children's Hospital

summary: CDKL5 deficiency disorder (CDD) is a rare developmental and epileptic encephalopathy resulting from variants in cyclin-dependent kinase-like 5 (CDKL5) that lead to impaired kinase activity or loss of function. CDD is one of the most common genetic etiologies identified in epilepsy cohorts. To study how CDKL5 variants impact human neuronal activity, gene expression and morphology, CDD patient-derived induced pluripotent stem cells and their isogenic controls were differentiated into excitatory neurons using either an NGN2 induction protocol or a guided cortical organoid differentiation. Patient-derived neurons from both differentiation paradigms had decreased phosphorylated EB2, a known molecular target of CDKL5. Induced neurons showed no detectable differences between cases and isogenic controls in network activity using a multielectrode array, or in MAP2+ neurite length, and only two genes were differentially expressed. However, patient-derived neurons from the organoid differentiation showed increased synchrony and weighted mean firing rate on the multielectrode array within the first month of network maturation. CDD patient-derived cortical neurons had lower expression of CDKL5 and HS3ST1, which may change the extracellular matrix around the synapse and contribute to hyperexcitability. Similar to the induced neurons, there were no differences in neurite length across or within patient-control cell lines. Induced neurons have poor cortical specification while the organoid derived neurons expressed cortical markers, suggesting that the changes in neuronal excitability and gene expression are specific to cortical excitatory neurons. Examining molecular mechanisms of early hyperexcitability in cortical neurons is a promising avenue for identification of CDD therapeutics.

middle: R

first: Dosh

last: Whye

first: Nickesha C

last: Anderson

first: Delaney

last: Wood

first: Nina R

last: Makhortova

first: Taryn

last: Polanco

first: Kristina H

last: Kim

first: Kathleen E

last: Donovan

first: Gayathri Rajaram

last: Srinivasan

first: Lorenzo

last: Vaccaro

first: Ashish

last: Jain

first: Davide

last: Cacchiarelli

first: Liang

last: Sun

first: Elizabeth D

last: Buttermore

first: Mustafa

last: Sahin


title: NMD-mediated control of Tor influences adaptation to nutrient and temperature conditions in Cryptococcus neoformans

city: Buffalo

first: Sean

last: Duffy

state: NY

address: 955 Main Street

department: Microbiology and Immunology

institute: SUNY at Buffalo

summary: The yeast Cryptococcus neoformans is an opportunistic human pathogen capable of surviving within various environmental conditions. The repertoire of antifungal agents effective in treating cryptococcal infection is limited, necessitating the identification of alternative treatment strategies. Nonsense-mediated decay (NMD) is an RNA decay mechanism that serves as a post-transcriptional regulator of gene expression.  While the absence of NMD in C. neoformans sensitizes cells to the antifungal fluconazole, the mechanism underlying this sensitivity and role of NMD in C. neoformans biology remained unexplored. Using phenotypic analysis and RNA-sequencing analysis, we identify basal dysregulation of thermal- and nutrient-adaptive genes and demonstrate temperature- and/or nutrient-dependent phenotypic suppression of upf1Δ phenotypes, including fluconazole sensitivity and resistance to rapamycin. We determine rapamycin co-treatment also suppresses the upf1Δ fluconazole sensitivity, implicating dysregulation of Tor signaling in phenotypic outcomes when NMD is absent. We then investigate Tor-sensitive signaling in the upf1Δ mutant, finding inhibition of cell wall integrity (CWI) signaling and hyperactivation of the kinase Gcn2, both of which returned to wildtype-like levels by either rapamycin treatment, nutrient limitation, or constitutive thermal stress. These results indicated NMD is required for appropriate regulation of Tor signaling in unstressed conditions and suggested upf1Δ phenotypes are driven in part by Tor hyperactivation. A phenotypic screen of mutants lacking Tor regulators revealed that deletion of the Tor-suppressing IML1 gene recapitulates upf1Δ phenotypes and signaling defects, consistent with Tor hyperactivation. Taken together, our results suggest NMD participates in the regulation of Tor signaling in C. neoformans. Future work will investigate how specific targets of NMD impact Tor signaling and promote fluconazole sensitivity in C. neoformans.

overall_design: RNA-seq profiling of wildtype and upf1 mutant strains in the H99 background grown to mid-log phase at 30°C and 1 hour after a shift to growth at 37°C

first: John

middle: C

last: Panepinto


title: Lcn2 deficiency leads to social impairments independent of maternal immune activation

city: Warsaw

first: Laboratory

last: of Sequencing

state: mazowieckie

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology PAS

summary: Maternal infection during pregnancy is a well-established risk factor for neurodevelopmental disorders (NDDs), yet the underlying molecular mechanisms remain poorly understood. Lipocalin-2 (Lcn2), an innate immune protein that is highly upregulated during infection, also affects neuronal and glial function. This study investigates the role of Lcn2 in shaping brain development, particularly after maternal immune activation (MIA). To mimic maternal infection, pregnant mice received intraperitoneal injections of either lipopolysaccharide (LPS) or saline on embryonic days 16 to 18 to model infection during the second trimester of pregnancy in humans. We first showed that Lcn2 mRNA is expressed in the fetal brain and that MIA significantly upregulates Lcn2 mRNA and protein in the hippocampus and neocortex of both sexes. To assess functional relevance, we employed Lcn2 heterozygous females to generate wild-type and Lcn2 KO offspring from the MIA and control groups. Both female and male offspring underwent a battery of behavioral assays. Lcn2 deletion and MIA independently induced deficits in social behavior and increased repetitive behavior phenotypes relevant to NDDs. However, their combination did not exacerbate these effects, suggesting an occlusion effect. Importantly, the impact of Lcn2 deletion and MIA appeared to be specific to social and repetitive behavior, as no deficits were observed in the learning and memory task.  To investigate potential shared molecular mechanisms, we performed RNA sequencing of the fetal forebrain 4 hours after the final LPS injection. This analysis revealed an overlapping group of differentially expressed genes in the Lcn2 KO and MIA groups, indicating convergence on similar transcriptional pathways that may underlie the observed behavioral phenotypes. These results suggest that while Lcn2 may not mediate the pathological effects of prenatal immune challenge, it plays a critical role in normal brain development.

overall_design: RNA-seq profiling of RNA isolated from the forebrain of WT or Lcn2KO mouse fetuses at E18, four hours after the final of three injections of LPS (40 μg/kg of body weight) or saline administered to Lcn2Het dams.

first: Martyna

last: Pekala

first: Sylwia

last: Zawiślak

first: Sandra

last: Romanis

first: Karolina

last: Nader

first: Aleksandra

last: Cabaj

first: Anna

last: Madecka

first: Alicja

last: Puścian

first: Ewelina

last: Knapska

first: Robert

last: Pawlak

first: Leszek

last: Kaczmarek

first: Katarzyna

last: Kalita


title: Steroid hormone antagonism reduces the rate of aortic rupture and improves survival in a mouse model of Vascular Ehlers-Danlos Syndrome

city: Baltimore

first: Elena

last: MacFarlane

state: Maryland

address: 733 N Broadway St

department: Department of Genetic Medicine

institute: Johns Hopkins

summary: Vascular Ehlers-Danlos syndrome (VEDS) carries a high risk of vascular rupture. In the Col3a1G938D/+ mouse model, the rate of aortic rupture accelerates postnatally, especially in males, concurrently with the rise in androgens. Here we show that this vulnerability is associated with the postnatal transition of the aorta to a non-synthetic state, and that androgen receptor (AR ) antagonism partially reversed this shift, resulting in a non-physiological increase in the expression of extracellular matrix components. Both pharmacological and genetic AR antagonism improved survival in males, while dual AR and mineralocorticoid (MR) inhibition, or selective MR antagonism, reduced the risk of aortic rupture in both sexes. In all major aortic cell types, there was substantial overlap in the transcriptional alterations imposed by AR, MR and dual AR/MR inhibition, suggesting that both AR/MR antagonism and selective targeting of the MR are potential therapeutic strategies in this condition.

overall_design: RNA-seq of wildtype and Vascular Ehlers-Danlos Syndrome (vEDS) model mice. Wildtype and vEDS mice include untreated control mice, mice treated with hydralazine, mice treated with a combination of bicalutamide and hydralazine, mice treated with a combination of spironolactone and hydralazine

first: Emily

last: Juzwiak

first: Caitlin

last: Bowen

first: Rhiannon

last: Edwards

first: Maya

last: Black

first: Anthony

last: Zeng

last: Bramel

first: Zachary

last: Burger

first: Harry

last: Dietz

last: MacFarlane Gallo


title: Host response to bacteria induces a shift towards the enteroendocrine cell lineage in the murine enteroid model

city: Toronto

first: Stephen

middle: E

last: Girardin

state: ON

address: 1 King's College Cir

country: Canada

institute: University of Toronto

summary: The host response to commensal and pathogenic bacteria has been extensively characterized using human cancer cell line models, but remains poorly defined in primary intestinal cellular systems. Recent evidence has demonstrated that mice lacking the Nod-like receptor (NLR) protein NLRC4 are susceptible to S. flexneri infection and thus represent a new model to study the mechanistic aspects of S. flexneri -host interaction. Using ileal organoids from wild type (WT) and Nlrc4-/- mice, we first confirmed that NLRC4 was required for the restriction of intracellular S. flexneri growth. Surprisingly, NLRC4 further mediated the detection of bacteria-free S. flexneri supernatants, suggesting that ileal organoids sample proteins from the type three secretion system (T3SS) to mediate a preemptive pyroptotic response to pathogens independently from invasion. Moreover, both invasive and non-invasive S. flexneri were found within Nlrc4-/- ileal organoids, suggesting that murine intestinal epithelial cells (IECs) may be capable of bacterial uptake. Transcriptional analysis further revealed that S. flexneri infection in Nlrc4-/- organoids resulted in the downregulation of inflammatory signaling, associated with an enrichment for markers of the enteroendocrine cell lineage (EEC). This finding was recapitulated in organoids in contact with a non-pathogenic strain of S. flexneri, suggesting that EEC expansion depended on either bacterial contact or pickup. Together, our results reveal unexpected characteristics of host-bacterial interaction in primary murine IECs, which may shape the response to the microbiota and enteric pathogens at the intestinal mucosal surface

overall_design: Nlrc4-/-Ripk2+/+ and Nlrc4-/-Ripk2-/- ileal organoids were infected with M90T Shigella, or treated with bacteria-free M90T Shigella supernatant. Uninfected organoids and TSB-treated organoids were used, respectively, as controls.

first: Marry

last: Nissan


title: Elucidating the role of DEAF1 in neurodevelopment and shared molecular pathways in high-risk autism genes using cortical organoids

city: NEW HAVEN

first: Museog

last: Choe

state: CT

address: 10 Amistad Street, Ste 214J

department: Genetics

institute: Yale University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD) and intellectual disability (ID), are highly heterogeneous conditions with strong genetic underpinnings. Among the numerous risk genes implicated in NDDs, DEAF1 has emerged as a key candidate, with pathogenic variants linked to ASD and DEAF1-associated neurodevelopmental disorder (DAND). However, its precise role in human neurodevelopment remains poorly understood. Human cortical organoids (hCOs) provide a physiologically relevant model that retains the authentic human genetic background, faithfully recapitulating fetal brain development while minimizing extrapolation errors associated with genetic variability. In this study, we investigate the role of DEAF1 in neurodevelopment and its implications for NDDs using hCOs. We demonstrate that DEAF1 mutations disrupt chromatin accessibility at neuronal gene loci in human embryonic stem cells (hESCs), leading to significant transcriptional alterations.

overall_design: The RNA-seq analysis was performed on cortical organoids CTRL or MUT at Day 75 while the ATAC-seq and ChIP-seq analysis was conducted on hESC states with or without DEAF1 MUT

first: Jonghun

last: Kim

first: Mu Seog

first: In-Hyun

last: Park


title: RLF and ZFP292 regulate bivalent genes through CoREST complex [ChIP-seq]

city: Toyonaka

first: Takamasa

last: Ito

state: Osaka

address: 1-1 Machikaneyama

department: Biological Science

country: Japan

institute: Osaka University

summary: This dataset includes ChIP-seq and RNA-seq data derived from mouse embryonic stem cells (mESCs) to investigate the roles of RLF and ZFP292 in transcriptional regulation and chromatin organization.

overall_design: ChIP-seq was performed in wild-type (WT), FLAG-tagged Rlf, FLAG-tagged Zfp292, and Rlf/Zfp292 double knockout cells.

first: T

first: C

last: Obuse


title: Development of a One-Step Knock-In CAR-NK immunotherapy for Large-scale, Off-the-Shelf Production [RNA-Seq]

city: Seoul

first: Mihue

last: Jang

address: 5, Hwarang-ro 14-gil, Seongbuk-gu

department: Medicinal Materials Research Center, Biomedical Research Division

country: South Korea

institute: Korea Institute of Science and Technology

summary: Chimeric antigen receptor (CAR)-engineered natural killer (NK) cells offer a promising immunotherapy for various malignancies. However, their efficacy in treating solid tumors is often compromised by the immunosuppressive tumor microenvironment (TME), where TGF-β1 plays a key role in inhibiting NK cell function. To address this challenge, our study focused on developing a simple, one-step process for generating CAR-NK cells, termed “one-step CAR-NK”, by simultaneously knocking out TGFβR2 and knocking in a CAR gene into human primary NK cells. We first demonstrated that knocking out TGFβR2 using CRISPR-Cas9 enhanced NK-mediated cancer killing abilities with upregulated CD107a expression when co-cultured with AsPC-1 cells. Additionally, we optimized the donor DNA by inserting a binding motif for dexamethasone, which encodes a CAR targeting mesothelin (MSLN) as a tumor antigen, to integrate into the TGFβR2 locus. Using electroporation, the Cas9 protein/gRNA complex combined with CAR donor DNA significantly increased the knock-in efficacy, resulting in potent cancer killing against solid tumors. Furthermore, we explored a two-step CAR-NK manufacturing process, using AAV to deliver DNA instead of naked DNA. This method also showed high KI efficacy and robust cancer-killing capabilities. As with the one-step process, the supplement of dexamethasone further improved NK functions in two-step CAR-NK cells. Thus, our one-step CAR-NK platform, particularly in the presence of dexamethasone, holds promise as off-the-shelf therapeutics with a simple and scalable manufacturing process for treating solid tumors.

overall_design: RNA-seq profiling of wild type human primary NK cells and human primary NK cell-derived CAR-NK cells treated with or without dexamethasone.


title: Genome-scale metabolic modelling uncovers cell-type specific signatures associated with APOE variants

city: Bethesda

first: Priyanka

middle: S.

last: Narayan

address: 9000 Rockville Pike

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: Natonal Institutes of Health

summary: Metabolic dysregulation is a key feature of Alzheimer’s disease (AD) pathogenesis. The ε4 variant of APOE gene (APOE4), coding for the lipid-transporter apolipoprotein E, is the strongest genetic risk factor for late-onset AD. Previous studies have investigated how APOE4 disrupts specific metabolic pathways within different cell types. In this study, we followed a broad, metabolite-centric approach to investigate how APOE4 reshapes cellular metabolism in a cell type-specific manner based on transcriptome and metabolome data. We integrated transcriptomics data from an isogenic set of iPSC-derived neurons, astrocytes, and microglia harboring APOE3 or APOE4 genotypes into a human genome-scale metabolic model. From this model, we identified metabolic pathways that differed between APOE3 and APOE4 cells. We then used metabolomics data from the same iPSC-derived cell types to validate pathways identified by the transcriptomic analysis. In addition to confirming previous reports of disrupted cholesterol and fatty acid metabolism, we also identified bile acid biosynthesis, folate metabolism, and thyroid hormone metabolism as novel pathways dysregulated in APOE4 cells. Moreover, we were able to detect similar metabolic dysregulation in human post-mortem transcriptomic data. By integrating transcriptomic and metabolomic data, our approach can enhance understanding of biological mechanisms associated with APOE4-associated metabolic dysregulation in AD.

overall_design: RNA-seq profiling of iPSC-derived microglia cells of APOE3 and APOE4 genotypes.

first: Dilara

last: Uzuner Odongo

first: Linling

last: Cheng

first: Linda

middle: G

last: Yang

first: Roxan

middle: A

last: Stephenson

middle: S

first: Tunahan

last: Çakır

first: Madhav

last: Thambisetty


title: Development of a One-Step Knock-In CAR-NK immunotherapy for Large-scale, Off-the-Shelf Production [ATAC-seq]

overall_design: ATAC-seq profiling of wild type human primary NK cells treated with or without dexamethasone.


title: Targeting branched-chain amino acids alleviates pulmonary fibrosis [ATAC-seq]

city: wuhan

first: Jie

last: Yao

state: 湖北

address: wuhan hubei province

country: China

institute: wuhan university

summary:
Purpose: Previous studies demonstrated that BCAA metabolic reprogramming induces idiopathic pulmonary fibrosis (IPF). This study investigates BCAA-mediated gene expression regulation in primary mouse lung fibroblasts (MLFs).
Methods: MLFs were cultured in three media conditions: complete medium (Complete), BCAA-free medium (Free), or BCAA-free medium supplemented with BCAAs (Free+BCAA) for 24 hours prior to TGF-β1 (20 ng/mL) stimulation for 48 hours. ATAC-seq analyses were conducted on treated MLFs.
Conclusions: BCAA plays a crucial role in modulating the chromatin state of key fibrotic genes.

overall_design: Primary mouse lung fibroblasts (MLFs) were isolated from lungs of 6–8-week-old mice using a combination of collagenase I digestion and differential adhesion and cultured in DMEM/F12 medium. ATAC-seq analyses were conducted on treated MLFs.

first: Miao

last: Lei

last: He

first: Su

last: Fang

first: Wanli

last: Peng

first: Wenxiang

last: Hu


title: Imidacloprid susceptibility is linked to life history regulation in honey bees (Apis mellifera)

city: Edmonton

first: Olav

last: Rueppell

state: Alberta

address: 11355 - Saskatchewan Drive

department: Biological Sciences

institute: University of Alberta

summary: The western honey bee (Apis mellifera) often encounters chemical stressors in the form of phytochemicals, or pesticide residues. The first line of defense against these agrochemicals is constitutively expressed detoxification enzymes such as cytochrome P450s.Honey bees with lower levels of constitutively expressed enzymes experience greater immediate stress, which can lead to death, sub-lethal effects, and precocious foraging, if nursing. Precocious foragers are young, less developed honey bees that are recruited into the foraging population, whereas normal-aged foragers are much older. These precocious foragers are less capable flyers, and are more likely to die during their flights, which can in turn further stress the colony due to reduced food stores. In our study, we hypothesize that chemical stress sensitivity is directly linked to the onset of precocious foraging. Additionally, we believe that precocious foragers are less suited for foraging due to their rushed development, and are likely more transcriptionally similar to nurses instead of older foragers. We measured the survival of honey bees taken from 26 different colonies when exposed to a chemical stressor over 48 hours. Honey bees from each of these colonies were also all added to the same colony, and we measured the age and number of foragers from each colony over a 2-week period. Lastly, we performed transcriptomics of young and old nurses and foragers. Our results suggest that chemical stress tolerance was linked to the honey bee’s origin colony. Moreover, we found no significant correlation of the honey bees’ chemical tolerance to the age at which they began foraging. Rather, we found that bees from more tolerant colonies exhibited lower volumes of foraging by two weeks. Furthermore, transcriptomic analysis showed that precocious foragers exhibited global gene expression patterns more closely aligned with nurses than with older foragers, reinforcing age as the primary determinant of gene expression profiles. Susceptible bees displayed distinct expression profiles compared to more tolerant ones across different life stages, with notable overlap in genes encoding cytochrome P450e and a vitellogenin receptor, highlighting their potential roles in stress response and behavioral maturation.

overall_design: RNA-seq and chemical mortality assay of nurse and forager bees of different origin colonies that have been concatenated into 3, equally dispersed replicate nuclear hives.

first: Gursimran

last: Toor

first: Robert

last: Lu


title: RLF and ZFP292 regulate bivalent genes through CoREST complex [RNA-seq]

first: Takamasa

last: Ito

overall_design: RNA-seq was conducted under two conditions—Serum/LIF (undifferentiated) and retinoic acid (RA, 72 h) treatment (differentiated)—in WT and Rlf/Zfp292 double knockout cells.

first: T

first: C

last: Obuse


title: Proton-activated chloride channel 1 is essential for innate host defense against bacterial sepsis

first: Markus

last: Bosmann

address: 72 E Concord Street

department: Pulmonary Centre, Department of Medicine

institute: Boston University

summary: Bacterial sepsis remains a devastating clinical problem. Here, we describe a protective role for the recently discovered acid-sensitive, proton-activated chloride channel, PACC1 (PAC/ASOR/TMEM206), during sepsis. Initially, we found PACC1 was enriched in healthy human and mouse mononuclear phagocytes, particularly macrophages, and differentially regulated by inflammatory stimuli, suggesting PACC1 involvement in innate immunity. To further investigate, we generated de novo Pacc1 knockout (−/−) mice, which presented without major immunologic abnormalities at baseline. Compared to wild type (WT), Pacc1−/− myeloid cells showed normal phagocytic uptake of acid-insensitive Escherichia coli BioParticles, but impaired development of the acidifying phagolysosome using acid-sensitive E. coli BioParticles. Transcriptomic profiling of Pacc1−/− macrophages revealed dysregulated phagolysosomal and cytokine networks (e.g., interferons). Because phagolysosomal bacterial clearance is essential to resolve infection, we challenged Pacc1−/− mice with intraperitoneal gram-negative E. coli sepsis. Pacc1−/− mice displayed increased bacterial burden, immune cell infiltration, inflammation, and lethality. In contrast, phagocytosis-independent E. coli lipopolysaccharide (LPS)-induced endotoxemia yielded comparable WT and Pacc1−/− survival, as well as similar inflammatory responses. Finally, we engineered Pacc1-floxed (fl/fl) mice crossed with a myeloid lineage Cre-deleter strain to interrogate myeloid cell–intrinsic PACC1 in vivo. Consistent with a predominate role for PACC1 during phagocytosis and bacterial clearance in these cells, LysM-Cre/Pacc1fl/fl mice exhibited impaired E. coli sepsis survival but indifferent endotoxemia phenotypes. In conclusion, PACC1 links sterilizing phagolysosomal activity with immune networks in sepsis pathobiology.

overall_design: Bone marrow-derived macrophages (BMDMs; 2x10^6) from wild type and Pacc1-/- (C57BL/6J-Pacc1em1Bosm/Bosm, MGI: 6283429) mice were plated in 6-well tissue-culture treated plates in macrophage media and allowed to attach for 2 hours. BMDMs were then either left unstimulated for 12h or stimulated with inactivated E. coli pHrodo Bioparticles at 100ug/mL for 12h (n=6 mice/group). RNA-seq was performed from these BMDMs.

first: Lucien

middle: P

last: Garo

first: Archana

last: Jayaraman


title: ChIPseq - Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of human beige adipocytes

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: Epigenetic regulation is a key determinant of adipocyte fate and function, conferring phenotypic plasticity to adipose tissue in response to metabolic and thermal challenges. To understand the spatiotemporal regulation of chromatin during the establishment of a beige thermogenic adipocyte phenotype, we analyzed the transcriptomic, epigenetic, and enhancer connectome dynamics during white and beige adipogenesis. Using a machine learning approach, we find that the white-specific transcriptional program is associated with promoter modulations of H3K2ac levels and chromatin accessibility. In contrast, beige-specific mitochondrial gene expression correlates with promoter changes in H3K4me3 levels. Adipocyte beiging is also mediated by a remodeling of the 3D genome involving the recruitment of short range enhancers targeting fatty acid oxidation and thermogenic genes. These increased promoter-enhancer contacts correlate with increased chromatin opening at sites enriched for C/EBP transcription factor motifs. We notably identify the C/EBP transcription factor NFIL3 as differentially bound between white and beige adipocytes at enhancers regulating PDK4, a key metabolic switch promoting fatty acid oxidation. Our results highlight a multimodal, pathway-specific regulation of the transcriptional program underlying the beige adipocyte phenotype.

overall_design: Primary human adipocyte stem cells from a single subject were differentiated into both beige and white adipocytes in the presence or absence of rosiglitazone, respectively, and harvested for Chromatin Immunoprecipation and sequencing (ChIP-Seq). Six histone post translational modifications (H3K27ac, H3K4me3, H3K4me1, H3K27me3, H3K36me3 and H3K9me3) were assayed before differentiation (day0) and 1, 3 and 15 days after induction of differentiation.  Four marks (H3K27ac, H3K4me3, H3K4me1, and H3K27me3) at day15 were previously published under accession GSE256260.

first: Sarah

last: Hazell Pickering

first: Mohamed

last: Abdelhalim

first: Natalia

middle: M

last: Galigniana

first: Anita

middle: L

last: Sørensen

first: Manuela

last: Zucknick

first: Nolwenn

last: Briand


title: Selective clonal attrition of high-affinity B cells in chronic viral infection

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Perturbed B cell responses and late formation of neutralizing antibodies are hallmarks of chronic infections but the mechanisms underlying the dysfunctional humoral responses remain poorly defined. We used adoptive transfer of monoclonal anti-viral B cells (KL25) in the context of chronic lymphocytic choriomeningitis virus (LCMV) infection in mice and we observed late clonal deletion of the KL25 cells. This process was governed by the binding affinity of the KL25 B cell receptor (BCR) to its target, the viral glycoprotein (GP), and the persistence of the antigen. We found that the loss of the KL25 B cells was independent of IFN-I inflammation, and it was the result of Blimp-1-dependent differentiation. The late deletion of high-affinity B cells in chronic infection may explain the delayed neutralizing antibody response to persistent pathogens. Strategies to counter B cell clonal deletion should help us improve humoral immunity against chronic infectious diseases

overall_design: On day -6,  4 mice were infected with high-affinity DOCILE infection (DOC) (S1-S4), and 4 mice were infected wtih low-affinity antigen (DOC-LAV) (S5-S8). Low numbers of LCMV-specific KL25 B cells were adoptively tranferred at day 0 and isolated from chronically infected recipients 14 days after adoptive transfer using FAC sorting.

first: Mirela

last: Dimitrova

first: Julien

last: Roux

first: Daniel

last: Pinschewer


title: Targeting branched-chain amino acids alleviates pulmonary fibrosis [scRNA-seq]

first: Jie

last: Yao

summary: We previously confirmed that BCAT2 was reduced in TGF-β1-treated mouse and human lung fibroblasts. Knockdown of BCAT2 significantly promoted COL1A1 expression in response to TGF-β1 treatment. However, the roles of BCAT2 on other cell types, changes in cellular states, and cellular interactions are currently unknown. Here, we used single-cell RNA sequencing to analysis healthy mouse lungs (WT_PBS), mouse lungs with bleomycin-induced fibrosis (WT_BLM), and heterozygous BCAT2+/− (BCAT2 Het) mouse lungs treated with BLM (Het_BLM). Notably, we observed a reduced number of epithelial cells in the BCAT2 Het mice (Figure 3M and S3L). In contrast, the fibroblast and macrophage populations were significantly increased in the BCAT2 Het mice compared to WT mice after bleomycin-induced lung injury.

overall_design: 10–12-week-old male C57BL/6 mice (WT and BCAT2 Het) were injected intratracheally with bleomycin (1.25 mg/kg) for 14 days. Lung tissues were collected to perform scRNA-seq.

first: Miao

last: Lei

last: He

first: Su

last: Fang

first: Wanli

last: Peng

first: Wenxiang

last: Hu


title: Dynamic rewiring of cell identity transcriptional programs by loss of ERG in aortic endothelial cells [CATS]

first: Kai

middle: Howson

last: Ellis

address: 686 Bay St

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

summary: The ETS transcription factor ERG is a critical transcription factor that establishes and maintains an EC identity program. ERG is downregulated in several chronic vascular diseases, including atherosclerosis, and has been implicated in suppressing endothelial-to-mesenchymal transition (EndMT). However, the dynamic phenotypic and transcriptional consequences of ERG loss in the endothelium is poorly understood. We knocked down ERG using siRNA and compared this transient ERG loss over time to chronic deletion of ERG in a CRISPR/Cas9 deletion line in aortic ECs. RNA-sequencing and ATAC-sequencing revealed profound and dynamic rewiring of endothelial and mesenchymal transcriptional programs. While EC identity was rapidly lost (24 hours knock-down) at the transcriptional level, barrier dysfunction required longer-term knock- down (72 hours). A mesenchymal gene network and enhanced cell migration also required 72 hours to manifest. Loss of ERG was accompanied by a rapid loss of occupancy of ETS motifs and a gain in open chromatin containing AP1 motifs. Inhibition of AP1, washout of ERG siRNA or expression of ERG protein in ERG knock-out cells, demonstrated that EndMT was reversible. Finally, ERG-regulated genes and regulatory elements were associated with human disease, demonstrating that this transcription factor may be a valuable target of future therapies for vascular diseases.

overall_design: To investigate the role of ERG in maintaining identity and function of the arterial endothelium, we generated ERG knockout (ΔERG) clones in telomerase-immortalized human aortic endothelial cells (teloHAECs) using a CRISPR/Cas9-mediated deletion of ERG exon 6. Gene expression was assesses in ΔERG compared ERG wildtype ERGWT cells using CATS mRNA-seq kit v2 with poly(A) selection and dual indexing as per the manufacturer’s recommendations.

first: Kristen

last: Schulz

first: Steven

last: Botts

first: Michael

middle: D

last: Wilson

first: Jason

last: Fish

first: Kathryn

last: Howe


title: Targeting branched-chain amino acids alleviates pulmonary fibrosis [CUT&Tag]

summary:
Purpose: We previously observed significant dysregulation in the expression of key BCAA metabolic genes during idiopathic pulmonary fibrosis (IPF). This study aims to elucidate the molecular mechanisms underlying BCAA metabolic genes dysregulation during IPF progression.
Methods: ATF4 CUT&Tag were performed in MLFs and PPARγ CUT&Tag were performed in MLFs treated with TGF-β1 (20 ng/mL) for 48 h.
Conclusions: ATF4 and PPARγ respectively regulate the expression of Slc7a5 and BCAA catabolic genes in primary mouse lung fibroblasts (MLFs)


title: Dynamic rewiring of cell identity transcriptional programs by loss of ERG in aortic endothelial cells [ATAC-Seq]

overall_design: To investigate the role of ERG in maintaining identity and function of the arterial endothelium, we generated ERG knockout (ΔERG) clones in telomerase-immortalized human aortic endothelial cells (teloHAECs) using a CRISPR/Cas9-mediated deletion of ERG exon 6. Chromatin accessibility was assessed using ATAC-sequencing


title: Targeting branched-chain amino acids alleviates pulmonary fibrosis [CUT&Tag, histone_modification]

summary:
Purpose: Previous studies demonstrated that BCAA metabolic reprogramming induces idiopathic pulmonary fibrosis (IPF). This study investigates BCAA-mediated gene expression regulation in primary mouse lung fibroblasts (MLFs).
Methods: MLFs were cultured in two media conditions: complete medium (Complete) or BCAA-free medium (Free) for 24 hours prior to TGF-β1 (20 ng/mL) stimulation for 48 hours. H3K4me3, H3K27ac, H3K27me3, H3K36me3, and H3K9me3 CUT&Tag analyses were conducted on treated MLFs.
Conclusions: BCAA plays a crucial role in modulating H3K36me3 of key fibrotic genes.

overall_design: Primary mouse lung fibroblasts (MLFs) were isolated from lungs of 6–8-week-old mice using a combination of collagenase I digestion and differential adhesion and cultured in DMEM/F12 medium. CUT&Tag analyses were conducted on treated MLFs.


title: RNA-seq - Multimodal remodeling of epigenetic and enhancer networks shapes the transcriptional landscape of beige adipocytes

first: Philippe

last: Collas

overall_design: Primary human adipocyte stem cells from a single subject were subjected to beige adipogenic differentiation (in the presence of rosiglitazone) for 24h (day 1) and 72 h (day 3). Adipogenic differentiation cocktail without rosiglitazone (white differentiation) was also assayed at 24h to act as a normalistion control.  Samples were harvested for RNA-Seq.   Complementary RNA-Seq from white differentiation and day15 white and beige differentiated adipocytes were previously published under accessions GSE176020 (donor A) and GSE256259 (subject 6).

first: Sarah

last: Hazell Pickering

first: Mohamed

last: Abdelhalim

first: Natalia

last: Galigniana

first: Anita

last: Sørensen

first: Manuela

last: Zucknick

last: Briand


title: Dynamic plasticity of gastric neck cells contributes to regeneration and metaplasia supported by myeloid-mesenchymal interactions

city: Bunkyo-ku

first: Junya

last: Arai

state: Tokyo

address: Clinical reserch center A #422 7-3-1 Hongo

institute: University of Tokyo

summary: Gastric mucosal homeostasis is maintained by tissue-resident stem cells. Following mucosal injury, both stem cells and a subset of differentiated cell types contribute to regeneration, coinciding with characteristic pathological changes such as atrophic gastritis and metaplasia. To comprehensively understand the cellular dynamics involved in this process, we performed single-cell and spatial transcriptomics using newly generated transgenic mice. In humans, gastric chief cell loss precedes parietal cell loss during the progression of atrophy and metaplasia. In mice, selective ablation of chief cells induces parietal cell loss and accelerates metaplasia development, validating the causal relationship underlying the decrease of these two lineages. Single-cell analysis confirmed robust stemness activity and metaplastic changes in neck cell clusters following either chief or parietal cell ablation, and lineage-tracing experiments revealed that neck cells serve as a source of metaplasia and regeneration. Mechanistically, mucosal injury recruits IL-1-expressing myeloid cells, which stimulates NRG1 production in stromal fibroblasts, leading to mucosal proliferation and regeneration mediated by activated neck cells. These findings highlight the plasticity and facultative stem cell function of gastric neck cells, which play a critical role in mucosal homeostasis and disease progression.

overall_design: We established genetically engineered mouse models designed to induce the selective ablation of chief and parietal cells.

first: Yoku

last: Hayakawa


title: Weak influence of light and time of day on transcriptional response to SAV3 infection in Atlantic salmon (Salmo salar) smolts

city: Tromsø

first: Alexander

middle: Christopher

last: West

state: Troms

address: Framstredet 39, Tromsø

department: Arctic Chronobiology and Physiology

institute: Universitetet i Tromsø

summary: Seventeen percent of aquaculture Atlantic salmon in Norway die after transfer from freshwater to seawater facilities, many from infectious disease. The degree to which these deaths are attributable to unseen weakness in smolt preparation is therefore an important concern. Strong evidence in mammals and supporting evidence in other teleosts show that the light environment shapes the immune response via entrainment of the circadian clock. These data are alarming as most smoltification protocols use constant light, which does not entrain the circadian clock and is associated with negative survival outcomes to disease challenge in other species. The goal of our study was to establish how different light environments affected the anti-viral immunity of Atlantic salmon smolts. To achieve this goal, we measured the transcriptional response of select type I and type II interferons and major histocompatibility complexes in the heart and head kidney following an intraperitoneal SAV3 viral challenge delivered under different lighting conditions. We began with two hypotheses. First, that compared with a regular light-dark cycle (long photoperiod; LP), constant light (LL) would have a weaker resistance to viral challenge in Atlantic salmon smolts. Second, that Atlantic salmon smolts kept in a regular light-dark cycle would have altered immune sensitivity between the light and dark phases. To test our first hypothesis, we photostimulated smoltification in parr through exposure to either LP or LL conditions for 6 weeks then challenged them by SAV3 infection. LP and LL groups showed indistinguishable measurements in classical smolt characteristics and comparable levels of SAV3 mRNA in the heart after 8 and 14 days post infection. They also showed comparable transcriptional responses of select type I interferons (IFNa, IFNb, IFNc) and both class I and class II major histocompatibility complexes (MHC I and MHC II) in both heart and head kidney tissue. IFNγ induction in the heart, however, was marked higher in the LL compared to the LP group. While this data suggests a heightened sensitivity of the LL group to SAV3 viral challenge, the consistent induction of MHC II, a key target gene of IFNγ signaling, to SAV3 infection in both LL and LP groups indicates that photoperiod may only have a minor impact on interferon regulation, rather than a more general influence on the viral immune response. To test our second hypothesis, we compared the transcriptomic response in the heart to SAV3 infection delivered either at the mid-light or mid-dark phase in the LP group. Both mid-light and mid-dark groups showed an upregulation of immune related genes and down-regulation of structural genes of mitochondria, but an analysis of the interaction between infection and time of day identified no differentially regulated genes. This second experiment suggests that, unlike in mammals, daily timing of viral infection may not play a major role in the immune response of Atlantic salmon.

overall_design: RNAseq profiling of hearts from Salmo salar. Parr were exposed to 6 weeks short photoperiod, then 6 weeks long photoperiod before intraperitoneal viral challenge with SAV3 or PBS at the mid-light or mid-dark timepoint. Hearts were collected 14 days after infection and snap frozen on dry ice before RNA processing.

first: Therese

last: Solberg

first: Chandra

last: Ravuri

first: Mattis

last: Jayme van Dalum

first: Jo

last: Espen Tau Strand

first: David

last: Hazlerigg

first: Eva

last: Stina Edholm


title: Targeting branched-chain amino acids alleviates pulmonary fibrosis [RNA-seq]

first: Jie

last: Yao

summary:
Purpose: Previous studies demonstrated that BCAA metabolic reprogramming induces idiopathic pulmonary fibrosis (IPF). This study investigates BCAA-mediated gene expression regulation in primary mouse lung fibroblasts (MLFs).
Methods: In vitro: MLFs were cultured in three media conditions: complete medium (Complete), BCAA-free medium (Free), or BCAA-free medium supplemented with BCAAs (Free+BCAA) or BCKA (Free+BCKA) for 24 hours prior to TGF-β1 (20 ng/mL) stimulation for 48 hours. Triplicate RNA-seq analyses were conducted on treated MLFs.
In vivo: Comparative RNA-seq profiling was performed on lung tissues from three experimental groups: PBS-treated controls, bleomycin (BLM)-exposed mice, and BLM-treated mice receiving BCAA supplementation (3 mmol/L in drinking water) or BCAA-free diets or BT2 treatment.
Conclusions: BCAA metabolism is essential for myofibroblast activation and mechanistically promotes lung fibrogenesis in both in vitro and in vivo models.

overall_design: In vitro: Primary mouse lung fibroblasts (MLFs) were isolated from lungs of 6–8-week-old mice using a combination of collagenase I digestion and differential adhesion and cultured in DMEM/F12 medium. Triplicate RNA-seq analyses were conducted on treated MLFs. In vivo: 10–12-week-old male C57BL/6 mice were randomly allocated into three batchs. Batch 1: ① Normal diet throughout (PBS); ② Normal diet for 7 days followed by intratracheal administration of 1.25 mg/kg BLM (BLM); ③ BCAA-supplemented drinking water (3 mM) for 7 days, followed by 1.25 mg/kg BLM (BLM+BCAA). Lung tissues were collected 14 days post-BLM treatment. Batch 2: ① Normal diet throughout (PBS); ② BLM administration (1.25 mg/kg) with normal diet (BLM); ③ BLM administration (1.25 mg/kg) for 7 days, followed by BCAA-free diet for 14 days (BLM+BCAA free). Lung tissues were collected 21 days post-BLM treatment. Batch 3:  ① Normal diet throughout (PBS); ② BLM administration (3.5 mg/kg) for 3 days, followed by daily intraperitoneal injection of 10% DMSO for 11 days (BLM); ③ BLM administration (3.5 mg/kg) for 3 days, followed by daily intraperitoneal injection of 20 mg/kg BT2 for 11 days (BLM+BT2). Lung tissues were collected 14 days post-BLM treatment.

first: Miao

last: Lei

last: He

first: Su

last: Fang

first: Wanli

last: Peng

first: Wenxiang

last: Hu


title: Macrophage-intrinsic and IL-9-dependent arginine metabolism promotes lung tumor growth

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: Tumor-associated macrophages are an abundant, tumor-infiltrating cell population that supports the evasion of tumor cells from anti-tumoral immune cell detection by generating an immunosuppressive tumor-immune microenvironment (TIME). The immunosuppressive function of macrophages is dictated by the cytokine environment. IL-9 is a pleiotropic cytokine that can be a positive or negative regulator of tumor growth. Our lab previously identified a pro-tumoral role of IL-9 by expanding lung interstitial macrophage populations and inducing the expression of arginase 1 (ARG1) to enhance tumor growth. However, the underlying mechanism by which IL-9R/ARG1+ interstitial macrophages promote tumor progression remains incomplete. Here, we demonstrate that macrophage-targeting nanoparticles containing Arg1 siRNA can therapeutically reduce tumor burden and reduce pro-tumor arginine-derived metabolite production. Furthermore, using bulk RNA sequencing of lung macrophages isolated from Il9r-/-:WT mixed-bone marrow chimeric mice, we demonstrate that IL-9 intrinsically alters the transcriptomic landscape of lung interstitial macrophages. Mechanistically, IL-9 promotes intrinsic Arg1 expression through an IRF4-dependent regulatory pathway and modulates arginine and polyamine concentration within interstitial macrophages and lung tissue, resulting in increased lung tumor growth and altered macrophage phenotypes. Thus, our work defines a pro-tumor mechanism of IL-9-responsive macrophages mediated by altered intrinsic arginine metabolism in lung interstitial macrophages that enhances lung tumor growth.

overall_design: To define the intrinsic transcriptional changes dependent on IL-9 signaling, we will perform RNAseq on interstitial macrophages using a mixed, bone marrow chimera mice in B16 lung tumor model. B6/boyj recipient mice will receive Il9r -/- and Boyj WT bone marrow. CD11c- and CD11c+ interstitial macrophaes were sorted and RNA isolated for bulk RNA-seq.

first: Anthony

last: Cannon

first: Mark

middle: H

last: Kaplan


title: Subtype-specific enhancer RNAs define transcriptional regulators and prognosis in breast cancers

city: Manchester

first: Aamena

middle: Y

last: Patel

address: Dover Street

country: United Kingdom

institute: University of Manchester

summary: Gene expression is tightly controlled by DNA elements called enhancers by associating with lineage-specific transcription factors. These enhancers transcribe noncoding RNAs (called enhancer RNAs or eRNAs). eRNA expression is an early indicator of transcription factor activity and is associated with treatment response and survival in cancer patients. By analysing ~ 300 000 eRNA loci profiled using RNA-sequencing data sets from 975 breast cancer patients using machine learning approaches, we categorised eRNAs specific to breast cancer molecular subtypes and survival. We associated these eRNAs with subtype-specific mRNAs to define proximal co-expressed regulatory eRNAs (ProxCReAm), which are enriched in pathways characteristic of their respective subtypes. Interestingly, cistrome and transcription factor motif analyses on these eRNAs highlighted involvement of diverse nuclear receptors (GR/AHR for luminal and GR/RAR for basal) and FOX factors in luminal regions. Moreover, luminal eRNAs were associated with better outcomes and Her2 eRNAs with worse outcomes in patients. Overall, we demonstrate that machine learning approaches performed on RNA-seq data sets can classify functionally relevant subtype-specific and prognostic eRNAs, which can identify critical gene pathways and transcription factor networks in breast cancer.

overall_design: Low input N3-kethoxal-assisted single stranded DNA sequencing (KAS-seq) protocol was performed on MCF7 cells, which is a ER+ LumA breast cancer line.

first: Nagarajan

last: Sankari

first: Mohan

last: Sumitra

first: Sheth

last: Jigar


title: Steroid Hormone Dependent Pathogenesis in Vascular Ehlers-Danlos Syndrome

first: Tyler

middle: J

last: Creamer

address: 733 N Broadway

department: Genetic Medicine

institute: Johns Hopkins University

summary: Vascular Ehlers-Danlos Syndrome (VEDS) is a genetic connective tissue disorder caused by heterozygous mutations in the COL3A1 gene encoding type III collagen which result in spontaneous rupture of the arteries, intestines, and gravid uterus. Aortic ruptures occur primarily in the descending thoracic aorta. Male VEDS patients experience a higher rate of catastrophic vascular events (dissections or ruptures) during puberty compared to females suggesting a role for androgens. Our Col3a1G938D/+ mouse model recapitulates the sexually dimorphic phenotype of spontaneous death due to aortic rupture in puberty. Our work with VEDS mice subjected to androgen receptor inhibition, through the use of a conditional allele for the androgen receptor (AR) to generate global Ar null mice or through the use of pharmacologic AR antagonism with bicalutamide, discovered that androgens drive sexual dimorphic survival. We also found a role for mineralocorticoid receptor signaling with the use of spironolactone, a dual AR and MR antagonist, and finerenone, a specific MR antagonist. Therefore, we employed single nucleus-RNAseq of the descending thoracic aorta to identify the molecular mechanism driving AR, MR, and dual AR/MR protection in VEDS male mice. We discovered AR or MR antagonism normalized expression of dysregulated transcripts in both VEDS endothelial cells (ECs) and vascular smooth muscle cells (VSMCs). In ECs, components of cell junctions and modulators of cell junction stability were dysregulated while transcripts encoding a contractile VSMC phenotype, integrin signaling, and focal adhesions were modulated in VSMCs.

overall_design: Untreated male Col3a1+/+ and Col3a1G938D/+ mice were used as controls to compare to male Col3a1G938D/+ mice that were treated with either 50mg/kg/day bicalutamide, 100mg/kg/day spironolactone, 5mg/kg/day finerenone, or 10ug/kg/day fludrocortisone from weaning until 60 days of age. The descending thoracic aortas of these six groups of mice were sent for snRNAseq at 60 days of age. All mice were maintained on a C57BL/6J background strain (The Jackson Laboratory, strain #000664).

first: Emily E

last: Juzwiak

first: Caitlin

last: Bowen

first: Cassie

last: Parks

last: Zeng

first: Emily

last: Bramel

first: Zachary

last: Burger

first: Elena

last: Gallo MacFarlane

first: Harry

last: Dietz


title: Slow RNAPII elongation facilitates early pluripotency cell transitions without reducing replication fork rates

city: Madrid

first: Maria

last: Gomez

address: Nicolas Cabrera, 1

country: Spain

institute: CBMSO(CSIC/UAM)

summary: We assess the impact of reducing transcription elongation rate during mESCs dedifferentiation, gaining insights into its effects on replication fork dynamics, gene expression, chromatin conformation, and alternative splicing.

overall_design: We analyze RNA-seq data in RNAPII-mutant and WT mESCs growing for 0, 1, 2, and 7 days in LIF/2i medium.

first: Sara

last: Martín-Vírgala

first: Joana

last: Segura

first: Alicia

last: Gallego

first: Ran

last: Tong

last: Tur-Gracia

first: Jesús Rafael

last: Rodriguez-Aguilera

first: Biswajit

last: Das

first: Javier

last: Isoler-Alcaraz

first: Carlos

last: Gallego-García

first: Shraddha

last: Shinde

first: Magdalena M.

last: Maslon

first: Andrei

last: Chabes

first: Lothar

last: Schermelleh

first: María

last: Gómez


title: Dynamic rewiring of cell identity transcriptional programs by loss of ERG in aortic endothelial cells [RNA]

first: Kai

last: Ellis

first: Kristen

last: Schulz

first: Steven

last: Botts

first: Michael

last: Wilson

first: Jason

last: Fish

first: Kathryn

last: Howe


title: Transcriptional and epigenetic programs of in vitro-expanded HSPCs and their T cell progenitors progeny

city: Pasadena

first: Brendan

middle: W

last: MacNabb

state: CA

address: 1200 E California Blvd

institute: California Institute of Technology

summary: Hematopoietic stem and progenitor cells (HSPCs) in the bone marrow are the ultimate sources of all hematopoietic lineage cells, including T cells.  However, gene expression programs and chromatin dynamics that guide the bone marrow progenitor cells to enter the T-development programs are not fully understood due to limited cell numbers and population heterogeneity.  By exploiting the in vitro HSPC expansion approach, which effectively expands HSPCs with high T cell potentials, we monitored the gene expression programs and chromatin accessibility changes underlying the transition from the bone marrow progenitor stages to early T cell development stages.  Notably, expanded HSPCs displayed strikingly similar chromatin accessibility profiles with early-stage T cell progenitors, representing their shared hematopoietic chromatin landscapes.  However, a select set of genomic regions and target genes were specifically regulated as cells first received the strong Notch signaling and engaged with T-development conditions. These events included a robust chromatin opening and transcriptional activation of the T cell receptor (TCR)-C beta locus. In addition, well-known stem and progenitor-associated transcription factors were sharply repressed, often concerted with broad chromatin accessibility losses at those loci.   These gene regulation targets were not an artifact of in vitro expanded HSPC-derived pro-T cells. The progeny of expanded HSPCs and freshly isolated HSPCs share the same T-lineage developmental trajectory at the single-cell transcriptome level, and their gene expression programs were highly similar. However, expanded HSPC-derived pro-T cells showed temporal differences in early T-development speed and progressed through pre-commitment stages slowly.  From cytokine and chemokine screening, we found that a brief Flt3L pre-treatment during the 4-5 days of the expansion period could moderately accelerate the T-development kinetics of expanded HSPCs. Thus, we compared the chromatin accessibility programs, H3K27ac and H3K27me3 histone marks, and gene expression programs upon Flt3L treatment.  Although chromatin state and transcriptional features were mostly not altered by Flt3L treatment at the bulk population levels, scRNA-seq results showed that a set of activation and stress-response genes were upregulated upon Flt3L stimulation. However, Flt3L-primed HSPCs developed through a normal T cell pathway.   Together, these datasets (1) provide comprehensive gene expression and chromatin accessibility profiles of expanded HSPCs and their progeny pro-T cells, (2) reveal molecular events accompanied by bone marrow progenitor cells transition to the T cell program, and (3) suggest a slight modification of the expansion protocol for the use of T cell biology studies by adding acute Flt3L treatment.

overall_design: ATAC-seq of in vivo DN thymocyte populations:  Thymi were pooled from 8-10 sex-matched mice (4.5 - 7 weeks old) per replicate. Each population was purified by flow cytometry cell sorting.

first: Boyoung

last: Shin

first: Samantha

last: Chang

first: Ellen

middle: V

last: Rothenberg


title: POLR1F promotes proliferation and stemness of anaplastic thyroid cancer by activating F2R/p38 MAPK signaling

city: Hangzhou

first: Minghua

last: Ge

address: Shangtang

institute: Zhejiang provincial people's hospital

summary: Anaplastic thyroid cancer (ATC) is one of the most aggressive cancers characterized with extremely rapid growth rate. Dysregulation of RNA polymerase (Pol) is critical for cancer development, but little is known about its role and mechanism in ATC. In the present study, the expressions of Pol family members were screened in a large-cohort proteome, which contained 113 ATCs and 20 normal thyroid samples. Combined with gene dependency score, we found RNA Polymerase I Subunit F (POLR1F) was significantly upregulated in ATC tissues with the strongest gene effect among the Pol family members. The results were confirmed in ATC tissues and cell lines, revealing that POLR1F was mainly located in nuclei and expressed stronger than normal thyrocytes. Silence of POLR1F in ATC cell lines significantly inhibited cell proliferation, colony formation, and sphere sizes. POLR1F knockdown dramatically reduced tumor growth of ATC xenografts both in zebrafish and nude mice. RNA sequencing analysis revealed that coagulation factor thrombin receptor (F2R) was a downstream target of POLR1F participating in p38 MAPK pathway. Silence of F2R significantly inhibited ATC cell proliferation, colony number, and the ability of sphere formation. F2R positively correlated with POLR1F and p38 MAPK signaling score. Both POLR1F and F2R knockdown evidently attenuated phosphorylation of p38 MAPK. Consistently, phosphorylation of p38 MAPK was reduced in ATC xenografts after POLR1F inhibition. These results demonstrate POLR1F was required for ATC growth and stemness by activating F2R/p38 MAPK signaling, shedding light on an essential role of POLR1F in maintaining ATC aggressiveness.

overall_design: To investigate the regulatory role of POLR1F on downstream genes, we silenced POLR1F in the 8505C cell line using siRNA for 24 hours, followed by RNA-seq analysis to assess gene expression profiles.

first: Yingying

last: Gong

first: Zongfu

last: Pan


title: Dysregulation of macrophage lipid metabolism underlies intracellular bacterial neuroinvasion [RNA-seq]

city: chongqing

first: zhou

last: sha

address: 55 University City South Road, Shapingba District, Chongqing, China

institute: chongqing university

summary: Acute infection of the central nervous system is one of the deadliest diseases, but the mechanisms by which intracellular bacteria infiltrate the brain remain poorly understood. Phagocytic cells are usually recognized as the battlefield on which war is waged against intracellular bacteria; however, little is known about how the intracellular bacteria take advantage of infected phagocytes to access the brain. In this study, we find that a novel CD36+ foamy macrophage subpopulation participates in penetration of the brain by intracellular bacteria. Biomechanical analysis reveals that abundant protrusions and adhesion molecules on foamy macrophages confer significant resistance to the mechanical stress of blood flow, thereby providing more opportunities for these macrophages to adhere to the vascular endothelial surface during neuroinvasion. Through metabolomics analysis, we find that macrophage lipid metabolism is recalibrated during bacterial neuroinvasion, and that β-hydroxybutyrate promotes the formation and survival of CD36+ foamy macrophages. Taken together, our findings uncover a pathway by which intracellular bacteria hijack macrophages to invade the brain, suggesting that lipid metabolism might play a role in the prevention or resolution of bacterial neuroinvasion.

overall_design: RNA-sequencing (RNA-seq) were performed with CD36+ macrophages isolated from peripheral blood and the sorted peritoneal macrophages treated with ox-LDL


title: Xist RNA Dependent and Independent Mechanisms Regulate Dynamic X Chromosome Inactivation in B Lymphocytes [WGBS]

city: Philadelphia

first: Montserrat

last: Anguera

state: PA

address: 3800 Spruce Street, Rosenthal Room 390EB

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

type: Methylation profiling by high throughput sequencing

summary: X-chromosome inactivation (XCI) maintenance in female B cells is dynamic (dXCI), where naïve cells lack cytological enrichment of Xist RNA and heterochromatic marks on the inactive X-chromosome (Xi), and these marks re-localize after stimulation. Here, we report the epigenetic profiling of silencing (H3K27me3, H2AK119Ub, H3K9me3, DNA methylation (DNAm)) and activating (H3K27ac) marks on the Xi during dXCI and investigate the requirement for Xist RNA in maintaining the Xi epigenetic landscape. We find that the Xi in naïve B cells is depleted for H2AK119Ub and H3K9me3 but enriched for DNAm and H3K27me3 which maintain an epigenetic memory of transcriptional silencing dependent on Xist RNA. Upon stimulation, Xist-independent H3K27me3 and Xist-dependent H2AK119Ub modifications accumulate across the Xi. Thus, naïve B cells maintain an epigenetic memory of silencing in the absence of Xist RNA localization via retention of DNAm and H3K27me3, and both H3K27me3 and H2AK119Ub accumulate on the Xi post-stimulation in an Xist-dependent and -independent manner. These data have critical implications for understanding molecular mechanisms underlying female-biased immune responses.

overall_design: Whole genome bisulfite sequencing analysis in F1 mus x cast CD23+ B cells that were unstimulated or stimulated for 24 hours with CpG (n = 3 per condition). F1 mus x cast is a hybrid mouse model of skewed XCI generated through mating female C57BL/6 mice harboring a heterozygous Xist deletion to male M. m. castaneous mice.

first: Natalie

last: Toothacre

middle: C


title: Ftsj1 deficiency influences diverse ncRNA networks in murine organs (circRNAs)

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

institute: University Medicine Greifswald

type: Non-coding RNA profiling by high throughput sequencing

summary: Beyond the regulation of mRNAs by individual ncRNA types, such as miRNAs or lncRNAs, their interplay as so-called competitive endogenous RNAs (ceRNAs) appears to play a pivotal role in diseases. In our study we aimed to get a holistic understanding of the tRNA 2’O-methyltransferase FTSJ1 and its regulatory role in the context of cognitive disability. Here, we investigated the impact of Ftsj1 deficiency on ceRNA networks across different mouse organs. Our study underscores the critical role of organ-specific ceRNA networks, particularly in metabolic regulation, and emphasizes the need for cross-organ analyses to unravel the complexity of ceRNA-mediated gene regulation. Our findings reveal a prominent ceRNA network in the liver, mediated by four hub miRNAs (miR-378d, miR-3076-5p, miR-3474, and miR-296-3p) and enriched with acetyl CoA-related genes, including Acly, Acss2, and Mvk. These genes are integral to fatty acid metabolism, which is heavily disrupted in both liver and kidney. In contrast, brain tissues exhibited minimal changes, suggesting only a limited impact directly related to Ftsj1 in this organ. These results suggest that the cognitive disability associated with Ftsj1 is driven by metabolic and ceRNA crosstalk along the liver-brain and kidney-brain axes. This dataset comprises the circRNA sequencing data used in our study.

overall_design: RNA-seq profiling of 3 Ftsj1-deficient and 3 wildtype mice with circRNA-seq in 5 different organs, brain, heart, kidney, liver, spleen.

first: Heiko

last: Dunkel

first: Andreas

last: Kuß

first: Lars

middle: R

last: Jensen

first: Jonah

last: Schreier

first: Franziska

last: Sperling

first: Oliver

last: von Bohlen und Halbach


title: Xist RNA Dependent and Independent Mechanisms Regulate Dynamic X Chromosome Inactivation in B Lymphocytes [CUTandRUN_PRC2]

overall_design: CUT&RUN analysis for the histone modification H3K27me3 in unstimulated CD23+ B cells. B cells originated from mice with an Ezh2 conditional deletion using CD19-cre (n=2 WT control and 2 cKO) or from female F1 mus x cast mice treated with the Ezh2 inhibitor EPZ6438 (n=1 DMSO control, 1 6-day EPZ treatment, 1 7-day EPZ treatment).

middle: E


title: A Respiratory Syncytial Virus trailer sequence modulates viral replication and copy-back defective viral genome generation and propagation kinetics

city: Rochester

first: Justin

last: Brennan

address: 601 Elmwood Ave.

department: Microbiology & Immunology

institute: University of Rochester Medical Center

summary: Copy-back defective viral genomes (cbDVGs) are key inducers of antiviral responses during negative-sense RNA virus infection. Once considered byproducts of in vitro viral replication, cbDVGs have since been detected in clinical specimens and implicated in affecting infection outcomes. The molecular mechanism of cbDVG generation remains unclear, thereby hindering our ability to manipulate cbDVG production during infection for therapeutic gain. Previous work showed that respiratory syncytial virus (RSV) cbDVG re-initiation sites cluster in trailer-end hotspots R1, R2, and R3, and that a poly-U mutation in R1 selectively reduced cbDVG formation at the mutated region. Here, we reported that a 10U mutation in R2 drastically reduced cbDVGs in this region in both minigenome and recombinant virus systems. Furthermore, during high-MOI passaging of the R2-10U virus, we observed delayed detection of cbDVGs with re-initiation sites in R1-R3 (trailer cbDVGs) compared to WT, while no differences in virus titers were observed. Interestingly, we observed the rapid emergence and accumulation of a viral variant bearing a 2-ribonucleotide deletion (R2-8U) within the R2-10U mutation sequence as early as P0. Compared to R2-10U, the R2-8U virus was stable, displayed faster generation and accumulation of trailer cbDVGs, restored cbDVGs with R2 re-initiation sites, and exhibited enhanced genomic replication. Overall, our data identify a sequence in the RSV trailer whose mutation critically modulates both viral replication and the generation/propagation of trailer cbDVGs. Our data also suggest that cbDVG generation, particularly near the trailer, may be an evolutionary tradeoff for more rapid virus genomic replication.

overall_design:
To investigate the impact of mutations in the RSV trailer sequence on the generation and accumulation of copy-back defective viral genomes we serially passaged WT, R2-10U, and R2-8U viruses at  MOI 5 to generate viral stocks enriched with cbDVGs (HD). Figure 3: total RNA was extracted from the supernatants of infected passage 10 (P10) cells for the WT and R2-10U viruses. Total RNA was extracted from the HD supernatants of passage 6 (P6) cells for R2-8U. To generate viral stocks with low cbDVG content (LD) WT and R2-10U passage 3 viruses were passaged at MOI 0.001 until passage 5 (P5) and total RNA was extracted from the supernatants of infected cells. For HD and LD viruses, 2 WT lineages (L1-L2) and 3 R2-10U lineages (L1-L3) were made by passaging in independent HEp2 cell infections. 1 R2-8U HD lineage was sequenced. Figure 6: passaging and RNA extraction were performed as described. Here, lineages refer to 2 independent instances of the RSV reverse genetic system. Note that HD virus passaging proceeded to P5 while LD passaging proceeded to P4. Additionally, note that HD and LD passaging began at P3, respectively. To confirm that the R2-8U mutation was not an artifact arising during transcription or RNA sequencing, an RSV mini genome construct bearing the R2-10U mutation was in vitro transcribed, DNase digested and lithium chloride purified prior to RNA-sequencing. Note that these files are named 10U_R1 and 10U_R2.
RNA-seq data was analyzed using the ViReMa algorithm to identify the break/rejoin junction sequences that are unique to cbDVGs and do not fully align to the viral reference genome.

first: Yan

last: Sun


title: Defective ventral neurogenesis due to midfetal Chd8 mutation drives autistic-like behavior in mice

city: Kanazawa

first: Kenta

last: Nitahara

state: Ishikawa

address: 13-1, Takaramachi

department: Department of Histology and Cellular Biology

institute: Kanazawa Univeristy

summary: Autism spectrum disorder (ASD) is a common neurodevelopmental condition characterized by behavioral abnormalities. Although mouse models have been widely adopted to recapitulate the pathology of ASD, the identification of specific neural abnormalities responsible for autistic-like behavior has remained challenging. Here we provide insight into this causal relation by identifying the critical period and cell type responsible for the development of such behavior in ASD model mice with a Chd8 mutation. We found that Chd8 mutation induced at embryonic day 14.5 gave rise to ASD-like behavioral phenotypes, including abnormal social interaction and increased anxiety-like behavior, as well as to accelerated cell-cycle exit and differentiation in ventral progenitor cells. Restoration of Chd8 expression in ventral progenitor cells ameliorated both the behavioral phenotypes and aberrant ventral differentiation in Chd8 mutant mice. Our findings indicate that Chd8 mutation during the midfetal period—in particular, in ventral progenitor cells—contributes to the development of autistic-like behavior.

overall_design: scRNA-seq analysis was performed using tdTomato-positive cells from the forebrains of mice at P5 (Chd8 control vs mutant). The target cells were isolated by fluorescence-activated cell sorting according to the presence or absence of tdTomato signal.

first: Atsuki

last: Kawamura

first: Masaaki

last: Nishiyama


title: Ftsj1 deficiency influences diverse ncRNA networks in murine organs (miRNAs)

summary: Beyond the regulation of mRNAs by individual ncRNA types, such as miRNAs or lncRNAs, their interplay as so-called competitive endogenous RNAs (ceRNAs) appears to play a pivotal role in diseases. In our study we aimed to get a holistic understanding of the tRNA 2’O-methyltransferase FTSJ1 and its regulatory role in the context of cognitive disability. Here, we investigated the impact of Ftsj1 deficiency on ceRNA networks across different mouse organs. Our study underscores the critical role of organ-specific ceRNA networks, particularly in metabolic regulation, and emphasizes the need for cross-organ analyses to unravel the complexity of ceRNA-mediated gene regulation. Our findings reveal a prominent ceRNA network in the liver, mediated by four hub miRNAs (miR-378d, miR-3076-5p, miR-3474, and miR-296-3p) and enriched with acetyl CoA-related genes, including Acly, Acss2, and Mvk. These genes are integral to fatty acid metabolism, which is heavily disrupted in both liver and kidney. In contrast, brain tissues exhibited minimal changes, suggesting only a limited impact directly related to Ftsj1 in this organ. These results suggest that the cognitive disability associated with Ftsj1 is driven by metabolic and ceRNA crosstalk along the liver-brain and kidney-brain axes. This dataset comprises the miRNA-seq data used in our study.

overall_design: RNA-seq profiling of 3 Ftsj1-deficient and 3 wildtype mice with degradome seq in 5 different organs, brain, heart, kidney, liver, spleen.


title: Disseminated tumor cell of colorectal cancer adopt the wound healing program of epidermal keratinocyte [RNA-seq]

city: Ariake

first: Ryoji

last: Yao

institute: Cancer Institute, JFCR

summary: Disseminated tumor cells (DTCs) are a critical cell population in the metastasis process, and understanding their features is essential for the development of cancer treatment. We show that DTCs of colorectal cancer (CRC) transiently adopted the cellular state resembling to the activated epidermal keratinocyte during wound healing. Using the orthotropic transplantation of patient derived organoids (PDOs), we demonstrated that collective migrating cell clusters in primary site did not contain cancer stem cells but contained cells expressing wound-inducible keratins. Mechanistically, inhibition of EZH2 methyltransferase and activation of YAP signaling synergistically promoted DTC phenotype and potentiated dissemination to the distant organs. Collectively, these observations demonstrated that CRC cells alter the cellular hierarchy and adopt re-epithelization program resembling to the tissue repair process to generate DTCs.

overall_design:
We established organoids from primary, disseminate and metastasis lesions, and the comparative analysis of expression profiles were performed.
PDOs established from primary lesions were treated with GSK126 and PY-60, and the comparative analysis of expression profiles were performed.


title: Ftsj1 deficiency influences diverse ncRNA networks in murine organs (degradome) [RNA-Seq]

summary: Beyond the regulation of mRNAs by individual ncRNA types, such as miRNAs or lncRNAs, their interplay as so-called competitive endogenous RNAs (ceRNAs) appears to play a pivotal role in diseases. In our study we aimed to get a holistic understanding of the tRNA 2’O-methyltransferase FTSJ1 and its regulatory role in the context of cognitive disability. Here, we investigated the impact of Ftsj1 deficiency on ceRNA networks across different mouse organs. Our study underscores the critical role of organ-specific ceRNA networks, particularly in metabolic regulation, and emphasizes the need for cross-organ analyses to unravel the complexity of ceRNA-mediated gene regulation. Our findings reveal a prominent ceRNA network in the liver, mediated by four hub miRNAs (miR-378d, miR-3076-5p, miR-3474, and miR-296-3p) and enriched with acetyl CoA-related genes, including Acly, Acss2, and Mvk. These genes are integral to fatty acid metabolism, which is heavily disrupted in both liver and kidney. In contrast, brain tissues exhibited minimal changes, suggesting only a limited impact directly related to Ftsj1 in this organ. These results suggest that the cognitive disability associated with Ftsj1 is driven by metabolic and ceRNA crosstalk along the liver-brain and kidney-brain axes. This dataset comprises the degradome sequencing data used in our study. Degradome expression levels were used to validate miRNA – mRNA interaction pairs.

overall_design: RNA-seq profiling of 3 Ftsj1-deficient and 3 wildtype mice with degradome seq in 5 different organs, brain, heart, kidney, liver, spleen.  (4 samples per genotype for Spleen)


address: 13-1 Takaramachi

department: Department of Histology and Cell Biology

institute: Graduate School of Medical Sciences, Kanazawa University

summary: Autism spectrum disorder (ASD) is characterized by its distinctive behavioral abnormality. Often mouse models were adopted to recapitulate the ASD pathology, however, difficulties reside in distinguishing neural abnormalities primarily responsible for the autistic behavior. Chromatin remodeler, CHD8, is encoded by the most frequently mutated gene in individuals with ASD. Here we investigated the etiology of the ASD due to CHD8 mutation by identifying the critical period to develop behavioral symptoms. By applying inducible Cre/loxP system and behavioral examinations, we discovered that neural stem cell-specific mutation of Chd8 at E14.5, but not at E17.5, manifested behavioral phenotypes. Single cell transcriptome analysis revealed that Chd8 mutation was associated with premature cell-cycle exit and differentiation at ventral progenitor cells. Furthermore, we generated a knock-in mouse to restore CHD8 expression in a Cre-dependent manner. CHD8 restoration in neural stem cells at E14.5 or ventral progenitor cells ameliorated behavioral phenotypes whereas the restoration in neural stem cells at E17.5 did not. These findings suggested that Chd8 mutation at 14.5 especially in ventral progenitor cells was associated with behavioral abnormality. The combination of behavioral examinations and transcriptome analysis allowed us to find the association between neural changes and behavioral symptoms.

overall_design: Nanostring CosMx Mouse Neuroscience Panel was applied to WT and Chd8 mutant brain at adulthood.


title: Ftsj1 deficiency influences diverse ncRNA networks in murine organs (poly-A-seq and rRNA-depletion-seq)

summary: Beyond the regulation of mRNAs by individual ncRNA types, such as miRNAs or lncRNAs, their interplay as so-called competitive endogenous RNAs (ceRNAs) appears to play a pivotal role in diseases. In our study we aimed to get a holistic understanding of the tRNA 2’O-methyltransferase FTSJ1 and its regulatory role in the context of cognitive disability. Here, we investigated the impact of Ftsj1 deficiency on ceRNA networks across different mouse organs. Our study underscores the critical role of organ-specific ceRNA networks, particularly in metabolic regulation, and emphasizes the need for cross-organ analyses to unravel the complexity of ceRNA-mediated gene regulation. Our findings reveal a prominent ceRNA network in the liver, mediated by four hub miRNAs (miR-378d, miR-3076-5p, miR-3474, and miR-296-3p) and enriched with acetyl CoA-related genes, including Acly, Acss2, and Mvk. These genes are integral to fatty acid metabolism, which is heavily disrupted in both liver and kidney. In contrast, brain tissues exhibited minimal changes, suggesting only a limited impact directly related to Ftsj1 in this organ. These results suggest that the cognitive disability associated with Ftsj1 is driven by metabolic and ceRNA crosstalk along the liver-brain and kidney-brain axes. This dataset comprises the poly-A and rRNA-depletion total RNA sequencing data used in our study for mRNAs and lncRNAs.

overall_design: RNA-seq profiling of 3 Ftsj1-deficient and 3 wildtype mice with poly-A-seq and rRNA-depletion-seq in 5 different organs, brain, heart, kidney, liver, spleen.


title: Dysregulation of macrophage lipid metabolism underlies intracellular bacterial neuroinvasion [liver]

overall_design: RNA-sequencing (RNA-seq) were performed of liver tissues collected from mice with mild infection, acute neuroinvasion and uninfected baseline


title: Dysregulation of macrophage lipid metabolism underlies intracellular bacterial neuroinvasion

overall_design: Single-cell RNA-sequencing (scRNA-seq) were performed of peripheral blood mononuclear cells (PBMCs) collected from mice in an acute meningitis model of L. monocytogenes infection.


title: NSUN2 promotes T-ALL cell growth as anRNA m5C methyltransferase

city: suzhou

first: Wenjuan

last: Ma

state: Jiang su

address: 199 Ren'ai Rd

department: Hematology Center Cyrus Tang medical institute

institute: Soochow University

summary: NSUN2 (NOP2/Sun RNA methyltransferase 2), a 5-methylcytosine (m5C) RNA methyltransferase is highly expressed and plays a proto-oncoprotein role in various cancers. However, the role of NSUN2 in T-ALL remains unknown, we aim to investigate the role of NSUN2 in T-ALL and delineate its underlying mechanism. Then RNA-Seq data were generated with NSUN2-silenced and control (scrambled) Jurkat cells from 3 independent RNA extracts. The differentially expressed transcripts comparing NSUN2-silenced cells with control cells are displayed.

overall_design: RNA-Seq data were generated with NSUN2-silenced and control (scrambled) Jurkat cells from 3 independent RNA extracts. The differentially expressed transcripts comparing NSUN2-silenced cells with scrambled cells are displayed.

first: Pan

last: Chen

first: Xingjie

last: Qin

first: Xiuyan

last: Zhang

first: Haixia

last: Zhou

first: Yun

last: Zhao

first: Lei


title: Alternative splicing-triggered mRNA decay informs splice-switching targets for neurodevelopmental disorders

status: Public on Mar 16 2026

city: Chicago

first: Xiaochang

state: IL

department: Department of Human Genetics

institute: University of Chicago

summary: Alternative splicing-triggered nonsense-mediated mRNA decay (AS-NMD) critically regulates gene expression, but the extent to which neuronal genes are regulated by AS-NMD remains understudied. Here, we identified more than 3,000 developmentally regulated AS-NMD exons in mouse and human brains, and validated them in cultured neurons. AS-NMD suppresses synaptic genes during brain development and differentially regulates more than 200 causal genes for neurodevelopmental disorders (NDDs). We detected an AS-NMD exon in GRIA2 and identified splice-switching antisense oligonucleotides that suppressed GRIA2 NMD and increased its functional isoforms. In summary, this study uncovers genes repressed by AS-NMD in the brain and nominates amenable splice-switching targets for treating dominant NDDs such as autism spectrum disorders and developmental epileptic encephalopathy.

overall_design: (1) Neuroa2 Upf1 siRNA and control. (2) Primary neurons from E16.5 CD1 mouse, CHX and DMSO.


title: A cellular cross-species RNA-seq atlas captures the transcriptional dynamics of myogenesis

city: Freising-Weihenstephan

first: Alexander

last: Bartelt

address: Gregor-Mendel-Str. 2

department: Chair of Translational Nutritional Medicine

institute: Technical University of Munich

summary: Skeletal muscle formation and regeneration is a tightly regulated process involving extensive transcriptional reprogramming as proliferating myoblasts fuse into mature myotubes. However, a comparative comprehensive analysis of the transcriptional landscape of humans and mouse myogenesis is missing. Here, we present a high-quality RNA-sequencing dataset profiling this transition in both mouse (C2C12) and human (LHCN-M2) myogenic cells. Samples were collected from proliferating myoblasts, the early differentiation phase, and from mature myocytes using identical protocols, ensuring stringent comparability. This unified dataset captures the major transcriptional shifts occurring in myoblasts, marking the onset of differentiation. Quality metrics, including PCA, read distribution, and clustering, confirmed high internal consistency across samples and species. Comparative analyses revealed shared global features of myogenesis but also distinct regulatory trajectories. Human differentiation showed early upregulation followed by suppression of metabolic and stress-related pathways, while structural and ECM-associated programs remained persistently elevated. In contrast, mouse C2C12 cells displayed early inflammatory activation and later enrichment of metabolic and contractile pathways typical of mature myotubes. Ortholog-based integration demonstrated decreasing cross-species correlation over time, indicating progressive reinforcement of species-specific differentiation programs. We additionally compared this bulk RNA-seq with tissue-derived myotubes from single-cell muscle datasets to determine which transcriptional programs are conserved in the in vitro models or which emerge only in vivo. This analysis delineates the conserved and context-specific features of myogenesis, identifying pathways that reflect culture-specific artifacts in both human and mouse muscle cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq profilling of differentiation of both mouse (C2C12) and human (LHCN-M2) myogenic cells

first: Fernando

last: Valdivieso Rivera

first: Anastasiia

last: Zenina

first: Carlos

last: H. Sponton


title: Effect of orthotopically transplanted pancreatic tumor on gene expression of subcutaneous white adipose tissue.

city: New York

first: Christine

last: Chio

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University Medical Center

summary: At 4-5 weeks post-surgery, a time when adipose depletion is robust by tumor progression, the transcriptome of sWAT from tumour-bearing mice is strongly enriched for oxidative phosphorylation as well as markers of adipose browning such as Elovl3, Ucp1, and Dio2 (Extended Data Fig. 6e).

overall_design: Pancreas ductal adenocarcinoma (PDAC) cells are orthotopically tranplanted to MSRA WT and MSRA full-body KO host, and subcutaneous adipose tissues are collected at 4-5 weeks post-surgery. Total RNA (RIN value > 7) was extracted from adipose tissues, and poly-A pull-down was performed to enrich mRNAs. Library construction was performed using Illumina TruSeq chemistry, with the final PCR step being modified using the KAPA HiFi HotStart Ready Mix. Libraries were sequenced using Element AVITI at Columbia Genome Center.


title: Xist RNA Dependent and Independent Mechanisms Regulate Dynamic X Chromosome Inactivation in B Lymphocytes [CUTandRUN_F1]

first: Montserrat

last: Anguera

overall_design: CUT&RUN analysis for the histone modifications H3K27me3, H2AK119Ub, H3K27ac, and H3K9me3 and the Polycomb subunits Ring1B and Suz12 in F1 mus x cast CD23+ B cells that were unstimulated or stimulated for 12 or 24 hours with CpG (n = 3-5 per condition). F1 mus x cast is a hybrid mouse model of skewed XCI generated through mating female C57BL/6 mice harboring a heterozygous Xist deletion to male M. m. castaneous mice.

first: Natalie

last: Toothacre


title: Environmentally Relevant Microplastic Inhalation Drives Pulmonary Fibrosis via a FABP5–FOXK2–PDGFA Macrophage Axis

city: Shanghai

first: manyi

last: pan

address: Manufacturing Bureau Road, Shanghai

department: Department of Respiratory and Critical Care Medicine

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

summary: Microplastics are increasingly detected in the atmosphere and human tissues, yet their long-term effects on lung biology remain unclear. Here, we identified multiple microplastic polymers in human lung tissues using pyrolysis–gas chromatography/mass spectrometry (Py-GC/MS). Using a chronic inhalation model with environmentally relevant concentrations, we show that microplastic exposure induces progressive pulmonary fibrosis in a particle size–dependent manner, with nanoscale particles producing stronger fibrogenic effects than micron-scale particles. Single-cell transcriptomics revealed expansion of Fabp5⁺ interstitial macrophages and early fibroblast activation specifically following nanoscale exposure. Cell–cell communication analysis identified PDGFA–PDGFRA signaling as a key mediator of macrophage–fibroblast interactions. Mechanistically, nanoscale microplastics activated a Fabp5–FOXK2–PDGFA transcriptional axis in macrophages, whereas micron-scale particles showed minimal activation. Fabp5 silencing suppressed this pathway and attenuated pulmonary fibrosis, revealing a macrophage-driven mechanism linking inhaled microplastics to fibrotic lung remodeling.

overall_design: To investigate the pulmonary effects of airborne microplastics, three types of microplastics with different particle sizes were selected: polyvinyl chloride with a diameter of 100 nm, polyethylene with a diameter of 100 nm, and polyvinyl chloride with a diameter of 1 μm. Based on the estimated respiratory rate of adult mice (~18 mL/min; approximately 25.92 L/day), and applying a 100-fold uncertainty factor, the calculated daily exposure dose of particulate matter was 14,644.8 particles/day. Microplastics were suspended in sterile saline at a concentration of 878.86 particles/μL, which was estimated according to reported airborne microplastic concentrations in Beijing in 2020. Mice were exposed to microplastics via intranasal instillation twice per week (50 μL per administration) for a total duration of 8 weeks.


title: Preconception exposures of female mice to a panel of metabolic disruptors induce sexually dimorphic metabolic perturbations in their offspring

city: Santa Cruz

last: Diaz-Castillo

state: California

address: 448 Physical Sciences Building

institute: University of California Santa Cruz

summary: In recent years, there has been a growing emphasis on research investigating the transmission across generations of the effects of exposure to environmental factors, which may predispose to chronic diseases. It has been hypothesized that the propagation of such effects is mediated by alterations in gene regulatory elements, such as DNA methylation, histone modifications, and non-coding RNAs. Studies in Drosophila and mice have demonstrated that the compartmentalization of eukaryotic genomes into heterochromatin and euchromatin can mediate multigenerational metabolism-disrupting effects elicited by exposure to various metabolism disruptors. These findings suggest that eukaryotic nuclear genomes may possess the capacity to integrate the impact of environmental cues in a metastable manner that is phenotypically relevant. Here, we present the results of a murine model to assess whether preconception exposure to three metabolism disruptors of distinct nature, including dietary factors and environmental toxicants, intended to emulate the complexity of human exposures, results in metabolic alterations in the offspring of exposed individuals. Our findings align with our central hypothesis but also open an unexpected avenue to explore whether preconception exposure to metabolism disruptors predisposes the offspring of exposed individuals to not only typical metabolic diseases such as obesity but also to complex metabolic-psychiatric conditions such as anorexia.

overall_design: We generated RNA-seq data from gonadal white adipose tissue (GWAT) and liver samples from 11-week-old female and male mice, first-generation (F1) descendants of five groups of female mice exposed for 3.5 weeks to the following combinations of treated water and diets: 0.1% dimethylsulfoxide (DMSO) in water and a control diet (CD; Envigo Teklad Diets TD.140148) [DMSO group], 5 nM tributyltin (TBT) and 0.1% DMSO in water and CD [5TBT group], 50 nM tributyltin and 0.1% DMSO in water and CD [50TBT group], 10 µg/L sodium meta(arsenite) (inorganic arsenic, iAs) and 0.1% DMSO in water and CD [IAS group], and 0.1% DMSO in water and Total Western Diet (TWD; Envigo Teklad Diets TD.110919) [TWD group]. A total of 100 samples were collected: 5 exposure groups x 2 F1 sexes x 2 tissues (GWAT and liver) x 5 biological replicates.

first: Stephanie

last: Aguiar

first: Raquel

last: Chamorro-Garcia


title: Suppression of antiviral innate immunity by the COX2-PGE2-PKA signaling axis by inhibiting the cytosolic mtDNA-dependent activation of STING

city: San Diego

first: Pham Thuy Tien

last: Vo

address: 3855 Health Sciences Dr

institute: University of California, San Diego

summary: The innate immune cGAS-STING pathway is activated by cytosolic doubled-stranded DNA (dsDNA) to induce type I interferon response, which is essential for antiviral and antitumor immunity. However, intrinsic STING activation during viral infection or within the tumor microenvironment is often insufficient to achieve complete viral clearance or tumor regression, indicating the presence of additional mechanisms that evades its activity. Here, we identified COX2/PGE2 as an intrinsic negative regulator of STING activation, particularly in response to cytosolic mitochondrial DNA (mtDNA) generated during HSV-1 infection. Mechanistically, we demonstrated that PGE2 signals through the EP4-PKA axis to induce mitophagy and facilitate the clearance of immunostimulatory cytosolic mtDNA, thereby dampening STING-mediated antiviral response. Furthermore, we discovered STOML2 as a direct downstream target of PKA, thereby linking mitochondrial quality control to innate immune signaling. Together, our findings established the COX2/PGE2/PKA axis as an intrinsic negative regulator of STING signaling, which may be targeted to potentiate STING-mediated antiviral and antitumor immunity.

overall_design: Total RNA extracted from THP-1-derived macrophages infected with HSV-1 (MOI = 1) in the presence or absence of PGE2 was subjected to paired-end 150bp sequencing on the Illumina NovaSeq X Plus sequencer at Novogene Co., Ltd.. Sequencing reads were aligned to GRCh38 human reference genome by STAR v2.7.9 using Gencode v38 annotations. Read count data was generated by RSEM v1.3.1.


title: DPM1 regulates ER-stress sensor IRE1 activity and antitumor immunity in colorectal cancer

city: Memphis

first: Douglas

last: Green

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St. Jude Children's Research Hospital

summary: This study investigates how DPM1 regulates the ER stress sensor IRE1 and how this impacts antitumor immunity in a colorectal cancer model. Single cell data were generated from tumor infiltrating T cells isolated from BALB/c mice bearing CT26 colorectal tumors. Wild-type and Dpm1 knockout tumors were profiled using 10x Genomics Chromium Single Cell 5' gene expression, feature barcode hashtags, and paired TCR VDJ libraries. Raw reads are available in SRA under BioProject PRJNA1435810.

overall_design: Tumor infiltrating T cells were isolated from CT26 tumors grown in BALB/c mice. Cells were pooled into four genotype-level pools (WT pool1, WT pool2, KO pool1, KO pool2). For each pool, 10x Genomics 5' gene expression, hashtag feature barcode (CITE-seq) and TCR V(D)J libraries were generated and sequenced on Illumina NovaSeq 6000. Processed data include feature-barcode count matrices (MEX) containing both Gene Expression and Antibody Capture features, feature_reference.csv files for hashtags, and TCR contig annotations and clonotypes.


title: Microbiota-derived polyphosphates govern mucosal immunity through multilevel suppression of STAT/IL-27 signaling  (multiome)

city: Boston

first: Markus

last: Bosmann

state: MA

address: 72 E Concord Street

institute: Boston University

summary: The interplay between gut bacteria and mucosal immune cells is crucial for maintaining intestinal homeostasis. Dysregulation of this immune-microbiome axis has been implicated in the pathogenesis of inflammatory bowel diseases, but the mechanisms driving the health-to-disease transition remain unclear. Here, we demonstrate that polyphosphates, a bacterial metabolite, influence mucosal immunity during both homeostasis and inflammation. Germ-free mice were monocolonized with polyphosphate competent Escherichia coli or a ∆ppk E. coli mutant strain deficient in polyphosphate production, affecting subsets of T cells and mononuclear phagocytes. Transfer of lamina propria immune cells into RAG1-/- mice indicated that polyphosphate-experienced T cells induced more severe colitis. Mechanistically, polyphosphate exposure suppressed chromatin accessibility of the Stat1, Stat3 and Il10 genes in CD4+ T cells. Ultra-pure polyphosphates corresponding to the molecular sizes produced by microbes decreased gene expression of STATs as observed by snRNA-seq, antagonized IL-27 production in mononuclear phagocytes through suppression of STAT1, and disrupted IL-27-induced STAT1/STAT3 phosphorylation in naïve CD4+ and CD8+ T cells. IL-27Rα-/- lamina propria immune cells were more aggressive in promoting colitis, suggesting that the paralyzing effects of polyphosphates on IL-27/IL-27Rα signaling are functionally significant. In conclusion, the intestinal microbiota utilizes polyphosphates to disrupt the protective balance of innate and adaptive immune cell networks.

overall_design: 4 individual sets of peritoneal cells were stimulated with long-chain polyphoshates for 18 hours or remained untreated. 7-AAD-CD45+ cells were flow sorted and single-nuclei ATAC and RNA-seq was performed.

first: Kevin

last: Brueck

first: Archana

last: Jayaraman


title: Study on the mechanism of toll-like receptor junction molecule TICAM1 promoting the occurrence and development of acute myeloid leukemia

first: Wenjuan

last: Ma

summary: TICAM1 is recruited into intracellular vesicles to mediate TLR3/4 signaling involved in innate immunity, however the role of this pathway in the pathogenesis of acute myeloid leukemia (AML) remains unknown. We found that in myelomonocytic (M4) and monocytic (M5) AML cells, TLR3/4 was highly expressed, and activation of TLR3/4-TICAM1 signaling was an independent indicator of poor prognosis. TLR3/4 agonists significantly promoted the proliferation of these subtypes of AML cells but inhibited the proliferation of other subtypes of AML cells. Silencing TICAM1 significantly inhibited the growth of M5 AML cells in vitro and in vivo, enhanced their chemotherapy sensitivity, and led to decreased phosphorylation of TBK1 and RIPK3. Using MLL-AF9-driven murine AML model, we investigated the molecular mechanism by which TLR3/4-TICAM1 signaling promotes AML cell growth and drug resistance in vivo and in vitro. Therefore, this study likely provides a new theoretical and experimental basis for the treatment of such disease.

overall_design: To explore the role of TICAM1 in AML, RNA seq analysis was performed on MOLM-13 cells that knocked down TICAM1 with Shrna

first: Lei

last: Zhang

first: Jiawei

last: Lin

first: Xiaonan

last: Zhou

first: Rongyao